diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 6f04cb035a..03325a1a22 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -27,10 +27,9 @@ Before a pull request can be merged, the following items must be checked: * [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this is to run the following in the **correct sequence** on - your local machine. Start with running [black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will - automatically reformat your code to PEP8 conventions and removes most issues. Then run - [ruff](https://ruff.rs). -* [ ] Docstrings have been added in the [Numpy docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html). + your local machine. Start with running [`ruff`](https://docs.astral.sh/ruff) and `ruff format` on your new code. This will + automatically reformat your code to PEP8 conventions and fix many linting issues. +* [ ] Doc strings have been added in the [Numpy docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html). Run [ruff](https://beta.ruff.rs/docs/rules/#pydocstyle-d) on your code. * [ ] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org) to type check your code. diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 37fbf3b594..d3d7488836 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -6,30 +6,30 @@ on: types: [completed] jobs: - deploy-docs: - # only run if commit is a push to master and the testing finished if: ${{ github.repository_owner == 'materialsproject' && github.event.workflow_run.conclusion == 'success' && github.event.workflow_run.event == 'push' && startsWith(github.event.workflow_run.head_branch, 'v0.') }} runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: ref: ${{ github.event.workflow_run.head_branch }} - name: Install pandoc run: sudo apt-get install pandoc - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: - python-version: '3.10' + python-version: "3.10" cache: pip cache-dependency-path: pyproject.toml - name: Install dependencies run: | python -m pip install --upgrade pip + # ase needed to get FrechetCellFilter used by ML force fields + pip install git+https://gitlab.com/ase/ase pip install .[strict,docs] - name: Build @@ -42,19 +42,18 @@ jobs: publish_dir: ./docs_build/ deploy-pypi: - # only run if commit is a push to master, the testing finished, and tagged as version if: github.repository_owner == 'materialsproject' && github.event.workflow_run.conclusion == 'success' && github.event.workflow_run.event == 'push' && startsWith(github.event.workflow_run.head_branch, 'v0.') runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: ref: ${{ github.event.workflow_run.head_branch }} - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: - python-version: '3.10' + python-version: "3.10" - name: Build run: | @@ -68,19 +67,18 @@ jobs: password: ${{ secrets.PYPI_PASSWORD }} deploy-github: - runs-on: ubuntu-latest needs: - deploy-pypi steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: ref: ${{ github.event.workflow_run.head_branch }} - name: Write release info run: | - awk 'BEGIN {p = 0} {a = 0 }; /^v\d*.\d*.\d*./ { p += 1; a = 1}; p + a == 1 { print } ' CHANGELOG.md | sed -e '1,1d' | sed -e '/./,$!d' -e :a -e '/^\n*$/{$d;N;ba' -e '}' > release_info.txt + awk 'BEGIN {p = 0} {a = 0 }; /^\#\#\ v\d*.\d*.\d*./ { p += 1; a = 1}; p + a == 1 { print } ' CHANGELOG.md | sed -e '1,1d' | sed -e '/./,$!d' -e :a -e '/^\n*$/{$d;N;ba' -e '}' > release_info.txt echo "" >> release_info.txt awk '/CONTRIBUTOR SECTION/{f=1; c=0} f' CHANGELOG.md >> release_info.txt diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index d66dfb87d3..6847853711 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -17,14 +17,14 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: ref: ${{ github.event.workflow_run.head_branch }} - name: Install pandoc run: sudo apt-get install pandoc - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: "3.10" cache: pip @@ -33,6 +33,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip + # ase needed to get FrechetCellFilter used by ML force fields + pip install git+https://gitlab.com/ase/ase pip install .[strict,docs] - name: Build diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index 04545793ac..2f1e31a4f6 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -6,14 +6,16 @@ on: tags: ["v*"] pull_request: workflow_dispatch: + repository_dispatch: + types: [pymatgen-ci-trigger] jobs: lint: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: "3.9" cache: pip @@ -34,25 +36,40 @@ jobs: python-version: ["3.9", "3.10", "3.11"] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - cache: pip - cache-dependency-path: pyproject.toml + + - name: Install enumlib + run: | + cd .. + git clone --recursive https://github.com/msg-byu/enumlib.git + cd enumlib/symlib/src + export F90=gfortran + make + cd ../../src + make enum.x + sudo mv enum.x /usr/local/bin/ + cd .. + sudo cp aux_src/makeStr.py /usr/local/bin/ + continue-on-error: true # This is not critical to succeed. - name: Install dependencies - # ERROR: Cannot install atomate2 and atomate2[strict,tests]==0.0.1 because these package versions have conflicting dependencies. - # The conflict is caused by: - # atomate2[strict,tests] 0.0.1 depends on pymatgen>=2023.10.4 - # atomate2[strict,tests] 0.0.1 depends on pymatgen==2023.10.4; extra == "strict" - # ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts - # chgnet 0.2.1 depends on pymatgen>=2023.5.31 - # emmet-core 0.70.0 depends on pymatgen>=2023.10.11 run: | python -m pip install --upgrade pip - pip install .[strict,tests] + mkdir -p ~/.abinit/pseudos + cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos + # ase needed to get FrechetCellFilter used by ML force fields + pip install git+https://gitlab.com/ase/ase + pip install .[strict,tests,abinit] + pip install torch-runstats + pip install --no-deps nequip==0.5.6 + + - name: Install pymatgen from master if triggered by pymatgen repo dispatch + if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger' + run: pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}' - name: Test env: @@ -69,9 +86,9 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: "3.10" cache: pip @@ -80,6 +97,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip + # ase needed to get FrechetCellFilter used by ML force fields + pip install git+https://gitlab.com/ase/ase pip install .[strict,docs] - name: Build diff --git a/.github/workflows/update-precommit.yml b/.github/workflows/update-precommit.yml index 0d6a43f422..273be7171f 100644 --- a/.github/workflows/update-precommit.yml +++ b/.github/workflows/update-precommit.yml @@ -2,7 +2,7 @@ name: pre-commit-auto-update on: schedule: - - cron: '0 0 1,14,28 * *' + - cron: "0 0 1,14,28 * *" workflow_dispatch: jobs: @@ -10,10 +10,10 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: 3.9 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 19ff60e958..34b2f96837 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,42 +1,27 @@ default_language_version: python: python3 +exclude: ^(.github/|tests/test_data/abinit/) repos: - repo: https://github.com/charliermarsh/ruff-pre-commit - rev: v0.1.1 + rev: v0.4.10 hooks: - id: ruff args: [--fix] + - id: ruff-format - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.5.0 + rev: v4.6.0 hooks: - id: check-yaml - id: fix-encoding-pragma args: [--remove] - id: end-of-file-fixer - id: trailing-whitespace -- repo: https://github.com/psf/black - rev: 23.10.0 - hooks: - - id: black - repo: https://github.com/asottile/blacken-docs rev: 1.16.0 hooks: - id: blacken-docs additional_dependencies: [black] exclude: README.md -- repo: https://github.com/pycqa/flake8 - rev: 6.1.0 - hooks: - - id: flake8 - entry: pflake8 - files: ^src/ - additional_dependencies: - - pyproject-flake8==6.0.0a1 - - flake8-bugbear==22.12.6 - - flake8-typing-imports==1.14.0 - - flake8-docstrings==1.6.0 - - flake8-rst-docstrings==0.3.0 - - flake8-rst==0.8.0 - repo: https://github.com/pre-commit/pygrep-hooks rev: v1.10.0 hooks: @@ -45,16 +30,15 @@ repos: - id: rst-directive-colons - id: rst-inline-touching-normal - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.6.1 + rev: v1.10.0 hooks: - id: mypy files: ^src/ additional_dependencies: - tokenize-rt==4.1.0 - - types-pkg_resources==0.1.2 - types-paramiko - repo: https://github.com/codespell-project/codespell - rev: v2.2.6 + rev: v2.3.0 hooks: - id: codespell stages: [commit, commit-msg] diff --git a/CHANGELOG.md b/CHANGELOG.md index 12c23befc0..ccea4304b9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,166 @@ # Change log +## v0.0.14 + +### New Features ๐ŸŽ‰ + +* Add lobster mp workflow by @JaGeo in https://github.com/materialsproject/atomate2/pull/634 +* Add FHI-aims DFT calculator by @tpurcell90 in https://github.com/materialsproject/atomate2/pull/562 +* Electrode Workflow by @jmmshn in https://github.com/materialsproject/atomate2/pull/655 +* Equation of state (EOS) workflows by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/623 + +### Bug Fixes ๐Ÿ› + +* Skip final LDAU/J/L/MAGMOM updates and fix setting MAGMOM via `user_incar_settings` by @JonathanSchmidt1 in https://github.com/materialsproject/atomate2/pull/648 +* Prep for next `pymatgen` release by @janosh in https://github.com/materialsproject/atomate2/pull/690 +* fix SC Matrix Checking Logic by @jmmshn in https://github.com/materialsproject/atomate2/pull/704 +* Fix elastic conventional structure by @mjwen in https://github.com/materialsproject/atomate2/pull/706 +* Add `KspacingMetalHandler` to VASP `_DEFAULT_HANDLERS` by @janosh in https://github.com/materialsproject/atomate2/pull/600 +* Fix import error [ijson] by @naik-aakash in https://github.com/materialsproject/atomate2/pull/708 +* Print invalid value and list valid ones in `PhononMaker` error messages by @janosh in https://github.com/materialsproject/atomate2/pull/728 +* Update minimum `monty` version, allow newer `pydantic` by @mkhorton in https://github.com/materialsproject/atomate2/pull/720 +* Fix phonon + Lobster flow by removing magmoms before passing to `phonopy` by @naik-aakash in https://github.com/materialsproject/atomate2/pull/751 +* Fix MP query by @utf in https://github.com/materialsproject/atomate2/pull/755 + +### Enhancements ๐Ÿ›  + +* add directory of task doc generation to phonon schema by @JaGeo in https://github.com/materialsproject/atomate2/pull/674 +* Ensure MP VASP sets don't use auto_ismear, few other fixes by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/673 +* Schema update > Update plot example LOBSTER workflow by @naik-aakash in https://github.com/materialsproject/atomate2/pull/682 +* Modify `BadInputSetWarning` logic for relaxations of a likely metal by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/727 +* Define `MLFF` `Enum` to ensure consistent force field names by @janosh in https://github.com/materialsproject/atomate2/pull/729 + +### Documentation ๐Ÿ“– + +* Update doc: adding metadata to flow by @naik-aakash in https://github.com/materialsproject/atomate2/pull/638 +* Fix hyperlink in Docs by @naik-aakash in https://github.com/materialsproject/atomate2/pull/686 +* Correct typo in doc by @JiQi535 in https://github.com/materialsproject/atomate2/pull/716 +* Fix docstring on `MatPesMetaGGAStaticSetGenerator` by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/725 +* Add `citation.cff` file, Zenodo record and readme "How to cite" section by @janosh in https://github.com/materialsproject/atomate2/pull/731 + +### House-Keeping ๐Ÿงน + +* Address TODO re missing asserts in `test_elastic_wf_with_mace()` by @janosh in https://github.com/materialsproject/atomate2/pull/679 +* Update lobsterpy version by @naik-aakash in https://github.com/materialsproject/atomate2/pull/683 +* Fix all ruff PT011 (not checking error message when testing exceptions) by @janosh in https://github.com/materialsproject/atomate2/pull/698 + +## New Contributors + +* @JonathanSchmidt1 made their first contribution in https://github.com/materialsproject/atomate2/pull/648 +* @rdguha1995 made their first contribution in https://github.com/materialsproject/atomate2/pull/161 +* @JiQi535 made their first contribution in https://github.com/materialsproject/atomate2/pull/716 + +**Full Changelog**: https://github.com/materialsproject/atomate2/compare/v0.0.13...v0.0.14 + +## v0.0.13 + +### BREAKING CHANGE + +The API of `Maker.maker` for all workflows (VASP, CP2K, force fields) have been modified. Previously, this function had custom arguments for previous calculation directories (e.g., `prev_vasp_dir`, `prev_cp2k_dir`). These arguments have been standardised to `prev_dir`. Accordingly, the approach used to chain workflows has now changed. + +### New Features ๐ŸŽ‰ + +* Add setting `VASP_RUN_DDEC6: bool = False` by @janosh in https://github.com/materialsproject/atomate2/pull/587 + +### Bug Fixes ๐Ÿ› + +* Resolve bandstructure datastore bug by @JaGeo in https://github.com/materialsproject/atomate2/pull/605 +* Fix `TypeError`: `PhononBSPlotter.save_plot()` got an unexpected keyword argument `img_format` by @janosh in https://github.com/materialsproject/atomate2/pull/625 +* `ForceFieldRelaxMaker` default `relax_cell` to `True` by @janosh in https://github.com/materialsproject/atomate2/pull/635 +* Replace ase `ExpCellFilter` with `FrechetCellFilter` in `Relaxer` by @janosh in https://github.com/materialsproject/atomate2/pull/636 +* update lobsterpy version and schemas to match new version changes by @naik-aakash in https://github.com/materialsproject/atomate2/pull/637 +* Default `create_thermal_displacements` to `False` in VASP and forcefield `PhononMaker` by @janosh in https://github.com/materialsproject/atomate2/pull/647 +* Fix import of ASE filters when user has installed from PyPI and not gitlab by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/650 +* Mark schema fields with `None` default as `Optional` to pass pydantic v2 validation by @danielzuegner in https://github.com/materialsproject/atomate2/pull/651 + +### Enhancements ๐Ÿ›  + +* Breaking: Unify previous directory `Maker` API by @janosh in https://github.com/materialsproject/atomate2/pull/593 +* Add keyword `incar_exclude: Sequence[str] = None` to `fake_run_vasp()` by @janosh in https://github.com/materialsproject/atomate2/pull/599 +* Allow `prv_dir` to be used more in defect wf by @jmmshn in https://github.com/materialsproject/atomate2/pull/585 +* Add MACE RelaxMaker and StaticMaker by @CompRhys in https://github.com/materialsproject/atomate2/pull/611 +* Update lobster task schema by @naik-aakash in https://github.com/materialsproject/atomate2/pull/529 +* Allow optimizer to be configured for MACE/GAP by @CompRhys in https://github.com/materialsproject/atomate2/pull/615 +* MACE Static/RelaxMakers default to loading `mace_mp` instead of test model by @janosh in https://github.com/materialsproject/atomate2/pull/614 +* Add optional 3rd static for PBE+U to `MatPesStaticFlowMaker` by @janosh in https://github.com/materialsproject/atomate2/pull/606 +* Use PyPI version of MACE by @utf in https://github.com/materialsproject/atomate2/pull/668 +* Multi step MD flow by @gpetretto in https://github.com/materialsproject/atomate2/pull/489 + +### Documentation ๐Ÿ“– + +* Add @CompRhys to `contributors.md` by @CompRhys in https://github.com/materialsproject/atomate2/pull/612 + +### House-Keeping ๐Ÿงน + +* Update GitHub Action versions by @janosh in https://github.com/materialsproject/atomate2/pull/640 +* Drop `flake8` by @janosh in https://github.com/materialsproject/atomate2/pull/658 +* Enable all `ruff` rules by default by @janosh in https://github.com/materialsproject/atomate2/pull/663 + +### New Contributors + +* @CompRhys made their first contribution in https://github.com/materialsproject/atomate2/pull/612 +* @danielzuegner made their first contribution in https://github.com/materialsproject/atomate2/pull/651 + +**Full Changelog**: https://github.com/materialsproject/atomate2/compare/v0.0.12...v0.0.13 + +## v0.0.12 + +* Breaking: default `Atomate2Settings.VASP_INHERIT_INCAR` to `False` by @janosh in https://github.com/materialsproject/atomate2/pull/594 + +### Bug Fixes ๐Ÿ› + +* Enforce magmom precedence in INCAR creation by @mattmcdermott in https://github.com/materialsproject/atomate2/pull/506 +* Warn on empty config by @janosh in https://github.com/materialsproject/atomate2/pull/522 +* CP2K use `calcs_reversed[0]` instead of `calcs_reversed[-1]` to not reverse again by @janosh in https://github.com/materialsproject/atomate2/pull/534 +* Fix wrong INCAR values in MP workflows by @janosh in https://github.com/materialsproject/atomate2/pull/550 +* Fix failing tests from Pydantic v2 migration by @hrushikesh-s in https://github.com/materialsproject/atomate2/pull/558 +* fixing pydantic v2 test errors by @hrushikesh-s in https://github.com/materialsproject/atomate2/pull/565 +* `parse_additional_json()` ignore `FW.json.gz` in output directories by @janosh in https://github.com/materialsproject/atomate2/pull/574 +* Fix `bandgap_tol` and delete `bandgap_override` on `MPMetaGGARelaxSetGenerator` by @janosh in https://github.com/materialsproject/atomate2/pull/553 +* Fix `VaspInputGenerator`'s `_set_kspacing` not respecting `auto_ismear = False` nor `auto_kspacing = False` by @janosh in https://github.com/materialsproject/atomate2/pull/576 +* Clean up VASP powerups, correct params in MP flows, test for `_set_u_params`, test for `_set_kspacing`, fix `_get_incar` method of `VaspInputSet` by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/561 +* Fix Lobster workflow by @JaGeo in https://github.com/materialsproject/atomate2/pull/583 +* Change `MatPesGGAPlusMetaGGAStaticMaker.output` to dict containing both statics by @janosh in https://github.com/materialsproject/atomate2/pull/586 +* Test MP + MatPES set generators by @janosh in https://github.com/materialsproject/atomate2/pull/596 + +### Enhancements ๐Ÿ›  + +* Add StructureMetadata as baseclass for output documents by @gpetretto in https://github.com/materialsproject/atomate2/pull/514 +* Materials Project GGA and meta-GGA workflows by @janosh in https://github.com/materialsproject/atomate2/pull/504 +* MP-compatible r2SCAN workflow (and a few general INCAR improvements) by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/362 +* Update to Pydantic v2 by @hrushikesh-s in https://github.com/materialsproject/atomate2/pull/567 +* Add MatPES GGA and r2SCAN static makers by @janosh in https://github.com/materialsproject/atomate2/pull/532 +* Move elastic workflow to common and build force-field elastic workflow by @JaGeo in https://github.com/materialsproject/atomate2/pull/581 + +### Documentation ๐Ÿ“– + +* Update @arosen93 to @Andrew-S-Rosen by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/516 +* Add Aaron Kaplan and Matthew McDermott to `contributors.md` by @janosh in https://github.com/materialsproject/atomate2/pull/560 +* Document architectural difference between atomate 1 and 2 by @janosh in https://github.com/materialsproject/atomate2/pull/381 +* Add Thomas Purcell to `contributors.md` by @tpurcell90 in https://github.com/materialsproject/atomate2/pull/568 +* Add Alex Bonkowski to contributors list by @JaGeo in https://github.com/materialsproject/atomate2/pull/573 +* Add @matthewkuner to contributors by @matthewkuner in https://github.com/materialsproject/atomate2/pull/575 +* Update contributors.md by @utf in https://github.com/materialsproject/atomate2/pull/579 + +### House-Keeping ๐Ÿงน + +* Remove `__all__` from all modules by @janosh in https://github.com/materialsproject/atomate2/pull/540 +* removed py38 support, and add py 3.11 support by @naik-aakash in https://github.com/materialsproject/atomate2/pull/537 +* Check full INCAR by default in `mock_vasp` fixture by @janosh in https://github.com/materialsproject/atomate2/pull/551 +* skip validate charge test by @jmmshn in https://github.com/materialsproject/atomate2/pull/563 +* Add some type annotations by @ab5424 in https://github.com/materialsproject/atomate2/pull/578 +* Future type annotations by @janosh in https://github.com/materialsproject/atomate2/pull/580 +* Use `numpy.testing.assert_allclose` over assert `np.(all|is)close` by @janosh in https://github.com/materialsproject/atomate2/pull/582 + +## New Contributors + +* @mattmcdermott made their first contribution in https://github.com/materialsproject/atomate2/pull/506 +* @tpurcell90 made their first contribution in https://github.com/materialsproject/atomate2/pull/568 +* @esoteric-ephemera made their first contribution in https://github.com/materialsproject/atomate2/pull/561 +* @ab5424 made their first contribution in https://github.com/materialsproject/atomate2/pull/578 + +**Full Changelog**: https://github.com/materialsproject/atomate2/compare/v0.0.11...v0.0.12 + ## v0.0.11 ### Task Document Changes @@ -7,17 +168,17 @@ Merge atomate2 VASP task document with the one in emmet. The changes to the atomate2 schemas are: -- `PsuedoPotentialSummary` -> `Potcar` - - `labels` -> `symbols` -- `AnalysisSymmary` -> `AnalysisDoc` - - `delta_volume_as_percent` -> `delta_volume_percent` -- `InputSummary` -> `InputDoc` -- `OutputSummary` -> `OutputDoc` - - `density` added -- `Status` -> `TaskState` -- `TaskDocument` -> `TaskDoc` - - `task_type added` -- `Status` -> `TaskState` +* `PsuedoPotentialSummary` -> `Potcar` + * `labels` -> `symbols` +* `AnalysisSymmary` -> `AnalysisDoc` + * `delta_volume_as_percent` -> `delta_volume_percent` +* `InputSummary` -> `InputDoc` +* `OutputSummary` -> `OutputDoc` + * `density` added +* `Status` -> `TaskState` +* `TaskDocument` -> `TaskDoc` + * `task_type added` +* `Status` -> `TaskState` ### VASP input set updates @@ -32,9 +193,9 @@ to stay the same. Two new options have been added to the `BaseVaspInputSetGenerator`: -- `auto_metal_kpoints`: If true and the system is metallic, try and use ` +* `auto_metal_kpoints`: If true and the system is metallic, try and use ` reciprocal_density_metal` instead of `reciprocal_density` for metallic systems. -- `auto_ismear`: If true, the values for ISMEAR and SIGMA will be set automatically +* `auto_ismear`: If true, the values for ISMEAR and SIGMA will be set automatically depending on the bandgap of the system. If the bandgap is not known (e.g., there is no previous VASP directory) then ISMEAR=0 and SIGMA=0.2; if the bandgap is zero (a metallic system) then ISMEAR=2 and SIGMA=0.2; if the system is an insulator, then @@ -42,78 +203,78 @@ reciprocal_density_metal` instead of `reciprocal_density` for metallic systems. ### New Features ๐ŸŽ‰ -- CP2K Support by @nwinner in https://github.com/materialsproject/atomate2/pull/157 -- Add forcefield schemas/makers to atomate2 by @matthewkuner in https://github.com/materialsproject/atomate2/pull/322 -- Add `m3gnet` support to Atomate2 by @matthewkuner in https://github.com/materialsproject/atomate2/pull/380 -- Phonons for forcefields by @JaGeo in https://github.com/materialsproject/atomate2/pull/398 +* CP2K Support by @nwinner in https://github.com/materialsproject/atomate2/pull/157 +* Add forcefield schemas/makers to atomate2 by @matthewkuner in https://github.com/materialsproject/atomate2/pull/322 +* Add `m3gnet` support to Atomate2 by @matthewkuner in https://github.com/materialsproject/atomate2/pull/380 +* Phonons for forcefields by @JaGeo in https://github.com/materialsproject/atomate2/pull/398 ### Bug Fixes ๐Ÿ› -- Fix Lobster Schema by @JaGeo in https://github.com/materialsproject/atomate2/pull/266 -- fix lso dos of lobster being not saved in schema by @naik-aakash in https://github.com/materialsproject/atomate2/pull/279 -- fix `_get_strong_bonds` function by @naik-aakash in https://github.com/materialsproject/atomate2/pull/289 -- [Bug Fix] For stringing defect calculations together by @jmmshn in https://github.com/materialsproject/atomate2/pull/292 -- BUGFIX `auto_lreal` by @jmmshn in https://github.com/materialsproject/atomate2/pull/297 -- Fix `Yb` PSP: change `Yb_2` to `Yb_3` by @janosh in https://github.com/materialsproject/atomate2/pull/319 -- Fix typo by @janosh in https://github.com/materialsproject/atomate2/pull/321 -- Fix overriding `magmoms` in `update_user_incar_settings(` by @janosh in https://github.com/materialsproject/atomate2/pull/375 -- Fix encoding of input `Molecule` coordinates in cclib `TaskDocument` by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/411 -- [FIX] fix elastic tensor flow by @mjwen in https://github.com/materialsproject/atomate2/pull/415 -- [BUG FIX] Edge case for Magmoms by @jmmshn in https://github.com/materialsproject/atomate2/pull/460 -- [FIX] Fix major bug that caused `user_incar_settings` to be overwritten in some cases by @matthewkuner in https://github.com/materialsproject/atomate2/pull/412 -- Test for `zip_outputs` by @gpetretto in https://github.com/materialsproject/atomate2/pull/503 +* Fix Lobster Schema by @JaGeo in https://github.com/materialsproject/atomate2/pull/266 +* fix lso dos of lobster being not saved in schema by @naik-aakash in https://github.com/materialsproject/atomate2/pull/279 +* fix `_get_strong_bonds` function by @naik-aakash in https://github.com/materialsproject/atomate2/pull/289 +* [Bug Fix] For stringing defect calculations together by @jmmshn in https://github.com/materialsproject/atomate2/pull/292 +* BUGFIX `auto_lreal` by @jmmshn in https://github.com/materialsproject/atomate2/pull/297 +* Fix `Yb` PSP: change `Yb_2` to `Yb_3` by @janosh in https://github.com/materialsproject/atomate2/pull/319 +* Fix typo by @janosh in https://github.com/materialsproject/atomate2/pull/321 +* Fix overriding `magmoms` in `update_user_incar_settings(` by @janosh in https://github.com/materialsproject/atomate2/pull/375 +* Fix encoding of input `Molecule` coordinates in cclib `TaskDocument` by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/411 +* [FIX] fix elastic tensor flow by @mjwen in https://github.com/materialsproject/atomate2/pull/415 +* [BUG FIX] Edge case for Magmoms by @jmmshn in https://github.com/materialsproject/atomate2/pull/460 +* [FIX] Fix major bug that caused `user_incar_settings` to be overwritten in some cases by @matthewkuner in https://github.com/materialsproject/atomate2/pull/412 +* Test for `zip_outputs` by @gpetretto in https://github.com/materialsproject/atomate2/pull/503 ### Enhancements ๐Ÿ›  -- Extension of Lobster schema and additional tests by @JaGeo in https://github.com/materialsproject/atomate2/pull/272 -- Use emmet VASP task document by @utf in https://github.com/materialsproject/atomate2/pull/269 -- VASP inputset updates by @utf in https://github.com/materialsproject/atomate2/pull/270 -- Linting by @utf in https://github.com/materialsproject/atomate2/pull/274 -- Improve Lobster workflow preconverge step, kpoints, docs by @JaGeo in https://github.com/materialsproject/atomate2/pull/277 -- add `has_doscar_lso` field to Lobsterout schema model and update lobsterpy version by @naik-aakash in https://github.com/materialsproject/atomate2/pull/286 -- added simple chg check by @jmmshn in https://github.com/materialsproject/atomate2/pull/320 -- Switch to emmet's `MoleculeMetadata` by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/301 -- Update update-precommit.yml by @utf in https://github.com/materialsproject/atomate2/pull/330 -- Update dependencies by @utf in https://github.com/materialsproject/atomate2/pull/329 -- Add missing molecule field to cclib TaskDocument by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/353 -- allow elastically unstable structures by @matthewkuner in https://github.com/materialsproject/atomate2/pull/355 -- update lobstertask schema: add bandoverlaps,grosspop and sitepotentials fields by @naik-aakash in https://github.com/materialsproject/atomate2/pull/404 -- Update CondensedBondingAnalysis schema by @naik-aakash in https://github.com/materialsproject/atomate2/pull/469 -- Phonon tweaks by @utf in https://github.com/materialsproject/atomate2/pull/276 -- Update to Defects WF by @jmmshn in https://github.com/materialsproject/atomate2/pull/430 -- Small change to `gunzip` to allow better restarting by @jmmshn in https://github.com/materialsproject/atomate2/pull/476 -- Remove VASP calc types schema by @mjwen in https://github.com/materialsproject/atomate2/pull/407 -- Optionally zip files at the end of jobs by @gpetretto in https://github.com/materialsproject/atomate2/pull/414 +* Extension of Lobster schema and additional tests by @JaGeo in https://github.com/materialsproject/atomate2/pull/272 +* Use emmet VASP task document by @utf in https://github.com/materialsproject/atomate2/pull/269 +* VASP inputset updates by @utf in https://github.com/materialsproject/atomate2/pull/270 +* Linting by @utf in https://github.com/materialsproject/atomate2/pull/274 +* Improve Lobster workflow preconverge step, kpoints, docs by @JaGeo in https://github.com/materialsproject/atomate2/pull/277 +* add `has_doscar_lso` field to Lobsterout schema model and update lobsterpy version by @naik-aakash in https://github.com/materialsproject/atomate2/pull/286 +* added simple chg check by @jmmshn in https://github.com/materialsproject/atomate2/pull/320 +* Switch to emmet's `MoleculeMetadata` by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/301 +* Update update-precommit.yml by @utf in https://github.com/materialsproject/atomate2/pull/330 +* Update dependencies by @utf in https://github.com/materialsproject/atomate2/pull/329 +* Add missing molecule field to cclib TaskDocument by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/353 +* allow elastically unstable structures by @matthewkuner in https://github.com/materialsproject/atomate2/pull/355 +* update lobstertask schema: add bandoverlaps,grosspop and sitepotentials fields by @naik-aakash in https://github.com/materialsproject/atomate2/pull/404 +* Update CondensedBondingAnalysis schema by @naik-aakash in https://github.com/materialsproject/atomate2/pull/469 +* Phonon tweaks by @utf in https://github.com/materialsproject/atomate2/pull/276 +* Update to Defects WF by @jmmshn in https://github.com/materialsproject/atomate2/pull/430 +* Small change to `gunzip` to allow better restarting by @jmmshn in https://github.com/materialsproject/atomate2/pull/476 +* Remove VASP calc types schema by @mjwen in https://github.com/materialsproject/atomate2/pull/407 +* Optionally zip files at the end of jobs by @gpetretto in https://github.com/materialsproject/atomate2/pull/414 ### Documentation ๐Ÿ“– -- Add more documentation for Lobster by @JaGeo in https://github.com/materialsproject/atomate2/pull/267 -- Use furo for docs theme by @utf in https://github.com/materialsproject/atomate2/pull/331 -- Update Lobster documentation by @JaGeo in https://github.com/materialsproject/atomate2/pull/376 -- Fix docs typos by @janosh in https://github.com/materialsproject/atomate2/pull/373 -- Update FireWorks section of docs by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/378 -- Add a copy button to code blocks by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/382 -- clean up doc, remove left-overs from amset example by @JaGeo in https://github.com/materialsproject/atomate2/pull/394 -- More details for lobster documentation by @JaGeo in https://github.com/materialsproject/atomate2/pull/431 -- Deploy docs on every commit to `main` by @janosh in https://github.com/materialsproject/atomate2/pull/422 -- Add clearer documentation on lobster worker by @JaGeo in https://github.com/materialsproject/atomate2/pull/440 -- Docs: add basic workflow tutorial by @rkingsbury in https://github.com/materialsproject/atomate2/pull/408 -- Use GitHub's `deploy-pages` action to deploy docs by @janosh in https://github.com/materialsproject/atomate2/pull/475 +* Add more documentation for Lobster by @JaGeo in https://github.com/materialsproject/atomate2/pull/267 +* Use furo for docs theme by @utf in https://github.com/materialsproject/atomate2/pull/331 +* Update Lobster documentation by @JaGeo in https://github.com/materialsproject/atomate2/pull/376 +* Fix docs typos by @janosh in https://github.com/materialsproject/atomate2/pull/373 +* Update FireWorks section of docs by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/378 +* Add a copy button to code blocks by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/382 +* clean up doc, remove left-overs from amset example by @JaGeo in https://github.com/materialsproject/atomate2/pull/394 +* More details for lobster documentation by @JaGeo in https://github.com/materialsproject/atomate2/pull/431 +* Deploy docs on every commit to `main` by @janosh in https://github.com/materialsproject/atomate2/pull/422 +* Add clearer documentation on lobster worker by @JaGeo in https://github.com/materialsproject/atomate2/pull/440 +* Docs: add basic workflow tutorial by @rkingsbury in https://github.com/materialsproject/atomate2/pull/408 +* Use GitHub's `deploy-pages` action to deploy docs by @janosh in https://github.com/materialsproject/atomate2/pull/475 ### House-Keeping ๐Ÿงน -- More `ruff` by @janosh in https://github.com/materialsproject/atomate2/pull/344 -- Move all type-hint only imports behind `if TYPE_CHECKING` by @janosh in https://github.com/materialsproject/atomate2/pull/354 -- `ruff` select `perflint` `flake8-slots` by @janosh in https://github.com/materialsproject/atomate2/pull/395 -- Bump `ruff` and fix `PERF401`: Use a list comprehension to create transformed list by @janosh in https://github.com/materialsproject/atomate2/pull/421 -- Simplify: `dict.get(key, None)` -> `dict.get(key)` by @janosh in https://github.com/materialsproject/atomate2/pull/429 -- `dict.setdefault` instead of `if key not in dict: dict[key] = ...` by @janosh in https://github.com/materialsproject/atomate2/pull/452 +* More `ruff` by @janosh in https://github.com/materialsproject/atomate2/pull/344 +* Move all type-hint only imports behind `if TYPE_CHECKING` by @janosh in https://github.com/materialsproject/atomate2/pull/354 +* `ruff` select `perflint` `flake8-slots` by @janosh in https://github.com/materialsproject/atomate2/pull/395 +* Bump `ruff` and fix `PERF401`: Use a list comprehension to create transformed list by @janosh in https://github.com/materialsproject/atomate2/pull/421 +* Simplify: `dict.get(key, None)` -> `dict.get(key)` by @janosh in https://github.com/materialsproject/atomate2/pull/429 +* `dict.setdefault` instead of `if key not in dict: dict[key] = ...` by @janosh in https://github.com/materialsproject/atomate2/pull/452 ## New Contributors -- @naik-aakash made their first contribution in https://github.com/materialsproject/atomate2/pull/279 -- @matthewkuner made their first contribution in https://github.com/materialsproject/atomate2/pull/322 -- @gpetretto made their first contribution in https://github.com/materialsproject/atomate2/pull/414 +* @naik-aakash made their first contribution in https://github.com/materialsproject/atomate2/pull/279 +* @matthewkuner made their first contribution in https://github.com/materialsproject/atomate2/pull/322 +* @gpetretto made their first contribution in https://github.com/materialsproject/atomate2/pull/414 **Full Changelog**: https://github.com/materialsproject/atomate2/compare/v0.0.10...v0.0.11) @@ -125,83 +286,83 @@ Lobster workflow with VASP implementation ([@JaGeo][jageo], [@naik-aakash][naik- New features: -- Defect formation energy workflow with VASP implementation ([@jmmshn][jmmshn], [#215](https://github.com/materialsproject/atomate2/pull/215)) -- Job to retrieve a structure from the MP API at run-time ([@mkhorton][mkhorton], [#176](https://github.com/materialsproject/atomate2/pull/176])) +* Defect formation energy workflow with VASP implementation ([@jmmshn][jmmshn], [#215](https://github.com/materialsproject/atomate2/pull/215)) +* Job to retrieve a structure from the MP API at run-time ([@mkhorton][mkhorton], [#176](https://github.com/materialsproject/atomate2/pull/176])) Enhancements: -- Documentation of phonon workflow ([@QuantumChemist][quantumchemist], [#232](https://github.com/materialsproject/atomate2/pull/232)) -- Refactor defect code ([@jmmshn][jmmshn], [#214](https://github.com/materialsproject/atomate2/pull/214)) -- Use `ruff` for linting ([@janosh][janosh], [#250](https://github.com/materialsproject/atomate2/pull/250)) +* Documentation of phonon workflow ([@QuantumChemist][quantumchemist], [#232](https://github.com/materialsproject/atomate2/pull/232)) +* Refactor defect code ([@jmmshn][jmmshn], [#214](https://github.com/materialsproject/atomate2/pull/214)) +* Use `ruff` for linting ([@janosh][janosh], [#250](https://github.com/materialsproject/atomate2/pull/250)) Bug fixes: -- Use correct k-point density in phonon workflow ([@JaGeo][jageo], [#177](https://github.com/materialsproject/atomate2/pull/177)) -- Fix use of `expanduser` path ([@nwinner][nwinner], [#180](https://github.com/materialsproject/atomate2/pull/180)) -- Correct `calcs_reversed` to be in the proper order ([@Zhuoying][zhuoying], [#182](https://github.com/materialsproject/atomate2/pull/182)) -- Bugfix for `store_volumetric_data` ([@jmmshn][jmmshn], [#212](https://github.com/materialsproject/atomate2/pull/212)) +* Use correct k-point density in phonon workflow ([@JaGeo][jageo], [#177](https://github.com/materialsproject/atomate2/pull/177)) +* Fix use of `expanduser` path ([@nwinner][nwinner], [#180](https://github.com/materialsproject/atomate2/pull/180)) +* Correct `calcs_reversed` to be in the proper order ([@Zhuoying][zhuoying], [#182](https://github.com/materialsproject/atomate2/pull/182)) +* Bugfix for `store_volumetric_data` ([@jmmshn][jmmshn], [#212](https://github.com/materialsproject/atomate2/pull/212)) ## v0.0.8 New features: -- VASP Phonopy workflow ([@JaGeo][jageo], [#137](https://github.com/materialsproject/atomate2/pull/137)) -- Molecular dynamics VASP job ([@mjwen][mjwen], [#134](https://github.com/materialsproject/atomate2/pull/134)) +* VASP Phonopy workflow ([@JaGeo][jageo], [#137](https://github.com/materialsproject/atomate2/pull/137)) +* Molecular dynamics VASP job ([@mjwen][mjwen], [#134](https://github.com/materialsproject/atomate2/pull/134)) Enhancements: -- Update IO classes to use pymatgen base classes ([@rkingsbury][rkingsbury], [#141](https://github.com/materialsproject/atomate2/pull/141)) -- Read and write VASP structures with higher precision ([@JaGeo][jageo], [#167](https://github.com/materialsproject/atomate2/pull/167)) +* Update IO classes to use pymatgen base classes ([@rkingsbury][rkingsbury], [#141](https://github.com/materialsproject/atomate2/pull/141)) +* Read and write VASP structures with higher precision ([@JaGeo][jageo], [#167](https://github.com/materialsproject/atomate2/pull/167)) Bug fixes: -- Fix code examples in docs ([@JaGeo][jageo], [#169](https://github.com/materialsproject/atomate2/pull/169)) -- Fix f-orbital DOS properties ([@Andrew-S-Rosen][arosen], [#138](https://github.com/materialsproject/atomate2/pull/138)) -- Fix `mock_run_vasp` testing to accept args ([@mjwen][mjwen], [#151](https://github.com/materialsproject/atomate2/pull/151)) -- Regenerate calc_types enum ([@mjwen][mjwen], [#153](https://github.com/materialsproject/atomate2/pull/153)) +* Fix code examples in docs ([@JaGeo][jageo], [#169](https://github.com/materialsproject/atomate2/pull/169)) +* Fix f-orbital DOS properties ([@Andrew-S-Rosen][arosen], [#138](https://github.com/materialsproject/atomate2/pull/138)) +* Fix `mock_run_vasp` testing to accept args ([@mjwen][mjwen], [#151](https://github.com/materialsproject/atomate2/pull/151)) +* Regenerate calc_types enum ([@mjwen][mjwen], [#153](https://github.com/materialsproject/atomate2/pull/153)) ## v0.0.7 New features: -- Include band-related features (e.g. band center, bandwidth, skewness, kurtosis) in +* Include band-related features (e.g. band center, bandwidth, skewness, kurtosis) in VASP schema ([@Andrew-S-Rosen][arosen], [#92](https://github.com/materialsproject/atomate2/pull/92)) -- Add `use_auto_ispin` and `update_user_potcar_functional` powerups +* Add `use_auto_ispin` and `update_user_potcar_functional` powerups Enhancements: -- Add `is_hubbard` and `hubbards` to VASP task doc. -- Migrate build system to pyproject.toml. -- Migrate docs to jupyter-book. -- Docs improvements ([@janosh][janosh], [@mjwen][mjwen]) +* Add `is_hubbard` and `hubbards` to VASP task doc. +* Migrate build system to pyproject.toml. +* Migrate docs to jupyter-book. +* Docs improvements ([@janosh][janosh], [@mjwen][mjwen]) Bug fixes: -- Fix HSE tags. -- Fix running bader. -- Make potcar_spec argument usable ([@jmmshn][jmmshn], [#83](https://github.com/materialsproject/atomate2/pull/83)) -- Replace monty which with shutil which ([@Andrew-S-Rosen][arosen], [#92](https://github.com/materialsproject/atomate2/pull/92)) -- Fix `calculate_deformation_potentials()` ([@janosh][janosh], [#94](https://github.com/materialsproject/atomate2/pull/94)) -- Fix gzipping of files with numerical suffixes ([@jmmshn][jmmshn], [#116](https://github.com/materialsproject/atomate2/pull/116)) +* Fix HSE tags. +* Fix running bader. +* Make potcar_spec argument usable ([@jmmshn][jmmshn], [#83](https://github.com/materialsproject/atomate2/pull/83)) +* Replace monty which with shutil which ([@Andrew-S-Rosen][arosen], [#92](https://github.com/materialsproject/atomate2/pull/92)) +* Fix `calculate_deformation_potentials()` ([@janosh][janosh], [#94](https://github.com/materialsproject/atomate2/pull/94)) +* Fix gzipping of files with numerical suffixes ([@jmmshn][jmmshn], [#116](https://github.com/materialsproject/atomate2/pull/116)) ## v0.0.6 New features: -- cclib task document supporting virtually all popular molecular DFT codes out-of-the-box +* cclib task document supporting virtually all popular molecular DFT codes out-of-the-box ([@Andrew-S-Rosen][arosen], [#64](https://github.com/materialsproject/atomate2/pull/64)) Enhancements: -- Add mag_density to VASP output doc ([@Andrew-S-Rosen][arosen], [#65](https://github.com/materialsproject/atomate2/pull/66)) -- Double relax maker now supports two different Makers ([@Andrew-S-Rosen][arosen], [#32](https://github.com/materialsproject/atomate2/pull/32)) +* Add mag_density to VASP output doc ([@Andrew-S-Rosen][arosen], [#65](https://github.com/materialsproject/atomate2/pull/66)) +* Double relax maker now supports two different Makers ([@Andrew-S-Rosen][arosen], [#32](https://github.com/materialsproject/atomate2/pull/32)) Bug fixes: -- Store band structure efermi in CalculationOutput ([@Andrew-S-Rosen][arosen], [#66](https://github.com/materialsproject/atomate2/pull/66)) -- Support for VASP6 and latest pymatgen ([@Andrew-S-Rosen][arosen], [#75](https://github.com/materialsproject/atomate2/pull/75)) -- Fixed atomate2 version string. -- Disabled orbital projections in the electron-phonon workflow. +* Store band structure efermi in CalculationOutput ([@Andrew-S-Rosen][arosen], [#66](https://github.com/materialsproject/atomate2/pull/66)) +* Support for VASP6 and latest pymatgen ([@Andrew-S-Rosen][arosen], [#75](https://github.com/materialsproject/atomate2/pull/75)) +* Fixed atomate2 version string. +* Disabled orbital projections in the electron-phonon workflow. ## v0.0.5 @@ -209,17 +370,17 @@ This version removed Python 3.7 support following numpy and pymatgen. New features: -- Base schema for molecule task documents ([@Andrew-S-Rosen][arosen], [#54](https://github.com/materialsproject/atomate2/pull/54)) +* Base schema for molecule task documents ([@Andrew-S-Rosen][arosen], [#54](https://github.com/materialsproject/atomate2/pull/54)) Bug fixes: -- Fix VASP relaxation using custodian "FULL_OPT" ([@Andrew-S-Rosen][arosen], [#42](https://github.com/materialsproject/atomate2/pull/42)) -- Fix supercell generation and input sets in electron-phonon workflow. -- Fix `HSEBSSetGenerator` INCAR settings. -- Fix issue with magnetism in SOC structures. -- Fix bug with Fermi level and IBRION=1 -- Better handling of URI generation. -- Tweak k-spacing formula to stop large band gaps giving negative values +* Fix VASP relaxation using custodian "FULL_OPT" ([@Andrew-S-Rosen][arosen], [#42](https://github.com/materialsproject/atomate2/pull/42)) +* Fix supercell generation and input sets in electron-phonon workflow. +* Fix `HSEBSSetGenerator` INCAR settings. +* Fix issue with magnetism in SOC structures. +* Fix bug with Fermi level and IBRION=1 +* Better handling of URI generation. +* Tweak k-spacing formula to stop large band gaps giving negative values ## v0.0.4 @@ -227,34 +388,34 @@ Lots of improvements and bug fixes this release. New features: -- AMSET workflow. -- Electron phonon band gap renormalisation workflow. -- Specific uniform and line mode band structure makers. -- Optics maker. -- Transmuter maker. +* AMSET workflow. +* Electron phonon band gap renormalisation workflow. +* Specific uniform and line mode band structure makers. +* Optics maker. +* Transmuter maker. Enhancements: -- Support for automatic handling of ISPIN. -- Add MP base sets ([@Andrew-S-Rosen][arosen], [#27](https://github.com/materialsproject/atomate2/pull/27)) -- Docs updates ([@Andrew-S-Rosen][arosen], [#13](https://github.com/materialsproject/atomate2/pull/13) [#17](https://github.com/materialsproject/atomate2/pull/17)) -- Options to strip band structure and DOS projects to reduce object sizes. -- Input sets now use generators to avoid serialization issues. -- Use smart efermi finding to remove errors with tetrahedron integration in VASP 6. -- Powerups can now work on `Maker` objects directly. +* Support for automatic handling of ISPIN. +* Add MP base sets ([@Andrew-S-Rosen][arosen], [#27](https://github.com/materialsproject/atomate2/pull/27)) +* Docs updates ([@Andrew-S-Rosen][arosen], [#13](https://github.com/materialsproject/atomate2/pull/13) [#17](https://github.com/materialsproject/atomate2/pull/17)) +* Options to strip band structure and DOS projects to reduce object sizes. +* Input sets now use generators to avoid serialization issues. +* Use smart efermi finding to remove errors with tetrahedron integration in VASP 6. +* Powerups can now work on `Maker` objects directly. Bug fixes: -- Use PBEsol by default. -- Increase number of significant figures when writing POSCAR files. -- Remove unused INCAR settings ([@Andrew-S-Rosen][arosen]) -- Add missing LASPH flags on vdW functionals ([@Andrew-S-Rosen][arosen], [#31](https://github.com/materialsproject/atomate2/pull/31)) -- Use `NSW=0` in static calculations ([@Andrew-S-Rosen][arosen], [#10](https://github.com/materialsproject/atomate2/pull/10)) -- `LREAL = False` in static jobs by default ([@Andrew-S-Rosen][arosen], [#23](https://github.com/materialsproject/atomate2/pull/23)) -- Add missing functionals in output schema ([@Andrew-S-Rosen][arosen], [#12](https://github.com/materialsproject/atomate2/pull/12)) -- Many output schema fixes. -- Better support for FireWorks. -- Support writing additional files in VASP jobs. +* Use PBEsol by default. +* Increase number of significant figures when writing POSCAR files. +* Remove unused INCAR settings ([@Andrew-S-Rosen][arosen]) +* Add missing LASPH flags on vdW functionals ([@Andrew-S-Rosen][arosen], [#31](https://github.com/materialsproject/atomate2/pull/31)) +* Use `NSW=0` in static calculations ([@Andrew-S-Rosen][arosen], [#10](https://github.com/materialsproject/atomate2/pull/10)) +* `LREAL = False` in static jobs by default ([@Andrew-S-Rosen][arosen], [#23](https://github.com/materialsproject/atomate2/pull/23)) +* Add missing functionals in output schema ([@Andrew-S-Rosen][arosen], [#12](https://github.com/materialsproject/atomate2/pull/12)) +* Many output schema fixes. +* Better support for FireWorks. +* Support writing additional files in VASP jobs. ## v0.0.3 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index ec5b8cf8f1..0c150f15d3 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,6 +1,6 @@ # Contributing to atomate2 -We love your input! We want to make contributing to as easy and +We love your input! We want to make contributing as easy and transparent as possible, whether it's: - Reporting a bug @@ -32,20 +32,20 @@ make quick and meaningful fixes. When we confirm your bug report, we'll move it to the GitHub issues where its progress can be further tracked. -## Contributing code modifications or additions through Github +## Contributing code modifications or additions through GitHub -We use github to host code, to track issues and feature requests, +We use GitHub to host code, to track issues and feature requests, as well as accept pull requests. We maintain a list of all contributors [here](https://materialsproject.github.io/atomate2/contributors.html). Pull requests are the best way to propose changes to the codebase. -Follow the [Github flow](https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow) +Follow the [GitHub flow](https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow) for more information on this procedure. The basic procedure for making a PR is: - Fork the repo and create your branch from master. -- Commit your improvements to your branch and push to your Github fork (repo). +- Commit your improvements to your branch and push to your GitHub fork (repo). - When you're finished, go to your fork and make a Pull Request. It will automatically update if you need to make further changes. diff --git a/README.md b/README.md index b2dc2e7b48..d7ac33791c 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,7 @@ [![code coverage](https://img.shields.io/codecov/c/gh/materialsproject/atomate2)](https://codecov.io/gh/materialsproject/atomate2) [![pypi version](https://img.shields.io/pypi/v/atomate2?color=blue)](https://pypi.org/project/atomate2) ![supported python versions](https://img.shields.io/pypi/pyversions/atomate2) +[![Zenodo](https://img.shields.io/badge/DOI-10.5281/zenodo.10677081-blue?logo=Zenodo&logoColor=white)](https://zenodo.org/records/10677081) [Documentation][docs] | [PyPI][pypi] | [GitHub][github] @@ -53,7 +54,7 @@ calculations will be performed: 4. A non-self-consistent calculation on a high symmetry k-point path (for the line mode band structure). -```python +```py from atomate2.vasp.flows.core import RelaxBandStructureMaker from jobflow import run_locally from pymatgen.core import Structure @@ -123,6 +124,23 @@ Atomate2 is released under a modified BSD license; the full text can be found [h The development of atomate2 has benefited from many people across several research groups. A full list of contributors can be found [here][contributors]. +## Citing atomate2 + +A journal submission for `atomate2` is planned. In the meantime, please use [`citation.cff`](citation.cff) and the [Zenodo record](https://zenodo.org/badge/latestdoi/306414371) to cite `atomate2`. + +```bib +@software{ganose_atomate2_2024, + author = {Ganose, Alex and Riebesell, Janosh and George, J. and Shen, Jimmy and S. Rosen, Andrew and Ashok Naik, Aakash and nwinner and Wen, Mingjian and rdguha1995 and Kuner, Matthew and Petretto, Guido and Zhu, Zhuoying and Horton, Matthew and Sahasrabuddhe, Hrushikesh and Kaplan, Aaron and Schmidt, Jonathan and Ertural, Christina and Kingsbury, Ryan and McDermott, Matt and Goodall, Rhys and Bonkowski, Alexander and Purcell, Thomas and Zรผgner, Daniel and Qi, Ji}, + doi = {10.5281/zenodo.10677081}, + license = {cc-by-4.0}, + month = jan, + title = {atomate2}, + url = {https://github.com/materialsproject/atomate2}, + version = {0.0.13}, + year = {2024} +} +``` + [pymatgen]: https://pymatgen.org [fireworks]: https://materialsproject.github.io/fireworks/ [jobflow]: https://materialsproject.github.io/jobflow/ diff --git a/citation.cff b/citation.cff new file mode 100644 index 0000000000..aff21df9aa --- /dev/null +++ b/citation.cff @@ -0,0 +1,116 @@ +cff-version: 1.2.0 +message: If you use this software, please cite it using these metadata. +title: atomate2 +doi: 10.5281/zenodo.10677081 +authors: + - given-names: Alex + family-names: Ganose + github: https://github.com/utf + affiliation: Imperial College London + orcid: 0000-0002-4486-3321 + - given-names: Janosh + family-names: Riebesell + github: https://github.com/janosh + affiliation: Cambridge University, Lawrence Berkeley National Laboratory + orcid: 0000-0001-5233-3462 + - given-names: Janine + family-names: George + github: https://github.com/JaGeo + affiliation: Federal Institute for Materials Research and Testing (BAM) + orcid: 0000-0001-8907-0336 + - given-names: Jimmy-Xuan + family-names: Shen + github: https://github.com/jmmshn + affiliation: Lawrence Livermore National Laboratory + orcid: 0000-0002-2743-7531 + - given-names: Andrew + family-names: Rosen + github: https://github.com/Andrew-S-Rosen + name-particle: S. + affiliation: Princeton University + orcid: 0000-0002-0141-7006 + - given-names: Aakash + family-names: Naik + github: https://github.com/naik-aakash + name-particle: Ashok + affiliation: Federal Institute for Materials Research and Testing (BAM) + - given-names: Nick + family-names: Winner + email: nwinner@berkeley.edu + github: https://github.com/nwinner + affiliation: University of California, Berkeley + - given-names: Mingjian + family-names: Wen + github: https://github.com/mjwen + affiliation: University of Houston + - given-names: Rishabh + family-names: Guha + github: https://github.com/rdguha1995 + affiliation: Lawrence Berkeley National Laboratory + - given-names: Matthew + family-names: Kuner + github: https://github.com/matthewkuner + affiliation: University of California, Berkeley + - given-names: Guido + family-names: Petretto + github: https://github.com/gpetretto + affiliation: Universitรฉ catholique de Louvain + - given-names: Zhuoying + family-names: Zhu + github: https://github.com/Zhuoying + affiliation: Lawrence Berkeley National Laboratory + - given-names: Matthew + family-names: Horton + github: https://github.com/mkhorton + affiliation: Microsoft Research + orcid: 0000-0001-7777-8871 + - given-names: Hrushikesh + family-names: Sahasrabuddhe + github: https://github.com/hrushikesh-s + affiliation: University of California, Berkeley + - given-names: Aaron + family-names: Kaplan + github: https://github.com/esoteric-ephemera + affiliation: Lawrence Berkeley National Laboratory + - given-names: Jonathan + family-names: Schmidt + github: https://github.com/JonathanSchmidt1 + affiliation: ETH Zurich + - given-names: Christina + family-names: Ertural + github: https://github.com/QuantumChemist + affiliation: Federal Institute for Materials Research and Testing (BAM) + - given-names: Ryan + family-names: Kingsbury + github: https://github.com/rkingsbury + affiliation: Princeton University + - given-names: Matt + family-names: McDermott + github: https://github.com/mattmcdermott + affiliation: Lawrence Berkeley National Laboratory + - given-names: Rhys + family-names: Goodall + github: https://github.com/CompRhys + affiliation: Chemix.ai + - given-names: Alexander + family-names: Bonkowski + github: https://github.com/ab5424 + affiliation: RWTH Aachen University + - given-names: Thomas + family-names: Purcell + github: https://github.com/tpurcell90 + affiliation: Fritz Haber Institute + - given-names: Daniel + family-names: Zรผgner + github: https://github.com/danielzuegner + affiliation: Microsoft Research + - given-names: Ji + family-names: Qi + github: https://github.com/JiQi535 + affiliation: University of California, San Diego +version: 0.0.13 +date-released: 2024-01-08 +repository-code: https://github.com/materialsproject/atomate2 +license: cc-by-4.0 +license-url: https://github.com/materialsproject/atomate2/blob/main/LICENSE +type: software diff --git a/docs/_static/fonts/lato-bold-italic.woff b/docs/_static/fonts/lato-bold-italic.woff new file mode 100644 index 0000000000..88ad05b9ff Binary files /dev/null and b/docs/_static/fonts/lato-bold-italic.woff differ diff --git a/docs/_static/fonts/lato-bold-italic.woff2 b/docs/_static/fonts/lato-bold-italic.woff2 new file mode 100644 index 0000000000..c4e3d804b5 Binary files /dev/null and b/docs/_static/fonts/lato-bold-italic.woff2 differ diff --git a/docs/_static/fonts/lato-bold.woff b/docs/_static/fonts/lato-bold.woff new file mode 100644 index 0000000000..c6dff51f06 Binary files /dev/null and b/docs/_static/fonts/lato-bold.woff differ diff --git a/docs/_static/fonts/lato-bold.woff2 b/docs/_static/fonts/lato-bold.woff2 new file mode 100644 index 0000000000..bb195043cf Binary files /dev/null and b/docs/_static/fonts/lato-bold.woff2 differ diff --git a/docs/_static/fonts/lato-normal-italic.woff b/docs/_static/fonts/lato-normal-italic.woff new file mode 100644 index 0000000000..76114bc033 Binary files /dev/null and b/docs/_static/fonts/lato-normal-italic.woff differ diff --git a/docs/_static/fonts/lato-normal-italic.woff2 b/docs/_static/fonts/lato-normal-italic.woff2 new file mode 100644 index 0000000000..3404f37e2e Binary files /dev/null and b/docs/_static/fonts/lato-normal-italic.woff2 differ diff --git a/docs/_static/fonts/lato-normal.woff b/docs/_static/fonts/lato-normal.woff new file mode 100644 index 0000000000..ae1307ff5f Binary files /dev/null and b/docs/_static/fonts/lato-normal.woff differ diff --git a/docs/_static/fonts/lato-normal.woff2 b/docs/_static/fonts/lato-normal.woff2 new file mode 100644 index 0000000000..3bf9843328 Binary files /dev/null and b/docs/_static/fonts/lato-normal.woff2 differ diff --git a/docs/about/contributors.md b/docs/about/contributors.md index 987bb88d8e..f5be8c945b 100644 --- a/docs/about/contributors.md +++ b/docs/about/contributors.md @@ -90,8 +90,8 @@ Lawrence Berkeley National Laboratory [0000-0003-3439-4856]: https://orcid.org/0000-0003-3439-4856 **Matthew McDermott** [![gh]][mattmcdermott] [![orc]][0000-0002-4071-3000] \ -PhD student \ -University of California, Berkeley +Postdoctoral Researcher \ +Lawrence Berkeley National Laboratory [mattmcdermott]: https://github.com/mattmcdermott [0000-0002-4071-3000]: https://orcid.org/0000-0002-4071-3000 @@ -103,6 +103,13 @@ University of Arizona [tpurcell90]: https://github.com/tpurcell90 [0000-0003-4564-7206]: https://orcid.org/0000-0003-4564-7206 +**Andrei Sobolev** [![gh]][ansobolev] [![orc]][0000-0001-5086-6601] \ +Software Scientist \ +MS1P e.V. + +[ansobolev]: https://github.com/ansobolev +[0000-0001-5086-6601]: https://orcid.org/0000-0001-5086-6601 + **Alexander Bonkowski** [![gh]][ab5424] [![orc]][0000-0002-0525-4742] \ PhD student in Chemistry \ RWTH Aachen University @@ -116,3 +123,9 @@ University of California, Berkeley [matthewkuner]: https://github.com/matthewkuner [0000-0002-8218-8558]: https://orcid.org/0000-0002-8218-8558 + +**Rhys Goodall** [![gh]][comprhys] [![orc]][0000-0002-6589-1700] \ +Hobbyist Contributor + +[comprhys]: https://github.com/comprhys +[0000-0002-6589-1700]: https://orcid.org/0000-0002-6589-1700 diff --git a/docs/about/license.md b/docs/about/license.md index f53342d160..e302813d6d 100644 --- a/docs/about/license.md +++ b/docs/about/license.md @@ -46,7 +46,7 @@ choose to make your Enhancements available either publicly, or directly to Lawrence Berkeley National Laboratory or its contributors, without imposing a separate written license agreement for such Enhancements, then you hereby grant the following license: -a non-exclusive, royalty-free perpetual license to install, use, +a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, distribute, and sublicense such enhancements or derivative works thereof, in binary and source code form. diff --git a/docs/conf.py b/docs/conf.py index b94d57786a..24df470d11 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -18,7 +18,7 @@ # -- Project information ----------------------------------------------------- project = "atomate2" -copyright = "2023, materialsproject" +copyright = "2023, materialsproject" # noqa: A001 author = "Alex Ganose" # The short X.Y version @@ -138,9 +138,8 @@ # -- Options for HTML output ------------------------------------------------- -# The theme to use for HTML and HTML Help pages. See the documentation for +# The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -# html_theme = "furo" html_theme_options = { "footer_icons": [ diff --git a/docs/dev/abinit_tests.md b/docs/dev/abinit_tests.md new file mode 100644 index 0000000000..faa75a3904 --- /dev/null +++ b/docs/dev/abinit_tests.md @@ -0,0 +1,165 @@ + +# Writing ABINIT Tests + +## Considerations + +Atomate2 includes tools to help write tests for ABINIT workflows. The primary +considerations with the atomate2 testing environment are listed below. + +### Pseudopotentials + +ABINIT heavily relies on pseudo potential tables accessible through abipy. These +tables are large in size or can be downloaded on the fly at input creation time. +Therefore, a smaller pseudopotential table is included for just a few elements. +Structures to be used for testing should be based on the missing elements should +be added to this pseudopotential table. + +Note that information from the real pseudopotential files is used in the creation +of the jobs and flows, hence fake pseudopotentials are not an option here. + +### File sizes + +The files produced by ABINIT are generally large and would overwhelm the size of the +atomate2 repository if not managed carefully. For example, density (DEN) and +wavefunction (WFK) files can easily be ten's of megabytes which can quickly add up. + +To overcome this, we only include essential ABINIT output files in the atomate2 test +folder. For example, DEN, WFK and other density information is not needed in most +instances. For these outputs files which can be required inputs for some jobs, fake +files are generated in the test folder and the linking copying of the files is checked +using these fake files. These fake files contain the information whether they are +a regular file or a symbolic link to another regular file. + +### ABINIT execution + +We cannot run ABINIT on the testing server due to the computational expense. Furthermore, +different versions/compilations of ABINIT may yield slightly different total energies +which are not important for our tests โ€“ we only test that (i) inputs are written +correctly, (ii) outputs are parsed correctly, and (iii) jobs are connected together +properly. + +This is achieved by "mocking" ABINIT execution. Instead of running ABINIT, we copy reference +output files into the current directory and then proceed with running the workflow. + +Note that it is still possible to run integration tests where ABINIT is executed by +passing the `--abinit-integration` option to pytest: + +```bash +pytest --abinit-integration +``` + +When executing tests with the real abinit, larger deviations are expected depending on +ABINIT version, compilation options, etc. + +## Generation of new tests + +Atomate2 provides an automatic procedure to prepare ABINIT data (reference files) +for use in atomate2 tests. It does this by: + +- Preparing a standard maker file that will be used to generate the reference files as + well as to run the tests. +- Create the flow or job using the maker file and a structure file (cif file or other). +- Copying ABINIT inputs and outputs into the correct directory structure and creating + the fake input and output files for large files when relevant. +- Providing a template unit test that is configured for the specific workflow. + +There are four stages to generating the test data: + +### 1. Create the maker file + +The `atm dev abinit-script-maker` command allows to prepare a template `create_maker.py` +script in the current directory. You should adapt this file for the maker you intend +to test. Try to make sure to use parameters that allow the generation to be executed +relatively fast. Additionally, with the integration testing capability for ABINIT +workflows, the faster the workflows can run, the better. + +After adapting the `create_maker.py` script for the maker to be tested, you should run +it: + +```bash +python create_maker.py +``` + +This will generate a `maker.json` containing the serialized version of the maker together +with additional metadata information, inter alia the string of the `create_maker.py` script +itself, the author and author mail (extracted from git config information), date of +generation, ... + +### 2. Generate the reference files + +The `atm dev abinit-generate-reference` command runs the workflow for a given structure +in the current directory using `jobflow`'s `run_locally` option. This will execute the +different abinit jobs of the flow in separated run folders, and dump an `outputs.json` +file with all the outputs of the flow. + +Note that the structure is specified either implicitly in an `initial_structure.json` +file: + +```bash +atm dev abinit-generate-reference +``` + +or explicitly, e.g. as a path to a CIF file: + +```bash +atm dev abinit-generate-reference /path/to/structure.cif +``` + +When an explicit structure file is passed to the `atm dev abinit-generate-reference` +command, the structure is dumped to an `initial_structure.json` file. + +### 3. Copy files to the test_data folder + +Now that the flow has been executed, the generated input and output files have to be +copied to the tests/test_data/abinit folder. This is achieved using the +`atm dev abinit-test-data` command: + +```bash +atm dev abinit-test-data TEST_NAME +``` + +You should change `TEST_NAME` to be a name for the workflow test. Note, `TEST_NAME` should not +contain spaces or punctuation. For example, the band structure workflow test data was +generated using `atm dev vasp-test-data Si_band_structure`. + +This will automatically detect whether the Maker is a Job Maker or a Flow Maker and +copy files in the corresponding `tests/test_data/abinit/jobs/NameOfMaker/TEST_NAME` +or `tests/test_data/abinit/flows/NameOfMaker/TEST_NAME` directory. It will create +the `NameOfMaker/TEST_NAME` directory structure and copy the information about the +Maker and initial structure, i.e. `maker.json`, `initial_structure.json` and +`make_info.json` if present. + +Each job of the flow has its own directory in the `TEST_NAME` directory, +with one directory for each "restart" (i.e. index of the job). The directory +for a given ABINIT run, hereafter referenced as `REF_RUN_FOLDER` thus has the +following structure: + +`tests/test_data/abinit/jobs_OR_flows/NameOfMaker/TEST_NAME/JOB_NAME/JOB_INDEX` + +where `JOB_NAME` is the name of the job and `JOB_INDEX` is the index of the job +(usually "1" unless the job is restarted). + +**Note:** For the script to run successfully, every job in the workflow must have +a unique name. For example, there cannot be two calculations called "relax". +Instead you should ensure they are named something like "relax 1" and "relax 2". + +Each `REF_RUN_FOLDER` contains: + +- A folder called "inputs" with the run.abi and abinit_input.json, as well as with the + indata, outdata and tmpdata directories. The indata directory potentially contains + the reference fake input files needed for the job to be executed (e.g. a fake link to a + previous DEN file). +- A folder called "outputs" with the run.abo, run.err, run.log, as well as with the + indata, outdata and tmpdata directories. In the indata, outdata and tmpdata directories, + the large files are replaced by fake reference files while the necessary files for the + workflow test execution are present. + +### 4. Write the test + +The `atm dev abinit-test-data` command also generates a template test method that is +configured to use the test data that was just generated. In this template test method, +the maker, the initial_structure and the reference paths (i.e. the mapping from the job +name and job index to the reference job folder) are automatically loaded from the test +folder. + +Add `assert` statements to validate the workflow outputs. diff --git a/docs/dev/vasp_tests.md b/docs/dev/vasp_tests.md index 60ec45e7ef..dcee0e69e9 100644 --- a/docs/dev/vasp_tests.md +++ b/docs/dev/vasp_tests.md @@ -59,7 +59,7 @@ The script should also contain some additional code that will allow `atm dev vasp-test-data` to process the reference data. Below we give an example used to generate the elastic constant workflow test data. -```python +```py from atomate2.vasp.flows.elastic import ElasticMaker from atomate2.vasp.powerups import update_user_kpoints_settings from pymatgen.core import Structure @@ -114,18 +114,17 @@ atm dev vasp-test-data WF_NAME ``` You should change WF_NAME to be a name for the workflow. Note, WF_NAME should not -contain spaces or punctuation. For example, the elastic constant workflow test data was -genenerated using `atm dev vasp-test-data Si_elastic`. +contain spaces or punctuation. For example, the elastic constant workflow test data was generated using `atm dev vasp-test-data Si_elastic`. This will generate a folder in the current directory called "WF_NAME" that contains the folders in the correct format. ````{note} By default, the script will only copy POTCAR, POSCAR, CONTCAR, KPOINTS, INCAR, -vasprun.xml, OUTCAR and json files to the WF_NAME folder. If additional files are +vasprun.xml, OUTCAR and JSON files to the WF_NAME folder. If additional files are needed for specific steps of the workflow you need to copy them in manually. A mapping from jobflow calculation folder to job folder in WF_NAME is given at the -to of the `atm dev vasp-test-data` script output. E.g., it will look something +top of the `atm dev vasp-test-data` script output. E.g., it will look something like ``` @@ -162,7 +161,7 @@ The most important part is the section that mocks VASP and configures which chec to perform on the input files. For the elastic constant workflow, it looks something like this: -```python +```py # mapping from job name to directory containing test files ref_paths = { "elastic relax 1/6": "Si_elastic/elastic_relax_1_6", @@ -215,7 +214,7 @@ the k-point density during the test. Finally, you should add `assert` statements to validate the workflow outputs. As an example, the full elastic workflow test is reproduced below. -```python +```py def test_elastic(mock_vasp, clean_dir): import numpy as np from jobflow import run_locally diff --git a/docs/dev/workflow_tutorial.md b/docs/dev/workflow_tutorial.md index cb7d9c2365..40d8c1a746 100644 --- a/docs/dev/workflow_tutorial.md +++ b/docs/dev/workflow_tutorial.md @@ -1,15 +1,15 @@ -# How to Develop a new workflow for `atomate2` +# How to develop a new `atomate2` workflow ## Anatomy of an `atomate2` computational workflow (i.e., what do I need to write?) -Every `atomate2` workflow is an instance of jobflow's `Flow ` class, which is a collection of Job and/or other `Flow` objects. So your end goal is to produce a `Flow `. +Every `atomate2` workflow is an instance of jobflow's `Flow` class, which is a collection of Job and/or other `Flow` objects. So your end goal is to produce a `Flow`. -In the context of computational materials science, `Flow ` objects are most easily created by a `Maker`, which contains a factory method make() that produces a `Flow `, given certain inputs. Typically, the input to `Maker`.make() includes atomic coordinate information in the form of a `pymatgen` `Structure` or `Molecule` object. So the basic signature looks like this: +In the context of computational materials science, `Flow` objects are most easily created by a `Maker`, which contains a factory method make() that produces a `Flow`, given certain inputs. Typically, the input to `Maker`.make() includes atomic coordinate information in the form of a `pymatgen` `Structure` or `Molecule` object. So the basic signature looks like this: -```python +```py class ExampleMaker(Maker): def make(self, coordinates: Structure) -> Flow: - # take the input coordinates and return a `Flow ` + # take the input coordinates and return a `Flow` return Flow(...) ``` @@ -18,7 +18,7 @@ The `Maker` class usually contains most of the calculation parameters and other One common task encountered in almost any materials science calculation is writing calculation input files to disk so they can be executed by the underlying software (e.g., VASP, Q-Chem, CP2K, etc.). This is preferably done via a `pymatgen` `InputSet` class. `InputSet` is essentially a dict-like container that specifies the files that need to be written, and their contents. Similarly to the way that `Maker` classes generate `Flow`s, `InputSet`s are most easily created by `InputGenerator` classes. `InputGenerator` have a method `get_input_set()` that typically takes atomic coordinates (e.g., a `Structure` or `Molecule` object) and produce an `InputSet`, e.g., -```python +```py class ExampleInputGenerator(InputGenerator): def get_input_set(self, coordinates: Structure) -> InputSet: # take the input coordinates, determine appropriate @@ -30,7 +30,7 @@ class ExampleInputGenerator(InputGenerator): **TODO - the code block below needs refinement. Not exactly sure how write_inputs() fits into a`Job`** -```python +```py class ExampleMaker(Maker): input_set_generator: ExampleInputGenerator = field( default_factory=ExampleInputGenerator @@ -49,15 +49,16 @@ Finally, most `atomate2` workflows return structured output in the form of "Task **TODO - extend code block above to illustrate TaskDoc usage** In summary, a new `atomate2` workflow consists of the following components: - - A `Maker` that actually generates the workflow - - One or more `Job` and/or `Flow ` classes that define the discrete steps in the workflow - - (optionally) an `InputGenerator` that produces a `pymatgen` `InputSet` for writing calculation input files - - (optionally) a `TaskDocument` that defines a schema for storing the output data + +- A `Maker` that actually generates the workflow +- One or more `Job` and/or `Flow` classes that define the discrete steps in the workflow +- (optionally) an `InputGenerator` that produces a `pymatgen` `InputSet` for writing calculation input files +- (optionally) a `TaskDocument` that defines a schema for storing the output data ## Where do I put my code? Because of the distributed design of the MP Software Ecosystem, writing a complete new workflow may involve making contributions to more than one GitHub repository. The following guidelines should help you understand where to put your contribution. - - All workflow code (`Job`, `Flow `, `Maker`) belongs in `atomate2` - - `InputSet` and `InputGenerator` code belongs in `pymatgen`. However, if you need to create these classes from scratch (i.e., you are working with a code that is not already supported in`pymatgen`), then it is recommended to include them in `atomate2` at first to facilitate rapid iteration. Once mature, they can be moved to `pymatgen` or to a `pymatgen` [addon package](https://pymatgen.org/addons). - - `TaskDocument` schemas should generally be developed in `atomate2` alongside the workflow code. We recommend that you first check emmet to see if there is an existing schema that matches what you need. If so, you can import it. If not, check [`cclib`](https://cclib.github.io/). `cclib` output can be imported via [`atomate2.common.schemas.TaskDocument`](https://github.com/materialsproject/atomate2/blob/main/src/atomate2/common/schemas/cclib.py). If neither code has what you need, then new schemas should be developed within `atomate2` (or `cclib`). +- All workflow code (`Job`, `Flow`, `Maker`) belongs in `atomate2` +- `InputSet` and `InputGenerator` code belongs in `pymatgen`. However, if you need to create these classes from scratch (i.e., you are working with a code that is not already supported in`pymatgen`), then it is recommended to include them in `atomate2` at first to facilitate rapid iteration. Once mature, they can be moved to `pymatgen` or to a `pymatgen` [addon package](https://pymatgen.org/addons). +- `TaskDocument` schemas should generally be developed in `atomate2` alongside the workflow code. We recommend that you first check emmet to see if there is an existing schema that matches what you need. If so, you can import it. If not, check [`cclib`](https://cclib.github.io/). `cclib` output can be imported via [`atomate2.common.schemas.TaskDocument`](https://github.com/materialsproject/atomate2/blob/main/src/atomate2/common/schemas/cclib.py). If neither code has what you need, then new schemas should be developed within `atomate2` (or `cclib`). diff --git a/docs/index.md b/docs/index.md index dbe5b9bec7..646fad8693 100644 --- a/docs/index.md +++ b/docs/index.md @@ -18,6 +18,7 @@ reference/index :caption: Developer Guide :hidden: dev/dev_install +dev/workflow_tutorial dev/vasp_tests ``` diff --git a/docs/user/atomate-1-vs-2.md b/docs/user/atomate-1-vs-2.md index 3aa317dfe9..8a54a1103f 100644 --- a/docs/user/atomate-1-vs-2.md +++ b/docs/user/atomate-1-vs-2.md @@ -2,6 +2,7 @@ This document contains introductory context for people coming from atomate 1. One of atomate2's core ideas is to allow scaling from a single material, to 100 materials, or 100,000 materials. Therefore, both local submission options and a connection to workflow managers such as FireWorks exist. We plan to support more workflow managers in the future to further ease job submission. + ## Relation between managers running the actual jobs and the workflow as written in `atomate2` There is no leakage between job manager and the workflow definition in `atomate2`. For example, Fireworks is not a required dependency of `atomate2` or `jobflow`. Any `atomate2` workflow can be run using the local manager or an extensible set of external providers, Fireworks just one among them. E.g. all tests are run with mocked calls to the executables using the local manager. diff --git a/docs/user/codes/vasp.md b/docs/user/codes/vasp.md index f3a2134d9a..cf24b76b23 100644 --- a/docs/user/codes/vasp.md +++ b/docs/user/codes/vasp.md @@ -232,6 +232,12 @@ converted into a dynamical matrix. To correct for polarization effects, a correc dynamical matrix based on BORN charges can be performed. Finally, phonon densities of states, phonon band structures and thermodynamic properties are computed. +```{warning} +The current implementation of the workflow does not consider the initial magnetic moments +for the determination of the symmetry of the structure; therefore, they are removed from the structure. +``` + + ```{note} It is heavily recommended to symmetrize the structure before passing it to this flow. Otherwise, a different space group might be detected and too @@ -241,7 +247,7 @@ adjust them if necessary. The default might not be strict enough for your specific case. ``` -### Lobster +### LOBSTER Perform bonding analysis with [LOBSTER](http://cohp.de/) and [LobsterPy](https://github.com/jageo/lobsterpy) @@ -258,9 +264,16 @@ VASP_CMD: <> LOBSTER_CMD: <> ``` +```{note} +A LOBSTER workflow with settings compatible to LOBSTER database (Naik, A.A., et al. Sci Data 10, 610 (2023). https://doi.org/10.1038/s41597-023-02477-5 , currently being integrated into Materials Project) is also available now, +which could be used by simply importing from atomate2.vasp.flows.mp > MPVaspLobsterMaker +instead of VaspLobsterMaker. Rest of the things to execute the workflow stays same as +shown below. +``` + The corresponding flow could, for example, be started with the following code: -```Python +```py from jobflow import SETTINGS from jobflow import run_locally from pymatgen.core.structure import Structure @@ -287,7 +300,7 @@ It is, however, computationally very beneficial to define two different types o Specifically, you might want to change the `_fworker` for the LOBSTER runs and define a separate `lobster` worker within FireWorks: -```python +```py from fireworks import LaunchPad from jobflow.managers.fireworks import flow_to_workflow from pymatgen.core.structure import Structure @@ -321,7 +334,7 @@ lpad.add_wf(wf) Outputs from the automatic analysis with LobsterPy can easily be extracted from the database and also plotted: -```python +```py from jobflow import SETTINGS from pymatgen.electronic_structure.cohp import Cohp from pymatgen.electronic_structure.plotter import CohpPlotter @@ -339,7 +352,7 @@ result = store.query_one( ) for number, (key, cohp) in enumerate( - result["output"]["lobsterpy_data"]["cohp_plot_data"].items() + result["output"]["lobsterpy_data"]["cohp_plot_data"]["data"].items() ): plotter = CohpPlotter() cohp = Cohp.from_dict(cohp) @@ -347,13 +360,50 @@ for number, (key, cohp) in enumerate( plotter.save_plot(f"plots_all_bonds{number}.pdf") for number, (key, cohp) in enumerate( - result["output"]["lobsterpy_data_cation_anion"]["cohp_plot_data"].items() + result["output"]["lobsterpy_data_cation_anion"]["cohp_plot_data"]["data"].items() ): plotter = CohpPlotter() cohp = Cohp.from_dict(cohp) plotter.add_cohp(key, cohp) plotter.save_plot(f"plots_cation_anion_bonds{number}.pdf") ``` +#### Running the LOBSTER workflow without database and with one job script only + +It is also possible to run the VASP-LOBSTER workflow with a minimal setup. +In this case, you will run the VASP calculations on the same node as the LOBSTER calculations. +In between, the different computations you will switch from MPI to OpenMP parallelization. + +For example, for a node with 48 cores, you could use an adapted version of the following SLURM script: + +```bash +#!/bin/bash +#SBATCH -J vasplobsterjob +#SBATCH -o ./%x.%j.out +#SBATCH -e ./%x.%j.err +#SBATCH -D ./ +#SBATCH --mail-type=END +#SBATCH --mail-user=you@you.de +#SBATCH --time=24:00:00 +#SBATCH --nodes=1 +#This needs to be adapted if you run with different cores +#SBATCH --ntasks=48 + +# ensure you load the modules to run VASP, e.g., module load vasp +module load my_vasp_module +# please activate the required conda environment +conda activate my_environment +cd my_folder +# the following script needs to contain the workflow +python xyz.py +``` + +The `LOBSTER_CMD` now needs an additional export of the number of threads. + +```yaml +VASP_CMD: <> +LOBSTER_CMD: OMP_NUM_THREADS=48 <> +``` + (modifying_input_sets)= Modifying input sets @@ -363,7 +413,7 @@ The inputs for a calculation can be modified in several ways. Every VASP job takes a {obj}`.VaspInputGenerator` as an argument (`input_set_generator`). One option is to specify an alternative input set generator: -```python +```py from atomate2.vasp.sets.core import StaticSetGenerator from atomate2.vasp.jobs.core import StaticMaker @@ -382,7 +432,7 @@ The second approach is to edit the job after it has been made. All VASP jobs hav the `input_set_generator` attribute maker will update the input set that gets written: -```python +```py static_job.maker.input_set_generator.user_incar_settings["LOPTICS"] = True ``` @@ -392,7 +442,7 @@ functions called "powerups" that can apply settings updates to all VASP jobs in These powerups also contain filters for the name of the job and the maker used to generate them. -```python +```py from atomate2.vasp.powerups import update_user_incar_settings from atomate2.vasp.flows.elastic import ElasticMaker from atomate2.vasp.flows.core import DoubleRelaxMaker @@ -469,7 +519,7 @@ All VASP workflows are constructed using the `Maker.make()` function. The argume for this function always include: - `structure`: A pymatgen structure. -- `prev_vasp_dir`: A previous VASP directory to copy output files from. +- `prev_dir`: A previous VASP directory to copy output files from. There are two options when chaining workflows: @@ -480,12 +530,12 @@ There are two options when chaining workflows: set KSPACING), and the magnetic moments. Some workflows will also use other outputs. For example, the Band Structure workflow will copy the CHGCAR file (charge density) from the previous calculation. This can be achieved by setting both the - `structure` and `prev_vasp_dir` arguments. + `structure` and `prev_dir` arguments. These two examples are illustrated in the code below, where we chain a relaxation calculation and a static calculation. -```python +```py from jobflow import Flow from atomate2.vasp.jobs.core import RelaxMaker, StaticMaker from pymatgen.core.structure import Structure @@ -500,7 +550,7 @@ static_job = StaticMaker().make(structure=relax_job.output.structure) # create a static job that will use additional outputs from the relaxation static_job = StaticMaker().make( - structure=relax_job.output.structure, prev_vasp_dir=relax_job.output.dir_name + structure=relax_job.output.structure, prev_dir=relax_job.output.dir_name ) # create a flow including the two jobs and set the output to be that of the static diff --git a/docs/user/fireworks.md b/docs/user/fireworks.md index defad2ca5a..abbdf440ae 100644 --- a/docs/user/fireworks.md +++ b/docs/user/fireworks.md @@ -13,9 +13,10 @@ FireWorks workflow using the {obj}`~jobflow.managers.fireworks.flow_to_workflow` The workflow can then be submitted to the launchpad in the usual way. For example, to submit an MgO band structure workflow using FireWorks: -```python +```py from fireworks import LaunchPad from atomate2.vasp.flows.core import RelaxBandStructureMaker +from atomate2.vasp.powerups import add_metadata_to_flow from jobflow.managers.fireworks import flow_to_workflow from pymatgen.core import Structure @@ -29,6 +30,14 @@ mgo_structure = Structure( # make a band structure flow to optimise the structure and obtain the band structure bandstructure_flow = RelaxBandStructureMaker().make(mgo_structure) +# (Optional) add metadata to the flow task document. +# Could be useful to filter specific results from the database. +# For e.g., adding material project ID for the compound, use following lines +bandstructure_flow = add_metadata_to_flow( + flow=bandstructure_flow, + additional_fields={"mp_id": "mp-190"}, +) + # convert the flow to a fireworks WorkFlow object wf = flow_to_workflow(bandstructure_flow) @@ -37,7 +46,7 @@ lpad = LaunchPad.auto_load() lpad.add_wf(wf) ``` -Additional details about interfacing Jobflow-based packages with FireWorks can be found in the [Running Jobflow with FireWorks](fw_guide) guide. +Additional details about interfacing Jobflow-based packages with FireWorks can be found in the [Running Jobflow with FireWorks][fw_guide] guide. [fireworks]: https://materialsproject.github.io/fireworks/ [fireworks_instructions]: https://materialsproject.github.io/jobflow/install_fireworks.html diff --git a/docs/user/install.md b/docs/user/install.md index d1ec9ecc39..781dd2d9fd 100644 --- a/docs/user/install.md +++ b/docs/user/install.md @@ -5,14 +5,14 @@ ## Introduction This guide will get you up and running in an environment for running high-throughput -workflows with atomate2. atomate2 is built on the pymatgen, custodian, jobflow, and -FireWorks libraries. Briefly: +workflows with atomate2. atomate2 is built on the `pymatgen`, `custodian`, `jobflow`, and +`FireWorks` libraries. Briefly: -- [pymatgen] is used to create input files and analyze the output of materials science codes. -- [custodian] runs your simulation code (e.g., VASP) and performs error checking/handling +- [`pymatgen`] is used to create input files and analyze the output of materials science codes. +- [`custodian`] runs your simulation code (e.g., VASP) and performs error checking/handling and checkpointing. -- [jobflow] is used to design computational workflows. -- [FireWorks] (optional) is used to manage and execute workflows on HPC machines. +- [`jobflow`] is used to design computational workflows. +- [`FireWorks`] (optional) is used to manage and execute workflows on HPC machines. Running and writing your own workflows are covered in later tutorials. For now, these topics will be covered in enough depth to get you set up and to help you know where to @@ -21,10 +21,10 @@ troubleshoot if you're having problems. Note that this installation tutorial is VASP-centric since almost all functionality currently in atomate2 pertains to VASP. -[pymatgen]: http://pymatgen.org -[custodian]: https://materialsproject.github.io/custodian -[fireworks]: https://materialsproject.github.io/fireworks -[jobflow]: https://materialsproject.github.io/jobflow +[`pymatgen`]: http://pymatgen.org +[`custodian`]: https://materialsproject.github.io/custodian +[`fireworks`]: https://materialsproject.github.io/fireworks +[`jobflow`]: https://materialsproject.github.io/jobflow ### Objectives @@ -76,16 +76,16 @@ MongoDB must be running and available to accept connections whenever you're runn workflows. Thus, it is strongly recommended that you have a server to run MongoDB or (simpler) use a hosting service. Your options are: -- Use a commercial service to host your MongoDB instance. These are typically the +1. Use a commercial service to host your MongoDB instance. These are typically the easiest to use and offer high-quality service but require payment for larger databases. [MongoDB Atlas](https://www.mongodb.com/cloud/atlas) offers a free 500 MB - server which is certainly enough to get started for small to medium size projects, and + server which is certainly enough to get started for small to medium-sized projects, and it is easy to upgrade or migrate your database if you exceed the free allocation. -- Contact your supercomputing center to see if they offer MongoDB hosting (e.g., NERSC +1. Contact your supercomputing center to see if they offer MongoDB hosting (e.g., NERSC has this, Google "request NERSC MongoDB database"). -- Self-host a MongoDB server. +1. Self-host a MongoDB server. -If you're just starting, we suggest the first (with a free plan) or second option +If you're just starting, we suggest option 1 (with a free plan) or 2 (if available to you). The third option will require you to open up network settings to accept outside connections properly which can sometimes be tricky. @@ -113,7 +113,7 @@ issues later in this tutorial, some options are: ## Create a directory scaffold for atomate2 -Installing atomate2 includes installation of codes, configuration files, and various +Installing atomate2 includes the installation of codes, configuration files, and various binaries and libraries. Thus, it is useful to create a directory structure that organizes all these items. @@ -140,7 +140,7 @@ Make sure to create a Python 3.8+ environment as recent versions of atomate2 onl support Python 3.8 and higher. ``` -We highly recommended that you organize your installation of the atomate2 and the other +We highly recommend that you organize your installation of the atomate2 and the other Python codes using a conda virtual environment. Some of the main benefits are: - Different Python projects that have conflicting packages can coexist on the same @@ -175,6 +175,16 @@ To install the packages run: pip install atomate2 ``` +If you would like to use more specialized capabilities of `atomate2` such as the phonon, Lobster or force field workflows, you would need to run one of + +```bash +pip install atomate2[phonons] +pip install atomate2[lobster] +pip install atomate2[forcefields] +``` + +See [`pyproject.toml`](https://github.com/materialsproject/atomate2/blob/main/pyproject.toml) for all available optional dependency sets. More detailed instructions can be found under [dev installation](../dev/dev_install.md). + ## Configure calculation output database The next step is to configure your MongoDB database that will be used to store @@ -194,7 +204,7 @@ that are unique only to these databases. Create the following files in `<>/config`. -### jobflow.yaml +### `jobflow.yaml` The `jobflow.yaml` file contains the credentials of the MongoDB server that will store calculation outputs. The `jobflow.yaml` file requires you to enter the basic database @@ -351,14 +361,13 @@ workflows. ### Define the workflow Workflows are written using the `jobflow` software. Essentially, individual stages of -a workflow are simple Python functions. Jobflow provides a way to connect jobs together -in a natural way. For more details on connecting jobs together see: -[](connecting_vasp_jobs). +a workflow are simple Python functions. Jobflow provides a way to connect jobs in a natural way. +For more details on connecting jobs see: [](connecting_vasp_jobs). Go to the directory where you would like your calculations to run (i.e., your scratch or work directory) and create a file called `relax.py` containing: -```python +```py from atomate2.vasp.jobs.core import RelaxMaker from jobflow import run_locally from pymatgen.core import Structure @@ -416,7 +425,7 @@ on the Grid Engine scheduler, this would be using `qsub job.sh`. Once the job is finished, you can connect to the output database and check the job output. -```python +```py from jobflow import SETTINGS store = SETTINGS.JOB_STORE diff --git a/docs/user/running-workflows.md b/docs/user/running-workflows.md index b6d0ef69f7..28322571af 100644 --- a/docs/user/running-workflows.md +++ b/docs/user/running-workflows.md @@ -7,7 +7,7 @@ Once you have a working installation of atomate2, you'll want to jump in and start running workflows. Atomate2 includes many workflows with reasonable settings that can get you started. This tutorial will quickly guide you through customizing and running a -workflow to calculate the bandstructure of MgO. +workflow to calculate the band structure of MgO. ### Objectives @@ -16,7 +16,7 @@ workflow to calculate the bandstructure of MgO. ### Prerequisites -In order for you to complete this tutorial you need +For you to complete this tutorial you need * A working installation of atomate2. @@ -60,7 +60,7 @@ workflow. Create a Python script named `mgo_bandstructure.py` with the following contents: -```python +```py from atomate2.vasp.flows.core import RelaxBandStructureMaker from jobflow import run_locally from pymatgen.core import Structure @@ -116,7 +116,7 @@ results will be in your database. Finally, we'll plot the results that we calculated. Simply run the following Python code, either as a script or on the Python prompt. -```python +```py from jobflow import SETTINGS from pymatgen.electronic_structure.plotter import DosPlotter, BSPlotter from pymatgen.electronic_structure.dos import CompleteDos @@ -136,7 +136,7 @@ dos = CompleteDos.from_dict(result["output"]["vasp_objects"]["dos"]) # plot the DOS dos_plotter = DosPlotter() dos_plotter.add_dos_dict(dos.get_element_dos()) -dos_plotter.save_plot("MgO-dos.pdf", xlim=(-10, 10), img_format="pdf") +dos_plotter.save_plot("MgO-dos.pdf", xlim=(-10, 10)) # get the line mode bandstructure from the database result = store.query_one( @@ -150,7 +150,7 @@ bandstructure = BandStructureSymmLine.from_dict( # plot the line mode band structure bs_plotter = BSPlotter(bandstructure) -bs_plotter.save_plot("MgO-bandstructure.pdf", img_format="pdf") +bs_plotter.save_plot("MgO-bandstructure.pdf") ``` If you open the saved figures, you should see a plot of your DOS and bandstructure! diff --git a/pyproject.toml b/pyproject.toml index 37cd52d785..cfcc443181 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,60 +27,84 @@ requires-python = ">=3.9" dependencies = [ "PyYAML", "click", - "custodian>=2023.3.10", - "emmet-core>=0.70.5", + "custodian>=2024.4.18", + "emmet-core==0.82.2", "jobflow>=0.1.11", - "monty>=2023.9.25", + "monty>=2024.2.2", "numpy", "pydantic-settings>=2.0.3", "pydantic>=2.0.1", - "pymatgen>=2023.10.11", + "pymatgen>=2024.4.13", ] [project.optional-dependencies] +abinit = ["abipy>=0.9.3"] amset = ["amset>=0.4.15", "pydash"] cclib = ["cclib"] mp = ["mp-api>=0.37.5"] phonons = ["phonopy>=1.10.8", "seekpath"] -lobster = ["lobsterpy>=0.3.2"] -defects = ["dscribe>=1.2.0", "pymatgen-analysis-defects>=2022.11.30"] -forcefields = ["chgnet>=0.2.2", "matgl>=0.8.3", "quippy-ase>=0.9.14"] +lobster = ["ijson>=3.2.2", "lobsterpy>=0.4.0"] +defects = [ + "dscribe>=1.2.0", + "pymatgen-analysis-defects>=2024.5.11", + "python-ulid", +] +forcefields = [ + "ase>=3.22.1", + "chgnet>=0.2.2", + "mace-torch>=0.3.3", + "matgl>=1.1.1", + "quippy-ase>=0.9.14", + "torch<=2.2.1", # incompatibility with dgl if newer versions are used +] docs = [ "FireWorks==2.0.3", - "autodoc_pydantic==2.0.1", - "furo==2023.9.10", - "ipython==8.16.1", + "autodoc_pydantic==2.1.0", + "furo==2024.5.6", + "ipython==8.25.0", "jsonschema[format]", "myst_parser==2.0.0", - "numpydoc==1.6.0", + "numpydoc==1.7.0", "sphinx-copybutton==0.5.2", "sphinx==7.2.6", - "sphinx_design==0.5.0", + "sphinx_design==0.6.0", ] dev = ["pre-commit>=2.12.1"] -tests = ["FireWorks==2.0.3", "pytest-cov==4.1.0", "pytest==7.4.2"] +tests = [ + "FireWorks==2.0.3", + "pytest-cov==5.0.0", + "pytest-mock==3.14.0", + "pytest==8.0.2", +] strict = [ "PyYAML==6.0.1", - "cclib==1.8", - "chgnet==0.2.2", + # must use >= for ase to not uninstall main branch install in CI + # last known working commit: https://gitlab.com/ase/ase@2bab58f4e + "ase>=3.22.1", + "cclib==1.8.1", + "chgnet==0.3.8", "click==8.1.7", - "custodian==2023.10.9", - "dscribe==2.1.0", - "emmet-core==0.70.5", - "jobflow==0.1.14", - "lobsterpy==0.3.2", - "matgl==0.8.3", - "monty==2023.9.25", - "mp-api==0.37.5", + "custodian==2024.4.18", + "dscribe==2.1.1", + "emmet-core==0.82.2", + "ijson==3.3.0", + "jobflow==0.1.17", + "lobsterpy==0.4.4", + "mace-torch>=0.3.3", + "matgl==1.1.2", + "monty==2024.5.24", + "mp-api==0.41.2", "numpy", - "phonopy==2.20.0", - "pydantic-settings==2.0.3", - "pydantic==2.4.2", - "pymatgen-analysis-defects==2023.8.22", - "pymatgen==2023.10.11", + "phonopy==2.24.3", + "pydantic-settings==2.3.3", + "pydantic==2.7.4", + "pymatgen-analysis-defects==2024.5.11", + "pymatgen==2024.6.10", + "python-ulid==2.7.0", "quippy-ase==0.9.14", "seekpath==2.1.0", - "typing-extensions==4.8.0", + "torch==2.2.1", + "typing-extensions==4.12.2", ] [project.scripts] @@ -102,21 +126,12 @@ atomate2 = ["py.typed"] method = "git" default-tag = "0.0.1" -[tool.flake8] -max-line-length = 88 -max-doc-length = 88 -select = "C, E, F, W, B" -extend-ignore = "E203, W503, E501, F401, RST21" -min-python-version = "3.8.0" -docstring-convention = "numpy" -rst-roles = "class, func, ref, obj" - [tool.mypy] ignore_missing_imports = true no_strict_optional = true [tool.pytest.ini_options] -addopts = "-p no:warnings --import-mode=importlib" +addopts = "-p no:warnings --import-mode=importlib --cov-config=pyproject.toml" filterwarnings = [ "ignore:.*POTCAR.*:UserWarning", "ignore:.*input structure.*:UserWarning", @@ -144,57 +159,58 @@ exclude_lines = [ [tool.ruff] target-version = "py39" -select = [ - "B", # flake8-bugbear - "C4", # flake8-comprehensions - "D", # pydocstyle - "E", # pycodestyle error - "EXE", # flake8-executable - "F", # pyflakes - "FA", # flake8-future-annotations - "FBT003", # boolean-positional-value-in-call - "FLY", # flynt - "I", # isort - "ICN", # flake8-import-conventions - "ISC", # flake8-implicit-str-concat - "PD", # pandas-vet - "PERF", # perflint - "PIE", # flake8-pie - "PL", # pylint - "PT", # flake8-pytest-style - "PYI", # flakes8-pyi - "Q", # flake8-quotes - "RET", # flake8-return - "RSE", # flake8-raise - "RUF", # Ruff-specific rules - "SIM", # flake8-simplify - "SLOT", # flake8-slots - "TCH", # flake8-type-checking - "TID", # flake8-tidy-imports - "UP", # pyupgrade - "W", # pycodestyle warning - "YTT", # flake8-2020 -] + +[tool.ruff.lint] +select = ["ALL"] ignore = [ + "ANN002", + "ANN003", + "ANN101", # missing self type annotation + "ANN102", # missing cls annotation + "ANN401", + "ARG002", # unused method argument + # "BLE001", + "C408", # Unnecessary (dict/list/tuple) call - remove call + "C901", # function too complex + "COM812", # trailing comma missing + "EM", # exception message must not use f-string literal + "ERA001", # found commented out code + "FBT001", + "FBT002", + "FIX002", + "G004", # logging uses fstring + "ISC001", "PD011", # pandas-use-of-dot-values "PERF203", # try-except-in-loop - "PLR", # pylint-refactor + "PLR0911", # too many returns + "PLR0912", # too many branches + "PLR0913", # too many arguments + "PLR0915", # too many local statements + "PLR2004", "PT004", # pytest-missing-fixture-name-underscore "PT006", # pytest-parametrize-names-wrong-type + "PT013", # pytest-incorrect-pytest-import + "PTH", # prefer Pathlib to os.path "RUF013", # implicit-optional - # TODO remove PT011, pytest.raises() should always check err msg - "PT011", # pytest-raises-too-broad - "PT013", # pytest-incorrect-pytest-import + "S324", # use of insecure hash function + "S507", # paramiko auto trust + "TD", # TODOs + "TRY003", # long message outside exception class ] pydocstyle.convention = "numpy" isort.known-first-party = ["atomate2"] +isort.split-on-trailing-comma = false + +[tool.ruff.format] +docstring-code-format = true -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "__init__.py" = ["F401"] -"**/tests/*" = ["D"] +"**/tests/*" = ["ANN", "ARG001", "D", "INP001", "PLR2004", "S101"] # flake8-type-checking (TCH): things inside TYPE_CHECKING aren't available # at runtime and so can't be used by pydantic models # flake8-future-annotations (FA): pipe operator for type unions only work in pydantic models in python 3.10+ "**/schemas/*" = ["FA", "TCH", "UP007"] "**/schemas.py" = ["FA", "TCH", "UP007"] "**/settings.py" = ["FA", "TCH", "UP007"] +"docs/*" = ["INP001"] diff --git a/src/atomate2/abinit/__init__.py b/src/atomate2/abinit/__init__.py new file mode 100644 index 0000000000..26ccf27793 --- /dev/null +++ b/src/atomate2/abinit/__init__.py @@ -0,0 +1 @@ +"""Module for ABINIT workflows.""" diff --git a/src/atomate2/abinit/files.py b/src/atomate2/abinit/files.py new file mode 100644 index 0000000000..af05b9f94d --- /dev/null +++ b/src/atomate2/abinit/files.py @@ -0,0 +1,141 @@ +"""Functions for manipulating Abinit files.""" + +from __future__ import annotations + +import logging +import os +from typing import TYPE_CHECKING + +from abipy.flowtk.utils import abi_extensions +from monty.serialization import loadfn + +from atomate2.abinit.utils.common import INDIR_NAME +from atomate2.utils.file_client import FileClient, auto_fileclient + +if TYPE_CHECKING: + from collections.abc import Iterable + from pathlib import Path + + from abipy.abio.inputs import AbinitInput + from pymatgen.core.structure import Structure + + from atomate2.abinit.sets.base import AbinitInputGenerator + + +logger = logging.getLogger(__name__) + + +ALL_ABIEXTS = abi_extensions() + + +def fname2ext(filepath: Path | str) -> None | str: + """Get the abinit extension of a given filename. + + This will return None if no extension is found. + """ + filename = os.path.basename(filepath) + if "_" not in filename: + return None + ext = filename.split("_")[-1].replace(".nc", "") + if ext not in ALL_ABIEXTS: + return None + return ext + + +@auto_fileclient +def out_to_in( + out_files: Iterable[tuple[str, str]], + src_host: str | None = None, + indir: Path | str = INDIR_NAME, + file_client: FileClient | None = None, + link_files: bool = True, +) -> None: + """ + Copy or link abinit output files to the Abinit input directory. + + Parameters + ---------- + out_files : list of tuples + The list of (abinit output filepath, abinit input filename) to be copied + or linked. + src_host : str or None + The source hostname used to specify a remote filesystem. Can be given as + either "username@remote_host" or just "remote_host" in which case the username + will be inferred from the current user. If ``None``, the local filesystem will + be used as the source. + indir : Path or str + The input directory for Abinit input files. + file_client : .FileClient + A file client to use for performing file operations. + link_files : bool + Whether to link the files instead of copying them. + """ + dest_dir = file_client.abspath(indir, host=None) + + for out_filepath, in_file in out_files: + src_file = file_client.abspath(out_filepath, host=src_host) + dest_file = os.path.join(dest_dir, in_file) + if link_files and src_host is None: + file_client.link(src_file, dest_file) + else: + file_client.copy(src_file, dest_file, src_host=src_host) + + +def load_abinit_input( + dirpath: Path | str, fname: str = "abinit_input.json" +) -> AbinitInput: + """Load the AbinitInput object from a given directory. + + Parameters + ---------- + dirpath + Directory to load the AbinitInput from. + fname + Name of the json file containing the AbinitInput. + + Returns + ------- + AbinitInput + The AbinitInput object. + """ + abinit_input_file = os.path.join(dirpath, f"{fname}") + if not os.path.exists(abinit_input_file): + raise NotImplementedError( + f"Cannot load AbinitInput from directory without {fname} file." + ) + + return loadfn(abinit_input_file) + + +def write_abinit_input_set( + structure: Structure, + input_set_generator: AbinitInputGenerator, + prev_outputs: str | Path | list[str] | None = None, + restart_from: str | Path | list[str] | None = None, + directory: str | Path = ".", +) -> None: + """Write the abinit inputs for a given structure using a given generator. + + Parameters + ---------- + structure + The structure for which the abinit inputs have to be written. + input_set_generator + The input generator used to write the abinit inputs. + prev_outputs + The list of previous directories needed for the calculation. + restart_from + The previous directory of the same calculation (in case of a restart). + Note that this should be provided as a list of one directory. + directory + Directory in which to write the abinit inputs. + """ + ais = input_set_generator.get_input_set( + structure=structure, + restart_from=restart_from, + prev_outputs=prev_outputs, + ) + if not ais.validate(): + raise RuntimeError("AbinitInputSet is not valid.") + + ais.write_input(directory=directory, make_dir=True, overwrite=False) diff --git a/src/atomate2/abinit/flows/__init__.py b/src/atomate2/abinit/flows/__init__.py new file mode 100644 index 0000000000..af583bc735 --- /dev/null +++ b/src/atomate2/abinit/flows/__init__.py @@ -0,0 +1 @@ +"""Flows for running ABINIT calculations.""" diff --git a/src/atomate2/abinit/flows/core.py b/src/atomate2/abinit/flows/core.py new file mode 100644 index 0000000000..8219ebd9aa --- /dev/null +++ b/src/atomate2/abinit/flows/core.py @@ -0,0 +1,139 @@ +"""Core abinit flow makers.""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +from jobflow import Flow, Maker + +from atomate2.abinit.jobs.core import ( + LineNonSCFMaker, + RelaxMaker, + StaticMaker, + UniformNonSCFMaker, +) + +if TYPE_CHECKING: + from pathlib import Path + + from pymatgen.core.structure import Structure + + from atomate2.abinit.jobs.base import BaseAbinitMaker + + +@dataclass +class BandStructureMaker(Maker): + """ + Maker to generate abinit band structures. + + This is a static calculation followed by two non-self-consistent field + calculations, one uniform and one line mode. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + scf_maker : .BaseAbinitMaker + The maker to use for the static calculation. + bs_maker : .BaseAbinitMaker + The maker to use for the non-self-consistent field calculations. + """ + + name: str = "band structure - dos" + static_maker: BaseAbinitMaker = field(default_factory=StaticMaker) + bs_maker: BaseAbinitMaker | None = field(default_factory=LineNonSCFMaker) + dos_maker: BaseAbinitMaker | None = field(default_factory=UniformNonSCFMaker) + + def make( + self, + structure: Structure, + restart_from: str | Path | None = None, + ) -> Flow: + """Create a band structure flow. + + Parameters + ---------- + structure : Structure + A pymatgen structure object. + restart_from : str or Path or None + One previous directory to restart from. + + Returns + ------- + Flow + A band structure flow. + """ + static_job = self.static_maker.make(structure, restart_from=restart_from) + jobs = [static_job] + + if self.dos_maker: + uniform_job = self.dos_maker.make( + prev_outputs=static_job.output.dir_name, + ) + jobs.append(uniform_job) + + if self.bs_maker: + line_job = self.bs_maker.make( + prev_outputs=static_job.output.dir_name, + ) + jobs.append(line_job) + + return Flow(jobs, name=self.name) + + +@dataclass +class RelaxFlowMaker(Maker): + """ + Maker to generate a relaxation flow with abinit. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + relaxation_makers : .BaseAbinitMaker + The maker or list of makers to use for the relaxation flow. + """ + + name: str = "relaxation" + relaxation_makers: list[Maker] = field( + default_factory=lambda: [ + RelaxMaker.ionic_relaxation(), + RelaxMaker.full_relaxation(), + ] + ) + + def make( + self, + structure: Structure | None = None, + restart_from: str | Path | None = None, + ) -> Flow: + """Create a relaxation flow. + + Parameters + ---------- + structure : Structure + A pymatgen structure object. + restart_from : str or Path or None + One previous directory to restart from. + + Returns + ------- + Flow + A relaxation flow. + """ + relax_job1 = self.relaxation_makers[0].make( + structure=structure, restart_from=restart_from + ) + jobs = [relax_job1] + for rlx_maker in self.relaxation_makers[1:]: + rlx_job = rlx_maker.make(restart_from=jobs[-1].output.dir_name) + jobs.append(rlx_job) + return Flow(jobs, output=jobs[-1].output, name=self.name) + + @classmethod + def ion_ioncell_relaxation(cls, *args, **kwargs) -> Flow: + """Create a double relaxation (ionic relaxation + full relaxation).""" + ion_rlx_maker = RelaxMaker.ionic_relaxation(*args, **kwargs) + ioncell_rlx_maker = RelaxMaker.full_relaxation(*args, **kwargs) + return cls(relaxation_makers=[ion_rlx_maker, ioncell_rlx_maker]) diff --git a/src/atomate2/abinit/jobs/__init__.py b/src/atomate2/abinit/jobs/__init__.py new file mode 100644 index 0000000000..53aa989eee --- /dev/null +++ b/src/atomate2/abinit/jobs/__init__.py @@ -0,0 +1 @@ +"""Jobs for running ABINIT calculations.""" diff --git a/src/atomate2/abinit/jobs/base.py b/src/atomate2/abinit/jobs/base.py new file mode 100644 index 0000000000..148089914b --- /dev/null +++ b/src/atomate2/abinit/jobs/base.py @@ -0,0 +1,244 @@ +"""Definition of base ABINIT job maker.""" + +from __future__ import annotations + +import logging +import os +import time +from dataclasses import dataclass, field +from pathlib import Path +from typing import TYPE_CHECKING, Any, ClassVar, NamedTuple + +import jobflow +from jobflow import Maker, Response, job + +from atomate2 import SETTINGS +from atomate2.abinit.files import write_abinit_input_set +from atomate2.abinit.run import run_abinit +from atomate2.abinit.schemas.calculation import TaskState +from atomate2.abinit.schemas.task import AbinitTaskDoc +from atomate2.abinit.utils.common import UnconvergedError +from atomate2.abinit.utils.history import JobHistory + +if TYPE_CHECKING: + from collections.abc import Sequence + + from abipy.flowtk.events import AbinitCriticalWarning + from pymatgen.core.structure import Structure + + from atomate2.abinit.sets.base import AbinitInputGenerator + +logger = logging.getLogger(__name__) + +__all__ = ["BaseAbinitMaker"] + + +class JobSetupVars(NamedTuple): + start_time: float + history: JobHistory + workdir: str + abipy_manager: None # To change in the future + wall_time: int | None + + +def setup_job( + structure: Structure, + prev_outputs: str | Path | list[str] | None, + restart_from: str | Path | list[str] | None, + history: JobHistory, + wall_time: int | None, +) -> JobSetupVars: + """Set up job.""" + # Get the start time. + start_time = time.time() + + if structure is None and prev_outputs is None and restart_from is None: + raise RuntimeError( + "At least one of structure, prev_outputs or " + "restart_from should be defined." + ) + + if history is None: + # Supposedly the first time the job is created + history = JobHistory() + elif restart_from is not None: + # We want to log the restart only if the restart_from is due to + # an automatic restart, not a restart from e.g. another scf or relax + # with different parameters. + history.log_restart() + + # Set up working directory + workdir = os.getcwd() + + # Log information about the start of the job + history.log_start(workdir=workdir, start_time=start_time) + + # Set up logging + log_handler = logging.FileHandler("atomate2_abinit.log") + log_handler.setFormatter(logging.Formatter(logging.BASIC_FORMAT)) + logging.getLogger("pymatgen.io.abinit").addHandler(log_handler) + logging.getLogger("abipy").addHandler(log_handler) + logging.getLogger("atomate2").addHandler(log_handler) + + # Load the atomate settings for abinit to get configuration parameters + # TODO: how to allow for tuned parameters on a per-job basis ? + # (similar to fw_spec-passed settings) + abipy_manager = None # Currently disabled as it is needed for autoparal, + # which is not yet supported + # abipy_manager = get_abipy_manager(SETTINGS) + + # set walltime, if possible + # TODO: see in set_walltime, where to put this walltime_command + # wall_time = wall_time + return JobSetupVars( + start_time=start_time, + history=history, + workdir=workdir, + abipy_manager=abipy_manager, + wall_time=wall_time, + ) + + +@dataclass +class BaseAbinitMaker(Maker): + """ + Base ABINIT job maker. + + Parameters + ---------- + input_set_generator : AbinitInputGenerator + Input generator to be used. + name : str + The job name. + wall_time : int + The wall time for the job. + run_abinit_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_abinit`. + task_document_kwargs : dict[str, Any] + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + """ + + input_set_generator: AbinitInputGenerator + name: str = "base abinit job" + wall_time: int | None = None + run_abinit_kwargs: dict[str, Any] = field(default_factory=dict) + task_document_kwargs: dict[str, Any] = field(default_factory=dict) + + # class variables + CRITICAL_EVENTS: ClassVar[Sequence[AbinitCriticalWarning]] = () + + def __post_init__(self) -> None: + """Process post-init configuration.""" + self.critical_events = list(self.CRITICAL_EVENTS) + + @property + def calc_type(self) -> str: + """Get the type of calculation for this maker.""" + return self.input_set_generator.calc_type + + @job + def make( + self, + structure: Structure | None = None, + prev_outputs: str | Path | list[str] | None = None, + restart_from: str | Path | list[str] | None = None, + history: JobHistory | None = None, + ) -> jobflow.Job: + """Get an ABINIT jobflow.Job. + + Parameters + ---------- + structure : Structure + A pymatgen structure object. + prev_outputs : TODO: add description from sets.base + restart_from : TODO: add description from sets.base + history : JobHistory + A JobHistory object containing the history of this job. + """ + # Setup job and get general job configuration + config = setup_job( + structure=structure, + prev_outputs=prev_outputs, + restart_from=restart_from, + history=history, + wall_time=self.wall_time, + ) + + # Write abinit input set + write_abinit_input_set( + structure=structure, + input_set_generator=self.input_set_generator, + prev_outputs=prev_outputs, + restart_from=restart_from, + directory=config.workdir, + ) + + # Run abinit + run_abinit( + wall_time=config.wall_time, + start_time=config.start_time, + **self.run_abinit_kwargs, + ) + + # parse Abinit outputs + + task_doc = AbinitTaskDoc.from_directory( + Path.cwd(), + **self.task_document_kwargs, + ) + task_doc.task_label = self.name + if len(task_doc.event_report.filter_types(self.critical_events)) > 0: + task_doc = task_doc.model_copy(update={"state": TaskState.UNCONVERGED}) + task_doc.calcs_reversed[-1] = task_doc.calcs_reversed[-1].model_copy( + update={"has_abinit_completed": TaskState.UNCONVERGED} + ) # optional I think + + return self.get_response( + task_document=task_doc, + history=config.history, + max_restarts=SETTINGS.ABINIT_MAX_RESTARTS, + prev_outputs=prev_outputs, + ) + + def get_response( + self, + task_document: AbinitTaskDoc, + history: JobHistory, + max_restarts: int = 5, + prev_outputs: str | tuple | list | Path | None = None, + ) -> Response: + """Get new job to restart abinit calculation.""" + if task_document.state == TaskState.SUCCESS: + return Response( + output=task_document, + ) + + if history.run_number > max_restarts: + # TODO: check here if we should stop jobflow or children or + # if we should throw an error. + unconverged_error = UnconvergedError( + self, + msg=f"Unconverged after {history.run_number} runs.", + abinit_input=task_document.input.abinit_input, + history=history, + ) + return Response( + output=task_document, + stop_children=True, + stop_jobflow=False, + stored_data={"error": unconverged_error}, + ) + + logger.info("Getting restart job.") + + new_job = self.make( + structure=task_document.structure, + restart_from=task_document.dir_name, + prev_outputs=prev_outputs, + history=history, + ) + + return Response( + output=task_document, + replace=new_job, + ) diff --git a/src/atomate2/abinit/jobs/core.py b/src/atomate2/abinit/jobs/core.py new file mode 100644 index 0000000000..0f7958c7ad --- /dev/null +++ b/src/atomate2/abinit/jobs/core.py @@ -0,0 +1,195 @@ +"""Core jobs for running ABINIT calculations.""" + +from __future__ import annotations + +import logging +from dataclasses import dataclass, field +from typing import TYPE_CHECKING, ClassVar + +from abipy.flowtk.events import ( + AbinitCriticalWarning, + NscfConvergenceWarning, + RelaxConvergenceWarning, + ScfConvergenceWarning, +) +from jobflow import Job, job + +from atomate2.abinit.jobs.base import BaseAbinitMaker +from atomate2.abinit.sets.core import ( + LineNonSCFSetGenerator, + NonSCFSetGenerator, + NonScfWfqInputGenerator, + RelaxSetGenerator, + StaticSetGenerator, + UniformNonSCFSetGenerator, +) + +if TYPE_CHECKING: + from collections.abc import Sequence + + from pymatgen.core.structure import Structure + + from atomate2.abinit.sets.base import AbinitInputGenerator + from atomate2.abinit.utils.history import JobHistory + +logger = logging.getLogger(__name__) + + +@dataclass +class StaticMaker(BaseAbinitMaker): + """Maker to create ABINIT scf jobs. + + Parameters + ---------- + name : str + The job name. + """ + + calc_type: str = "scf" + name: str = "Scf calculation" + input_set_generator: AbinitInputGenerator = field( + default_factory=StaticSetGenerator + ) + + CRITICAL_EVENTS: ClassVar[Sequence[AbinitCriticalWarning]] = ( + ScfConvergenceWarning, + ) + + +@dataclass +class LineNonSCFMaker(BaseAbinitMaker): + """Maker to create a jobs with a non-scf ABINIT calculation along a line. + + Parameters + ---------- + name : str + The job name. + """ + + calc_type: str = "nscf_line" + name: str = "Line non-Scf calculation" + input_set_generator: AbinitInputGenerator = field( + default_factory=LineNonSCFSetGenerator + ) + + CRITICAL_EVENTS: ClassVar[Sequence[AbinitCriticalWarning]] = ( + NscfConvergenceWarning, + ) + + +@dataclass +class UniformNonSCFMaker(BaseAbinitMaker): + """Maker to create a jobs with a non-scf ABINIT calculation along a line. + + Parameters + ---------- + name : str + The job name. + """ + + calc_type: str = "nscf_uniform" + name: str = "Uniform non-Scf calculation" + input_set_generator: AbinitInputGenerator = field( + default_factory=UniformNonSCFSetGenerator + ) + + CRITICAL_EVENTS: ClassVar[Sequence[AbinitCriticalWarning]] = ( + NscfConvergenceWarning, + ) + + +@dataclass +class NonSCFMaker(BaseAbinitMaker): + """Maker to create non SCF calculations.""" + + calc_type: str = "nscf" + name: str = "non-Scf calculation" + + input_set_generator: AbinitInputGenerator = field( + default_factory=NonSCFSetGenerator + ) + + # Non dataclass variables: + CRITICAL_EVENTS: ClassVar[Sequence[AbinitCriticalWarning]] = ( + NscfConvergenceWarning, + ) + + @job + def make( + self, + structure: Structure | None = None, + prev_outputs: str | list[str] | None = None, + restart_from: str | list[str] | None = None, + history: JobHistory | None = None, + mode: str = "uniform", + ) -> Job: + """Run a non-scf ABINIT job. + + Parameters + ---------- + structure : .Structure + A pymatgen structure object. + mode : str + Type of band structure calculation. Options are: + - "line": Full band structure along symmetry lines. + - "uniform": Uniform mesh band structure. + """ + self.input_set_generator.mode = mode + + return super().make.original( + self, + structure=structure, + prev_outputs=prev_outputs, + restart_from=restart_from, + history=history, + ) + + +@dataclass +class NonSCFWfqMaker(NonSCFMaker): + """Maker to create non SCF calculations for the WFQ.""" + + calc_type: str = "nscf_wfq" + name: str = "non-Scf calculation" + + input_set_generator: AbinitInputGenerator = field( + default_factory=NonScfWfqInputGenerator + ) + + # Non dataclass variables: + CRITICAL_EVENTS: ClassVar[Sequence[AbinitCriticalWarning]] = ( + NscfConvergenceWarning, + ) + + +@dataclass +class RelaxMaker(BaseAbinitMaker): + """Maker to create relaxation calculations.""" + + calc_type: str = "relax" + input_set_generator: AbinitInputGenerator = field(default_factory=RelaxSetGenerator) + name: str = "Relaxation calculation" + + # non-dataclass variables + CRITICAL_EVENTS: ClassVar[Sequence[AbinitCriticalWarning]] = ( + RelaxConvergenceWarning, + ) + + @classmethod + def ionic_relaxation(cls, *args, **kwargs) -> Job: + """Create an ionic relaxation maker.""" + # TODO: add the possibility to tune the RelaxInputGenerator options + # in this class method. + return cls( + input_set_generator=RelaxSetGenerator(*args, relax_cell=False, **kwargs), + name=cls.name + " (ions only)", + ) + + @classmethod + def full_relaxation(cls, *args, **kwargs) -> Job: + """Create a full relaxation maker.""" + # TODO: add the possibility to tune the RelaxInputGenerator options + # in this class method. + return cls( + input_set_generator=RelaxSetGenerator(*args, relax_cell=True, **kwargs) + ) diff --git a/src/atomate2/abinit/powerups.py b/src/atomate2/abinit/powerups.py new file mode 100644 index 0000000000..42df5f7ce8 --- /dev/null +++ b/src/atomate2/abinit/powerups.py @@ -0,0 +1,226 @@ +"""Powerups for performing common modifications on ABINIT jobs and flows.""" + +from __future__ import annotations + +from copy import deepcopy +from typing import Any + +from jobflow import Flow, Job, Maker +from pymatgen.io.abinit.abiobjects import KSampling + +from atomate2.abinit.jobs.base import BaseAbinitMaker + + +def update_maker_kwargs( + class_filter: Maker | None, + dict_mod_updates: dict, + flow: Job | Flow | Maker, + name_filter: str | None, +) -> Job | Flow | Maker: + """ + Update an object inside a Job, a Flow or a Maker. + + A generic method to be shared for more specific updates that will + build the dict_mod_updates. + + Parameters + ---------- + flow : .Job or .Flow or .Maker + A job, flow or Maker. + dict_mod_updates : dict + The updates to apply. + name_filter : str or None + A filter for the name of the jobs. + class_filter : Maker or None + A filter for the class used to generate the flows. Note the class + filter will match any subclasses. + + Returns + ------- + Job or Flow or Maker + A copy of the input modified flow/job/maker. + """ + updated_flow = deepcopy(flow) + if isinstance(updated_flow, Maker): + updated_flow = updated_flow.update_kwargs( + {"_set": dict_mod_updates}, + name_filter=name_filter, + class_filter=class_filter, + dict_mod=True, + ) + else: + updated_flow.update_maker_kwargs( + {"_set": dict_mod_updates}, + name_filter=name_filter, + class_filter=class_filter, + dict_mod=True, + ) + return updated_flow + + +def update_user_abinit_settings( + flow: Job | Flow | Maker, + abinit_updates: dict[str, Any], + name_filter: str | None = None, + class_filter: type[Maker] | None = BaseAbinitMaker, +) -> Job | Flow | Maker: + """ + Update the user_abinit_settings of any AbinitInputGenerator in the flow. + + Alternatively, if a Maker is supplied, the user_abinit_settings of the maker will + be updated. + + Note, this returns a copy of the original Job/Flow/Maker. I.e., the update does not + happen in place. + + Parameters + ---------- + flow : .Job or .Flow or .Maker + A job, flow or Maker. + abinit_updates : dict + The updates to apply. Existing keys in user_abinit_settings will not be modified + unless explicitly specified in ``abinit_updates``. + name_filter : str or None + A filter for the name of the jobs. + class_filter : Maker or None + A filter for the BaseAbinitMaker class used to generate the flows. Note the + class filter will match any subclasses. + + Returns + ------- + Job or Flow or Maker + A copy of the input flow/job/maker modified to use the updated abinit settings. + """ + dict_mod_updates = { + f"input_set_generator->user_abinit_settings->{k}": v + for k, v in abinit_updates.items() + } + + return update_maker_kwargs(class_filter, dict_mod_updates, flow, name_filter) + + +def update_factory_kwargs( + flow: Job | Flow | Maker, + factory_updates: dict[str, Any], + name_filter: str | None = None, + class_filter: type[Maker] | None = BaseAbinitMaker, +) -> Job | Flow | Maker: + """ + Update the factory_kwargs of any AbinitInputGenerator in the flow. + + Alternatively, if a Maker is supplied, the factory_kwargs of the maker will + be updated. + + Note, this returns a copy of the original Job/Flow/Maker. I.e., the update does not + happen in place. + + Parameters + ---------- + flow : .Job or .Flow or .Maker + A job, flow or Maker. + factory_updates : dict + The updates to apply. Existing keys in factory_kwargs will not be modified + unless explicitly specified in ``factory_updates``. + name_filter : str or None + A filter for the name of the jobs. + class_filter : Maker or None + A filter for the BaseAbinitMaker class used to generate the flows. Note the + class filter will match any subclasses. + + Returns + ------- + Job or Flow or Maker + A copy of the input flow/job/maker modified to use the updated factory settings. + """ + dict_mod_updates = { + f"input_set_generator->factory_kwargs->{k}": v + for k, v in factory_updates.items() + } + + return update_maker_kwargs(class_filter, dict_mod_updates, flow, name_filter) + + +def update_user_kpoints_settings( + flow: Job | Flow | Maker, + kpoints_updates: dict[str, Any] | KSampling, + name_filter: str | None = None, + class_filter: type[Maker] | None = BaseAbinitMaker, +) -> Job | Flow | Maker: + """ + Update the user_kpoints_settings of any AbinitInputGenerator in the flow. + + Alternatively, if a Maker is supplied, the user_kpoints_settings of the maker will + be updated. + + Note, this returns a copy of the original Job/Flow/Maker. I.e., the update does not + happen in place. + + Parameters + ---------- + flow : .Job or .Flow or .Maker + A job, flow or Maker. + kpoints_updates : dict + The updates to apply. Can be specified as a dictionary or as a KSampling object. + If a dictionary is supplied, existing keys in user_kpoints_settings will not be + modified unless explicitly specified in ``kpoints_updates``. + name_filter : str or None + A filter for the name of the jobs. + class_filter : Maker or None + A filter for the BaseAbinitMaker class used to generate the flows. Note the + class filter will match any subclasses. + + Returns + ------- + Job or Flow or Maker + A copy of the input flow/job/maker modified to use the updated kpoints settings. + """ + if isinstance(kpoints_updates, KSampling): + dict_mod_updates = { + "input_set_generator->user_kpoints_settings": kpoints_updates + } + else: + dict_mod_updates = { + f"input_set_generator->user_kpoints_settings->{k}": v + for k, v in kpoints_updates.items() + } + + return update_maker_kwargs(class_filter, dict_mod_updates, flow, name_filter) + + +def update_generator_attributes( + flow: Job | Flow | Maker, + generator_updates: dict[str, Any], + name_filter: str | None = None, + class_filter: type[Maker] | None = BaseAbinitMaker, +) -> Job | Flow | Maker: + """ + Update any attribute of any AbinitInputGenerator in the flow. + + Alternatively, if a Maker is supplied, the attributes of the maker will + be updated. + + Note, this returns a copy of the original Job/Flow/Maker. I.e., the update does not + happen in place. + + Parameters + ---------- + flow : .Job or .Flow or .Maker + A job, flow or Maker. + generator_updates : dict + The updates to apply to the input generator. + name_filter : str or None + A filter for the name of the jobs. + class_filter : Maker or None + A filter for the BaseAbinitMaker class used to generate the flows. Note the + class filter will match any subclasses. + + Returns + ------- + Job or Flow or Maker + A copy of the input flow/job/maker modified to use the updated factory settings. + """ + dict_mod_updates = { + f"input_set_generator->{k}": v for k, v in generator_updates.items() + } + + return update_maker_kwargs(class_filter, dict_mod_updates, flow, name_filter) diff --git a/src/atomate2/abinit/run.py b/src/atomate2/abinit/run.py new file mode 100644 index 0000000000..8137c57ba2 --- /dev/null +++ b/src/atomate2/abinit/run.py @@ -0,0 +1,64 @@ +"""Functions to run ABINIT.""" + +from __future__ import annotations + +import logging +import subprocess +import time + +from abipy.flowtk.qutils import time2slurm + +from atomate2 import SETTINGS +from atomate2.abinit.utils.common import ( + INPUT_FILE_NAME, + LOG_FILE_NAME, + STDERR_FILE_NAME, +) + +__all__ = ["run_abinit"] + + +SLEEP_TIME_STEP = 30 + + +logger = logging.getLogger(__name__) + + +def run_abinit( + abinit_cmd: str = None, + mpirun_cmd: str = None, + wall_time: int = None, + start_time: float = None, +) -> None: + """Run ABINIT.""" + abinit_cmd = abinit_cmd or SETTINGS.ABINIT_CMD + mpirun_cmd = mpirun_cmd or SETTINGS.ABINIT_MPIRUN_CMD + start_time = start_time or time.time() + command = [mpirun_cmd, abinit_cmd] if mpirun_cmd is not None else [abinit_cmd] + + max_end_time = 0.0 + if wall_time is not None: + abinit_timelimit = wall_time + if abinit_timelimit > 480: + # TODO: allow tuning this timelimit buffer for abinit, + # e.g. using a config variable or possibly per job + abinit_timelimit -= 240 + command.extend(["--timelimit", time2slurm(abinit_timelimit)]) + max_end_time = start_time + wall_time + + command.append(INPUT_FILE_NAME) + + with open(LOG_FILE_NAME, "w") as stdout, open(STDERR_FILE_NAME, "w") as stderr: + process = subprocess.Popen(command, stdout=stdout, stderr=stderr) # noqa: S603 + + if wall_time is not None: + while True: + time.sleep(SLEEP_TIME_STEP) + if process.poll() is not None: + break + current_time = time.time() + remaining_time = max_end_time - current_time + if remaining_time < 5 * SLEEP_TIME_STEP: + process.terminate() + + process.wait() diff --git a/src/atomate2/abinit/schemas/__init__.py b/src/atomate2/abinit/schemas/__init__.py new file mode 100644 index 0000000000..8074968c44 --- /dev/null +++ b/src/atomate2/abinit/schemas/__init__.py @@ -0,0 +1 @@ +"""Definition of schemas for results of ABINIT calculations.""" diff --git a/src/atomate2/abinit/schemas/calculation.py b/src/atomate2/abinit/schemas/calculation.py new file mode 100644 index 0000000000..15b8cff682 --- /dev/null +++ b/src/atomate2/abinit/schemas/calculation.py @@ -0,0 +1,274 @@ +"""Schemas for Abinit calculation objects.""" + +from __future__ import annotations + +import logging +import os +from datetime import datetime, timezone +from pathlib import Path +from typing import Optional, Union + +from abipy.electrons.gsr import GsrFile +from abipy.flowtk import events +from abipy.flowtk.utils import File +from emmet.core.math import Matrix3D, Vector3D +from jobflow.utils import ValueEnum +from pydantic import BaseModel, Field +from pymatgen.core import Structure +from typing_extensions import Self + +from atomate2.abinit.utils.common import LOG_FILE_NAME, MPIABORTFILE, get_event_report + +logger = logging.getLogger(__name__) + + +class TaskState(ValueEnum): + """Abinit calculation state.""" + + SUCCESS = "successful" + FAILED = "failed" + UNCONVERGED = "unconverged" + + +class AbinitObject(ValueEnum): + """Types of Abinit data objects.""" + + DOS = "dos" + BAND_STRUCTURE = "band_structure" + ELECTRON_DENSITY = "electron_density" # e_density + WFN = "wfn" # Wavefunction file + TRAJECTORY = "trajectory" + + +class CalculationOutput(BaseModel): + """Document defining Abinit calculation outputs. + + Parameters + ---------- + energy: float + The final total DFT energy for the calculation + energy_per_atom: float + The final DFT energy per atom for the calculation + structure: Structure + The final pymatgen Structure of the system + efermi: float + The Fermi level from the calculation in eV + forces: List[Vector3D] + Forces acting on each atom + stress: Matrix3D + The stress on the cell + is_metal: bool + Whether the system is metallic + bandgap: float + The band gap from the calculation in eV + cbm: float + The conduction band minimum in eV (if system is not metallic + vbm: float + The valence band maximum in eV (if system is not metallic) + """ + + energy: float = Field( + None, description="The final total DFT energy for the calculation" + ) + energy_per_atom: float = Field( + None, description="The final DFT energy per atom for the calculation" + ) + + structure: Union[Structure] = Field( + None, description="The final structure from the calculation" + ) + + efermi: float = Field( + None, description="The Fermi level from the calculation in eV" + ) + + forces: Optional[list[Vector3D]] = Field( + None, description="Forces acting on each atom" + ) + stress: Optional[Matrix3D] = Field(None, description="The stress on the cell") + is_metal: Optional[bool] = Field(None, description="Whether the system is metallic") + bandgap: Optional[float] = Field( + None, description="The band gap from the calculation in eV" + ) + direct_bandgap: Optional[float] = Field( + None, description="The direct band gap from the calculation in eV" + ) + cbm: Optional[float] = Field( + None, + description="The conduction band minimum, or LUMO for molecules, in eV " + "(if system is not metallic)", + ) + vbm: Optional[float] = Field( + None, + description="The valence band maximum, or HOMO for molecules, in eV " + "(if system is not metallic)", + ) + + @classmethod + def from_abinit_gsr( + cls, + output: GsrFile, # Must use auto_load kwarg when passed + ) -> Self: + """Create an Abinit output document from Abinit outputs. + + Parameters + ---------- + output: .AbinitOutput + An AbinitOutput object. + + Returns + ------- + The Abinit calculation output document. + """ + structure = output.structure # final structure by default for GSR + + # In case no conduction bands were included + try: + cbm = output.ebands.get_edge_state("cbm").eig + bandgap = output.ebands.fundamental_gaps[ + 0 + ].energy # [0] for one spin channel only + direct_bandgap = output.ebands.direct_gaps[0].energy + except ValueError: + cbm = None + bandgap = None + direct_bandgap = None + + electronic_output = { + "efermi": float(output.ebands.fermie), + "vbm": output.ebands.get_edge_state("vbm").eig, + "cbm": cbm, + "bandgap": bandgap, + "direct_bandgap": direct_bandgap, + } + + forces = None + if output.cart_forces is not None: + forces = output.cart_forces.tolist() + + stress = None + if output.cart_stress_tensor is not None: + stress = output.cart_stress_tensor.tolist() + + return cls( + structure=structure, + energy=output.energy, + energy_per_atom=output.energy_per_atom, + **electronic_output, + forces=forces, + stress=stress, + ) + + +class Calculation(BaseModel): + """Full Abinit calculation inputs and outputs. + + Parameters + ---------- + dir_name: str + The directory for this Abinit calculation + abinit_version: str + Abinit version used to perform the calculation + has_abinit_completed: .TaskState + Whether Abinit completed the calculation successfully + output: .CalculationOutput + The Abinit calculation output + completed_at: str + Timestamp for when the calculation was completed + output_file_paths: Dict[str, str] + Paths (relative to dir_name) of the Abinit output files + associated with this calculation + """ + + dir_name: str = Field(None, description="The directory for this Abinit calculation") + abinit_version: str = Field( + None, description="Abinit version used to perform the calculation" + ) + has_abinit_completed: TaskState = Field( + None, description="Whether Abinit completed the calculation successfully" + ) + output: CalculationOutput = Field(None, description="The Abinit calculation output") + completed_at: str = Field( + None, description="Timestamp for when the calculation was completed" + ) + event_report: events.EventReport = Field( + None, description="Event report of this abinit job." + ) + output_file_paths: Optional[dict[str, str]] = Field( + None, + description="Paths (relative to dir_name) of the Abinit output files " + "associated with this calculation", + ) + + @classmethod + def from_abinit_files( + cls, + dir_name: Path | str, + task_name: str, + abinit_gsr_file: Path | str = "out_GSR.nc", + abinit_log_file: Path | str = LOG_FILE_NAME, + abinit_abort_file: Path | str = MPIABORTFILE, + ) -> tuple[Self, dict[AbinitObject, dict]]: + """Create an Abinit calculation document from a directory and file paths. + + Parameters + ---------- + dir_name: Path or str + The directory containing the calculation outputs. + task_name: str + The task name. + abinit_gsr_file: Path or str + Path to the GSR output of abinit job, relative to dir_name. + abinit_log_file: Path or str + Path to the main log of abinit job, relative to dir_name. + abinit_abort_file: Path or str + Path to the main abort file of abinit job, relative to dir_name. + + Returns + ------- + .Calculation + An Abinit calculation document. + """ + dir_name = Path(dir_name) + abinit_gsr_file = dir_name / abinit_gsr_file + abinit_log_file = dir_name / abinit_log_file + abinit_abort_file = dir_name / abinit_abort_file + + abinit_gsr = GsrFile.from_file(abinit_gsr_file) + + completed_at = str( + datetime.fromtimestamp(os.stat(abinit_log_file).st_mtime, tz=timezone.utc) + ) + + output_doc = CalculationOutput.from_abinit_gsr(abinit_gsr) + + report = None + has_abinit_completed = TaskState.FAILED + # TODO: How to detect which status it has here ? + # UNCONVERGED would be for scf/nscf/relax when it's not yet converged + # FAILED should be for a job that failed for other reasons. + # What about a job that has been killed by the run_abinit (i.e. before + # Slurm or PBS kills it) ? + + try: + report = get_event_report( + ofile=File(abinit_log_file), mpiabort_file=File(abinit_abort_file) + ) + if report.run_completed: + has_abinit_completed = TaskState.SUCCESS + + except (ValueError, RuntimeError, Exception) as exc: + msg = f"{cls} exception while parsing event_report:\n{exc}" + logger.critical(msg) + + instance = cls( + dir_name=str(dir_name), + task_name=task_name, + abinit_version=abinit_gsr.abinit_version, + has_abinit_completed=has_abinit_completed, + completed_at=completed_at, + output=output_doc, + event_report=report, + ) + + return instance, None # abinit_objects, diff --git a/src/atomate2/abinit/schemas/task.py b/src/atomate2/abinit/schemas/task.py new file mode 100644 index 0000000000..07a66d3fa8 --- /dev/null +++ b/src/atomate2/abinit/schemas/task.py @@ -0,0 +1,390 @@ +"""A definition of a MSON document representing an Abinit task.""" + +from __future__ import annotations + +import logging +from collections.abc import Sequence +from pathlib import Path +from typing import Any, Optional, Union + +from abipy.abio.inputs import AbinitInput +from abipy.flowtk import events +from emmet.core.math import Matrix3D, Vector3D +from emmet.core.structure import StructureMetadata +from pydantic import BaseModel, Field +from pymatgen.core import Structure +from typing_extensions import Self + +from atomate2.abinit.files import load_abinit_input +from atomate2.abinit.schemas.calculation import AbinitObject, Calculation, TaskState +from atomate2.abinit.utils.common import LOG_FILE_NAME, MPIABORTFILE +from atomate2.utils.datetime import datetime_str +from atomate2.utils.path import get_uri, strip_hostname + +logger = logging.getLogger(__name__) + + +class InputDoc(BaseModel): + """Summary of the inputs for an Abinit calculation. + + Parameters + ---------- + structure: Structure + The final pymatgen Structure of the final system + """ + + structure: Union[Structure] = Field(None, description="The input structure object") + abinit_input: AbinitInput = Field( + None, description="AbinitInput used to perform calculation." + ) + xc: str = Field( + None, description="Exchange-correlation functional used if not the default" + ) + + @classmethod + def from_abinit_calc_doc(cls, calc_doc: Calculation) -> Self: + """Create a summary from an abinit CalculationDocument. + + Parameters + ---------- + calc_doc: .Calculation + An Abinit calculation document. + + Returns + ------- + .InputDoc + The calculation input summary. + """ + abinit_input = load_abinit_input(calc_doc.dir_name) + return cls( + structure=abinit_input.structure, + abinit_input=abinit_input, + xc=str(abinit_input.pseudos[0].xc.name), + ) + + +class OutputDoc(BaseModel): + """Summary of the outputs for an Abinit calculation. + + Parameters + ---------- + structure: Structure + The final pymatgen Structure of the final system + trajectory: List[Structure] + The trajectory of output structures + energy: float + The final total DFT energy for the last calculation + energy_per_atom: float + The final DFT energy per atom for the last calculation + bandgap: float + The DFT bandgap for the last calculation + cbm: float + CBM for this calculation + vbm: float + VBM for this calculation + forces: List[Vector3D] + Forces on atoms from the last calculation + stress: Matrix3D + Stress on the unit cell from the last calculation + """ + + structure: Union[Structure] = Field(None, description="The output structure object") + trajectory: Optional[Sequence[Union[Structure]]] = Field( + None, description="The trajectory of output structures" + ) + energy: float = Field( + None, description="The final total DFT energy for the last calculation" + ) + energy_per_atom: float = Field( + None, description="The final DFT energy per atom for the last calculation" + ) + bandgap: Optional[float] = Field( + None, description="The DFT bandgap for the last calculation" + ) + cbm: Optional[float] = Field(None, description="CBM for this calculation") + vbm: Optional[float] = Field(None, description="VBM for this calculation") + forces: Optional[list[Vector3D]] = Field( + None, description="Forces on atoms from the last calculation" + ) + stress: Optional[Matrix3D] = Field( + None, description="Stress on the unit cell from the last calculation" + ) + + @classmethod + def from_abinit_calc_doc(cls, calc_doc: Calculation) -> Self: + """Create a summary from an abinit CalculationDocument. + + Parameters + ---------- + calc_doc: .Calculation + An Abinit calculation document. + + Returns + ------- + .OutputDoc + The calculation output summary. + """ + return cls( + structure=calc_doc.output.structure, + energy=calc_doc.output.energy, + energy_per_atom=calc_doc.output.energy_per_atom, + bandgap=calc_doc.output.bandgap, + cbm=calc_doc.output.cbm, + vbm=calc_doc.output.vbm, + forces=calc_doc.output.forces, + stress=calc_doc.output.stress, + ) + + +class AbinitTaskDoc(StructureMetadata): + """Definition of Abinit task document. + + Parameters + ---------- + dir_name: str + The directory for this Abinit task + last_updated: str + Timestamp for when this task document was last updated + completed_at: str + Timestamp for when this task was completed + input: .InputDoc + The input to the first calculation + output: .OutputDoc + The output of the final calculation + structure: Structure + Final output structure from the task + state: .TaskState + State of this task + included_objects: List[.AbinitObject] + List of Abinit objects included with this task document + abinit_objects: Dict[.AbinitObject, Any] + Abinit objects associated with this task + task_label: str + A description of the task + tags: List[str] + Metadata tags for this task document + author: str + Author extracted from transformations + icsd_id: str + International crystal structure database id of the structure + calcs_reversed: List[.Calculation] + The inputs and outputs for all Abinit runs in this task. + transformations: Dict[str, Any] + Information on the structural transformations, parsed from a + transformations.json file + custodian: Any + Information on the custodian settings used to run this + calculation, parsed from a custodian.json file + additional_json: Dict[str, Any] + Additional json loaded from the calculation directory + """ + + dir_name: Optional[str] = Field( + None, description="The directory for this Abinit task" + ) + last_updated: Optional[str] = Field( + default_factory=datetime_str, + description="Timestamp for when this task document was last updated", + ) + completed_at: Optional[str] = Field( + None, description="Timestamp for when this task was completed" + ) + input: Optional[InputDoc] = Field( + None, description="The input to the first calculation" + ) + output: Optional[OutputDoc] = Field( + None, description="The output of the final calculation" + ) + structure: Union[Structure] = Field( + None, description="Final output atoms from the task" + ) + state: Optional[TaskState] = Field(None, description="State of this task") + event_report: Optional[events.EventReport] = Field( + None, description="Event report of this abinit job." + ) + included_objects: Optional[list[AbinitObject]] = Field( + None, description="List of Abinit objects included with this task document" + ) + abinit_objects: Optional[dict[AbinitObject, Any]] = Field( + None, description="Abinit objects associated with this task" + ) + task_label: Optional[str] = Field(None, description="A description of the task") + tags: Optional[list[str]] = Field( + None, description="Metadata tags for this task document" + ) + author: Optional[str] = Field( + None, description="Author extracted from transformations" + ) + icsd_id: Optional[str] = Field( + None, description="International crystal structure database id of the structure" + ) + calcs_reversed: Optional[list[Calculation]] = Field( + None, description="The inputs and outputs for all Abinit runs in this task." + ) + transformations: Optional[dict[str, Any]] = Field( + None, + description="Information on the structural transformations, parsed from a " + "transformations.json file", + ) + custodian: Any = Field( + None, + description="Information on the custodian settings used to run this " + "calculation, parsed from a custodian.json file", + ) + additional_json: Optional[dict[str, Any]] = Field( + None, description="Additional json loaded from the calculation directory" + ) + + @classmethod + def from_directory( + cls, + dir_name: Path | str, + additional_fields: dict[str, Any] = None, + **abinit_calculation_kwargs, + ) -> Self: + """Create a task document from a directory containing Abinit files. + + Parameters + ---------- + dir_name: Path or str + The path to the folder containing the calculation outputs. + additional_fields: Dict[str, Any] + Dictionary of additional fields to add to output document. + **abinit_calculation_kwargs + Additional parsing options that will be passed to the + :obj:`.Calculation.from_abinit_files` function. + + Returns + ------- + .AbinitTaskDoc + A task document for the calculation. + """ + logger.info(f"Getting task doc in: {dir_name}") + + if additional_fields is None: + additional_fields = {} + + dir_name = Path(dir_name) + task_files = _find_abinit_files(dir_name) + + if len(task_files) == 0: + raise FileNotFoundError("No Abinit files found!") + + calcs_reversed = [] + all_abinit_objects = [] + for task_name, files in task_files.items(): + calc_doc, abinit_objects = Calculation.from_abinit_files( + dir_name, task_name, **files, **abinit_calculation_kwargs + ) + calcs_reversed.append(calc_doc) + all_abinit_objects.append(abinit_objects) + + tags = additional_fields.get("tags") + + dir_name = get_uri(dir_name) # convert to full uri path + dir_name = strip_hostname( + dir_name + ) # VT: TODO to put here?necessary with laptop at least... + + # only store objects from last calculation + # TODO: make this an option + abinit_objects = all_abinit_objects[-1] + included_objects = None + if abinit_objects: + included_objects = list(abinit_objects.keys()) + + # rewrite the original structure save! + + if isinstance(calcs_reversed[-1].output.structure, Structure): + attr = "from_structure" + dat = { + "structure": calcs_reversed[-1].output.structure, + "meta_structure": calcs_reversed[-1].output.structure, + "include_structure": True, + } + doc = getattr(cls, attr)(**dat) + ddict = doc.dict() + + data = { + "abinit_objects": abinit_objects, + "calcs_reversed": calcs_reversed, + "completed_at": calcs_reversed[-1].completed_at, + "dir_name": dir_name, + "event_report": calcs_reversed[-1].event_report, + "included_objects": included_objects, + "input": InputDoc.from_abinit_calc_doc(calcs_reversed[0]), + "meta_structure": calcs_reversed[-1].output.structure, + "output": OutputDoc.from_abinit_calc_doc(calcs_reversed[-1]), + "state": calcs_reversed[-1].has_abinit_completed, + "structure": calcs_reversed[-1].output.structure, + "tags": tags, + } + + doc = cls(**ddict) + doc = doc.model_copy(update=data) + return doc.model_copy(update=additional_fields, deep=True) + + +def _find_abinit_files( + path: Path | str, +) -> dict[str, Any]: + """Find Abinit files in a directory. + + Only files in folders with names matching a task name (or alternatively files + with the task name as an extension, e.g., abinit.out) will be returned. + + Abinit files in the current directory will be given the task name "standard". + + Parameters + ---------- + path: str or Path + Path to a directory to search. + + Returns + ------- + dict[str, Any] + The filenames of the calculation outputs for each Abinit task, + given as a ordered dictionary of:: + + { + task_name: { + "abinit_output_file": abinit_output_filename, + """ + task_names = ["precondition"] + [f"relax{i}" for i in range(9)] + path = Path(path) + task_files = {} + + def _get_task_files(files: list[Path], suffix: str = "") -> dict: + abinit_files = {} + for file in files: + # Here we make assumptions about the output file naming + if file.match(f"*outdata/out_GSR{suffix}*"): + abinit_files["abinit_gsr_file"] = Path(file).relative_to(path) + elif file.match(f"*{LOG_FILE_NAME}{suffix}*"): + abinit_files["abinit_log_file"] = Path(file).relative_to(path) + elif file.match(f"*{MPIABORTFILE}{suffix}*"): + abinit_files["abinit_abort_file"] = Path(file).relative_to(path) + + return abinit_files + + for task_name in task_names: + subfolder_match = list(path.glob(f"{task_name}/*")) + suffix_match = list(path.glob(f"*.{task_name}*")) + if len(subfolder_match) > 0: + # subfolder match + task_files[task_name] = _get_task_files(subfolder_match) + elif len(suffix_match) > 0: + # try extension schema + task_files[task_name] = _get_task_files( + suffix_match, suffix=f".{task_name}" + ) + + if len(task_files) == 0: + # get any matching file from the root folder + standard_files = _get_task_files( + list(path.glob("*")) + list(path.glob("outdata/*")) + ) + if len(standard_files) > 0: + task_files["standard"] = standard_files + + return task_files diff --git a/src/atomate2/abinit/sets/__init__.py b/src/atomate2/abinit/sets/__init__.py new file mode 100644 index 0000000000..62c07f26b2 --- /dev/null +++ b/src/atomate2/abinit/sets/__init__.py @@ -0,0 +1 @@ +"""Module defining ABINIT input sets used in atomate2.""" diff --git a/src/atomate2/abinit/sets/base.py b/src/atomate2/abinit/sets/base.py new file mode 100644 index 0000000000..1092784bc6 --- /dev/null +++ b/src/atomate2/abinit/sets/base.py @@ -0,0 +1,810 @@ +"""Module defining base abinit input set and generator.""" + +from __future__ import annotations + +import copy +import json +import logging +import os +from dataclasses import dataclass, field +from pathlib import Path +from typing import TYPE_CHECKING, Any, Callable + +import numpy as np +from abipy.abio.inputs import AbinitInput, MultiDataset +from abipy.flowtk.psrepos import get_repo_from_name +from abipy.flowtk.utils import Directory, irdvars_for_ext +from monty.json import MontyEncoder, jsanitize +from pymatgen.io.abinit.abiobjects import KSampling, KSamplingModes +from pymatgen.io.abinit.pseudos import Pseudo, PseudoTable +from pymatgen.io.core import InputGenerator, InputSet +from pymatgen.io.vasp import Kpoints +from pymatgen.symmetry.analyzer import SpacegroupAnalyzer +from pymatgen.symmetry.bandstructure import HighSymmKpath + +from atomate2 import SETTINGS +from atomate2.abinit.files import fname2ext, load_abinit_input, out_to_in +from atomate2.abinit.utils.common import ( + INDATA_PREFIX, + INDATAFILE_PREFIX, + INDIR_NAME, + INPUT_FILE_NAME, + OUTDATA_PREFIX, + OUTDATAFILE_PREFIX, + OUTDIR_NAME, + TMPDATA_PREFIX, + TMPDIR_NAME, + InitializationError, + get_final_structure, +) + +if TYPE_CHECKING: + from collections.abc import Iterable, Sequence + + from pymatgen.core.structure import Structure + + +logger = logging.getLogger(__name__) + + +class AbinitInputSet(InputSet): + """ + A class to represent a set of Abinit inputs. + + Parameters + ---------- + abinit_input + An AbinitInput object. + input_files + A list of input files needed for the calculation. The corresponding + file reading variables (ird***) should be present in the abinit_input. + """ + + def __init__( + self, + abinit_input: AbinitInput, + input_files: Iterable[tuple[str, str]] | None = None, + link_files: bool = True, + ) -> None: + self.input_files = input_files + self.link_files = link_files + super().__init__( + inputs={ + INPUT_FILE_NAME: abinit_input, + "abinit_input.json": json.dumps( + abinit_input.as_dict(), cls=MontyEncoder + ), + } + ) + + def write_input( + self, + directory: str | Path, + make_dir: bool = True, + overwrite: bool = True, + zip_inputs: bool = False, + ) -> None: + """Write Abinit input files to a directory.""" + # TODO: do we allow zipping ? not sure if it really makes sense for abinit as + # the abinit input set also sets up links to previous files, sets up the + # indir, outdir and tmpdir, ... + self.inputs["abinit_input.json"] = json.dumps( + jsanitize(self.abinit_input.as_dict()) + ) + super().write_input( + directory=directory, + make_dir=make_dir, + overwrite=overwrite, + zip_inputs=zip_inputs, + ) + del self.inputs["abinit_input.json"] + indir, _outdir, _tmpdir = self.set_workdir(workdir=directory) + + if self.input_files: + out_to_in( + out_files=self.input_files, + indir=indir.path, + link_files=self.link_files, + ) + + def validate(self) -> bool: + """Validate the input set. + + Check that all files in the input directory + have their corresponding ird variables. + """ + if not self.input_files: + return True + for _out_filepath, in_file in self.input_files: + ext = fname2ext(in_file) + if ext is None: + return False + irdvars = irdvars_for_ext(ext) + for irdvar, irdval in irdvars.items(): + if irdvar not in self.abinit_input: + return False + if self.abinit_input[irdvar] != irdval: + return False + return True + + @property + def abinit_input(self) -> AbinitInput: + """Get the AbinitInput object.""" + return self[INPUT_FILE_NAME] + + @staticmethod + def set_workdir(workdir: Path | str) -> tuple[Directory, Directory, Directory]: + """Set up the working directory. + + This also sets up and creates standard input, output and temporary directories. + """ + workdir = os.path.abspath(workdir) + + # Directories with input|output|temporary data. + indir = Directory(os.path.join(workdir, INDIR_NAME)) + outdir = Directory(os.path.join(workdir, OUTDIR_NAME)) + tmpdir = Directory(os.path.join(workdir, TMPDIR_NAME)) + + # Create dirs for input, output and tmp data. + indir.makedirs() + outdir.makedirs() + tmpdir.makedirs() + + return indir, outdir, tmpdir + + def set_vars(self, *args, **kwargs) -> dict: + """Set the values of abinit variables. + + This sets the abinit variables in the abipy AbinitInput object. + + One can pass a dictionary mapping the abinit variables to their values or + the abinit variables as keyword arguments. A combination of the two + options is also allowed. + + Returns + ------- + dict + dictionary with the variables that have been added. + """ + return self.abinit_input.set_vars(*args, **kwargs) + + def remove_vars(self, keys: Iterable[str] | str, strict: bool = True) -> dict: + """Remove the abinit variables listed in keys. + + This removes the abinit variables from the abipy AbinitInput object. + + Parameters + ---------- + keys + string or list of strings with the names of the abinit variables + to be removed. + strict + whether to raise a KeyError if one of the abinit variables to be + removed is not present. + + Returns + ------- + dict + dictionary with the variables that have been removed. + """ + return self.abinit_input.remove_vars(keys=keys, strict=strict) + + def runlevel(self) -> set[str]: + """Get the set of strings defining the calculation type.""" + return self.abinit_input.runlevel + + def set_structure(self, structure: Any) -> Structure: + """Set the structure for this input set. + + This basically forwards the setting of the structure to the abipy + AbinitInput object. + """ + return self.abinit_input.set_structure(structure) + + def deepcopy(self) -> AbinitInputSet: + """Deep copy of the input set.""" + return copy.deepcopy(self) + + +def as_pseudo_table(pseudos: str | Sequence[Pseudo]) -> PseudoTable: + """Get the pseudos as a PseudoTable object. + + Parameters + ---------- + pseudos + Pseudopotentials as a list of pseudopotentials files, a single + pseudopotential file, a string representing a pseudo repository. + + Returns + ------- + PseudoTable + Table of pseudopotentials. + """ + # get the PseudoTable from the PseudoRepo + if isinstance(pseudos, str): + # in case a single path to a pseudopotential file has been passed + if os.path.isfile(pseudos): + return PseudoTable(pseudos) + pseudo_repo_name, table_name = pseudos.rsplit(":", 1) + repo = get_repo_from_name(pseudo_repo_name) + if not repo.is_installed(): + msg = ( + f"Pseudo repository {pseudo_repo_name} is not installed " + f"in {repo.dirpath}. " + f"Use abips.py to install it." + ) + raise RuntimeError(msg) + return repo.get_pseudos(table_name) + return PseudoTable(pseudos) + + +@dataclass +class AbinitInputGenerator(InputGenerator): + """ + A class to generate Abinit input sets. + + Parameters + ---------- + factory + A callable that generates an AbinitInput or MultiDataset object. + calc_type + A short description of the calculation type + pseudos + Define the pseudopotentials that should be used for the calculation. + Can be an instance of a PseudoTable, a list of strings with the paths of + the pseudopotential files or a string with the name of a PseudoDojo table + (https://github.com/PseudoDojo/), followed by the accuracy of the pseudos + in that table, separated by a colon. This requires that the PseudoTable + is installed in the system. + Set to None if no pseudopotentials should be set, as coming from a previous + AbinitInput. + factory_kwargs + A dictionary to customize the values for the arguments of the factory + function. + user_abinit_settings + A dictionary that allows to set any Abinit variable in the AbinitInput + after it has been generated from the factory function. This will override + any value or default previously set. Set a value to None to remove it + from the input. + user_kpoints_settings + Allow user to override kpoints setting by supplying a dict. E.g., + ``{"reciprocal_density": 1000}``. User can also supply a KSampling object. + restart_from_deps: + Defines the files that needs to be linked from previous calculations in + case of restart. The format is a tuple where each element is a list of + "|" separated run levels (as defined in the AbinitInput object) followed + by a colon and a list of "|" list of extensions of files that needs to + be linked. The runlevel defines the type of calculations from which the + file can be linked. An example is (f"{NSCF}:WFK",). + prev_outputs_deps + Defines the files that needs to be linked from previous calculations and + are required for the execution of the current calculation. + The format is a tuple where each element is a list of "|" separated + run levels (as defined in the AbinitInput object) followed by a colon and + a list of "|" list of extensions of files that needs to be linked. + The runlevel defines the type of calculations from which the file can + be linked. An example is (f"{NSCF}:WFK",). + factory_prev_inputs_kwargs + A dictionary defining the source of the of one or more previous + AbinitInput in case they are required by a factory to build a new + AbinitInput. The key should match the name of the argument of the factory + function and the value should be a tuple with the runlevels of the + compatible types of AbinitInput that can be used. + force_gamma + Force gamma centered kpoint generation. + symprec + Tolerance for symmetry finding, used for line mode band structure k-points. + """ + + factory: Callable + calc_type: str = "abinit_calculation" + pseudos: str | list[str] | PseudoTable | None = "ONCVPSP-PBE-SR-PDv0.4:standard" + factory_kwargs: dict = field(default_factory=dict) + user_abinit_settings: dict = field(default_factory=dict) + user_kpoints_settings: dict | KSampling = field(default_factory=dict) + restart_from_deps: str | tuple | None = None + prev_outputs_deps: str | tuple | None = None + factory_prev_inputs_kwargs: dict | None = None + force_gamma: bool = True + symprec: float = SETTINGS.SYMPREC + + def get_input_set( + self, + structure: Structure = None, + restart_from: str | tuple | list | Path | None = None, + prev_outputs: str | tuple | list | Path | None = None, + ) -> AbinitInputSet: + """Generate an AbinitInputSet object. + + Here we assume that restart_from is a directory and prev_outputs is + a list of directories. We also assume there is an abinit_input.json file + in each of these directories containing the AbinitInput object used to + execute abinit. + + Parameters + ---------- + structure : Structure + Pymatgen Structure object. + restart_from : str or Path or list or tuple + Directory (as a str or Path) or list/tuple of 1 directory (as a str + or Path) to restart from. + prev_outputs : str or Path or list or tuple + Directory (as a str or Path) or list/tuple of directories (as a str + or Path) needed as dependencies for the AbinitInputSet generated. + """ + # Get the pseudos as a PseudoTable + pseudos = as_pseudo_table(self.pseudos) if self.pseudos else None + + restart_from = self.check_format_prev_dirs(restart_from) + prev_outputs = self.check_format_prev_dirs(prev_outputs) + + all_irdvars = {} + input_files = [] + if restart_from is not None: + # Use the previous abinit input + abinit_input = load_abinit_input(restart_from[0]) + # Update with the abinit input with the final structure + structure = get_final_structure(restart_from[0]) + abinit_input.set_structure(structure=structure) + # Files for restart (e.g. continue a not yet converged + # scf/nscf/relax calculation) + irdvars, files = self.resolve_deps( + restart_from, deps=self.restart_from_deps + ) + all_irdvars.update(irdvars) + input_files.extend(files) + else: + if prev_outputs is not None and not self.prev_outputs_deps: + raise RuntimeError( + f"Previous outputs not allowed for {type(self).__name__}." + ) + abinit_input = self.get_abinit_input( + structure=structure, + pseudos=pseudos, + prev_outputs=prev_outputs, + ) + # Always reset the ird variables. + abinit_input.pop_irdvars() + + # Files that are dependencies (e.g. band structure calculations + # need the density). + if prev_outputs: + irdvars, files = self.resolve_deps(prev_outputs, self.prev_outputs_deps) + all_irdvars.update(irdvars) + input_files.extend(files) + + # Set ird variables and extra variables. + abinit_input.set_vars(all_irdvars) + abinit_input.set_vars(self.user_abinit_settings) + + abinit_input["indata_prefix"] = (f'"{INDATA_PREFIX}"',) + abinit_input["outdata_prefix"] = (f'"{OUTDATA_PREFIX}"',) + abinit_input["tmpdata_prefix"] = (f'"{TMPDATA_PREFIX}"',) + + # TODO: where/how do we set up/pass down link_files ? + return AbinitInputSet( + abinit_input=abinit_input, + input_files=input_files, + link_files=True, + ) + + def check_format_prev_dirs( + self, prev_dirs: str | tuple | list | Path | None + ) -> list[str] | None: + """Check and format the prev_dirs (restart or dependency).""" + if prev_dirs is None: + return None + if isinstance(prev_dirs, (str, Path)): + return [str(prev_dirs)] + return [str(prev_dir) for prev_dir in prev_dirs] + + def resolve_deps( + self, prev_dirs: list[str], deps: str | tuple, check_runlevel: bool = True + ) -> tuple[dict, list]: + """Resolve dependencies. + + This method assumes that prev_dirs is in the correct format, i.e. + a list of directories as str or Path. + """ + input_files = [] + deps_irdvars = {} + for prev_dir in prev_dirs: + if check_runlevel: + abinit_input = load_abinit_input(prev_dir) + for dep in deps: + runlevel = set(dep.split(":")[0].split("|")) + exts = list(dep.split(":")[1].split("|")) + if not check_runlevel or runlevel.intersection(abinit_input.runlevel): + irdvars, inp_files = self.resolve_dep_exts( + prev_dir=prev_dir, exts=exts + ) + input_files.extend(inp_files) + deps_irdvars.update(irdvars) + + return deps_irdvars, input_files + + def resolve_prev_inputs( + self, prev_dirs: list[str], prev_inputs_kwargs: dict + ) -> dict[str, AbinitInput]: + """ + Find suitable abinit inputs from the previous outputs. + + Also retrieves the final structure from the previous outputs + and replace it in the selected abinit input. + + This method assumes that prev_dirs is in the correct format, i.e. + a list of directories as str or Path. + """ + abinit_inputs = {} + for prev_dir in prev_dirs: + abinit_input = load_abinit_input(prev_dir) + for var_name, runlevels in prev_inputs_kwargs.items(): + if abinit_input.runlevel and abinit_input.runlevel.intersection( + runlevels + ): + if var_name in abinit_inputs: + msg = ( + "Multiple previous inputs match the " + "requirements as inputs for the factory" + ) + raise RuntimeError(msg) + final_structure = get_final_structure(prev_dir) + abinit_input.set_structure(final_structure) + abinit_inputs[var_name] = abinit_input + + n_found = len(abinit_inputs) + n_required = len(self.factory_prev_inputs_kwargs) + if n_found != n_required: + raise RuntimeError( + f"Should have exactly {n_found} previous output. Found {n_required}" + ) + + return abinit_inputs + + @staticmethod + def _get_in_file_name(out_filepath: str) -> str: + in_file = os.path.basename(out_filepath) + in_file = in_file.replace(OUTDATAFILE_PREFIX, INDATAFILE_PREFIX, 1) + + return os.path.basename(in_file).replace("WFQ", "WFK", 1) + + @staticmethod + def resolve_dep_exts(prev_dir: str, exts: list[str]) -> tuple: + """Return irdvars and corresponding file for a given dependency. + + This method assumes that prev_dir is in the correct format, + i.e. a directory as a str or Path. + """ + prev_outdir = Directory(os.path.join(prev_dir, OUTDIR_NAME)) + inp_files = [] + + for ext in exts: + # TODO: how to check that we have the files we need ? + # Should we raise if don't find at least one file for a given extension ? + if ext in ("1WF", "1DEN"): + # Special treatment for 1WF and 1DEN files + if ext == "1WF": + files = prev_outdir.find_1wf_files() + elif ext == "1DEN": + files = prev_outdir.find_1den_files() + else: + raise RuntimeError("Should not occur.") + if files is not None: + inp_files = [ + (f.path, AbinitInputGenerator._get_in_file_name(f.path)) + for f in files + ] + irdvars = irdvars_for_ext(ext) + break + elif ext == "DEN": + # Special treatment for DEN files + # In case of relaxations or MD, there may be several TIM?_DEN files + # First look for the standard out_DEN file. + # If not found, look for the last TIM?_DEN file. + out_den = prev_outdir.path_in(f"{OUTDATAFILE_PREFIX}_DEN") + if os.path.exists(out_den): + irdvars = irdvars_for_ext("DEN") + inp_files.append( + (out_den, AbinitInputGenerator._get_in_file_name(out_den)) + ) + break + last_timden = prev_outdir.find_last_timden_file() + if last_timden is not None: + if last_timden.path.endswith(".nc"): + in_file_name = f"{INDATAFILE_PREFIX}_DEN.nc" + else: + in_file_name = f"{INDATAFILE_PREFIX}_DEN" + inp_files.append((last_timden.path, in_file_name)) + irdvars = irdvars_for_ext("DEN") + break + else: + out_file = prev_outdir.has_abiext(ext) + irdvars = irdvars_for_ext(ext) + if out_file: + inp_files.append( + (out_file, AbinitInputGenerator._get_in_file_name(out_file)) + ) + break + else: + msg = f"Cannot find {' or '.join(exts)} file to restart from." + logger.error(msg) + raise InitializationError(msg) + return irdvars, inp_files + + def get_abinit_input( + self, + structure: Structure | None = None, + pseudos: PseudoTable | None = None, + prev_outputs: list[str] | None = None, + abinit_settings: dict | None = None, + factory_kwargs: dict | None = None, + kpoints_settings: dict | KSampling | None = None, + input_index: int | None = None, + ) -> AbinitInput: + """Generate the AbinitInput for the input set. + + Uses the defined factory function and additional parameters from user + and subclasses. + + Parameters + ---------- + structure + A structure. + pseudos + A pseudopotential table. + prev_outputs + A list of previous output directories. + abinit_settings + A dictionary with additional abinit keywords to set. + factory_kwargs + A dictionary with additional factory keywords to set. + kpoints_settings + A dictionary or a KSampling object with additional settings + for the k-points. + input_index + The index to be used to select the AbinitInput in case a factory + returns a MultiDataset. + + Returns + ------- + An AbinitInput + """ + total_factory_kwargs = dict(self.factory_kwargs) if self.factory_kwargs else {} + if self.factory_prev_inputs_kwargs: + if not prev_outputs: + raise RuntimeError( + f"No previous_outputs. Required for {type(self).__name__}." + ) + + # TODO consider cases where structure might be defined even if + # factory_prev_inputs_kwargs is present. + if structure is not None: + raise RuntimeError( + "Structure not supported if factory_prev_inputs_kwargs is defined" + ) + + abinit_inputs = self.resolve_prev_inputs( + prev_outputs, self.factory_prev_inputs_kwargs + ) + total_factory_kwargs.update(abinit_inputs) + + elif structure is None: + msg = ( + f"Structure is mandatory for {type(self).__name__} " + f"generation since no previous output is used." + ) + raise RuntimeError(msg) + + if not self.prev_outputs_deps and prev_outputs: + msg = ( + f"Previous outputs not allowed for {type(self).__name__} " + "Consider if restart_from argument of get_input_set method " + "can fit your needs instead." + ) + raise RuntimeError(msg) + + if structure: + total_factory_kwargs["structure"] = structure + if pseudos: + total_factory_kwargs["pseudos"] = pseudos + if factory_kwargs: + total_factory_kwargs.update(factory_kwargs) + + generated_input = self.factory(**total_factory_kwargs) + + if input_index is not None: + generated_input = generated_input[input_index] + + self._set_kpt_vars(generated_input, kpoints_settings) + + if abinit_settings: + generated_input.set_vars(abinit_settings) + if self.user_abinit_settings: + generated_input.set_vars(self.user_abinit_settings) + + # remove the None values. They will not be printed in the input file + # but can cause issues when checking if the values are present in the input. + self._clean_none(generated_input) + + return generated_input + + def _set_kpt_vars( + self, + abinit_input: AbinitInput | MultiDataset, + kpoints_settings: dict | KSampling | None, + ) -> None: + """ + Update the kpoints variables, according to the options selected. + + Parameters + ---------- + abinit_input + An AbinitInput to be updated. + kpoints_settings + The options to set the kpoints variable. + """ + ksampling = self._get_kpoints(abinit_input.structure, kpoints_settings) + if ksampling: + kpt_related_vars = [ + "kpt", + "kptbounds", + "kptnrm", + "kptns", + "kptns_hf", + "kptopt", + "kptrlatt", + "kptrlen", + "ndivk", + "ndivsm", + "ngkpt", + "nkpath", + "nkpt", + "nshiftk", + "shiftk", + "wtk", + ] + abinit_input.pop_vars(kpt_related_vars) + abinit_input.set_vars(**ksampling.abivars) + + @staticmethod + def _clean_none(abinit_input: AbinitInput | MultiDataset) -> None: + """ + Remove the variables whose value is set to None from the AbinitInput. + + Parameters + ---------- + abinit_input + An AbinitInput to modify. + """ + if not isinstance(abinit_input, MultiDataset): + abinit_input = [abinit_input] + + for ai in abinit_input: + for k, v in list(ai.items()): + if v is None: + ai.remove_vars(k) + + def _get_kpoints( + self, + structure: Structure, + kpoints_updates: dict[str, Any] | None, + ) -> KSampling | None: + """Get the kpoints file.""" + kpoints_updates = {} if kpoints_updates is None else kpoints_updates + + # use user setting if set otherwise default to base config settings + if self.user_kpoints_settings != {}: + kconfig = copy.deepcopy(self.user_kpoints_settings) + elif kpoints_updates: + kconfig = kpoints_updates + else: + return None + + if isinstance(kconfig, KSampling): + return kconfig + + explicit = ( + kconfig.get("explicit") + or len(kconfig.get("added_kpoints", [])) > 0 + or "zero_weighted_reciprocal_density" in kconfig + or "zero_weighted_line_density" in kconfig + ) + + base_kpoints = None + if kconfig.get("line_density"): + # handle line density generation + kpath = HighSymmKpath(structure, **kconfig.get("kpath_kwargs", {})) + frac_k_points, _k_points_labels = kpath.get_kpoints( + line_density=kconfig["line_density"], coords_are_cartesian=False + ) + base_kpoints = KSampling( + mode=KSamplingModes.automatic, + num_kpts=len(frac_k_points), + kpts=frac_k_points, + kpts_weights=[1] * len(frac_k_points), + comment="Non SCF run along symmetry lines", + ) + elif kconfig.get("grid_density") or kconfig.get("reciprocal_density"): + # handle regular weighted k-point grid generation + if kconfig.get("grid_density"): + vasp_kpoints = Kpoints.automatic_density( + structure, int(kconfig["grid_density"]), self.force_gamma + ) + base_kpoints = KSampling( + mode=KSamplingModes.monkhorst, + num_kpts=0, + kpts=vasp_kpoints.kpts, + kpt_shifts=vasp_kpoints.kpts_shift, + comment=vasp_kpoints.comment, + ) + elif kconfig.get("reciprocal_density"): + vasp_kpoints = Kpoints.automatic_density_by_vol( + structure, kconfig["reciprocal_density"], self.force_gamma + ) + base_kpoints = KSampling( + mode=KSamplingModes.monkhorst, + num_kpts=0, + kpts=vasp_kpoints.kpts, + kpt_shifts=vasp_kpoints.kpts_shift, + comment=vasp_kpoints.comment, + ) + if explicit: + sga = SpacegroupAnalyzer(structure, symprec=self.symprec) + mesh = sga.get_ir_reciprocal_mesh(base_kpoints.kpts[0]) + base_kpoints = KSampling( + mode=KSamplingModes.automatic, + num_kpts=len(mesh), + kpts=[i[0] for i in mesh], + kpts_weights=[i[1] for i in mesh], + comment="Uniform grid", + ) + else: + # if not explicit that means no other options have been specified + # so we can return the k-points as is + return base_kpoints + + added_kpoints = None + if kconfig.get("added_kpoints"): + added_kpoints = KSampling( + mode=KSamplingModes.automatic, + num_kpts=len(kconfig.get("added_kpoints")), + kpts=kconfig.get("added_kpoints"), + kpts_weights=[0] * len(kconfig.get("added_kpoints")), + comment="Specified k-points only", + ) + + if base_kpoints and not added_kpoints: + return base_kpoints + if added_kpoints and not base_kpoints: + return added_kpoints + + # do some sanity checking + if not (base_kpoints or added_kpoints): + raise ValueError("Invalid k-point generation algo.") + + return _combine_kpoints(base_kpoints, added_kpoints) + + +def _combine_kpoints(*kpoints_objects: KSampling) -> KSampling: + """Combine k-points files together.""" + kpoints = [] + weights = [] + + for kpoints_object in filter(None, kpoints_objects): + if not kpoints_object.mode == KSamplingModes.automatic: + raise ValueError( + "Can only combine kpoints with mode=KSamplingModes.automatic" + ) + + weights.append(kpoints_object.kpts_weights) + kpoints.append(kpoints_object.kpts) + + weights = np.concatenate(weights).tolist() + kpoints = np.concatenate(kpoints) + return KSampling( + mode=KSamplingModes.automatic, + num_kpts=len(kpoints), + kpts=kpoints, + kpts_weights=weights, + comment="Combined k-points", + ) diff --git a/src/atomate2/abinit/sets/core.py b/src/atomate2/abinit/sets/core.py new file mode 100644 index 0000000000..f75a5adc09 --- /dev/null +++ b/src/atomate2/abinit/sets/core.py @@ -0,0 +1,227 @@ +"""Module defining core Abinit input set generators.""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import TYPE_CHECKING, Callable + +import numpy as np +from abipy.abio.factories import ( + dos_from_gsinput, + ebands_from_gsinput, + ion_ioncell_relax_input, + nscf_from_gsinput, + scf_input, +) +from abipy.abio.input_tags import MOLECULAR_DYNAMICS, NSCF, RELAX, SCF + +from atomate2.abinit.sets.base import AbinitInputGenerator + +if TYPE_CHECKING: + from abipy.abio.inputs import AbinitInput + from pymatgen.core import Structure + from pymatgen.io.abinit import PseudoTable + from pymatgen.io.abinit.abiobjects import KSampling + + +GS_RESTART_FROM_DEPS = (f"{SCF}|{RELAX}|{MOLECULAR_DYNAMICS}:WFK|DEN",) + + +@dataclass +class StaticSetGenerator(AbinitInputGenerator): + """Common class for ground-state generators.""" + + calc_type: str = "static" + factory: Callable = scf_input + restart_from_deps: tuple = GS_RESTART_FROM_DEPS + + def get_abinit_input( + self, + structure: Structure | None = None, + pseudos: PseudoTable | None = None, + prev_outputs: list[str] | None = None, + abinit_settings: dict | None = None, + factory_kwargs: dict | None = None, + kpoints_settings: dict | KSampling | None = None, + input_index: int | None = None, + ) -> AbinitInput: + """Generate the AbinitInput for the input set. + + Removes some standard variables related to relaxation. + """ + # disable relax options in case they are present (from a restart) + scf_abinit_settings = { + "ionmov": None, + "optcell": None, + "ntime": None, + } + if abinit_settings: + scf_abinit_settings.update(abinit_settings) + + return super().get_abinit_input( + structure=structure, + pseudos=pseudos, + prev_outputs=prev_outputs, + abinit_settings=scf_abinit_settings, + factory_kwargs=factory_kwargs, + kpoints_settings=kpoints_settings, + ) + + +@dataclass +class NonSCFSetGenerator(AbinitInputGenerator): + """Class to generate Abinit non-SCF input sets.""" + + calc_type: str = "nscf" + factory: Callable = nscf_from_gsinput + pseudos: str | list[str] | PseudoTable | None = None + restart_from_deps: tuple = (f"{NSCF}:WFK",) + prev_outputs_deps: tuple = (f"{SCF}:DEN",) + nbands_factor: float = 1.2 + factory_kwargs: dict = field(default_factory=dict) + + factory_prev_inputs_kwargs: dict | None = field( + default_factory=lambda: {"gs_input": (SCF,)} + ) + + def get_abinit_input( + self, + structure: Structure | None = None, + pseudos: PseudoTable | None = None, + prev_outputs: list[str] | None = None, + abinit_settings: dict | None = None, + factory_kwargs: dict | None = None, + kpoints_settings: dict | KSampling | None = None, + input_index: int | None = None, + ) -> AbinitInput: + """Get AbinitInput object for Non-SCF calculation.""" + factory_kwargs = dict(factory_kwargs) if factory_kwargs else {} + factory_kwargs["nband"] = self._get_nband(prev_outputs) + + return super().get_abinit_input( + structure=structure, + pseudos=pseudos, + prev_outputs=prev_outputs, + abinit_settings=abinit_settings, + factory_kwargs=factory_kwargs, + kpoints_settings=kpoints_settings, + ) + + def _get_nband(self, prev_outputs: list[str] | None) -> int: + abinit_inputs = self.resolve_prev_inputs( + prev_outputs, self.factory_prev_inputs_kwargs + ) + if len(abinit_inputs) != 1: + raise RuntimeError( + f"Should have exactly one previous output. Found {len(abinit_inputs)}" + ) + previous_abinit_input = next(iter(abinit_inputs.values())) + n_band = previous_abinit_input.get( + "nband", + previous_abinit_input.structure.num_valence_electrons( + previous_abinit_input.pseudos + ), + ) + return int(np.ceil(n_band * self.nbands_factor)) + + +@dataclass +class LineNonSCFSetGenerator(NonSCFSetGenerator): + """Class to generate Abinit non-SCF input sets.""" + + calc_type: str = "nscf_line" + factory: Callable = ebands_from_gsinput + + +@dataclass +class UniformNonSCFSetGenerator(NonSCFSetGenerator): + """Class to generate Abinit non-SCF input sets.""" + + calc_type: str = "nscf_uniform" + factory: Callable = dos_from_gsinput + + +@dataclass +class NonScfWfqInputGenerator(AbinitInputGenerator): + """Input set generator for Non-Scf Wfq calculations.""" + + calc_type: str = "nscf_wfq" + + wfq_tol: dict = field(default_factory=lambda: {"tolwfr": 1e-18}) + + restart_from_deps: tuple = (f"{NSCF}:WFQ",) + prev_outputs_deps: tuple = (f"{SCF}:DEN",) + + def get_abinit_input( + self, + structure: Structure | None = None, + pseudos: PseudoTable | None = None, + prev_outputs: list[str] | None = None, + abinit_settings: dict | None = None, + factory_kwargs: dict | None = None, + kpoints_settings: dict | KSampling | None = None, + input_index: int | None = None, + ) -> AbinitInput: + """Get AbinitInput object for Non-SCF Wfq calculation.""" + raise NotImplementedError + + +@dataclass +class DdkInputGenerator(AbinitInputGenerator): + """Input set generator for Non-Scf Wfq calculations.""" + + calc_type: str = "ddk" + + def get_abinit_input( + self, + structure: Structure | None = None, + pseudos: PseudoTable | None = None, + prev_outputs: list[str] | None = None, + abinit_settings: dict | None = None, + factory_kwargs: dict | None = None, + kpoints_settings: dict | KSampling | None = None, + input_index: int | None = None, + ) -> AbinitInput: + """Get the abinit input for Ddk calculation.""" + raise NotImplementedError + + +@dataclass +class RelaxSetGenerator(AbinitInputGenerator): + """Common class for ground-state generators.""" + + calc_type: str = "relaxation" + factory: Callable = ion_ioncell_relax_input + restart_from_deps: tuple = GS_RESTART_FROM_DEPS + relax_cell: bool = True + tolmxf: float = 5e-5 + + def get_abinit_input( + self, + structure: Structure | None = None, + pseudos: PseudoTable | None = None, + prev_outputs: list[str] | None = None, + abinit_settings: dict | None = None, + factory_kwargs: dict | None = None, + kpoints_settings: dict | KSampling | None = None, + input_index: int | None = None, + ) -> AbinitInput: + """Generate the AbinitInput for the input set. + + Sets tolmxf and determines the index of the MultiDataset. + """ + abinit_settings = abinit_settings or {} + # TODO move tolmxf to the factory? + abinit_settings["tolmxf"] = self.tolmxf + if input_index is None: + input_index = 1 if self.relax_cell else 0 + + return super().get_abinit_input( + structure=structure, + pseudos=pseudos, + prev_outputs=prev_outputs, + abinit_settings=abinit_settings, + factory_kwargs=factory_kwargs, + kpoints_settings=kpoints_settings, + input_index=input_index, + ) diff --git a/src/atomate2/abinit/utils/__init__.py b/src/atomate2/abinit/utils/__init__.py new file mode 100644 index 0000000000..3bdfec301d --- /dev/null +++ b/src/atomate2/abinit/utils/__init__.py @@ -0,0 +1,3 @@ +"""Tools to generate ABINIT inputs.""" + +"""A collection of helper utils found in atomate2 package.""" diff --git a/src/atomate2/abinit/utils/common.py b/src/atomate2/abinit/utils/common.py new file mode 100644 index 0000000000..75593abc8a --- /dev/null +++ b/src/atomate2/abinit/utils/common.py @@ -0,0 +1,433 @@ +"""Module with common file names and classes used for Abinit flows.""" + +from __future__ import annotations + +import logging +import os +from typing import TYPE_CHECKING + +from abipy.abio.outputs import AbinitOutputFile +from abipy.dfpt.ddb import DdbFile +from abipy.electrons.gsr import GsrFile +from abipy.flowtk import events +from abipy.flowtk.utils import Directory, File +from monty.json import MSONable +from monty.serialization import MontyDecoder + +if TYPE_CHECKING: + from pathlib import Path + + from abipy.abio.inputs import AbinitInput + from abipy.core.structure import Structure + from abipy.flowtk.events import EventReport + from jobflow import Flow, Job + from typing_extensions import Self + + from atomate2.abinit.utils.history import JobHistory + +TMPDIR_NAME = "tmpdata" +OUTDIR_NAME = "outdata" +INDIR_NAME = "indata" +TMPDATAFILE_PREFIX = "tmp" +OUTDATAFILE_PREFIX = "out" +INDATAFILE_PREFIX = "in" +TMPDATA_PREFIX = os.path.join(TMPDIR_NAME, TMPDATAFILE_PREFIX) +OUTDATA_PREFIX = os.path.join(OUTDIR_NAME, OUTDATAFILE_PREFIX) +INDATA_PREFIX = os.path.join(INDIR_NAME, INDATAFILE_PREFIX) +STDERR_FILE_NAME = "run.err" +LOG_FILE_NAME = "run.log" +OUTPUT_FILE_NAME = "run.abo" +OUTNC_FILE_NAME = "out_OUT.nc" +INPUT_FILE_NAME: str = "run.abi" +MPIABORTFILE = "__ABI_MPIABORTFILE__" +DUMMY_FILENAME = "__DUMMY__" +ELPHON_OUTPUT_FILE_NAME = "run.abo_elphon" +DDK_FILES_FILE_NAME = "ddk.files" +HISTORY_JSON = "history.json" + + +logger = logging.getLogger(__name__) + + +class ErrorCode: + """Error code to classify the errors.""" + + ERROR = "Error" + UNRECOVERABLE = "Unrecoverable" + UNCLASSIFIED = "Unclassified" + UNCONVERGED = "Unconverged" + UNCONVERGED_PARAMETERS = "Unconverged_parameters" + INITIALIZATION = "Initialization" + RESTART = "Restart" + POSTPROCESS = "Postprocess" + WALLTIME = "Walltime" + + +class AbiAtomateError(Exception): + """Base class for the abinit errors in atomate.""" + + ERROR_CODE = ErrorCode.ERROR + + def __init__(self, msg: str) -> None: + super().__init__(msg) + self.msg = msg + + def to_dict(self) -> dict: + """Create dictionary representation of the error.""" + return {"error_code": self.ERROR_CODE, "msg": self.msg} + + +class AbinitRuntimeError(AbiAtomateError): + """Exception raised for errors during Abinit calculation. + + Contains the information about the errors and warning extracted from + the output files. + Initialized with a job, uses it to prepare a suitable error message. + """ + + ERROR_CODE = ErrorCode.ERROR + + def __init__( + self, + job: Job | Flow | None = None, + msg: str | None = None, + num_errors: int | None = None, + num_warnings: int | None = None, + errors: list | None = None, + warnings: list | None = None, + ) -> None: + """Construct AbinitRuntimeError object. + + If the job has a report all the information will be extracted from it, + otherwise the arguments will be used. + + Parameters + ---------- + job + the atomate2 job + msg + the error message + num_errors + number of errors in the abinit execution. Only used if job doesn't + have a report. + num_warnings + number of warning in the abinit execution. Only used if job doesn't + have a report. + errors + list of errors in the abinit execution. Only used if job doesn't + have a report. + warnings + list of warnings in the abinit execution. Only used if job doesn't + have a report. + """ + # This can handle both the cases of DECODE_MONTY=True and False + # (Since it has a from_dict method). + super().__init__(msg) + self.job = job + if ( + self.job is not None + and hasattr(self.job, "report") + and self.job.report is not None + ): + report = self.job.report + self.num_errors = report.num_errors + self.num_warnings = report.num_warnings + self.errors = report.errors + self.warnings = report.warnings + else: + self.num_errors = num_errors + self.num_warnings = num_warnings + self.errors = errors + self.warnings = warnings + self.msg = msg + + def to_dict(self) -> dict: + """Create dictionary representation of the error.""" + dct = {"num_errors": self.num_errors, "num_warnings": self.num_warnings} + if self.errors: + errors = [error.as_dict() for error in self.errors] + dct["errors"] = errors + if self.warnings: + warnings = [warning.as_dict() for warning in self.warnings] + dct["warnings"] = warnings + if self.msg: + dct["error_message"] = self.msg + + dct["error_code"] = self.ERROR_CODE + dct["@module"] = type(self).__module__ + dct["@class"] = type(self).__name__ + + return dct + + def as_dict(self) -> dict: + """Create dictionary representation of the error.""" + return self.to_dict() + + @classmethod + def from_dict(cls, d: dict) -> Self: + """Create instance of the error from its dictionary representation.""" + dec = MontyDecoder() + warnings = ( + [dec.process_decoded(w) for w in d["warnings"]] if "warnings" in d else [] + ) + errors = [dec.process_decoded(w) for w in d["errors"]] if "errors" in d else [] + msg = d.get("error_message") + + return cls( + warnings=warnings, + errors=errors, + num_errors=d["num_errors"], + num_warnings=d["num_warnings"], + msg=msg, + ) + + +class UnconvergedError(AbinitRuntimeError): + """Exception raised when a calculation didn't converge after the max restarts.""" + + ERROR_CODE = ErrorCode.UNCONVERGED + + def __init__( + self, + job: Job | Flow | None = None, + msg: str | None = None, + num_errors: int | None = None, + num_warnings: int | None = None, + errors: list | None = None, + warnings: list | None = None, + abinit_input: AbinitInput | None = None, + restart_info: RestartInfo | None = None, + history: JobHistory | None = None, + ) -> None: + """Construct UnconvergedError object. + + If the job has a report all the information will be extracted from it, + otherwise the arguments will be used. + It contains information that can be used to further restart the job. + + Parameters + ---------- + job + the atomate2 job + msg + the error message + num_errors + number of errors in the abinit execution. Only used if job doesn't + have a report. + num_warnings + number of warning in the abinit execution. Only used if job doesn't + have a report. + errors + list of errors in the abinit execution. Only used if job doesn't + have a report. + warnings + list of warnings in the abinit execution. Only used if job doesn't + have a report. + abinit_input + the last AbinitInput used. + restart_info + the RestartInfo required to restart the job. + history + The history of the job. + """ + super().__init__(job, msg, num_errors, num_warnings, errors, warnings) + self.abinit_input = abinit_input + self.restart_info = restart_info + self.history = history + + def to_dict(self) -> dict: + """Create dictionary representation of the error.""" + dct = super().to_dict() + dct["abinit_input"] = self.abinit_input.as_dict() if self.abinit_input else None + dct["restart_info"] = self.restart_info.as_dict() if self.restart_info else None + dct["history"] = self.history.as_dict() if self.history else None + dct["@module"] = type(self).__module__ + dct["@class"] = type(self).__name__ + return dct + + @classmethod + def from_dict(cls, d: dict) -> Self: + """Create instance of the error from its dictionary representation.""" + dec = MontyDecoder() + warnings = ( + [dec.process_decoded(w) for w in d["warnings"]] if "warnings" in d else [] + ) + errors = [dec.process_decoded(w) for w in d["errors"]] if "errors" in d else [] + if "abinit_input" in d and d["abinit_input"] is not None: + abinit_input = dec.process_decoded(d["abinit_input"]) + else: + abinit_input = None + if "restart_info" in d and d["restart_info"] is not None: + restart_info = dec.process_decoded(d["restart_info"]) + else: + restart_info = None + if "history" in d and d["history"] is not None: + history = dec.process_decoded(d["history"]) + else: + history = None + return cls( + warnings=warnings, + errors=errors, + num_errors=d["num_errors"], + num_warnings=d["num_warnings"], + msg=d["error_message"], + abinit_input=abinit_input, + restart_info=restart_info, + history=history, + ) + + +class WalltimeError(AbiAtomateError): + """Exception raised when the calculation didn't complete in time.""" + + ERROR_CODE = ErrorCode.WALLTIME + + +class InitializationError(AbiAtomateError): + """Exception raised if errors are present during the initialization of the job.""" + + ERROR_CODE = ErrorCode.INITIALIZATION + + +class RestartError(InitializationError): + """Exception raised if errors show up during the set up of the restart.""" + + ERROR_CODE = ErrorCode.RESTART + + +class PostProcessError(AbiAtomateError): + """Exception raised if problems are encountered during the post processing.""" + + ERROR_CODE = ErrorCode.POSTPROCESS + + +class RestartInfo(MSONable): + """Object that contains the information about the restart of a job.""" + + def __init__(self, previous_dir: Path | str, num_restarts: int = 0) -> None: + self.previous_dir = previous_dir + # self.reset = reset + self.num_restarts = num_restarts + + def as_dict(self) -> dict: + """Create dictionary representation of the error.""" + return { + "previous_dir": self.previous_dir, + # "reset": self.reset, + "num_restarts": self.num_restarts, + "@module": type(self).__module__, + "@class": type(self).__name__, + } + + @classmethod + def from_dict(cls, d: dict) -> Self: + """Create instance of the error from its dictionary representation.""" + return cls( + previous_dir=d["previous_dir"], + # reset=d["reset"], + num_restarts=d["num_restarts"], + ) + + @property + def prev_outdir(self) -> Directory: + """Get the Directory pointing to the output directory of the previous step.""" + return Directory(os.path.join(self.previous_dir, OUTDIR_NAME)) + + @property + def prev_indir(self) -> Directory: + """Get the Directory pointing to the input directory of the previous step.""" + return Directory(os.path.join(self.previous_dir, INDIR_NAME)) + + +def get_final_structure(dir_name: Path | str) -> Structure: + """Get the final/last structure of a calculation in a given directory. + + This functions tries to get the structure: + 1. from the output file of abinit (run.abo). + 2. from the gsr file of abinit (out_GSR.nc). + """ + gsr_path = Directory(os.path.join(dir_name, OUTDIR_NAME)).has_abiext("GSR") + if gsr_path: + # Open the GSR file. + try: + gsr_file = GsrFile(gsr_path) + except Exception: + logging.exception("Exception occurred") + else: + return gsr_file.structure + + ddb_path = Directory(os.path.join(dir_name, OUTDIR_NAME)).has_abiext("DDB") + if ddb_path: + # Open the GSR file. + try: + ddb_file = DdbFile(ddb_path) + except Exception: + logging.exception("Exception occurred") + else: + return ddb_file.structure + + out_path = File(os.path.join(dir_name, OUTPUT_FILE_NAME)) + if out_path.exists: + try: + ab_out = AbinitOutputFile.from_file(out_path.path) + except Exception: + logging.exception("Exception occurred") + else: + return ab_out.final_structure + + raise RuntimeError("Could not get final structure.") + + +def get_event_report(ofile: File, mpiabort_file: File) -> EventReport | None: + """Get report from abinit calculation. + + This analyzes the main output file for possible Errors or Warnings. + It will check the presence of an MPIABORTFILE if not output file is found. + + Parameters + ---------- + ofile : File + Output file to be parsed. Should be either the standard abinit + output or the log file (stdout). + mpiabort_file : File + + Returns + ------- + EventReport + Report of the abinit calculation or None if no output file exists. + """ + parser = events.EventsParser() + + if not ofile.exists: + if not mpiabort_file.exists: + return None + # ABINIT abort file without log! + + return parser.parse(mpiabort_file.path) + + try: + report = parser.parse(ofile.path) + + # Add events found in the ABI_MPIABORTFILE. + if mpiabort_file.exists: + logger.critical("Found ABI_MPIABORTFILE!") + abort_report = parser.parse(mpiabort_file.path) + if len(abort_report) == 0: + logger.warning("ABI_MPIABORTFILE but empty") + else: + if len(abort_report) != 1: + logger.critical("Found more than one event in ABI_MPIABORTFILE") + + # Add it to the initial report only if it differs + # from the last one found in the main log file. + last_abort_event = abort_report[-1] + if report and last_abort_event != report[-1]: + report.append(last_abort_event) + else: + report.append(last_abort_event) + except (ValueError, RuntimeError, Exception) as exc: + # Return a report with an error entry with info on the exception. + logger.critical(f"{ofile}: Exception while parsing ABINIT events:\n {exc!s}") + return parser.report_exception(ofile.path, exc) + else: + return report diff --git a/src/atomate2/abinit/utils/history.py b/src/atomate2/abinit/utils/history.py new file mode 100644 index 0000000000..dc51659e30 --- /dev/null +++ b/src/atomate2/abinit/utils/history.py @@ -0,0 +1,240 @@ +"""Job history related objects.""" + +from __future__ import annotations + +import collections +import logging +import os +import traceback +from typing import TYPE_CHECKING, Any + +from monty.json import MontyDecoder, MSONable, jsanitize + +from atomate2.abinit.utils.common import OUTDIR_NAME + +if TYPE_CHECKING: + from pathlib import Path + + from abipy.abio.inputs import AbinitInput + from abipy.flowtk.events import AbinitEvent + from abipy.flowtk.utils import Directory + from jobflow import Flow, Job + from typing_extensions import Self + +logger = logging.getLogger(__name__) + + +class JobHistory(collections.deque, MSONable): + """History class for tracking the creation and actions performed during a job. + + The objects provided should be MSONable, thus dicts, lists or MSONable objects. + The expected items are dictionaries, transformations, corrections, autoparal, + restart/reset and initializations (when factories will be handled). + Possibly, the first item should contain information about the starting point + of the job. + This object will be forwarded during job restarts and resets, in order to keep + track of the full history of the job. + """ + + def as_dict(self) -> dict: + """Create dictionary representation of the history.""" + items = [i.as_dict() if hasattr(i, "as_dict") else i for i in self] + + return { + "items": items, + "@module": type(self).__module__, + "@class": type(self).__name__, + } + + @classmethod + def from_dict(cls, d: dict) -> Self: + """Create instance of the history from its dictionary representation.""" + dec = MontyDecoder() + return cls([dec.process_decoded(i) for i in d["items"]]) + + def log_initialization( + self, job: Job | Flow, initialization_info: Any | None = None + ) -> None: + """Log initialization information about the job.""" + details = {"job_class": job.__class__.__name__} + if initialization_info: + details["initialization_info"] = initialization_info + self.append(JobEvent(JobEvent.INITIALIZED, details=details)) + + def log_corrections(self, corrections: Any | None) -> None: + """Log corrections applied to the job.""" + self.append(JobEvent(JobEvent.CORRECTIONS, corrections)) + + def log_restart(self) -> None: + """Log that the job is restarted.""" + self.append( + JobEvent( + JobEvent.RESTART, + ) + ) + + def log_start(self, workdir: Path | str | Directory, start_time: Any) -> None: + """Log that the job has started.""" + self.append( + JobEvent( + JobEvent.START, + details={"workdir": workdir, "start_time": start_time}, + ) + ) + + def log_end(self, workdir: Path | str | Directory) -> None: + """Log that the job has ended.""" + self.append( + JobEvent( + JobEvent.END, + details={"workdir": workdir}, + ) + ) + + @property + def num_restarts(self) -> int: + """Get the number of restarts of the job.""" + # TODO: what happens if a job starts but does not end (e.g. killed by walltime) + # how should we count the number of restarts ? do we need both START and + # RESTART events ? One could assume there is one "start" and the following + # are restarts. + return len( + self.get_events_by_types(JobEvent.RESTART) + ) # [event for event in self if event.event_type == JobEvent.RESTART]) + + @property + def run_number(self) -> int: + """Get the number of the run.""" + return len(self.get_events_by_types(JobEvent.START)) + + @property + def prev_dir(self) -> str: + """Get the last run directory.""" + return os.path.join( + self.get_events_by_types(JobEvent.END)[-1].details["workdir"] + ) + + @property + def prev_outdir(self) -> str: + """Get the output directory of the last run.""" + return os.path.join(self.prev_dir, OUTDIR_NAME) + + @property + def is_first_run(self) -> bool: + """Determine if it is the first run of the job from the history.""" + nstart = len(self.get_events_by_types(JobEvent.START)) + if nstart == 0: + raise RuntimeError( + "Calling is_first_run when the start of the job has not been logged." + ) + return nstart == 1 + + def log_autoparal(self, optconf: Any) -> None: + """Log autoparal execution.""" + self.append(JobEvent(JobEvent.AUTOPARAL, details={"optconf": optconf})) + + def log_unconverged(self) -> None: + """Log that the job is not converged.""" + self.append(JobEvent(JobEvent.UNCONVERGED)) + + def log_finalized(self, final_input: AbinitInput | None = None) -> None: + """Log that the job is finalized.""" + details = {"total_run_time": self.get_total_run_time()} + if final_input: + details["final_input"] = final_input + self.append(JobEvent(JobEvent.FINALIZED, details=details)) + + def log_converge_params( + self, unconverged_params: dict, abiinput: AbinitInput + ) -> None: + """Log the change of user-defined convergence parameters. + + An example is the convergence with respect to dilatmx when relaxing a structure. + """ + params = {} + for param, new_value in unconverged_params.items(): + params[param] = { + "old_value": abiinput.get(param, "Default"), + "new_value": new_value, + } + self.append(JobEvent(JobEvent.UNCONVERGED_PARAMS, details={"params": params})) + + def log_error(self, exc: Any) -> None: + """Log an error in the job.""" + tb = traceback.format_exc() + event_details = {"stacktrace": tb} + # If the exception is serializable, save its details + try: + exception_details = exc.to_dict() + except AttributeError: + exception_details = None + except BaseException: + logger.exception("Exception couldn't be serialized") + exception_details = None + if exception_details: + event_details["exception_details"] = exception_details + self.append(JobEvent(JobEvent.ERROR, details=event_details)) + + def log_abinit_stop(self, run_time: Any | None = None) -> None: + """Log that abinit has stopped.""" + self.append(JobEvent(JobEvent.ABINIT_STOP, details={"run_time": run_time})) + + def get_events_by_types(self, types: list | AbinitEvent) -> list: + """Return the events in history of the selected types. + + Parameters + ---------- + types + Single type or list of types. + """ + types = types if isinstance(types, (list, tuple)) else [types] + + return [e for e in self if e.event_type in types] + + def get_total_run_time(self) -> Any: + """Get the total run time based summing the abinit stop event run times.""" + total_run_time = 0 + for te in self.get_events_by_types(JobEvent.ABINIT_STOP): + run_time = te.details.get("run_time", None) + if run_time: + total_run_time += run_time + + return total_run_time + + +class JobEvent(MSONable): + """Object used to categorize the events in the JobHistory.""" + + INITIALIZED = "initialized" + CORRECTIONS = "corrections" + START = "start" + END = "end" + RESTART = "restart" + AUTOPARAL = "autoparal" + UNCONVERGED = "unconverged" + FINALIZED = "finalized" + UNCONVERGED_PARAMS = "unconverged parameters" + ERROR = "error" + ABINIT_STOP = "abinit stop" + + def __init__(self, event_type: AbinitEvent, details: Any | None = None) -> None: + # TODO: add when and where the JobEvent occurred ? + """Construct JobEvent object.""" + self.event_type = event_type + self.details = details + + def as_dict(self) -> dict: + """Create dictionary representation of the job event.""" + dct = {"event_type": self.event_type} + if self.details: + dct["details"] = jsanitize(self.details, strict=True) + dct["@module"] = type(self).__module__ + dct["@class"] = type(self).__name__ + return dct + + @classmethod + def from_dict(cls, d: dict) -> Self: + """Create instance of the job event from its dictionary representation.""" + dec = MontyDecoder() + details = dec.process_decoded(d["details"]) if "details" in d else None + return cls(event_type=d["event_type"], details=details) diff --git a/src/atomate2/abinit/utils/settings.py b/src/atomate2/abinit/utils/settings.py new file mode 100644 index 0000000000..31fa79d317 --- /dev/null +++ b/src/atomate2/abinit/utils/settings.py @@ -0,0 +1,18 @@ +"""Settings for abinit flows in atomate2.""" + +from typing import Any + +from abipy.flowtk.tasks import TaskManager + + +def get_abipy_manager(settings: Any) -> TaskManager: + """Get abipy manager. + + Parameters + ---------- + settings + Abinit atomate2 settings. + """ + if settings.ABIPY_MANAGER_FILE: + return TaskManager.from_file(settings.ABIPY_MANAGER_FILE) + return TaskManager.from_user_config() diff --git a/src/atomate2/aims/__init__.py b/src/atomate2/aims/__init__.py new file mode 100644 index 0000000000..f81a7f8131 --- /dev/null +++ b/src/atomate2/aims/__init__.py @@ -0,0 +1 @@ +"""FHI-aims interface for atomate2.""" diff --git a/src/atomate2/aims/files.py b/src/atomate2/aims/files.py new file mode 100644 index 0000000000..c9ab46a2fc --- /dev/null +++ b/src/atomate2/aims/files.py @@ -0,0 +1,150 @@ +"""Functions dealing with FHI-aims files.""" + +from __future__ import annotations + +import logging +from glob import glob +from pathlib import Path +from typing import TYPE_CHECKING + +from atomate2.common.files import copy_files, get_zfile, gunzip_files +from atomate2.utils.file_client import FileClient, auto_fileclient +from atomate2.utils.path import strip_hostname + +if TYPE_CHECKING: + from collections.abc import Sequence + + from pymatgen.core import Molecule, Structure + from pymatgen.io.aims.sets.base import AimsInputGenerator + +logger = logging.getLogger(__name__) + + +@auto_fileclient +def copy_aims_outputs( + src_dir: Path | str, + src_host: str | None = None, + additional_aims_files: list[str] | None = None, + restart_to_input: bool = False, + file_client: FileClient | None = None, +) -> None: + """ + Copy FHI-aims output files to the current directory (inspired by CP2K plugin). + + Parameters + ---------- + src_dir : str or Path + The source directory. + src_host : str or None + The source hostname used to specify a remote filesystem. Can be given as + either "username@remote_host" or just "remote_host" in which case the username + will be inferred from the current user. If ``None``, the local filesystem will + be used as the source. + additional_aims_files : list[str] + Additional files to copy + restart_to_input : bool + Move the aims restart files to by the aims input in the new directory + file_client : .FileClient + A file client to use for performing file operations. + """ + src_dir = strip_hostname(src_dir) + logger.info(f"Copying FHI-aims inputs from {src_dir}") + directory_listing = file_client.listdir(src_dir, host=src_host) + # additional files like bands, DOS, *.cube, whatever + additional_files = additional_aims_files or [] + + # copy files + # (no need to copy aims.out by default; it can be added to additional_aims_files + # explicitly if needed) + files: list[str] = ( + ["hessian.aims", "geometry.in.next_step", "*.csc"] if restart_to_input else [] + ) + + files += [ + Path(f).name + for pattern in set(files + additional_files) + for f in glob((Path(src_dir) / pattern).as_posix()) + ] + + all_files = [ + get_zfile(directory_listing, str(r), allow_missing=True) for r in files + ] + all_files = [f for f in all_files if f] + + copy_files( + src_dir, + src_host=src_host, + include_files=all_files, + file_client=file_client, + ) + + zipped_files = [f for f in all_files if f.name.endswith("gz")] + + gunzip_files( + include_files=zipped_files, + allow_missing=True, + file_client=file_client, + ) + + logger.info("Finished copying inputs") + + +def write_aims_input_set( + structure: Structure | Molecule, + input_set_generator: AimsInputGenerator, + directory: str | Path = ".", + prev_dir: str | Path | None = None, + **kwargs, +) -> None: + """ + Write FHI-aims input set. + + Parameters + ---------- + structure : Structure or Molecule + A to write the input set for. + input_set_generator : .AimsInputGenerator + An GHI-aims input set generator. + directory : str or Path + The directory to write the input files to. + prev_dir : str or Path or None + If the input set is to be initialized from a previous calculation, + the previous calc directory + **kwargs + Keyword arguments to pass to :obj:`.AimsInputSet.write_input`. + """ + properties = kwargs.get("properties", []) + aims_is = input_set_generator.get_input_set( + structure, prev_dir=prev_dir, properties=properties + ) + + logger.info("Writing FHI-aims input set.") + aims_is.write_input(directory, **kwargs) + + +@auto_fileclient +def cleanup_aims_outputs( + directory: Path | str, + host: str | None = None, + file_patterns: Sequence[str] = (), + file_client: FileClient | None = None, +) -> None: + """Remove unnecessary files. + + Parameters + ---------- + directory: Path or str + Directory containing files + host: str or None + File client host + file_patterns: Sequence[str] + Glob patterns to find files for deletion. + file_client: .FileClient + A file client to use for performing file operations. + """ + files_to_delete = [] + for pattern in file_patterns: + files_to_delete.extend(file_client.glob(Path(directory) / pattern, host=host)) + + for file in files_to_delete: + file_client.remove(file) diff --git a/src/atomate2/aims/flows/__init__.py b/src/atomate2/aims/flows/__init__.py new file mode 100644 index 0000000000..ef12453673 --- /dev/null +++ b/src/atomate2/aims/flows/__init__.py @@ -0,0 +1 @@ +"""Workflows for FHI-aims.""" diff --git a/src/atomate2/aims/flows/core.py b/src/atomate2/aims/flows/core.py new file mode 100644 index 0000000000..5ac2160533 --- /dev/null +++ b/src/atomate2/aims/flows/core.py @@ -0,0 +1,107 @@ +"""(Work)flows for FHI-aims.""" + +from __future__ import annotations + +from copy import deepcopy +from dataclasses import dataclass, field +from pathlib import Path +from typing import TYPE_CHECKING, Any + +from jobflow import Flow, Maker +from pymatgen.io.aims.sets.core import RelaxSetGenerator + +from atomate2.aims.jobs.core import RelaxMaker + +if TYPE_CHECKING: + from pymatgen.core import Molecule, Structure + from typing_extensions import Self + + from atomate2.aims.jobs.base import BaseAimsMaker + + +@dataclass +class DoubleRelaxMaker(Maker): + """Double relaxation maker for FHI-aims. + + A maker to perform a double relaxation in FHI-aims (first with light, + and then with tight species_defaults). + + Parameters + ---------- + name : str + A name for the flow + relax_maker1: .BaseAimsMaker + A maker that generates the first relaxation + relax_maker2: .BaseAimsMaker + A maker that generates the second relaxation + """ + + name: str = "Double relaxation" + relax_maker1: BaseAimsMaker = field(default_factory=RelaxMaker) + relax_maker2: BaseAimsMaker = field(default_factory=RelaxMaker) + + def make( + self, + structure: Structure | Molecule, + prev_dir: str | Path | None = None, + ) -> Flow: + """Create a flow with two chained relaxations. + + Parameters + ---------- + structure : Structure or Molecule + The structure to relax. + prev_dir : str or Path or None + A previous FHI-aims calculation directory to copy output files from. + """ + relax1 = self.relax_maker1.make(structure, prev_dir=prev_dir) + relax1.name += " 1" + + relax2 = self.relax_maker2.make( + relax1.output.structure, prev_dir=relax1.output.dir_name + ) + relax2.name += " 2" + + return Flow([relax1, relax2], relax2.output, name=self.name) + + @classmethod + def from_parameters( + cls, + parameters: dict[str, Any], + species_defaults: list[str] | tuple[str, str] = ("light", "tight"), + ) -> Self: + """Create the maker from an ASE parameter set. + + Creates a DoubleRelaxFlow for the same parameters with two different + species defaults. + + Parameters + ---------- + parameters : dict + a dictionary with calculation parameters + species_defaults: list | tuple + paths for species defaults to use relative to the given `species_dir` + in parameters + """ + # various checks + if len(species_defaults) != 2: + raise ValueError( + "Two species defaults directories must be provided for DoubleRelaxFlow" + ) + if "species_dir" not in parameters: + raise KeyError("Provided parameters do not include species_dir") + species_dir = Path(parameters["species_dir"]) + for basis_set in species_defaults: + if not (species_dir / basis_set).exists(): + basis_set_dir = (species_dir / basis_set).as_posix() + raise OSError( + f"The species defaults directory {basis_set_dir} does not exist" + ) + + # now the actual work begins + makers = [] + for basis_set in species_defaults: + parameters["species_dir"] = (species_dir / basis_set).as_posix() + input_set = RelaxSetGenerator(user_params=deepcopy(parameters)) + makers.append(RelaxMaker(input_set_generator=input_set)) + return cls(relax_maker1=makers[0], relax_maker2=makers[1]) diff --git a/src/atomate2/aims/flows/gw.py b/src/atomate2/aims/flows/gw.py new file mode 100644 index 0000000000..d63d103cf5 --- /dev/null +++ b/src/atomate2/aims/flows/gw.py @@ -0,0 +1,39 @@ +"""GW workflows for FHI-aims with automatic convergence.""" + +from dataclasses import dataclass, field + +from atomate2.aims.jobs.convergence import ConvergenceMaker +from atomate2.aims.jobs.core import GWMaker + + +@dataclass +class GWConvergenceMaker(ConvergenceMaker): + """A maker to perform a GW workflow with automatic convergence in FHI-aims. + + Basically a .ConvergenceMaker with adjusted defaults. Employs the fact that + GW calculations in FHI-aims scale as O(N^4) with a large prefactor, which makes + running a DFT part for any structure negligible with respect to the GW + postprocessing. + + Parameters + ---------- + name : str + A name for the job + maker: .GWMaker + A maker for the run + criterion_name: str + A name for the convergence criterion. Must be in the run results + epsilon: float + A difference in criterion value for subsequent runs + convergence_field: str + An input parameter that changes to achieve convergence + convergence_steps: Iterable + An iterable of the possible values for the convergence field. + If the iterable is depleted and the convergence is not reached, + then the job is failed + """ + + name: str = "GW convergence" + maker: GWMaker = field(default_factory=GWMaker) + criterion_name: str = "bandgap" + epsilon: float = 0.1 diff --git a/src/atomate2/aims/flows/phonons.py b/src/atomate2/aims/flows/phonons.py new file mode 100644 index 0000000000..2f2db8b6f1 --- /dev/null +++ b/src/atomate2/aims/flows/phonons.py @@ -0,0 +1,155 @@ +"""Defines the phonon workflows for FHI-aims.""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +from atomate2.aims.jobs.core import RelaxMaker, StaticMaker +from atomate2.aims.jobs.phonons import ( + PhononDisplacementMaker, + PhononDisplacementMakerSocket, +) +from atomate2.common.flows.phonons import BasePhononMaker + +if TYPE_CHECKING: + from atomate2.aims.jobs.base import BaseAimsMaker + + +@dataclass +class PhononMaker(BasePhononMaker): + """Maker to calculate harmonic phonons with FHI-aims and Phonopy. + + Calculate the harmonic phonons of a material. Initially, a tight structural + relaxation is performed to obtain a structure without forces on the atoms. + Subsequently, supercells with one displaced atom are generated and accurate + forces are computed for these structures. With the help of phonopy, these + forces are then converted into a dynamical matrix. To correct for polarization + effects, a correction of the dynamical matrix based on BORN charges can + be performed. Finally, phonon densities of states, phonon band structures + and thermodynamic properties are computed. + + .. Note:: + It is heavily recommended to symmetrize the structure before passing it to + this flow. Otherwise, a different space group might be detected and too + many displacement calculations will be generated. + It is recommended to check the convergence parameters here and + adjust them if necessary. The default might not be strict enough + for your specific case. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + sym_reduce : bool + Whether to reduce the number of deformations using symmetry. + symprec : float + Symmetry precision to use in the + reduction of symmetry to find the primitive/conventional cell + (use_primitive_standard_structure, use_conventional_standard_structure) + and to handle all symmetry-related tasks in phonopy + displacement: float + displacement distance for phonons + min_length: float + min length of the supercell that will be built + prefer_90_degrees: bool + if set to True, supercell algorithm will first try to find a supercell + with 3 90 degree angles + get_supercell_size_kwargs: dict + kwargs that will be passed to get_supercell_size to determine supercell size + use_symmetrized_structure: str + allowed strings: "primitive", "conventional", None + + - "primitive" will enforce to start the phonon computation + from the primitive standard structure + according to Setyawan, W., & Curtarolo, S. (2010). + High-throughput electronic band structure calculations: + Challenges and tools. Computational Materials Science, + 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010. + This makes it possible to use certain k-path definitions + with this workflow. Otherwise, we must rely on seekpath + - "conventional" will enforce to start the phonon computation + from the conventional standard structure + according to Setyawan, W., & Curtarolo, S. (2010). + High-throughput electronic band structure calculations: + Challenges and tools. Computational Materials Science, + 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010. + We will however use seekpath and primitive structures + as determined by from phonopy to compute the phonon band structure + bulk_relax_maker : .BaseAimsMaker or None + A maker to perform a tight relaxation on the bulk. + Set to ``None`` to skip the + bulk relaxation + static_energy_maker : .BaseAimsMaker or None + A maker to perform the computation of the DFT energy on the bulk. + Set to ``None`` to skip the + static energy computation + born_maker: .BaseAimsMaker or None + Maker to compute the BORN charges. + phonon_displacement_maker : .BaseAimsMaker or None + Maker used to compute the forces for a supercell. + generate_frequencies_eigenvectors_kwargs : dict + Keyword arguments passed to :obj:`generate_frequencies_eigenvectors`. + create_thermal_displacements: bool + Bool that determines if thermal_displacement_matrices are computed + kpath_scheme: str + scheme to generate kpoints. Please be aware that + you can only use seekpath with any kind of cell + Otherwise, please use the standard primitive structure + Available schemes are: + "seekpath", "hinuma", "setyawan_curtarolo", "latimer_munro". + "seekpath" and "hinuma" are the same definition but + seekpath can be used with any kind of unit cell as + it relies on phonopy to handle the relationship + to the primitive cell and not pymatgen + code: str + determines the dft or forcefield code. + store_force_constants: bool + if True, force constants will be stored + socket: bool + If True, use the socket for the calculation + """ + + name: str = "phonon" + sym_reduce: bool = True + symprec: float = 1e-4 + displacement: float = 0.01 + min_length: float | None = 20.0 + prefer_90_degrees: bool = True + get_supercell_size_kwargs: dict = field(default_factory=dict) + use_symmetrized_structure: str | None = None + create_thermal_displacements: bool = True + generate_frequencies_eigenvectors_kwargs: dict = field(default_factory=dict) + kpath_scheme: str = "seekpath" + store_force_constants: bool = True + socket: bool = False + code: str = "aims" + bulk_relax_maker: BaseAimsMaker | None = field( + default_factory=RelaxMaker.full_relaxation + ) + static_energy_maker: BaseAimsMaker | None = field(default_factory=StaticMaker) + born_maker: BaseAimsMaker | None = None + phonon_displacement_maker: BaseAimsMaker | None = None + + def __post_init__(self) -> None: + """Set the default phonon_displacement_maker. + + Set the displacement maker based on whether the socket communicator is used + """ + if self.phonon_displacement_maker is None: + if self.socket: + self.phonon_displacement_maker = PhononDisplacementMakerSocket() + else: + self.phonon_displacement_maker = PhononDisplacementMaker() + + @property + def prev_calc_dir_argname(self) -> str: + """Name of argument informing static maker of previous calculation directory. + + As this differs between different DFT codes (e.g., VASP, CP2K), it + has been left as a property to be implemented by the inheriting class. + + Note: this is only applicable if a relax_maker is specified; i.e., two + calculations are performed for each ordering (relax -> static) + """ + return "prev_dir" diff --git a/src/atomate2/aims/jobs/__init__.py b/src/atomate2/aims/jobs/__init__.py new file mode 100644 index 0000000000..f6d79b2728 --- /dev/null +++ b/src/atomate2/aims/jobs/__init__.py @@ -0,0 +1 @@ +"""Define all FHI-aims jobs.""" diff --git a/src/atomate2/aims/jobs/base.py b/src/atomate2/aims/jobs/base.py new file mode 100644 index 0000000000..e2a190b0fd --- /dev/null +++ b/src/atomate2/aims/jobs/base.py @@ -0,0 +1,137 @@ +"""Defines the base FHI-aims Maker.""" + +from __future__ import annotations + +import logging +from dataclasses import dataclass, field +from pathlib import Path +from typing import TYPE_CHECKING, Any + +from jobflow import Maker, Response, job +from monty.serialization import dumpfn +from pymatgen.io.aims.sets.base import AimsInputGenerator + +from atomate2 import SETTINGS +from atomate2.aims.files import ( + cleanup_aims_outputs, + copy_aims_outputs, + write_aims_input_set, +) +from atomate2.aims.run import run_aims, should_stop_children +from atomate2.aims.schemas.task import AimsTaskDoc +from atomate2.common.files import gzip_output_folder + +if TYPE_CHECKING: + from pymatgen.core import Molecule, Structure + +logger = logging.getLogger(__name__) + +# Input files. +# Exclude those that are also outputs +_INPUT_FILES = [ + "geometry.in", + "control.in", +] + +# Output files. +_OUTPUT_FILES = ["aims.out", "geometry.in.next_step", "hessian.aims", "*.cube", "*.csc"] + +# Files to zip: inputs, outputs and additionally generated files +_FILES_TO_ZIP = _INPUT_FILES + _OUTPUT_FILES + + +@dataclass +class BaseAimsMaker(Maker): + """ + Base FHI-aims job maker. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .AimsInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict[str, Any] + Keyword arguments that will get passed to :obj:`.write_aims_input_set`. + copy_aims_kwargs : dict[str, Any] + Keyword arguments that will get passed to :obj:`.copy_aims_outputs`. + run_aims_kwargs : dict[str, Any] + Keyword arguments that will get passed to :obj:`.run_aims`. + task_document_kwargs : dict[str, Any] + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + stop_children_kwargs : dict[str, Any] + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict[str, Any] + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + store_output_data: bool + Whether the job output (TaskDoc) should be stored in the JobStore through + the response. + """ + + name: str = "base" + input_set_generator: AimsInputGenerator = field(default_factory=AimsInputGenerator) + write_input_set_kwargs: dict[str, Any] = field(default_factory=dict) + copy_aims_kwargs: dict[str, Any] = field(default_factory=dict) + run_aims_kwargs: dict[str, Any] = field(default_factory=dict) + task_document_kwargs: dict[str, Any] = field(default_factory=dict) + stop_children_kwargs: dict[str, Any] = field(default_factory=dict) + write_additional_data: dict[str, Any] = field(default_factory=dict) + store_output_data: bool = True + + @job + def make( + self, + structure: Structure | Molecule, + prev_dir: str | Path | None = None, + ) -> Response: + """Run an FHI-aims calculation. + + Parameters + ---------- + structure : Structure or Molecule + A pymatgen Structure object to create the calculation for. + prev_dir : str or Path or None + A previous FHI-aims calculation directory to copy output files from. + """ + # copy previous inputs if needed (governed by self.copy_aims_kwargs) + if prev_dir is not None: + copy_aims_outputs(prev_dir, **self.copy_aims_kwargs) + + # write aims input files + self.write_input_set_kwargs["prev_dir"] = prev_dir + write_aims_input_set( + structure, self.input_set_generator, **self.write_input_set_kwargs + ) + + # write any additional data + for filename, data in self.write_additional_data.items(): + dumpfn(data, filename.replace(":", ".")) + + # run FHI-aims + run_aims(**self.run_aims_kwargs) + + # parse FHI-aims outputs + task_doc = AimsTaskDoc.from_directory(Path.cwd(), **self.task_document_kwargs) + task_doc.task_label = self.name + + # decide whether child jobs should proceed + stop_children = should_stop_children(task_doc, **self.stop_children_kwargs) + + # cleanup files to save disk space + cleanup_aims_outputs(directory=Path.cwd()) + + # gzip folder + gzip_output_folder( + directory=Path.cwd(), + setting=SETTINGS.VASP_ZIP_FILES, + files_list=_FILES_TO_ZIP, + ) + + return Response( + stop_children=stop_children, + output=task_doc if self.store_output_data else None, + ) diff --git a/src/atomate2/aims/jobs/convergence.py b/src/atomate2/aims/jobs/convergence.py new file mode 100644 index 0000000000..b29e4be1c9 --- /dev/null +++ b/src/atomate2/aims/jobs/convergence.py @@ -0,0 +1,134 @@ +"""Defines the base FHI-aims convergence jobs.""" + +from __future__ import annotations + +import json +from dataclasses import dataclass, field +from pathlib import Path +from typing import TYPE_CHECKING + +from jobflow import Flow, Maker, Response, job + +from atomate2.aims.jobs.base import BaseAimsMaker +from atomate2.aims.schemas.task import ConvergenceSummary + +if TYPE_CHECKING: + from pymatgen.core import Molecule, Structure + +CONVERGENCE_FILE_NAME = "convergence.json" # make it a constant? + + +@dataclass +class ConvergenceMaker(Maker): + """Defines a convergence workflow with a maximum number of steps. + + A job that performs convergence run for a given number of steps. Stops either + when all steps are done, or when the convergence criterion is reached, that is when + the absolute difference between the subsequent values of the convergence field is + less than a given epsilon. + + Parameters + ---------- + convergence_field: str + An input parameter that changes to achieve convergence + convergence_steps: Iterable + An iterable of the possible values for the convergence field. + If the iterable is depleted and the convergence is not reached, + then the job is failed + name : str + A name for the job + maker: .BaseAimsMaker + A maker for the run + criterion_name: str + A name for the convergence criterion. Must be in the run results + epsilon: float + A difference in criterion value for subsequent runs + """ + + convergence_field: str + convergence_steps: list | tuple + name: str = "convergence" + maker: BaseAimsMaker = field(default_factory=BaseAimsMaker) + criterion_name: str = "energy_per_atom" + epsilon: float = 0.001 + + @job + def make( + self, + structure: Structure | Molecule, + prev_dir: str | Path | None = None, + convergence_data: dict | None = None, + prev_output_value: float | None = None, + ) -> ConvergenceSummary: + """Create a top-level flow controlling convergence iteration. + + Parameters + ---------- + structure : Structure or Molecule + a structure to run a job + prev_dir : str or Path or None + An FHI-aims calculation directory in which previous run contents are stored + convergence_data : dict or None + The convergence information to date. + prev_output_value : float or None + The output value being converged from the previous aims calculation. + """ + # getting the calculation index + idx = 0 + converged = False + if convergence_data is not None: + idx = convergence_data["idx"] + convergence_data["convergence_field_values"].append( + self.convergence_steps[idx] + ) + convergence_data["criterion_values"].append(prev_output_value) + if len(convergence_data["criterion_values"]) > 1: + # checking for convergence + converged = ( + abs(prev_output_value - convergence_data["criterion_values"][-2]) + < self.epsilon + ) + idx += 1 + else: + convergence_data = { + "criterion_name": self.criterion_name, + "criterion_values": [], + "convergence_field_name": self.convergence_field, + "convergence_field_values": [], + "epsilon": self.epsilon, + } + convergence_data.update(idx=idx, converged=converged) + + if prev_dir is not None: + split_prev_dir = str(prev_dir).split(":")[-1] + convergence_file = Path(split_prev_dir) / CONVERGENCE_FILE_NAME + with open(convergence_file, "w") as file: + json.dump(convergence_data, file) + + if idx < len(self.convergence_steps) and not converged: + # finding next jobs + next_base_job = self.maker.make(structure, prev_dir=prev_dir) + next_base_job.update_maker_kwargs( + { + "_set": { + f"input_set_generator->user_params->" + f"{self.convergence_field}": self.convergence_steps[idx] + } + }, + dict_mod=True, + ) + next_base_job.append_name(append_str=f" {idx}") + + next_job = self.make( + structure, + prev_dir=next_base_job.output.dir_name, + convergence_data=convergence_data, + prev_output_value=getattr( + next_base_job.output.output, self.criterion_name + ), + ) + + replace_flow = Flow([next_base_job, next_job], output=next_base_job.output) + return Response(replace=replace_flow) + + return ConvergenceSummary.from_data(structure, convergence_data) diff --git a/src/atomate2/aims/jobs/core.py b/src/atomate2/aims/jobs/core.py new file mode 100644 index 0000000000..4bfca85377 --- /dev/null +++ b/src/atomate2/aims/jobs/core.py @@ -0,0 +1,227 @@ +"""Define all Core FHI-aims jobs.""" + +from __future__ import annotations + +import logging +from collections.abc import Sequence +from dataclasses import dataclass, field +from pathlib import Path +from typing import TYPE_CHECKING + +from jobflow import Response, job +from monty.serialization import dumpfn +from pymatgen.io.aims.parsers import read_aims_output +from pymatgen.io.aims.sets.bs import BandStructureSetGenerator, GWSetGenerator +from pymatgen.io.aims.sets.core import ( + RelaxSetGenerator, + SocketIOSetGenerator, + StaticSetGenerator, +) + +from atomate2 import SETTINGS +from atomate2.aims.files import cleanup_aims_outputs, write_aims_input_set +from atomate2.aims.jobs.base import _FILES_TO_ZIP, BaseAimsMaker +from atomate2.aims.run import run_aims_socket, should_stop_children +from atomate2.aims.schemas.task import AimsTaskDoc +from atomate2.common.files import gzip_output_folder + +if TYPE_CHECKING: + from pymatgen.core import Molecule, Structure + from pymatgen.io.aims.sets.base import AimsInputGenerator + +logger = logging.getLogger(__name__) + + +@dataclass +class StaticMaker(BaseAimsMaker): + """Maker to create FHI-aims SCF jobs. + + Parameters + ---------- + calc_type: str + The type key for the calculation + name: str + The job name + input_set_generator: .AimsInputGenerator + The InputGenerator for the calculation + """ + + calc_type: str = "scf" + name: str = "SCF Calculation" + input_set_generator: AimsInputGenerator = field(default_factory=StaticSetGenerator) + + +@dataclass +class RelaxMaker(BaseAimsMaker): + """Maker to create relaxation calculations. + + Parameters + ---------- + calc_type: str + The type key for the calculation + name: str + The job name + input_set_generator: .AimsInputGenerator + The InputGenerator for the calculation + """ + + calc_type: str = "relax" + name: str = "Relaxation calculation" + input_set_generator: AimsInputGenerator = field(default_factory=RelaxSetGenerator) + + @classmethod + def fixed_cell_relaxation(cls, *args, **kwargs) -> RelaxMaker: + """Create a fixed cell relaxation maker.""" + return cls( + input_set_generator=RelaxSetGenerator(*args, relax_cell=False, **kwargs), + name=cls.name + " (fixed cell)", + ) + + @classmethod + def full_relaxation(cls, *args, **kwargs) -> RelaxMaker: + """Create a full relaxation maker.""" + return cls( + input_set_generator=RelaxSetGenerator(*args, relax_cell=True, **kwargs) + ) + + +@dataclass +class SocketIOStaticMaker(BaseAimsMaker): + """Maker for the SocketIO calculator in FHI-aims. + + Parameters + ---------- + calc_type: str + The type key for the calculation + name: str + The job name + host: str + The name of the host to maintain the socket server on + port: int + The port number the socket server will listen on + input_set_generator: .AimsInputGenerator + The InputGenerator for the calculation + """ + + calc_type: str = "multi_scf" + name: str = "SCF Calculations Socket" + host: str = "localhost" + port: int = 12345 + input_set_generator: AimsInputGenerator = field( + default_factory=SocketIOSetGenerator + ) + + @job + def make( + self, + structure: list[Structure | Molecule], + prev_dir: str | Path | None = None, + ) -> Response: + """Run multiple FHI-aims calculation with the socket. + + Calculate the properties for multiple structures using the same parameters + using socket communication to speed up the calculations. + + Parameters + ---------- + structure : list[Molecule | Structure] + The list of structure objects to run FHI-aims on + prev_dir : str or Path or None + A previous FHI-aims calculation directory to copy output files from. + + Returns + ------- + The output response for the calculations + """ + # copy previous inputs + if not isinstance(structure, list): + structure = [structure] + + from_prev = prev_dir is not None + if from_prev: + hostless_prev_dir = str(prev_dir).split(":")[1] + images = read_aims_output(f"{hostless_prev_dir}/aims.out") + if not isinstance(images, Sequence): + images = [images] + + for img in images: + img.calc = None + + for ii in range(-1 * len(structure), 0, -1): + if structure[ii] in images: + del structure[ii] + + # write aims input files + self.write_input_set_kwargs["prev_dir"] = prev_dir + write_aims_input_set( + structure[0], self.input_set_generator, **self.write_input_set_kwargs + ) + + # write any additional data + for filename, data in self.write_additional_data.items(): + dumpfn(data, filename.replace(":", ".")) + + # run FHI-aims + run_aims_socket(structure, **self.run_aims_kwargs) + + # parse FHI-aims outputs + task_doc = AimsTaskDoc.from_directory(Path.cwd(), **self.task_document_kwargs) + task_doc.task_label = self.name + + # decide whether child jobs should proceed + stop_children = should_stop_children(task_doc, **self.stop_children_kwargs) + + # cleanup files to save disk space + cleanup_aims_outputs(directory=Path.cwd()) + + # gzip folder + gzip_output_folder( + directory=Path.cwd(), + setting=SETTINGS.VASP_ZIP_FILES, + files_list=_FILES_TO_ZIP, + ) + + return Response( + stop_children=stop_children, + output=task_doc if self.store_output_data else None, + ) + + +@dataclass +class BandStructureMaker(BaseAimsMaker): + """A job Maker for a band structure calculation. + + Parameters + ---------- + calc_type: str + The type key for the calculation + name: str + The job name + input_set_generator: .BandStructureSetGenerator + The InputGenerator for the calculation + """ + + calc_type = "band_structure" + name: str = "bands" + input_set_generator: BandStructureSetGenerator = field( + default_factory=BandStructureSetGenerator + ) + + +@dataclass +class GWMaker(BaseAimsMaker): + """A job Maker for a GW band structure calculation. + + Parameters + ---------- + calc_type: str + The type key for the calculation + name: str + The job name + input_set_generator: .GWSetGenerator + The InputGenerator for the calculation + """ + + calc_type = "gw" + name: str = "GW" + input_set_generator: GWSetGenerator = field(default_factory=GWSetGenerator) diff --git a/src/atomate2/aims/jobs/phonons.py b/src/atomate2/aims/jobs/phonons.py new file mode 100644 index 0000000000..e19faca568 --- /dev/null +++ b/src/atomate2/aims/jobs/phonons.py @@ -0,0 +1,63 @@ +"""Define the PhononDisplacementMakers for FHI-aims.""" + +from dataclasses import dataclass, field + +from pymatgen.io.aims.sets.base import AimsInputGenerator +from pymatgen.io.aims.sets.core import SocketIOSetGenerator, StaticSetGenerator + +from atomate2.aims.jobs.base import BaseAimsMaker +from atomate2.aims.jobs.core import SocketIOStaticMaker + + +@dataclass +class PhononDisplacementMaker(BaseAimsMaker): + """ + Maker to perform a static calculation as a part of the finite displacement method. + + The input set is for a static run with tighter convergence parameters. + Both the k-point mesh density and convergence parameters + are stricter than a normal relaxation. + + Parameters + ---------- + name: str + The job name. + input_set_generator: .AimsInputGenerator + A generator used to make the input set. + """ + + name: str = "phonon static aims" + + input_set_generator: AimsInputGenerator = field( + default_factory=lambda: StaticSetGenerator( + user_params={"compute_forces": True}, + user_kpoints_settings={"density": 5.0, "even": True}, + ) + ) + + +@dataclass +class PhononDisplacementMakerSocket(SocketIOStaticMaker): + """ + Maker to perform a static calculation as a part of the finite displacement method. + + The input set is for a static run with tighter convergence parameters. + Both the k-point mesh density and convergence parameters + are stricter than a normal relaxation. + + Parameters + ---------- + name: str + The job name. + input_set_generator: .AimsInputGenerator + A generator used to make the input set. + """ + + name: str = "phonon static aims socket" + + input_set_generator: AimsInputGenerator = field( + default_factory=lambda: SocketIOSetGenerator( + user_params={"compute_forces": True}, + user_kpoints_settings={"density": 5.0, "even": True}, + ) + ) diff --git a/src/atomate2/aims/run.py b/src/atomate2/aims/run.py new file mode 100644 index 0000000000..1d2294f55e --- /dev/null +++ b/src/atomate2/aims/run.py @@ -0,0 +1,123 @@ +"""An FHI-aims jobflow runner.""" + +from __future__ import annotations + +import json +import logging +import os +import subprocess +from os.path import expandvars +from typing import TYPE_CHECKING + +from ase.calculators.aims import Aims +from ase.calculators.socketio import SocketIOCalculator +from monty.json import MontyDecoder +from pymatgen.io.ase import AseAtomsAdaptor + +from atomate2 import SETTINGS + +if TYPE_CHECKING: + from pymatgen.core import Molecule, Structure + + from atomate2.aims.schemas.task import AimsTaskDoc +logger = logging.getLogger(__name__) + + +def run_aims( + aims_cmd: str = None, +) -> None: + """ + Run FHI-aims. + + Parameters + ---------- + aims_cmd : str + The command used to run FHI-aims (defaults to SETTINGS.AIMS_CMD). + """ + if aims_cmd is None: + aims_cmd = SETTINGS.AIMS_CMD + + aims_cmd = expandvars(aims_cmd) + + logger.info(f"Running command: {aims_cmd}") + return_code = subprocess.call(["/bin/bash", "-c", aims_cmd], env=os.environ) # noqa: S603 + logger.info(f"{aims_cmd} finished running with return code: {return_code}") + + +def should_stop_children( + task_document: AimsTaskDoc, + handle_unsuccessful: bool | str = True, +) -> bool: + """ + Decide whether child jobs should continue. + + Parameters + ---------- + task_document : .TaskDoc + An FHI-aims task document. + handle_unsuccessful : bool or str + This is a three-way toggle on what to do if your job looks OK, but is actually + not converged (either electronic or ionic): + + - `True`: Mark job as completed, but stop children. + - `False`: Do nothing, continue with workflow as normal. + - `"error"`: Throw an error. + + Returns + ------- + bool + Whether to stop child jobs. + """ + if task_document.state == "successful": + return False + + if isinstance(handle_unsuccessful, bool): + return handle_unsuccessful + + if handle_unsuccessful == "error": + raise RuntimeError("Job was not successful (not converged)!") + + raise RuntimeError(f"Unknown option for handle_unsuccessful: {handle_unsuccessful}") + + +def run_aims_socket( + structures_to_calculate: list[Structure | Molecule], aims_cmd: str = None +) -> None: + """Use the ASE interface to run FHI-aims from the socket. + + Parameters + ---------- + structures_to_calculate: list[Structure or Molecule] + The list of structures to run scf calculations on + aims_cmd: str + The aims command to use (defaults to SETTINGS.AIMS_CMD). + """ + ase_adaptor = AseAtomsAdaptor() + atoms_to_calculate = [ + ase_adaptor.get_atoms(structure) for structure in structures_to_calculate + ] + + with open("parameters.json") as param_file: + parameters = json.load(param_file, cls=MontyDecoder) + if aims_cmd: + parameters["aims_command"] = aims_cmd + elif "aims_command" not in parameters: + parameters["aims_command"] = SETTINGS.AIMS_CMD + + calculator = Aims(**parameters) + port = parameters["use_pimd_wrapper"][1] + atoms = atoms_to_calculate[0].copy() + + with SocketIOCalculator(calc=calculator, port=port) as calc: + for atoms_calc in atoms_to_calculate: + # Delete prior calculation results + calc.results.clear() + + # Reset atoms information to the new cell + atoms.info = atoms_calc.info + atoms.cell = atoms_calc.cell + atoms.positions = atoms_calc.positions + + calc.calculate(atoms, system_changes=["positions", "cell"]) + + calc.close() diff --git a/src/atomate2/aims/schemas/__init__.py b/src/atomate2/aims/schemas/__init__.py new file mode 100644 index 0000000000..ea67ae1600 --- /dev/null +++ b/src/atomate2/aims/schemas/__init__.py @@ -0,0 +1 @@ +"""Define the schemas for FHI-aims.""" diff --git a/src/atomate2/aims/schemas/calculation.py b/src/atomate2/aims/schemas/calculation.py new file mode 100644 index 0000000000..9077f9798e --- /dev/null +++ b/src/atomate2/aims/schemas/calculation.py @@ -0,0 +1,455 @@ +"""Schemas for FHI-aims calculation objects.""" + +from __future__ import annotations + +import os +from collections.abc import Sequence +from datetime import datetime, timezone +from pathlib import Path +from typing import TYPE_CHECKING, Any, Optional, Union + +import numpy as np +from ase.spectrum.band_structure import BandStructure +from jobflow.utils import ValueEnum +from pydantic import BaseModel, Field +from pymatgen.core import Molecule, Structure +from pymatgen.core.trajectory import Trajectory +from pymatgen.electronic_structure.dos import Dos +from pymatgen.io.aims.outputs import AimsOutput +from pymatgen.io.common import VolumetricData +from typing_extensions import Self + +if TYPE_CHECKING: + from emmet.core.math import Matrix3D, Vector3D + +STORE_VOLUMETRIC_DATA = ("total_density",) + + +def ensure_stress_full(input_stress: Sequence[float] | Matrix3D) -> Matrix3D: + """Test if the stress if a voigt vector and if so convert it to a 3x3 matrix.""" + if np.array(input_stress).shape == (3, 3): + return np.array(input_stress) + + xx, yy, zz, yz, xz, xy = np.array(input_stress).flatten() + return np.array([[xx, xy, xz], [xy, yy, yz], [xz, yz, zz]]) + + +class TaskState(ValueEnum): + """FHI-aims calculation state.""" + + SUCCESS = "successful" + FAILED = "failed" + + +class AimsObject(ValueEnum): + """Types of FHI-aims data objects.""" + + DOS = "dos" + BAND_STRUCTURE = "band_structure" + ELECTRON_DENSITY = "electron_density" # e_density + WFN = "wfn" # Wavefunction file + TRAJECTORY = "trajectory" + + +class CalculationOutput(BaseModel): + """Document defining FHI-aims calculation outputs. + + Parameters + ---------- + energy: float + The final total DFT energy for the calculation + energy_per_atom: float + The final DFT energy per atom for the calculation + structure: Structure or Molecule + The final pymatgen Structure or Molecule of the system + efermi: float + The Fermi level from the calculation in eV + forces: List[Vector3D] + Forces acting on each atom + all_forces: List[List[Vector3D]] + Forces acting on each atom for each structure in the output file + stress: Matrix3D + The stress on the cell + stresses: List[Matrix3D] + The atomic virial stresses + is_metal: bool + Whether the system is metallic + bandgap: float + The band gap from the calculation in eV + cbm: float + The conduction band minimum in eV (if system is not metallic + vbm: float + The valence band maximum in eV (if system is not metallic) + atomic_steps: list[Structure or Molecule] + Structures for each ionic step" + """ + + energy: float = Field( + None, description="The final total DFT energy for the calculation" + ) + energy_per_atom: float = Field( + None, description="The final DFT energy per atom for the calculation" + ) + + structure: Union[Structure, Molecule] = Field( + None, description="The final structure from the calculation" + ) + + efermi: Optional[float] = Field( + None, description="The Fermi level from the calculation in eV" + ) + + forces: Optional[list[Vector3D]] = Field( + None, description="Forces acting on each atom" + ) + all_forces: Optional[list[list[Vector3D]]] = Field( + None, + description="Forces acting on each atom for each structure in the output file", + ) + stress: Optional[Matrix3D] = Field(None, description="The stress on the cell") + stresses: Optional[list[Matrix3D]] = Field( + None, description="The atomic virial stresses" + ) + + is_metal: Optional[bool] = Field(None, description="Whether the system is metallic") + bandgap: Optional[float] = Field( + None, description="The band gap from the calculation in eV" + ) + cbm: float = Field( + None, + description="The conduction band minimum, or LUMO for molecules, in eV " + "(if system is not metallic)", + ) + vbm: Optional[float] = Field( + None, + description="The valence band maximum, or HOMO for molecules, in eV " + "(if system is not metallic)", + ) + atomic_steps: list[Union[Structure, Molecule]] = Field( + None, description="Structures for each ionic step" + ) + + @classmethod + def from_aims_output( + cls, + output: AimsOutput, # Must use auto_load kwarg when passed + # store_trajectory: bool = False, + ) -> Self: + """Create an FHI-aims output document from FHI-aims outputs. + + Parameters + ---------- + output: .AimsOutput + An AimsOutput object. + store_trajectory: bool + A flag setting to store output trajectory + + Returns + ------- + The FHI-aims calculation output document. + """ + structure = output.final_structure + + electronic_output = { + "efermi": getattr(output, "fermi_energy", None), + "vbm": output.vbm, + "cbm": output.cbm, + "bandgap": output.band_gap, + "direct_bandgap": output.direct_band_gap, + } + + forces = getattr(output, "forces", None) + + stress = None + if output.stress is not None: + stress = ensure_stress_full(output.stress).tolist() + + stresses = None + if output.stresses is not None: + stresses = [ensure_stress_full(st).tolist() for st in output.stresses] + + all_forces = None + if not any(ff is None for ff in output.all_forces): + all_forces = [f if (f is not None) else None for f in output.all_forces] + + return cls( + structure=structure, + energy=output.final_energy, + energy_per_atom=output.final_energy / len(structure.species), + **electronic_output, + atomic_steps=output.structures, + forces=forces, + stress=stress, + stresses=stresses, + all_forces=all_forces, + ) + + +class Calculation(BaseModel): + """Full FHI-aims calculation inputs and outputs. + + Parameters + ---------- + dir_name: str + The directory for this FHI-aims calculation + aims_version: str + FHI-aims version used to perform the calculation + has_aims_completed: .TaskState + Whether FHI-aims completed the calculation successfully + output: .CalculationOutput + The FHI-aims calculation output + completed_at: str + Timestamp for when the calculation was completed + output_file_paths: Dict[str, str] + Paths (relative to dir_name) of the FHI-aims output files + associated with this calculation + """ + + dir_name: str = Field( + None, description="The directory for this FHI-aims calculation" + ) + aims_version: str = Field( + None, description="FHI-aims version used to perform the calculation" + ) + has_aims_completed: TaskState = Field( + None, description="Whether FHI-aims completed the calculation successfully" + ) + output: CalculationOutput = Field( + None, description="The FHI-aims calculation output" + ) + completed_at: str = Field( + None, description="Timestamp for when the calculation was completed" + ) + output_file_paths: dict[str, str] = Field( + None, + description="Paths (relative to dir_name) of the FHI-aims output files " + "associated with this calculation", + ) + + @classmethod + def from_aims_files( + cls, + dir_name: Path | str, + task_name: str, + aims_output_file: Path | str = "aims.out", + volumetric_files: list[str] = None, + parse_dos: str | bool = False, + parse_bandstructure: str | bool = False, + store_trajectory: bool = False, + # store_scf: bool = False, + store_volumetric_data: Optional[Sequence[str]] = STORE_VOLUMETRIC_DATA, + ) -> tuple[Self, dict[AimsObject, dict]]: + """Create an FHI-aims calculation document from a directory and file paths. + + Parameters + ---------- + dir_name: Path or str + The directory containing the calculation outputs. + task_name: str + The task name. + aims_output_file: Path or str + Path to the main output of aims job, relative to dir_name. + volumetric_files: List[str] + Path to volumetric (Cube) files, relative to dir_name. + parse_dos: str or bool + Whether to parse the DOS. Can be: + + - "auto": Only parse DOS if there are no ionic steps. + - True: Always parse DOS. + - False: Never parse DOS. + + parse_bandstructure: str or bool + How to parse the bandstructure. Can be: + + - "auto": Parse the bandstructure with projections for NSCF calculations + and decide automatically if it's line or uniform mode. + - "line": Parse the bandstructure as a line mode calculation with + projections + - True: Parse the bandstructure as a uniform calculation with + projections . + - False: Parse the band structure without projects and just store + vbm, cbm, band_gap, is_metal and efermi rather than the full + band structure object. + + store_trajectory: bool + Whether to store the ionic steps as a pmg trajectory object, which can be + pushed, to a bson data store, instead of as a list od dicts. Useful for + large trajectories. + store_scf: bool + Whether to store the SCF convergence data. + store_volumetric_data: Sequence[str] or None + Which volumetric files to store. + + Returns + ------- + .Calculation + An FHI-aims calculation document. + """ + dir_name = Path(dir_name) + aims_output_file = dir_name / aims_output_file + + volumetric_files = [] if volumetric_files is None else volumetric_files + aims_output = AimsOutput.from_outfile(aims_output_file) + + completed_at = str( + datetime.fromtimestamp(os.stat(aims_output_file).st_mtime, tz=timezone.utc) + ) + + output_file_paths = _get_output_file_paths(volumetric_files) + aims_objects: dict[AimsObject, Any] = _get_volumetric_data( + dir_name, output_file_paths, store_volumetric_data + ) + + dos = _parse_dos(parse_dos, aims_output) + if dos is not None: + aims_objects[AimsObject.DOS] = dos # type: ignore # noqa: PGH003 + + bandstructure = _parse_bandstructure(parse_bandstructure, aims_output) + if bandstructure is not None: + aims_objects[AimsObject.BANDSTRUCTURE] = bandstructure # type: ignore # noqa: PGH003 + + output_doc = CalculationOutput.from_aims_output(aims_output) + + has_aims_completed = ( + TaskState.SUCCESS if aims_output.completed else TaskState.FAILED + ) + + if store_trajectory: + traj = _parse_trajectory(aims_output=aims_output) + aims_objects[AimsObject.TRAJECTORY] = traj # type: ignore # noqa: PGH003 + + instance = cls( + dir_name=str(dir_name), + task_name=task_name, + aims_version=aims_output.aims_version, + has_aims_completed=has_aims_completed, + completed_at=completed_at, + output=output_doc, + output_file_paths={k.name.lower(): v for k, v in output_file_paths.items()}, + ) + + return instance, aims_objects + + +def _get_output_file_paths(volumetric_files: list[str]) -> dict[AimsObject, str]: + """Get the output file paths for FHI-aims output files. + + Parameters + ---------- + volumetric_files: List[str] + A list of volumetric files associated with the calculation. + + Returns + ------- + Dict[AimsObject, str] + A mapping between the Aims object type and the file path. + """ + output_file_paths = {} + for aims_object in AimsObject: # type: ignore # noqa: PGH003 + for volumetric_file in volumetric_files: + if aims_object.name in str(volumetric_file): + output_file_paths[aims_object] = str(volumetric_file) + return output_file_paths + + +def _get_volumetric_data( + dir_name: Path, + output_file_paths: dict[AimsObject, str], + store_volumetric_data: Optional[Sequence[str]], +) -> dict[AimsObject, VolumetricData]: + """ + Load volumetric data files from a directory. + + Parameters + ---------- + dir_name: Path + The directory containing the files. + output_file_paths: Dict[.AimsObject, str] + A dictionary mapping the data type to file path relative to dir_name. + store_volumetric_data: Sequence[str] or None + The volumetric data files to load. + + Returns + ------- + Dict[AimsObject, VolumetricData] + A dictionary mapping the FHI-aims object data type (`AimsObject.total_density`, + `AimsObject.electron_density`, etc) to the volumetric data object. + """ + if store_volumetric_data is None or len(store_volumetric_data) == 0: + return {} + + volumetric_data = {} + for file_type, file in output_file_paths.items(): + if file_type.name not in store_volumetric_data: + continue + try: + volumetric_data[file_type] = VolumetricData.from_cube( + (dir_name / file).as_posix() + ) + except Exception as err: + raise ValueError(f"Failed to parse {file_type} at {file}.") from err + + return volumetric_data + + +def _parse_dos(parse_dos: str | bool, aims_output: AimsOutput) -> Optional[Dos]: + """Parse DOS outputs from FHI-aims calculation. + + Parameters + ---------- + parse_dos: str or bool + Whether to parse the DOS. Can be: + - "auto": Only parse DOS if there are no ionic steps. + - True: Always parse DOS. + - False: Never parse DOS. + aims_output: .AimsOutput + The output object for the calculation being parsed. + + Returns + ------- + A Dos object if parse_dos is set accordingly. + """ + if parse_dos == "auto": + if len(aims_output.ionic_steps) == 0: + return aims_output.complete_dos + return None + if parse_dos: + return aims_output.complete_dos + return None + + +def _parse_bandstructure( + parse_bandstructure: str | bool, aims_output: AimsOutput +) -> Optional[BandStructure]: + """ + Get the band structure. + + Parameters + ---------- + parse_bandstructure: str or bool + Whether to parse. Does not support the auto/line distinction currently. + aims_ouput: .AimsOutput + The output object to parse + + Returns + ------- + The bandstructure + """ + if parse_bandstructure: + return aims_output.band_structure + return None + + +def _parse_trajectory(aims_output: AimsOutput) -> Optional[Trajectory]: + """Grab a Trajectory object given an FHI-aims output object. + + Parameters + ---------- + aims_ouput: .AimsOutput + The output object to parse + + Returns + ------- + The trajectory for the calculation + """ + return aims_output.structures diff --git a/src/atomate2/aims/schemas/task.py b/src/atomate2/aims/schemas/task.py new file mode 100644 index 0000000000..c3e537100c --- /dev/null +++ b/src/atomate2/aims/schemas/task.py @@ -0,0 +1,715 @@ +"""A definition of a MSON document representing an FHI-aims task.""" + +from __future__ import annotations + +import json +import logging +from collections.abc import Sequence +from pathlib import Path +from typing import Any, Optional, Union + +import numpy as np +from emmet.core.math import Matrix3D, Vector3D +from emmet.core.structure import MoleculeMetadata, StructureMetadata +from emmet.core.tasks import get_uri +from pydantic import BaseModel, Field +from pymatgen.core import Molecule, Structure +from pymatgen.entries.computed_entries import ComputedEntry +from typing_extensions import Self + +from atomate2.aims.schemas.calculation import AimsObject, Calculation, TaskState +from atomate2.aims.utils import datetime_str + +_VOLUMETRIC_FILES = ("total_density", "spin_density", "eigenstate_density") +logger = logging.getLogger(__name__) + + +class AnalysisDoc(BaseModel): + """Calculation relaxation summary. + + Parameters + ---------- + delta_volume: float + Absolute change in volume + delta_volume_as_percent: float + Percentage change in volume + max_force: float + Maximum force on the atoms + errors: List[str] + Errors from the FHI-aims output + """ + + delta_volume: Optional[float] = Field(None, description="Absolute change in volume") + delta_volume_as_percent: Optional[float] = Field( + None, description="Percentage change in volume" + ) + max_force: Optional[float] = Field(None, description="Maximum force on the atoms") + errors: Optional[list[str]] = Field( + None, description="Errors from the FHI-aims output" + ) + + @classmethod + def from_aims_calc_docs(cls, calc_docs: list[Calculation]) -> Self: + """Create analysis summary from FHI-aims calculation documents. + + Parameters + ---------- + calc_docs: List[.Calculation] + FHI-aims calculation documents. + + Returns + ------- + .AnalysisDoc + Summary object + """ + delta_vol = None + percent_delta_vol = None + + final_calc = calc_docs[-1] + max_force = None + if final_calc.has_aims_completed == TaskState.SUCCESS: + max_force = _get_max_force(final_calc) + + return cls( + delta_volume=delta_vol, + delta_volume_as_percent=percent_delta_vol, + max_force=max_force, + errors=[], + ) + + +class Species(BaseModel): + """A representation of the most important information about each type of species. + + Parameters + ---------- + element: str + Element assigned to this atom kind + species_defaults: str + Basis set for this atom kind + """ + + element: str = Field(None, description="Element assigned to this atom kind") + species_defaults: str = Field(None, description="Basis set for this atom kind") + + +class SpeciesSummary(BaseModel): + """A summary of species defaults. + + Parameters + ---------- + species_defaults: Dict[str, .Species] + Dictionary mapping atomic kind labels to their info + """ + + species_defaults: dict[str, Species] = Field( + None, description="Dictionary mapping atomic kind labels to their info" + ) + + @classmethod + def from_species_info(cls, species_info: dict[str, dict[str, Any]]) -> Self: + """Initialize from the atomic_kind_info dictionary. + + Parameters + ---------- + species_info: Dict[str, Dict[str, Any]] + The information for the basis set for the calculation + + Returns + ------- + The SpeciesSummary + """ + dct: dict[str, dict[str, Any]] = {"species_defaults": {}} + for kind, info in species_info.items(): + dct["species_defaults"][kind] = { + "element": info["element"], + "species_defaults": info["species_defaults"], + } + return cls(**dct) + + +class InputDoc(BaseModel): + """Summary of inputs for an FHI-aims calculation. + + Parameters + ---------- + structure: Structure or Molecule + The input pymatgen Structure or Molecule of the system + species_info: .SpeciesSummary + Summary of the species defaults used for each atom kind + xc: str + Exchange-correlation functional used if not the default + """ + + structure: Union[Structure, Molecule] = Field( + None, description="The input structure object" + ) + species_info: SpeciesSummary = Field( + None, description="Summary of the species defaults used for each atom kind" + ) + xc: str = Field( + None, description="Exchange-correlation functional used if not the default" + ) + + @classmethod + def from_aims_calc_doc(cls, calc_doc: Calculation) -> Self: + """Create calculation input summary from a calculation document. + + Parameters + ---------- + calc_doc: .Calculation + An FHI-aims calculation document. + + Returns + ------- + .InputDoc + A summary of the input structure and parameters. + """ + summary = SpeciesSummary.from_species_info(calc_doc.input.species_info) + + return cls( + structure=calc_doc.input.structure, + atomic_kind_info=summary, + xc=str(calc_doc.run_type), + ) + + +class OutputDoc(BaseModel): + """Summary of the outputs for an FHI-aims calculation. + + Parameters + ---------- + structure: Structure or Molecule + The final pymatgen Structure or Molecule of the final system + trajectory: List[Structure or Molecule] + The trajectory of output structures + energy: float + The final total DFT energy for the last calculation + energy_per_atom: float + The final DFT energy per atom for the last calculation + bandgap: float + The DFT bandgap for the last calculation + cbm: float + CBM for this calculation + vbm: float + VBM for this calculation + forces: List[Vector3D] + Forces on atoms from the last calculation + stress: Matrix3D + Stress on the unit cell from the last calculation + all_forces: List[List[Vector3D]] + Forces on atoms from all calculations. + """ + + structure: Union[Structure, Molecule] = Field( + None, description="The output structure object" + ) + trajectory: Sequence[Union[Structure, Molecule]] = Field( + None, description="The trajectory of output structures" + ) + energy: float = Field( + None, description="The final total DFT energy for the last calculation" + ) + energy_per_atom: float = Field( + None, description="The final DFT energy per atom for the last calculation" + ) + bandgap: Optional[float] = Field( + None, description="The DFT bandgap for the last calculation" + ) + cbm: Optional[float] = Field(None, description="CBM for this calculation") + vbm: Optional[float] = Field(None, description="VBM for this calculation") + forces: Optional[list[Vector3D]] = Field( + None, description="Forces on atoms from the last calculation" + ) + stress: Optional[Matrix3D] = Field( + None, description="Stress on the unit cell from the last calculation" + ) + all_forces: Optional[list[list[Vector3D]]] = Field( + None, description="Forces on atoms from all calculations." + ) + + @classmethod + def from_aims_calc_doc(cls, calc_doc: Calculation) -> Self: + """Create a summary from an aims CalculationDocument. + + Parameters + ---------- + calc_doc: .Calculation + An FHI-aims calculation document. + + Returns + ------- + .OutputDoc + The calculation output summary. + """ + return cls( + structure=calc_doc.output.structure, + energy=calc_doc.output.energy, + energy_per_atom=calc_doc.output.energy_per_atom, + bandgap=calc_doc.output.bandgap, + cbm=calc_doc.output.cbm, + vbm=calc_doc.output.vbm, + forces=calc_doc.output.forces, + stress=calc_doc.output.stress, + all_forces=calc_doc.output.all_forces, + trajectory=calc_doc.output.atomic_steps, + ) + + +class ConvergenceSummary(BaseModel): + """Summary of the outputs for an FHI-aims convergence calculation. + + Parameters + ---------- + structure: Structure or Molecule + The output structure object + converged: bool + Is convergence achieved? + convergence_criterion_name: str + The output name of the convergence criterion + convergence_field_name: str + The name of the input setting to study convergence against + convergence_criterion_value: float + The output value of the convergence criterion + convergence_field_value: Any + The last value of the input setting to study convergence against + asked_epsilon: float + The difference in the values for the convergence criteria that was asked for + actual_epsilon: float + The actual difference in the convergence criteria values + """ + + structure: Union[Structure, Molecule] = Field( + None, description="The pymatgen object of the output structure" + ) + converged: bool = Field(None, description="Is convergence achieved?") + + convergence_criterion_name: str = Field( + None, description="The output name of the convergence criterion" + ) + convergence_field_name: str = Field( + None, description="The name of the input setting to study convergence against" + ) + convergence_criterion_value: float = Field( + None, description="The output value of the convergence criterion" + ) + convergence_field_value: Any = Field( + None, + description="The last value of the input setting to study convergence against", + ) + asked_epsilon: Optional[float] = Field( + None, + description="The difference in the values for the convergence criteria that was" + " asked for", + ) + actual_epsilon: float = Field( + None, + description="The actual difference in the convergence criteria values", + ) + + @classmethod + def from_aims_calc_doc(cls, calc_doc: Calculation) -> Self: + """Create a summary from an FHI-aims calculation document. + + Parameters + ---------- + calc_doc: .Calculation + An FHI-aims calculation document. + + Returns + ------- + .ConvergenceSummary + The summary for convergence runs. + """ + from atomate2.aims.jobs.convergence import CONVERGENCE_FILE_NAME + + job_dir = calc_doc.dir_name.split(":")[-1] + + convergence_file = Path(job_dir) / CONVERGENCE_FILE_NAME + if not convergence_file.exists(): + raise ValueError( + f"Did not find the convergence json file {CONVERGENCE_FILE_NAME}" + " in {calc_doc.dir_name}" + ) + + with open(convergence_file) as file: + convergence_data = json.load(file) + + return cls( + structure=calc_doc.output.structure, + converged=convergence_data["converged"], + convergence_criterion_name=convergence_data["criterion_name"], + convergence_field_name=convergence_data["convergence_field_name"], + convergence_criterion_value=convergence_data["criterion_values"][-1], + convergence_field_value=convergence_data["convergence_field_values"][-1], + asked_epsilon=None, + actual_epsilon=abs( + convergence_data["criterion_values"][-2] + - convergence_data["criterion_values"][-1] + ), + ) + + @classmethod + def from_data( + cls, structure: Structure | Molecule, convergence_data: dict[str, Any] + ) -> Self: + """Create a summary from the convergence data dictionary. + + Parameters + ---------- + structure : Structure | Molecule + a Pymatgen structure object + + convergence_data: dict[str, Any] + A dictionary containing convergence data for the run. + + Returns + ------- + .ConvergenceSummary + The summary for convergence runs. + """ + return cls( + structure=structure, + converged=convergence_data["converged"], + convergence_criterion_name=convergence_data["criterion_name"], + convergence_field_name=convergence_data["convergence_field_name"], + convergence_criterion_value=convergence_data["criterion_values"][-1], + convergence_field_value=convergence_data["convergence_field_values"][-1], + asked_epsilon=convergence_data["epsilon"], + actual_epsilon=abs( + convergence_data["criterion_values"][-2] + - convergence_data["criterion_values"][-1] + ), + ) + + +class AimsTaskDoc(StructureMetadata, MoleculeMetadata): + """Definition of FHI-aims task document. + + Parameters + ---------- + dir_name: str + The directory for this FHI-aims task + last_updated: str + Timestamp for this task document was last updated + completed_at: str + Timestamp for when this task was completed + input: .InputDoc + The input to the first calculation + output: .OutputDoc + The output of the final calculation + structure: Structure or Molecule + Final output structure from the task + state: .TaskState + State of this task + included_objects: List[.AimsObject] + List of FHI-aims objects included with this task document + aims_objects: Dict[.AimsObject, Any] + FHI-aims objects associated with this task + entry: ComputedEntry + The ComputedEntry from the task doc + analysis: .AnalysisDoc + Summary of structural relaxation and forces + task_label: str + A description of the task + tags: List[str] + Metadata tags for this task document + author: str + Author extracted from transformations + icsd_id: str + International crystal structure database id of the structure + calcs_reversed: List[.Calculation] + The inputs and outputs for all FHI-aims runs in this task. + transformations: Dict[str, Any] + Information on the structural transformations, parsed from a + transformations.json file + custodian: Any + Information on the custodian settings used to run this + calculation, parsed from a custodian.json file + additional_json: Dict[str, Any] + Additional json loaded from the calculation directory + """ + + dir_name: str = Field(None, description="The directory for this FHI-aims task") + last_updated: str = Field( + default_factory=datetime_str, + description="Timestamp for this task document was last updated", + ) + completed_at: str = Field( + None, description="Timestamp for when this task was completed" + ) + input: Optional[InputDoc] = Field( + None, description="The input to the first calculation" + ) + output: OutputDoc = Field(None, description="The output of the final calculation") + structure: Union[Structure, Molecule] = Field( + None, description="Final output atoms from the task" + ) + state: TaskState = Field(None, description="State of this task") + included_objects: Optional[list[AimsObject]] = Field( + None, description="List of FHI-aims objects included with this task document" + ) + aims_objects: Optional[dict[AimsObject, Any]] = Field( + None, description="FHI-aims objects associated with this task" + ) + entry: Optional[ComputedEntry] = Field( + None, description="The ComputedEntry from the task doc" + ) + analysis: AnalysisDoc = Field( + None, description="Summary of structural relaxation and forces" + ) + task_label: str = Field(None, description="A description of the task") + tags: Optional[list[str]] = Field( + None, description="Metadata tags for this task document" + ) + author: Optional[str] = Field( + None, description="Author extracted from transformations" + ) + icsd_id: Optional[str] = Field( + None, description="International crystal structure database id of the structure" + ) + calcs_reversed: Optional[list[Calculation]] = Field( + None, description="The inputs and outputs for all FHI-aims runs in this task." + ) + transformations: Optional[dict[str, Any]] = Field( + None, + description="Information on the structural transformations, parsed from a " + "transformations.json file", + ) + custodian: Any = Field( + None, + description="Information on the custodian settings used to run this " + "calculation, parsed from a custodian.json file", + ) + additional_json: Optional[dict[str, Any]] = Field( + None, description="Additional json loaded from the calculation directory" + ) + + @classmethod + def from_directory( + cls, + dir_name: Path | str, + volumetric_files: Sequence[str] = _VOLUMETRIC_FILES, + additional_fields: dict[str, Any] = None, + **aims_calculation_kwargs, + ) -> Self: + """Create a task document from a directory containing FHi-aims files. + + Parameters + ---------- + dir_name: Path or str + The path to the folder containing the calculation outputs. + volumetric_files: Sequence[str] + A volumetric files to search for. + additional_fields: Dict[str, Any] + Dictionary of additional fields to add to output document. + **aims_calculation_kwargs + Additional parsing options that will be passed to the + :obj:`.Calculation.from_aims_files` function. + + Returns + ------- + .AimsTaskDoc + A task document for the calculation. + """ + logger.info(f"Getting task doc in: {dir_name}") + + if additional_fields is None: + additional_fields = {} + + dir_name = Path(dir_name) + task_files = _find_aims_files(dir_name, volumetric_files=volumetric_files) + + if len(task_files) == 0: + raise FileNotFoundError("No FHI-aims files found!") + + calcs_reversed = [] + all_aims_objects = [] + for task_name, files in task_files.items(): + calc_doc, aims_objects = Calculation.from_aims_files( + dir_name, task_name, **files, **aims_calculation_kwargs + ) + calcs_reversed.append(calc_doc) + all_aims_objects.append(aims_objects) + + analysis = AnalysisDoc.from_aims_calc_docs(calcs_reversed) + tags = additional_fields.get("tags") + + dir_name = get_uri(dir_name) # convert to full uri path + + # only store objects from last calculation + # TODO: make this an option + aims_objects = all_aims_objects[-1] + included_objects = None + if aims_objects: + included_objects = list(aims_objects.keys()) + + # rewrite the original structure save! + + data = { + "structure": calcs_reversed[-1].output.structure, + "meta_structure": calcs_reversed[-1].output.structure, + "dir_name": dir_name, + "calcs_reversed": calcs_reversed, + "analysis": analysis, + "tags": tags, + "completed_at": calcs_reversed[-1].completed_at, + "output": OutputDoc.from_aims_calc_doc(calcs_reversed[-1]), + "state": _get_state(calcs_reversed, analysis), + "entry": cls.get_entry(calcs_reversed), + "aims_objects": aims_objects, + "included_objects": included_objects, + } + doc = cls(**data) + return doc.model_copy(update=additional_fields, deep=True) + + @staticmethod + def get_entry( + calc_docs: list[Calculation], job_id: Optional[str] = None + ) -> ComputedEntry: + """Get a computed entry from a list of FHI-aims calculation documents. + + Parameters + ---------- + calc_docs: List[.Calculation] + A list of FHI-aims calculation documents. + job_id: Optional[str] + The job identifier. + + Returns + ------- + ComputedEntry + A computed entry. + """ + entry_dict = { + "correction": 0.0, + "entry_id": job_id, + "composition": calc_docs[-1].output.structure.formula, + "energy": calc_docs[-1].output.energy, + "parameters": { + # Required to be compatible with MontyEncoder for the ComputedEntry + # "run_type": str(calc_docs[-1].run_type), + "run_type": "AIMS run" + }, + "data": { + "last_updated": datetime_str(), + }, + } + return ComputedEntry.from_dict(entry_dict) + + +def _find_aims_files( + path: Path | str, + volumetric_files: Sequence[str] = _VOLUMETRIC_FILES, +) -> dict[str, Any]: + """Find FHI-aims files in a directory. + + Only files in folders with names matching a task name (or alternatively files + with the task name as an extension, e.g., aims.out) will be returned. + + FHI-aims files in the current directory will be given the task name "standard". + + Parameters + ---------- + path: str or Path + Path to a directory to search. + volumetric_files: Sequence[str] + Volumetric files to search for. + + Returns + ------- + dict[str, Any] + The filenames of the calculation outputs for each FHI-aims task, + given as a ordered dictionary of:: + + { + task_name: { + "aims_output_file": aims_output_filename, + "volumetric_files": [v_hartree file, e_density file, etc], + """ + task_names = ["precondition"] + [f"relax{i}" for i in range(9)] + path = Path(path) + task_files = {} + + def _get_task_files( + files: list[Path], suffix: str = "" + ) -> dict[str, list[str | Path] | Path | str]: + aims_files: dict[str, list[str | Path] | Path | str] = {} + vol_files: list[str | Path] = [] + for file in files: + # Here we make assumptions about the output file naming + if file.match(f"*aims.out{suffix}*"): + aims_files["aims_output_file"] = Path(file).name + for vol in volumetric_files: + _files = [f.name for f in files if f.match(f"*{vol}*cube{suffix}*")] + if _files: + vol_files.append(_files[0]) + + if len(vol_files) > 0: + # add volumetric files if some were found or other cp2k files were found + aims_files["volumetric_files"] = vol_files + + return aims_files + + for task_name in task_names: + subfolder_match = list(path.glob(f"{task_name}/*")) + suffix_match = list(path.glob(f"*.{task_name}*")) + if len(subfolder_match) > 0: + # subfolder match + task_files[task_name] = _get_task_files(subfolder_match) + elif len(suffix_match) > 0: + # try extension schema + task_files[task_name] = _get_task_files( + suffix_match, suffix=f".{task_name}" + ) + + if len(task_files) == 0: + # get any matching file from the root folder + standard_files = _get_task_files(list(path.glob("*"))) + if len(standard_files) > 0: + task_files["standard"] = standard_files + + return task_files + + +def _get_max_force(calc_doc: Calculation) -> Optional[float]: + """Get max force acting on atoms from a calculation document. + + Parameters + ---------- + calc_doc: .Calculation + The calculation doc to get the max force + + Returns + ------- + float + The maximum force + """ + forces = calc_doc.output.forces + if forces is not None: + forces = np.array(forces) + return max(np.linalg.norm(forces, axis=1)) + return None + + +def _get_state(calc_docs: list[Calculation], analysis: AnalysisDoc) -> TaskState: + """Get state from calculation documents and relaxation analysis. + + Parameters + ---------- + calc_docs: List[.Calculations] + The calculation to get the state from + analysis: .AnalysisDoc + The summary of the analysis + + Returns + ------- + .TaskState + The status of the calculation + """ + all_calcs_completed = all( + c.has_aims_completed == TaskState.SUCCESS for c in calc_docs + ) + if len(analysis.errors) == 0 and all_calcs_completed: + return TaskState.SUCCESS # type: ignore # noqa: PGH003 + return TaskState.FAILED # type: ignore # noqa: PGH003 diff --git a/src/atomate2/aims/utils/__init__.py b/src/atomate2/aims/utils/__init__.py new file mode 100644 index 0000000000..21d63e822e --- /dev/null +++ b/src/atomate2/aims/utils/__init__.py @@ -0,0 +1,15 @@ +"""A collection of helper utils found in atomate2 package.""" + +from datetime import datetime, timezone + + +def datetime_str() -> str: + """ + Get a string representation of the current time. + + Returns + ------- + str + The current time. + """ + return str(datetime.now(tz=timezone.utc)) diff --git a/src/atomate2/aims/utils/bands.py b/src/atomate2/aims/utils/bands.py new file mode 100644 index 0000000000..ead5651a26 --- /dev/null +++ b/src/atomate2/aims/utils/bands.py @@ -0,0 +1,62 @@ +"""Some utilities of dealing with bands. + +Copied from GIMS as of now; should be in its own dedicated FHI-aims python package. +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, TypedDict + +from pymatgen.symmetry.bandstructure import HighSymmKpath + +if TYPE_CHECKING: + from pymatgen.core.structure import Structure + + +class _SegmentDict(TypedDict): + coords: list[list[float]] + labels: list[str] + length: int + + +def prepare_band_input(structure: Structure, density: float = 20) -> list: + """Prepare the band information needed for the FHI-aims control.in file. + + Parameters + ---------- + structure: Structure + The structure for which the band path is calculated + density: float + Number of kpoints per Angstrom. + """ + bp = HighSymmKpath(structure) + points, labels = bp.get_kpoints(line_density=density, coords_are_cartesian=False) + lines_and_labels: list[_SegmentDict] = [] + current_segment: _SegmentDict | None = None + for label_, coords in zip(labels, points): + # rename the Gamma point label + label = "G" if label_ in ("GAMMA", "\\Gamma", "ฮ“") else label_ + if label: + if current_segment is None: + current_segment = _SegmentDict( + coords=[coords], labels=[label], length=1 + ) + else: + current_segment["coords"].append(coords) + current_segment["labels"].append(label) + current_segment["length"] += 1 + lines_and_labels.append(current_segment) + current_segment = None + else: + current_segment["length"] += 1 + + bands = [] + for segment in lines_and_labels: + start, end = segment["coords"] + lstart, lend = segment["labels"] + bands.append( + f"band {start[0]:9.5f}{start[1]:9.5f}{start[2]:9.5f} " + f"{end[0]:9.5f}{end[1]:9.5f}{end[2]:9.5f} {segment['length']:4d} " + f"{lstart:3}{lend:3}" + ) + return bands diff --git a/src/atomate2/aims/utils/common.py b/src/atomate2/aims/utils/common.py new file mode 100644 index 0000000000..00a96c64db --- /dev/null +++ b/src/atomate2/aims/utils/common.py @@ -0,0 +1,44 @@ +"""Module with common file names and classes used for FHI-aims flows.""" + +import contextlib +import os +import shutil +from collections.abc import Generator + +TMPDIR_NAME = "tmpdir" +OUTPUT_FILE_NAME: str = "aims.out" +CONTROL_FILE_NAME: str = "control.in" +PARAMS_JSON_FILE_NAME: str = "parameters.json" +GEOMETRY_FILE_NAME: str = "geometry.in" + + +@contextlib.contextmanager +def cwd(path: str, mkdir: bool = False, rmdir: bool = False) -> Generator: + """Change cwd intermediately. + + Example + ------- + >>> with cwd(some_path): + >>> do so some stuff in some_path + >>> do so some other stuff in old cwd + + Parameters + ---------- + path: str or Path + Path to change working directory to + mkdir: bool + If True make path if it does not exist + rmdir: bool + If True remove the working directory upon exiting + """ + cwd = os.getcwd() + + if os.path.exists(path) is False and mkdir: + os.makedirs(path) + + os.chdir(path) + yield + + os.chdir(cwd) + if rmdir: + shutil.rmtree(path) diff --git a/src/atomate2/aims/utils/units.py b/src/atomate2/aims/utils/units.py new file mode 100644 index 0000000000..51ea034922 --- /dev/null +++ b/src/atomate2/aims/utils/units.py @@ -0,0 +1,12 @@ +"""Define the Units for FHI-aims calculations.""" + +from numpy import pi + +PI = pi +EV = 1.602176634e-19 # [J] CODATA 2002 +THZ = 1e12 +AMU = 1.66053906660e-27 # [kg] CODATA 2002 +AA = 1e-10 + +omegaToTHz = (EV / AA**2 / AMU) ** 0.5 / THZ / 2 / PI # noqa: N816 +ev_per_A3_to_kbar = EV / AA**3 / 1e8 # noqa: N816 diff --git a/src/atomate2/amset/jobs.py b/src/atomate2/amset/jobs.py index ef098d3a56..fb576b4982 100644 --- a/src/atomate2/amset/jobs.py +++ b/src/atomate2/amset/jobs.py @@ -42,19 +42,18 @@ class AmsetMaker(Maker): def make( self, settings: dict, - prev_amset_dir: str | Path = None, + prev_dir: str | Path = None, wavefunction_dir: str | Path = None, deformation_dir: str | Path = None, bandstructure_dir: str | Path = None, ) -> Response: - """ - Run an AMSET calculation. + """Run an AMSET calculation. Parameters ---------- settings : dict Amset settings. - prev_amset_dir : str or Path + prev_dir : str or Path A previous AMSET calculation directory to copy output files from. The previous directory is also used to check for transport convergence. wavefunction_dir : str or Path @@ -66,14 +65,12 @@ def make( band_structure_data.json). """ # copy previous inputs - from_prev = prev_amset_dir is not None - if prev_amset_dir is not None: - copy_amset_files(prev_amset_dir) + from_prev = prev_dir is not None + if prev_dir is not None: + copy_amset_files(prev_dir) else: if bandstructure_dir is None: - raise ValueError( - "Either prev_amset_dir or bandstructure_dir must be set" - ) + raise ValueError("Either prev_dir or bandstructure_dir must be set") copy_amset_files(bandstructure_dir) @@ -116,7 +113,7 @@ def make( if self.resubmit and not converged: replace = self.make( {"interpolation_factor": settings.get("interpolation_factor", 10) + 5}, - prev_amset_dir=task_doc.dir_name, + prev_dir=task_doc.dir_name, ) return Response(output=task_doc, replace=replace) diff --git a/src/atomate2/amset/run.py b/src/atomate2/amset/run.py index 19bc8e5e40..7cf0e3a8af 100644 --- a/src/atomate2/amset/run.py +++ b/src/atomate2/amset/run.py @@ -17,7 +17,7 @@ def run_amset() -> None: # Run AMSET using the command line as calling from python can cause issues # with multiprocessing with open("std_out.log", "w") as f_std, open("std_err.log", "w") as f_err: - subprocess.call(["amset", "run"], stdout=f_std, stderr=f_err) + subprocess.call(["amset", "run"], stdout=f_std, stderr=f_err) # noqa: S603, S607 def check_converged( diff --git a/src/atomate2/amset/schemas.py b/src/atomate2/amset/schemas.py index 875ae67568..005cf7278d 100644 --- a/src/atomate2/amset/schemas.py +++ b/src/atomate2/amset/schemas.py @@ -3,7 +3,7 @@ import logging import re from pathlib import Path -from typing import Any, Union +from typing import TYPE_CHECKING, Any, Union import numpy as np from emmet.core.math import Matrix3D, Vector3D @@ -23,6 +23,9 @@ amset = None +if TYPE_CHECKING: + from typing_extensions import Self + logger = logging.getLogger(__name__) @@ -144,9 +147,8 @@ def from_directory( dir_name: Union[Path, str], additional_fields: dict[str, Any] = None, include_mesh: bool = False, - ) -> "AmsetTaskDocument": - """ - Create a task document from a directory containing VASP files. + ) -> Self: + """Create a task document from a directory containing VASP files. Parameters ---------- @@ -189,8 +191,8 @@ def from_directory( } if include_mesh: # remove duplicated data - for k in ("doping", "temperatures", "fermi_levels", "structure"): - mesh.pop(k) + for key in ("doping", "temperatures", "fermi_levels", "structure"): + mesh.pop(key) mesh_kwargs["mesh"] = cast_dict_list(mesh) diff --git a/src/atomate2/cli/dev.py b/src/atomate2/cli/dev.py index ffa5b0130f..7e80b5fa66 100644 --- a/src/atomate2/cli/dev.py +++ b/src/atomate2/cli/dev.py @@ -1,6 +1,16 @@ """Module containing command line scripts for developers.""" +from __future__ import annotations + +from typing import TYPE_CHECKING, Any + import click +from monty.json import jsanitize + +if TYPE_CHECKING: + from pathlib import Path + + from jobflow import Maker @click.group(context_settings={"help_option_names": ["-h", "--help"]}) @@ -9,15 +19,32 @@ def dev() -> None: @dev.command(context_settings={"help_option_names": ["-h", "--help"]}) -@click.argument("test_dir") -def vasp_test_data(test_dir) -> None: +@click.argument( + "test_dir", +) +@click.option( + "--additional_file", + "-a", + multiple=True, + help="list of additional files to copy from each completed VASP directory. " + "Example: `--additional_file CHGCAR --additional_file LOCPOT`", +) +def vasp_test_data(test_dir: str | Path, additional_file: list[str]) -> None: """Generate test data for VASP unit tests. This script expects there is an outputs.json file and job folders in the current directory. Please refer to the atomate2 documentation on writing unit tests for more information. + + Parameters + ---------- + test_dir + The directory to write the test data to. + Should not contain spaces or punctuation. + additional_files + list of additional files to copy from each completed VASP directory. + Example: `--additional_file CHGCAR --additional_file LOCPOT`, """ - import sys import warnings from pathlib import Path from pprint import pformat @@ -34,7 +61,7 @@ def vasp_test_data(test_dir) -> None: if test_dir.exists(): click.echo("test_data folder already exists, refusing to overwrite it") - sys.exit() + raise SystemExit(1) test_dir.mkdir() @@ -103,6 +130,7 @@ def vasp_test_data(test_dir) -> None: "vasprun*", "OUTCAR*", "*.json*", + *additional_file, ], allow_missing=True, ) @@ -113,7 +141,7 @@ def vasp_test_data(test_dir) -> None: [f" {v} -> {k}" for k, v in original_mapping.items()] ) - run_vasp_kwargs = {k: {"incar_settings": ["NSW", "ISMEAR"]} for k in mapping} + run_vasp_kwargs = {key: {"incar_settings": ["NSW", "ISMEAR"]} for key in mapping} run_vasp_kwargs_str = pformat(run_vasp_kwargs).replace("\n", "\n ") test_function_str = f"""Test files generated in test_data. @@ -154,12 +182,466 @@ def test_my_flow(mock_vasp, clean_dir, si_structure): assert output1.output.energy == pytest.approx(-10.85037078) """ - print(test_function_str) + print(test_function_str) # noqa: T201 -def _potcar_to_potcar_spec(potcar_filename, output_filename) -> None: +def _potcar_to_potcar_spec(potcar_filename: str | Path, output_filename: Path) -> None: """Convert a POTCAR file to a POTCAR.spec file.""" from pymatgen.io.vasp import Potcar potcar = Potcar.from_file(potcar_filename) output_filename.write_text("\n".join(potcar.symbols)) + + +@dev.command(context_settings={"help_option_names": ["-h", "--help"]}) +def abinit_script_maker() -> None: + """Generate template script for abinit makers.""" + import os + import sys + + script_fname = "create_maker.py" + if os.path.exists(script_fname): + click.echo(f"{script_fname} already exists, refusing to overwrite it") + sys.exit() + out = [ + "from atomate2.abinit.flows.core import BandStructureMaker", + "from atomate2.abinit.jobs.core import StaticMaker, LineNonSCFMaker", + "from atomate2.abinit.powerups import update_factory_kwargs, update_generator_attributes", # noqa: E501 + "from atomate2.cli.dev import save_abinit_maker", + "", + "", + "# The following lines define the maker.", + "# Adapt for specific job/flow maker test.", + "maker = BandStructureMaker()", + "maker = update_factory_kwargs(maker, dict(kppa=10, ecut=4.0, nband=4), class_filter=StaticMaker)", # noqa: E501 + "maker = update_factory_kwargs(maker, dict(ndivsm=2), class_filter=LineNonSCFMaker)", # noqa: E501 + "maker = update_generator_attributes(maker, dict(nbands_factor=1.5), class_filter=LineNonSCFMaker)", # noqa: E501 + "", + "# Save the maker and metadata to maker.json", + "save_abinit_maker(maker)", + "", + ] + with open(script_fname, "w") as file: + file.write("\n".join(out)) + + +@dev.command(context_settings={"help_option_names": ["-h", "--help"]}) +@click.argument("structure_file", required=False) +@click.option("--make-kwargs", "-mk", required=False) +def abinit_generate_reference(structure_file: str, make_kwargs: dict) -> None: + """Generate reference files for abinit test. + + This script expects there is a maker.json file and a structure file. The structure + file can either be "initial_structure.json" or another file that can be opened by + pymatgen. Keyword arguments can also be passed down to the Maker's make method + through the make_kwargs option. + + NB: note that all the files in the folder will be compressed, in light of a copy to + the test folder, unless the --no-compress is selected. + """ + from jobflow import JobStore, run_locally + from maggma.stores.mongolike import MemoryStore + from monty.serialization import dumpfn, loadfn + from pymatgen.core.structure import Structure + + # get the structure + if structure_file: + struct = Structure.from_file(filename=structure_file) + struct.to(filename="initial_structure.json") + else: + struct = Structure.from_file(filename="initial_structure.json") + + # initialize the maker from the maker.json file + maker_info = loadfn("maker.json") + maker = maker_info["maker"] + + # make the flow and dump the keyword arguments passed to the Maker's make method + # if it is not empty + make_kwargs = make_kwargs or {} + flow_or_job = maker.make(structure=struct, **make_kwargs) + if make_kwargs: + dumpfn({"make_kwargs": make_kwargs}, "make_info.json") + + # run the workflow using a custom store so that we can easily compile test data + store = JobStore(MemoryStore(), additional_stores={"data": MemoryStore()}) + run_locally(flow_or_job, store=store, create_folders=True) + + # dump all of the job outputs to the outputs.json file in the current directory + outputs = list(store.query(load=True)) + dumpfn(outputs, "outputs.json") + + +@dev.command(context_settings={"help_option_names": ["-h", "--help"]}) +@click.argument("test_name") +@click.option("--test-data-dir", required=False) +@click.option( + "--force", + is_flag=True, + default=False, + help="Whether to force overwrite of existing folders/files.", +) +def abinit_test_data(test_name: str, test_data_dir: str | None, force: bool) -> None: + """Copy test data for ABINIT unit tests. + + This script expects there is a maker.json file, an initial_structure.json file, + an outputs.json file and job folders in the current directory. Please refer to + the atomate2 documentation on writing unit tests for more information. + """ + import sys + import warnings + from pathlib import Path + + from monty.serialization import dumpfn, loadfn + from monty.shutil import compress_dir + + from atomate2.abinit.schemas.core import AbinitTaskDocument + from atomate2.common.files import copy_files + from atomate2.utils.path import strip_hostname + + if test_data_dir is None: + abinit_test_data_dir = ( + Path(__file__).parent + / ".." + / ".." + / ".." + / "tests" + / "test_data" + / "abinit" + ) + else: + abinit_test_data_dir = Path(test_data_dir) / "abinit" + + if not abinit_test_data_dir.exists(): + click.echo( + "The following test_data/abinit " + f"directory does not exist: {abinit_test_data_dir}" + ) + sys.exit() + + warnings.filterwarnings("ignore", module="pymatgen") + + maker_info = loadfn("maker.json") + maker = maker_info["maker"] + + maker_name = maker.__class__.__name__ + # take the module path and exclude the first two elements + # (i.e. "atomate2" and "abinit") + module_path = maker.__module__.split(".")[2:] + maker_dir = abinit_test_data_dir / Path(*module_path) / maker_name + if not maker_dir.exists(): + maker_dir.mkdir(parents=True) + test_dir = maker_dir / test_name + + def _makedir(directory: Path, force_overwrite: bool) -> None: + if not directory.exists(): + directory.mkdir() + elif not force_overwrite: + click.echo(f"folder ({directory}) already exists, refusing to overwrite it") + sys.exit() + + _makedir(test_dir, force_overwrite=force) + + outputs = loadfn("outputs.json") + + task_labels = [ + o["output"].task_label for o in outputs if isinstance(o, AbinitTaskDocument) + ] + + if len(task_labels) != len(set(task_labels)): + raise ValueError("Not all jobs have unique names") + + original_mapping = {} + mapping: dict[Any, Any] = {} + + def _fake_dirdata( + src_dir: Path, + dest_dir: Path, + dirdata_name: str, + include_files: list | None = None, + include_fake_files: list | None = None, + force_overwrite: bool = False, + allow_missing: bool = True, + ) -> None: + src_dirdata = src_dir / dirdata_name + if not src_dirdata.exists(): + raise RuntimeError(f"Source directory {src_dirdata} does not exist") + dest_dirdata = dest_dir / dirdata_name + _makedir(dest_dirdata, force_overwrite=force_overwrite) + empty_file = dest_dirdata / ".empty" + empty_file.write_text( + "Empty file for git to be able to have an empty directory" + ) + if include_files: + copy_files( + src_dirdata, + dest_dirdata, + include_files=include_files, + allow_missing=allow_missing, + ) + if include_fake_files: + for fname in include_fake_files: + src_fpath = src_dirdata / fname + dest_fpath = dest_dirdata / fname + if not src_fpath.exists(): + if allow_missing: + continue + raise RuntimeError(f"File {src_fpath} does not exist") + if src_fpath.is_symlink(): + dest_fpath.write_text(f"SYMBOLIC_LINK TO {src_fpath.resolve()}") + elif src_fpath.is_file(): + dest_fpath.write_text("REGULAR_FILE") + else: + raise RuntimeError( + "File is not a symbolic link nor a regular file." + ) + + def _fake_dirs( + src_dir: Path, + dest_dir: Path, + indata_files: list | None = None, + outdata_files: list | None = None, + tmpdata_files: list | None = None, + indata_fake_files: list | None = None, + outdata_fake_files: list | None = None, + tmpdata_fake_files: list | None = None, + force_overwrite: bool = False, + allow_missing: bool = True, + ) -> None: + for dirdata_name, data_files, data_fake_files in zip( + ("indata", "outdata", "tmpdata"), + (indata_files, outdata_files, tmpdata_files), + (indata_fake_files, outdata_fake_files, tmpdata_fake_files), + ): + _fake_dirdata( + src_dir=src_dir, + dest_dir=dest_dir, + dirdata_name=dirdata_name, + include_files=data_files, + include_fake_files=data_fake_files, + force_overwrite=force_overwrite, + allow_missing=allow_missing, + ) + + for output in outputs: + if not isinstance(output["output"], AbinitTaskDocument): + # this is not an Abinit job + continue + + job_name = output["output"].task_label + orig_job_dir = Path(strip_hostname(output["output"].dir_name)) + folder_name = output["output"].task_label.replace("/", "_").replace(" ", "_") + index_job = str(output["index"]) + + job_dir = test_dir / folder_name + _makedir(job_dir, force_overwrite=force) + job_index_dir = job_dir / index_job + _makedir(job_index_dir, force_overwrite=force) + + job_index_dir = job_index_dir.resolve() + + job_index_dir_parts = job_index_dir.parts + indices = _find_sub_list( + ( + "atomate2", + "tests", + "test_data", + "abinit", + ), + job_index_dir_parts, + ) + if len(indices) != 1: + raise RuntimeError( + "Could not find job_test's " + "atomate2/tests/test_data/abinit-based root dir" + ) + job_index_dir_for_mapping = Path(*job_index_dir_parts[indices[0][1] :]) + if job_name not in mapping: + mapping[job_name] = {} + if index_job in mapping[job_name]: + raise RuntimeError( + f"Job index {index_job} for " + f"{job_name} Job is already present in the mapping" + ) + mapping[job_name][index_job] = str(job_index_dir_for_mapping) + original_mapping[str(job_index_dir)] = orig_job_dir + + # create input folder and copy across files + input_dir = job_index_dir / "inputs" + _makedir(input_dir, force_overwrite=force) + + copy_files( + orig_job_dir, + input_dir, + include_files=[ + "run.abi", + "abinit_input.json", + ], + allow_missing=False, + ) + _fake_dirs( + src_dir=orig_job_dir, + dest_dir=input_dir, + indata_files=None, + outdata_files=None, + tmpdata_files=None, + indata_fake_files=["in_DEN", "in_WFK"], + outdata_fake_files=None, + tmpdata_fake_files=None, + force_overwrite=force, + allow_missing=True, + ) + # create output folder and copy across files + output_dir = job_index_dir / "outputs" + _makedir(output_dir, force_overwrite=force) + copy_files( + orig_job_dir, + output_dir, + include_files=[ + "run.abo", + "run.err", + "run.log", + ], + allow_missing=False, + ) + _fake_dirs( + src_dir=orig_job_dir, + dest_dir=output_dir, + indata_files=None, + outdata_files=["out_GSR.nc", "out_FATBANDS.nc"], + tmpdata_files=None, + indata_fake_files=None, + outdata_fake_files=["out_DEN", "out_WFK"], + tmpdata_fake_files=None, + force_overwrite=force, + allow_missing=True, + ) + + dumpfn(mapping, "ref_paths.json") + flow_files = ["maker.json", "initial_structure.json", "ref_paths.json"] + if Path("make_info.json").exists(): + flow_files.append("make_info.json") + copy_files(".", test_dir, include_files=flow_files) + original_mapping_str = "\n".join( + [f" {v} -> {k}" for k, v in original_mapping.items()] + ) + + compress_dir(test_dir) + + # starting index of the parts of the test_dir that needs to be used in the + # example script. Looks for the last occurrence of the "abinit" part of the path. + for i, p in enumerate(reversed(test_dir.parts)): + if p == "abinit": + index_part = -i + break + else: + raise RuntimeError("Did not find 'abinit' in the test path") + test_function_str = f"""Test files generated in test_data. + +Please ensure that all other necessary files are included in the test_data, such as +run.abi, run.abo, run.log, etc. as well as indata, outdata and tmpdata directories +with their respective relevant reference files. +Include additional files only if they are absolutely necessary otherwise they will +increase the size of the atomate2 repository. + +A mapping from the original job folders to the formatted folders is: +{original_mapping_str} + +An example test using the generated test data is provided below. Be sure to update +this test with the particulars for your system. For more examples, see the existing +tests in atomate2/tests/abinit/jobs and atomate2/tests/abinit/flows. + +class Test{maker_name}: + def test_run_{test_name}(self, mock_abinit, abinit_test_dir, clean_dir): + from jobflow import run_locally + from pymatgen.core.structure import Structure + from monty.serialization import loadfn + from atomate2.abinit.schemas.core import AbinitTaskDocument + + # load the initial structure, the maker and the ref_paths from the test_dir + test_dir = abinit_test_dir / {" / ".join( + [f'"{part}"' for part in test_dir.parts[index_part:]] + )} + structure = Structure.from_file(test_dir / "initial_structure.json.gz") + maker_info = loadfn(test_dir / "maker.json.gz") + maker = maker_info["maker"] + ref_paths = loadfn(test_dir / "ref_paths.json.gz") + + mock_abinit(ref_paths) + + # make the flow or job, run it and ensure that it finished running successfully + flow_or_job = maker.make(structure) + responses = run_locally(flow_or_job, create_folders=True, ensure_success=True) + + # validation the outputs of the flow or job + output1 = responses[flow_or_job.uuid][1].output + assert isinstance(output1, AbinitTaskDocument) + assert output1.structure == structure + assert output1.run_number == 1 + """ + + print(test_function_str) # noqa: T201 + + +def save_abinit_maker(maker: Maker) -> None: + """Save maker, the script used to create it and additional metadata.""" + import inspect + import json + import shutil + import subprocess + import warnings + from datetime import datetime, timezone + + caller_frame = inspect.stack()[1] + caller_filename_full = caller_frame.filename + with open(caller_filename_full) as file: + script_str = file.read() + git = shutil.which("git") + author = None + author_mail = None + if git: + name = subprocess.run( + "git config user.name".split(), # noqa: S603 + capture_output=True, + encoding="utf-8", + check=True, + ) + mail = subprocess.run( + "git config user.email".split(), # noqa: S603 + capture_output=True, + encoding="utf-8", + check=True, + ) + if name.returncode == 0: + author = name.stdout.strip() + else: + warnings.warn( + "Author could not be detected from git. " + "You may want to manually set it in the 'maker.json' file.", + stacklevel=2, + ) + if mail.returncode == 0: + author_mail = mail.stdout.strip() + else: + warnings.warn( + "Author email could not be detected from git. " + "You may want to manually set it in the 'maker.json' file.", + stacklevel=2, + ) + with open("maker.json", "w") as file: + json.dump( + { + "author": author, + "author_mail": author_mail, + "created_on": str(datetime.now(tz=timezone.utc)), + "maker": jsanitize(maker.as_dict()), + "script": script_str, + }, + file, + ) + + +def _find_sub_list(sublist: list | tuple, mainlist: list | tuple) -> list: + sll = len(sublist) + inds = [i for i, e in enumerate(mainlist) if e == sublist[0]] + + return [(ind, ind + sll) for ind in inds if mainlist[ind : ind + sll] == sublist] diff --git a/src/atomate2/common/builders/__init__.py b/src/atomate2/common/builders/__init__.py new file mode 100644 index 0000000000..01fa60d707 --- /dev/null +++ b/src/atomate2/common/builders/__init__.py @@ -0,0 +1 @@ +"""DFT code agnostic builders.""" diff --git a/src/atomate2/common/builders/magnetism.py b/src/atomate2/common/builders/magnetism.py new file mode 100644 index 0000000000..242f10b65b --- /dev/null +++ b/src/atomate2/common/builders/magnetism.py @@ -0,0 +1,206 @@ +"""Module defining DFT code agnostic magnetic orderings builder.""" + +from __future__ import annotations + +from typing import TYPE_CHECKING + +from emmet.core.utils import jsanitize +from maggma.builders import Builder +from monty.serialization import MontyDecoder +from pymatgen.analysis.structure_matcher import StructureMatcher + +from atomate2.common.schemas.magnetism import MagneticOrderingsDocument + +if TYPE_CHECKING: + from collections.abc import Iterator + + from maggma.core import Store + + +class MagneticOrderingsBuilder(Builder): + """Builder to analyze the results of magnetic orderings calculations. + + This job will process the output documents of the calculations and return new + documents with relevant parameters (such as the total magnetization, whether the + ordering changed, whether the particular ordering is the ground state, etc.). This + is especially useful for performing postprocessing of magnetic ordering + calculations. + + Parameters + ---------- + tasks : .Store + Store of task documents. + magnetic_orderings : .Store + Store for magnetic ordering documents. + query : dict + Dictionary query to limit tasks to be analyzed. + structure_match_stol : float + Numerical site tolerance for structure equivalence. Default is 0.3. + structure_match_ltol : float + Numerical length tolerance for structure equivalence. Default is 0.3 + structure_match_angle_tol : float + Numerical angle tolerance in degrees for structure equivalence. Default is 5. + **kwargs : dict + Keyword arguments that will be passed to the Builder init. + """ + + def __init__( + self, + tasks: Store, + magnetic_orderings: Store, + query: dict = None, + structure_match_stol: float = 0.3, + structure_match_ltol: float = 0.2, + structure_match_angle_tol: float = 5, + **kwargs, + ) -> None: + self.tasks = tasks + self.magnetic_orderings = magnetic_orderings + self.query = query or {} + self.structure_match_stol = structure_match_stol + self.structure_match_ltol = structure_match_ltol + self.structure_match_angle_tol = structure_match_angle_tol + + self.kwargs = kwargs + + super().__init__(sources=[tasks], targets=[magnetic_orderings], **kwargs) + + def ensure_indexes(self) -> None: + """Ensure indices on the tasks and magnetic orderings collections.""" + self.tasks.ensure_index("output.formula_pretty") + self.tasks.ensure_index("last_updated") + self.magnetic_orderings.ensure_index("last_updated") + + def get_items(self) -> Iterator[list[dict]]: + """Get all items to process into magnetic ordering documents. + + This step does a first grouping by formula (which is fast) and then the magnetic + orderings are grouped by parent structure. + + Yields + ------ + list of dict + A list of magnetic ordering relaxation or static task outputs, grouped by + formula. + """ + self.logger.info("Magnetic orderings builder started") + self.logger.debug("Adding/ensuring indices...") + self.ensure_indexes() + + criteria = dict(self.query) + criteria.update({"metadata.ordering": {"$exists": True}}) + self.logger.info("Grouping by formula...") + num_formulas = len( + self.tasks.distinct("output.formula_pretty", criteria=criteria) + ) + results = self.tasks.groupby("output.formula_pretty", criteria=criteria) + + for n_formula, (keys, docs) in enumerate(results): + formula = keys["output"]["formula_pretty"] + self.logger.debug( + "Getting %s (Formula %d of %d)", formula, n_formula + 1, num_formulas + ) + decoded_docs = MontyDecoder().process_decoded(docs) + grouped_tasks = _group_orderings( + decoded_docs, + self.structure_match_ltol, + self.structure_match_stol, + self.structure_match_angle_tol, + ) + n_groups = len(grouped_tasks) + for n_group, group in enumerate(grouped_tasks): + self.logger.debug( + "Found %d tasks for %s (Parent structure %d of %d)", + len(group), + formula, + n_group + 1, + n_groups, + ) + yield group + + def process_item(self, tasks: list[dict]) -> list[MagneticOrderingsDocument]: + """Process magnetic ordering relaxation/static calculations into documents. + + The magnetic ordering tasks will be grouped based on their parent structure + (i.e., the structure before the magnetic ordering transformation was applied). + See _group_orderings for more details. + + Parameters + ---------- + tasks : list[dict] + A list of magnetic ordering tasks grouped by same formula. + + Returns + ------- + list of .MagneticOrderingsDocument + A list of magnetic ordering documents (one for each unique parent + structure). + """ + self.logger.debug("Processing %s", tasks[0]["output"].formula_pretty) + + if not tasks: + return [] + + return jsanitize( + MagneticOrderingsDocument.from_tasks(tasks).model_dump(), + allow_bson=True, + ) + + def update_targets(self, items: list[MagneticOrderingsDocument]) -> None: + """Insert new magnetic orderings into the magnetic orderings Store. + + Parameters + ---------- + items : list of .MagneticOrderingsDocument + A list of magnetic ordering documents to add to the database. + """ + self.logger.info("Updating %s magnetic orderings documents", len(items)) + self.magnetic_orderings.update(items, key="ground_state_uuid") + + +def _group_orderings( + tasks: list[dict], ltol: float, stol: float, angle_tol: float +) -> list[list[dict]]: + """Group ordering tasks by their parent structure. + + This is useful for distinguishing between different polymorphs (i.e., same formula). + + Parameters + ---------- + tasks : list[dict] + A list of ordering tasks. + tol : float + Numerical tolerance for structure equivalence. + + Returns + ------- + list[list[dict]] + The tasks grouped by their parent structure. + """ + tasks = [dict(task) for task in tasks] + + grouped_tasks = [[tasks[0]]] + sm = StructureMatcher(ltol=ltol, stol=stol, angle_tol=angle_tol) + + for task in tasks[1:]: + parent_structure = MontyDecoder().process_decoded( + task["metadata"]["parent_structure"] + ) + + match = False + for group in grouped_tasks: + group_parent_structure = MontyDecoder().process_decoded( + group[0]["metadata"]["parent_structure"] + ) + + # parent structure lattice/coords may be same but in different order + # so we need to be more rigorous in checking equivalence + if sm.fit(parent_structure, group_parent_structure): + group.append(task) + match = True + break + + if not match: + grouped_tasks.append([task]) + + return MontyDecoder().process_decoded(grouped_tasks) diff --git a/src/atomate2/common/files.py b/src/atomate2/common/files.py index d9ed4a3b35..ebc818bb6b 100644 --- a/src/atomate2/common/files.py +++ b/src/atomate2/common/files.py @@ -19,6 +19,7 @@ def copy_files( prefix: str = "", allow_missing: bool = False, file_client: FileClient | None = None, + link_files: bool = False, ) -> None: r""" Copy files between source and destination folders. @@ -49,6 +50,9 @@ def copy_files( directory. file_client : .FileClient A file client to use for performing file operations. + link_files : bool + Whether to link the files instead of copying them. This option will raise an + error if it is used in combination with a file_client. """ src_dir = file_client.abspath(src_dir, host=src_host) if dest_dir is None: @@ -63,7 +67,10 @@ def copy_files( to_file = Path(file.parent) / f"{prefix}{file.name}" to_file = (dest_dir / to_file).with_suffix(file.suffix + suffix) try: - file_client.copy(from_file, to_file, src_host=src_host) + if link_files and src_host is None: + file_client.link(from_file, to_file) + else: + file_client.copy(from_file, to_file, src_host=src_host) except FileNotFoundError: if not allow_missing: raise @@ -326,7 +333,9 @@ def find_and_filter_files( def get_zfile( - directory_listing: list[Path], base_name: str, allow_missing: bool = False + directory_listing: list[Path], + base_name: str, + allow_missing: bool = False, ) -> Path | None: """ Find gzipped or non-gzipped versions of a file in a directory listing. @@ -347,7 +356,7 @@ def get_zfile( found, then ``None`` will be returned. """ for file in directory_listing: - if file.name in [base_name, f"{base_name}.gz", f"{base_name}.GZ"]: + if file.name in (base_name, f"{base_name}.gz", f"{base_name}.GZ"): return file if allow_missing: diff --git a/src/atomate2/common/flows/defect.py b/src/atomate2/common/flows/defect.py index 9dca7ca9fd..1c34f0e0c5 100644 --- a/src/atomate2/common/flows/defect.py +++ b/src/atomate2/common/flows/defect.py @@ -5,7 +5,6 @@ import logging from abc import ABC, abstractmethod from dataclasses import dataclass -from pathlib import Path from typing import TYPE_CHECKING from jobflow import Flow, Job, Maker, OutputReference @@ -21,9 +20,13 @@ ) if TYPE_CHECKING: + from pathlib import Path + import numpy.typing as npt + from emmet.core.tasks import TaskDoc from pymatgen.analysis.defects.core import Defect from pymatgen.core.structure import Structure + from pymatgen.entries.computed_entries import ComputedStructureEntry logger = logging.getLogger(__name__) @@ -60,8 +63,7 @@ def make( charge_state1: int, charge_state2: int, ) -> Flow: - """ - Make a job for the calculation of the configuration coordinate diagram. + """Make a job for the calculation of the configuration coordinate diagram. Parameters ---------- @@ -110,7 +112,7 @@ def make( struct2, distortions=self.distortions, static_maker=self.static_maker, - prev_vasp_dir=dir1, + prev_dir=dir1, add_name="q1", add_info={"relaxed_uuid": relax1.uuid, "distorted_uuid": relax2.uuid}, ) @@ -120,7 +122,7 @@ def make( struct1, distortions=self.distortions, static_maker=self.static_maker, - prev_vasp_dir=dir2, + prev_dir=dir2, add_name="q2", add_info={"relaxed_uuid": relax2.uuid, "distorted_uuid": relax1.uuid}, ) @@ -165,7 +167,7 @@ class FormationEnergyMaker(Maker, ABC): A maker to perform a atomic-position-only relaxation on the defect charge states. Since these calculations are expensive and the settings might get messy, it is recommended for each implementation of this maker to check - some of the most important settings in the `relax_maker`. Please see + some of the most important settings in the `relax_maker`. Please see `FormationEnergyMaker.validate_maker` for more details. bulk_relax_maker: Maker @@ -216,7 +218,7 @@ class FormationEnergyMaker(Maker, ABC): .. note:: Once we remove the requirement for explicit bulk supercell calculations, - this setting will be removed. It is only needed because the bulk supercell + this setting will be removed. It is only needed because the bulk supercell locpot is currently needed for the finite-size correction calculation. Output format for the DefectEntry data: @@ -278,7 +280,7 @@ def make( If provided, the bulk supercell calculation will be skipped. supercell_matrix: NDArray | None The supercell transformation matrix. If None, the supercell matrix - will be computed automatically. If `bulk_supercell_dir` is provided, + will be computed automatically. If `bulk_supercell_dir` is provided, this parameter will be ignored. defect_index : int | str Additional index to give unique names to the defect calculations. @@ -295,6 +297,7 @@ def make( uc_structure=defect.structure, relax_maker=self.bulk_relax_maker, sc_mat=supercell_matrix, + get_planar_locpot=self.get_planar_locpot, ) sc_mat = get_sc_job.output["sc_mat"] lattice = get_sc_job.output["sc_struct"].lattice @@ -305,8 +308,8 @@ def make( get_sc_job = get_supercell_from_prv_calc( uc_structure=defect.structure, prv_calc_dir=bulk_supercell_dir, + sc_entry_and_locpot_from_prv=self.sc_entry_and_locpot_from_prv, sc_mat_ref=supercell_matrix, - structure_from_prv=self.structure_from_prv, ) sc_mat = get_sc_job.output["sc_mat"] lattice = get_sc_job.output["lattice"] @@ -329,12 +332,6 @@ def make( jobs.extend([get_sc_job, spawn_output]) if self.collect_defect_entry_data: - if isinstance(bulk_supercell_dir, (str, Path)): - raise NotImplementedError( - "DefectEntery creation only works when you are explicitly " - "calculating the bulk supercell. This is because the bulk " - "SC energy parsing from previous calculations is not implemented." - ) collection_job = get_defect_entry( charge_state_summary=spawn_output.output, bulk_summary=get_sc_job.output, @@ -348,8 +345,10 @@ def make( ) @abstractmethod - def structure_from_prv(self, previous_dir: str) -> Structure: - """Copy the output structure from previous directory. + def sc_entry_and_locpot_from_prv( + self, previous_dir: str + ) -> tuple[ComputedStructureEntry, dict]: + """Copy the output ComputedStructureEntry and Locpot from previous directory. Parameters ---------- @@ -358,7 +357,25 @@ def structure_from_prv(self, previous_dir: str) -> Structure: Returns ------- - structure: Structure + entry: ComputedStructureEntry + """ + + @abstractmethod + def get_planar_locpot(self, task_doc: TaskDoc) -> dict: + """Get the Planar Locpot from the TaskDoc. + + This is needed just in case the planar average locpot is stored in different + part of the TaskDoc for different codes. + + Parameters + ---------- + task_doc: TaskDoc + The task document. + + Returns + ------- + planar_locpot: dict + The planar average locpot. """ @abstractmethod diff --git a/src/atomate2/common/flows/elastic.py b/src/atomate2/common/flows/elastic.py index eaaf4d7d81..256e0753e9 100644 --- a/src/atomate2/common/flows/elastic.py +++ b/src/atomate2/common/flows/elastic.py @@ -7,7 +7,6 @@ from typing import TYPE_CHECKING from jobflow import Flow, Maker, OnMissing -from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from atomate2 import SETTINGS from atomate2.common.jobs.elastic import ( @@ -15,6 +14,7 @@ generate_elastic_deformations, run_elastic_deformations, ) +from atomate2.common.jobs.utils import structure_to_conventional if TYPE_CHECKING: from pathlib import Path @@ -60,6 +60,11 @@ class BaseElasticMaker(Maker, ABC): bulk relaxation. elastic_relax_maker : .BaseVaspMaker or .ForceFieldRelaxMaker Maker used to generate elastic relaxations. + max_failed_deformations: int or float + Maximum number of deformations allowed to fail to proceed with the fitting + of the elastic tensor. If an int the absolute number of deformations. If + a float between 0 an 1 the maximum fraction of deformations. If None any + number of deformations allowed. generate_elastic_deformations_kwargs : dict Keyword arguments passed to :obj:`generate_elastic_deformations`. fit_elastic_tensor_kwargs : dict @@ -76,6 +81,7 @@ class BaseElasticMaker(Maker, ABC): elastic_relax_maker: BaseVaspMaker | ForceFieldRelaxMaker = ( None # constant volume optimization ) + max_failed_deformations: int | float | None = None generate_elastic_deformations_kwargs: dict = field(default_factory=dict) fit_elastic_tensor_kwargs: dict = field(default_factory=dict) task_document_kwargs: dict = field(default_factory=dict) @@ -87,14 +93,13 @@ def make( equilibrium_stress: Matrix3D = None, conventional: bool = False, ) -> Flow: - """ - Make flow to calculate the elastic constant. + """Make flow to calculate the elastic constant. Parameters ---------- structure : .Structure A pymatgen structure. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous vasp calculation directory to use for copying outputs. equilibrium_stress : tuple of tuple of float The equilibrium stress of the (relaxed) structure, if known. @@ -116,8 +121,9 @@ def make( equilibrium_stress = bulk.output.output.stress if conventional: - sga = SpacegroupAnalyzer(structure, symprec=self.symprec) - structure = sga.get_conventional_standard_structure() + stc = structure_to_conventional(structure, self.symprec) + jobs.append(stc) + structure = stc.output deformations = generate_elastic_deformations( structure, @@ -139,6 +145,7 @@ def make( equilibrium_stress=equilibrium_stress, order=self.order, symprec=self.symprec if self.sym_reduce else None, + max_failed_deformations=self.max_failed_deformations, **self.fit_elastic_tensor_kwargs, **self.task_document_kwargs, ) @@ -156,7 +163,7 @@ def make( @property @abstractmethod - def prev_calc_dir_argname(self): + def prev_calc_dir_argname(self) -> str: """Name of argument informing static maker of previous calculation directory. As this differs between different DFT codes (e.g., VASP, CP2K), it diff --git a/src/atomate2/common/flows/electrode.py b/src/atomate2/common/flows/electrode.py new file mode 100644 index 0000000000..cb6a17ee4a --- /dev/null +++ b/src/atomate2/common/flows/electrode.py @@ -0,0 +1,183 @@ +"""Flow for electrode analysis.""" + +from __future__ import annotations + +import logging +from abc import ABC, abstractmethod +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +from jobflow import Flow, Maker +from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher + +from atomate2.common.jobs.electrode import ( + RelaxJobSummary, + get_computed_entries, + get_insertion_electrode_doc, + get_stable_inserted_results, + get_structure_group_doc, +) + +if TYPE_CHECKING: + from pathlib import Path + + from pymatgen.alchemy import ElementLike + from pymatgen.core.structure import Structure + from pymatgen.entries.computed_entries import ComputedEntry + from pymatgen.io.vasp.outputs import VolumetricData + +logger = logging.getLogger(__name__) + +__author__ = "Jimmy Shen" +__email__ = "jmmshn@gmail.com" + + +@dataclass +class ElectrodeInsertionMaker(Maker, ABC): + """Attempt ion insertion into a structure. + + The basic unit for cation insertion is: + [get_stable_inserted_structure]: + (static) -> (chgcar analysis) -> + N x (relax) -> (return best structure) + + The workflow is: + [relax structure] + [get_stable_inserted_structure] + [get_stable_inserted_structure] + [get_stable_inserted_structure] + ... until the insertion is no longer topotactic. + + This workflow requires the users to provide the following functions: + self.get_charge_density(task_doc: TaskDoc): + Get the charge density of a TaskDoc output from a calculation. + self.update_static_maker(): + Ensure that the static maker will store the desired data. + + If you use this workflow please cite the following paper: + Shen, J.-X., Horton, M., & Persson, K. A. (2020). + A charge-density-based general cation insertion algorithm for + generating new Li-ion cathode materials. + npj Computational Materials, 6(161), 1โ€”7. + doi: 10.1038/s41524-020-00422-3 + + Attributes + ---------- + name: str + The name of the flow created by this maker. + relax_maker: RelaxMaker + A maker to perform relaxation calculations. + bulk_relax_maker: Maker + A separate maker to perform the first bulk relaxation calculation. + If None, the relax_maker will be used. + static_maker: Maker + A maker to perform static calculations. + structure_matcher: StructureMatcher + The structure matcher to use to determine if additional insertion is needed. + """ + + relax_maker: Maker + static_maker: Maker + bulk_relax_maker: Maker | None = None + name: str = "ion insertion" + structure_matcher: StructureMatcher = field( + default_factory=lambda: StructureMatcher( + comparator=ElementComparator(), + ) + ) + + def __post_init__(self) -> None: + """Ensure that the static maker will store the desired data.""" + self.update_static_maker() + + def make( + self, + structure: Structure, + inserted_element: ElementLike, + n_steps: int | None, + insertions_per_step: int = 4, + working_ion_entry: ComputedEntry | None = None, + ) -> Flow: + """Make the flow. + + Parameters + ---------- + structure: + Structure to insert ion into. + inserted_species: + Species to insert. + n_steps: int + The maximum number of sequential insertion steps to attempt. + insertions_per_step: int + The maximum number of ion insertion sites to attempt. + + Returns + ------- + Flow for ion insertion. + """ + # First relax the structure + if self.bulk_relax_maker: + relax = self.bulk_relax_maker.make(structure) + else: + relax = self.relax_maker.make(structure) + # add ignored_species to the structure matcher + sm = _add_ignored_species(self.structure_matcher, inserted_element) + # Get the inserted structure + new_entries_job = get_stable_inserted_results( + structure=relax.output.structure, + inserted_element=inserted_element, + structure_matcher=sm, + static_maker=self.static_maker, + relax_maker=self.relax_maker, + get_charge_density=self.get_charge_density, + n_steps=n_steps, + insertions_per_step=insertions_per_step, + ) + relaxed_summary = RelaxJobSummary( + structure=relax.output.structure, + entry=relax.output.entry, + dir_name=relax.output.dir_name, + uuid=relax.output.uuid, + ) + get_entries_job = get_computed_entries(new_entries_job.output, relaxed_summary) + structure_group_job = get_structure_group_doc( + get_entries_job.output, ignored_species=str(inserted_element) + ) + jobs = [relax, new_entries_job, get_entries_job, structure_group_job] + output = structure_group_job.output + if working_ion_entry: + insertion_electrode_job = get_insertion_electrode_doc( + get_entries_job.output, working_ion_entry + ) + jobs.append(insertion_electrode_job) + output = insertion_electrode_job.output + return Flow(jobs=jobs, output=output) + + @abstractmethod + def get_charge_density(self, prev_dir: Path | str) -> VolumetricData: + """Get the charge density of a structure. + + Parameters + ---------- + prev_dir: + The previous directory where the static calculation was performed. + + Returns + ------- + The charge density. + """ + + @abstractmethod + def update_static_maker(self) -> None: + """Ensure that the static maker will store the desired data.""" + + +def _add_ignored_species( + structure_matcher: StructureMatcher, species: ElementLike +) -> StructureMatcher: + """Add an ignored species to a structure matcher.""" + sm_dict = structure_matcher.as_dict() + ignored_species = set(sm_dict.get("ignored_species", set())) + ignored_species.add(str(species)) + sm_dict["ignored_species"] = list(ignored_species) + return StructureMatcher.from_dict(sm_dict) diff --git a/src/atomate2/common/flows/eos.py b/src/atomate2/common/flows/eos.py new file mode 100644 index 0000000000..ec64d1988e --- /dev/null +++ b/src/atomate2/common/flows/eos.py @@ -0,0 +1,188 @@ +"""Define common EOS flow agnostic to electronic-structure code.""" + +from __future__ import annotations + +import contextlib +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +import numpy as np +from jobflow import Flow, Maker + +from atomate2.common.jobs.eos import PostProcessEosEnergy, apply_strain_to_structure + +if TYPE_CHECKING: + from pathlib import Path + + from jobflow import Job + from pymatgen.core import Structure + + from atomate2.common.jobs.eos import EOSPostProcessor + + +@dataclass +class CommonEosMaker(Maker): + """ + Generate equation of state data. + + First relax a structure using relax_maker. + Then perform a series of deformations on the relaxed structure, and + evaluate single-point energies with static_maker. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + initial_relax_maker : .Maker | None + Maker to relax the input structure, defaults to None (no initial relaxation). + eos_relax_maker : .Maker + Maker to relax deformed structures for the EOS fit. + static_maker : .Maker | None + Maker to generate statics after each relaxation, defaults to None. + strain : tuple[float] + Percentage linear strain to apply as a deformation, default = -5% to 5%. + number_of_frames : int + Number of strain calculations to do for EOS fit, default = 6. + postprocessor : .atomate2.common.jobs.EOSPostProcessor + Optional postprocessing step, defaults to + `atomate2.common.jobs.PostProcessEosEnergy`. + _store_transformation_information : .bool = False + Whether to store the information about transformations. Unfortunately + needed at present to handle issues with emmet and pydantic validation + TODO: remove this when clash is fixed + """ + + name: str = "EOS Maker" + initial_relax_maker: Maker = None + eos_relax_maker: Maker = None + static_maker: Maker = None + linear_strain: tuple[float, float] = (-0.05, 0.05) + number_of_frames: int = 6 + postprocessor: EOSPostProcessor = field(default_factory=PostProcessEosEnergy) + _store_transformation_information: bool = False + + def make(self, structure: Structure, prev_dir: str | Path = None) -> Flow: + """Run an EOS flow. + + Parameters + ---------- + structure : Structure + A pymatgen structure object. + prev_dir : str or Path or None + A previous calculation directory to copy output files from. + + Returns + ------- + .Flow, an EOS flow + """ + jobs: dict[str, list[Job]] = {key: [] for key in ("relax", "static", "utility")} + + job_types: tuple[str, ...] = ( + ("relax", "static") if self.static_maker else ("relax",) + ) + flow_output: dict[str, dict] = { + key: {quantity: [] for quantity in ("energy", "volume", "stress")} + for key in job_types + } + + # First step: optional relaxation of structure + if self.initial_relax_maker: + relax_flow = self.initial_relax_maker.make( + structure=structure, prev_dir=prev_dir + ) + relax_flow.name = "EOS equilibrium relaxation" + + flow_output["initial_relax"] = { + "E0": relax_flow.output.output.energy, + "V0": relax_flow.output.structure.volume, + } + structure = relax_flow.output.structure + prev_dir = relax_flow.output.dir_name + jobs["relax"].append(relax_flow) + + if self.static_maker: + equil_static = self.static_maker.make( + structure=structure, prev_dir=prev_dir + ) + equil_static.name = "EOS equilibrium static" + flow_output["initial_static"] = { + "E0": equil_static.output.output.energy, + "V0": equil_static.output.structure.volume, + } + jobs["static"].append(equil_static) + + strain_l, strain_delta = np.linspace( + self.linear_strain[0], + self.linear_strain[1], + self.number_of_frames, + retstep=True, + ) + + if self.initial_relax_maker: + # Cell without applied strain already included from relax/equilibrium steps. + # Perturb this point (or these points) if included + zero_strain_mask = np.abs(strain_l) < 1e-15 + if np.any(zero_strain_mask): + nzs = len(strain_l[zero_strain_mask]) + shift = strain_delta / (nzs + 1.0) * np.linspace(-1.0, 1.0, nzs) + strain_l[np.abs(strain_l) < 1e-15] += shift + + deformation_l = [(np.identity(3) * (1.0 + eps)).tolist() for eps in strain_l] + + # apply strain to structures, return list of transformations + transformations = apply_strain_to_structure(structure, deformation_l) + jobs["utility"] += [transformations] + + for frame_idx in range(self.number_of_frames): + if self._store_transformation_information: + with contextlib.suppress(Exception): + # write details of the transformation to the + # transformations.json file. This file will automatically get + # added to the task document and allow the elastic builder + # to reconstruct the elastic document. Note the ":" + # is automatically converted to a "." in the filename. + self.eos_relax_maker.write_additional_data[ + "transformations:json" + ] = transformations.output[frame_idx] + + relax_job = self.eos_relax_maker.make( + structure=transformations.output[frame_idx].final_structure, + prev_dir=prev_dir, + ) + relax_job.name += f" deformation {frame_idx}" + jobs["relax"].append(relax_job) + + if self.static_maker: + static_job = self.static_maker.make( + structure=relax_job.output.structure, + prev_dir=relax_job.output.dir_name, + ) + static_job.name += f" {frame_idx}" + jobs["static"].append(static_job) + + for key in job_types: + for idx in range(len(jobs[key])): + output = jobs[key][idx].output.output + flow_output[key]["energy"] += [output.energy] + flow_output[key]["volume"] += [output.structure.volume] + flow_output[key]["stress"] += [output.stress] + + if self.postprocessor is not None: + min_points = self.postprocessor.min_data_points + if len(jobs["relax"]) < min_points: + raise ValueError( + "To perform least squares EOS fit with " + f"{type(self.postprocessor).__name__}, you must specify " + f"self.number_of_frames >= {min_points}." + ) + + post_process = self.postprocessor.make(flow_output) + post_process.name = self.name + " postprocessing" + flow_output = post_process.output + jobs["utility"] += [post_process] + + job_list = [] + for key in jobs: + job_list += jobs[key] + + return Flow(jobs=job_list, output=flow_output, name=self.name) diff --git a/src/atomate2/common/flows/magnetism.py b/src/atomate2/common/flows/magnetism.py new file mode 100644 index 0000000000..2f5a15bbd0 --- /dev/null +++ b/src/atomate2/common/flows/magnetism.py @@ -0,0 +1,190 @@ +"""Flows for calculating magnetic orderings and other magnetism-related tasks.""" + +from __future__ import annotations + +import warnings +from abc import ABC +from dataclasses import dataclass, field +from typing import TYPE_CHECKING, Literal + +from jobflow import Flow, Maker +from pymatgen.core import Element + +from atomate2.common.jobs.magnetism import ( + enumerate_magnetic_orderings, + postprocess_orderings, + run_ordering_calculations, +) +from atomate2.vasp.jobs.core import RelaxMaker, StaticMaker +from atomate2.vasp.sets.core import StaticSetGenerator + +if TYPE_CHECKING: + from collections.abc import Sequence + + from pymatgen.core.structure import Structure + + +__all__ = ["MagneticOrderingsMaker"] + + +@dataclass +class MagneticOrderingsMaker(Maker, ABC): + """Maker to calculate possible collinear magnetic orderings for a material. + + Given an input structure, possible magnetic orderings will be enumerated and ranked + based on symmetry up to a maximum number of orderings. Each ordering will be + optionally relaxed and a higher quality static calculation performed to obtain a + total energy. The lowest energy ordering is the predicted ground-state collinear + ordering. + + This Maker can be trivially implemented for your DFT code of choice by + utilizing the appropriate static/relax makers. However, for postprocessing to + work correctly, one must ensure that the calculation outputs can be processed into a + MagneticOrderingsDocument. As the TaskDoc class is currently defined only for + VASP, one should ensure that the task document returned during their DFT runs + contains the necessary parameters (e.g., TaskDoc.input.magnetic_moments). + This warning will be removed once a universal TaskDoc is implemented (Issue #741). + + This workflow was benchmarked with VASP for a wide range of test materials and + originally implemented in atomate (v1) for VASP as the MagneticOrderingsWF. Please + refer to the following paper for more information and cite appropriately: + + Horton, M.K., Montoya, J.H., Liu, M. et al. High-throughput prediction of the + ground-state collinear magnetic order of inorganic materials using Density + Functional Theory. npj Computational Materials 5, 64 (2019). + https://doi.org/10.1038/s41524-019-0199-7 + + .. Note:: + Good performance of this workflow is ultimately dependent on an appropriate + choice of Hubbard U, Hund J values and/or the functional. The defaults will work + well for many transition metal oxides. + + Parameters + ---------- + name : str + Name of the flows produced by this Maker. + static_maker : Maker + Maker used to perform static calculations for total energy. VASP is selected as + the default DFT code (atomate2.vasp.jobs.StaticMaker). + relax_maker : Maker | None + Maker used to perform relaxations of the enumerated structures. VASP is selected + as the default DFT code (atomate2.vasp.jobs.RelaxMaker). If this field is None, + relaxations will be skipped (i.e., only static calculations are performed). + default_magmoms : dict | None + Optional default mapping of magnetic elements to their initial magnetic moments + in ฮผB. Generally these are chosen to be high-spin, since they can relax to a + low-spin configuration during a DFT electronic configuration. If None, will use + the default values provided in pymatgen/analysis/magnetism/default_magmoms.yaml. + strategies : tuple[str] + Different ordering strategies to use. Choose from ferromagnetic, + antiferromagnetic, antiferromagnetic_by_motif, ferrimagnetic_by_motif, + ferrimagnetic_by_species, or nonmagnetic. Here, "motif", means to use a + different ordering parameter for symmetry inequivalent sites. + automatic : bool + If True, will automatically choose sensible strategies. Defaults to True. + truncate_by_symmetry : bool + If True, will remove very unsymmetrical orderings that are likely physically + implausible. Defaults to True. + transformation_kwargs : dict | None + Keyword arguments provided to MagOrderingTransformation in pymatgen. Defaults to + None. + """ + + name: str = "magnetic_orderings" + static_maker: Maker = field( + default_factory=lambda: StaticMaker( + input_set_generator=StaticSetGenerator(user_incar_settings={"EDIFF": 1e-7}) + ) + ) + relax_maker: Maker | None = field(default_factory=RelaxMaker) + default_magmoms: dict[Element, float] | None = None + strategies: Sequence[ + Literal[ + "ferromagnetic", + "antiferromagnetic", + "antiferromagnetic_by_motif", + "ferrimagnetic_by_motif", + "ferrimagnetic_by_species", + "nonmagnetic", + ] + ] = ("ferromagnetic", "antiferromagnetic") + automatic: bool = True + truncate_by_symmetry: bool = True + transformation_kwargs: dict | None = None + + def __post_init__(self) -> None: + """Ensure that the static and relax makers come from the same base maker. + + This ensures that the same DFT code is used for both calculations. + """ + if self.relax_maker is None: + warnings.warn( + ( + "No relax_maker provided, relaxations will be skipped. Please be" + " sure that this is intended!" + ), + stacklevel=2, + ) + else: + static_base_maker_name = self.static_maker.__class__.__mro__[1].__name__ + relax_base_maker_name = self.relax_maker.__class__.__mro__[1].__name__ + if relax_base_maker_name != static_base_maker_name: + warnings.warn( + "The provided static and relax makers do not use the " + "same DFT code! Please check the base maker used.", + stacklevel=2, + ) + + def make( + self, + structure: Structure, + ) -> Flow: + """Make a flow to calculate collinear magnetic orderings for a given structure. + + Parameters + ---------- + structure : Structure + A pymatgen structure object. + + Returns + ------- + flow: Flow + The magnetic ordering workflow. + """ + jobs = [] + + if Element("Co") in structure.elements: + warnings.warn( + ( + "Co detected in structure! Please consider testing both low-spin" + " and high-spin configurations. The current default for Co (without" + " oxidation state) is high-spin. Refer to the defaults in" + " pymatgen/analysis/magnetism/default_magmoms.yaml for more" + " information. " + ), + stacklevel=2, + ) + + orderings = enumerate_magnetic_orderings( + structure, + default_magmoms=self.default_magmoms, + strategies=self.strategies, + automatic=self.automatic, + truncate_by_symmetry=self.truncate_by_symmetry, + transformation_kwargs=self.transformation_kwargs, + ) + + calculations = run_ordering_calculations( + orderings.output, # pylint: disable=no-member + static_maker=self.static_maker, + relax_maker=self.relax_maker, + ) + + postprocessing = postprocess_orderings(calculations.output) + jobs = [orderings, calculations, postprocessing] + + return Flow( + jobs=jobs, + output=postprocessing.output, + name=f"{self.name} ({structure.composition.reduced_formula})", + ) diff --git a/src/atomate2/common/flows/phonons.py b/src/atomate2/common/flows/phonons.py new file mode 100644 index 0000000000..3d6edf9a21 --- /dev/null +++ b/src/atomate2/common/flows/phonons.py @@ -0,0 +1,370 @@ +"""Flows for calculating phonons.""" + +from __future__ import annotations + +from abc import ABC, abstractmethod +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +from jobflow import Flow, Maker + +from atomate2.common.jobs.phonons import ( + generate_frequencies_eigenvectors, + generate_phonon_displacements, + get_supercell_size, + get_total_energy_per_cell, + run_phonon_displacements, +) +from atomate2.common.jobs.utils import structure_to_conventional, structure_to_primitive + +if TYPE_CHECKING: + from pathlib import Path + + from emmet.core.math import Matrix3D + from pymatgen.core.structure import Structure + + from atomate2.aims.jobs.base import BaseAimsMaker + from atomate2.forcefields.jobs import ForceFieldRelaxMaker, ForceFieldStaticMaker + from atomate2.vasp.jobs.base import BaseVaspMaker + +SUPPORTED_CODES = frozenset(("vasp", "aims", "forcefields")) + + +@dataclass +class BasePhononMaker(Maker, ABC): + """ + Maker to calculate harmonic phonons with a DFT/force field code and Phonopy. + + Calculate the harmonic phonons of a material. Initially, a tight structural + relaxation is performed to obtain a structure without forces on the atoms. + Subsequently, supercells with one displaced atom are generated and accurate + forces are computed for these structures. With the help of phonopy, these + forces are then converted into a dynamical matrix. To correct for polarization + effects, a correction of the dynamical matrix based on BORN charges can + be performed. Finally, phonon densities of states, phonon band structures + and thermodynamic properties are computed. + + .. Note:: + It is heavily recommended to symmetrize the structure before passing it to + this flow. Otherwise, a different space group might be detected and too + many displacement calculations will be generated. + It is recommended to check the convergence parameters here and + adjust them if necessary. The default might not be strict enough + for your specific case. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + sym_reduce : bool + Whether to reduce the number of deformations using symmetry. + symprec : float + Symmetry precision to use in the + reduction of symmetry to find the primitive/conventional cell + (use_primitive_standard_structure, use_conventional_standard_structure) + and to handle all symmetry-related tasks in phonopy + displacement: float + displacement distance for phonons + min_length: float + min length of the supercell that will be built + prefer_90_degrees: bool + if set to True, supercell algorithm will first try to find a supercell + with 3 90 degree angles + get_supercell_size_kwargs: dict + kwargs that will be passed to get_supercell_size to determine supercell size + use_symmetrized_structure: str + allowed strings: "primitive", "conventional", None + + - "primitive" will enforce to start the phonon computation + from the primitive standard structure + according to Setyawan, W., & Curtarolo, S. (2010). + High-throughput electronic band structure calculations: + Challenges and tools. Computational Materials Science, + 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010. + This makes it possible to use certain k-path definitions + with this workflow. Otherwise, we must rely on seekpath + - "conventional" will enforce to start the phonon computation + from the conventional standard structure + according to Setyawan, W., & Curtarolo, S. (2010). + High-throughput electronic band structure calculations: + Challenges and tools. Computational Materials Science, + 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010. + We will however use seekpath and primitive structures + as determined by from phonopy to compute the phonon band structure + bulk_relax_maker: .ForceFieldRelaxMaker, .BaseAimsMaker, .BaseVaspMaker, or None + A maker to perform a tight relaxation on the bulk. + Set to ``None`` to skip the + bulk relaxation + static_energy_maker: .ForceFieldRelaxMaker, .BaseAimsMaker, .BaseVaspMaker, or None + A maker to perform the computation of the DFT energy on the bulk. + Set to ``None`` to skip the + static energy computation + born_maker: .ForceFieldStaticMaker, .BaseAsimsMaker, .BaseVaspMaker, or None + Maker to compute the BORN charges. + phonon_displacement_maker: .ForceFieldStaticMaker, .BaseAimsMaker, .BaseVaspMaker + Maker used to compute the forces for a supercell. + generate_frequencies_eigenvectors_kwargs : dict + Keyword arguments passed to :obj:`generate_frequencies_eigenvectors`. + create_thermal_displacements: bool + Bool that determines if thermal_displacement_matrices are computed + kpath_scheme: str + scheme to generate kpoints. Please be aware that + you can only use seekpath with any kind of cell + Otherwise, please use the standard primitive structure + Available schemes are: + "seekpath", "hinuma", "setyawan_curtarolo", "latimer_munro". + "seekpath" and "hinuma" are the same definition but + seekpath can be used with any kind of unit cell as + it relies on phonopy to handle the relationship + to the primitive cell and not pymatgen + code: str + determines the dft or force field code. + store_force_constants: bool + if True, force constants will be stored + socket: bool + If True, use the socket for the calculation + """ + + name: str = "phonon" + sym_reduce: bool = True + symprec: float = 1e-4 + displacement: float = 0.01 + min_length: float | None = 20.0 + prefer_90_degrees: bool = True + get_supercell_size_kwargs: dict = field(default_factory=dict) + use_symmetrized_structure: str | None = None + bulk_relax_maker: ForceFieldRelaxMaker | BaseVaspMaker | BaseAimsMaker | None = None + static_energy_maker: ForceFieldRelaxMaker | BaseVaspMaker | BaseAimsMaker | None = ( + None + ) + born_maker: ForceFieldStaticMaker | BaseVaspMaker | None = None + phonon_displacement_maker: ForceFieldStaticMaker | BaseVaspMaker | BaseAimsMaker = ( + None + ) + create_thermal_displacements: bool = True + generate_frequencies_eigenvectors_kwargs: dict = field(default_factory=dict) + kpath_scheme: str = "seekpath" + code: str = None + store_force_constants: bool = True + socket: bool = False + + def make( + self, + structure: Structure, + prev_dir: str | Path | None = None, + born: list[Matrix3D] | None = None, + epsilon_static: Matrix3D | None = None, + total_dft_energy_per_formula_unit: float | None = None, + supercell_matrix: Matrix3D | None = None, + ) -> Flow: + """Make flow to calculate the phonon properties. + + Parameters + ---------- + structure : Structure + A pymatgen structure object. Please start with a structure + that is nearly fully optimized as the internal optimizers + have very strict settings! + prev_dir : str or Path or None + A previous calculation directory to use for copying outputs. + born: Matrix3D + Instead of recomputing born charges and epsilon, these values can also be + provided manually. If born and epsilon_static are provided, the born run + will be skipped it can be provided in the VASP convention with information + for every atom in unit cell. Please be careful when converting structures + within in this workflow as this could lead to errors + epsilon_static: Matrix3D + The high-frequency dielectric constant to use instead of recomputing born + charges and epsilon. If born, epsilon_static are provided, the born run + will be skipped + total_dft_energy_per_formula_unit: float + It has to be given per formula unit (as a result in corresponding Doc). + Instead of recomputing the energy of the bulk structure every time, this + value can also be provided in eV. If it is provided, the static run will be + skipped. This energy is the typical output dft energy of the dft workflow. + No conversion needed. + supercell_matrix: list + Instead of min_length, also a supercell_matrix can be given, e.g. + [[1.0,0.0,0.0],[0.0,1.0,0.0],[0.0,0.0,1.0] + """ + use_symmetrized_structure = self.use_symmetrized_structure + kpath_scheme = self.kpath_scheme + valid_structs = (None, "primitive", "conventional") + if use_symmetrized_structure not in valid_structs: + raise ValueError( + f"Invalid {use_symmetrized_structure=}, use one of {valid_structs}" + ) + + if use_symmetrized_structure != "primitive" and kpath_scheme != "seekpath": + raise ValueError( + f"You can't use {kpath_scheme=} with the primitive standard " + "structure, please use seekpath" + ) + + valid_schemes = ("seekpath", "hinuma", "setyawan_curtarolo", "latimer_munro") + if kpath_scheme not in valid_schemes: + raise ValueError( + f"{kpath_scheme=} is not implemented, use one of {valid_schemes}" + ) + + if self.code is None or self.code not in SUPPORTED_CODES: + raise ValueError( + "The code variable must be passed and it must be a supported code." + f" Supported codes are: {SUPPORTED_CODES}" + ) + + jobs = [] + + # TODO: should this be after or before structural optimization as the + # optimization could change the symmetry we could add a tutorial and point out + # that the structure should be nearly optimized before the phonon workflow + if self.use_symmetrized_structure == "primitive": + # These structures are compatible with many + # of the kpath algorithms that are used for Materials Project + prim_job = structure_to_primitive(structure, self.symprec) + jobs.append(prim_job) + structure = prim_job.output + elif self.use_symmetrized_structure == "conventional": + # it could be beneficial to use conventional standard structures to arrive + # faster at supercells with right angles + conv_job = structure_to_conventional(structure, self.symprec) + jobs.append(conv_job) + structure = conv_job.output + + optimization_run_job_dir = None + optimization_run_uuid = None + + if self.bulk_relax_maker is not None: + # optionally relax the structure + bulk_kwargs = {} + if self.prev_calc_dir_argname is not None: + bulk_kwargs[self.prev_calc_dir_argname] = prev_dir + bulk = self.bulk_relax_maker.make(structure, **bulk_kwargs) + jobs.append(bulk) + structure = bulk.output.structure + prev_dir = bulk.output.dir_name + optimization_run_job_dir = bulk.output.dir_name + optimization_run_uuid = bulk.output.uuid + + # if supercell_matrix is None, supercell size will be determined after relax + # maker to ensure that cell lengths are really larger than threshold + if supercell_matrix is None: + supercell_job = get_supercell_size( + structure, + self.min_length, + self.prefer_90_degrees, + **self.get_supercell_size_kwargs, + ) + jobs.append(supercell_job) + supercell_matrix = supercell_job.output + + # Computation of static energy + total_dft_energy = None + static_run_job_dir = None + static_run_uuid = None + if (self.static_energy_maker is not None) and ( + total_dft_energy_per_formula_unit is None + ): + static_job_kwargs = {} + if self.prev_calc_dir_argname is not None: + static_job_kwargs[self.prev_calc_dir_argname] = prev_dir + static_job = self.static_energy_maker.make( + structure=structure, **static_job_kwargs + ) + jobs.append(static_job) + total_dft_energy = static_job.output.output.energy + static_run_job_dir = static_job.output.dir_name + static_run_uuid = static_job.output.uuid + prev_dir = static_job.output.dir_name + elif total_dft_energy_per_formula_unit is not None: + # to make sure that one can reuse results from Doc + compute_total_energy_job = get_total_energy_per_cell( + total_dft_energy_per_formula_unit, structure + ) + jobs.append(compute_total_energy_job) + total_dft_energy = compute_total_energy_job.output + + # get a phonon object from phonopy + displacements = generate_phonon_displacements( + structure=structure, + supercell_matrix=supercell_matrix, + displacement=self.displacement, + sym_reduce=self.sym_reduce, + symprec=self.symprec, + use_symmetrized_structure=self.use_symmetrized_structure, + kpath_scheme=self.kpath_scheme, + code=self.code, + ) + jobs.append(displacements) + + # perform the phonon displacement calculations + displacement_calcs = run_phonon_displacements( + displacements=displacements.output, + structure=structure, + supercell_matrix=supercell_matrix, + phonon_maker=self.phonon_displacement_maker, + socket=self.socket, + prev_dir_argname=self.prev_calc_dir_argname, + prev_dir=prev_dir, + ) + jobs.append(displacement_calcs) + + # Computation of BORN charges + born_run_job_dir = None + born_run_uuid = None + if self.born_maker is not None and (born is None or epsilon_static is None): + born_kwargs = {} + if self.prev_calc_dir_argname is not None: + born_kwargs[self.prev_calc_dir_argname] = prev_dir + born_job = self.born_maker.make(structure, **born_kwargs) + jobs.append(born_job) + + # I am not happy how we currently access "born" charges + # This is very vasp specific code aims and forcefields + # do not support this at the moment, if this changes we have + # to update this section + epsilon_static = born_job.output.calcs_reversed[0].output.epsilon_static + born = born_job.output.calcs_reversed[0].output.outcar["born"] + born_run_job_dir = born_job.output.dir_name + born_run_uuid = born_job.output.uuid + + phonon_collect = generate_frequencies_eigenvectors( + supercell_matrix=supercell_matrix, + displacement=self.displacement, + sym_reduce=self.sym_reduce, + symprec=self.symprec, + use_symmetrized_structure=self.use_symmetrized_structure, + kpath_scheme=self.kpath_scheme, + code=self.code, + structure=structure, + displacement_data=displacement_calcs.output, + epsilon_static=epsilon_static, + born=born, + total_dft_energy=total_dft_energy, + static_run_job_dir=static_run_job_dir, + static_run_uuid=static_run_uuid, + born_run_job_dir=born_run_job_dir, + born_run_uuid=born_run_uuid, + optimization_run_job_dir=optimization_run_job_dir, + optimization_run_uuid=optimization_run_uuid, + create_thermal_displacements=self.create_thermal_displacements, + store_force_constants=self.store_force_constants, + **self.generate_frequencies_eigenvectors_kwargs, + ) + + jobs.append(phonon_collect) + + # create a flow including all jobs for a phonon computation + return Flow(jobs, phonon_collect.output) + + @property + @abstractmethod + def prev_calc_dir_argname(self) -> str | None: + """Name of argument informing static maker of previous calculation directory. + + As this differs between different DFT codes (e.g., VASP, CP2K), it + has been left as a property to be implemented by the inheriting class. + + Note: this is only applicable if a relax_maker is specified; i.e., two + calculations are performed for each ordering (relax -> static) + """ diff --git a/src/atomate2/common/jobs/__init__.py b/src/atomate2/common/jobs/__init__.py index 77701f2bf8..cb42134aa8 100644 --- a/src/atomate2/common/jobs/__init__.py +++ b/src/atomate2/common/jobs/__init__.py @@ -1,2 +1,3 @@ """DFT code agnostic jobs.""" + from .utils import structure_to_conventional, structure_to_primitive diff --git a/src/atomate2/common/jobs/defect.py b/src/atomate2/common/jobs/defect.py index 769f553b9e..7871c01cef 100644 --- a/src/atomate2/common/jobs/defect.py +++ b/src/atomate2/common/jobs/defect.py @@ -17,6 +17,7 @@ from pymatgen.entries.computed_entries import ComputedStructureEntry from atomate2.common.schemas.defects import CCDDocument +from atomate2.utils.path import strip_hostname if TYPE_CHECKING: from collections.abc import Iterable @@ -59,8 +60,8 @@ def get_charged_structures(structure: Structure, charges: Iterable) -> list[Stru A dictionary with the two structures with the charge states added. """ structs_out = [structure.copy() for _ in charges] - for i, q in enumerate(charges): - structs_out[i].set_charge(q) + for idx, q in enumerate(charges): + structs_out[idx].set_charge(q) return structs_out @@ -70,7 +71,7 @@ def spawn_energy_curve_calcs( distorted_structure: Structure, distortions: Iterable[float], static_maker: StaticMaker, - prev_vasp_dir: str | Path | None = None, + prev_dir: str | Path | None = None, add_name: str = "", add_info: dict | None = None, ) -> Response: @@ -107,15 +108,15 @@ def spawn_energy_curve_calcs( distorted_structure, nimages=s_distortions ) # add all the distorted structures - for i, d_struct in enumerate(distorted_structures): - static_job = static_maker.make(d_struct, prev_vasp_dir=prev_vasp_dir) - suffix = f" {i}" if add_name == "" else f" {add_name} {i}" + for idx, d_struct in enumerate(distorted_structures): + static_job = static_maker.make(d_struct, prev_dir=prev_dir) + suffix = f" {idx}" if add_name == "" else f" {add_name} {idx}" # write some provenances data in info.json file info = { "relaxed_structure": relaxed_structure, "distorted_structure": distorted_structure, - "distortion": s_distortions[i], + "distortion": s_distortions[idx], } if add_info is not None: info.update(add_info) @@ -185,9 +186,9 @@ def get_ccd_documents( @job def get_supercell_from_prv_calc( uc_structure: Structure, - prv_calc_dir: str | Path | None = None, + prv_calc_dir: str | Path, + sc_entry_and_locpot_from_prv: Callable, sc_mat_ref: NDArray | None = None, - structure_from_prv: Callable | None = None, ) -> dict: """Get the supercell from the previous calculation. @@ -201,22 +202,25 @@ def get_supercell_from_prv_calc( The directory of the previous calculation. sc_mat : NDArray The supercell matrix. If not None, use this to validate the extracted supercell. - structure_from_prv : Callable - Function to get the supercell structure from the previous calculation. + sc_entry_and_locpot_from_prv : Callable + Function to get the supercell ComputedStructureEntry and Locpot from the + previous calculation. Returns ------- Response: Output containing the supercell transformation and the dir_name """ - sc_structure = structure_from_prv(prv_calc_dir) + prv_calc_dir = strip_hostname(prv_calc_dir) + sc_entry, plnr_locpot = sc_entry_and_locpot_from_prv(prv_calc_dir) + sc_structure = sc_entry.structure sc_mat_prv, _ = get_matched_structure_mapping( uc_struct=uc_structure, sc_struct=sc_structure ) if sc_mat_ref is not None: - latt_ref = Lattice(sc_mat_ref) - latt_prv = Lattice(sc_mat_prv) + latt_ref = (uc_structure * sc_mat_ref).lattice + latt_prv = (uc_structure * sc_mat_prv).lattice if not ( np.allclose(sorted(latt_ref.abc), sorted(latt_prv.abc)) and np.allclose(sorted(latt_ref.angles), sorted(latt_prv.angles)) @@ -225,7 +229,15 @@ def get_supercell_from_prv_calc( "The supercell matrix extracted from the previous calculation " "does not match the the desired supercell shape." ) - return {"sc_mat": sc_mat_prv, "lattice": Lattice(sc_structure.lattice.matrix)} + return { + "sc_entry": sc_entry, + "sc_struct": sc_structure, + "sc_mat": sc_mat_prv, + "dir_name": prv_calc_dir, + "lattice": Lattice(sc_structure.lattice.matrix), + "uuid": None, + "locpot_plnr": plnr_locpot, + } @job(name="bulk supercell") @@ -233,6 +245,7 @@ def bulk_supercell_calculation( uc_structure: Structure, relax_maker: RelaxMaker, sc_mat: NDArray | None = None, + get_planar_locpot: Callable | None = None, ) -> Response: """Bulk Supercell calculation. @@ -246,12 +259,19 @@ def bulk_supercell_calculation( The relax maker to use. sc_mat : NDArray | None The supercell matrix used to construct the simulation cell. + get_plnr_locpot : Callable | None + A function to get the Locpot from the output of the task document. Returns ------- Response: Output a dictionary containing the bulk supercell calculation summary. """ + if get_planar_locpot is None: + + def get_planar_locpot(task_doc: TaskDoc) -> NDArray: + return task_doc.calcs_reversed[0].output.locpot + logger.info("Running bulk supercell calculation. Running...") sc_mat = get_sc_fromstruct(uc_structure) if sc_mat is None else sc_mat sc_mat = np.array(sc_mat) @@ -270,7 +290,7 @@ def bulk_supercell_calculation( "sc_mat": sc_mat.tolist(), "dir_name": relax_output.dir_name, "uuid": relax_job.uuid, - "locpot_plnr": relax_output.calcs_reversed[0].output.locpot, + "locpot_plnr": get_planar_locpot(relax_output), } flow = Flow([relax_job], output=summary_d) return Response(replace=flow) @@ -309,7 +329,7 @@ def spawn_defect_q_jobs( By default only the defect object and charge state are stored. relaxed_sc_lattice: The lattice of the relaxed supercell. If provided, the lattice parameters - of the supercell will be set to value specified. Otherwise, the lattice it will + of the supercell will be set to value specified. Otherwise, the lattice it will only by set by `defect.structure` and `sc_mat`. validate_charge: Whether to validate the charge states of the defect after the atomic relaxation. @@ -409,11 +429,11 @@ def check_charge_state(charge_state: int, task_structure: Structure) -> Response @job def get_defect_entry(charge_state_summary: dict, bulk_summary: dict) -> list[dict]: """Get a defect entry from a defect calculation and a bulk calculation.""" - bulk_sc_entry = bulk_summary["sc_entry"] - bulk_struct_entry = ComputedStructureEntry( - structure=bulk_summary["sc_struct"], - energy=bulk_sc_entry.energy, - ) + bulk_struct_entry = bulk_summary["sc_entry"] + # bulk_struct_entry = ComputedStructureEntry( + # structure=bulk_summary["sc_struct"], + # energy=bulk_sc_entry.energy, + # ) bulk_dir_name = bulk_summary["dir_name"] bulk_locpot = bulk_summary["locpot_plnr"] defect_ent_res = [] @@ -438,7 +458,7 @@ def get_defect_entry(charge_state_summary: dict, bulk_summary: dict) -> list[dic "defect_locpot": defect_locpot, "bulk_dir_name": bulk_dir_name, "bulk_locpot": bulk_locpot, - "bulk_uuid": bulk_summary.get("uuid", None), + "bulk_uuid": bulk_summary.get("uuid"), "defect_uuid": qq_summary.get("uuid", None), } ) diff --git a/src/atomate2/common/jobs/elastic.py b/src/atomate2/common/jobs/elastic.py index 171968b344..253977f99a 100644 --- a/src/atomate2/common/jobs/elastic.py +++ b/src/atomate2/common/jobs/elastic.py @@ -128,7 +128,7 @@ def run_elastic_deformations( """ relaxations = [] outputs = [] - for i, deformation in enumerate(deformations): + for idx, deformation in enumerate(deformations): # deform the structure dst = DeformStructureTransformation(deformation=deformation) ts = TransformedStructure(structure, transformations=[dst]) @@ -146,7 +146,7 @@ def run_elastic_deformations( elastic_job_kwargs[prev_dir_argname] = prev_dir # create the job relax_job = elastic_relax_maker.make(deformed_structure, **elastic_job_kwargs) - relax_job.append_name(f" {i + 1}/{len(deformations)}") + relax_job.append_name(f" {idx + 1}/{len(deformations)}") relaxations.append(relax_job) # extract the outputs we want @@ -172,6 +172,7 @@ def fit_elastic_tensor( fitting_method: str = SETTINGS.ELASTIC_FITTING_METHOD, symprec: float = SETTINGS.SYMPREC, allow_elastically_unstable_structs: bool = True, + max_failed_deformations: float | None = None, ) -> ElasticDocument: """ Analyze stress/strain data to fit the elastic tensor and related properties. @@ -200,14 +201,21 @@ def fit_elastic_tensor( allow_elastically_unstable_structs : bool Whether to allow the ElasticDocument to still complete in the event that the structure is elastically unstable. + max_failed_deformations: int or float + Maximum number of deformations allowed to fail to proceed with the fitting + of the elastic tensor. If an int the absolute number of deformations. If + a float between 0 an 1 the maximum fraction of deformations. If None any + number of deformations allowed. """ stresses = [] deformations = [] uuids = [] job_dirs = [] + failed_uuids = [] for data in deformation_data: # stress could be none if the deformation calculation failed if data["stress"] is None: + failed_uuids.append(data["uuid"]) continue stresses.append(Stress(data["stress"])) @@ -215,6 +223,20 @@ def fit_elastic_tensor( uuids.append(data["uuid"]) job_dirs.append(data["job_dir"]) + if max_failed_deformations is not None: + if 0 < max_failed_deformations < 1: + fraction_failed = len(failed_uuids) / len(deformation_data) + if fraction_failed > max_failed_deformations: + raise RuntimeError( + f"{fraction_failed} fraction of deformation calculations have " + f"failed, maximum fraction allowed: {max_failed_deformations}" + ) + elif len(failed_uuids) > max_failed_deformations: + raise RuntimeError( + f"{len(failed_uuids)} deformation calculations have failed, maximum " + f"allowed: {max_failed_deformations}" + ) + logger.info("Analyzing stress/strain data") return ElasticDocument.from_stresses( @@ -228,4 +250,5 @@ def fit_elastic_tensor( equilibrium_stress=equilibrium_stress, symprec=symprec, allow_elastically_unstable_structs=allow_elastically_unstable_structs, + failed_uuids=failed_uuids, ) diff --git a/src/atomate2/common/jobs/electrode.py b/src/atomate2/common/jobs/electrode.py new file mode 100644 index 0000000000..1d3786c077 --- /dev/null +++ b/src/atomate2/common/jobs/electrode.py @@ -0,0 +1,305 @@ +"""Jobs for electrode analysis.""" + +from __future__ import annotations + +import logging +from typing import TYPE_CHECKING, Callable, NamedTuple + +from emmet.core.electrode import InsertionElectrodeDoc +from emmet.core.structure_group import StructureGroupDoc +from jobflow import Flow, Maker, Response, job +from pymatgen.analysis.defects.generators import ChargeInterstitialGenerator +from pymatgen.entries.computed_entries import ComputedStructureEntry + +if TYPE_CHECKING: + from pathlib import Path + + from pymatgen.alchemy import ElementLike + from pymatgen.analysis.structure_matcher import StructureMatcher + from pymatgen.core import Structure + from pymatgen.entries.computed_entries import ComputedEntry + from pymatgen.io.vasp.outputs import VolumetricData + + +logger = logging.getLogger(__name__) + +__author__ = "Jimmy Shen" +__email__ = "jmmshn@gmail.com" + + +class RelaxJobSummary(NamedTuple): + """A summary of a relaxation job.""" + + structure: Structure + entry: ComputedEntry + dir_name: str + uuid: str + + +@job +def get_stable_inserted_results( + structure: Structure, + inserted_element: ElementLike, + structure_matcher: StructureMatcher, + static_maker: Maker, + relax_maker: Maker, + get_charge_density: Callable, + insertions_per_step: int = 4, + n_steps: int | None = None, + n_inserted: int = 0, +) -> Response: + """Attempt ion insertion. + + The basic unit for cation insertion is: + [get_stable_inserted_structure]: + (static) -> N x (chgcar analysis -> relax) -> (return best structure) + + Parameters + ---------- + structure: + The structure to insert into. + inserted_species: + The species to insert. + structure_matcher: + The structure matcher to use to determine if additional + insertion is needed. + static_maker: + A maker to perform static calculations. + relax_maker: + A maker to perform relaxation calculations. + get_charge_density: + A function to get the charge density from a previous calculation. + Whether to use the AECCAR0 and AECCAR2 files for the charge density. + This is often necessary since the CHGCAR file has spurious effects near the + core which often breaks the min-filter algorithms used to identify the local + minima. + insertions_per_step: + The maximum number of ion insertion sites to attempt. + n_steps: + The maximum number of steps to perform. + n_inserted: + The number of ions inserted so far, used to help assign a unique name to the + different jobs. + """ + if structure is None: + return [] + if n_steps is not None and n_steps <= 0: + return [] + # append job name + add_name = f"{n_inserted}" + + static_job = static_maker.make(structure=structure) + chg_job = get_charge_density_job(static_job.output.dir_name, get_charge_density) + insertion_job = get_inserted_structures( + chg_job.output, + inserted_species=inserted_element, + insertions_per_step=insertions_per_step, + ) + relax_jobs = get_relaxed_job_summaries( + structures=insertion_job.output, relax_maker=relax_maker, append_name=add_name + ) + + min_en_job = get_min_energy_summary( + relaxed_summaries=relax_jobs.output, + ref_structure=structure, + structure_matcher=structure_matcher, + ) + nn_step = n_steps - 1 if n_steps is not None else None + next_step = get_stable_inserted_results( + structure=min_en_job.output[0], + inserted_element=inserted_element, + structure_matcher=structure_matcher, + static_maker=static_maker, + relax_maker=relax_maker, + get_charge_density=get_charge_density, + insertions_per_step=insertions_per_step, + n_steps=nn_step, + n_inserted=n_inserted + 1, + ) + + for job_ in [static_job, chg_job, insertion_job, min_en_job, relax_jobs, next_step]: + job_.append_name(f" {add_name}") + combine_job = get_computed_entries(next_step.output, min_en_job.output) + replace_flow = Flow( + jobs=[ + static_job, + chg_job, + insertion_job, + relax_jobs, + min_en_job, + next_step, + combine_job, + ], + output=combine_job.output, + ) + return Response(replace=replace_flow) + + +@job +def get_computed_entries( + multi: list[ComputedEntry], single: RelaxJobSummary | None +) -> list[ComputedEntry]: + """Add a single new entry to a list of entries. + + Parameters + ---------- + multi: The list of entries. + single: Possible tuple containing the new entry + + Returns + ------- + The list of entries with the new entry added. + """ + if single is None: + return multi + # keep the [1] for now, if jobflow supports NamedTuple, we can do this much cleaner + s_ = RelaxJobSummary._make(single) + s_.entry.entry_id = s_.uuid + ent = ComputedStructureEntry( + structure=s_.structure, + energy=s_.entry.energy, + parameters=s_.entry.parameters, + data=s_.entry.data, + entry_id=s_.uuid, + ) + return [*multi, ent] + + +@job(output_schema=StructureGroupDoc) +def get_structure_group_doc( + computed_entries: list[ComputedEntry], ignored_species: str +) -> Response: + """Take in `ComputedEntry` and return a `StructureGroupDoc`.""" + for ient in computed_entries: + ient.data["material_id"] = ient.entry_id + return StructureGroupDoc.from_grouped_entries( + computed_entries, ignored_specie=ignored_species + ) + + +@job(output_schema=InsertionElectrodeDoc) +def get_insertion_electrode_doc( + computed_entries: ComputedEntry, working_ion_entry: ComputedEntry +) -> Response: + """Return a `InsertionElectrodeDoc`.""" + for ient in computed_entries: + ient.data["material_id"] = ient.entry_id + return InsertionElectrodeDoc.from_entries( + computed_entries, working_ion_entry, battery_id=None + ) + + +@job +def get_inserted_structures( + chg: VolumetricData, + inserted_species: ElementLike, + insertions_per_step: int = 4, + charge_insertion_generator: ChargeInterstitialGenerator | None = None, +) -> list[Structure]: + """Get the inserted structures. + + Parameters + ---------- + chg: The charge density. + inserted_species: The species to insert. + insertions_per_step: The maximum number of ion insertion sites to attempt. + charge_insertion_generator: The charge insertion generator to use, + tolerances should be set here. + + + Returns + ------- + The inserted structures. + """ + if charge_insertion_generator is None: + charge_insertion_generator = ChargeInterstitialGenerator() + gen = charge_insertion_generator.generate(chg, insert_species=[inserted_species]) + inserted_structures = [defect.defect_structure for defect in gen] + return inserted_structures[:insertions_per_step] + + +@job +def get_relaxed_job_summaries( + structures: list[Structure], + relax_maker: Maker, + append_name: str = "", +) -> Response: + """Spawn relaxation jobs. + + Parameters + ---------- + structures: The structures to relax. + relax_maker: The maker to use to spawn relaxation jobs. + + Returns + ------- + The relaxation jobs. + """ + relax_jobs = [] + outputs = [] + for ii, structure in enumerate(structures): + job_ = relax_maker.make(structure=structure) + relax_jobs.append(job_) + job_.append_name(f" {append_name} ({ii})") + d_ = { + "structure": job_.output.structure, + "entry": job_.output.entry, + "dir_name": job_.output.dir_name, + "uuid": job_.output.uuid, + } + outputs.append(RelaxJobSummary(**d_)) + + replace_flow = Flow(relax_jobs, output=outputs) + return Response(replace=replace_flow, output=outputs) + + +@job +def get_min_energy_summary( + relaxed_summaries: list[RelaxJobSummary], + ref_structure: Structure, + structure_matcher: StructureMatcher, +) -> Response: + """Get the structure with the lowest energy. + + Parameters + ---------- + structures: The structures to compare. + ref_structure: The reference structure to compare to. + structure_matcher: The structure matcher to use to compare structures. + + Returns + ------- + The structure with the lowest energy. + """ + # Since the outputs parser will see a NamedTuple and immediately convert it to + # a list We have to convert the list of lists to a list of NamedTuples + relaxed_summaries = list(map(RelaxJobSummary._make, relaxed_summaries)) + topotactic_summaries = [ + summary + for summary in relaxed_summaries + if structure_matcher.fit(ref_structure, summary.structure) + ] + + if len(topotactic_summaries) == 0: + return None + + return min(topotactic_summaries, key=lambda x: x.entry.energy_per_atom) + + +@job +def get_charge_density_job( + prev_dir: Path | str, + get_charge_density: Callable, +) -> VolumetricData: + """Get the charge density from a task document. + + Parameters + ---------- + prev_dir: The previous directory where the static calculation was performed. + get_charge_density: A function to get the charge density from a task document. + + Returns + ------- + The charge density. + """ + return get_charge_density(prev_dir) diff --git a/src/atomate2/common/jobs/eos.py b/src/atomate2/common/jobs/eos.py new file mode 100644 index 0000000000..7c5886cbc6 --- /dev/null +++ b/src/atomate2/common/jobs/eos.py @@ -0,0 +1,359 @@ +"""Define common jobs used in EOS workflows, electronic-structure code agnostic.""" + +from __future__ import annotations + +from typing import TYPE_CHECKING + +import numpy as np +from jobflow import job +from monty.json import MSONable +from pymatgen.alchemy.materials import TransformedStructure +from pymatgen.analysis.eos import EOS, EOSError +from pymatgen.transformations.standard_transformations import ( + DeformStructureTransformation, +) +from scipy.optimize import leastsq + +if TYPE_CHECKING: + from collections.abc import Sequence + from typing import Any + + from jobflow import Job + from pymatgen.core import Structure + + +class EOSPostProcessor(MSONable): + """ + Fit data to an EOS. + + name : str + Name of the class + eos_attrs : tuple[str,...] + Physical quantities that can enter the EOS fit + job_types : tuple[str,...] + Types of jobs included in the EOS data + min_data_points : int or None + Minimum number of data points needed to perform a fit. + """ + + name: str = "EOS postprocessor" + eos_attrs: tuple[str, ...] = ("energy", "volume", "stress", "pressure") + job_types: tuple[str, ...] = ("relax", "static") + min_data_points: int | None = None + + def __init__(self) -> None: + self.results: dict[str, dict] = {} + + def sort_by_quantity(self, quantity: str = "volume") -> None: + """ + Sort input data by given kwarg. + + Parameters + ---------- + quantity : str = "volume" + kwarg to sort by + """ + for job_type in self._use_job_types: + sort_by_vol = np.argsort(self.results[job_type][quantity]) + for key in self.eos_attrs: + if self.results[job_type].get(key): + self.results[job_type][key] = [ + self.results[job_type][key][index] for index in sort_by_vol + ] + + def eval(self) -> None: + """Fit the EOS according to a user-implemented function.""" + raise NotImplementedError + + def fit(self, eos_flow_output: dict[str, Any]) -> None: + """ + Fit the EOS. + + Parameters + ---------- + eos_flow_output : dict + Volume, energy, and (optionally) stress and pressure data in dict form, + { + "relax" and "static" : { + "energy": list, + "volume": list, + "stress": list + }, + "initial_": {"E0": float, "V0": float} , + for in ("relax", "static") + } + """ + self.results.update(eos_flow_output) + self._use_job_types = [key for key in self.job_types if self.results.get(key)] + if self.min_data_points and any( + len(self.results[job_type].get("volume", [])) < self.min_data_points + for job_type in self._use_job_types + ): + raise ValueError( + f"{type(self)} requires {self.min_data_points} frames to fit an EOS." + ) + + self.sort_by_quantity() + self.eval() + + @job + def make(self, eos_flow_output: dict[str, Any]) -> Job: + """Run the fit as a jobflow job. + + Parameters + ---------- + eos_flow_output : dict + Volume, energy, and (optionally) stress and pressure data in dict form, + { + "relax" and "static" : { + "energy": list, + "volume": list, + "stress": list + }, + "initial_": {"E0": float, "V0": float} , + for in ("relax", "static") + } + """ + self.fit(eos_flow_output) + return self.results + + +class PostProcessEosEnergy(EOSPostProcessor): + """ + Fit energy vs. volume data to an EOS. + + Parameters + ---------- + eos_flow_output : dict + Volume, energy, and (optionally) stress and pressure data in dict form, + { + "relax" and "static" : { + "energy": list, + "volume": list, + "stress": list + }, + "initial_": {"E0": float, "V0": float} , + for in ("relax", "static") + } + name : str + Name of the class + eos_attrs : tuple[str,...] + Physical quantities that can enter the EOS fit + job_types : tuple[str,...] + Types of jobs included in the EOS data + min_data_points : int or None + Minimum number of data points needed to perform a fit. + eos_models : tuple[str,...] + List of names of EOSes to fit to. + """ + + name: str = "EOS energy vs volume fit" + min_data_points: int | None = 4 + eos_models: tuple[str, ...] = ( + "murnaghan", + "birch", + "birch_murnaghan", + "pourier_tarantola", + "vinet", + ) + + def eval(self) -> None: + """Fit the input data to each EOS in `self.eos_models.""" + for jobtype in self._use_job_types: + self.results[jobtype]["EOS"] = {} + for eos_name in self.eos_models: + try: + eos = EOS(eos_name=eos_name).fit( + self.results[jobtype]["volume"], self.results[jobtype]["energy"] + ) + self.results[jobtype]["EOS"][eos_name] = { + **eos.results, + "b0 GPa": float(eos.b0_GPa), + } + except EOSError as exc: + self.results[jobtype]["EOS"][eos_name] = {"exception": str(exc)} + + +class PostProcessEosPressure(EOSPostProcessor): + """ + Fit pressure vs. volume data to an EOS. + + Parameters + ---------- + eos_flow_output : dict + Volume, energy, and (optionally) stress and pressure data in dict form, + { + "relax" and "static" : { + "energy": list, + "volume": list, + "stress": list + }, + "initial_": {"E0": float, "V0": float} , + for in ("relax", "static") + } + name : str + Name of the class + eos_attrs : tuple[str,...] + Physical quantities that can enter the EOS fit + job_types : tuple[str,...] + Types of jobs included in the EOS data + min_data_points : int or None + Minimum number of data points needed to perform a fit. + + If only stresses are specified, it is assumed that the elements of "stress" + are 3 x 3 tensors, and the pressure is computed as + pressure = Trace(stress tensor)/3 + The overall sign is irrelevant for a successful fit, as the overall sign + of the pressure indicates internal/external stress. + """ + + name: str = "EOS pressure vs volume fit" + min_data_points: int | None = 3 + + @staticmethod + def _birch_murnaghan_pressure( + volume: float, b0: float, b1: float, v0: float + ) -> float: + """ + Compute pressure from Birch-Murnaghan equation of state. + + Parameters + ---------- + volume : float + A single volume or list of them to evaluate the pressure. + b0 : float + The Birch-Murnaghan (BM) bulk modulus at the equilibrium volume V = v0 + b1 : float + The derivative of the bulk modulus wrt pressure at v0 + v0 : float + The equilibrium volume + + Returns + ------- + float : the BM pressure + + BM EOS for E(V) has the form + E(V) = E0 + 9 B0 V0 / 16 * ( + (B1 - 4)*eta**6 + (14 - 3*B1)*eta**4 + (3*B1 - 16)*eta**2 + 6 - B1 + ) + eta = (V0/V)**(1/3). + This function computes p = - dE / dV via the chain rule, + p = d E / d eta * (- d eta / dV) + = eta**4/(3*V0) * d E / d eta + """ + eta = (v0 / volume) ** (1.0 / 3.0) + return ( + 3 + * b0 + * eta**5 + / 8.0 + * (3 * (b1 - 4) * eta**4 + 2 * (14.0 - 3 * b1) * eta**2 + 3 * b1 - 16.0) + ) + + def _initial_fit(self) -> dict: + """Generate initial polynomial fit for p(V) curve. + + p(V) / V = a + b V + c V**2 + """ + init_pars = {} + for jobtype in self._use_job_types: + if self.results[jobtype].get("stress") and ( + not self.results[jobtype].get("pressure") + ): + self.results[jobtype]["pressure"] = [ + 1.0 / 3.0 * np.trace(np.array(stress_tensor)) + for stress_tensor in self.results[jobtype]["stress"] + ] + poly_pars = np.polyfit( + self.results[jobtype]["volume"], + np.array(self.results[jobtype]["pressure"]) + / np.array(self.results[jobtype]["volume"]), + deg=2, + ) + + radicand = poly_pars[1] ** 2 - 4.0 * poly_pars[0] * poly_pars[2] + if radicand < 0.0: + v0 = self.results[jobtype]["volume"][ + np.argmin(self.results[jobtype]["energy"]) + ] + else: + min_abs_pressure = 1e20 + for i in range(2): + _v0 = (-poly_pars[1] + (-1) ** i * radicand ** (0.5)) / ( + 2.0 * poly_pars[0] + ) + pressure = _v0 * np.polyval(poly_pars, _v0) + if _v0 > 0.0 and abs(pressure) < min_abs_pressure: + min_abs_pressure = abs(pressure) + v0 = _v0 + + b0 = -( + 3 * poly_pars[0] * v0**3 + 2 * poly_pars[1] * v0**2 + poly_pars[0] * v0 + ) + b1 = ( + v0 + * (9 * poly_pars[0] * v0**2 + 4 * poly_pars[1] * v0 + poly_pars[0]) + / b0 + ) + + init_pars[jobtype] = [b0, b1, v0] + + return init_pars + + def _objective(self, pars: Sequence, jobtype: str) -> float: + return np.array( + self.results[jobtype]["pressure"] + ) - self._birch_murnaghan_pressure( + np.array(self.results[jobtype]["volume"]), *pars + ) + + def eval(self) -> None: + """Fit the input data to the Birch-Murnaghan pressure EOS.""" + initial_pars = self._initial_fit() + for jobtype in self._use_job_types: + eos_params, ierr = leastsq( + self._objective, initial_pars[jobtype], args=(jobtype,) + ) + + self.results[jobtype]["EOS"] = {} + if ierr not in (1, 2, 3, 4): + self.results[jobtype]["EOS"]["exception"] = ( + "Optimal EOS parameters not found." + ) + else: + for i, key in enumerate(["b0", "b1", "v0"]): + self.results[jobtype]["EOS"][key] = eos_params[i] + + +@job +def apply_strain_to_structure(structure: Structure, deformations: list) -> list: + """ + Apply strain(s) to input structure and return transformation(s) as list. + + Parameters + ---------- + structure: .Structure + Input structure to apply strain to + deformations: list[.Deformation] + A list of deformations to apply **independently** to the input + structure, in anticipation of performing an EOS fit. + Deformations should be of the form of a 3x3 matrix, e.g., + [[1.2, 0., 0.], [0., 1.2, 0.], [0., 0., 1.2]] + or + ((1.2, 0., 0.), (0., 1.2, 0.), (0., 0., 1.2)) + + Returns + ------- + list + A list of .TransformedStructure objects corresponding to the + list of input deformations. + """ + transformations = [] + for deformation in deformations: + # deform the structure + ts = TransformedStructure( + structure, + transformations=[DeformStructureTransformation(deformation=deformation)], + ) + transformations += [ts] + return transformations diff --git a/src/atomate2/common/jobs/magnetism.py b/src/atomate2/common/jobs/magnetism.py new file mode 100644 index 0000000000..6243c35270 --- /dev/null +++ b/src/atomate2/common/jobs/magnetism.py @@ -0,0 +1,177 @@ +"""Jobs used for enumeration/calculation of collinear magnetic orderings.""" + +from __future__ import annotations + +import logging +from typing import TYPE_CHECKING, Literal + +from jobflow import Flow, Maker, Response, job +from pymatgen.analysis.magnetism.analyzer import MagneticStructureEnumerator + +from atomate2.common.schemas.magnetism import MagneticOrderingsDocument + +if TYPE_CHECKING: + from collections.abc import Sequence + + from emmet.core.tasks import TaskDoc + from pymatgen.core.structure import Structure + + +logger = logging.getLogger(__name__) + + +@job(name="enumerate orderings") +def enumerate_magnetic_orderings( + structure: Structure, + default_magmoms: dict[str, float] | None = None, + strategies: Sequence[ + Literal[ + "ferromagnetic", + "antiferromagnetic", + "antiferromagnetic_by_motif", + "ferrimagnetic_by_motif", + "ferrimagnetic_by_species", + "nonmagnetic", + ] + ] = ("ferromagnetic", "antiferromagnetic"), + automatic: bool = True, + truncate_by_symmetry: bool = True, + transformation_kwargs: dict | None = None, +) -> tuple[list[Structure], list[str]]: + """Enumerate possible collinear magnetic orderings for a given structure. + + This method is a wrapper around pymatgen's `MagneticStructureEnumerator`. Please see + the corresponding documentation in pymatgen for more detailed descriptions. + + Parameters + ---------- + structure : Structure + Input structure + default_magmoms : dict[str, float] + Optional default mapping of magnetic elements to their initial magnetic moments + in ฮผB. Generally these are chosen to be high-spin, since they can relax to a + low-spin configuration during a DFT electronic configuration. If None, will use + the default values provided in pymatgen/analysis/magnetism/default_magmoms.yaml. + strategies : Sequence[Literal["ferromagnetic", "antiferromagnetic", ...]] + Different ordering strategies to use, choose from: ferromagnetic, + antiferromagnetic, antiferromagnetic_by_motif, ferrimagnetic_by_motif and + ferrimagnetic_by_species (here, "motif", means to use a different ordering + parameter for symmetry inequivalent sites). Defaults to + ("ferromagnetic", "antiferromagnetic"). + automatic : bool + If True, will automatically choose sensible strategies + truncate_by_symmetry: : bool + If True, will remove very unsymmetrical orderings that are likely physically + implausible + transformation_kwargs : dict + Keyword arguments to pass to MagOrderingTransformation, to change automatic cell + size limits, etc. + + Returns + ------- + Ordered structures, origins (e.g., "fm", "afm") + """ + enumerator = MagneticStructureEnumerator( + structure, + default_magmoms=default_magmoms, + strategies=strategies, + automatic=automatic, + truncate_by_symmetry=truncate_by_symmetry, + transformation_kwargs=transformation_kwargs, + ) + + return enumerator.ordered_structures, enumerator.ordered_structure_origins + + +@job(name="run orderings") +def run_ordering_calculations( + orderings: tuple[Sequence[Structure], Sequence[str]], + static_maker: Maker, + relax_maker: Maker | None, +) -> Response: + """Run calculations for a list of enumerated orderings. + + This job will automatically replace itself with calculations. + + Parameters + ---------- + orderings : tuple[Sequence[Structure], Sequence[str]] + A tuple containing a sequence of ordered structures and another sequence of + strings indicating the origin of each structure (e.g., "fm", "afm"). + static_maker : .Maker + A Maker to use to generate jobs for calculating the energies of the orderings. + This is required. + relax_maker : .Maker | None + An optional Maker to use to generate jobs for relaxing the structures (before + static calculations). + + Returns + ------- + Replaces the job with a Flow that will run all calculations. + """ + jobs = [] + num_orderings = len(orderings[0]) + for idx, (struct, origin) in enumerate(zip(*orderings)): + name = f"{idx + 1}/{num_orderings} ({origin})" + + parent_structure = struct.copy() + parent_structure.remove_spin() + metadata = {"parent_structure": parent_structure, "ordering": origin} + + parent_uuid = None + static_job_kwargs = {} # previous calc dir only + if relax_maker is not None: + relax_job = relax_maker.make(struct) + relax_job.append_name(" " + name) + relax_job.metadata.update(metadata) # type: ignore[union-attr] + jobs.append(relax_job) + + structure = relax_job.output.structure + parent_uuid = relax_job.output.uuid + static_job_kwargs["prev_dir"] = relax_job.output.dir_name + + static_job = static_maker.make(structure, **static_job_kwargs) + static_job.append_name(" " + name) + + metadata["parent_uuid"] = parent_uuid + static_job.metadata.update(metadata) # type: ignore[union-attr] + + jobs.append(static_job) + + flow = Flow( + jobs, + output=[(j.output, j.metadata, j.uuid) for j in jobs], # type: ignore[union-attr] + ) + return Response(replace=flow) + + +@job(name="postprocess orderings") +def postprocess_orderings( + tasks_metadata_uuids: list[tuple[TaskDoc, dict, str]], +) -> MagneticOrderingsDocument: + """Identify ground state ordering and build summary document. + + This job performs the same analysis as that performed by the + MagneticOrderingsBuilder. It is provided here for convenience and runs automatically + at the conclusion of a successful MagneticOrderingsFlow. + + Parameters + ---------- + tasks_metadata_uuids : list[tuple[TaskDoc, dict, str]] + A list of tuples containing the output task document, metadata, and uuid for + each job. This format is used to construct a dict that mimics how job data is + stored and provided to the builder input. + build_doc_fn : Callable[[list[dict]], MagneticOrderingsDocument] + A function to build the summary document from a list of dicts. + + Returns + ------- + MagneticOrderingsDocument + A summary document containing the ground state ordering and other information. + """ + tasks = [ + {"output": output, "metadata": metadata, "uuid": uuid} # mimic builder input + for output, metadata, uuid in tasks_metadata_uuids + ] + + return MagneticOrderingsDocument.from_tasks(tasks) diff --git a/src/atomate2/common/jobs/phonons.py b/src/atomate2/common/jobs/phonons.py index e788917c1b..8a0c927e80 100644 --- a/src/atomate2/common/jobs/phonons.py +++ b/src/atomate2/common/jobs/phonons.py @@ -4,12 +4,12 @@ import contextlib import logging -from dataclasses import dataclass, field +import warnings from typing import TYPE_CHECKING +import numpy as np from jobflow import Flow, Response, job from phonopy import Phonopy -from phonopy.units import VaspToTHz from pymatgen.core import Structure from pymatgen.io.phonopy import get_phonopy_structure, get_pmg_structure from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine @@ -18,18 +18,17 @@ CubicSupercellTransformation, ) -from atomate2.common.schemas.phonons import ForceConstants, PhononBSDOSDoc -from atomate2.vasp.jobs.base import BaseVaspMaker -from atomate2.vasp.sets.core import StaticSetGenerator +from atomate2.common.schemas.phonons import ForceConstants, PhononBSDOSDoc, get_factor if TYPE_CHECKING: from pathlib import Path - import numpy as np from emmet.core.math import Matrix3D + from atomate2.aims.jobs.base import BaseAimsMaker from atomate2.forcefields.jobs import ForceFieldStaticMaker - from atomate2.vasp.sets.base import VaspInputGenerator + from atomate2.vasp.jobs.base import BaseVaspMaker + logger = logging.getLogger(__name__) @@ -39,7 +38,7 @@ def get_total_energy_per_cell( total_dft_energy_per_formula_unit: float, structure: Structure ) -> float: """ - Job that computes total dft energy of the cell. + Job that computes total DFT energy of the cell. Parameters ---------- @@ -74,47 +73,36 @@ def get_supercell_size( **kwargs: Additional parameters that can be set. """ - kwargs.setdefault("min_atoms", None) kwargs.setdefault("force_diagonal", False) + common_kwds = dict( + min_length=min_length, + min_atoms=kwargs.get("min_atoms"), + force_diagonal=kwargs["force_diagonal"], + ) if not prefer_90_degrees: - kwargs.setdefault("max_atoms", None) transformation = CubicSupercellTransformation( - min_length=min_length, - min_atoms=kwargs["min_atoms"], - max_atoms=kwargs["max_atoms"], - force_diagonal=kwargs["force_diagonal"], - force_90_degrees=False, + **common_kwds, max_atoms=kwargs.get("max_atoms"), force_90_degrees=False ) transformation.apply_transformation(structure=structure) - else: - max_atoms = kwargs.get("max_atoms", 1000) - kwargs.setdefault("angle_tolerance", 1e-2) try: transformation = CubicSupercellTransformation( - min_length=min_length, - min_atoms=kwargs["min_atoms"], - max_atoms=max_atoms, - force_diagonal=kwargs["force_diagonal"], + **common_kwds, + max_atoms=kwargs.get("max_atoms", 1200), force_90_degrees=True, - angle_tolerance=kwargs["angle_tolerance"], + angle_tolerance=kwargs.get("angle_tolerance", 1e-2), ) transformation.apply_transformation(structure=structure) except AttributeError: - kwargs.setdefault("max_atoms", None) - transformation = CubicSupercellTransformation( - min_length=min_length, - min_atoms=kwargs["min_atoms"], - max_atoms=kwargs["max_atoms"], - force_diagonal=kwargs["force_diagonal"], - force_90_degrees=False, + **common_kwds, max_atoms=kwargs.get("max_atoms"), force_90_degrees=False ) transformation.apply_transformation(structure=structure) - return transformation.transformation_matrix.tolist() + # matrix from pymatgen has to be transposed + return transformation.transformation_matrix.transpose().tolist() @job(data=[Structure]) @@ -150,19 +138,34 @@ def generate_phonon_displacements( code: code to perform the computations """ - cell = get_phonopy_structure(structure) - if code == "vasp": - factor = VaspToTHz + warnings.warn( + "Initial magnetic moments will not be considered for the determination " + "of the symmetry of the structure and thus will be removed now.", + stacklevel=1, + ) + cell = get_phonopy_structure( + structure.remove_site_property(property_name="magmom") + if "magmom" in structure.site_properties + else structure + ) + factor = get_factor(code) + # a bit of code repetition here as I currently # do not see how to pass the phonopy object? if use_symmetrized_structure == "primitive" and kpath_scheme != "seekpath": - primitive_matrix: list[list[float]] | str = [ - [1.0, 0.0, 0.0], - [0.0, 1.0, 0.0], - [0.0, 0.0, 1.0], - ] + primitive_matrix: np.ndarray | str = np.eye(3) else: primitive_matrix = "auto" + + # TARP: THIS IS BAD! Including for discussions sake + if cell.magnetic_moments is not None and primitive_matrix == "auto": + if np.any(cell.magnetic_moments != 0.0): + raise ValueError( + "For materials with magnetic moments, " + "use_symmetrized_structure must be 'primitive'" + ) + cell.magnetic_moments = None + phonon = Phonopy( cell, supercell_matrix, @@ -221,7 +224,7 @@ def generate_frequencies_eigenvectors( displacement_data: dict outputs from displacements total_dft_energy: float - total dft energy in eV per cell + total DFT energy in eV per cell epsilon_static: Matrix3D The high-frequency dielectric constant born: Matrix3D @@ -230,7 +233,9 @@ def generate_frequencies_eigenvectors( Additional parameters that are passed to PhononBSDOSDoc.from_forces_born """ return PhononBSDOSDoc.from_forces_born( - structure=structure, + structure=structure.remove_site_property(property_name="magmom") + if "magmom" in structure.site_properties + else structure, supercell_matrix=supercell_matrix, displacement=displacement, sym_reduce=sym_reduce, @@ -248,31 +253,37 @@ def generate_frequencies_eigenvectors( @job(data=["forces", "displaced_structures"]) def run_phonon_displacements( - displacements, + displacements: list[Structure], structure: Structure, - supercell_matrix, - phonon_maker: BaseVaspMaker | ForceFieldStaticMaker = None, - prev_vasp_dir: str | Path = None, + supercell_matrix: Matrix3D, + phonon_maker: BaseVaspMaker | ForceFieldStaticMaker | BaseAimsMaker = None, + prev_dir: str | Path = None, + prev_dir_argname: str = None, + socket: bool = False, ) -> Flow: """ Run phonon displacements. - Note, this job will replace itself with N displacement calculations. + Note, this job will replace itself with N displacement calculations, + or a single socket calculation for all displacements. Parameters ---------- - displacements + displacements: Sequence + All displacements to calculate structure: Structure object Fully optimized structure used for phonon computations. supercell_matrix: Matrix3D supercell matrix for meta data - phonon_maker : .BaseVaspMaker - A VaspMaker to use to generate the elastic relaxation jobs. - prev_vasp_dir : str or Path or None - A previous vasp calculation directory to use for copying outputs. + phonon_maker : .BaseVaspMaker or .ForceFieldStaticMaker or .BaseAimsMaker + A maker to use to generate dispacement calculations + prev_dir: str or Path + The previous working directory + prev_dir_argname: str + argument name for the prev_dir variable + socket: bool + If True use the socket-io interface to increase performance """ - if phonon_maker is None: - phonon_maker = PhononDisplacementMaker() phonon_jobs = [] outputs: dict[str, list] = { "displacement_number": [], @@ -280,85 +291,50 @@ def run_phonon_displacements( "uuids": [], "dirs": [], } + phonon_job_kwargs = {} + if prev_dir is not None and prev_dir_argname is not None: + phonon_job_kwargs[prev_dir_argname] = prev_dir - for i, displacement in enumerate(displacements): - if prev_vasp_dir is not None: - phonon_job = phonon_maker.make(displacement, prev_vasp_dir=prev_vasp_dir) - else: - phonon_job = phonon_maker.make(displacement) - phonon_job.append_name(f" {i + 1}/{len(displacements)}") - - # we will add some meta data + if socket: + phonon_job = phonon_maker.make(displacements, **phonon_job_kwargs) info = { - "displacement_number": i, "original_structure": structure, "supercell_matrix": supercell_matrix, - "displaced_structure": displacement, + "displaced_structures": displacements, } - with contextlib.suppress(Exception): - phonon_job.update_maker_kwargs( - {"_set": {"write_additional_data->phonon_info:json": info}}, - dict_mod=True, - ) - + phonon_job.update_maker_kwargs( + {"_set": {"write_additional_data->phonon_info:json": info}}, dict_mod=True + ) phonon_jobs.append(phonon_job) - outputs["displacement_number"].append(i) - outputs["uuids"].append(phonon_job.output.uuid) - outputs["dirs"].append(phonon_job.output.dir_name) - outputs["forces"].append(phonon_job.output.output.forces) + outputs["displacement_number"] = list(range(len(displacements))) + outputs["uuids"] = [phonon_job.output.uuid] * len(displacements) + outputs["dirs"] = [phonon_job.output.dir_name] * len(displacements) + outputs["forces"] = phonon_job.output.output.all_forces + else: + for idx, displacement in enumerate(displacements): + if prev_dir is not None: + phonon_job = phonon_maker.make(displacement, prev_dir=prev_dir) + else: + phonon_job = phonon_maker.make(displacement) + phonon_job.append_name(f" {idx + 1}/{len(displacements)}") + + # we will add some meta data + info = { + "displacement_number": idx, + "original_structure": structure, + "supercell_matrix": supercell_matrix, + "displaced_structure": displacement, + } + with contextlib.suppress(Exception): + phonon_job.update_maker_kwargs( + {"_set": {"write_additional_data->phonon_info:json": info}}, + dict_mod=True, + ) + phonon_jobs.append(phonon_job) + outputs["displacement_number"].append(idx) + outputs["uuids"].append(phonon_job.output.uuid) + outputs["dirs"].append(phonon_job.output.dir_name) + outputs["forces"].append(phonon_job.output.output.forces) displacement_flow = Flow(phonon_jobs, outputs) return Response(replace=displacement_flow) - - -@dataclass -class PhononDisplacementMaker(BaseVaspMaker): - """ - Maker to perform a static calculation as a part of the finite displacement method. - - The input set is for a static run with tighter convergence parameters. - Both the k-point mesh density and convergence parameters - are stricter than a normal relaxation. - - Parameters - ---------- - name : str - The job name. - input_set_generator : .VaspInputGenerator - A generator used to make the input set. - write_input_set_kwargs : dict - Keyword arguments that will get passed to :obj:`.write_vasp_input_set`. - copy_vasp_kwargs : dict - Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`. - run_vasp_kwargs : dict - Keyword arguments that will get passed to :obj:`.run_vasp`. - task_document_kwargs : dict - Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. - stop_children_kwargs : dict - Keyword arguments that will get passed to :obj:`.should_stop_children`. - write_additional_data : dict - Additional data to write to the current directory. Given as a dict of - {filename: data}. Note that if using FireWorks, dictionary keys cannot contain - the "." character which is typically used to denote file extensions. To avoid - this, use the ":" character, which will automatically be converted to ".". E.g. - ``{"my_file:txt": "contents of the file"}``. - """ - - name: str = "phonon static" - input_set_generator: VaspInputGenerator = field( - default_factory=lambda: StaticSetGenerator( - user_kpoints_settings={"reciprocal_density": 100}, - user_incar_settings={ - "IBRION": 2, - "ISIF": 3, - "ENCUT": 700, - "EDIFF": 1e-7, - "LAECHG": False, - "LREAL": False, - "ALGO": "Normal", - "NSW": 0, - "LCHARG": False, - }, - auto_ispin=True, - ) - ) diff --git a/src/atomate2/common/jobs/utils.py b/src/atomate2/common/jobs/utils.py index dffcec0d4e..c305a85ed2 100644 --- a/src/atomate2/common/jobs/utils.py +++ b/src/atomate2/common/jobs/utils.py @@ -40,7 +40,7 @@ def structure_to_conventional( structure: Structure, symprec: float = SETTINGS.SYMPREC ) -> Structure: """ - Job hat creates a standard conventional structure. + Job that creates a standard conventional structure. Parameters ---------- @@ -112,12 +112,12 @@ def retrieve_structure_from_materials_project( with MPRester() as mpr: if use_task_id: - doc = mpr.tasks.get_data_by_id(material_id_or_task_id, fields=["structure"]) + doc = mpr.tasks.search(material_id_or_task_id, fields=["structure"])[0] task_id = material_id_or_task_id else: - doc = mpr.materials.get_data_by_id( + doc = mpr.materials.search( material_id_or_task_id, fields=["structure", "origins"] - ) + )[0] origins = {prop.name: prop for prop in doc.origins} task_id = str(origins["structure"].task_id) diff --git a/src/atomate2/common/powerups.py b/src/atomate2/common/powerups.py new file mode 100644 index 0000000000..b4f8bddb2d --- /dev/null +++ b/src/atomate2/common/powerups.py @@ -0,0 +1,76 @@ +"""Utilities for modifying workflow.""" + +from __future__ import annotations + +from typing import TYPE_CHECKING + +if TYPE_CHECKING: + from jobflow import Flow, Maker + + +def add_metadata_to_flow( + flow: Flow, additional_fields: dict, class_filter: Maker +) -> Flow: + """ + Return the flow with additional field(metadata) to the task doc. + + This allows adding metadata to the task-docs, could be useful + to query results from DB. + + Parameters + ---------- + flow: + additional_fields : dict + A dict with metadata. + class_filter: .Maker + The Maker to which additional metadata needs to be added + + Returns + ------- + Flow + Flow with added metadata to the task-doc. + """ + flow.update_maker_kwargs( + { + "_set": { + f"task_document_kwargs->additional_fields->{field}": value + for field, value in additional_fields.items() + } + }, + dict_mod=True, + class_filter=class_filter, + ) + + return flow + + +def update_custodian_handlers( + flow: Flow, custom_handlers: tuple, class_filter: Maker +) -> Flow: + """ + Return the flow with custom custodian handlers for VASP jobs. + + This allows user to selectively set error correcting handlers for VASP jobs + or completely unset error handlers. + + Parameters + ---------- + flow: + custom_handlers : tuple + A tuple with custodian handlers. + class_filter: .Maker + The Maker to which custom custodian handler needs to be added + + Returns + ------- + Flow + Flow with modified custodian handlers. + """ + code = class_filter.name.split(" ")[1] + flow.update_maker_kwargs( + {"_set": {f"run_{code}_kwargs->handlers": custom_handlers}}, + dict_mod=True, + class_filter=class_filter, + ) + + return flow diff --git a/src/atomate2/common/schemas/cclib.py b/src/atomate2/common/schemas/cclib.py index 0a473736c5..d6d681df4d 100644 --- a/src/atomate2/common/schemas/cclib.py +++ b/src/atomate2/common/schemas/cclib.py @@ -3,7 +3,7 @@ import logging import os from pathlib import Path -from typing import Any, Optional, TypeVar, Union +from typing import Any, Optional, Union from emmet.core.structure import MoleculeMetadata from monty.dev import requires @@ -11,6 +11,7 @@ from pydantic import Field from pymatgen.core import Molecule from pymatgen.core.periodic_table import Element +from typing_extensions import Self from atomate2 import __version__ from atomate2.utils.datetime import datetime_str @@ -23,7 +24,6 @@ logger = logging.getLogger(__name__) -_T = TypeVar("_T", bound="TaskDocument") class TaskDocument(MoleculeMetadata, extra="allow"): # type: ignore[call-arg] @@ -34,22 +34,28 @@ class TaskDocument(MoleculeMetadata, extra="allow"): # type: ignore[call-arg] For the list of supported packages, see https://cclib.github.io """ - molecule: Molecule = Field(None, description="Final output molecule from the task") - energy: float = Field(None, description="Final total energy") - dir_name: str = Field(None, description="Directory where the output is parsed") - logfile: str = Field( + molecule: Optional[Molecule] = Field( + None, description="Final output molecule from the task" + ) + energy: Optional[float] = Field(None, description="Final total energy") + dir_name: Optional[str] = Field( + None, description="Directory where the output is parsed" + ) + logfile: Optional[str] = Field( None, description="Path to the log file used in the post-processing analysis" ) - attributes: dict = Field( + attributes: Optional[dict] = Field( None, description="Computed properties and calculation outputs" ) - metadata: dict = Field( + metadata: Optional[dict] = Field( None, description="Calculation metadata, including input parameters and runtime " "statistics", ) - task_label: str = Field(None, description="A description of the task") - tags: list[str] = Field(None, description="Optional tags for this task document") + task_label: Optional[str] = Field(None, description="A description of the task") + tags: Optional[list[str]] = Field( + None, description="Optional tags for this task document" + ) last_updated: str = Field( default_factory=datetime_str, description="Timestamp for this task document was last updated", @@ -61,16 +67,15 @@ class TaskDocument(MoleculeMetadata, extra="allow"): # type: ignore[call-arg] @classmethod @requires(cclib, "The cclib TaskDocument requires cclib to be installed.") def from_logfile( - cls: type[_T], + cls, dir_name: Union[str, Path], logfile_extensions: Union[str, list[str]], store_trajectory: bool = False, additional_fields: Optional[dict[str, Any]] = None, analysis: Optional[Union[str, list[str]]] = None, proatom_dir: Optional[Union[Path, str]] = None, - ) -> "TaskDocument": - """ - Create a TaskDocument from a log file. + ) -> Self: + """Create a TaskDocument from a log file. For a full description of each field, see https://cclib.github.io/data.html. @@ -250,7 +255,7 @@ def from_logfile( @requires(cclib, "cclib_calculate requires cclib to be installed.") def cclib_calculate( - cclib_obj, + cclib_obj: Any, method: str, cube_file: Union[Path, str], proatom_dir: Union[Path, str], @@ -285,47 +290,43 @@ def cclib_calculate( ) method = method.lower() - cube_methods = ["bader", "ddec6", "hirshfeld"] + cube_methods = ("bader", "ddec6", "hirshfeld") if method in cube_methods and not cube_file: - raise FileNotFoundError( - f"A cube file must be provided for {method}. Returning None." - ) - if method in ["ddec6", "hirshfeld"] and not proatom_dir: + raise FileNotFoundError(f"A cube file must be provided for {method}.") + if method in ("ddec6", "hirshfeld") and not proatom_dir: if os.getenv("PROATOM_DIR") is None: - raise OSError("PROATOM_DIR environment variable not set. Returning None.") + raise OSError("PROATOM_DIR environment variable not set.") proatom_dir = os.path.expandvars(os.environ["PROATOM_DIR"]) - if proatom_dir and not os.path.exists(proatom_dir): - raise FileNotFoundError( - f"Protatom directory {proatom_dir} does not exist. Returning None." - ) + if proatom_dir and not os.path.isdir(proatom_dir): + raise FileNotFoundError(f"{proatom_dir=} does not exist.") if cube_file and method in cube_methods: vol = volume.read_from_cube(str(cube_file)) if method == "bader": - m = Bader(cclib_obj, vol) + _method = Bader(cclib_obj, vol) elif method == "bickelhaupt": - m = Bickelhaupt(cclib_obj) + _method = Bickelhaupt(cclib_obj) elif method == "cpsa": - m = CSPA(cclib_obj) + _method = CSPA(cclib_obj) elif method == "ddec6": - m = DDEC6(cclib_obj, vol, str(proatom_dir)) + _method = DDEC6(cclib_obj, vol, str(proatom_dir)) elif method == "density": - m = Density(cclib_obj) + _method = Density(cclib_obj) elif method == "hirshfeld": - m = Hirshfeld(cclib_obj, vol, str(proatom_dir)) + _method = Hirshfeld(cclib_obj, vol, str(proatom_dir)) elif method == "lpa": - m = LPA(cclib_obj) + _method = LPA(cclib_obj) elif method == "mbo": - m = MBO(cclib_obj) + _method = MBO(cclib_obj) elif method == "mpa": - m = MPA(cclib_obj) + _method = MPA(cclib_obj) else: - raise ValueError(f"{method} is not supported.") + raise ValueError(f"{method=} is not supported.") try: - m.calculate() + _method.calculate() except AttributeError: return None @@ -345,20 +346,20 @@ def cclib_calculate( ] calc_attributes = {} for attribute in avail_attributes: - if hasattr(m, attribute): - calc_attributes[attribute] = getattr(m, attribute) + if hasattr(_method, attribute): + calc_attributes[attribute] = getattr(_method, attribute) return calc_attributes def _get_homos_lumos( - moenergies: list[list[float]], homo_indices: list[int] + mo_energies: list[list[float]], homo_indices: list[int] ) -> tuple[list[float], Optional[list[float]], Optional[list[float]]]: """ Calculate the HOMO, LUMO, and HOMO-LUMO gap energies in eV. Parameters ---------- - moenergies + mo_energies List of MO energies. For restricted calculations, List[List[float]] is length one. For unrestricted, it is length two. homo_indices @@ -374,13 +375,15 @@ def _get_homos_lumos( The HOMO-LUMO gaps (eV), calculated as LUMO_alpha-HOMO_alpha and LUMO_beta-HOMO_beta """ - homo_energies = [moenergies[i][h] for i, h in enumerate(homo_indices)] - # Make sure that the HOMO+1 (i.e. LUMO) is in moenergies (sometimes virtual + homo_energies = [mo_energies[idx][homo] for idx, homo in enumerate(homo_indices)] + # Make sure that the HOMO+1 (i.e. LUMO) is in MO energies (sometimes virtual # orbitals aren't printed in the output) - for i, h in enumerate(homo_indices): - if len(moenergies[i]) < h + 2: + for idx, homo in enumerate(homo_indices): + if len(mo_energies[idx]) < homo + 2: return homo_energies, None, None - lumo_energies = [moenergies[i][h + 1] for i, h in enumerate(homo_indices)] + lumo_energies = [ + mo_energies[idx][homo + 1] for idx, homo in enumerate(homo_indices) + ] homo_lumo_gaps = [ lumo_energies[i] - homo_energies[i] for i in range(len(homo_energies)) ] diff --git a/src/atomate2/common/schemas/defects.py b/src/atomate2/common/schemas/defects.py index 2853172a4a..c91912d6bb 100644 --- a/src/atomate2/common/schemas/defects.py +++ b/src/atomate2/common/schemas/defects.py @@ -1,6 +1,8 @@ """General schemas for defect workflow outputs.""" import logging +from collections.abc import Sequence +from itertools import starmap from typing import Any, Callable, Optional, Union import numpy as np @@ -10,6 +12,7 @@ from pymatgen.analysis.defects.thermo import DefectEntry, FormationEnergyDiagram from pymatgen.core import Structure from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry +from typing_extensions import Self logger = logging.getLogger(__name__) @@ -22,43 +25,52 @@ class FormationEnergyDiagramDocument(BaseModel): will not necessarily have all the entries in the phase diagram computed. """ - bulk_entry: ComputedStructureEntry = Field( - None, description="The ComputedEntry representing the bulk structure." + bulk_entry: Optional[ComputedStructureEntry] = Field( + None, + description="The ComputedEntry representing the bulk structure.", ) - defect_entries: list[DefectEntry] = Field( - None, description="The defect entries for the formation energy diagram." + defect_entries: Optional[list[DefectEntry]] = Field( + None, + description="The defect entries for the formation energy diagram.", ) - pd_entries: list[ComputedEntry] = Field( - None, description="The entries used to construct the phase diagram." + pd_entries: Optional[list[ComputedEntry]] = Field( + None, + description="The entries used to construct the phase diagram.", ) - vbm: float = Field( - None, description="The VBM of the pristine supercell calculation." + vbm: Optional[float] = Field( + None, + description="The VBM of the pristine supercell calculation.", ) - band_gap: float = Field( - None, description="The band gap of the pristine supercell calculation." + band_gap: Optional[float] = Field( + None, + description="The band gap of the pristine supercell calculation.", ) - inc_inf_values: bool = Field( - None, description="Whether or not to include infinite values in the diagram." + inc_inf_values: Optional[bool] = Field( + None, + description="Whether or not to include infinite values in the diagram.", ) - defect: Defect = Field( - None, description="The defect for which the diagram is being calculated." + defect: Optional[Defect] = Field( + None, + description="The defect for which the diagram is being calculated.", ) - bulk_sc_dir: str = Field( - None, description="The directory name of the pristine supercell calculation." + bulk_sc_dir: Optional[str] = Field( + None, + description="The directory name of the pristine supercell calculation.", ) - defect_sc_dirs: dict[int, str] = Field( - None, description="The directory names of the charged defect calculations." + defect_sc_dirs: Optional[dict[int, str]] = Field( + None, + description="The directory names of the charged defect calculations.", ) - dielectric: Union[float, list[list[float]]] = Field( + dielectric: Optional[Union[float, list[list[float]]]] = Field( None, description="The dielectric constant or tensor, can be used to compute " "finite-size corrections.", @@ -66,8 +78,10 @@ class FormationEnergyDiagramDocument(BaseModel): @classmethod def from_formation_energy_diagram( - cls, fed: FormationEnergyDiagram, **kwargs - ) -> "FormationEnergyDiagramDocument": + cls, + fed: FormationEnergyDiagram, + **kwargs, + ) -> Self: """Create a document from a `FormationEnergyDiagram` object. Args: @@ -87,7 +101,8 @@ def from_formation_energy_diagram( ) def as_formation_energy_diagram( - self, pd_entries: Optional[list[ComputedEntry]] = None + self, + pd_entries: Optional[list[ComputedEntry]] = None, ) -> FormationEnergyDiagram: """Create a `FormationEnergyDiagram` object from the document. @@ -113,38 +128,41 @@ def as_formation_energy_diagram( class CCDDocument(BaseModel): """Configuration-coordinate definition of configuration-coordinate diagram.""" - q1: int = Field(None, description="Charge state 1.") - q2: int = Field(None, description="Charge state 2.") - structure1: Structure = Field( - None, description="The structure of defect (supercell) in charge state (q2)." + q1: Optional[int] = Field(None, description="Charge state 1.") + q2: Optional[int] = Field(None, description="Charge state 2.") + structure1: Optional[Structure] = Field( + None, + description="The structure of defect (supercell) in charge state (q2).", ) - structure2: Structure = Field( - None, description="The structure of defect (supercell) in charge state (q2)." + structure2: Optional[Structure] = Field( + None, + description="The structure of defect (supercell) in charge state (q2).", ) - distortions1: list[float] = Field( + distortions1: Optional[list[float]] = Field( None, description="The distortions of the defect (supercell) in charge state (q1).", ) - distortions2: list[float] = Field( + distortions2: Optional[list[float]] = Field( None, description="The distortions of the defect (supercell) in charge state (q2).", ) - - energies1: list[float] = Field( - None, description="The energies of the defect (supercell) in charge state (q1)." + energies1: Optional[list[float]] = Field( + None, + description="The energies of the defect (supercell) in charge state (q1).", ) - energies2: list[float] = Field( - None, description="The energies of the defect (supercell) in charge state (q2)." + energies2: Optional[list[float]] = Field( + None, + description="The energies of the defect (supercell) in charge state (q2).", ) - static_dirs1: list[str] = Field( + static_dirs1: Optional[list[str]] = Field( None, description="Directories of distorted calculations for the defect (supercell) " "in charge state (q1).", ) - static_dirs2: list[str] = Field( + static_dirs2: Optional[list[str]] = Field( None, description="Directories of distorted calculations for the defect (supercell) " "in charge state (q2).", @@ -162,13 +180,13 @@ class CCDDocument(BaseModel): "charge state (q2).", ) - relaxed_index1: int = Field( + relaxed_index1: Optional[int] = Field( None, description="The index of the static calculation in that corresponds to the " "relaxed charge state (q1).", ) - relaxed_index2: int = Field( + relaxed_index2: Optional[int] = Field( None, description="The index of the static calculation in that corresponds to the " "relaxed charge state (q2).", @@ -187,7 +205,7 @@ def from_task_outputs( static_uuids2: list[str], relaxed_uuid1: str, relaxed_uuid2: str, - ) -> "CCDDocument": + ) -> Self: """Create a CCDDocument from a lists of structures and energies. The directories and the UUIDs of the static calculations are also provided as @@ -221,23 +239,22 @@ def from_task_outputs( UUID of relaxed calculation in charge state (q2). """ - def get_ent( - struct: Structure, energy: float, dir_name, uuid + def get_cs_entry( + struct: Structure, energy: float, dir_name: str, uuid: str ) -> ComputedStructureEntry: - return ComputedStructureEntry( - structure=struct, - energy=energy, - data={"dir_name": dir_name, "uuid": uuid}, - ) + data = {"dir_name": dir_name, "uuid": uuid} + return ComputedStructureEntry(structure=struct, energy=energy, data=data) - entries1 = [ - get_ent(s, e, d, u) - for s, e, d, u in zip(structures1, energies1, static_dirs1, static_uuids1) - ] - entries2 = [ - get_ent(s, e, d, u) - for s, e, d, u in zip(structures2, energies2, static_dirs2, static_uuids2) - ] + entries1 = list( + starmap( + get_cs_entry, zip(structures1, energies1, static_dirs1, static_uuids1) + ) + ) + entries2 = list( + starmap( + get_cs_entry, zip(structures2, energies2, static_dirs2, static_uuids2) + ) + ) return cls.from_entries(entries1, entries2, relaxed_uuid1, relaxed_uuid2) @@ -248,9 +265,8 @@ def from_entries( entries2: list[ComputedStructureEntry], relaxed_uuid1: Optional[str] = None, relaxed_uuid2: Optional[str] = None, - ) -> "CCDDocument": - """ - Create a CCDTaskDocument from a list of distorted calculations. + ) -> Self: + """Create a CCDTaskDocument from a list of distorted calculations. Parameters ---------- @@ -262,17 +278,18 @@ def from_entries( UUID of relaxed calculation in charge state (q1). relaxed_uuid1 UUID of relaxed calculation in charge state (q2). - """ - def find_entry(entries, uuid) -> tuple[int, ComputedStructureEntry]: + def find_entry( + entries: Sequence[ComputedStructureEntry], uuid: str + ) -> tuple[int, ComputedStructureEntry]: """Find the entry with the given UUID.""" - for itr, entry in enumerate(entries): + for idx, entry in enumerate(entries): if entry.data["uuid"] == uuid: - return itr, entry + return idx, entry raise ValueError(f"Could not find entry with UUID: {uuid}") - def dQ_entries(e1, e2) -> float: + def dQ_entries(e1: ComputedStructureEntry, e2: ComputedStructureEntry) -> float: # noqa: N802 """Get the displacement between two entries.""" return get_dQ(e1.structure, e2.structure) @@ -287,10 +304,16 @@ def dQ_entries(e1, e2) -> float: idx2, ent_r2 = find_entry(entries2, relaxed_uuid2) s_entries1, distortions1 = sort_pos_dist( - entries1, ent_r1, ent_r2, dist=dQ_entries + entries1, + ent_r1, + ent_r2, + dist=dQ_entries, ) s_entries2, distortions2 = sort_pos_dist( - entries2, ent_r1, ent_r2, dist=dQ_entries + entries2, + ent_r1, + ent_r2, + dist=dQ_entries, ) energies1 = [entry.energy for entry in s_entries1] @@ -314,26 +337,29 @@ def dQ_entries(e1, e2) -> float: relaxed_index2=idx2, ) - def get_taskdocs(self) -> list[list[TaskDoc]]: + def get_taskdocs(self) -> tuple[list[TaskDoc], list[TaskDoc]]: """Get the distorted task documents.""" - def remove_host_name(dir_name) -> str: + def remove_host_name(dir_name: str) -> str: return dir_name.split(":")[-1] - return [ - [ - TaskDoc.from_directory(remove_host_name(dir_name)) - for dir_name in self.static_dirs1 - ], - [ - TaskDoc.from_directory(remove_host_name(dir_name)) - for dir_name in self.static_dirs2 - ], + static1_task_docs = [ + TaskDoc.from_directory(remove_host_name(dir_name)) + for dir_name in self.static_dirs1 ] + static2_task_docs = [ + TaskDoc.from_directory(remove_host_name(dir_name)) + for dir_name in self.static_dirs2 + ] + + return static1_task_docs, static2_task_docs def sort_pos_dist( - list_in: list[Any], s1: Any, s2: Any, dist: Callable + list_in: list[Any], + s1: Any, + s2: Any, + dist: Callable, ) -> tuple[list[Any], list[float]]: """ Sort a list defined when we can only compute a positive-definite distance. @@ -364,19 +390,19 @@ def sort_pos_dist( """ d1 = [dist(s, s1) for s in list_in] d2 = [dist(s, s2) for s in list_in] - D0 = dist(s1, s2) + d0 = dist(s1, s2) d_vs_s = [] for q1, q2, s in zip(d1, d2, list_in): sign = +1 - if q1 < q2 and q2 > D0: + if q1 < q2 and q2 > d0: sign = -1 d_vs_s.append((sign * q1, s)) d_vs_s.sort() return [s for _, s in d_vs_s], [d for d, _ in d_vs_s] -def get_dQ(ref: Structure, distorted: Structure) -> float: +def get_dQ(ref: Structure, distorted: Structure) -> float: # noqa: N802 """ Calculate dQ from the initial and final structures. @@ -397,6 +423,6 @@ def get_dQ(ref: Structure, distorted: Structure) -> float: [ x[0].distance(x[1]) ** 2 * x[0].specie.atomic_mass for x in zip(ref, distorted) - ] - ) + ], + ), ) diff --git a/src/atomate2/common/schemas/elastic.py b/src/atomate2/common/schemas/elastic.py index a596e1ae6d..ddd06ca0db 100644 --- a/src/atomate2/common/schemas/elastic.py +++ b/src/atomate2/common/schemas/elastic.py @@ -1,5 +1,7 @@ """Schemas for elastic tensor fitting and related properties.""" + from copy import deepcopy +from enum import Enum from typing import Optional import numpy as np @@ -16,6 +18,7 @@ from pymatgen.core import Structure from pymatgen.core.tensors import TensorMapping from pymatgen.symmetry.analyzer import SpacegroupAnalyzer +from typing_extensions import Self from atomate2 import SETTINGS @@ -23,51 +26,61 @@ class DerivedProperties(BaseModel): """Properties derived from an elastic tensor.""" - k_voigt: float = Field(None, description="Voigt average of the bulk modulus.") - k_reuss: float = Field(None, description="Reuss average of the bulk modulus.") - k_vrh: float = Field( + k_voigt: Optional[float] = Field( + None, description="Voigt average of the bulk modulus." + ) + k_reuss: Optional[float] = Field( + None, description="Reuss average of the bulk modulus." + ) + k_vrh: Optional[float] = Field( None, description="Voigt-Reuss-Hill average of the bulk modulus." ) - g_voigt: float = Field(None, description="Voigt average of the shear modulus.") - g_reuss: float = Field(None, description="Reuss average of the shear modulus.") - g_vrh: float = Field( + g_voigt: Optional[float] = Field( + None, description="Voigt average of the shear modulus." + ) + g_reuss: Optional[float] = Field( + None, description="Reuss average of the shear modulus." + ) + g_vrh: Optional[float] = Field( None, description="Voigt-Reuss-Hill average of the shear modulus." ) - universal_anisotropy: float = Field( + universal_anisotropy: Optional[float] = Field( None, description="Universal elastic anisotropy." ) - homogeneous_poisson: float = Field(None, description="Homogeneous poisson ratio.") - y_mod: float = Field( + homogeneous_poisson: Optional[float] = Field( + None, description="Homogeneous poisson ratio." + ) + y_mod: Optional[float] = Field( None, description="Young's modulus (SI units) from the Voight-Reuss-Hill averages of " "the bulk and shear moduli.", ) - trans_v: float = Field( + trans_v: Optional[float] = Field( None, description="Transverse sound velocity (SI units) obtained from the " "Voigt-Reuss-Hill average bulk modulus.", ) - long_v: float = Field( + long_v: Optional[float] = Field( None, description="Longitudinal sound velocity (SI units) obtained from the " "Voigt-Reuss-Hill average bulk modulus.", ) - snyder_ac: float = Field( + snyder_ac: Optional[float] = Field( None, description="Synder's acoustic sound velocity (SI units)." ) - snyder_opt: float = Field( + snyder_opt: Optional[float] = Field( None, description="Synder's optical sound velocity (SI units)." ) - snyder_total: float = Field( + snyder_total: Optional[float] = Field( None, description="Synder's total sound velocity (SI units)." ) clark_thermalcond: Optional[float] = Field( None, description="Clarke's thermal conductivity (SI units)." ) - cahill_thermalcond: float = Field( + cahill_thermalcond: Optional[float] = Field( None, description="Cahill's thermal conductivity (SI units)." ) - debye_temperature: float = Field( + debye_temperature: Optional[float] = Field( None, description="Debye temperature from longitudinal and transverse sound " "velocities (SI units).", @@ -77,55 +90,69 @@ class DerivedProperties(BaseModel): class FittingData(BaseModel): """Data used to fit elastic tensors.""" - cauchy_stresses: list[Matrix3D] = Field( + cauchy_stresses: Optional[list[Matrix3D]] = Field( None, description="The Cauchy stresses used to fit the elastic tensor." ) - strains: list[Matrix3D] = Field( + strains: Optional[list[Matrix3D]] = Field( None, description="The strains used to fit the elastic tensor." ) - pk_stresses: list[Matrix3D] = Field( + pk_stresses: Optional[list[Matrix3D]] = Field( None, description="The Piola-Kirchoff stresses used to fit the elastic tensor." ) - deformations: list[Matrix3D] = Field( + deformations: Optional[list[Matrix3D]] = Field( None, description="The deformations corresponding to each strain state." ) - uuids: list[str] = Field(None, description="The uuids of the deformation jobs.") - job_dirs: list[Optional[str]] = Field( + uuids: Optional[list[str]] = Field( + None, description="The uuids of the deformation jobs." + ) + job_dirs: Optional[list[Optional[str]]] = Field( None, description="The directories where the deformation jobs were run." ) + failed_uuids: Optional[list[str]] = Field( + None, description="The uuids of perturbations that were not completed" + ) class ElasticTensorDocument(BaseModel): """Raw and standardized elastic tensors.""" - raw: MatrixVoigt = Field(None, description="Raw elastic tensor.") - ieee_format: MatrixVoigt = Field(None, description="Elastic tensor in IEEE format.") + raw: Optional[MatrixVoigt] = Field(None, description="Raw elastic tensor.") + ieee_format: Optional[MatrixVoigt] = Field( + None, description="Elastic tensor in IEEE format." + ) + + +class ElasticWarnings(Enum): + """Warnings for elastic document.""" + + FAILED_PERTURBATIONS: str = "failed_perturbations" class ElasticDocument(StructureMetadata): """Document containing elastic tensor information and related properties.""" - structure: Structure = Field( + structure: Optional[Structure] = Field( None, description="The structure for which the elastic data is calculated." ) - elastic_tensor: ElasticTensorDocument = Field( + elastic_tensor: Optional[ElasticTensorDocument] = Field( None, description="Fitted elastic tensor." ) eq_stress: Optional[Matrix3D] = Field( None, description="The equilibrium stress of the structure." ) - derived_properties: DerivedProperties = Field( + derived_properties: Optional[DerivedProperties] = Field( None, description="Properties derived from the elastic tensor." ) - fitting_data: FittingData = Field( + fitting_data: Optional[FittingData] = Field( None, description="Data used to fit the elastic tensor." ) - fitting_method: str = Field( + fitting_method: Optional[str] = Field( None, description="Method used to fit the elastic tensor." ) - order: int = Field( + order: Optional[int] = Field( None, description="Order of the expansion of the elastic tensor." ) + warnings: Optional[list[str]] = Field(None, description="Warnings.") @classmethod def from_stresses( @@ -140,9 +167,9 @@ def from_stresses( equilibrium_stress: Optional[Matrix3D] = None, symprec: float = SETTINGS.SYMPREC, allow_elastically_unstable_structs: bool = True, - ) -> "ElasticDocument": - """ - Create an elastic document from strains and stresses. + failed_uuids: list[str] = None, + ) -> Self: + """Create an elastic document from strains and stresses. Parameters ---------- @@ -172,11 +199,14 @@ def from_stresses( allow_elastically_unstable_structs : bool Whether to allow the ElasticDocument to still complete in the event that the structure is elastically unstable. + failed_uuids: list of str + The uuids of perturbations that were not completed """ strains = [d.green_lagrange_strain for d in deformations] + elastic_warnings = [] if symprec is not None: - strains, stresses, uuids, job_dirs = _expand_strains( + strains, stresses, uuids, job_dirs = expand_strains( structure, strains, stresses, uuids, job_dirs, symprec ) @@ -221,6 +251,9 @@ def from_stresses( eq_stress = eq_stress.tolist() if eq_stress is not None else eq_stress + if failed_uuids: + elastic_warnings.append(ElasticWarnings.FAILED_PERTURBATIONS.value) + return cls.from_structure( structure=structure, meta_structure=structure, @@ -238,11 +271,13 @@ def from_stresses( deformations=[d.tolist() for d in deformations], uuids=uuids, job_dirs=job_dirs, + failed_uuids=failed_uuids, ), + warnings=elastic_warnings or None, ) -def _expand_strains( +def expand_strains( structure: Structure, strains: list[Strain], stresses: list[Stress], @@ -265,7 +300,7 @@ def _expand_strains( `generate_elastic_deformations()`. """ sga = SpacegroupAnalyzer(structure, symprec=symprec) - symmops = sga.get_symmetry_operations(cartesian=True) + symm_ops = sga.get_symmetry_operations(cartesian=True) full_strains = deepcopy(strains) full_stresses = deepcopy(stresses) @@ -273,9 +308,9 @@ def _expand_strains( full_job_dirs = deepcopy(job_dirs) mapping = TensorMapping(full_strains, [True for _ in full_strains]) - for i, strain in enumerate(strains): - for symmop in symmops: - rotated_strain = strain.transform(symmop) + for idx, strain in enumerate(strains): + for symm_op in symm_ops: + rotated_strain = strain.transform(symm_op) # check if we have more than one perturbed strain component if sum(np.abs(rotated_strain.voigt) > tol) > 1: @@ -290,8 +325,8 @@ def _expand_strains( # expand the other properties full_strains.append(rotated_strain) - full_stresses.append(stresses[i].transform(symmop)) - full_uuids.append(uuids[i]) - full_job_dirs.append(job_dirs[i]) + full_stresses.append(stresses[idx].transform(symm_op)) + full_uuids.append(uuids[idx]) + full_job_dirs.append(job_dirs[idx]) return full_strains, full_stresses, full_uuids, full_job_dirs diff --git a/src/atomate2/common/schemas/magnetism.py b/src/atomate2/common/schemas/magnetism.py new file mode 100644 index 0000000000..c63db089ea --- /dev/null +++ b/src/atomate2/common/schemas/magnetism.py @@ -0,0 +1,437 @@ +"""Schemas for magnetic ordering calculations.""" + +from __future__ import annotations + +from typing import Optional + +import numpy as np +from emmet.core.tasks import TaskDoc +from pydantic import BaseModel, Field +from pymatgen.analysis.magnetism.analyzer import ( + CollinearMagneticStructureAnalyzer, + Ordering, +) +from pymatgen.core.structure import Structure + + +class MagneticOrderingInput(BaseModel): + """Defines the input structure/ordering for a magnetic ordering calculation. + + This is embedded in the MagneticOrderingOutput and MagneticOrderingRelaxation + documents. + """ + + structure: Optional[Structure] = Field(None, description="Input structure") + ordering: Optional[Ordering] = Field( + None, + description=( + "The magnetic ordering of the input structure, " + "as defined in pymatgen.analysis.magnetism.analyzer." + ), + ) + magmoms: Optional[list[float]] = Field( + None, description="Magnetic moments of the structure." + ) + symmetry: Optional[str] = Field(None, description="Detected space group symbol.") + + +class MagneticOrderingRelaxation(BaseModel): + """Defines the relaxation information for a magnetic ordering calculation. + + This is embedded within the MagneticOrderingOutput. + """ + + uuid: Optional[str] = Field(None, description="Unique ID of the calculation.") + dir_name: Optional[str] = Field(None, description="Directory of the calculation.") + input: Optional[MagneticOrderingInput] = Field( + None, description="Input ordering information." + ) + structure: Optional[Structure] = Field( + None, description="Final structure from the calculation." + ) + symmetry_changed: Optional[bool] = Field( + None, description="Whether or not symmetry changed." + ) + ordering_changed: Optional[bool] = Field( + None, + description=( + "Specifies whether or not the magnetic ordering changed during the" + " calculation." + ), + ) + ordering: Optional[Ordering] = Field( + None, description="Final ordering from the calculation." + ) + magmoms: Optional[list[float]] = Field( + None, description="Magnetic moments of the structure." + ) + symmetry: Optional[str] = Field(None, description="Detected space group symbol.") + energy: Optional[float] = Field( + None, description="Final energy result from the calculation." + ) + energy_per_atom: Optional[float] = Field(None, description="Final energy per atom.") + total_magnetization: Optional[float] = Field( + None, + description=( + "Total magnetization as a sum of individual atomic moments in " + "the calculated unit cell." + ), + ) + total_magnetization_per_formula_unit: Optional[float] = Field( + None, description="Total magnetization normalized to per formula unit." + ) + total_magnetization_per_unit_volume: Optional[float] = Field( + None, description="Total magnetiation normalized to per unit volume." + ) + + @classmethod + def from_structures_and_energies( + cls, + input_structure: Structure, + output_structure: Structure, + output_energy: float, + uuid: str | None = None, + dir_name: str | None = None, + ) -> MagneticOrderingRelaxation: + """Construct a relaxation output doc from structures and energies.""" + return cls( + uuid=uuid, + dir_name=dir_name, + structure=output_structure, + energy=output_energy, + energy_per_atom=output_energy / output_structure.num_sites, + **_compare_ordering_and_symmetry(input_structure, output_structure), + ) + + @classmethod + def from_task_document( + cls, task_document: TaskDoc, uuid: str | None = None + ) -> MagneticOrderingRelaxation: + """Construct a MagneticOrderingRelaxation from a task document. + + This does not include the uuid, which must be provided separately. + + .. Warning:: Currently, the TaskDoc defined in emmet is VASP-specific. + Ensure that the TaskDoc provided contains an InputDoc with a magnetic + moments field. + """ + dir_name = task_document.dir_name + structure = task_document.structure + input_structure = task_document.input.structure + if not input_structure.site_properties.get("magmom"): + input_structure.add_site_property( # input struct likely has no magmoms + "magmom", task_document.input.magnetic_moments + ) + energy = task_document.output.energy + + return cls.from_structures_and_energies( + input_structure=input_structure, + output_structure=structure, + output_energy=energy, + uuid=uuid, + dir_name=dir_name, + ) + + +class MagneticOrderingOutput(BaseModel): + """Defines the output for a *static* magnetic ordering calculation. + + This is used within the construction of the MagneticOrderingDocument. If a + relaxation was performed, this information will be stored within the relax_output + field. + """ + + uuid: Optional[str] = Field(None, description="Unique ID of the calculation.") + dir_name: Optional[str] = Field(None, description="Directory of the calculation.") + input: Optional[MagneticOrderingInput] = Field( + None, description="Input ordering information." + ) + structure: Optional[Structure] = Field( + None, description="Final structure from the calculation." + ) + ordering: Optional[Ordering] = Field( + None, + description=( + "The magnetic ordering of the output structure, " + "as defined in pymatgen.analysis.magnetism.analyzer." + ), + ) + magmoms: Optional[list[float]] = Field( + None, description="Magnetic moments of the structure." + ) + symmetry: Optional[str] = Field(None, description="Detected space group symbol.") + energy: Optional[float] = Field( + None, description="Final energy result from the calculation." + ) + energy_per_atom: Optional[float] = Field(None, description="Final energy per atom.") + total_magnetization: Optional[float] = Field( + None, + description=( + "Total magnetization as a sum of individual atomic moments in " + "the calculated unit cell." + ), + ) + total_magnetization_per_formula_unit: Optional[float] = Field( + None, description="Total magnetization normalized to per formula unit." + ) + total_magnetization_per_unit_volume: Optional[float] = Field( + None, description="Total magnetiation normalized to per unit volume." + ) + ordering_changed: Optional[bool] = Field( + None, + description=( + "Specifies whether or not the magnetic ordering changed during the" + " calculation." + ), + ) + symmetry_changed: Optional[bool] = Field( + None, + description=( + "Specifies whether or not the symmetry changed during the calculation." + ), + ) + energy_above_ground_state_per_atom: Optional[float] = Field( + None, description="Energy per atom above the calculated ground state ordering." + ) + relax_output: Optional[MagneticOrderingRelaxation] = Field( + None, description="Relaxation output, if relaxation performed." + ) + energy_diff_relax_static: Optional[float] = Field( + None, + description=( + "Difference in energy between relaxation and final static calculation, if" + " relaxation performed (useful for benchmarking). Specifically, this is" + " calculated as energy[static] - energy[relax]." + ), + ) + + @classmethod + def from_structures_and_energies( + cls, + input_structure: Structure, + output_structure: Structure, + output_energy: float, + relax_output: MagneticOrderingRelaxation | None = None, + uuid: str | None = None, + dir_name: str | None = None, + ground_state_energy_per_atom: float | None = None, + ) -> MagneticOrderingOutput: + """Construct a MagneticOrderingOutput doc from structures and energies.""" + energy_diff_relax_static = ( + relax_output.energy - output_energy if relax_output else None + ) + output_energy_per_atom = output_energy / output_structure.num_sites + energy_above_ground_state_per_atom = ( + output_energy_per_atom - ground_state_energy_per_atom + if ground_state_energy_per_atom + else None + ) + return cls( + uuid=uuid, + dir_name=dir_name, + structure=output_structure, + energy=output_energy, + relax_output=relax_output, + energy_diff_relax_static=energy_diff_relax_static, + energy_per_atom=output_energy_per_atom, + energy_above_ground_state_per_atom=energy_above_ground_state_per_atom, + **_compare_ordering_and_symmetry(input_structure, output_structure), + ) + + @classmethod + def from_task_document( + cls, + task_document: TaskDoc, + uuid: str | None = None, + relax_output: MagneticOrderingRelaxation | None = None, + ) -> MagneticOrderingOutput: + """Construct a MagneticOrderingOutput from a task document. + + This does not include the uuid, which must be set separately. + + .. Warning:: Currently, the TaskDoc defined in emmet is VASP-specific. + Ensure that the TaskDoc provided contains an InputDoc with a + magnetic moments field. + """ + dir_name = task_document.dir_name + structure = task_document.structure + input_structure = task_document.input.structure + if not input_structure.site_properties.get("magmom"): + input_structure.add_site_property( # input struct likely has no magmoms + "magmom", task_document.input.magnetic_moments + ) + energy = task_document.output.energy + + return cls.from_structures_and_energies( + input_structure=input_structure, + output_structure=structure, + output_energy=energy, + uuid=uuid, + dir_name=dir_name, + relax_output=relax_output, + ) + + +class MagneticOrderingsDocument(BaseModel): + """Final document containing information about calculated magnetic orderings. + + Includes description of the ground state ordering. This document is returned by the + MagneticOrderingsBuilder corresponding to your DFT code. + """ + + formula: Optional[str] = Field( + None, + description="Formula taken from pymatgen.core.structure.Structure.formula.", + ) + formula_pretty: Optional[str] = Field( + None, + description="Cleaned representation of the formula", + ) + parent_structure: Optional[Structure] = Field( + None, + description=( + "The parent structure from which individual magnetic " + "orderings are generated." + ), + ) + outputs: Optional[list[MagneticOrderingOutput]] = Field( + None, + description="All magnetic ordering calculation results for this structure.", + ) + ground_state_uuid: Optional[str] = Field( + None, description="UUID of the ground state ordering." + ) + ground_state_structure: Optional[Structure] = Field( + None, description="Ground state structure." + ) + ground_state_ordering: Optional[Ordering] = Field( + None, description="Ground state magnetic ordering." + ) + ground_state_energy: Optional[float] = Field( + None, description="Ground state energy." + ) + ground_state_energy_per_atom: Optional[float] = Field( + None, description="Ground state energy, normalized per atom." + ) + + @classmethod + def from_outputs( + cls, + outputs: list[MagneticOrderingOutput], + parent_structure: Structure, + ) -> MagneticOrderingsDocument: + """Construct a MagneticOrderingDocument from a list of output docs. + + This is general and should not need to be implemented for a specific DFT code. + """ + formula = outputs[0].structure.formula + formula_pretty = outputs[0].structure.composition.reduced_formula + + ground_state = min(outputs, key=lambda struct: struct.energy_per_atom) + ground_state_energy_per_atom = ground_state.energy_per_atom + for output in outputs: + output.energy_above_ground_state_per_atom = ( + output.energy_per_atom - ground_state_energy_per_atom + ) + + return cls( + formula=formula, + formula_pretty=formula_pretty, + parent_structure=parent_structure, + outputs=outputs, + ground_state_uuid=ground_state.uuid, + ground_state_structure=ground_state.structure, + ground_state_ordering=ground_state.ordering, + ground_state_energy=ground_state.energy, + ground_state_energy_per_atom=ground_state.energy_per_atom, + ) + + @classmethod + def from_tasks(cls, tasks: list[dict]) -> MagneticOrderingsDocument: + """Construct a MagneticOrderingsDocument from a list of task dicts. + + .. Note:: this function assumes the tasks contain the keys "output" and + "metadata". These keys are automatically constructed when jobflow stores its + outputs; however, you may need to put the data in this format if using this + manually (as in a postprocessing job). + """ + parent_structure = tasks[0]["metadata"]["parent_structure"] + + relax_tasks, static_tasks = [], [] + for task in tasks: + if task["output"].task_type.value.lower() == "structure optimization": + relax_tasks.append(task) + elif task["output"].task_type.value.lower() == "static": + static_tasks.append(task) + + outputs = [] + for task in static_tasks: + relax_output = None + for r_task in relax_tasks: + if r_task["uuid"] == task["metadata"]["parent_uuid"]: + relax_output = MagneticOrderingRelaxation.from_task_document( + r_task["output"], + uuid=r_task["uuid"], + ) + break + output = MagneticOrderingOutput.from_task_document( + task["output"], + uuid=task["uuid"], + relax_output=relax_output, + ) + outputs.append(output) + + return cls.from_outputs(outputs, parent_structure=parent_structure) + + +def _compare_ordering_and_symmetry( + input_structure: Structure, output_structure: Structure +) -> dict: + """Compare ordering and symmetry of input and output structures. + + This is especially useful for debugging purposes. + """ + # process input structure + input_analyzer = CollinearMagneticStructureAnalyzer(input_structure, threshold=0.61) + input_ordering = input_analyzer.ordering + input_magmoms = input_analyzer.magmoms + input_symmetry = input_structure.get_space_group_info()[0] + + # process output structure + output_analyzer = CollinearMagneticStructureAnalyzer( + output_structure, threshold=0.61 + ) + output_ordering = output_analyzer.ordering + output_magmoms = output_analyzer.magmoms + output_symmetry = output_structure.get_space_group_info()[0] + total_magnetization = output_analyzer.total_magmoms + num_formula_units = ( + output_structure.composition.get_reduced_composition_and_factor()[1] + ) + total_magnetization_per_formula_unit = total_magnetization / num_formula_units + total_magnetization_per_unit_volume = total_magnetization / output_structure.volume + + # compare + ordering_changed = not np.array_equal( + np.sign(input_analyzer.magmoms), np.sign(output_magmoms) + ) + symmetry_changed = output_symmetry != input_symmetry + + input_doc = MagneticOrderingInput( + structure=input_structure, + ordering=input_ordering, + magmoms=list(input_magmoms), + symmetry=input_symmetry, + ) + + return { + "input": input_doc, + "magmoms": list(output_magmoms), + "ordering": output_ordering, + "symmetry": output_symmetry, + "ordering_changed": ordering_changed, + "symmetry_changed": symmetry_changed, + "total_magnetization": total_magnetization, + "total_magnetization_per_formula_unit": total_magnetization_per_formula_unit, + "total_magnetization_per_unit_volume": total_magnetization_per_unit_volume, + } diff --git a/src/atomate2/common/schemas/phonons.py b/src/atomate2/common/schemas/phonons.py index 73aed8e11d..a594afa623 100644 --- a/src/atomate2/common/schemas/phonons.py +++ b/src/atomate2/common/schemas/phonons.py @@ -2,6 +2,7 @@ import copy import logging +from pathlib import Path from typing import Optional, Union import numpy as np @@ -26,10 +27,39 @@ from pymatgen.phonon.plotter import PhononBSPlotter, PhononDosPlotter from pymatgen.symmetry.bandstructure import HighSymmKpath from pymatgen.symmetry.kpath import KPathSeek +from typing_extensions import Self + +from atomate2.aims.utils.units import omegaToTHz logger = logging.getLogger(__name__) +def get_factor(code: str) -> float: + """ + Get the frequency conversion factor to THz for each code. + + Parameters + ---------- + code: str + The code to get the conversion factor for + + Returns + ------- + float + The correct conversion factor + + Raises + ------ + ValueError + If code is not defined + """ + if code in ["forcefields", "vasp"]: + return VaspToTHz + if code == "aims": + return omegaToTHz # Based on CODATA 2002 + raise ValueError(f"Frequency conversion factor for code ({code}) not defined.") + + class PhononComputationalSettings(BaseModel): """Collection to store computational settings for the phonon computation.""" @@ -48,15 +78,15 @@ class ThermalDisplacementData(BaseModel): "cutoff frequency in THz to avoid numerical issues in the " "computation of the thermal displacement parameters" ) - thermal_displacement_matrix_cif: list[list[Matrix3D]] = Field( + thermal_displacement_matrix_cif: Optional[list[list[Matrix3D]]] = Field( None, description="field including thermal displacement matrices in CIF format" ) - thermal_displacement_matrix: list[list[Matrix3D]] = Field( + thermal_displacement_matrix: Optional[list[list[Matrix3D]]] = Field( None, description="field including thermal displacement matrices in Cartesian " "coordinate system", ) - temperatures_thermal_displacements: list[int] = Field( + temperatures_thermal_displacements: Optional[list[int]] = Field( None, description="temperatures at which the thermal displacement matrices" "have been computed", @@ -86,10 +116,10 @@ def __init__(self, force_constants: list[list[Matrix3D]]) -> None: class PhononJobDirs(BaseModel): """Collection to save all job directories relevant for the phonon run.""" - displacements_job_dirs: list[Optional[str]] = Field( + displacements_job_dirs: Optional[list[Optional[str]]] = Field( None, description="The directories where the displacement jobs were run." ) - static_run_job_dir: Optional[str] = Field( + static_run_job_dir: Optional[Optional[str]] = Field( None, description="Directory where static run was performed." ) born_run_job_dir: Optional[str] = Field( @@ -98,50 +128,52 @@ class PhononJobDirs(BaseModel): optimization_run_job_dir: Optional[str] = Field( None, description="Directory where optimization run was performed." ) + taskdoc_run_job_dir: Optional[str] = Field( + None, description="Directory where task doc was generated." + ) -class PhononBSDOSDoc(StructureMetadata): +class PhononBSDOSDoc(StructureMetadata, extra="allow"): # type: ignore[call-arg] """Collection of all data produced by the phonon workflow.""" - structure: Structure = Field( - None, - description="Structure of Materials Project.", + structure: Optional[Structure] = Field( + None, description="Structure of Materials Project." ) - phonon_bandstructure: PhononBandStructureSymmLine = Field( + phonon_bandstructure: Optional[PhononBandStructureSymmLine] = Field( None, description="Phonon band structure object.", ) - phonon_dos: PhononDos = Field( + phonon_dos: Optional[PhononDos] = Field( None, description="Phonon density of states object.", ) - free_energies: list[float] = Field( + free_energies: Optional[list[float]] = Field( None, description="vibrational part of the free energies in J/mol per " "formula unit for temperatures in temperature_list", ) - heat_capacities: list[float] = Field( + heat_capacities: Optional[list[float]] = Field( None, description="heat capacities in J/K/mol per " "formula unit for temperatures in temperature_list", ) - internal_energies: list[float] = Field( + internal_energies: Optional[list[float]] = Field( None, - description="internal energies in J/mol per " + description="internal energies in J/mol per " "formula unit for temperatures in temperature_list", ) - entropies: list[float] = Field( + entropies: Optional[list[float]] = Field( None, description="entropies in J/(K*mol) per formula unit" "for temperatures in temperature_list ", ) - temperatures: list[int] = Field( + temperatures: Optional[list[int]] = Field( None, description="temperatures at which the vibrational" " part of the free energies" @@ -150,7 +182,7 @@ class PhononBSDOSDoc(StructureMetadata): total_dft_energy: Optional[float] = Field("total DFT energy per formula unit in eV") - has_imaginary_modes: bool = Field( + has_imaginary_modes: Optional[bool] = Field( None, description="if true, structure has imaginary modes" ) @@ -206,9 +238,8 @@ def from_forces_born( epsilon_static: Matrix3D = None, born: Matrix3D = None, **kwargs, - ) -> "PhononBSDOSDoc": - """ - Generate collection of phonon data. + ) -> Self: + """Generate collection of phonon data. Parameters ---------- @@ -228,7 +259,7 @@ def from_forces_born( code: str which code was used for computation displacement_data: - output of the VASP displacement runs + output of the displacement data total_dft_energy: float total energy in eV per cell epsilon_static: Matrix3D @@ -238,21 +269,26 @@ def from_forces_born( **kwargs: additional arguments """ - if code == "vasp": - factor = VaspToTHz + factor = get_factor(code) # This opens the opportunity to add support for other codes # that are supported by phonopy cell = get_phonopy_structure(structure) - if use_symmetrized_structure == "primitive" and kpath_scheme != "seekpath": - primitive_matrix: Union[list[list[float]], str] = [ - [1.0, 0.0, 0.0], - [0.0, 1.0, 0.0], - [0.0, 0.0, 1.0], - ] + if use_symmetrized_structure == "primitive": + primitive_matrix: Union[np.ndarray, str] = np.eye(3) else: primitive_matrix = "auto" + + # TARP: THIS IS BAD! Including for discussions sake + if cell.magnetic_moments is not None and primitive_matrix == "auto": + if np.any(cell.magnetic_moments != 0.0): + raise ValueError( + "For materials with magnetic moments, " + "use_symmetrized_structure must be 'primitive'" + ) + cell.magnetic_moments = None + phonon = Phonopy( cell, supercell_matrix, @@ -263,6 +299,7 @@ def from_forces_born( ) phonon.generate_displacements(distance=displacement) set_of_forces = [np.array(forces) for forces in displacement_data["forces"]] + if born is not None and epsilon_static is not None: if len(structure) == len(born): borns, epsilon = symmetrize_borns_and_epsilon( @@ -292,11 +329,11 @@ def from_forces_born( # Produces all force constants phonon.produce_force_constants(forces=set_of_forces) - # with phonon.load("phonopy.yaml") the phonopy API can be used + # with phonopy.load("phonopy.yaml") the phonopy API can be used phonon.save("phonopy.yaml") # get phonon band structure - kpath_dict, kpath_concrete = cls.get_kpath( + kpath_dict, kpath_concrete = PhononBSDOSDoc.get_kpath( structure=get_pmg_structure(phonon.primitive), kpath_scheme=kpath_scheme, symprec=symprec, @@ -307,7 +344,7 @@ def from_forces_born( kpath_concrete, npoints=kwargs.get("npoints_band", 101) ) - # phonon band structures will always be cmouted + # phonon band structures will always be computed filename_band_yaml = "phonon_band_structure.yaml" # TODO: potentially add kwargs to avoid computation of eigenvectors @@ -322,10 +359,8 @@ def from_forces_born( filename_band_yaml, labels_dict=kpath_dict, has_nac=born is not None ) new_plotter = PhononBSPlotter(bs=bs_symm_line) - new_plotter.save_plot( - "phonon_band_structure.eps", - img_format=kwargs.get("img_format", "eps"), + filename=kwargs.get("filename_bs", "phonon_band_structure.pdf"), units=kwargs.get("units", "THz"), ) @@ -335,13 +370,13 @@ def from_forces_born( ) # gets data for visualization on website - yaml is also enough - if kwargs.get("band_structure_eigenvectors", False): + if kwargs.get("band_structure_eigenvectors"): bs_symm_line.write_phononwebsite("phonon_website.json") # get phonon density of states filename_dos_yaml = "phonon_dos.yaml" - kpoint_density_dos = kwargs.get("kpoint_density_dos", 7000) + kpoint_density_dos = kwargs.get("kpoint_density_dos", 7_000) kpoint = Kpoints.automatic_density( structure=get_pmg_structure(phonon.primitive), kppa=kpoint_density_dos, @@ -354,8 +389,7 @@ def from_forces_born( new_plotter_dos = PhononDosPlotter() new_plotter_dos.add_dos(label="total", dos=dos) new_plotter_dos.save_plot( - filename="phonon_dos.eps", - img_format=kwargs.get("img_format", "eps"), + filename=kwargs.get("filename_dos", "phonon_dos.pdf"), units=kwargs.get("units", "THz"), ) @@ -366,32 +400,32 @@ def from_forces_born( free_energies = [ dos.helmholtz_free_energy( - structure=get_pmg_structure(phonon.primitive), t=temperature + temp=temp, structure=get_pmg_structure(phonon.primitive) ) - for temperature in temperature_range + for temp in temperature_range ] entropies = [ - dos.entropy(structure=get_pmg_structure(phonon.primitive), t=temperature) - for temperature in temperature_range + dos.entropy(temp=temp, structure=get_pmg_structure(phonon.primitive)) + for temp in temperature_range ] internal_energies = [ dos.internal_energy( - structure=get_pmg_structure(phonon.primitive), t=temperature + temp=temp, structure=get_pmg_structure(phonon.primitive) ) - for temperature in temperature_range + for temp in temperature_range ] heat_capacities = [ - dos.cv(structure=get_pmg_structure(phonon.primitive), t=temperature) - for temperature in temperature_range + dos.cv(temp=temp, structure=get_pmg_structure(phonon.primitive)) + for temp in temperature_range ] # will compute thermal displacement matrices # for the primitive cell (phonon.primitive!) # only this is available in phonopy - if kwargs.get("create_thermal_displacements", False): + if kwargs.get("create_thermal_displacements"): phonon.run_mesh( kpoint.kpts[0], with_eigenvectors=True, is_mesh_symmetry=False ) @@ -410,19 +444,14 @@ def from_forces_born( kwargs.get("tmax_thermal_displacements", 500), kwargs.get("tstep_thermal_displacements", 100), ) - for i, temp in enumerate(temperature_range_thermal_displacements): + for idx, temp in enumerate(temperature_range_thermal_displacements): phonon.thermal_displacement_matrices.write_cif( - phonon.primitive, - i, - filename="tdispmat_" + str(temp) + "K.cif", + phonon.primitive, idx, filename=f"tdispmat_{temp}K.cif" ) - tdisp_mat = ( - phonon._thermal_displacement_matrices.thermal_displacement_matrices.tolist() - ) + _disp_mat = phonon._thermal_displacement_matrices # noqa: SLF001 + tdisp_mat = _disp_mat.thermal_displacement_matrices.tolist() - tdisp_mat_cif = ( - phonon._thermal_displacement_matrices.thermal_displacement_matrices_cif.tolist() - ) + tdisp_mat_cif = _disp_mat.thermal_displacement_matrices_cif.tolist() else: tdisp_mat = None @@ -456,20 +485,21 @@ def from_forces_born( epsilon_static=epsilon.tolist() if epsilon is not None else None, supercell_matrix=phonon.supercell_matrix.tolist(), primitive_matrix=phonon.primitive_matrix.tolist(), - code="vasp", + code=code, thermal_displacement_data={ "temperatures_thermal_displacements": temperature_range_thermal_displacements.tolist(), # noqa: E501 "thermal_displacement_matrix_cif": tdisp_mat_cif, "thermal_displacement_matrix": tdisp_mat, "freq_min_thermal_displacements": freq_min_thermal_displacements, } - if kwargs.get("create_thermal_displacements", False) + if kwargs.get("create_thermal_displacements") else None, jobdirs={ "displacements_job_dirs": displacement_data["dirs"], "static_run_job_dir": kwargs["static_run_job_dir"], "born_run_job_dir": kwargs["born_run_job_dir"], "optimization_run_job_dir": kwargs["optimization_run_job_dir"], + "taskdoc_run_job_dir": str(Path.cwd()), }, uuids={ "displacements_uuids": displacement_data["uuids"], @@ -488,8 +518,7 @@ def from_forces_born( def get_kpath( structure: Structure, kpath_scheme: str, symprec: float, **kpath_kwargs ) -> tuple: - """ - Get high-symmetry points in k-space in phonopy format. + """Get high-symmetry points in k-space in phonopy format. Parameters ---------- @@ -501,22 +530,20 @@ def get_kpath( **kpath_kwargs: additional parameters that can be passed to this method as a dict """ - if kpath_scheme in [ - "setyawan_curtarolo", - "latimer_munro", - "hinuma", - ]: - highsymmkpath = HighSymmKpath( + if kpath_scheme in ("setyawan_curtarolo", "latimer_munro", "hinuma"): + high_symm_kpath = HighSymmKpath( structure, path_type=kpath_scheme, symprec=symprec, **kpath_kwargs ) - kpath = highsymmkpath.kpath + kpath = high_symm_kpath.kpath elif kpath_scheme == "seekpath": - highsymmkpath = KPathSeek(structure, symprec=symprec, **kpath_kwargs) - kpath = highsymmkpath._kpath + high_symm_kpath = KPathSeek(structure, symprec=symprec, **kpath_kwargs) + kpath = high_symm_kpath._kpath # noqa: SLF001 + else: + raise ValueError(f"Unexpected {kpath_scheme=}") path = copy.deepcopy(kpath["path"]) - for ilabelset, labelset in enumerate(kpath["path"]): - for ilabel, label in enumerate(labelset): - path[ilabelset][ilabel] = kpath["kpoints"][label] + for set_idx, label_set in enumerate(kpath["path"]): + for lbl_idx, label in enumerate(label_set): + path[set_idx][lbl_idx] = kpath["kpoints"][label] return kpath["kpoints"], path diff --git a/src/atomate2/common/utils.py b/src/atomate2/common/utils.py index 5fd1c29167..4829e0b98c 100644 --- a/src/atomate2/common/utils.py +++ b/src/atomate2/common/utils.py @@ -112,11 +112,11 @@ def parse_transformations( def parse_additional_json(dir_name: Path) -> dict[str, Any]: - """Parse additional json files in the directory.""" + """Parse additional JSON files in the directory.""" additional_json = {} for filename in dir_name.glob("*.json*"): key = filename.name.split(".")[0] - # ignore FW.json(.gz) so jobflow doesn't try to parse prev_vasp_dir + # ignore FW.json(.gz) so jobflow doesn't try to parse prev_dir # OutputReferences was causing atomate2 MP workflows to fail with ValueError: # Could not resolve reference 7f5a7f14-464c-4a5b-85f9-8d11b595be3b not in store # or cache contact @janosh in case of questions diff --git a/src/atomate2/cp2k/drones.py b/src/atomate2/cp2k/drones.py index c17f350a43..b009e61d41 100644 --- a/src/atomate2/cp2k/drones.py +++ b/src/atomate2/cp2k/drones.py @@ -40,21 +40,21 @@ def assimilate(self, path: str | Path | None = None) -> TaskDocument: TaskDocument A CP2K task document. """ - if path is None: - path = Path.cwd() + path = path or Path.cwd() try: doc = TaskDocument.from_directory(path, **self.task_document_kwargs) except Exception: import traceback - logger.error(f"Error in {Path(path).absolute()}\n{traceback.format_exc()}") + logger.exception( + f"Error in {Path(path).absolute()}\n{traceback.format_exc()}" + ) raise return doc def get_valid_paths(self, path: tuple[str, list[str], list[str]]) -> list[str]: - """ - Get valid paths to assimilate. + """Get valid paths to assimilate. There are some restrictions on the valid directory structures: diff --git a/src/atomate2/cp2k/files.py b/src/atomate2/cp2k/files.py index 6091219fa2..67eb45c6fd 100644 --- a/src/atomate2/cp2k/files.py +++ b/src/atomate2/cp2k/files.py @@ -38,7 +38,7 @@ def copy_cp2k_outputs( For folders containing multiple calculations (e.g., suffixed with relax1, relax2, etc), this function will only copy the files with the highest numbered suffix and - the suffix will be removed. Additional cp2k files will be also be copied with the + the suffix will be removed. Additional cp2k files will be also be copied with the same suffix applied. Lastly, this function will gunzip any gzipped files. Parameters @@ -62,7 +62,7 @@ def copy_cp2k_outputs( relax_ext = get_largest_relax_extension(src_dir, src_host, file_client=file_client) directory_listing = file_client.listdir(src_dir, host=src_host) restart_file = None - additional_cp2k_files = additional_cp2k_files if additional_cp2k_files else [] + additional_cp2k_files = additional_cp2k_files or [] # find required files o = Cp2kOutput(src_dir / get_zfile(directory_listing, "cp2k.out"), auto_load=False) @@ -102,8 +102,10 @@ def copy_cp2k_outputs( # rename files to remove relax extension if relax_ext: files_to_rename = { - k.name.replace(".gz", ""): k.name.replace(relax_ext, "").replace(".gz", "") - for k in all_files + file.name.replace(".gz", ""): file.name.replace(relax_ext, "").replace( + ".gz", "" + ) + for file in all_files } rename_files(files_to_rename, allow_missing=True, file_client=file_client) @@ -149,7 +151,7 @@ def get_largest_relax_extension( return "" numbers = [re.search(r".relax(\d+)", file.name).group(1) for file in relax_files] - max_relax = max(numbers, key=lambda x: int(x)) + max_relax = max(numbers, key=int) return f".relax{max_relax}" diff --git a/src/atomate2/cp2k/flows/core.py b/src/atomate2/cp2k/flows/core.py index 209545ed47..f52f2912b9 100644 --- a/src/atomate2/cp2k/flows/core.py +++ b/src/atomate2/cp2k/flows/core.py @@ -23,6 +23,7 @@ from pathlib import Path from pymatgen.core.structure import Structure + from typing_extensions import Self from atomate2.cp2k.jobs.base import BaseCp2kMaker @@ -46,17 +47,14 @@ class DoubleRelaxMaker(Maker): relax_maker1: Maker = field(default_factory=RelaxMaker) relax_maker2: Maker = field(default_factory=RelaxMaker) - def make( - self, structure: Structure, prev_cp2k_dir: str | Path | None = None - ) -> Flow: - """ - Create a flow with two chained relaxations. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Create a flow with two chained relaxations. Parameters ---------- structure : .Structure A pymatgen structure object. - prev_cp2k_dir : str or Path or None + prev_dir : str or Path or None A previous Cp2k calculation directory to copy output files from. Returns @@ -64,18 +62,18 @@ def make( Flow A flow containing two relaxations. """ - relax1 = self.relax_maker1.make(structure, prev_cp2k_dir=prev_cp2k_dir) + relax1 = self.relax_maker1.make(structure, prev_dir=prev_dir) relax1.name += " 1" relax2 = self.relax_maker2.make( - relax1.output.structure, prev_cp2k_dir=relax1.output.dir_name + relax1.output.structure, prev_dir=relax1.output.dir_name ) relax2.name += " 2" return Flow([relax1, relax2], relax2.output, name=self.name) @classmethod - def from_relax_maker(cls, relax_maker: BaseCp2kMaker) -> DoubleRelaxMaker: + def from_relax_maker(cls, relax_maker: BaseCp2kMaker) -> Self: """ Instantiate the DoubleRelaxMaker with two relax makers of the same type. @@ -114,17 +112,14 @@ class BandStructureMaker(Maker): static_maker: Maker = field(default_factory=StaticMaker) bs_maker: Maker = field(default_factory=NonSCFMaker) - def make( - self, structure: Structure, prev_cp2k_dir: str | Path | None = None - ) -> Flow: - """ - Create a band structure flow. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Create a band structure flow. Parameters ---------- structure : Structure A pymatgen structure object. - prev_cp2k_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns @@ -132,7 +127,7 @@ def make( Flow A band structure flow. """ - static_job = self.static_maker.make(structure, prev_cp2k_dir=prev_cp2k_dir) + static_job = self.static_maker.make(structure, prev_dir=prev_dir) jobs = [static_job] outputs = {} @@ -140,7 +135,7 @@ def make( if bandstructure_type in ("both", "uniform"): uniform_job = self.bs_maker.make( static_job.output.structure, - prev_cp2k_dir=static_job.output.dir_name, + prev_dir=static_job.output.dir_name, mode="uniform", ) uniform_job.name += " uniform" @@ -154,7 +149,7 @@ def make( if bandstructure_type in ("both", "line"): line_job = self.bs_maker.make( static_job.output.structure, - prev_cp2k_dir=static_job.output.dir_name, + prev_dir=static_job.output.dir_name, mode="line", ) line_job.name += " line" @@ -192,17 +187,14 @@ class RelaxBandStructureMaker(Maker): relax_maker: Maker = field(default_factory=DoubleRelaxMaker) band_structure_maker: Maker = field(default_factory=BandStructureMaker) - def make( - self, structure: Structure, prev_cp2k_dir: str | Path | None = None - ) -> Flow: - """ - Run a relaxation and then calculate the uniform and line mode band structures. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Run a relaxation, then calculate the uniform and line mode band structures. Parameters ---------- structure: .Structure A pymatgen structure object. - prev_cp2k_dir : str or Path or None + prev_dir : str or Path or None A previous CP2K calculation directory to copy output files from. Returns @@ -210,9 +202,9 @@ def make( Flow A relax and band structure flow. """ - relax_job = self.relax_maker.make(structure, prev_cp2k_dir=prev_cp2k_dir) + relax_job = self.relax_maker.make(structure, prev_dir=prev_dir) bs_flow = self.band_structure_maker.make( - relax_job.output.structure, prev_cp2k_dir=relax_job.output.dir_name + relax_job.output.structure, prev_dir=relax_job.output.dir_name ) return Flow([relax_job, bs_flow], bs_flow.output, name=self.name) @@ -265,17 +257,14 @@ def __post_init__(self) -> None: updates, self.hybrid_maker.input_set_generator.user_input_settings ) - def make( - self, structure: Structure, prev_cp2k_dir: str | Path | None = None - ) -> Job: - """ - Make a hybrid flow. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Job: + """Make a hybrid flow. Parameters ---------- structure: .Structure A pymatgen structure object. - prev_cp2k_dir : str or Path or None + prev_dir : str or Path or None A previous CP2K calculation directory to copy output files from. Returns @@ -285,13 +274,13 @@ def make( """ jobs = [] if self.initialize_with_pbe: - initialization = self.pbe_maker.make(structure, prev_cp2k_dir) + initialization = self.pbe_maker.make(structure, prev_dir) jobs.append(initialization) hyb = self.hybrid_maker.make( initialization.output.structure if self.initialize_with_pbe else structure, - prev_cp2k_dir=initialization.output.dir_name + prev_dir=initialization.output.dir_name if self.initialize_with_pbe - else prev_cp2k_dir, + else prev_dir, ) jobs.append(hyb) return Flow(jobs, output=hyb.output, name=self.name) diff --git a/src/atomate2/cp2k/jobs/base.py b/src/atomate2/cp2k/jobs/base.py index eb28e89c96..6d5608dbd0 100644 --- a/src/atomate2/cp2k/jobs/base.py +++ b/src/atomate2/cp2k/jobs/base.py @@ -129,16 +129,15 @@ class BaseCp2kMaker(Maker): @cp2k_job def make( - self, structure: Structure, prev_cp2k_dir: str | Path | None = None + self, structure: Structure, prev_dir: str | Path | None = None ) -> Response: - """ - Run a CP2K calculation. + """Run a CP2K calculation. Parameters ---------- structure : Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous CP2K calculation directory to copy output files from. """ # Apply transformations if they are present @@ -155,9 +154,9 @@ def make( self.write_additional_data.setdefault("transformations:json", t_json) # copy previous inputs - from_prev = prev_cp2k_dir is not None - if prev_cp2k_dir is not None: - copy_cp2k_outputs(prev_cp2k_dir, **self.copy_cp2k_kwargs) + from_prev = prev_dir is not None + if prev_dir is not None: + copy_cp2k_outputs(prev_dir, **self.copy_cp2k_kwargs) # write cp2k input files self.write_input_set_kwargs["from_prev"] = from_prev diff --git a/src/atomate2/cp2k/jobs/core.py b/src/atomate2/cp2k/jobs/core.py index 568a97d5cb..1704ffba36 100644 --- a/src/atomate2/cp2k/jobs/core.py +++ b/src/atomate2/cp2k/jobs/core.py @@ -300,17 +300,16 @@ class NonSCFMaker(BaseCp2kMaker): def make( self, structure: Structure, - prev_cp2k_dir: str | Path | None, + prev_dir: str | Path | None, mode: str = "uniform", ) -> None: - """ - Run a non-scf CP2K job. + """Run a non-scf CP2K job. Parameters ---------- structure : .Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous CP2K calculation directory to copy output files from. mode : str Type of band structure calculation. Options are: @@ -325,7 +324,7 @@ def make( # copy previous inputs self.copy_cp2k_kwargs.setdefault("additional_cp2k_files", ("wfn",)) - return super().make.original(self, structure, prev_cp2k_dir) + return super().make.original(self, structure, prev_dir) @dataclass @@ -376,16 +375,15 @@ class TransmuterMaker(BaseCp2kMaker): def make( self, structure: Structure, - prev_cp2k_dir: str | Path | None = None, + prev_dir: str | Path | None = None, ) -> None: - """ - Run a transmuter Cp2k job. + """Run a transmuter Cp2k job. Parameters ---------- structure : Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous Cp2k calculation directory to copy output files from. """ transformations = get_transformations( @@ -399,7 +397,7 @@ def make( tjson = transmuter.transformed_structures[-1] self.write_additional_data.setdefault("transformations:json", tjson) - return super().make.original(self, structure, prev_cp2k_dir) + return super().make.original(self, structure, prev_dir) @dataclass diff --git a/src/atomate2/cp2k/powerups.py b/src/atomate2/cp2k/powerups.py index 35e696d781..205b30c39f 100644 --- a/src/atomate2/cp2k/powerups.py +++ b/src/atomate2/cp2k/powerups.py @@ -8,6 +8,8 @@ from jobflow import Flow, Job, Maker from pymatgen.io.vasp import Kpoints +from atomate2.common.powerups import add_metadata_to_flow as base_add_metadata_to_flow +from atomate2.common.powerups import update_custodian_handlers as base_custodian_handler from atomate2.cp2k.jobs.base import BaseCp2kMaker @@ -45,12 +47,14 @@ def update_user_input_settings( A copy of the input flow/job/maker modified to use the updated input settings. """ - # Convert nested dictionary updates for cp2k inpt settings + # Convert nested dictionary updates for cp2k input settings # into dict_mod update format - def nested_to_dictmod(d, kk="input_set_generator->user_input_settings") -> dict: + def nested_to_dictmod( + dct: dict, kk: str = "input_set_generator->user_input_settings" + ) -> dict: d2 = {} - for k, v in d.items(): - k2 = kk + f"->{k}" + for k, v in dct.items(): + k2 = f"{kk}->{k}" if isinstance(v, dict): d2.update(nested_to_dictmod(v, kk=k2)) else: @@ -138,3 +142,57 @@ def update_user_kpoints_settings( dict_mod=True, ) return updated_flow + + +def add_metadata_to_flow( + flow: Flow, additional_fields: dict, class_filter: Maker = BaseCp2kMaker +) -> Flow: + """ + Return the Cp2k flow with additional field(metadata) to the task doc. + + This allows adding metadata to the task-docs, could be useful + to query results from DB. + + Parameters + ---------- + flow: + additional_fields : dict + A dict with metadata. + class_filter: .BaseCp2kMaker + The Maker to which additional metadata needs to be added + + Returns + ------- + Flow + Flow with added metadata to the task-doc. + """ + return base_add_metadata_to_flow( + flow=flow, class_filter=class_filter, additional_fields=additional_fields + ) + + +def update_cp2k_custodian_handlers( + flow: Flow, custom_handlers: tuple, class_filter: Maker = BaseCp2kMaker +) -> Flow: + """ + Return the flow with custom custodian handlers for Cp2k jobs. + + This allows user to selectively set error correcting handlers for Cp2k jobs + or completely unset error handlers. + + Parameters + ---------- + flow: + custom_handlers : tuple + A tuple with custodian handlers. + class_filter: .BaseCp2kMaker + The Maker to which custom custodian handler needs to be added + + Returns + ------- + Flow + Flow with modified custodian handlers. + """ + return base_custodian_handler( + flow=flow, custom_handlers=custom_handlers, class_filter=class_filter + ) diff --git a/src/atomate2/cp2k/run.py b/src/atomate2/cp2k/run.py index 1693fdb34e..3e5334cce4 100644 --- a/src/atomate2/cp2k/run.py +++ b/src/atomate2/cp2k/run.py @@ -104,7 +104,7 @@ def run_cp2k( if job_type == JobType.DIRECT: logger.info(f"Running command: {cp2k_cmd}") - return_code = subprocess.call(cp2k_cmd, shell=True) + return_code = subprocess.call(cp2k_cmd, shell=True) # noqa: S602 logger.info(f"{cp2k_cmd} finished running with returncode: {return_code}") return if job_type == JobType.NORMAL: diff --git a/src/atomate2/cp2k/schemas/calc_types/_generate.py b/src/atomate2/cp2k/schemas/calc_types/_generate.py index 51a013a280..8881a144c3 100644 --- a/src/atomate2/cp2k/schemas/calc_types/_generate.py +++ b/src/atomate2/cp2k/schemas/calc_types/_generate.py @@ -1,6 +1,8 @@ """Module to define various calculation types as Enums for CP2K.""" + from itertools import product from pathlib import Path +from typing import Any from monty.serialization import loadfn @@ -18,19 +20,18 @@ _RUN_TYPES = [] for functional_class in _RUN_TYPE_DATA: for rt in _RUN_TYPE_DATA[functional_class]: - for vdw in ["", "-RVV10", "-LMKLL", "-DRSLL", "-D3", "-D2", "-D3(BJ)"]: - for u in ["", "+U"]: + for vdw in ("", "-RVV10", "-LMKLL", "-DRSLL", "-D3", "-D2", "-D3(BJ)"): + for u in ("", "+U"): _RUN_TYPES.append(f"{rt}{vdw}{u}") # noqa: PERF401 -def get_enum_source(enum_name, doc, items) -> str: +def get_enum_source(enum_name: str, doc: str, items: dict[str, Any]) -> str: header = f""" class {enum_name}(ValueEnum): \"\"\" {doc} \"\"\"\n """ - items = [f' {const} = "{val}"' for const, val in items.items()] - return header + "\n".join(items) + return header + "\n".join(f' {key} = "{val}"' for key, val in items.items()) run_type_enum = get_enum_source( @@ -52,11 +53,11 @@ class {enum_name}(ValueEnum): ) -def get_calc_type_key(rt) -> str: - """Conveniece function for readability.""" - s = "_".join(rt.split()) - s = s.replace("+", "_").replace("-", "_").replace("(", "_").replace(")", "") - return f"{s}" +def get_calc_type_key(rt: str) -> str: + """Get the calc_type key from the run_type. Convenience function for readability.""" + out = "_".join(rt.split()) + out = out.replace("+", "_").replace("-", "_").replace("(", "_").replace(")", "") + return f"{out}" calc_type_enum = get_enum_source( @@ -69,8 +70,8 @@ def get_calc_type_key(rt) -> str: ) -with open(Path(__file__).parent / "enums.py", "w") as f: - f.write( +with open(Path(__file__).parent / "enums.py", "w") as file: + file.write( """\"\"\" Autogenerated Enums for CP2K RunType, TaskType, and CalcType Do not edit this by hand. Edit generate.py or run_types.yaml instead @@ -79,9 +80,9 @@ def get_calc_type_key(rt) -> str: """ ) - f.write(run_type_enum) - f.write("\n\n") - f.write(task_type_enum) - f.write("\n\n") - f.write(calc_type_enum) - f.write("\n") + file.write(run_type_enum) + file.write("\n\n") + file.write(task_type_enum) + file.write("\n\n") + file.write(calc_type_enum) + file.write("\n") diff --git a/src/atomate2/cp2k/schemas/calc_types/utils.py b/src/atomate2/cp2k/schemas/calc_types/utils.py index a22971088c..f564131144 100644 --- a/src/atomate2/cp2k/schemas/calc_types/utils.py +++ b/src/atomate2/cp2k/schemas/calc_types/utils.py @@ -1,5 +1,6 @@ """Module to define various calculation types as Enums for CP2K.""" -from collections.abc import Iterable + +from collections.abc import Iterable, Sequence from pathlib import Path from monty.serialization import loadfn @@ -17,11 +18,11 @@ def run_type(inputs: dict) -> RunType: This is adapted from pymatgen to be far less unstable. Args: - dft: dictionary of dft parameters (standard from task doc) + dft: dictionary of DFT parameters (standard from task doc) """ dft = inputs.get("dft") - def _variant_equal(v1, v2) -> bool: + def _variant_equal(v1: Sequence, v2: Sequence) -> bool: """Determine if two run_types are equal.""" if isinstance(v1, str) and isinstance(v2, str): return v1.strip().upper() == v2.strip().upper() @@ -72,12 +73,12 @@ def task_type(inputs: dict) -> TaskType: cp2k_run_type = inputs.get("cp2k_global", {}).get("Run_type", "") ci = Cp2kInput.from_dict(inputs["cp2k_input"]) - if cp2k_run_type.upper() in [ + if cp2k_run_type.upper() in ( "ENERGY", "ENERGY_FORCE", "WAVEFUNCTION_OPTIMIZATION", "WFN_OPT", - ]: + ): if ci.check("FORCE_EVAL/DFT/SCF"): tmp = ci["force_eval"]["dft"]["scf"].get("MAX_SCF", Keyword("", 50)) if tmp.values[0] == 1: @@ -100,34 +101,34 @@ def task_type(inputs: dict) -> TaskType: else: calc_type.append("Static") - elif cp2k_run_type.upper() in ["GEO_OPT", "GEOMETRY_OPTIMIZATION", "CELL_OPT"]: + elif cp2k_run_type.upper() in ("GEO_OPT", "GEOMETRY_OPTIMIZATION", "CELL_OPT"): calc_type.append("Structure Optimization") elif cp2k_run_type.upper() == "BAND": calc_type.append("Band") - elif cp2k_run_type.upper() in ["MOLECULAR_DYNAMICS", "MD"]: + elif cp2k_run_type.upper() in ("MOLECULAR_DYNAMICS", "MD"): calc_type.append("Molecular Dynamics") - elif cp2k_run_type.upper() in ["MONTE_CARLO", "MC", "TMC", "TAMC"]: + elif cp2k_run_type.upper() in ("MONTE_CARLO", "MC", "TMC", "TAMC"): calc_type.append("Monte Carlo") - elif cp2k_run_type.upper() in ["LINEAR_RESPONSE", "LR"]: + elif cp2k_run_type.upper() in ("LINEAR_RESPONSE", "LR"): calc_type.append("Linear Response") - elif cp2k_run_type.upper() in ["VIBRATIONAL_ANALYSIS", "NORMAL_MODES"]: + elif cp2k_run_type.upper() in ("VIBRATIONAL_ANALYSIS", "NORMAL_MODES"): calc_type.append("Vibrational Analysis") - elif cp2k_run_type.upper() in ["ELECTRONIC_SPECTRA", "SPECTRA"]: + elif cp2k_run_type.upper() in ("ELECTRONIC_SPECTRA", "SPECTRA"): calc_type.append("Electronic Spectra") elif cp2k_run_type.upper() == "NEGF": calc_type.append("Non-equilibrium Green's Function") - elif cp2k_run_type.upper() in ["PINT", "DRIVER"]: + elif cp2k_run_type.upper() in ("PINT", "DRIVER"): calc_type.append("Path Integral") - elif cp2k_run_type.upper() in ["RT_PROPAGATION", "EHRENFEST_DYN"]: + elif cp2k_run_type.upper() in ("RT_PROPAGATION", "EHRENFEST_DYN"): calc_type.append("Real-time propagation") elif cp2k_run_type.upper() == "BSSE": diff --git a/src/atomate2/cp2k/schemas/calculation.py b/src/atomate2/cp2k/schemas/calculation.py index 4a70dab8c9..c9a1214ad6 100644 --- a/src/atomate2/cp2k/schemas/calculation.py +++ b/src/atomate2/cp2k/schemas/calculation.py @@ -2,7 +2,7 @@ import logging import os -from datetime import datetime +from datetime import datetime, timezone from pathlib import Path from shutil import which from typing import Any, Optional, Union @@ -18,6 +18,7 @@ from pymatgen.io.common import VolumetricData from pymatgen.io.cp2k.inputs import BasisFile, DataFile, PotentialFile from pymatgen.io.cp2k.outputs import Cp2kOutput, parse_energy_file +from typing_extensions import Self from atomate2 import SETTINGS from atomate2.cp2k.schemas.calc_types import ( @@ -84,23 +85,23 @@ class CalculationInput(BaseModel): @field_validator("atomic_kind_info", mode="before") @classmethod - def remove_unnecessary(cls, atomic_kind_info) -> dict: + def remove_unnecessary(cls, atomic_kind_info: dict) -> dict: """Remove unnecessary entry from atomic_kind_info.""" - for k in atomic_kind_info: - if "total_pseudopotential_energy" in atomic_kind_info[k]: - del atomic_kind_info[k]["total_pseudopotential_energy"] + for key in atomic_kind_info: + if "total_pseudopotential_energy" in atomic_kind_info[key]: + del atomic_kind_info[key]["total_pseudopotential_energy"] return atomic_kind_info @field_validator("dft", mode="before") @classmethod - def cleanup_dft(cls, dft) -> dict: + def cleanup_dft(cls, dft: dict) -> dict: """Convert UKS strings to UKS=True.""" if any(v.upper() == "UKS" for v in dft.values()): dft["UKS"] = True return dft @classmethod - def from_cp2k_output(cls, output: Cp2kOutput) -> "CalculationInput": + def from_cp2k_output(cls, output: Cp2kOutput) -> Self: """Initialize from Cp2kOutput object.""" return cls( structure=output.initial_structure, @@ -117,9 +118,8 @@ class RunStatistics(BaseModel): total_time: float = Field(0, description="The total CPU time for this calculation") @classmethod - def from_cp2k_output(cls, output: Cp2kOutput) -> "RunStatistics": - """ - Create a run statistics document from an CP2K Output object. + def from_cp2k_output(cls, output: Cp2kOutput) -> Self: + """Create a run statistics document from an CP2K Output object. Parameters ---------- @@ -186,9 +186,8 @@ def from_cp2k_output( v_hartree: Optional[VolumetricData] = None, store_trajectory: bool = False, store_scf: bool = False, - ) -> "CalculationOutput": - """ - Create a CP2K output document from CP2K outputs. + ) -> Self: + """Create a CP2K output document from CP2K outputs. Parameters ---------- @@ -302,9 +301,8 @@ def from_cp2k_files( store_volumetric_data: Optional[ tuple[str] ] = SETTINGS.CP2K_STORE_VOLUMETRIC_DATA, - ) -> tuple["Calculation", dict[Cp2kObject, dict]]: - """ - Create a CP2K calculation document from a directory and file paths. + ) -> tuple[Self, dict[Cp2kObject, dict]]: + """Create a CP2K calculation document from a directory and file paths. Parameters ---------- @@ -336,9 +334,9 @@ def from_cp2k_files( vbm, cbm, band_gap, is_metal and efermi rather than the full band structure object. - average_v_hartree + average_v_hartree : bool = True Whether to store the average of the V_HARTREE along the crystal axes. - run_bader + run_bader : bool = False Whether to run bader on the charge density. strip_dos_projections : bool Whether to strip the element and site projections from the density of @@ -347,13 +345,13 @@ def from_cp2k_files( strip_bandstructure_projections : bool Whether to strip the element and site projections from the band structure. This can help reduce the size of DOS objects in systems with many atoms. - store_trajectory: + store_trajectory : bool = False Whether to store the ionic steps as a pmg trajectory object, which can be pushed, to a bson data store, instead of as a list od dicts. Useful for large trajectories. - store_scf: + store_scf : bool = False Whether to store the SCF convergence data. - store_volumetric_data + store_volumetric_data : tuple[str] | None = SETTINGS.CP2K_STORE_VOLUMETRIC_DATA Which volumetric files to store. Returns @@ -366,7 +364,9 @@ def from_cp2k_files( volumetric_files = [] if volumetric_files is None else volumetric_files cp2k_output = Cp2kOutput(cp2k_output_file, auto_load=True) - completed_at = str(datetime.fromtimestamp(os.stat(cp2k_output_file).st_mtime)) + completed_at = str( + datetime.fromtimestamp(os.stat(cp2k_output_file).st_mtime, tz=timezone.utc) + ) output_file_paths = _get_output_file_paths(volumetric_files) cp2k_objects: dict[Cp2kObject, Any] = _get_volumetric_data( @@ -394,9 +394,9 @@ def from_cp2k_files( # TODO vasp version calls bader_analysis_from_path but cp2k # cube files don't support that yet, do it manually bader = { - "min_dist": [d["min_dist"] for d in ba.data], - "charge": [d["charge"] for d in ba.data], - "atomic_volume": [d["atomic_vol"] for d in ba.data], + "min_dist": [dct["min_dist"] for dct in ba.data], + "charge": [dct["charge"] for dct in ba.data], + "atomic_volume": [dct["atomic_vol"] for dct in ba.data], "vacuum_charge": ba.vacuum_charge, "vacuum_volume": ba.vacuum_volume, "reference_used": bool(ba.chgref_filename), @@ -479,9 +479,7 @@ def _get_basis_and_potential_files(dir_name: Path) -> dict[Cp2kObject, DataFile] """ data: dict[Cp2kObject, DataFile] = {} if Path.exists(dir_name / "BASIS"): - data[Cp2kObject.BASIS] = BasisFile.from_file( # type: ignore[index] - str(dir_name / "BASIS") - ) + data[Cp2kObject.BASIS] = BasisFile.from_file(str(dir_name / "BASIS")) # type: ignore[index] if Path.exists(dir_name / "POTENTIAL"): data[Cp2kObject.POTENTIAL] = PotentialFile.from_file( # type: ignore[index] str(dir_name / "POTENTIAL") diff --git a/src/atomate2/cp2k/schemas/task.py b/src/atomate2/cp2k/schemas/task.py index 8f8c0384b5..46072fd7de 100644 --- a/src/atomate2/cp2k/schemas/task.py +++ b/src/atomate2/cp2k/schemas/task.py @@ -1,8 +1,9 @@ """Core definition of a CP2K task document.""" + import logging from collections import OrderedDict from pathlib import Path -from typing import Any, Optional, TypeVar, Union +from typing import Any, Optional, Union import numpy as np from emmet.core.math import Matrix3D, Vector3D @@ -12,6 +13,7 @@ from pymatgen.entries.computed_entries import ComputedEntry from pymatgen.io.cp2k.inputs import Cp2kInput from pymatgen.io.cp2k.utils import natural_keys +from typing_extensions import Self from atomate2 import SETTINGS, __version__ from atomate2.common.utils import ( @@ -29,7 +31,6 @@ from atomate2.utils.path import get_uri logger = logging.getLogger(__name__) -_T = TypeVar("_T", bound="TaskDocument") _VOLUMETRIC_FILES = ("v_hartree", "ELECTRON_DENSITY", "SPIN_DENSITY") @@ -45,9 +46,8 @@ class AnalysisSummary(BaseModel): errors: list[str] = Field(None, description="Errors from the VASP drone") @classmethod - def from_cp2k_calc_docs(cls, calc_docs: list[Calculation]) -> "AnalysisSummary": - """ - Create analysis summary from CP2K calculation documents. + def from_cp2k_calc_docs(cls, calc_docs: list[Calculation]) -> Self: + """Create analysis summary from CP2K calculation documents. Parameters ---------- @@ -118,7 +118,7 @@ class AtomicKindSummary(BaseModel): ) @classmethod - def from_atomic_kind_info(cls, atomic_kind_info: dict) -> "AtomicKindSummary": + def from_atomic_kind_info(cls, atomic_kind_info: dict) -> Self: """Initialize from the atomic_kind_info dictionary.""" d: dict[str, dict[str, Any]] = {"atomic_kinds": {}} for kind, info in atomic_kind_info.items(): @@ -149,9 +149,8 @@ class InputSummary(BaseModel): ) @classmethod - def from_cp2k_calc_doc(cls, calc_doc: Calculation) -> "InputSummary": - """ - Create calculation input summary from a calculation document. + def from_cp2k_calc_doc(cls, calc_doc: Calculation) -> Self: + """Create calculation input summary from a calculation document. Parameters ---------- @@ -199,9 +198,8 @@ class OutputSummary(BaseModel): ) @classmethod - def from_cp2k_calc_doc(cls, calc_doc: Calculation) -> "OutputSummary": - """ - Create a summary of CP2K calculation outputs from a CP2K calculation document. + def from_cp2k_calc_doc(cls, calc_doc: Calculation) -> Self: + """Make a summary of CP2K calculation outputs from a CP2K calculation document. Parameters ---------- @@ -305,22 +303,21 @@ class TaskDocument(StructureMetadata, MoleculeMetadata): @classmethod def from_directory( - cls: type[_T], + cls, dir_name: Union[Path, str], volumetric_files: tuple[str, ...] = _VOLUMETRIC_FILES, store_additional_json: bool = SETTINGS.CP2K_STORE_ADDITIONAL_JSON, additional_fields: dict[str, Any] = None, **cp2k_calculation_kwargs, - ) -> "TaskDocument": - """ - Create a task document from a directory containing CP2K files. + ) -> Self: + """Create a task document from a directory containing CP2K files. Parameters ---------- dir_name The path to the folder containing the calculation outputs. store_additional_json - Whether to store additional json files found in the calculation directory. + Whether to store additional JSON files found in the calculation directory. volumetric_files Volumetric files to search for. additional_fields @@ -421,8 +418,7 @@ def from_directory( def get_entry( calc_docs: list[Calculation], job_id: Optional[str] = None ) -> ComputedEntry: - """ - Get a computed entry from a list of CP2K calculation documents. + """Get a computed entry from a list of CP2K calculation documents. Parameters ---------- @@ -486,7 +482,7 @@ def _find_cp2k_files( path = Path(path) task_files = OrderedDict() - def _get_task_files(files, suffix="") -> dict[str, Any]: + def _get_task_files(files: list[Path], suffix: str = "") -> dict[str, Any]: cp2k_files: dict[str, Any] = {} vol_files = [] for file in files: diff --git a/src/atomate2/cp2k/sets/base.py b/src/atomate2/cp2k/sets/base.py index 7aa3fdb0c5..203af8047a 100644 --- a/src/atomate2/cp2k/sets/base.py +++ b/src/atomate2/cp2k/sets/base.py @@ -5,13 +5,13 @@ import os from copy import deepcopy from dataclasses import dataclass, field +from importlib.resources import files as get_mod_path from pathlib import Path from typing import Any import numpy as np from monty.io import zopen from monty.serialization import loadfn -from pkg_resources import resource_filename from pymatgen.core.structure import Molecule, Structure from pymatgen.io.core import InputGenerator, InputSet from pymatgen.io.cp2k.inputs import ( @@ -29,8 +29,8 @@ from atomate2 import SETTINGS -_BASE_CP2K_SET = loadfn(resource_filename("atomate2.cp2k.sets", "BaseCp2kSet.yaml")) -_BASE_GAPW_SET = loadfn(resource_filename("atomate2.cp2k.sets", "BaseAllSet.yaml")) +_BASE_CP2K_SET = loadfn(get_mod_path("atomate2.cp2k.sets") / "BaseCp2kSet.yaml") +_BASE_GAPW_SET = loadfn(get_mod_path("atomate2.cp2k.sets") / "BaseAllSet.yaml") class Cp2kInputSet(InputSet): @@ -41,8 +41,7 @@ def __init__( cp2k_input: Cp2kInput, optional_files: dict | None = None, ) -> None: - """ - Initialize the set. + """Initialize the set. Parameters ---------- @@ -72,9 +71,7 @@ def __init__( structure definition to an external file in order to keep the main input file neat. This use case requires "@include" parameters (see pymatgen.io.cp2k or the cp2k manual) - (3) Other custom data files like vdw kernel tables, truncated coulomb - tables, classical MD potential parameters. - + (3) Other custom data files like vdw kernel tables, truncated coulomb. """ self.cp2k_input = cp2k_input self.optional_files = optional_files or {} @@ -85,8 +82,7 @@ def write_input( make_dir: bool = True, overwrite: bool = True, ) -> None: - """ - Write Cp2k input file to a directory. + """Write Cp2k input file to a directory. Parameters ---------- @@ -106,21 +102,20 @@ def write_input( } inputs.update(self.optional_files) - for k, v in inputs.items(): - fn = v.get("filename") - obj = v.get("object") - if v is not None and (overwrite or not (directory / k).exists()): - with zopen(directory / fn, "wt") as f: - f.write(str(obj)) - elif not overwrite and (directory / fn).exists(): - raise FileExistsError(f"{directory / fn} already exists.") + for key, val in inputs.items(): + filename = val.get("filename") + obj = val.get("object") + if val is not None and (overwrite or not (directory / key).exists()): + with zopen(directory / filename, "wt") as file: + file.write(str(obj)) + elif not overwrite and (directory / filename).exists(): + raise FileExistsError(f"{directory / filename} already exists.") @staticmethod def from_directory( directory: str | Path, optional_files: dict = None ) -> Cp2kInputSet: - """ - Load a set of CP2K inputs from a directory. + """Load a set of CP2K inputs from a directory. Parameters ---------- @@ -135,7 +130,7 @@ def from_directory( cp2k_input = Cp2kInput.from_file(directory / "cp2k.inp") else: raise FileNotFoundError - optional_files = optional_files if optional_files else {} + optional_files = optional_files or {} optional = {} for filename, obj in optional_files.items(): optional[filename] = { @@ -148,14 +143,7 @@ def from_directory( # TODO Validation @property def is_valid(self) -> bool: - """ - Whether the input set is valid. - - Returns - ------- - bool - Whether the input set is valid. - """ + """Whether the input set is valid.""" return True @@ -196,8 +184,7 @@ def get_input_set( prev_dir: str | Path = None, optional_files: dict | None = None, ) -> Cp2kInputSet: - """ - Get a CP2K input set. + """Get a CP2K input set. Note, if both ``structure`` and ``prev_dir`` are set, then the structure specified will be preferred over the final structure from the last CP2K run. @@ -216,7 +203,7 @@ def get_input_set( Cp2kInput A Cp2k input set. """ - structure, prev_input, cp2k_output = self._get_previous(structure, prev_dir) + structure, prev_input, _cp2k_output = self._get_previous(structure, prev_dir) input_updates = self.get_input_updates( structure, @@ -237,7 +224,7 @@ def get_input_set( prev_input, input_updates, ) - optional_files = optional_files if optional_files else {} + optional_files = optional_files or {} optional_files["basis"] = { "filename": "BASIS", "object": self._get_basis_file(cp2k_input=cp2k_input), @@ -250,8 +237,7 @@ def get_input_set( return Cp2kInputSet(cp2k_input=cp2k_input, optional_files=optional_files) def get_input_updates(self, structure: Structure, prev_input: Cp2kInput) -> dict: - """ - Get updates to the cp2k input for this calculation type. + """Get updates to the cp2k input for this calculation type. Parameters ---------- @@ -274,8 +260,7 @@ def get_input_updates(self, structure: Structure, prev_input: Cp2kInput) -> dict def get_kpoints_updates( self, structure: Structure, prev_input: Cp2kInput = None ) -> dict: - """ - Get updates to the kpoints configuration for this calculation type. + """Get updates to the kpoints configuration for this calculation type. Note, these updates will be ignored if the user has set user_kpoint_settings. @@ -302,7 +287,7 @@ def _get_previous( ) -> tuple[Structure, Cp2kInput, Cp2kOutput]: """Load previous calculation outputs and decide which structure to use.""" if structure is None and prev_dir is None: - raise ValueError("Either structure or prev_dir must be set.") + raise ValueError("Either structure or prev_dir must be set") prev_input = {} prev_structure = None @@ -317,7 +302,7 @@ def _get_previous( return structure, prev_input, cp2k_output - def _get_structure(self, structure) -> Structure: + def _get_structure(self, structure: Structure) -> Structure: """Get the standardized structure.""" if self.sort_structure and hasattr(structure, "get_sorted_structure"): structure = structure.get_sorted_structure() @@ -360,8 +345,7 @@ def _get_input( return cp2k_input def _get_basis_file(self, cp2k_input: Cp2kInput) -> BasisFile: - """ - Get the basis sets for the input object and convert them to a basis file object. + """Get input object's basis sets and convert them to a basis file object. Allows calculation to execute if the basis sets are not available on the execution resource. @@ -377,8 +361,7 @@ def _get_basis_file(self, cp2k_input: Cp2kInput) -> BasisFile: return BasisFile(objects=basis_sets) def _get_potential_file(self, cp2k_input: Cp2kInput) -> PotentialFile: - """ - Get the potentials and convert them to a potential file object. + """Get the potentials and convert them to a potential file object. Allows calculation to execute if the potentials are not available on the execution resource. @@ -405,37 +388,37 @@ def _get_kpoints( # use user setting if set otherwise default to base config settings if self.user_kpoints_settings != {}: - kconfig = deepcopy(self.user_kpoints_settings) + kpt_config = deepcopy(self.user_kpoints_settings) else: # apply updates to k-points config - kconfig = deepcopy(self.config_dict.get("KPOINTS", {})) - kconfig.update(kpoints_updates) + kpt_config = deepcopy(self.config_dict.get("KPOINTS", {})) + kpt_config.update(kpoints_updates) - if isinstance(kconfig, Kpoints): - return kconfig + if isinstance(kpt_config, Kpoints): + return kpt_config explicit = ( - kconfig.get("explicit", False) - or len(kconfig.get("added_kpoints", [])) > 0 - or "zero_weighted_reciprocal_density" in kconfig - or "zero_weighted_line_density" in kconfig + kpt_config.get("explicit") + or len(kpt_config.get("added_kpoints", [])) > 0 + or "zero_weighted_reciprocal_density" in kpt_config + or "zero_weighted_line_density" in kpt_config ) # handle length generation first as this doesn't support any additional options - if kconfig.get("length"): + if kpt_config.get("length"): if explicit: raise ValueError( "length option cannot be used with explicit k-point generation, " "added_kpoints, or zero weighted k-points." ) # If length is in kpoints settings use Kpoints.automatic - return Kpoints.automatic(kconfig["length"]) + return Kpoints.automatic(kpt_config["length"]) base_kpoints = None - if kconfig.get("line_density"): + if kpt_config.get("line_density"): # handle line density generation - kpath = HighSymmKpath(structure, **kconfig.get("kpath_kwargs", {})) + kpath = HighSymmKpath(structure, **kpt_config.get("kpath_kwargs", {})) frac_k_points, k_points_labels = kpath.get_kpoints( - line_density=kconfig["line_density"], coords_are_cartesian=False + line_density=kpt_config["line_density"], coords_are_cartesian=False ) base_kpoints = Kpoints( comment="Non SCF run along symmetry lines", @@ -445,15 +428,15 @@ def _get_kpoints( labels=k_points_labels, kpts_weights=[1] * len(frac_k_points), ) - elif kconfig.get("grid_density") or kconfig.get("reciprocal_density"): + elif kpt_config.get("grid_density") or kpt_config.get("reciprocal_density"): # handle regular weighted k-point grid generation - if kconfig.get("grid_density"): + if kpt_config.get("grid_density"): base_kpoints = Kpoints.automatic_density( - structure, int(kconfig["grid_density"]), self.force_gamma + structure, int(kpt_config["grid_density"]), self.force_gamma ) - if kconfig.get("reciprocal_density"): + if kpt_config.get("reciprocal_density"): base_kpoints = Kpoints.automatic_density_by_vol( - structure, kconfig["reciprocal_density"], self.force_gamma + structure, kpt_config["reciprocal_density"], self.force_gamma ) if explicit: sga = SpacegroupAnalyzer(structure, symprec=self.symprec) @@ -471,11 +454,11 @@ def _get_kpoints( return base_kpoints zero_weighted_kpoints = None - if kconfig.get("zero_weighted_line_density"): + if kpt_config.get("zero_weighted_line_density"): # zero_weighted k-points along line mode path kpath = HighSymmKpath(structure) frac_k_points, k_points_labels = kpath.get_kpoints( - line_density=kconfig["zero_weighted_line_density"], + line_density=kpt_config["zero_weighted_line_density"], coords_are_cartesian=False, ) zero_weighted_kpoints = Kpoints( @@ -486,9 +469,11 @@ def _get_kpoints( labels=k_points_labels, kpts_weights=[0] * len(frac_k_points), ) - elif kconfig.get("zero_weighted_reciprocal_density"): + elif kpt_config.get("zero_weighted_reciprocal_density"): zero_weighted_kpoints = Kpoints.automatic_density_by_vol( - structure, kconfig["zero_weighted_reciprocal_density"], self.force_gamma + structure, + kpt_config["zero_weighted_reciprocal_density"], + self.force_gamma, ) sga = SpacegroupAnalyzer(structure, symprec=self.symprec) mesh = sga.get_ir_reciprocal_mesh(zero_weighted_kpoints.kpts[0]) @@ -501,14 +486,14 @@ def _get_kpoints( ) added_kpoints = None - if kconfig.get("added_kpoints"): + if kpt_config.get("added_kpoints"): added_kpoints = Kpoints( comment="Specified k-points only", style=Kpoints.supported_modes.Reciprocal, - num_kpts=len(kconfig.get("added_kpoints")), - kpts=kconfig.get("added_kpoints"), - labels=["user-defined"] * len(kconfig.get("added_kpoints")), - kpts_weights=[0] * len(kconfig.get("added_kpoints")), + num_kpts=len(kpt_config.get("added_kpoints")), + kpts=kpt_config.get("added_kpoints"), + labels=["user-defined"] * len(kpt_config.get("added_kpoints")), + kpts_weights=[0] * len(kpt_config.get("added_kpoints")), ) if base_kpoints and not (added_kpoints or zero_weighted_kpoints): @@ -517,7 +502,7 @@ def _get_kpoints( return added_kpoints # do some sanity checking - if "line_density" in kconfig and zero_weighted_kpoints: + if "line_density" in kpt_config and zero_weighted_kpoints: raise ValueError( "Cannot combined line_density and zero weighted k-points options" ) @@ -542,7 +527,7 @@ def _combine_kpoints(*kpoints_objects: Kpoints) -> Kpoints: weights = [] for kpoints_object in filter(None, kpoints_objects): - if not kpoints_object.style == Kpoints.supported_modes.Reciprocal: + if kpoints_object.style != Kpoints.supported_modes.Reciprocal: raise ValueError( "Can only combine kpoints with style=Kpoints.supported_modes.Reciprocal" ) diff --git a/src/atomate2/cp2k/sets/core.py b/src/atomate2/cp2k/sets/core.py index bc007ea2d5..9eb0f1cccc 100644 --- a/src/atomate2/cp2k/sets/core.py +++ b/src/atomate2/cp2k/sets/core.py @@ -172,8 +172,7 @@ def get_kpoints_updates( structure: Structure, prev_input: Cp2kInput = None, ) -> dict: - """ - Get updates to the kpoints configuration for a non-self consistent VASP job. + """Get updates to the kpoints configuration for a non-self consistent VASP job. Note, these updates will be ignored if the user has set user_kpoint_settings. diff --git a/src/atomate2/forcefields/__init__.py b/src/atomate2/forcefields/__init__.py index 8ffc66eacd..a76400755f 100644 --- a/src/atomate2/forcefields/__init__.py +++ b/src/atomate2/forcefields/__init__.py @@ -1 +1,14 @@ """Tools and functions common to all forcefields.""" + +from enum import Enum + + +class MLFF(Enum): # TODO inherit from StrEnum when 3.11+ + """Names of ML force fields.""" + + MACE = "MACE" + GAP = "GAP" + M3GNet = "M3GNet" + CHGNet = "CHGNet" + Forcefield = "Forcefield" # default placeholder option + Nequip = "Nequip" diff --git a/src/atomate2/forcefields/flows/__init__.py b/src/atomate2/forcefields/flows/__init__.py index 1b434193d9..2090e63c6f 100644 --- a/src/atomate2/forcefields/flows/__init__.py +++ b/src/atomate2/forcefields/flows/__init__.py @@ -1,2 +1,3 @@ """Flows for forcefields.""" + from .relax import CHGNetVaspRelaxMaker, M3GNetVaspRelaxMaker diff --git a/src/atomate2/forcefields/flows/elastic.py b/src/atomate2/forcefields/flows/elastic.py index b3d6533ef5..c97a73e126 100644 --- a/src/atomate2/forcefields/flows/elastic.py +++ b/src/atomate2/forcefields/flows/elastic.py @@ -45,6 +45,11 @@ class ElasticMaker(BaseElasticMaker): bulk_relax_maker : .ForceFieldRelaxMaker or None A maker to perform a tight relaxation on the bulk. Set to ``None`` to skip the bulk relaxation. + max_failed_deformations: int or float + Maximum number of deformations allowed to fail to proceed with the fitting + of the elastic tensor. If an int the absolute number of deformations. If + a float between 0 an 1 the maximum fraction of deformations. If None any + number of deformations allowed. elastic_relax_maker : .ForceFieldRelaxMaker Maker used to generate elastic relaxations. generate_elastic_deformations_kwargs : dict @@ -69,12 +74,13 @@ class ElasticMaker(BaseElasticMaker): relax_cell=False, relax_kwargs={"fmax": 0.00001} ) ) # constant volume relaxation + max_failed_deformations: int | float | None = None generate_elastic_deformations_kwargs: dict = field(default_factory=dict) fit_elastic_tensor_kwargs: dict = field(default_factory=dict) task_document_kwargs: dict = field(default_factory=dict) @property - def prev_calc_dir_argname(self): + def prev_calc_dir_argname(self) -> str | None: """Name of argument informing static maker of previous calculation directory. As this differs between different DFT codes (e.g., VASP, CP2K), it @@ -83,4 +89,3 @@ def prev_calc_dir_argname(self): Note: this is only applicable if a relax_maker is specified; i.e., two calculations are performed for each ordering (relax -> static) """ - return diff --git a/src/atomate2/forcefields/flows/eos.py b/src/atomate2/forcefields/flows/eos.py new file mode 100644 index 0000000000..2208e34f82 --- /dev/null +++ b/src/atomate2/forcefields/flows/eos.py @@ -0,0 +1,138 @@ +"""Flows to generate EOS fits using CHGNet, M3GNet, or MACE.""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +from atomate2.common.flows.eos import CommonEosMaker +from atomate2.forcefields.jobs import CHGNetRelaxMaker, M3GNetRelaxMaker, MACERelaxMaker + +if TYPE_CHECKING: + from jobflow import Maker + + +@dataclass +class CHGNetEosMaker(CommonEosMaker): + """ + Generate equation of state data using the CHGNet ML forcefield. + + First relax a structure using relax_maker. + Then perform a series of deformations on the relaxed structure, and + relax atomic positions within the cell. For ML forcefields, there + is no distinction between relax and static energies, unlike in a VASP + calculation. Therefore these EosMakers default to static_maker = None. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + initial_relax_maker : .Maker | None + Maker to relax the input structure, defaults to None (no initial relaxation). + eos_relax_maker : .Maker + Maker to relax deformationed structures for the EOS fit. + static_maker : .Maker | None + Maker to generate statics after each relaxation, defaults to None. + strain : tuple[float] + Percentage linear strain to apply as a deformation, default = -5% to 5%. + number_of_frames : int + Number of strain calculations to do for EOS fit, default = 6. + postprocessor : .job + Optional postprocessing step, defaults to + `atomate2.common.jobs.PostProcessEosEnergy`. + _store_transformation_information : .bool = False + Whether to store the information about transformations. Unfortunately + needed at present to handle issues with emmet and pydantic validation + TODO: remove this when clash is fixed + """ + + name: str = "CHGNet EOS Maker" + initial_relax_maker: Maker = field(default_factory=CHGNetRelaxMaker) + eos_relax_maker: Maker = field( + default_factory=lambda: CHGNetRelaxMaker(relax_cell=False) + ) + static_maker: Maker = None + + +@dataclass +class M3GNetEosMaker(CommonEosMaker): + """ + Generate equation of state data using the M3GNet ML forcefield. + + First relax a structure using relax_maker. + Then perform a series of deformations on the relaxed structure, and + relax atomic positions within the cell. For ML forcefields, there + is no distinction between relax and static energies, unlike in a VASP + calculation. Therefore these EosMakers default to static_maker = None. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + initial_relax_maker : .Maker | None + Maker to relax the input structure, defaults to None (no initial relaxation). + eos_relax_maker : .Maker + Maker to relax deformationed structures for the EOS fit. + static_maker : .Maker | None + Maker to generate statics after each relaxation, defaults to None. + strain : tuple[float] + Percentage linear strain to apply as a deformation, default = -5% to 5%. + number_of_frames : int + Number of strain calculations to do for EOS fit, default = 6. + postprocessor : .job + Optional postprocessing step, defaults to + `atomate2.common.jobs.PostProcessEosEnergy`. + _store_transformation_information : .bool = False + Whether to store the information about transformations. Unfortunately + needed at present to handle issues with emmet and pydantic validation + TODO: remove this when clash is fixed + """ + + name: str = "M3GNet EOS Maker" + initial_relax_maker: Maker = field(default_factory=M3GNetRelaxMaker) + eos_relax_maker: Maker = field( + default_factory=lambda: M3GNetRelaxMaker(relax_cell=False) + ) + static_maker: Maker = None + + +@dataclass +class MACEEosMaker(CommonEosMaker): + """ + Generate equation of state data using the MACE ML forcefield. + + First relax a structure using relax_maker. + Then perform a series of deformations on the relaxed structure, and + relax atomic positions within the cell. For ML forcefields, there + is no distinction between relax and static energies, unlike in a VASP + calculation. Therefore these EosMakers default to static_maker = None. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + initial_relax_maker : .Maker | None + Maker to relax the input structure, defaults to None (no initial relaxation). + eos_relax_maker : .Maker + Maker to relax deformationed structures for the EOS fit. + static_maker : .Maker | None + Maker to generate statics after each relaxation, defaults to None. + strain : tuple[float] + Percentage linear strain to apply as a deformation, default = -5% to 5%. + number_of_frames : int + Number of strain calculations to do for EOS fit, default = 6. + postprocessor : .job + Optional postprocessing step, defaults to + `atomate2.common.jobs.PostProcessEosEnergy`. + _store_transformation_information : .bool = False + Whether to store the information about transformations. Unfortunately + needed at present to handle issues with emmet and pydantic validation + TODO: remove this when clash is fixed + """ + + name: str = "MACE EOS Maker" + initial_relax_maker: Maker = field(default_factory=MACERelaxMaker) + eos_relax_maker: Maker = field( + default_factory=lambda: MACERelaxMaker(relax_cell=False) + ) + static_maker: Maker = None diff --git a/src/atomate2/forcefields/flows/phonons.py b/src/atomate2/forcefields/flows/phonons.py index ad76c76eee..61b9740c63 100644 --- a/src/atomate2/forcefields/flows/phonons.py +++ b/src/atomate2/forcefields/flows/phonons.py @@ -3,18 +3,9 @@ from __future__ import annotations from dataclasses import dataclass, field -from typing import TYPE_CHECKING +from typing import Literal -from jobflow import Flow, Maker - -from atomate2.common.jobs.phonons import ( - generate_frequencies_eigenvectors, - generate_phonon_displacements, - get_supercell_size, - get_total_energy_per_cell, - run_phonon_displacements, -) -from atomate2.common.jobs.utils import structure_to_conventional, structure_to_primitive +from atomate2.common.flows.phonons import BasePhononMaker from atomate2.forcefields.jobs import ( CHGNetRelaxMaker, CHGNetStaticMaker, @@ -22,15 +13,9 @@ ForceFieldStaticMaker, ) -if TYPE_CHECKING: - from emmet.core.math import Matrix3D - from pymatgen.core.structure import Structure - - from atomate2.vasp.jobs.base import BaseVaspMaker - @dataclass -class PhononMaker(Maker): +class PhononMaker(BasePhononMaker): """ Maker to calculate harmonic phonons with a force field. @@ -91,15 +76,17 @@ class PhononMaker(Maker): 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010. We will however use seekpath and primitive structures as determined by from phonopy to compute the phonon band structure - bulk_relax_maker : .BaseVaspMaker or None + bulk_relax_maker : .ForceFieldRelaxMaker or None A maker to perform a tight relaxation on the bulk. Set to ``None`` to skip the bulk relaxation - static_energy_maker : .BaseVaspMaker or None + static_energy_maker : .ForceFieldRelaxMaker or None A maker to perform the computation of the DFT energy on the bulk. Set to ``None`` to skip the static energy computation - phonon_displacement_maker : .BaseVaspMaker or None + born_maker: .ForceFieldStaticMaker or None + Maker to compute the BORN charges. + phonon_displacement_maker : .ForceFieldStaticMaker or None Maker used to compute the forces for a supercell. generate_frequencies_eigenvectors_kwargs : dict Keyword arguments passed to :obj:`generate_frequencies_eigenvectors`. @@ -116,11 +103,11 @@ class PhononMaker(Maker): it relies on phonopy to handle the relationship to the primitive cell and not pymatgen code: str - determines the dft code. currently only vasp is implemented. - This keyword might enable the implementation of other codes - in the future + determines the dft or force field code. store_force_constants: bool if True, force constants will be stored + socket: bool + If True, use the socket for the calculation """ name: str = "phonon" @@ -130,192 +117,31 @@ class PhononMaker(Maker): min_length: float | None = 20.0 prefer_90_degrees: bool = True get_supercell_size_kwargs: dict = field(default_factory=dict) - use_symmetrized_structure: str | None = None - bulk_relax_maker: BaseVaspMaker | ForceFieldRelaxMaker | None = field( + use_symmetrized_structure: Literal["primitive", "conventional"] | None = None + bulk_relax_maker: ForceFieldRelaxMaker | None = field( default_factory=lambda: CHGNetRelaxMaker(relax_kwargs={"fmax": 0.00001}) ) - static_energy_maker: BaseVaspMaker | ForceFieldStaticMaker | None = field( + static_energy_maker: ForceFieldStaticMaker | None = field( default_factory=CHGNetStaticMaker ) - phonon_displacement_maker: BaseVaspMaker | ForceFieldStaticMaker = field( + phonon_displacement_maker: ForceFieldStaticMaker = field( default_factory=CHGNetStaticMaker ) - create_thermal_displacements: bool = True + create_thermal_displacements: bool = False generate_frequencies_eigenvectors_kwargs: dict = field(default_factory=dict) kpath_scheme: str = "seekpath" - code: str = "vasp" store_force_constants: bool = True + code: str = "forcefields" + born_maker: ForceFieldStaticMaker | None = None - def make( - self, - structure: Structure, - born: list[Matrix3D] | None = None, - epsilon_static: Matrix3D | None = None, - total_dft_energy_per_formula_unit: float | None = None, - supercell_matrix: Matrix3D | None = None, - ) -> Flow: - """ - Make flow to calculate the phonon properties. - - Parameters - ---------- - structure : .Structure - A pymatgen structure. Please start with a structure - that is nearly fully optimized as the internal optimizers - have very strict settings! - born: Matrix3D - The born charges and epsilon can be provided manually. - It can be provided in the VASP convention with information for - every atom in unit cell. Please be careful when converting - structures within in this workflow as this could lead to errors - epsilon_static: Matrix3D - The high-frequency dielectric constant. - total_dft_energy_per_formula_unit: float - It has to be given per formula unit (as a result in corresponding Doc) - Instead of recomputing the energy of the bulk structure every time, - this value can also be provided in eV. If it is provided, - the static run will be skipped. This energy is the typical - output dft energy of the dft workflow. No conversion needed. - supercell_matrix: list - instead of min_length, also a supercell_matrix can - be given, e.g. [[1.0,0.0,0.0],[0.0,1.0,0.0],[0.0,0.0,1.0] - """ - if self.use_symmetrized_structure not in [None, "primitive", "conventional"]: - raise ValueError( - "use_symmetrized_structure can only be primitive, conventional, None" - ) - - if ( - not self.use_symmetrized_structure == "primitive" - and self.kpath_scheme != "seekpath" - ): - raise ValueError( - "You can only use other kpath schemes with the primitive standard " - "structure" - ) - - if self.kpath_scheme not in [ - "seekpath", - "hinuma", - "setyawan_curtarolo", - "latimer_munro", - ]: - raise ValueError("kpath scheme is not implemented") + @property + def prev_calc_dir_argname(self) -> None: + """Name of argument informing static maker of previous calculation directory. - jobs = [] + As this differs between different DFT codes (e.g., VASP, CP2K), it + has been left as a property to be implemented by the inheriting class. - # TODO: should this be after or before structural - # optimization as the optimization could change - # the symmetry - # we could add a tutorial and point out that the structure - # should be nearly optimized before the phonon workflow - if self.use_symmetrized_structure == "primitive": - # These structures are compatible with many - # of the kpath algorithms that are used for Materials Project - prim_job = structure_to_primitive(structure, self.symprec) - jobs.append(prim_job) - structure = prim_job.output - elif self.use_symmetrized_structure == "conventional": - # it could be beneficial to use conventional - # standard structures to arrive faster at supercells with right - # angles - conv_job = structure_to_conventional(structure, self.symprec) - jobs.append(conv_job) - structure = conv_job.output - - if self.bulk_relax_maker is not None: - # optionally relax the structure - bulk = self.bulk_relax_maker.make(structure) - jobs.append(bulk) - structure = bulk.output.structure - optimization_run_job_dir = bulk.output.dir_name - # bulk.output.dir_name - optimization_run_uuid = bulk.output.uuid - else: - optimization_run_job_dir = None - optimization_run_uuid = None - - # if supercell_matrix is None, supercell size will be determined - # after relax maker to ensure that cell lengths are really larger - # than threshold - if supercell_matrix is None: - supercell_job = get_supercell_size( - structure, - self.min_length, - self.prefer_90_degrees, - **self.get_supercell_size_kwargs, - ) - jobs.append(supercell_job) - supercell_matrix = supercell_job.output - - # get a phonon object from phonopy - displacements = generate_phonon_displacements( - structure=structure, - supercell_matrix=supercell_matrix, - displacement=self.displacement, - sym_reduce=self.sym_reduce, - symprec=self.symprec, - use_symmetrized_structure=self.use_symmetrized_structure, - kpath_scheme=self.kpath_scheme, - code=self.code, - ) - jobs.append(displacements) - - # perform the phonon displacement calculations - vasp_displacement_calcs = run_phonon_displacements( - displacements=displacements.output, - structure=structure, - supercell_matrix=supercell_matrix, - phonon_maker=self.phonon_displacement_maker, - ) - jobs.append(vasp_displacement_calcs) - - # Computation of static energy - if (self.static_energy_maker is not None) and ( - total_dft_energy_per_formula_unit is None - ): - static_job = self.static_energy_maker.make(structure=structure) - jobs.append(static_job) - total_dft_energy = static_job.output.output.energy - static_run_job_dir = static_job.output.dir_name - static_run_uuid = static_job.output.uuid - else: - if total_dft_energy_per_formula_unit is not None: - # to make sure that one can reuse results from Doc - compute_total_energy_job = get_total_energy_per_cell( - total_dft_energy_per_formula_unit, structure - ) - jobs.append(compute_total_energy_job) - total_dft_energy = compute_total_energy_job.output - else: - total_dft_energy = None - static_run_job_dir = None - static_run_uuid = None - - phonon_collect = generate_frequencies_eigenvectors( - supercell_matrix=supercell_matrix, - displacement=self.displacement, - sym_reduce=self.sym_reduce, - symprec=self.symprec, - use_symmetrized_structure=self.use_symmetrized_structure, - kpath_scheme=self.kpath_scheme, - code=self.code, - structure=structure, - displacement_data=vasp_displacement_calcs.output, - epsilon_static=epsilon_static, - born=born, - total_dft_energy=total_dft_energy, - static_run_job_dir=static_run_job_dir, - static_run_uuid=static_run_uuid, - born_run_job_dir=None, - born_run_uuid=None, - optimization_run_job_dir=optimization_run_job_dir, - optimization_run_uuid=optimization_run_uuid, - create_thermal_displacements=self.create_thermal_displacements, - store_force_constants=self.store_force_constants, - **self.generate_frequencies_eigenvectors_kwargs, - ) - - jobs.append(phonon_collect) - # create a flow including all jobs for a phonon computation - return Flow(jobs, phonon_collect.output) + Note: this is only applicable if a relax_maker is specified; i.e., two + calculations are performed for each ordering (relax -> static) + """ + return diff --git a/src/atomate2/forcefields/flows/relax.py b/src/atomate2/forcefields/flows/relax.py index 27ca123927..3a2d6c6f15 100644 --- a/src/atomate2/forcefields/flows/relax.py +++ b/src/atomate2/forcefields/flows/relax.py @@ -7,6 +7,7 @@ from jobflow import Flow, Maker +from atomate2.forcefields import MLFF from atomate2.forcefields.jobs import CHGNetRelaxMaker, M3GNetRelaxMaker from atomate2.vasp.jobs.core import RelaxMaker @@ -31,13 +32,12 @@ class CHGNetVaspRelaxMaker(Maker): Maker to generate a VASP relaxation job. """ - name: str = "CHGNet relax followed by a VASP relax" + name: str = f"{MLFF.CHGNet} relax followed by a VASP relax" chgnet_maker: CHGNetRelaxMaker = field(default_factory=CHGNetRelaxMaker) vasp_maker: BaseVaspMaker = field(default_factory=RelaxMaker) def make(self, structure: Structure) -> Flow: - """ - Create a flow with a CHGNet (pre)relaxation followed by a VASP relaxation. + """Create a flow with a CHGNet (pre)relaxation followed by a VASP relaxation. Parameters ---------- @@ -50,7 +50,7 @@ def make(self, structure: Structure) -> Flow: A flow containing a CHGNet relaxation followed by a VASP relaxation """ chgnet_relax_job = self.chgnet_maker.make(structure) - chgnet_relax_job.name = "CHGNet pre-relax" + chgnet_relax_job.name = f"{MLFF.CHGNet} pre-relax" vasp_job = self.vasp_maker.make(chgnet_relax_job.output.structure) @@ -72,13 +72,12 @@ class M3GNetVaspRelaxMaker(Maker): Maker to generate a VASP relaxation job. """ - name: str = "M3GNet relax followed by a VASP relax" + name: str = f"{MLFF.M3GNet} relax followed by a VASP relax" m3gnet_maker: M3GNetRelaxMaker = field(default_factory=M3GNetRelaxMaker) vasp_maker: BaseVaspMaker = field(default_factory=RelaxMaker) def make(self, structure: Structure) -> Flow: - """ - Create a flow with a M3GNet (pre)relaxation followed by a VASP relaxation. + """Create a flow with a M3GNet (pre)relaxation followed by a VASP relaxation. Parameters ---------- @@ -91,7 +90,7 @@ def make(self, structure: Structure) -> Flow: A flow containing a M3GNet relaxation followed by a VASP relaxation """ m3gnet_relax_job = self.m3gnet_maker.make(structure) - m3gnet_relax_job.name = "M3GNet pre-relax" + m3gnet_relax_job.name = f"{MLFF.M3GNet} pre-relax" vasp_job = self.vasp_maker.make(m3gnet_relax_job.output.structure) diff --git a/src/atomate2/forcefields/jobs.py b/src/atomate2/forcefields/jobs.py index 8680c25e59..d6f94ff94e 100644 --- a/src/atomate2/forcefields/jobs.py +++ b/src/atomate2/forcefields/jobs.py @@ -3,70 +3,142 @@ from __future__ import annotations import logging +import os from dataclasses import dataclass, field from typing import TYPE_CHECKING +from ase.units import GPa as _GPa_to_eV_per_A3 from jobflow import Maker, job +from pymatgen.core.trajectory import Trajectory +from atomate2.forcefields import MLFF from atomate2.forcefields.schemas import ForceFieldTaskDocument -from atomate2.forcefields.utils import Relaxer +from atomate2.forcefields.utils import Relaxer, ase_calculator, revert_default_dtype if TYPE_CHECKING: from pathlib import Path + from typing import Callable + from ase.calculators.calculator import Calculator from pymatgen.core.structure import Structure logger = logging.getLogger(__name__) +_FORCEFIELD_DATA_OBJECTS = [Trajectory] + + +def forcefield_job(method: Callable) -> job: + """ + Decorate the ``make`` method of forcefield job makers. + + This is a thin wrapper around :obj:`~jobflow.core.job.Job` that configures common + settings for all forcefield jobs. For example, it ensures that large data objects + (currently only trajectories) are all stored in the atomate2 data store. + It also configures the output schema to be a ForceFieldTaskDocument :obj:`.TaskDoc`. + + Any makers that return forcefield jobs (not flows) should decorate the + ``make`` method with @forcefield_job. For example: + + .. code-block:: python + + class MyForcefieldMaker(Maker): + @forcefield_job + def make(structure): + # code to run forcefield job. + pass + + Parameters + ---------- + method : callable + A Maker.make method. This should not be specified directly and is + implied by the decorator. + + Returns + ------- + callable + A decorated version of the make function that will generate forcefield jobs. + """ + return job( + method, data=_FORCEFIELD_DATA_OBJECTS, output_schema=ForceFieldTaskDocument + ) + @dataclass class ForceFieldRelaxMaker(Maker): """ Base Maker to calculate forces and stresses using any force field. + Should be subclassed to use a specific force field. By default, + the code attempts to use the `self.force_field_name` attr to look + up a predefined forcefield. To overwrite this behavior, redefine `self.calculator`. + Parameters ---------- name : str The job name. force_field_name : str The name of the force field. - relax_cell : bool + relax_cell : bool = True Whether to allow the cell shape/volume to change during relaxation. + fix_symmetry : bool = False + Whether to fix the symmetry during relaxation. + Refines the symmetry of the initial structure. + symprec : float = 1e-2 + Tolerance for symmetry finding in case of fix_symmetry. steps : int Maximum number of ionic steps allowed during relaxation. relax_kwargs : dict Keyword arguments that will get passed to :obj:`Relaxer.relax`. optimizer_kwargs : dict Keyword arguments that will get passed to :obj:`Relaxer()`. + calculator_kwargs : dict + Keyword arguments that will get passed to the ASE calculator. task_document_kwargs : dict Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. """ - name: str = "Forcefield relax" - force_field_name: str = "Forcefield" - relax_cell: bool = False + name: str = "Force field relax" + force_field_name: str = f"{MLFF.Forcefield}" + relax_cell: bool = True + fix_symmetry: bool = False + symprec: float = 1e-2 steps: int = 500 relax_kwargs: dict = field(default_factory=dict) optimizer_kwargs: dict = field(default_factory=dict) + calculator_kwargs: dict = field(default_factory=dict) task_document_kwargs: dict = field(default_factory=dict) - @job(output_schema=ForceFieldTaskDocument) - def make(self, structure: Structure) -> ForceFieldTaskDocument: + @forcefield_job + def make( + self, structure: Structure, prev_dir: str | Path | None = None + ) -> ForceFieldTaskDocument: """ Perform a relaxation of a structure using a force field. Parameters ---------- structure: .Structure - pymatgen structure. + pymatgen structure. + prev_dir : str or Path or None + A previous calculation directory to copy output files from. Unused, just + added to match the method signature of other makers. """ if self.steps < 0: logger.warning( "WARNING: A negative number of steps is not possible. " "Behavior may vary..." ) - - result = self._relax(structure) + self.task_document_kwargs.setdefault("dir_name", os.getcwd()) + + with revert_default_dtype(): + relaxer = Relaxer( + self.calculator, + relax_cell=self.relax_cell, + fix_symmetry=self.fix_symmetry, + symprec=self.symprec, + **self.optimizer_kwargs, + ) + result = relaxer.relax(structure, steps=self.steps, **self.relax_kwargs) return ForceFieldTaskDocument.from_ase_compatible_result( self.force_field_name, @@ -75,17 +147,25 @@ def make(self, structure: Structure) -> ForceFieldTaskDocument: self.steps, self.relax_kwargs, self.optimizer_kwargs, + self.fix_symmetry, + self.symprec, **self.task_document_kwargs, ) - def _relax(self, structure: Structure) -> dict: - raise NotImplementedError + @property + def calculator(self) -> Calculator: + """ASE calculator, can be overwritten by user.""" + return ase_calculator(self.force_field_name, **self.calculator_kwargs) @dataclass class ForceFieldStaticMaker(ForceFieldRelaxMaker): """ - Maker to calculate forces and stresses using the CHGNet force field. + Maker to calculate forces and stresses using any force field. + + Note that while `steps = 1` by default, the user could override + this setting along with cell shape relaxation (`relax_cell = False` + by default). Parameters ---------- @@ -93,45 +173,21 @@ class ForceFieldStaticMaker(ForceFieldRelaxMaker): The job name. force_field_name : str The name of the force field. + calculator_kwargs : dict + Keyword arguments that will get passed to the ASE calculator. task_document_kwargs : dict Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. """ - name: str = "ForceField static" - force_field_name: str = "Forcefield" + name: str = "Force field static" + force_field_name: str = "Force field" + relax_cell: bool = False + steps: int = 1 + relax_kwargs: dict = field(default_factory=dict) + optimizer_kwargs: dict = field(default_factory=dict) + calculator_kwargs: dict = field(default_factory=dict) task_document_kwargs: dict = field(default_factory=dict) - @job(output_schema=ForceFieldTaskDocument) - def make(self, structure: Structure) -> ForceFieldTaskDocument: - """ - Perform a static evaluation using a force field. - - Parameters - ---------- - structure: .Structure - pymatgen structure. - """ - if self.steps < 0: - logger.warning( - "WARNING: A negative number of steps is not possible. " - "Behavior may vary..." - ) - - result = self._evaluate_static(structure) - - return ForceFieldTaskDocument.from_ase_compatible_result( - self.force_field_name, - result, - relax_cell=False, - steps=1, - relax_kwargs=None, - optimizer_kwargs=None, - **self.task_document_kwargs, - ) - - def _evaluate_static(self, structure: Structure) -> dict: - raise NotImplementedError - @dataclass class CHGNetRelaxMaker(ForceFieldRelaxMaker): @@ -142,33 +198,37 @@ class CHGNetRelaxMaker(ForceFieldRelaxMaker): ---------- force_field_name : str The name of the force field. - relax_cell : bool + relax_cell : bool = True Whether to allow the cell shape/volume to change during relaxation. + fix_symmetry : bool = False + Whether to fix the symmetry during relaxation. + Refines the symmetry of the initial structure. + symprec : float = 1e-2 + Tolerance for symmetry finding in case of fix_symmetry. steps : int Maximum number of ionic steps allowed during relaxation. relax_kwargs : dict Keyword arguments that will get passed to :obj:`Relaxer.relax`. optimizer_kwargs : dict Keyword arguments that will get passed to :obj:`Relaxer()`. + calculator_kwargs : dict + Keyword arguments that will get passed to the ASE calculator. task_document_kwargs : dict Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. """ - name: str = "CHGNet relax" - force_field_name = "CHGNet" - relax_cell: bool = False + name: str = f"{MLFF.CHGNet} relax" + force_field_name: str = f"{MLFF.CHGNet}" + relax_cell: bool = True + fix_symmetry: bool = False + symprec: float = 1e-2 steps: int = 500 relax_kwargs: dict = field(default_factory=dict) optimizer_kwargs: dict = field(default_factory=dict) task_document_kwargs: dict = field(default_factory=dict) - - def _relax(self, structure: Structure) -> dict: - from chgnet.model import StructOptimizer - - relaxer = StructOptimizer(**self.optimizer_kwargs) - return relaxer.relax( - structure, relax_cell=self.relax_cell, steps=self.steps, **self.relax_kwargs - ) + calculator_kwargs: dict = field( + default_factory=lambda: {"stress_weight": _GPa_to_eV_per_A3} + ) @dataclass @@ -180,19 +240,18 @@ class CHGNetStaticMaker(ForceFieldStaticMaker): ---------- name : str The job name. + calculator_kwargs : dict + Keyword arguments that will get passed to the ASE calculator. task_document_kwargs : dict Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. """ - name: str = "CHGNet static" - force_field_name = "CHGNet" + name: str = f"{MLFF.CHGNet} static" + force_field_name: str = f"{MLFF.CHGNet}" task_document_kwargs: dict = field(default_factory=dict) - - def _evaluate_static(self, structure: Structure) -> dict: - from chgnet.model import StructOptimizer - - relaxer = StructOptimizer() - return relaxer.relax(structure, steps=1) + calculator_kwargs: dict = field( + default_factory=lambda: {"stress_weight": _GPa_to_eV_per_A3} + ) @dataclass @@ -206,45 +265,100 @@ class M3GNetRelaxMaker(ForceFieldRelaxMaker): The job name. force_field_name : str The name of the force field. - relax_cell : bool + relax_cell : bool = True Whether to allow the cell shape/volume to change during relaxation. + fix_symmetry : bool = False + Whether to fix the symmetry during relaxation. + Refines the symmetry of the initial structure. + symprec : float = 1e-2 + Tolerance for symmetry finding in case of fix_symmetry. steps : int Maximum number of ionic steps allowed during relaxation. relax_kwargs : dict Keyword arguments that will get passed to :obj:`Relaxer.relax`. optimizer_kwargs : dict Keyword arguments that will get passed to :obj:`Relaxer()`. + calculator_kwargs : dict + Keyword arguments that will get passed to the ASE calculator. task_document_kwargs : dict Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. """ - name: str = "M3GNet relax" - force_field_name: str = "M3GNet" - relax_cell: bool = False + name: str = f"{MLFF.M3GNet} relax" + force_field_name: str = f"{MLFF.M3GNet}" + relax_cell: bool = True + fix_symmetry: bool = False + symprec: float = 1e-2 steps: int = 500 relax_kwargs: dict = field(default_factory=dict) optimizer_kwargs: dict = field(default_factory=dict) task_document_kwargs: dict = field(default_factory=dict) + calculator_kwargs: dict = field( + default_factory=lambda: {"stress_weight": _GPa_to_eV_per_A3} + ) - def _relax(self, structure: Structure) -> dict: - import matgl - from matgl.ext.ase import Relaxer - # Note: the below code was taken from the matgl repo examples. - # Load pre-trained M3GNet model (currently uses the MP-2021.2.8 database) - pot = matgl.load_model("M3GNet-MP-2021.2.8-PES") +@dataclass +class NequipRelaxMaker(ForceFieldRelaxMaker): + """ + Maker to perform a relaxation using a Nequip force field. - relaxer = Relaxer( - potential=pot, - relax_cell=self.relax_cell, - **self.optimizer_kwargs, - ) + Parameters + ---------- + name : str + The job name. + force_field_name : str + The name of the force field. + relax_cell : bool = True + Whether to allow the cell shape/volume to change during relaxation. + fix_symmetry : bool = False + Whether to fix the symmetry during relaxation. + Refines the symmetry of the initial structure. + symprec : float = 1e-2 + Tolerance for symmetry finding in case of fix_symmetry. + steps : int + Maximum number of ionic steps allowed during relaxation. + relax_kwargs : dict + Keyword arguments that will get passed to :obj:`Relaxer.relax`. + optimizer_kwargs : dict + Keyword arguments that will get passed to :obj:`Relaxer()`. + calculator_kwargs : dict + Keyword arguments that will get passed to the ASE calculator. + task_document_kwargs : dict + Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. + """ - return relaxer.relax( - structure, - steps=self.steps, - **self.relax_kwargs, - ) + name: str = f"{MLFF.Nequip} relax" + force_field_name: str = f"{MLFF.Nequip}" + relax_cell: bool = True + fix_symmetry: bool = False + symprec: float = 1e-2 + steps: int = 500 + relax_kwargs: dict = field(default_factory=dict) + optimizer_kwargs: dict = field(default_factory=dict) + task_document_kwargs: dict = field(default_factory=dict) + + +@dataclass +class NequipStaticMaker(ForceFieldStaticMaker): + """ + Maker to calculate energies, forces and stresses using a nequip force field. + + Parameters + ---------- + name : str + The job name. + force_field_name : str + The name of the force field. + calculator_kwargs : dict + Keyword arguments that will get passed to the ASE calculator. + task_document_kwargs : dict + Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. + """ + + name: str = f"{MLFF.Nequip} static" + force_field_name: str = f"{MLFF.Nequip}" + task_document_kwargs: dict = field(default_factory=dict) @dataclass @@ -258,31 +372,89 @@ class M3GNetStaticMaker(ForceFieldStaticMaker): The job name. force_field_name : str The name of the force field. + calculator_kwargs : dict + Keyword arguments that will get passed to the ASE calculator. task_document_kwargs : dict Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. """ - name: str = "M3GNet static" - force_field_name: str = "M3GNet" + name: str = f"{MLFF.M3GNet} static" + force_field_name: str = f"{MLFF.M3GNet}" task_document_kwargs: dict = field(default_factory=dict) + calculator_kwargs: dict = field( + default_factory=lambda: {"stress_weight": _GPa_to_eV_per_A3} + ) - def _evaluate_static(self, structure: Structure) -> dict: - import matgl - from matgl.ext.ase import Relaxer - # Note: the below code was taken from the matgl repo examples. - # Load pre-trained M3GNet model (currently uses the MP-2021.2.8 database) - pot = matgl.load_model("M3GNet-MP-2021.2.8-PES") +@dataclass +class MACERelaxMaker(ForceFieldRelaxMaker): + """ + Base Maker to calculate forces and stresses using a MACE potential. - relaxer = Relaxer( - potential=pot, - relax_cell=False, - ) + Parameters + ---------- + name : str + The job name. + force_field_name : str + The name of the force field. + relax_cell : bool = True + Whether to allow the cell shape/volume to change during relaxation. + fix_symmetry : bool = False + Whether to fix the symmetry during relaxation. + Refines the symmetry of the initial structure. + symprec : float = 1e-2 + Tolerance for symmetry finding in case of fix_symmetry. + steps : int + Maximum number of ionic steps allowed during relaxation. + relax_kwargs : dict + Keyword arguments that will get passed to :obj:`Relaxer.relax`. + optimizer_kwargs : dict + Keyword arguments that will get passed to :obj:`Relaxer()`. + calculator_kwargs : dict + Keyword arguments that will get passed to the ASE calculator. E.g. the "model" + key configures which checkpoint to load with mace.calculators.MACECalculator(). + Can be a URL starting with https://. If not set, loads the universal MACE-MP + trained for Matbench Discovery on the MPtrj dataset available at + https://figshare.com/articles/dataset/22715158. + task_document_kwargs : dict + Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. + """ - return relaxer.relax( - structure, - steps=1, - ) + name: str = f"{MLFF.MACE} relax" + force_field_name: str = f"{MLFF.MACE}" + relax_cell: bool = True + fix_symmetry: bool = False + symprec: float = 1e-2 + steps: int = 500 + relax_kwargs: dict = field(default_factory=dict) + optimizer_kwargs: dict = field(default_factory=dict) + task_document_kwargs: dict = field(default_factory=dict) + + +@dataclass +class MACEStaticMaker(ForceFieldStaticMaker): + """ + Base Maker to calculate forces and stresses using a MACE potential. + + Parameters + ---------- + name : str + The job name. + force_field_name : str + The name of the force field. + calculator_kwargs : dict + Keyword arguments that will get passed to the ASE calculator. E.g. the "model" + key configures which checkpoint to load with mace.calculators.MACECalculator(). + Can be a URL starting with https://. If not set, loads the universal MACE-MP + trained for Matbench Discovery on the MPtrj dataset available at + https://figshare.com/articles/dataset/22715158. + task_document_kwargs : dict + Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. + """ + + name: str = f"{MLFF.MACE} static" + force_field_name: str = f"{MLFF.MACE}" + task_document_kwargs: dict = field(default_factory=dict) @dataclass @@ -296,45 +468,40 @@ class GAPRelaxMaker(ForceFieldRelaxMaker): The job name. force_field_name : str The name of the force field. - relax_cell : bool + relax_cell : bool = True Whether to allow the cell shape/volume to change during relaxation. + fix_symmetry : bool = False + Whether to fix the symmetry during relaxation. + Refines the symmetry of the initial structure. + symprec : float = 1e-2 + Tolerance for symmetry finding in case of fix_symmetry. steps : int Maximum number of ionic steps allowed during relaxation. relax_kwargs : dict Keyword arguments that will get passed to :obj:`Relaxer.relax`. optimizer_kwargs : dict Keyword arguments that will get passed to :obj:`Relaxer()`. + calculator_kwargs : dict + Keyword arguments that will get passed to the ASE calculator. task_document_kwargs : dict Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. - potential_args_str: str - args_str for :obj: quippy.potential.Potential()'. - potential_param_filename: str|Path - param_file_name for :obj: quippy.potential.Potential()'. - potential_kwargs: dict - Further kwargs for :obj: quippy.potential.Potential()'. """ - name: str = "GAP relax" - force_field_name: str = "GAP" - relax_cell: bool = False + name: str = f"{MLFF.GAP} relax" + force_field_name: str = f"{MLFF.GAP}" + relax_cell: bool = True + fix_symmetry: bool = False + symprec: float = 1e-2 steps: int = 500 relax_kwargs: dict = field(default_factory=dict) optimizer_kwargs: dict = field(default_factory=dict) + calculator_kwargs: dict = field( + default_factory=lambda: { + "args_str": "IP GAP", + "param_filename": "gap.xml", + } + ) task_document_kwargs: dict = field(default_factory=dict) - potential_args_str: str | Path = "IP GAP" - potential_param_file_name: str = "gap.xml" - potential_kwargs: dict = field(default_factory=dict) - - def _relax(self, structure: Structure) -> dict: - from quippy.potential import Potential - - calculator = Potential( - args_str=self.potential_args_str, - param_filename=str(self.potential_param_file_name), - **self.potential_kwargs, - ) - relaxer = Relaxer(calculator, relax_cell=self.relax_cell) - return relaxer.relax(structure, steps=self.steps, **self.relax_kwargs) @dataclass @@ -348,29 +515,18 @@ class GAPStaticMaker(ForceFieldStaticMaker): The job name. force_field_name : str The name of the force field. + calculator_kwargs : dict + Keyword arguments that will get passed to the ASE calculator. task_document_kwargs : dict Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. - potential_args_str: str - args_str for :obj: quippy.potential.Potential()'. - potential_param_filename: str | Path - param_file_name for :obj: quippy.potential.Potential()'. - potential_kwargs: dict - Further kwargs for :obj: quippy.potential.Potential()'. """ - name: str = "GAP static" - force_field_name: str = "GAP" - potential_args_str: str = "IP GAP" - potential_param_file_name: str | Path = "gap.xml" - potential_kwargs: dict = field(default_factory=dict) - - def _evaluate_static(self, structure: Structure) -> dict: - from quippy.potential import Potential - - calculator = Potential( - args_str=self.potential_args_str, - param_filename=str(self.potential_param_file_name), - **self.potential_kwargs, - ) - relaxer = Relaxer(calculator, relax_cell=False) - return relaxer.relax(structure, steps=1) + name: str = f"{MLFF.GAP} static" + force_field_name: str = f"{MLFF.GAP}" + task_document_kwargs: dict = field(default_factory=dict) + calculator_kwargs: dict = field( + default_factory=lambda: { + "args_str": "IP GAP", + "param_filename": "gap.xml", + } + ) diff --git a/src/atomate2/forcefields/md.py b/src/atomate2/forcefields/md.py new file mode 100644 index 0000000000..b2462c1d79 --- /dev/null +++ b/src/atomate2/forcefields/md.py @@ -0,0 +1,379 @@ +"""Makers to perform MD with forcefields.""" + +from __future__ import annotations + +from collections.abc import Sequence +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +import numpy as np +from ase import units +from ase.md.andersen import Andersen +from ase.md.langevin import Langevin +from ase.md.md import MolecularDynamics +from ase.md.npt import NPT +from ase.md.nptberendsen import NPTBerendsen +from ase.md.nvtberendsen import NVTBerendsen +from ase.md.velocitydistribution import ( + MaxwellBoltzmannDistribution, + Stationary, + ZeroRotation, +) +from ase.md.verlet import VelocityVerlet +from jobflow import Maker +from pymatgen.io.ase import AseAtomsAdaptor +from scipy.interpolate import interp1d +from scipy.linalg import schur + +from atomate2.forcefields import MLFF +from atomate2.forcefields.jobs import forcefield_job +from atomate2.forcefields.schemas import ForcefieldResult, ForceFieldTaskDocument +from atomate2.forcefields.utils import ( + TrajectoryObserver, + ase_calculator, + revert_default_dtype, +) + +if TYPE_CHECKING: + from pathlib import Path + from typing import Literal + + from ase.calculators.calculator import Calculator + from pymatgen.core.structure import Structure + +_valid_dynamics: dict[str, tuple[str, ...]] = { + "nve": ("velocityverlet",), + "nvt": ("nose-hoover", "langevin", "andersen", "berendsen"), + "npt": ("nose-hoover", "berendsen"), +} + +_preset_dynamics: dict = { + "nve_velocityverlet": VelocityVerlet, + "nvt_andersen": Andersen, + "nvt_berendsen": NVTBerendsen, + "nvt_langevin": Langevin, + "nvt_nose-hoover": NPT, + "npt_berendsen": NPTBerendsen, + "npt_nose-hoover": NPT, +} + + +@dataclass +class ForceFieldMDMaker(Maker): + """ + Perform MD with a force field. + + Note the the following units are consistent with the VASP MD implementation: + - `temperature` in Kelvin (TEBEG and TEEND) + - `time_step` in femtoseconds (POTIM) + - `pressure` in kB (PSTRESS) + + The default dynamics is Langevin NVT consistent with VASP MD, with the friction + coefficient set to 10 ps^-1 (LANGEVIN_GAMMA). + + For the rest of preset dynamics (`_valid_dynamics`) and custom dynamics inherited + from ASE (`MolecularDynamics`), the user can specify the dynamics as a string or an + ASE class into the `dynamics` attribute. In this case, please consult the ASE + documentation for the parameters and units to pass into the ASE MD function through + `ase_md_kwargs`. + + Parameters + ---------- + name : str + The name of the MD Maker + force_field_name : str + The name of the forcefield (for provenance) + time_step : float | None = None. + The timestep of the MD run in fs. + If `None`, defaults to 0.5 fs if a structure contains an isotope of + hydrogen and 2 fs otherwise. + n_steps : int = 1000 + The number of MD steps to run + ensemble : str = "nvt" + The ensemble to use. Valid ensembles are nve, nvt, or npt + temperature: float | Sequence | np.ndarray | None. + The temperature in Kelvin. If a sequence or 1D array, the temperature + schedule will be interpolated linearly between the given values. If a + float, the temperature will be constant throughout the run. + pressure: float | Sequence | None = None + The pressure in kilobar. If a sequence or 1D array, the pressure + schedule will be interpolated linearly between the given values. If a + float, the pressure will be constant throughout the run. + dynamics : str | ASE .MolecularDynamics = "langevin" + The dynamical thermostat to use. If dynamics is an ASE .MolecularDynamics + object, this uses the option specified explicitly by the user. + See _valid_dynamics for a list of pre-defined options when + specifying dynamics as a string. + ase_md_kwargs : dict | None = None + Options except for temperature and pressure to pass into the ASE MD function + calculator_kwargs : dict + kwargs to pass to the ASE calculator class + traj_file : str | Path | None = None + If a str or Path, the name of the file to save the MD trajectory to. + If None, the trajectory is not written to disk + traj_file_fmt : Literal["ase","pmg"] + The format of the trajectory file to write. If "ase", writes an + ASE trajectory, if "pmg", writes a Pymatgen trajectory. + traj_interval : int + The step interval for saving the trajectories. + mb_velocity_seed : int | None = None + If an int, a random number seed for generating initial velocities + from a Maxwell-Boltzmann distribution. + zero_linear_momentum : bool = False + Whether to initialize the atomic velocities with zero linear momentum + zero_angular_momentum : bool = False + Whether to initialize the atomic velocities with zero angular momentum + task_document_kwargs: dict + Options to pass to the TaskDoc. Default choice + {"store_trajectory": "partial", "ionic_step_data": ("energy",),} + is consistent with atomate2.vasp.md.MDMaker + """ + + name: str = "Forcefield MD" + force_field_name: str = f"{MLFF.Forcefield}" + time_step: float | None = None + n_steps: int = 1000 + ensemble: Literal["nve", "nvt", "npt"] = "nvt" + dynamics: str | MolecularDynamics = "langevin" + temperature: float | Sequence | np.ndarray | None = 300.0 + pressure: float | Sequence | np.ndarray | None = None + ase_md_kwargs: dict | None = None + calculator_kwargs: dict = field(default_factory=dict) + traj_file: str | Path | None = None + traj_file_fmt: Literal["pmg", "ase"] = "ase" + traj_interval: int = 1 + mb_velocity_seed: int | None = None + zero_linear_momentum: bool = False + zero_angular_momentum: bool = False + task_document_kwargs: dict = field( + default_factory=lambda: { + "store_trajectory": "partial", + "ionic_step_data": ("energy",), # energy is required in ionic steps + } + ) + + @staticmethod + def _interpolate_quantity(values: Sequence | np.ndarray, n_pts: int) -> np.ndarray: + """Interpolate temperature / pressure on a schedule.""" + n_vals = len(values) + return np.interp( + np.linspace(0, n_vals - 1, n_pts + 1), + np.linspace(0, n_vals - 1, n_vals), + values, + ) + + def _get_ensemble_schedule(self) -> None: + if self.ensemble == "nve": + # Disable thermostat and barostat + self.temperature = np.nan + self.pressure = np.nan + self.t_schedule = np.full(self.n_steps + 1, self.temperature) + self.p_schedule = np.full(self.n_steps + 1, self.pressure) + return + + if isinstance(self.temperature, Sequence) or ( + isinstance(self.temperature, np.ndarray) and self.temperature.ndim == 1 + ): + self.t_schedule = self._interpolate_quantity(self.temperature, self.n_steps) + # NOTE: In ASE Langevin dynamics, the temperature are normally + # scalars, but in principle one quantity per atom could be specified by giving + # an array. This is not implemented yet here. + else: + self.t_schedule = np.full(self.n_steps + 1, self.temperature) + + if self.ensemble == "nvt": + self.pressure = np.nan + self.p_schedule = np.full(self.n_steps + 1, self.pressure) + return + + if isinstance(self.pressure, Sequence) or ( + isinstance(self.pressure, np.ndarray) and self.pressure.ndim == 1 + ): + self.p_schedule = self._interpolate_quantity(self.pressure, self.n_steps) + elif isinstance(self.pressure, np.ndarray) and self.pressure.ndim == 4: + self.p_schedule = interp1d( + np.arange(self.n_steps + 1), self.pressure, kind="linear" + ) + else: + self.p_schedule = np.full(self.n_steps + 1, self.pressure) + + def _get_ensemble_defaults(self) -> None: + """Update ASE MD kwargs with defaults consistent with VASP MD.""" + self.ase_md_kwargs = self.ase_md_kwargs or {} + + if self.ensemble == "nve": + self.ase_md_kwargs.pop("temperature", None) + self.ase_md_kwargs.pop("temperature_K", None) + self.ase_md_kwargs.pop("externalstress", None) + elif self.ensemble == "nvt": + self.ase_md_kwargs["temperature_K"] = self.t_schedule[0] + self.ase_md_kwargs.pop("externalstress", None) + elif self.ensemble == "npt": + self.ase_md_kwargs["temperature_K"] = self.t_schedule[0] + self.ase_md_kwargs["externalstress"] = self.p_schedule[0] * 1e3 * units.bar + + if isinstance(self.dynamics, str) and self.dynamics.lower() == "langevin": + self.ase_md_kwargs["friction"] = self.ase_md_kwargs.get( + "friction", + 10.0 * 1e-3 / units.fs, # Same default as in VASP: 10 ps^-1 + ) + + @forcefield_job + def make( + self, + structure: Structure, + prev_dir: str | Path | None = None, + ) -> ForceFieldTaskDocument: + """ + Perform MD on a structure using a force field. + + Parameters + ---------- + structure: .Structure + pymatgen structure. + prev_dir : str or Path or None + A previous calculation directory to copy output files from. Unused, just + added to match the method signature of other makers. + """ + self._get_ensemble_schedule() + self._get_ensemble_defaults() + + if self.time_step is None: + # If a structure contains an isotope of hydrogen, set default `time_step` + # to 0.5 fs, and 2 fs otherwise. + has_h_isotope = any(element.Z == 1 for element in structure.composition) + self.time_step = 0.5 if has_h_isotope else 2.0 + + initial_velocities = structure.site_properties.get("velocities") + + if isinstance(self.dynamics, str): + # Use known dynamics if `self.dynamics` is a str + self.dynamics = self.dynamics.lower() + if self.dynamics not in _valid_dynamics[self.ensemble]: + raise ValueError( + f"{self.dynamics} thermostat not available for {self.ensemble}." + f"Available {self.ensemble} thermostats are:" + " ".join(_valid_dynamics[self.ensemble]) + ) + + if self.ensemble == "nve" and self.dynamics is None: + self.dynamics = "velocityverlet" + md_func = _preset_dynamics[f"{self.ensemble}_{self.dynamics}"] + + elif issubclass(self.dynamics, MolecularDynamics): + # Allow user to explicitly run ASE Dynamics class + md_func = self.dynamics + + atoms = structure.to_ase_atoms() + + if md_func is NPT: + # Note that until md_func is instantiated, isinstance(md_func,NPT) is False + # ASE NPT implementation requires upper triangular cell + schur_decomp, _ = schur(atoms.get_cell(complete=True), output="complex") + atoms.set_cell(schur_decomp.real, scale_atoms=True) + + if initial_velocities: + atoms.set_velocities(initial_velocities) + elif not np.isnan(self.t_schedule).any(): + MaxwellBoltzmannDistribution( + atoms=atoms, + temperature_K=self.t_schedule[0], + rng=np.random.default_rng(seed=self.mb_velocity_seed), + ) + if self.zero_linear_momentum: + Stationary(atoms) + if self.zero_angular_momentum: + ZeroRotation(atoms) + + with revert_default_dtype(): + atoms.calc = self.calculator + + md_observer = TrajectoryObserver(atoms, store_md_outputs=True) + + md_runner = md_func( + atoms=atoms, timestep=self.time_step * units.fs, **self.ase_md_kwargs + ) + + md_runner.attach(md_observer, interval=self.traj_interval) + + def _callback(dyn: MolecularDynamics = md_runner) -> None: + if self.ensemble == "nve": + return + dyn.set_temperature(temperature_K=self.t_schedule[dyn.nsteps]) + if self.ensemble == "nvt": + return + dyn.set_stress(self.p_schedule[dyn.nsteps] * 1e3 * units.bar) + + md_runner.attach(_callback, interval=1) + md_runner.run(steps=self.n_steps) + + if self.traj_file is not None: + md_observer.save(filename=self.traj_file, fmt=self.traj_file_fmt) + + structure = AseAtomsAdaptor.get_structure(atoms) + + self.task_document_kwargs = self.task_document_kwargs or {} + + return ForceFieldTaskDocument.from_ase_compatible_result( + self.force_field_name, + ForcefieldResult( + final_structure=structure, + trajectory=md_observer.to_pymatgen_trajectory(None), + ), + relax_cell=(self.ensemble == "npt"), + steps=self.n_steps, + relax_kwargs=None, + optimizer_kwargs=None, + **self.task_document_kwargs, + ) + + @property + def calculator(self) -> Calculator: + """ASE calculator, can be overwritten by user.""" + return ase_calculator(self.force_field_name, **self.calculator_kwargs) + + +@dataclass +class MACEMDMaker(ForceFieldMDMaker): + """Perform an MD run with MACE.""" + + name: str = f"{MLFF.MACE} MD" + force_field_name: str = f"{MLFF.MACE}" + calculator_kwargs: dict = field( + default_factory=lambda: {"default_dtype": "float32"} + ) + + +@dataclass +class M3GNetMDMaker(ForceFieldMDMaker): + """Perform an MD run with M3GNet.""" + + name: str = f"{MLFF.M3GNet} MD" + force_field_name: str = f"{MLFF.M3GNet}" + + +@dataclass +class CHGNetMDMaker(ForceFieldMDMaker): + """Perform an MD run with CHGNet.""" + + name: str = f"{MLFF.CHGNet} MD" + force_field_name: str = f"{MLFF.CHGNet}" + + +@dataclass +class GAPMDMaker(ForceFieldMDMaker): + """Perform an MD run with GAP.""" + + name: str = f"{MLFF.GAP} MD" + force_field_name: str = f"{MLFF.GAP}" + calculator_kwargs: dict = field( + default_factory=lambda: {"args_str": "IP GAP", "param_filename": "gap.xml"} + ) + + +@dataclass +class NequipMDMaker(ForceFieldMDMaker): + """Perform an MD run with nequip.""" + + name: str = f"{MLFF.Nequip} MD" + force_field_name: str = f"{MLFF.Nequip}" diff --git a/src/atomate2/forcefields/schemas.py b/src/atomate2/forcefields/schemas.py index 4efb7f032b..d474d22ffb 100644 --- a/src/atomate2/forcefields/schemas.py +++ b/src/atomate2/forcefields/schemas.py @@ -1,17 +1,41 @@ -"""Job to prerelax a structure using an MD Potential.""" +"""Schema definitions for force field tasks.""" -from typing import Optional +from typing import Any, Optional from ase.stress import voigt_6_to_full_3x3_stress from ase.units import GPa from emmet.core.math import Matrix3D, Vector3D from emmet.core.structure import StructureMetadata -from pydantic import BaseModel, Extra, Field +from emmet.core.utils import ValueEnum +from emmet.core.vasp.calculation import StoreTrajectoryOption +from pydantic import BaseModel, Field from pymatgen.core.structure import Structure -from pymatgen.io.ase import AseAtomsAdaptor +from pymatgen.core.trajectory import Trajectory +from typing_extensions import Self +from atomate2.forcefields import MLFF -class IonicStep(BaseModel, extra=Extra.allow): # type: ignore[call-arg] + +class ForcefieldResult(dict): + """Schema to store outputs in ForceFieldTaskDocument.""" + + def __init__(self, **kwargs: Any) -> None: + kwargs = { + "final_structure": None, + "trajectory": None, + "is_force_converged": None, + **kwargs, + } + super().__init__(**kwargs) + + +class ForcefieldObject(ValueEnum): + """Types of forcefield data objects.""" + + TRAJECTORY = "trajectory" + + +class IonicStep(BaseModel, extra="allow"): # type: ignore[call-arg] """Document defining the information at each ionic step.""" energy: float = Field(None, description="The free energy.") @@ -19,7 +43,9 @@ class IonicStep(BaseModel, extra=Extra.allow): # type: ignore[call-arg] None, description="The forces on each atom." ) stress: Optional[Matrix3D] = Field(None, description="The stress on the lattice.") - structure: Structure = Field(None, description="The structure at this step.") + structure: Optional[Structure] = Field( + None, description="The structure at this step." + ) class InputDoc(BaseModel): @@ -30,6 +56,16 @@ class InputDoc(BaseModel): None, description="Whether cell lattice was allowed to change during relaxation.", ) + fix_symmetry: bool = Field( + None, + description=( + "Whether to fix the symmetry of the structure during relaxation. " + "Refines the symmetry of the initial structure." + ), + ) + symprec: float = Field( + None, description="Tolerance for symmetry finding in case of fix_symmetry." + ) steps: int = Field( None, description="Maximum number of steps allowed during relaxation." ) @@ -102,6 +138,21 @@ class ForceFieldTaskDocument(StructureMetadata): None, description="Directory where the force field calculations are performed." ) + included_objects: Optional[list[ForcefieldObject]] = Field( + None, description="list of forcefield objects included with this task document" + ) + forcefield_objects: Optional[dict[ForcefieldObject, Any]] = Field( + None, description="Forcefield objects associated with this task" + ) + + is_force_converged: Optional[bool] = Field( + None, + description=( + "Whether the calculation is converged with respect " + "to interatomic forces." + ), + ) + @classmethod def from_ase_compatible_result( cls, @@ -111,10 +162,13 @@ def from_ase_compatible_result( steps: int, relax_kwargs: dict = None, optimizer_kwargs: dict = None, + fix_symmetry: bool = False, + symprec: float = 1e-2, ionic_step_data: tuple = ("energy", "forces", "magmoms", "stress", "structure"), - ) -> "ForceFieldTaskDocument": - """ - Create a ForceFieldTaskDocument for a Task that has ASE-compatible outputs. + store_trajectory: StoreTrajectoryOption = StoreTrajectoryOption.NO, + **task_document_kwargs, + ) -> Self: + """Create a ForceFieldTaskDocument for a Task that has ASE-compatible outputs. Parameters ---------- @@ -124,6 +178,10 @@ def from_ase_compatible_result( The outputted results from the task. relax_cell : bool Whether the cell shape/volume was allowed to change during the task. + fix_symmetry : bool + Whether to fix the symmetry of the structure during relaxation. + symprec : float + Tolerance for symmetry finding in case of fix_symmetry. steps : int Maximum number of ionic steps allowed during relaxation. relax_kwargs : dict @@ -132,29 +190,33 @@ def from_ase_compatible_result( Keyword arguments that will get passed to :obj:`Relaxer()`. ionic_step_data : tuple Which data to save from each ionic step. + store_trajectory: + whether to set the StoreTrajectoryOption + task_document_kwargs : dict + Additional keyword args passed to :obj:`.ForceFieldTaskDocument()`. """ - trajectory = result["trajectory"].__dict__ + trajectory = result["trajectory"] - # NOTE: units for stresses were converted from ev/Angstromยณ to kbar - # (* -1 from standard output) - # and to 3x3 matrix to comply with MP convention - for i in range(len(trajectory["stresses"])): - trajectory["stresses"][i] = voigt_6_to_full_3x3_stress( - trajectory["stresses"][i] * -10 / GPa - ) + n_steps = len(trajectory) - species = AseAtomsAdaptor.get_structure(trajectory["atoms"]).species + # NOTE: convert stress units from eV/Aยณ to kBar (* -1 from standard output) + # and to 3x3 matrix to comply with MP convention + for idx in range(n_steps): + if trajectory.frame_properties[idx].get("stress") is not None: + trajectory.frame_properties[idx]["stress"] = voigt_6_to_full_3x3_stress( + [ + val * -10 / GPa + for val in trajectory.frame_properties[idx]["stress"] + ] + ) - input_structure = Structure( - lattice=trajectory["cells"][0], - coords=trajectory["atom_positions"][0], - species=species, - coords_are_cartesian=True, - ) + input_structure = trajectory[0] input_doc = InputDoc( structure=input_structure, relax_cell=relax_cell, + fix_symmetry=fix_symmetry, + symprec=symprec, steps=steps, relax_kwargs=relax_kwargs, optimizer_kwargs=optimizer_kwargs, @@ -164,69 +226,55 @@ def from_ase_compatible_result( # number of steps for static calculations. if steps <= 1: steps = 1 - for key in trajectory: - trajectory[key] = [trajectory[key][0]] + n_steps = 1 + trajectory = Trajectory.from_structures( + structures=[trajectory[0]], + frame_properties=[trajectory.frame_properties[0]], + constant_lattice=False, + ) output_structure = input_structure else: output_structure = result["final_structure"] - final_energy = trajectory["energies"][-1] - final_energy_per_atom = trajectory["energies"][-1] / input_structure.num_sites - final_forces = trajectory["forces"][-1].tolist() - final_stress = trajectory["stresses"][-1].tolist() - - n_steps = len(trajectory["energies"]) + final_energy = trajectory.frame_properties[-1]["energy"] + final_energy_per_atom = final_energy / input_structure.num_sites + final_forces = trajectory.frame_properties[-1]["forces"] + final_stress = trajectory.frame_properties[-1]["stress"] ionic_steps = [] - for i in range(n_steps): - cur_energy = ( - trajectory["energies"][i] if "energy" in ionic_step_data else None - ) - cur_forces = ( - trajectory["forces"][i].tolist() - if "forces" in ionic_step_data - else None - ) - cur_stress = ( - trajectory["stresses"][i].tolist() - if "stress" in ionic_step_data + for idx in range(n_steps): + _ionic_step_data = { + key: trajectory.frame_properties[idx][key] + if key in ionic_step_data else None - ) + for key in ("energy", "forces", "stress") + } - if "structure" in ionic_step_data: - cur_structure = Structure( - lattice=trajectory["cells"][i], - coords=trajectory["atom_positions"][i], - species=species, - coords_are_cartesian=True, - ) - else: - cur_structure = None - - # include "magmoms" in :obj:`cur_ionic_step` if the trajectory has "magmoms" - if "magmoms" in trajectory: - cur_ionic_step = IonicStep( - energy=cur_energy, - forces=cur_forces, - magmoms=( - trajectory["magmoms"][i].tolist() + cur_structure = trajectory[idx] if "structure" in ionic_step_data else None + + # include "magmoms" in :obj:`ionic_step` if the trajectory has "magmoms" + if "magmoms" in trajectory.frame_properties[idx]: + _ionic_step_data.update( + { + "magmoms": trajectory.frame_properties[idx]["magmoms"] if "magmoms" in ionic_step_data else None - ), - stress=cur_stress, - structure=cur_structure, + } ) - # otherwise do not include "magmoms" in :obj:`cur_ionic_step` - elif "magmoms" not in trajectory: - cur_ionic_step = IonicStep( - energy=cur_energy, - forces=cur_forces, - stress=cur_stress, - structure=cur_structure, - ) + ionic_step = IonicStep( + structure=cur_structure, + **_ionic_step_data, + ) + + ionic_steps.append(ionic_step) - ionic_steps.append(cur_ionic_step) + forcefield_objects: dict[ForcefieldObject, Any] = {} + if store_trajectory != StoreTrajectoryOption.NO: + # For VASP calculations, the PARTIAL trajectory option removes + # electronic step info. There is no equivalent for forcefields, + # so we just save the same info for FULL and PARTIAL options. + forcefield_objects[ForcefieldObject.TRAJECTORY] = trajectory # type: ignore[index] output_doc = OutputDoc( structure=output_structure, @@ -238,14 +286,22 @@ def from_ase_compatible_result( n_steps=n_steps, ) - if forcefield_name == "M3GNet": - import matgl - - version = matgl.__version__ - elif forcefield_name == "CHGNet": - import chgnet - - version = chgnet.__version__ + # map force field name to its package name + pkg_names = { + str(k): v + for k, v in { + MLFF.M3GNet: "matgl", + MLFF.CHGNet: "chgnet", + MLFF.MACE: "mace-torch", + MLFF.GAP: "quippy-ase", + MLFF.Nequip: "nequip", + }.items() + } + pkg_name = pkg_names.get(forcefield_name) + if pkg_name: + import importlib.metadata + + version = importlib.metadata.version(pkg_name) else: version = "Unknown" return cls.from_structure( @@ -255,4 +311,8 @@ def from_ase_compatible_result( output=output_doc, forcefield_name=forcefield_name, forcefield_version=version, + included_objects=list(forcefield_objects.keys()), + forcefield_objects=forcefield_objects, + is_force_converged=result.get("is_force_converged"), + **task_document_kwargs, ) diff --git a/src/atomate2/forcefields/utils.py b/src/atomate2/forcefields/utils.py index 0e99b606bd..ec65b5d282 100644 --- a/src/atomate2/forcefields/utils.py +++ b/src/atomate2/forcefields/utils.py @@ -6,34 +6,58 @@ and the following copyright applies: Copyright (c) 2022, Materials Virtual Lab. """ + from __future__ import annotations import contextlib import io -import pickle +import json import sys +import warnings +from contextlib import contextmanager from typing import TYPE_CHECKING -from ase.constraints import ExpCellFilter -from ase.optimize.bfgs import BFGS -from ase.optimize.bfgslinesearch import BFGSLineSearch -from ase.optimize.fire import FIRE -from ase.optimize.lbfgs import LBFGS, LBFGSLineSearch -from ase.optimize.mdmin import MDMin +import numpy as np +from ase.calculators.calculator import PropertyNotImplementedError +from ase.calculators.singlepoint import SinglePointCalculator +from ase.constraints import FixSymmetry +from ase.io import Trajectory as AseTrajectory +from ase.optimize import BFGS, FIRE, LBFGS, BFGSLineSearch, LBFGSLineSearch, MDMin from ase.optimize.sciopt import SciPyFminBFGS, SciPyFminCG +from monty.json import MontyDecoder +from monty.serialization import dumpfn from pymatgen.core.structure import Molecule, Structure +from pymatgen.core.trajectory import Trajectory as PmgTrajectory from pymatgen.io.ase import AseAtomsAdaptor +from atomate2.forcefields import MLFF +from atomate2.forcefields.schemas import ForcefieldResult + +try: + from ase.filters import FrechetCellFilter +except ImportError: + FrechetCellFilter = None + warnings.warn( + "Due to errors in the implementation of gradients in the ASE" + " ExpCellFilter, we recommend installing ASE from gitlab\n" + " pip install git+https://gitlab.com/ase/ase.git\n" + "rather than PyPi to access FrechetCellFilter. See\n" + " https://wiki.fysik.dtu.dk/ase/ase/filters.html#the-frechetcellfilter-class\n" + "for more details. Otherwise, you must specify an alternate ASE Filter.", + stacklevel=2, + ) + if TYPE_CHECKING: + from collections.abc import Generator from os import PathLike - from typing import Any + from typing import Any, Literal - import numpy as np from ase import Atoms from ase.calculators.calculator import Calculator + from ase.filters import Filter + from ase.io.trajectory import TrajectoryReader from ase.optimize.optimize import Optimizer - OPTIMIZERS = { "FIRE": FIRE, "BFGS": BFGS, @@ -46,15 +70,53 @@ } +def _get_pymatgen_trajectory_from_observer( + trajectory_observer: Any, frame_property_keys: list[str] +) -> PmgTrajectory: + to_singular = {"energies": "energy", "stresses": "stress"} + + if hasattr(trajectory_observer, "as_dict"): + traj = trajectory_observer.as_dict() + else: + traj = trajectory_observer.__dict__ + + n_md_steps = len(traj["cells"]) + species = AseAtomsAdaptor.get_structure(traj["atoms"]).species + + structures = [ + Structure( + lattice=traj["cells"][idx], + coords=traj["atom_positions"][idx], + species=species, + coords_are_cartesian=True, + ) + for idx in range(n_md_steps) + ] + + frame_properties = [ + { + to_singular.get(key, key): traj[key][idx] + for key in frame_property_keys + if key in traj + } + for idx in range(n_md_steps) + ] + + return PmgTrajectory.from_structures( + structures, + frame_properties=frame_properties, + constant_lattice=False, + ) + + class TrajectoryObserver: """Trajectory observer. This is a hook in the relaxation process that saves the intermediate structures. """ - def __init__(self, atoms: Atoms) -> None: - """ - Initialize the Observer. + def __init__(self, atoms: Atoms, store_md_outputs: bool = False) -> None: + """Initialize the Observer. Parameters ---------- @@ -68,18 +130,43 @@ def __init__(self, atoms: Atoms) -> None: self.energies: list[float] = [] self.forces: list[np.ndarray] = [] self.stresses: list[np.ndarray] = [] + + self._store_magmoms = True + self.magmoms: list[np.ndarray] = [] + self.atom_positions: list[np.ndarray] = [] self.cells: list[np.ndarray] = [] + self._store_md_outputs = store_md_outputs + # `self.{velocities,temperatures}` always initialized, + # but data is only stored / saved to trajectory for MD runs + self.velocities: list[np.ndarray] = [] + self.temperatures: list[float] = [] + def __call__(self) -> None: """Save the properties of an Atoms during the relaxation.""" - # TODO: maybe include magnetic moments self.energies.append(self.compute_energy()) self.forces.append(self.atoms.get_forces()) - self.stresses.append(self.atoms.get_stress()) + # MD needs kinetic energy parts of stress, relaxations do not + # When _store_md_outputs is True, ideal gas contribution to + # stress is included. + self.stresses.append( + self.atoms.get_stress(include_ideal_gas=self._store_md_outputs) + ) + + if self._store_magmoms: + try: + self.magmoms.append(self.atoms.get_magnetic_moments()) + except PropertyNotImplementedError: + self._store_magmoms = False + self.atom_positions.append(self.atoms.get_positions()) self.cells.append(self.atoms.get_cell()[:]) + if self._store_md_outputs: + self.velocities.append(self.atoms.get_velocities()) + self.temperatures.append(self.atoms.get_temperature()) + def compute_energy(self) -> float: """ Calculate the energy, here we just use the potential energy. @@ -90,9 +177,11 @@ def compute_energy(self) -> float: """ return self.atoms.get_potential_energy() - def save(self, filename: str | PathLike) -> None: + def save( + self, filename: str | PathLike | None, fmt: Literal["pmg", "ase"] = "ase" + ) -> None: """ - Save the trajectory file. + Save the trajectory file using monty.serialization. Parameters ---------- @@ -102,18 +191,97 @@ def save(self, filename: str | PathLike) -> None: ------- None """ - with open(filename, "wb") as f: - pickle.dump( - { - "energy": self.energies, - "forces": self.forces, - "stresses": self.stresses, - "atom_positions": self.atom_positions, - "cell": self.cells, - "atomic_number": self.atoms.get_atomic_numbers(), - }, - f, - ) + filename = str(filename) if filename is not None else None + if fmt == "pmg": + self.to_pymatgen_trajectory(filename=filename) + elif fmt == "ase": + self.to_ase_trajectory(filename=filename) + + def to_ase_trajectory( + self, filename: str | None = "atoms.traj" + ) -> TrajectoryReader: + """ + Convert to an ASE .Trajectory. + + Parameters + ---------- + filename : str | None + Name of the file to write the ASE trajectory to. + If None, no file is written. + """ + for idx in range(len(self.cells)): + atoms = self.atoms.copy() + atoms.set_positions(self.atom_positions[idx]) + atoms.set_cell(self.cells[idx]) + + if self._store_md_outputs: + atoms.set_velocities(self.velocities[idx]) + + kwargs = { + "energy": self.energies[idx], + "forces": self.forces[idx], + "stress": self.stresses[idx], + } + if self._store_magmoms: + kwargs["magmom"] = self.magmoms[idx] + + atoms.calc = SinglePointCalculator(atoms=atoms, **kwargs) + with AseTrajectory(filename, "a" if idx > 0 else "w", atoms=atoms) as file: + file.write() + + return AseTrajectory(filename, "r") + + def to_pymatgen_trajectory( + self, filename: str | None = "trajectory.json.gz" + ) -> PmgTrajectory: + """ + Convert the trajectory to a pymatgen .Trajectory object. + + Parameters + ---------- + filename : str or None + Name of the file to write the pymatgen trajectory to. + If None, no file is written. + """ + frame_property_keys = ["energy", "forces", "stress"] + if self._store_magmoms: + frame_property_keys += ["magmoms"] + if self._store_md_outputs: + frame_property_keys += ["velocities", "temperature"] + + traj = _get_pymatgen_trajectory_from_observer( + self, frame_property_keys=frame_property_keys + ) + + if filename: + dumpfn(traj, filename) + + return traj + + def as_dict(self) -> dict: + """Make JSONable dict representation of the Trajectory.""" + traj_dict = { + "energy": self.energies, + "forces": self.forces, + "stress": self.stresses, + "atom_positions": self.atom_positions, + "cells": self.cells, + "atoms": self.atoms, + "atomic_number": self.atoms.get_atomic_numbers(), + } + + if self._store_magmoms: + traj_dict["magmoms"] = self.magmoms + + if self._store_md_outputs: + traj_dict.update(velocities=self.velocities, temperature=self.temperatures) + # sanitize dict + for key in traj_dict: + if all(isinstance(val, np.ndarray) for val in traj_dict[key]): + traj_dict[key] = [val.tolist() for val in traj_dict[key]] + elif isinstance(traj_dict[key], np.ndarray): + traj_dict[key] = traj_dict[key].tolist() + return traj_dict class Relaxer: @@ -124,20 +292,23 @@ def __init__( calculator: Calculator, optimizer: Optimizer | str = "FIRE", relax_cell: bool = True, + fix_symmetry: bool = False, + symprec: float = 1e-2, ) -> None: - """ - Initialize the Relaxer. + """Initialize the Relaxer. Parameters ---------- calculator (ase Calculator): an ase calculator optimizer (str or ase Optimizer): the optimization algorithm. relax_cell (bool): if True, cell parameters will be optimized. + fix_symmetry (bool): if True, symmetry will be fixed during relaxation. + symprec (float): Tolerance for symmetry finding in case of fix_symmetry. """ self.calculator = calculator if isinstance(optimizer, str): - optimizer_obj = OPTIMIZERS.get(optimizer, None) + optimizer_obj = OPTIMIZERS.get(optimizer) elif optimizer is None: raise ValueError("Optimizer cannot be None") else: @@ -146,6 +317,8 @@ def __init__( self.opt_class: Optimizer = optimizer_obj self.relax_cell = relax_cell self.ase_adaptor = AseAtomsAdaptor() + self.fix_symmetry = fix_symmetry + self.symprec = symprec def relax( self, @@ -155,20 +328,28 @@ def relax( traj_file: str = None, interval: int = 1, verbose: bool = False, + cell_filter: Filter = FrechetCellFilter, **kwargs, - ) -> dict[str, Any]: + ) -> ForcefieldResult: """ Relax the structure. Parameters ---------- - atoms (Atoms): the atoms for relaxation - fmax (float): total force tolerance for relaxation convergence. - steps (int): max number of steps for relaxation - traj_file (str): the trajectory file for saving - interval (int): the step interval for saving the trajectories - verbose (bool): if True, screenoutput will be shown. - kwargs: further kwargs. + atoms : Atoms + The atoms for relaxation. + fmax : float + Total force tolerance for relaxation convergence. + steps : int + Max number of steps for relaxation. + traj_file : str + The trajectory file for saving. + interval : int + The step interval for saving the trajectories. + verbose : bool + If True, screen output will be shown. + **kwargs + Further kwargs. Returns ------- @@ -176,22 +357,106 @@ def relax( """ if isinstance(atoms, (Structure, Molecule)): atoms = self.ase_adaptor.get_atoms(atoms) + if self.fix_symmetry: + atoms.set_constraint(FixSymmetry(atoms, symprec=self.symprec)) atoms.set_calculator(self.calculator) - stream = sys.stdout if verbose else io.StringIO() - with contextlib.redirect_stdout(stream): + with contextlib.redirect_stdout(sys.stdout if verbose else io.StringIO()): obs = TrajectoryObserver(atoms) if self.relax_cell: - atoms = ExpCellFilter(atoms) + atoms = cell_filter(atoms) optimizer = self.opt_class(atoms, **kwargs) optimizer.attach(obs, interval=interval) optimizer.run(fmax=fmax, steps=steps) obs() if traj_file is not None: obs.save(traj_file) - if isinstance(atoms, ExpCellFilter): + if isinstance(atoms, cell_filter): atoms = atoms.atoms - return { - "final_structure": self.ase_adaptor.get_structure(atoms), - "trajectory": obs, - } + struct = self.ase_adaptor.get_structure(atoms) + traj = obs.to_pymatgen_trajectory(None) + is_force_conv = all( + np.linalg.norm(traj.frame_properties[-1]["forces"][idx]) < abs(fmax) + for idx in range(len(struct)) + ) + return ForcefieldResult( + final_structure=struct, trajectory=traj, is_force_converged=is_force_conv + ) + + +def ase_calculator(calculator_meta: str | dict, **kwargs: Any) -> Calculator | None: + """ + Create an ASE calculator from a given set of metadata. + + Parameters + ---------- + calculator_meta : str or dict + If a str, should be one of `atomate2.forcefields.MLFF`. + If a dict, should be decodable by `monty.json.MontyDecoder`. + For example, one can also call the CHGNet calculator as follows + ``` + calculator_meta = { + "@module": "chgnet.model.dynamics", + "@callable": "CHGNetCalculator" + } + ``` + args : optional args to pass to a calculator + kwargs : optional kwargs to pass to a calculator + + Returns + ------- + ASE .Calculator + """ + calculator = None + + if isinstance(calculator_meta, str) and calculator_meta in map(str, MLFF): + calculator_name = MLFF(calculator_meta.split("MLFF.")[-1]) + + if calculator_name == MLFF.CHGNet: + from chgnet.model.dynamics import CHGNetCalculator + + calculator = CHGNetCalculator(**kwargs) + + elif calculator_name == MLFF.M3GNet: + import matgl + from matgl.ext.ase import PESCalculator + + potential = matgl.load_model("M3GNet-MP-2021.2.8-PES") + calculator = PESCalculator(potential, **kwargs) + + elif calculator_name == MLFF.MACE: + from mace.calculators import mace_mp + + calculator = mace_mp(**kwargs) + + elif calculator_name == MLFF.GAP: + from quippy.potential import Potential + + calculator = Potential(**kwargs) + + elif calculator_name == MLFF.Nequip: + from nequip.ase import NequIPCalculator + + calculator = NequIPCalculator.from_deployed_model(**kwargs) + + elif isinstance(calculator_meta, dict): + calc_cls = MontyDecoder().decode(json.dumps(calculator_meta)) + calculator = calc_cls(**kwargs) + + return calculator + + +@contextmanager +def revert_default_dtype() -> Generator[None, None, None]: + """Context manager for torch.default_dtype. + + Reverts it to whatever torch.get_default_dtype() was when entering the context. + + Originally added for use with MACE(Relax|Static)Maker. + https://github.com/ACEsuit/mace/issues/328 + """ + import torch + + orig = torch.get_default_dtype() + yield + torch.set_default_dtype(orig) diff --git a/src/atomate2/lobster/files.py b/src/atomate2/lobster/files.py index 2121ce3255..8cfbb5c640 100644 --- a/src/atomate2/lobster/files.py +++ b/src/atomate2/lobster/files.py @@ -18,6 +18,7 @@ "COHPCAR.lobster", "COOPCAR.lobster", "DOSCAR.lobster", + "DOSCAR.LSO.lobster", "GROSSPOP.lobster", "ICOHPLIST.lobster", "ICOOPLIST.lobster", diff --git a/src/atomate2/lobster/jobs.py b/src/atomate2/lobster/jobs.py index af4aac1856..aef254c64d 100644 --- a/src/atomate2/lobster/jobs.py +++ b/src/atomate2/lobster/jobs.py @@ -9,7 +9,7 @@ from jobflow import Maker, job from pymatgen.electronic_structure.cohp import CompleteCohp from pymatgen.electronic_structure.dos import LobsterCompleteDos -from pymatgen.io.lobster import Lobsterin +from pymatgen.io.lobster import Bandoverlaps, Icohplist, Lobsterin from atomate2 import SETTINGS from atomate2.common.files import gzip_output_folder @@ -56,14 +56,21 @@ class LobsterMaker(Maker): run_lobster_kwargs: dict = field(default_factory=dict) calculation_type: str = "standard" - @job(output_schema=LobsterTaskDocument, data=[CompleteCohp, LobsterCompleteDos]) + @job( + output_schema=LobsterTaskDocument, + data=[ + CompleteCohp, + LobsterCompleteDos, + Bandoverlaps, + Icohplist, + ], + ) def make( self, wavefunction_dir: str | Path = None, basis_dict: dict | None = None, ) -> LobsterTaskDocument: - """ - Run a LOBSTER calculation. + """Run a LOBSTER calculation. Parameters ---------- diff --git a/src/atomate2/lobster/run.py b/src/atomate2/lobster/run.py index f3d4c19d9d..a2fd9af480 100644 --- a/src/atomate2/lobster/run.py +++ b/src/atomate2/lobster/run.py @@ -78,7 +78,7 @@ def run_lobster( if job_type == JobType.DIRECT: logger.info(f"Running command: {lobster_cmd}") - return_code = subprocess.call(lobster_cmd, shell=True) + return_code = subprocess.call(lobster_cmd, shell=True) # noqa: S602 logger.info(f"{lobster_cmd} finished running with returncode: {return_code}") return diff --git a/src/atomate2/lobster/schemas.py b/src/atomate2/lobster/schemas.py index 876809baa2..573e4506c5 100644 --- a/src/atomate2/lobster/schemas.py +++ b/src/atomate2/lobster/schemas.py @@ -1,5 +1,7 @@ """Module defining lobster document schemas.""" +import gzip +import json import logging import time from pathlib import Path @@ -8,9 +10,11 @@ import numpy as np from emmet.core.structure import StructureMetadata from monty.dev import requires +from monty.json import MontyDecoder, jsanitize +from monty.os.path import zpath from pydantic import BaseModel, Field from pymatgen.core import Structure -from pymatgen.electronic_structure.cohp import CompleteCohp +from pymatgen.electronic_structure.cohp import Cohp, CompleteCohp from pymatgen.electronic_structure.dos import LobsterCompleteDos from pymatgen.io.lobster import ( Bandoverlaps, @@ -23,74 +27,86 @@ MadelungEnergies, SitePotential, ) +from typing_extensions import Self from atomate2 import __version__ from atomate2.utils.datetime import datetime_str try: + import ijson from lobsterpy.cohp.analyze import Analysis from lobsterpy.cohp.describe import Description except ImportError: + ijson = None Analysis = None Description = None + logger = logging.getLogger(__name__) class LobsteroutModel(BaseModel): """Definition of computational settings from the LOBSTER computation.""" - restart_from_projection: bool = Field( + restart_from_projection: Optional[bool] = Field( None, description="Bool indicating if the run has been restarted from a projection", ) - lobster_version: str = Field(None, description="Lobster version") - threads: int = Field(None, description="Number of threads that Lobster ran on") - dft_program: str = Field(None, description="DFT program was used for this run") - charge_spilling: list = Field(None, description="Absolute charge spilling") - total_spilling: list = Field(None, description="Total spilling") - elements: list = Field(None, description="Elements in structure") - basis_type: list = Field(None, description="Basis set used in Lobster") - basis_functions: list = Field(None, description="basis_functions") - timing: Any = Field(None, description="Dict with infos on timing") - warning_lines: list = Field(None, description="Warnings") - info_orthonormalization: list = Field( + lobster_version: Optional[str] = Field(None, description="Lobster version") + threads: Optional[int] = Field( + None, description="Number of threads that Lobster ran on" + ) + dft_program: Optional[str] = Field( + None, description="DFT program was used for this run" + ) + charge_spilling: list[float] = Field(description="Absolute charge spilling") + total_spilling: list[float] = Field(description="Total spilling") + elements: list[str] = Field(description="Elements in structure") + basis_type: list[str] = Field(description="Basis set used in Lobster") + basis_functions: list[list[str]] = Field(description="basis_functions") + timing: dict[str, dict[str, str]] = Field(description="Dict with infos on timing") + warning_lines: Optional[list] = Field(None, description="Warnings") + info_orthonormalization: Optional[list] = Field( None, description="additional information on orthonormalization" ) - info_lines: list = Field( + info_lines: Optional[list] = Field( None, description="list of strings with additional info lines" ) - has_doscar: bool = Field(None, description="Bool indicating if DOSCAR is present.") - has_doscar_lso: bool = Field( + has_doscar: Optional[bool] = Field( + None, description="Bool indicating if DOSCAR is present." + ) + has_doscar_lso: Optional[bool] = Field( None, description="Bool indicating if DOSCAR.LSO is present." ) - has_cohpcar: bool = Field( + has_cohpcar: Optional[bool] = Field( None, description="Bool indicating if COHPCAR is present." ) - has_coopcar: bool = Field( + has_coopcar: Optional[bool] = Field( None, description="Bool indicating if COOPCAR is present." ) - has_cobicar: bool = Field( + has_cobicar: Optional[bool] = Field( None, description="Bool indicating if COBICAR is present." ) - has_charge: bool = Field(None, description="Bool indicating if CHARGE is present.") - has_madelung: bool = Field( + has_charge: Optional[bool] = Field( + None, description="Bool indicating if CHARGE is present." + ) + has_madelung: Optional[bool] = Field( None, description="Bool indicating if Site Potentials and Madelung file is present.", ) - has_projection: bool = Field( + has_projection: Optional[bool] = Field( None, description="Bool indicating if projection file is present." ) - has_bandoverlaps: bool = Field( + has_bandoverlaps: Optional[bool] = Field( None, description="Bool indicating if BANDOVERLAPS file is present" ) - has_fatbands: bool = Field( + has_fatbands: Optional[bool] = Field( None, description="Bool indicating if Fatbands are present." ) - has_grosspopulation: bool = Field( + has_grosspopulation: Optional[bool] = Field( None, description="Bool indicating if GROSSPOP file is present." ) - has_density_of_energies: bool = Field( + has_density_of_energies: Optional[bool] = Field( None, description="Bool indicating if DensityofEnergies is present" ) @@ -98,10 +114,8 @@ class LobsteroutModel(BaseModel): class LobsterinModel(BaseModel): """Definition of input settings for the LOBSTER computation.""" - cohpstartenergy: float = Field( - None, description="Start energy for COHP computation" - ) - cohpendenergy: float = Field(None, description="End energy for COHP computation") + cohpstartenergy: float = Field(description="Start energy for COHP computation") + cohpendenergy: float = Field(description="End energy for COHP computation") gaussiansmearingwidth: Optional[float] = Field( None, description="Set the smearing width in eV,default is 0.2 (eV)" @@ -113,51 +127,146 @@ class LobsterinModel(BaseModel): cohpsteps: Optional[float] = Field( None, description="Number steps in COHPCAR; similar to NEDOS of VASP" ) - basisset: str = Field(None, description="basis set of computation") + basisset: str = Field(description="basis set of computation") cohpgenerator: str = Field( - None, - description="Build the list of atom pairs to be analyzed using given distance", + description="Build the list of atom pairs to be analyzed using given distance" ) - saveprojectiontofile: bool = Field( + saveprojectiontofile: Optional[bool] = Field( None, description="Save the results of projections" ) lsodos: Optional[bool] = Field( None, description="Writes DOS output from the orthonormalized LCAO basis" ) - basisfunctions: list = Field( - None, description="Specify the basis functions for element" + basisfunctions: list[str] = Field( + description="Specify the basis functions for element" + ) + + +class Bonding(BaseModel): + """Model describing bonding field of BondsInfo.""" + + integral: Optional[float] = Field( + None, description="Integral considering only bonding contributions from COHPs" + ) + perc: Optional[float] = Field( + None, description="Percentage of bonding contribution" + ) + + +class Antibonding(BaseModel): + """Model describing antibonding field of BondsInfo.""" + + integral: Optional[float] = Field( + None, + description="Integral considering only anti-bonding contributions from COHPs", + ) + perc: Optional[float] = Field( + None, description="Percentage of anti-bonding contribution" + ) + + +class BondsInfo(BaseModel): + """Model describing bonds field of SiteInfo.""" + + ICOHP_mean: str = Field(..., description="Mean of ICOHPs of relevant bonds") + ICOHP_sum: str = Field(..., description="Sum of ICOHPs of relevant bonds") + has_antibdg_states_below_Efermi: bool = Field( # noqa: N815 + ..., + description="Indicates if antibonding interactions below efermi are detected", + ) + number_of_bonds: int = Field( + ..., description="Number of bonds considered in the analysis" + ) + bonding: Bonding = Field(description="Model describing bonding contributions") + antibonding: Antibonding = Field( + description="Model describing anti-bonding contributions" + ) + + +class SiteInfo(BaseModel): + """Outer model describing sites field of Sites model.""" + + env: str = Field( + ..., + description="The coordination environment identified from " + "the LobsterPy analysis", + ) + bonds: dict[str, BondsInfo] = Field( + ..., + description="A dictionary with keys as atomic-specie as key " + "and BondsInfo model as values", + ) + ion: str = Field(..., description="Ion to which the atom is bonded") + charge: float = Field(..., description="Mulliken charge of the atom") + relevant_bonds: list[str] = Field( + ..., + description="List of bond labels from the LOBSTER files i.e. for e.g. " + " from ICOHPLIST.lobster/ COHPCAR.lobster", + ) + + +class Sites(BaseModel): + """Model describing, sites field of CondensedBondingAnalysis.""" + + sites: dict[int, SiteInfo] = Field( + ..., + description="A dictionary with site index as keys and SiteInfo model as values", + ) + + +class CohpPlotData(BaseModel): + """Model describing the cohp_plot_data field of CondensedBondingAnalysis.""" + + data: dict[str, Cohp] = Field( + ..., + description="A dictionary with plot labels from LobsterPy " + "automatic analysis as keys and Cohp objects as values", + ) + + +class DictIons(BaseModel): + """Model describing final_dict_ions field of CondensedBondingAnalysis.""" + + data: dict[str, dict[str, int]] = Field( + ..., + description="Dict consisting information on environments of cations " + "and counts for them", + ) + + +class DictBonds(BaseModel): + """Model describing final_dict_bonds field of CondensedBondingAnalysis.""" + + data: dict[str, dict[str, Union[float, bool]]] = Field( + ..., description="Dict consisting information on ICOHPs per bond type" ) class CondensedBondingAnalysis(BaseModel): """Definition of condensed bonding analysis data from LobsterPy ICOHP.""" - formula: str = Field(None, description="Pretty formula of the structure") - max_considered_bond_length: Any = Field( - None, description="Maximum bond length considered in bonding analysis" + formula: str = Field(description="Pretty formula of the structure") + max_considered_bond_length: float = Field( + description="Maximum bond length considered in bonding analysis" ) - limit_icohp: list = Field( - None, description="ICOHP range considered in co-ordination environment analysis" + limit_icohp: list[Union[str, float]] = Field( + description="ICOHP range considered in co-ordination environment analysis" ) number_of_considered_ions: int = Field( - None, description="number of ions detected based on Mulliken/L๏ฟฝwdin Charges" + ..., description="number of ions detected based on Mulliken/Lรถwdin Charges" ) - sites: dict = Field( - None, - description="Dict object that describes bond summary stats, " - "bonding/antibonding percentage and its coordination environment", + sites: Sites = Field( + ..., + description="Bonding information at inequivalent sites in the structure", ) type_charges: str = Field( - None, - description="Charge type considered for assigning valences in bonding analysis", + description="Charge type considered for assigning valences in bonding analysis" ) cutoff_icohp: float = Field( - None, description="Percent limiting the ICOHP values to be considered" " relative to strongest ICOHP", ) summed_spins: bool = Field( - None, description="Bool that states if the spin channels in the " "cohp_plot_data are summed.", ) @@ -167,25 +276,23 @@ class CondensedBondingAnalysis(BaseModel): " bonding/anti-bonding percentages in the bond" " if set to None, all energies up-to the Fermi is considered", ) - cohp_plot_data: dict = Field( - None, - description="Stores the COHP plot data based on relevant bond labels " - "for site as keys", + cohp_plot_data: CohpPlotData = Field( + ..., + description="Plotting data for the relevant bonds from LobsterPy analysis", ) which_bonds: str = Field( - None, description="Specifies types of bond considered in LobsterPy analysis", ) - final_dict_bonds: dict = Field( - None, + final_dict_bonds: DictBonds = Field( + ..., description="Dict consisting information on ICOHPs per bond type", ) - final_dict_ions: dict = Field( - None, - description="Dict consisting information on environments of cations", + final_dict_ions: DictIons = Field( + ..., + description="Model that describes final_dict_ions field", ) run_time: float = Field( - None, description="Time needed to run Lobsterpy condensed bonding analysis" + ..., description="Time needed to run Lobsterpy condensed bonding analysis" ) @classmethod @@ -193,32 +300,49 @@ def from_directory( cls, dir_name: Union[str, Path], save_cohp_plots: bool = True, + lobsterpy_kwargs: dict = None, plot_kwargs: dict = None, which_bonds: str = "all", ) -> tuple: - """ - Create a task document from a directory containing LOBSTER files. + """Create a task document from a directory containing LOBSTER files. Parameters ---------- dir_name : path or str The path to the folder containing the calculation outputs. - save_cohp_plots : bool + save_cohp_plots : bool. Bool to indicate whether automatic cohp plots and jsons from lobsterpy will be generated. - plot_kwargs : dict + lobsterpy_kwargs : dict. + kwargs to change default lobsterpy automatic analysis parameters. + plot_kwargs : dict. kwargs to change plotting options in lobsterpy. - which_bonds: str + which_bonds: str. mode for condensed bonding analysis: "cation-anion" and "all". """ plot_kwargs = plot_kwargs or {} + lobsterpy_kwargs = lobsterpy_kwargs or {} dir_name = Path(dir_name) - cohpcar_path = dir_name / "COHPCAR.lobster.gz" - charge_path = dir_name / "CHARGE.lobster.gz" - structure_path = dir_name / "POSCAR.gz" - icohplist_path = dir_name / "ICOHPLIST.lobster.gz" - icobilist_path = dir_name / "ICOBILIST.lobster.gz" - icooplist_path = dir_name / "ICOOPLIST.lobster.gz" + cohpcar_path = Path(zpath(dir_name / "COHPCAR.lobster")) + charge_path = Path(zpath(dir_name / "CHARGE.lobster")) + structure_path = Path(zpath(dir_name / "POSCAR")) + icohplist_path = Path(zpath(dir_name / "ICOHPLIST.lobster")) + icobilist_path = Path(zpath(dir_name / "ICOBILIST.lobster")) + icooplist_path = Path(zpath(dir_name / "ICOOPLIST.lobster")) + + # Update lobsterpy analysis parameters with user supplied parameters + lobsterpy_kwargs_updated = { + "are_cobis": False, + "are_coops": False, + "cutoff_icohp": 0.10, + "noise_cutoff": 0.1, + "orbital_cutoff": 0.05, + "orbital_resolved": False, + "start": None, + "summed_spins": False, # we will always use spin polarization here + "type_charge": None, + **lobsterpy_kwargs, + } try: start = time.time() @@ -227,9 +351,8 @@ def from_directory( path_to_icohplist=icohplist_path, path_to_cohpcar=cohpcar_path, path_to_charge=charge_path, - summed_spins=False, # we will always use spin polarization here - cutoff_icohp=0.10, which_bonds=which_bonds, + **lobsterpy_kwargs_updated, ) cba_run_time = time.time() - start # initialize lobsterpy condensed bonding analysis @@ -251,20 +374,22 @@ def from_directory( cba_cohp_plot_data[label_str + label] = cohp describe = Description(analysis_object=analyse) + limit_icohp_val = list(cba["limit_icohp"]) + _replace_inf_values(limit_icohp_val) condensed_bonding_analysis = CondensedBondingAnalysis( formula=cba["formula"], max_considered_bond_length=cba["max_considered_bond_length"], - limit_icohp=cba["limit_icohp"], + limit_icohp=limit_icohp_val, number_of_considered_ions=cba["number_of_considered_ions"], - sites=cba["sites"], + sites=Sites(**cba), type_charges=analyse.type_charge, - cohp_plot_data=cba_cohp_plot_data, + cohp_plot_data=CohpPlotData(data=cba_cohp_plot_data), cutoff_icohp=analyse.cutoff_icohp, - summed_spins=False, + summed_spins=lobsterpy_kwargs_updated.get("summed_spins"), which_bonds=analyse.which_bonds, - final_dict_bonds=analyse.final_dict_bonds, - final_dict_ions=analyse.final_dict_ions, + final_dict_bonds=DictBonds(data=analyse.final_dict_bonds), + final_dict_ions=DictIons(data=analyse.final_dict_ions), run_time=cba_run_time, ) if save_cohp_plots: @@ -276,32 +401,207 @@ def from_directory( ) import json - with open( - dir_name / f"condensed_bonding_analysis_{which_bonds}.json", "w" - ) as fp: + filename = dir_name / f"condensed_bonding_analysis_{which_bonds}" + with open(f"{filename}.json", "w") as fp: json.dump(analyse.condensed_bonding_analysis, fp) - with open( - dir_name / f"condensed_bonding_analysis_{which_bonds}.txt", "w" - ) as fp: + with open(f"{filename}.txt", "w") as fp: for line in describe.text: fp.write(f"{line}\n") # Read in strongest icohp values - sb_icohp, sb_icobi, sb_icoop = _identify_strongest_bonds( + sb = _identify_strongest_bonds( analyse=analyse, icobilist_path=icobilist_path, icohplist_path=icohplist_path, icooplist_path=icooplist_path, ) - return ( - condensed_bonding_analysis, - describe, - sb_icobi, - sb_icohp, - sb_icoop, - ) + except ValueError: - return (None, None, None, None, None) + return None, None, None + else: + return condensed_bonding_analysis, describe, sb + + +class DosComparisons(BaseModel): + """Model describing the DOS comparisons field in the CalcQualitySummary model.""" + + tanimoto_orb_s: Optional[float] = Field( + None, + description="Tanimoto similarity index between s orbital of " + "VASP and LOBSTER DOS", + ) + tanimoto_orb_p: Optional[float] = Field( + None, + description="Tanimoto similarity index between p orbital of " + "VASP and LOBSTER DOS", + ) + tanimoto_orb_d: Optional[float] = Field( + None, + description="Tanimoto similarity index between d orbital of " + "VASP and LOBSTER DOS", + ) + tanimoto_orb_f: Optional[float] = Field( + None, + description="Tanimoto similarity index between f orbital of " + "VASP and LOBSTER DOS", + ) + tanimoto_summed: Optional[float] = Field( + None, + description="Tanimoto similarity index for summed PDOS between " + "VASP and LOBSTER", + ) + e_range: list[Union[float, None]] = Field( + description="Energy range used for evaluating the Tanimoto similarity index" + ) + n_bins: Optional[int] = Field( + None, + description="Number of bins used for discretizing the VASP and LOBSTER PDOS" + "(Affects the Tanimoto similarity index)", + ) + + +class ChargeComparisons(BaseModel): + """Model describing the charges field in the CalcQualitySummary model.""" + + bva_mulliken_agree: Optional[bool] = Field( + None, + description="Bool indicating whether atoms classification as cation " + "or anion based on Mulliken charge signs of LOBSTER " + "agree with BVA analysis", + ) + bva_loewdin_agree: Optional[bool] = Field( + None, + description="Bool indicating whether atoms classification as cations " + "or anions based on Loewdin charge signs of LOBSTER " + "agree with BVA analysis", + ) + + +class BandOverlapsComparisons(BaseModel): + """Model describing the Band overlaps field in the CalcQualitySummary model.""" + + file_exists: bool = Field( + description="Boolean indicating whether the bandOverlaps.lobster " + "file is generated during the LOBSTER run", + ) + limit_maxDeviation: Optional[float] = Field( # noqa: N815 + None, + description="Limit set for maximal deviation in pymatgen parser", + ) + has_good_quality_maxDeviation: Optional[bool] = Field( # noqa: N815 + None, + description="Boolean indicating whether the deviation at each k-point " + "is within the threshold set using limit_maxDeviation " + "for analyzing the bandOverlaps.lobster file data", + ) + max_deviation: Optional[float] = Field( + None, + description="Maximum deviation from ideal identity matrix from the observed in " + "the bandOverlaps.lobster file", + ) + percent_kpoints_abv_limit: Optional[float] = Field( + None, + description="Percent of k-points that show deviations above " + "the limit_maxDeviation threshold set in pymatgen parser.", + ) + + +class ChargeSpilling(BaseModel): + """Model describing the Charge spilling field in the CalcQualitySummary model.""" + + abs_charge_spilling: float = Field( + description="Absolute charge spilling value from the LOBSTER calculation.", + ) + abs_total_spilling: float = Field( + description="Total charge spilling percent from the LOBSTER calculation.", + ) + + +class CalcQualitySummary(BaseModel): + """Model describing the calculation quality of lobster run.""" + + minimal_basis: bool = Field( + description="Denotes whether the calculation used the minimal basis for the " + "LOBSTER computation", + ) + charge_spilling: ChargeSpilling = Field( + description="Model describing the charge spilling from the LOBSTER runs", + ) + charge_comparisons: Optional[ChargeComparisons] = Field( + None, + description="Model describing the charge sign comparison results", + ) + band_overlaps_analysis: Optional[BandOverlapsComparisons] = Field( + None, + description="Model describing the band overlap file analysis results", + ) + dos_comparisons: Optional[DosComparisons] = Field( + None, + description="Model describing the VASP and LOBSTER PDOS comparisons results", + ) + + @classmethod + @requires(Analysis, "lobsterpy must be installed to create an CalcQualitySummary.") + def from_directory( + cls, + dir_name: Union[Path, str], + calc_quality_kwargs: dict = None, + ) -> Self: + """Make a LOBSTER calculation quality summary from directory with LOBSTER files. + + Parameters + ---------- + dir_name : path or str + The path to the folder containing the calculation outputs. + calc_quality_kwargs : dict + kwargs to change calc quality analysis options in lobsterpy. + + Returns + ------- + CalcQualitySummary + A task document summarizing quality of the lobster calculation. + """ + dir_name = Path(dir_name) + calc_quality_kwargs = calc_quality_kwargs or {} + band_overlaps_path = Path(zpath(dir_name / "bandOverlaps.lobster")) + charge_path = Path(zpath(dir_name / "CHARGE.lobster")) + doscar_path = Path( + zpath( + dir_name / "DOSCAR.LSO.lobster" + if Path(zpath(dir_name / "DOSCAR.LSO.lobster")).exists() + else Path(zpath(dir_name / "DOSCAR.lobster")) + ) + ) + lobsterin_path = Path(zpath(dir_name / "lobsterin")) + lobsterout_path = Path(zpath(dir_name / "lobsterout")) + potcar_path = ( + Path(zpath(dir_name / "POTCAR")) + if Path(zpath(dir_name / "POTCAR")).exists() + else None + ) + structure_path = Path(zpath(dir_name / "POSCAR")) + vasprun_path = Path(zpath(dir_name / "vasprun.xml")) + + # Update calc quality kwargs supplied by user + calc_quality_kwargs_updated = { + "e_range": [-20, 0], + "dos_comparison": True, + "n_bins": 256, + "bva_comp": True, + **calc_quality_kwargs, + } + cal_quality_dict = Analysis.get_lobster_calc_quality_summary( + path_to_poscar=structure_path, + path_to_vasprun=vasprun_path, + path_to_charge=charge_path, + path_to_potcar=potcar_path, + path_to_doscar=doscar_path, + path_to_lobsterin=lobsterin_path, + path_to_lobsterout=lobsterout_path, + path_to_bandoverlaps=band_overlaps_path, + **calc_quality_kwargs_updated, + ) + return CalcQualitySummary(**cal_quality_dict) class StrongestBonds(BaseModel): @@ -310,238 +610,266 @@ class StrongestBonds(BaseModel): LobsterPy is used for the extraction. """ - which_bonds: str = Field( + which_bonds: Optional[str] = Field( None, description="Denotes whether the information " "is for cation-anion pairs or all bonds", ) - are_coops: bool = Field( - None, description="Denotes whether the file consists of ICOOPs" + strongest_bonds_icoop: Optional[dict] = Field( + None, + description="Dict with infos on bond strength and bond length based on ICOOP.", ) - are_cobis: bool = Field( - None, description="Denotes whether the file consists of ICOBIs" + strongest_bonds_icohp: Optional[dict] = Field( + None, + description="Dict with infos on bond strength and bond length based on ICOHP.", ) - strongest_bonds: dict = Field( + strongest_bonds_icobi: Optional[dict] = Field( None, - description="Dict with infos on bond strength and bond length,.", + description="Dict with infos on bond strength and bond length based on ICOBI.", ) -class LobsterTaskDocument(StructureMetadata): +class LobsterTaskDocument(StructureMetadata, extra="allow"): # type: ignore[call-arg] """Definition of LOBSTER task document.""" - structure: Structure = Field(None, description="The structure used in this task") - dir_name: Any = Field(None, description="The directory for this Lobster task") + structure: Structure = Field(description="The structure used in this task") + dir_name: Union[str, Path] = Field( + description="The directory for this Lobster task" + ) last_updated: str = Field( default_factory=datetime_str, description="Timestamp for this task document was last updated", ) - charges: dict = Field( + charges: Optional[Charge] = Field( None, - description="Atomic charges dict from LOBSTER" - " based on Mulliken and Loewdin charge analysis", + description="pymatgen Charge obj. Contains atomic charges based on Mulliken " + "and Loewdin charge analysis", ) - lobsterout: LobsteroutModel = Field(None, description="Lobster out data") - lobsterin: LobsterinModel = Field(None, description="Lobster calculation inputs") - lobsterpy_data: CondensedBondingAnalysis = Field( + lobsterout: LobsteroutModel = Field(description="Lobster out data") + lobsterin: LobsterinModel = Field(description="Lobster calculation inputs") + lobsterpy_data: Optional[CondensedBondingAnalysis] = Field( None, description="Model describing the LobsterPy data" ) - lobsterpy_text: str = Field( - None, - description="Stores LobsterPy automatic analysis summary text", + lobsterpy_text: Optional[str] = Field( + None, description="Stores LobsterPy automatic analysis summary text" ) - strongest_bonds_icohp: StrongestBonds = Field( - None, description="Describes the strongest cation-anion ICOHP bonds" + calc_quality_summary: Optional[CalcQualitySummary] = Field( + None, + description="Model summarizing results of lobster runs like charge spillings, " + "band overlaps, DOS comparisons with VASP runs and quantum chemical LOBSTER " + "charge sign comparisons with BVA method", ) - strongest_bonds_icoop: StrongestBonds = Field( - None, description="Describes the strongest cation-anion ICOOP bonds" + calc_quality_text: Optional[str] = Field( + None, description="Stores calculation quality analysis summary text" ) - strongest_bonds_icobi: StrongestBonds = Field( - None, description="Describes the strongest cation-anion ICOBI bonds" + strongest_bonds: Optional[StrongestBonds] = Field( + None, + description="Describes the strongest cation-anion ICOOP, ICOBI and ICOHP bonds", ) - lobsterpy_data_cation_anion: CondensedBondingAnalysis = Field( + lobsterpy_data_cation_anion: Optional[CondensedBondingAnalysis] = Field( None, description="Model describing the LobsterPy data" ) - lobsterpy_text_cation_anion: str = Field( + lobsterpy_text_cation_anion: Optional[str] = Field( None, description="Stores LobsterPy automatic analysis summary text", ) - strongest_bonds_icohp_cation_anion: StrongestBonds = Field( - None, description="Describes the strongest cation-anion ICOHP bonds" - ) - strongest_bonds_icoop_cation_anion: StrongestBonds = Field( - None, description="Describes the strongest cation-anion ICOOP bonds" - ) - strongest_bonds_icobi_cation_anion: StrongestBonds = Field( - None, description="Describes the strongest cation-anion ICOBI bonds" - ) - - cohp_data: CompleteCohp = Field( - None, description="pymatgen CompleteCohp object with COHP data" - ) - coop_data: CompleteCohp = Field( - None, description="pymatgen CompleteCohp object with COOP data" - ) - cobi_data: CompleteCohp = Field( - None, description="pymatgen CompleteCohp object with COBI data" + strongest_bonds_cation_anion: Optional[StrongestBonds] = Field( + None, + description="Describes the strongest cation-anion ICOOP, ICOBI and ICOHP bonds", ) - dos: LobsterCompleteDos = Field( + dos: Optional[LobsterCompleteDos] = Field( None, description="pymatgen pymatgen.io.lobster.Doscar.completedos data" ) lso_dos: Optional[LobsterCompleteDos] = Field( None, description="pymatgen pymatgen.io.lobster.Doscar.completedos data" ) - madelung_energies: dict = Field( + madelung_energies: Optional[MadelungEnergies] = Field( None, - description="Madelung energies dict from" - " LOBSTER based on Mulliken and Loewdin charges", + description="pymatgen Madelung energies obj. Contains madelung energies" + "based on Mulliken and Loewdin charges", ) - site_potentials: dict = Field( + site_potentials: Optional[SitePotential] = Field( None, - description="Site potentials dict from" - " LOBSTER based on Mulliken and Loewdin charges", + description="pymatgen Site potentials obj. Contains site potentials " + "based on Mulliken and Loewdin charges", ) - - gross_populations: dict = Field( + gross_populations: Optional[Grosspop] = Field( None, - description="Gross populations dict from" - " LOBSTER based on Mulliken and Loewdin charges with" - "each site as a key and the gross population as a value.", + description="pymatgen Grosspopulations obj. Contains gross populations " + " based on Mulliken and Loewdin charges ", ) - - band_overlaps: Optional[dict] = Field( + band_overlaps: Optional[Bandoverlaps] = Field( None, - description="Band overlaps data for each k-point from" + description="pymatgen Bandoverlaps obj for each k-point from" " bandOverlaps.lobster file if it exists", ) + cohp_data: Optional[CompleteCohp] = Field( + None, description="pymatgen CompleteCohp object with COHP data" + ) + coop_data: Optional[CompleteCohp] = Field( + None, description="pymatgen CompleteCohp object with COOP data" + ) + cobi_data: Optional[CompleteCohp] = Field( + None, description="pymatgen CompleteCohp object with COBI data" + ) + icohp_list: Optional[Icohplist] = Field( + None, description="pymatgen Icohplist object with ICOHP data" + ) + icoop_list: Optional[Icohplist] = Field( + None, description="pymatgen Icohplist object with ICOOP data" + ) + icobi_list: Optional[Icohplist] = Field( + None, description="pymatgen Icohplist object with ICOBI data" + ) schema: str = Field( __version__, description="Version of atomate2 used to create the document" ) @classmethod - @requires(Analysis, "lobsterpy must be installed to create an LobsterTaskDocument.") + @requires( + Analysis, + "LobsterTaskDocument requires `lobsterpy` and `ijson` to function properly. " + "Please reinstall atomate2 using atomate2[lobster]", + ) def from_directory( cls, dir_name: Union[Path, str], additional_fields: dict = None, + add_coxxcar_to_task_document: bool = False, + analyze_outputs: bool = True, + calc_quality_kwargs: dict = None, + lobsterpy_kwargs: dict = None, + plot_kwargs: dict = None, store_lso_dos: bool = False, save_cohp_plots: bool = True, - plot_kwargs: dict = None, - ) -> "LobsterTaskDocument": - """ - Create a task document from a directory containing LOBSTER files. + save_cba_jsons: bool = True, + save_computational_data_jsons: bool = False, + ) -> Self: + """Create a task document from a directory containing LOBSTER files. Parameters ---------- - dir_name : path or str + dir_name : path or str. The path to the folder containing the calculation outputs. - additional_fields : dict + additional_fields : dict. Dictionary of additional fields to add to output document. - store_lso_dos : bool + add_coxxcar_to_task_document : bool. + Bool to indicate whether to add COHPCAR, COOPCAR, COBICAR data objects + to the task document. + analyze_outputs: bool. + If True, will enable lobsterpy analysis. + calc_quality_kwargs : dict. + kwargs to change calc quality summary options in lobsterpy. + lobsterpy_kwargs : dict. + kwargs to change default lobsterpy automatic analysis parameters. + plot_kwargs : dict. + kwargs to change plotting options in lobsterpy. + store_lso_dos : bool. Whether to store the LSO DOS. - save_cohp_plots : bool + save_cohp_plots : bool. Bool to indicate whether automatic cohp plots and jsons from lobsterpy will be generated. - plot_kwargs : dict - kwargs to change plotting options in lobsterpy. + save_cba_jsons : bool. + Bool to indicate whether condensed bonding analysis jsons + should be saved, consists of outputs from lobsterpy analysis, + calculation quality summary, lobster dos, charges and madelung energies + save_computational_data_jsons : bool. + Bool to indicate whether computational data jsons + should be saved Returns ------- LobsterTaskDocument A task document for the lobster calculation. """ - additional_fields = additional_fields or {} + additional_fields = {} if additional_fields is None else additional_fields dir_name = Path(dir_name) # Read in lobsterout and lobsterin - lobsterout_doc = Lobsterout(dir_name / "lobsterout.gz").get_doc() + lobsterout_doc = Lobsterout(Path(zpath(dir_name / "lobsterout"))).get_doc() lobster_out = LobsteroutModel(**lobsterout_doc) - lobster_in = LobsterinModel(**Lobsterin.from_file(dir_name / "lobsterin.gz")) - - icohplist_path = dir_name / "ICOHPLIST.lobster.gz" - cohpcar_path = dir_name / "COHPCAR.lobster.gz" - charge_path = dir_name / "CHARGE.lobster.gz" - cobicar_path = dir_name / "COBICAR.lobster.gz" - coopcar_path = dir_name / "COOPCAR.lobster.gz" - doscar_path = dir_name / "DOSCAR.lobster.gz" - structure_path = dir_name / "POSCAR.gz" - madelung_energies_path = dir_name / "MadelungEnergies.lobster.gz" - site_potentials_path = dir_name / "SitePotentials.lobster.gz" - gross_populations_path = dir_name / "GROSSPOP.lobster.gz" - band_overlaps_path = dir_name / "bandOverlaps.lobster.gz" + lobster_in = LobsterinModel( + **Lobsterin.from_file(Path(zpath(dir_name / "lobsterin"))) + ) + + icohplist_path = Path(zpath(dir_name / "ICOHPLIST.lobster")) + icooplist_path = Path(zpath(dir_name / "ICOOPLIST.lobster")) + icobilist_path = Path(zpath(dir_name / "ICOBILIST.lobster")) + cohpcar_path = Path(zpath(dir_name / "COHPCAR.lobster")) + charge_path = Path(zpath(dir_name / "CHARGE.lobster")) + cobicar_path = Path(zpath(dir_name / "COBICAR.lobster")) + coopcar_path = Path(zpath(dir_name / "COOPCAR.lobster")) + doscar_path = Path(zpath(dir_name / "DOSCAR.lobster")) + structure_path = Path(zpath(dir_name / "POSCAR")) + madelung_energies_path = Path(zpath(dir_name / "MadelungEnergies.lobster")) + site_potentials_path = Path(zpath(dir_name / "SitePotentials.lobster")) + gross_populations_path = Path(zpath(dir_name / "GROSSPOP.lobster")) + band_overlaps_path = Path(zpath(dir_name / "bandOverlaps.lobster")) + + icohp_list = icoop_list = icobi_list = None + if icohplist_path.exists(): + icohp_list = Icohplist(filename=icohplist_path) + if icooplist_path.exists(): + icoop_list = Icohplist(filename=icooplist_path, are_coops=True) + if icobilist_path.exists(): + icobi_list = Icohplist(filename=icobilist_path, are_cobis=True) # Do automatic bonding analysis with LobsterPy - condensed_bonding_analysis = None - sb_icobi = None - sb_icohp = None - sb_icoop = None - struct = None - describe = None struct = Structure.from_file(structure_path) # will perform two condensed bonding analysis computations - if icohplist_path.exists() and cohpcar_path.exists() and charge_path.exists(): - ( - condensed_bonding_analysis, - describe, - sb_icobi, - sb_icohp, - sb_icoop, - ) = CondensedBondingAnalysis.from_directory( + condensed_bonding_analysis = None + condensed_bonding_analysis_ionic = None + sb_all = None + sb_ionic = None + calc_quality_summary = None + calc_quality_text = None + describe = None + describe_ionic = None + if analyze_outputs: + if ( + icohplist_path.exists() + and cohpcar_path.exists() + and charge_path.exists() + ): + ( + condensed_bonding_analysis, + describe, + sb_all, + ) = CondensedBondingAnalysis.from_directory( + dir_name, + save_cohp_plots=save_cohp_plots, + plot_kwargs=plot_kwargs, + lobsterpy_kwargs=lobsterpy_kwargs, + which_bonds="all", + ) + ( + condensed_bonding_analysis_ionic, + describe_ionic, + sb_ionic, + ) = CondensedBondingAnalysis.from_directory( + dir_name, + save_cohp_plots=save_cohp_plots, + plot_kwargs=plot_kwargs, + lobsterpy_kwargs=lobsterpy_kwargs, + which_bonds="cation-anion", + ) + # Get lobster calculation quality summary data + + calc_quality_summary = CalcQualitySummary.from_directory( dir_name, - save_cohp_plots=save_cohp_plots, - plot_kwargs=plot_kwargs, - which_bonds="all", + calc_quality_kwargs=calc_quality_kwargs, ) - ( - condensed_bonding_analysis_ionic, - describe_ionic, - sb_icobi_ionic, - sb_icohp_ionic, - sb_icoop_ionic, - ) = CondensedBondingAnalysis.from_directory( - dir_name, - save_cohp_plots=save_cohp_plots, - plot_kwargs=plot_kwargs, - which_bonds="cation-anion", + + calc_quality_text = Description.get_calc_quality_description( + calc_quality_summary.model_dump() ) + # Read in charges charges = None if charge_path.exists(): - charge = Charge(charge_path) - charges = {"Mulliken": charge.Mulliken, "Loewdin": charge.Loewdin} - - # Read in COHP, COBI, COOP plots - cohp_obj = None - if cohpcar_path.exists(): - cohp_obj = CompleteCohp.from_file( - fmt="LOBSTER", - structure_file=structure_path, - filename=cohpcar_path, - are_coops=False, - are_cobis=False, - ) - - coop_obj = None - if coopcar_path.exists(): - coop_obj = CompleteCohp.from_file( - fmt="LOBSTER", - structure_file=structure_path, - filename=coopcar_path, - are_coops=True, - are_cobis=False, - ) - - cobi_obj = None - if cobicar_path.exists(): - cobi_obj = CompleteCohp.from_file( - fmt="LOBSTER", - structure_file=structure_path, - filename=cobicar_path, - are_coops=False, - are_cobis=True, - ) + charges = Charge(filename=charge_path) # Read in DOS dos = None @@ -551,7 +879,7 @@ def from_directory( # Read in LSO DOS lso_dos = None - doscar_lso_path = dir_name / "DOSCAR.LSO.lobster.gz" + doscar_lso_path = Path(zpath(dir_name / "DOSCAR.LSO.lobster")) if store_lso_dos and doscar_lso_path.exists(): doscar_lso_lobster = Doscar( doscar=doscar_lso_path, structure_file=structure_path @@ -561,44 +889,55 @@ def from_directory( # Read in Madelung energies madelung_energies = None if madelung_energies_path.exists(): - madelung_obj = MadelungEnergies(filename=madelung_energies_path) - - madelung_energies = { - "Mulliken": madelung_obj.madelungenergies_Mulliken, - "Loewdin": madelung_obj.madelungenergies_Loewdin, - "Ewald_splitting": madelung_obj.ewald_splitting, - } + madelung_energies = MadelungEnergies(filename=madelung_energies_path) # Read in Site Potentials site_potentials = None if site_potentials_path.exists(): - site_potentials_obj = SitePotential(filename=site_potentials_path) - - site_potentials = { - "Mulliken": site_potentials_obj.sitepotentials_Mulliken, - "Loewdin": site_potentials_obj.sitepotentials_Loewdin, - "Ewald_splitting": site_potentials_obj.ewald_splitting, - } + site_potentials = SitePotential(filename=site_potentials_path) # Read in Gross Populations gross_populations = None if gross_populations_path.exists(): - gross_populations_obj = Grosspop(filename=gross_populations_path) - - gross_populations = {} - for atom_index, gross_pop in enumerate( - gross_populations_obj.list_dict_grosspop - ): - gross_populations[atom_index] = gross_pop + gross_populations = Grosspop(filename=gross_populations_path) # Read in Band overlaps band_overlaps = None if band_overlaps_path.exists(): - band_overlaps_obj = Bandoverlaps(filename=band_overlaps_path) + band_overlaps = Bandoverlaps(filename=band_overlaps_path) - band_overlaps = {} - for spin, value in band_overlaps_obj.bandoverlapsdict.items(): - band_overlaps[str(spin.value)] = value + # Read in COHPCAR, COBICAR, COOPCAR + cohp_obj = None + coop_obj = None + cobi_obj = None + + if add_coxxcar_to_task_document: + if cohpcar_path.exists(): + cohp_obj = CompleteCohp.from_file( + fmt="LOBSTER", + structure_file=structure_path, + filename=cohpcar_path, + are_coops=False, + are_cobis=False, + ) + + if coopcar_path.exists(): + coop_obj = CompleteCohp.from_file( + fmt="LOBSTER", + structure_file=structure_path, + filename=coopcar_path, + are_coops=True, + are_cobis=False, + ) + + if cobicar_path.exists(): + cobi_obj = CompleteCohp.from_file( + fmt="LOBSTER", + structure_file=structure_path, + filename=cobicar_path, + are_coops=False, + are_cobis=True, + ) doc = cls.from_structure( structure=struct, @@ -609,20 +948,16 @@ def from_directory( # include additional fields for cation-anion lobsterpy_data=condensed_bonding_analysis, lobsterpy_text=" ".join(describe.text) if describe is not None else None, - strongest_bonds_icohp=sb_icohp, - strongest_bonds_icoop=sb_icoop, - strongest_bonds_icobi=sb_icobi, + strongest_bonds=sb_all, lobsterpy_data_cation_anion=condensed_bonding_analysis_ionic, lobsterpy_text_cation_anion=" ".join(describe_ionic.text) if describe_ionic is not None else None, - strongest_bonds_icohp_cation_anion=sb_icohp_ionic, - strongest_bonds_icoop_cation_anion=sb_icoop_ionic, - strongest_bonds_icobi_cation_anion=sb_icobi_ionic, - # include additional fields for all bonds - cohp_data=cohp_obj, - coop_data=coop_obj, - cobi_data=cobi_obj, + strongest_bonds_cation_anion=sb_ionic, + calc_quality_summary=calc_quality_summary, + calc_quality_text=" ".join(calc_quality_text) + if calc_quality_text is not None + else None, dos=dos, lso_dos=lso_dos, charges=charges, @@ -630,8 +965,214 @@ def from_directory( site_potentials=site_potentials, gross_populations=gross_populations, band_overlaps=band_overlaps, + # include additional fields for all bonds + cohp_data=cohp_obj, + coop_data=coop_obj, + cobi_data=cobi_obj, + icohp_list=icohp_list, + icoop_list=icoop_list, + icobi_list=icobi_list, ) - return doc.copy(update=additional_fields) + + if save_cba_jsons and analyze_outputs: + cba_json_save_dir = dir_name / "cba.json.gz" + with gzip.open(cba_json_save_dir, "wt", encoding="UTF-8") as file: + # Write the json in iterable format + # (Necessary to load large JSON files via ijson) + file.write("[") + if ( + doc.lobsterpy_data_cation_anion is not None + ): # check if cation-anion analysis failed + lobsterpy_analysis_type = ( + doc.lobsterpy_data_cation_anion.which_bonds.replace("-", "_") + ) + data = { + f"{lobsterpy_analysis_type}_bonds": { + "lobsterpy_data": doc.lobsterpy_data_cation_anion, + "lobsterpy_text": [ + "".join(doc.lobsterpy_text_cation_anion) + ], + "strongest_bonds": doc.strongest_bonds_cation_anion, + } + } + else: + data = {"cation_anion_bonds": {}} + monty_encoded_json_doc = jsanitize( + data, allow_bson=True, strict=True, enum_values=True + ) + json.dump(monty_encoded_json_doc, file) + file.write(",") + # add all-bonds data + lobsterpy_analysis_type = doc.lobsterpy_data.which_bonds + data = { + f"{lobsterpy_analysis_type}_bonds": { + "lobsterpy_data": doc.lobsterpy_data, + "lobsterpy_text": ["".join(doc.lobsterpy_text)], + "strongest_bonds": doc.strongest_bonds, + } + } + monty_encoded_json_doc = jsanitize( + data, allow_bson=True, strict=True, enum_values=True + ) + json.dump(monty_encoded_json_doc, file) + file.write(",") + data = { + "madelung_energies": doc.madelung_energies + } # add madelung energies + monty_encoded_json_doc = jsanitize( + data, allow_bson=True, strict=True, enum_values=True + ) + json.dump(monty_encoded_json_doc, file) + file.write(",") + data = {"charges": doc.charges} # add charges + monty_encoded_json_doc = jsanitize( + data, allow_bson=True, strict=True, enum_values=True + ) + json.dump(monty_encoded_json_doc, file) + file.write(",") + data = { + "calc_quality_summary": doc.calc_quality_summary + } # add calc quality summary dict + monty_encoded_json_doc = jsanitize( + data, allow_bson=True, strict=True, enum_values=True + ) + json.dump(monty_encoded_json_doc, file) + file.write(",") + data = { + "calc_quality_text": ["".join(doc.calc_quality_text)] # type: ignore[dict-item] + } # add calc quality summary dict + monty_encoded_json_doc = jsanitize( + data, allow_bson=True, strict=True, enum_values=True + ) + json.dump(monty_encoded_json_doc, file) + file.write(",") + data = {"dos": doc.dos} # add NON LSO of lobster + monty_encoded_json_doc = jsanitize( + data, allow_bson=True, strict=True, enum_values=True + ) + json.dump(monty_encoded_json_doc, file) + file.write(",") + data = {"lso_dos": doc.lso_dos} # add LSO DOS of lobster + monty_encoded_json_doc = jsanitize( + data, allow_bson=True, strict=True, enum_values=True + ) + json.dump(monty_encoded_json_doc, file) + file.write(",") + data = {"builder_meta": doc.builder_meta} # add builder metadata + monty_encoded_json_doc = jsanitize( + data, allow_bson=False, strict=True, enum_values=True + ) + json.dump(monty_encoded_json_doc, file) + del data, monty_encoded_json_doc + file.write("]") + + if save_computational_data_jsons: + computational_data_json_save_dir = dir_name / "computational_data.json.gz" + fields_to_exclude = [ + "nsites", + "elements", + "nelements", + "formula_anonymous", + "chemsys", + "volume", + "density", + "density_atomic", + "symmetry", + ] + # Always add cohp, cobi and coop data to the jsons if files exists + if cohpcar_path.exists() and doc.cohp_data is None: + cohp_obj = CompleteCohp.from_file( + fmt="LOBSTER", + structure_file=structure_path, + filename=cohpcar_path, + are_coops=False, + are_cobis=False, + ) + doc.cohp_data = cohp_obj + + if coopcar_path.exists() and doc.coop_data is None: + coop_obj = CompleteCohp.from_file( + fmt="LOBSTER", + structure_file=structure_path, + filename=coopcar_path, + are_coops=True, + are_cobis=False, + ) + doc.coop_data = coop_obj + + if cobicar_path.exists() and doc.cobi_data is None: + cobi_obj = CompleteCohp.from_file( + fmt="LOBSTER", + structure_file=structure_path, + filename=cobicar_path, + are_coops=False, + are_cobis=True, + ) + doc.cobi_data = cobi_obj + with gzip.open( + computational_data_json_save_dir, "wt", encoding="UTF-8" + ) as file: + # Write the json in iterable format + # (Necessary to load large JSON files via ijson) + file.write("[") + for attribute in doc.model_fields: + if attribute not in fields_to_exclude: + # Use monty encoder to automatically convert pymatgen + # objects and other data json compatible dict format + data = { + attribute: jsanitize( + getattr(doc, attribute), + allow_bson=False, + strict=True, + enum_values=True, + ) + } + json.dump(data, file) + if attribute != list(doc.model_fields.keys())[-1]: + file.write(",") # add comma separator between two dicts + del data + file.write("]") + + # Again unset the cohp, cobi and coop data fields if not desired in the DB + if not add_coxxcar_to_task_document: + doc.cohp_data = None + doc.coop_data = None + doc.cobi_data = None + + return doc.model_copy(update=additional_fields) + + +def _replace_inf_values(data: Union[dict[Any, Any], list[Any]]) -> None: + """ + Replace the -inf value in dictionary and with the string representation '-Infinity'. + + Parameters + ---------- + data : dict + dictionary to recursively iterate over + + Returns + ------- + data + Dictionary with replaced -inf values. + + """ + if isinstance(data, dict): + for key, value in data.items(): + if isinstance(value, (dict, list)): + _replace_inf_values( + value + ) # Recursively process nested dictionaries and lists + elif value == float("-inf"): + data[key] = "-Infinity" # Replace -inf with a string representation + elif isinstance(data, list): + for index, item in enumerate(data): + if isinstance(item, (dict, list)): + _replace_inf_values( + item + ) # Recursively process nested dictionaries and lists + elif item == float("-inf"): + data[index] = "-Infinity" # Replace -inf with a string representation def _identify_strongest_bonds( @@ -639,7 +1180,7 @@ def _identify_strongest_bonds( icobilist_path: Path, icohplist_path: Path, icooplist_path: Path, -) -> list[StrongestBonds]: +) -> StrongestBonds: """ Identify the strongest bonds and convert them into StrongestBonds objects. @@ -656,16 +1197,16 @@ def _identify_strongest_bonds( Returns ------- - list[StrongestBonds] - List of StrongestBonds + StrongestBonds """ data = [ - (icohplist_path, False, False), - (icobilist_path, True, False), - (icooplist_path, False, True), + (icohplist_path, False, False, "icohp"), + (icobilist_path, True, False, "icobi"), + (icooplist_path, False, True, "icoop"), ] output = [] - for file, are_cobis, are_coops in data: + model_data = {"which_bonds": analyse.which_bonds} + for file, are_cobis, are_coops, prop in data: if file.exists(): icohplist = Icohplist( filename=file, @@ -678,17 +1219,17 @@ def _identify_strongest_bonds( are_cobis=are_cobis, are_coops=are_coops, ) + model_data[f"strongest_bonds_{prop}"] = bond_dict output.append( StrongestBonds( - are_cobis=are_cobis, - are_coops=are_coops, strongest_bonds=bond_dict, which_bonds=analyse.which_bonds, ) ) else: + model_data[f"strongest_bonds_{prop}"] = {} output.append(None) - return output + return StrongestBonds(**model_data) # Don't we have this in pymatgen somewhere? @@ -700,19 +1241,19 @@ def _get_strong_bonds( Parameters ---------- - bondlist : dict + bondlist : dict. dict including bonding information - are_cobis : bool + are_cobis : bool. True if these are cobis - are_coops : bool + are_coops : bool. True if these are coops - relevant_bonds : dict + relevant_bonds : dict. Dict include all bonds that are considered. Returns ------- dict - Dictionary including strongest bonds. + Dictionary including the strongest bonds. """ bonds = [] icohp_all = [] @@ -731,45 +1272,94 @@ def _get_strong_bonds( sep_icohp: list[list[float]] = [[] for _ in range(len(bond_labels_unique))] sep_lengths: list[list[float]] = [[] for _ in range(len(bond_labels_unique))] - for i, val in enumerate(bond_labels_unique): + for idx, val in enumerate(bond_labels_unique): for j, val2 in enumerate(bonds): if val == val2: - sep_icohp[i].append(icohp_all[j]) - sep_lengths[i].append(lengths[j]) + sep_icohp[idx].append(icohp_all[j]) + sep_lengths[idx].append(lengths[j]) if are_cobis and not are_coops: - prop = "ICOBI" + prop = "icobi" elif not are_cobis and are_coops: - prop = "ICOOP" + prop = "icoop" else: - prop = "ICOHP" + prop = "icohp" bond_dict = {} - for i, lab in enumerate(bond_labels_unique): + for idx, lab in enumerate(bond_labels_unique): label = lab.split("-") label.sort() for rel_bnd in relevant_bonds: rel_bnd_list = rel_bnd.split("-") rel_bnd_list.sort() if label == rel_bnd_list: - if prop == "ICOHP": - index = np.argmin(sep_icohp[i]) + if prop == "icohp": + index = np.argmin(sep_icohp[idx]) bond_dict.update( { rel_bnd: { - prop: min(sep_icohp[i]), - "length": sep_lengths[i][index], + "bond_strength": min(sep_icohp[idx]), + "length": sep_lengths[idx][index], } } ) else: - index = np.argmax(sep_icohp[i]) + index = np.argmax(sep_icohp[idx]) bond_dict.update( { rel_bnd: { - prop: max(sep_icohp[i]), - "length": sep_lengths[i][index], + "bond_strength": max(sep_icohp[idx]), + "length": sep_lengths[idx][index], } } ) return bond_dict + + +def read_saved_json( + filename: str, pymatgen_objs: bool = True, query: str = "structure" +) -> dict[str, Any]: + """ + Read the data from *.json.gz file corresponding to query. + + Uses ijson to parse specific keys(memory efficient) + + Parameters + ---------- + filename: str. + name of the json file to read + pymatgen_objs: bool. + if True will convert structure,coop, cobi, cohp and dos to pymatgen objects + query: str or None. + field name to query from the json file. If None, all data will be returned. + + Returns + ------- + dict + Returns a dictionary with lobster task json data corresponding to query. + """ + with gzip.open(filename, "rb") as file: + lobster_data = { + field: data + for obj in ijson.items(file, "item", use_float=True) + for field, data in obj.items() + if query is None or query in obj + } + if not lobster_data: + raise ValueError( + "Please recheck the query argument. " + f"No data associated to the requested 'query={query}' " + f"found in the JSON file" + ) + if pymatgen_objs: + for query_key, value in lobster_data.items(): + if isinstance(value, dict): + lobster_data[query_key] = MontyDecoder().process_decoded(value) + elif "lobsterpy_data" in query_key: + for field in lobster_data[query_key].__fields__: + val = MontyDecoder().process_decoded( + getattr(lobster_data[query_key], field) + ) + setattr(lobster_data[query_key], field, val) + + return lobster_data diff --git a/src/atomate2/qchem/__init__.py b/src/atomate2/qchem/__init__.py new file mode 100644 index 0000000000..d9f4ad8957 --- /dev/null +++ b/src/atomate2/qchem/__init__.py @@ -0,0 +1 @@ +"""Module for QChem workflows.""" diff --git a/src/atomate2/qchem/drones.py b/src/atomate2/qchem/drones.py new file mode 100644 index 0000000000..793686da6e --- /dev/null +++ b/src/atomate2/qchem/drones.py @@ -0,0 +1,83 @@ +"""Drones for parsing VASP calculations and realtd outputs.""" + +from __future__ import annotations + +import logging +import os +from pathlib import Path + +from emmet.core.qc_tasks import TaskDoc +from pymatgen.apps.borg.hive import AbstractDrone + +logger = logging.getLogger(__name__) + + +class QChemDrone(AbstractDrone): + """ + A QChem drone to parse QChem outputs. + + Parameters + ---------- + **task_document_kwargs + Additional keyword args passed to :obj: `.TaskDoc.from_directory`. + """ + + def __init__(self, **task_document_kwargs) -> None: + self.task_document_kwargs = task_document_kwargs + + def assimilate(self, path: str | Path | None = None) -> TaskDoc: + """ + Parse QChem output files and return the output document. + + Parameters + ---------- + path : str pr Path or None + Path to the directory containing mol.qout and other output files. + + + Returns + ------- + TaskDocument + A QChem task document + """ + path = path or Path.cwd() + try: + doc = TaskDoc.from_directory(path, **self.task_document_kwargs) + except Exception: + import traceback + + logger.exception( + f"Error in {Path(path).absolute()}\n{traceback.format_exc()}" + ) + raise + return doc + + def get_valid_paths(self, path: tuple[str, list[str], list[str]]) -> list[str]: + """Get valid paths to assimilate. + + Parameters + ---------- + path : tuple of (str, list of str, list of str) + Input path as a tuple generated from ``os.walk``, i.e., (parent, subdirs, + files). + + Returns + ------- + list of str + A list of paths to assimilate. + """ + parent, subdirs, _ = path + task_names = ["mol.qout.*"] + combined_paths = [parent + os.sep + sdir for sdir in subdirs] + rpath = [] + for cpath in combined_paths: + fnames = os.listdir(cpath) + if any(name.startswith("mol.qout.") for name in fnames): + rpath.append(parent) + + if ( + not any(parent.endswith(os.sep + r) for r in task_names) + and len(list(Path(parent).glob("mol.qout*"))) > 0 + ): + rpath.append(parent) + return rpath diff --git a/src/atomate2/qchem/files.py b/src/atomate2/qchem/files.py new file mode 100644 index 0000000000..c1116155b9 --- /dev/null +++ b/src/atomate2/qchem/files.py @@ -0,0 +1,128 @@ +"""Functions for manipulating QChem files.""" + +from __future__ import annotations + +import logging +import re +from pathlib import Path +from typing import TYPE_CHECKING + +from atomate2.common.files import copy_files, get_zfile, gunzip_files, rename_files +from atomate2.utils.file_client import FileClient, auto_fileclient +from atomate2.utils.path import strip_hostname + +if TYPE_CHECKING: + from collections.abc import Sequence + + +logger = logging.getLogger(__name__) + + +@auto_fileclient +def copy_qchem_outputs( + src_dir: Path | str, + src_host: str | None = None, + additional_qchem_files: Sequence[str] = (), + file_client: FileClient | None = None, +) -> None: + """ + Copy QChem output files to the current directory. + + For folders containing multiple calculations (e.g., suffixed with opt_1, opt_2, + etc), this function will only copy the files with the highest numbered suffix + and the suffix will be removed. Additional qchem files will be also be copied + with the same suffix applied. + Lastly, this function will gunzip any gzipped files. + + Parameters + ---------- + src_dir : str or Path + The source directory. + src_host : str or None + The source hostname used to specify a remote filesystem. Can be given as + either "username@remote_host" or just "remote_host" in which case the username + will be inferred from the current user. If ``None``, the local filesystem will + be used as the source. + additional_qchem_files : list of str + Additional files to copy. + file_client : .FileClient + A file client to use for performing file operations. + """ + src_dir = strip_hostname(src_dir) # TODO: Handle hostnames properly. + + logger.info(f"Copying QChem inputs from {src_dir}") + opt_ext = get_largest_opt_extension(src_dir, src_host, file_client=file_client) + directory_listing = file_client.listdir(src_dir, host=src_host) + + # find required files + files = ("mol.qin", "mol.qout", *tuple(additional_qchem_files)) + required_files = [get_zfile(directory_listing, r + opt_ext) for r in files] + + copy_files( + src_dir, + src_host=src_host, + include_files=required_files, + file_client=file_client, + ) + + gunzip_files( + include_files=required_files, + allow_missing=True, + file_client=file_client, + ) + + # rename files to remove opt extension + if opt_ext: + all_files = required_files + files_to_rename = { + file.name.replace(".gz", ""): file.name.replace(opt_ext, "").replace( + ".gz", "" + ) + for file in all_files + } + rename_files(files_to_rename, allow_missing=True, file_client=file_client) + + logger.info("Finished copying inputs") + + +@auto_fileclient +def get_largest_opt_extension( + directory: Path | str, + host: str | None = None, + file_client: FileClient | None = None, +) -> str: + """ + Get the largest numbered opt extension of files in a directory. + + For example, if listdir gives ["mol.qout.opt_0.gz", "mol.qout.opt_1.gz"], + this function will return ".opt_1". + + Parameters + ---------- + directory : str or Path + A directory to search. + host : str or None + The hostname used to specify a remote filesystem. Can be given as either + "username@remote_host" or just "remote_host" in which case the username will be + inferred from the current user. If ``None``, the local filesystem will be used. + file_client : .FileClient + A file client to use for performing file operations. + + Returns + ------- + str + The opt extension or an empty string if there were not multiple relaxations. + """ + opt_files = file_client.glob(Path(directory) / "*.opt*", host=host) + if len(opt_files) == 0: + return "" + numbers = [] + for file in opt_files: + match = re.search(r"\.opt_(\d+)", file.name) + if match: + numbers.append(match.group(1)) + + if not numbers: + return "" # No matches found + max_relax = max(numbers, key=int) + return f".opt_{max_relax}" diff --git a/src/atomate2/qchem/jobs/__init__.py b/src/atomate2/qchem/jobs/__init__.py new file mode 100644 index 0000000000..5d086b0016 --- /dev/null +++ b/src/atomate2/qchem/jobs/__init__.py @@ -0,0 +1 @@ +"""Jobs for running QChem calculations.""" diff --git a/src/atomate2/qchem/jobs/base.py b/src/atomate2/qchem/jobs/base.py new file mode 100644 index 0000000000..d67322917c --- /dev/null +++ b/src/atomate2/qchem/jobs/base.py @@ -0,0 +1,144 @@ +"""Definition of a base QChem Maker.""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from pathlib import Path +from typing import TYPE_CHECKING, Callable + +from emmet.core.qc_tasks import TaskDoc +from jobflow import Maker, Response, job +from monty.serialization import dumpfn +from monty.shutil import gzip_dir +from pymatgen.io.qchem.inputs import QCInput + +from atomate2.qchem.files import copy_qchem_outputs +from atomate2.qchem.run import run_qchem, should_stop_children +from atomate2.qchem.sets.base import QCInputGenerator + +if TYPE_CHECKING: + from pymatgen.core.structure import Molecule + + +def qchem_job(method: Callable) -> job: + """ + Decorate the ``make`` method of QChem job makers. + + This is a thin wrapper around :obj:`~jobflow.core.job.Job` that configures common + settings for all QChem jobs. It also configures the output schema to be a QChem + :obj:`.TaskDoc`. + + Any makers that return QChem jobs (not flows) should decorate the ``make`` method + with @qchem_job. For example: + + .. code-block:: python + + class MyQChemMaker(BaseQChemMaker): + @qchem_job + def make(molecule): + # code to run QChem job. + pass + + Parameters + ---------- + method : callable + A BaseQChemMaker.make method. This should not be specified directly and is + implied by the decorator. + + Returns + ------- + callable + A decorated version of the make function that will generate QChem jobs. + """ + return job(method, data=QCInput, output_schema=TaskDoc) + + +@dataclass +class BaseQCMaker(Maker): + """ + Base QChem job maker. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .QChemInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_qchem_input_set`. + copy_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_qchem_outputs`. + run_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_qchem`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "base qchem job" + input_set_generator: QCInputGenerator = field( + default_factory=lambda: QCInputGenerator( + job_type="sp", scf_algorithm="diis", basis_set="def2-qzvppd" + ) + ) + write_input_set_kwargs: dict = field(default_factory=dict) + copy_qchem_kwargs: dict = field(default_factory=dict) + run_qchem_kwargs: dict = field(default_factory=dict) + task_document_kwargs: dict = field(default_factory=dict) + stop_children_kwargs: dict = field(default_factory=dict) + write_additional_data: dict = field(default_factory=dict) + + @qchem_job + def make( + self, molecule: Molecule, prev_qchem_dir: str | Path | None = None + ) -> Response: + """Run a QChem calculation. + + Parameters + ---------- + molecule : Molecule + A pymatgen molecule object. + prev_qchem_dir : str or Path or None + A previous QChem calculation directory to copy output files from. + """ + # copy previous inputs + from_prev = prev_qchem_dir is not None + if prev_qchem_dir is not None: + copy_qchem_outputs(prev_qchem_dir, **self.copy_qchem_kwargs) + + self.write_input_set_kwargs.setdefault("from_prev", from_prev) + + # write qchem input files + # self.input_set_generator.get_input_set(molecule).write_inputs() + self.input_set_generator.get_input_set(molecule) + + # write any additional data + for filename, data in self.write_additional_data.items(): + dumpfn(data, filename.replace(":", ".")) + + # run qchem + run_qchem(**self.run_qchem_kwargs) + + # parse qchem outputs + task_doc = TaskDoc.from_directory(Path.cwd(), **self.task_document_kwargs) + # task_doc.task_label = self.name + task_doc.task_type = self.name + + # decide whether child jobs should proceed + stop_children = should_stop_children(task_doc, **self.stop_children_kwargs) + + # gzip folder + gzip_dir(".") + + return Response( + stop_children=stop_children, + stored_data={"custodian": task_doc.custodian}, + output=task_doc, + ) diff --git a/src/atomate2/qchem/jobs/core.py b/src/atomate2/qchem/jobs/core.py new file mode 100644 index 0000000000..b0d7987d1f --- /dev/null +++ b/src/atomate2/qchem/jobs/core.py @@ -0,0 +1,236 @@ +"""Core jobs for running QChem calculations.""" + +from __future__ import annotations + +import logging +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +if TYPE_CHECKING: + from atomate2.qchem.sets.base import QCInputGenerator + +from atomate2.qchem.jobs.base import BaseQCMaker +from atomate2.qchem.sets.core import ( + ForceSetGenerator, + FreqSetGenerator, + OptSetGenerator, + PESScanSetGenerator, + SinglePointSetGenerator, + TransitionStateSetGenerator, +) + +# from custodian.qchem.handlers import ( +# QChemErrorHandler, +# ) + + +logger = logging.getLogger(__name__) + + +@dataclass +class SinglePointMaker(BaseQCMaker): + """ + Maker to create QChem single point calculation jobs. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .QChemInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_qchem_input_set`. + copy_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_qchem_outputs`. + run_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_qchem`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDocument.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "single point" + input_set_generator: QCInputGenerator = field( + default_factory=SinglePointSetGenerator + ) + + +@dataclass +class OptMaker(BaseQCMaker): + """ + Maker to create QChem optimization jobs. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .QChemInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_qchem_input_set`. + copy_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_qchem_outputs`. + run_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_qchem`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDocument.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "optimization" + input_set_generator: QCInputGenerator = field(default_factory=OptSetGenerator) + + +@dataclass +class ForceMaker(BaseQCMaker): + """ + QChem Maker for a Force Job. + + Maker to create QChem job to converge electron density + and calculate the gradient and atomic forces. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .QChemInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_qchem_input_set`. + copy_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_qchem_outputs`. + run_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_qchem`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDocument.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "force" + input_set_generator: QCInputGenerator = field(default_factory=ForceSetGenerator) + + +@dataclass +class TransitionStateMaker(BaseQCMaker): + """ + Maker to create QChem transition state structure optimization jobs. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .QChemInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_qchem_input_set`. + copy_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_qchem_outputs`. + run_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_qchem`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDocument.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "transition state" + input_set_generator: QCInputGenerator = field( + default_factory=TransitionStateSetGenerator + ) + + +@dataclass +class FreqMaker(BaseQCMaker): + """ + Maker to create QChem job for frequency calculations. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .QChemInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_qchem_input_set`. + copy_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_qchem_outputs`. + run_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_qchem`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDocument.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "frequency" + input_set_generator: QCInputGenerator = field(default_factory=FreqSetGenerator) + + +@dataclass +class PESScanMaker(BaseQCMaker): + """ + Maker for a PES Scan job. + + Maker to create a QChem job which perform a potential energy surface + scan by varying bond lengths, angles, + and/or dihedral angles in a molecule. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .QChemInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_qchem_input_set`. + copy_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_qchem_outputs`. + run_qchem_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_qchem`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDocument.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "PES scan" + input_set_generator: QCInputGenerator = field(default_factory=PESScanSetGenerator) diff --git a/src/atomate2/qchem/run.py b/src/atomate2/qchem/run.py new file mode 100644 index 0000000000..9010dc7b68 --- /dev/null +++ b/src/atomate2/qchem/run.py @@ -0,0 +1,143 @@ +"""Functions to run QChem in atomate 2.""" + +from __future__ import annotations + +import logging +import shlex +from os.path import expandvars +from typing import TYPE_CHECKING, Any + +from custodian import Custodian +from custodian.qchem.handlers import QChemErrorHandler +from custodian.qchem.jobs import QCJob +from jobflow.utils import ValueEnum + +from atomate2 import SETTINGS + +if TYPE_CHECKING: + from collections.abc import Sequence + + from custodian.custodian import ErrorHandler + from emmet.core.qc_tasks import TaskDoc + + +_DEFAULT_HANDLERS = (QChemErrorHandler,) + +logger = logging.getLogger(__name__) + + +class JobType(ValueEnum): + """ + Type of QChem job. + + - ``DIRECT``: Run QChem without using custodian. + - ``NORMAL``: Normal custodian :obj:`.QCJob`. + """ + + DIRECT = "direct" + NORMAL = "normal" + + +def run_qchem( + job_type: JobType | str = JobType.NORMAL, + qchem_cmd: str = SETTINGS.QCHEM_CMD, + max_errors: int = SETTINGS.QCHEM_CUSTODIAN_MAX_ERRORS, + scratch_dir: str = SETTINGS.CUSTODIAN_SCRATCH_DIR, + handlers: Sequence[ErrorHandler] = _DEFAULT_HANDLERS, + # wall_time: int | None = None, + qchem_job_kwargs: dict[str, Any] = None, + custodian_kwargs: dict[str, Any] = None, +) -> None: + """ + Run QChem. + + Supports running QChem with or without custodian (see :obj:`JobType`). + + Parameters + ---------- + job_type : str or .JobType + The job type. + qchem_cmd : str + The command used to run the standard version of QChem. + max_errors : int + The maximum number of errors allowed by custodian. + scratch_dir : str + The scratch directory used by custodian. + handlers : list of .ErrorHandler + The error handlers used by custodian. + wall_time : int + The maximum wall time. If set, a WallTimeHandler will be added to the list + of handlers. + qchem_job_kwargs : dict + Keyword arguments that are passed to :obj:`.QCJob`. + custodian_kwargs : dict + Keyword arguments that are passed to :obj:`.Custodian`. + """ + qchem_job_kwargs = {} if qchem_job_kwargs is None else qchem_job_kwargs + custodian_kwargs = {} if custodian_kwargs is None else custodian_kwargs + + qchem_cmd = expandvars(qchem_cmd) + split_qchem_cmd = shlex.split(qchem_cmd) + + if job_type == JobType.NORMAL: + jobs = [ + QCJob( + split_qchem_cmd, max_cores=SETTINGS.QCHEM_MAX_CORES, **qchem_job_kwargs + ) + ] + else: + raise ValueError(f"Unsupported job type: {job_type}") + + c = Custodian( + handlers, + jobs, + max_errors=max_errors, + scratch_dir=scratch_dir, + **custodian_kwargs, + ) + + logger.info("Running QChem using custodian.") + c.run() + + +def should_stop_children( + task_document: TaskDoc, + handle_unsuccessful: bool | str = SETTINGS.QCHEM_HANDLE_UNSUCCESSFUL, +) -> bool: + """ + Parse QChem outputs and decide whether child jobs should continue. + + Parameters + ---------- + task_document : .TaskDocument + A QChem task document. + handle_unsuccessful : bool or str + This is a three-way toggle on what to do if your job looks OK, but is actually + unconverged (either electronic or ionic): + + - `True`: Mark job as completed, but stop children. + - `False`: Do nothing, continue with workflow as normal. + - `"error"`: Throw an error. + + Returns + ------- + bool + Whether to stop child jobs. + """ + if task_document.state == "successful": + if isinstance(handle_unsuccessful, bool): + return handle_unsuccessful + + if handle_unsuccessful == "error": + raise RuntimeError( + "Job was successful but children jobs need to be stopped!" + ) + return False + + if task_document.state == "unsuccessful": + raise RuntimeError( + "Job was not successful (perhaps your job did not converge within the " + "limit of electronic/ionic iterations)!" + ) + + raise RuntimeError(f"Unknown option for defuse_unsuccessful: {handle_unsuccessful}") diff --git a/src/atomate2/qchem/sets/__init__.py b/src/atomate2/qchem/sets/__init__.py new file mode 100644 index 0000000000..1ad67fe896 --- /dev/null +++ b/src/atomate2/qchem/sets/__init__.py @@ -0,0 +1 @@ +"""Module defining QChem input sets used in atomate2.""" diff --git a/src/atomate2/qchem/sets/base.py b/src/atomate2/qchem/sets/base.py new file mode 100644 index 0000000000..9592b5dfef --- /dev/null +++ b/src/atomate2/qchem/sets/base.py @@ -0,0 +1,425 @@ +"""Module defining base QChem input set and generator.""" + +from __future__ import annotations + +import os +from dataclasses import dataclass, field +from pathlib import Path +from typing import TYPE_CHECKING, Any, Literal + +from monty.io import zopen +from pymatgen.io.core import InputGenerator, InputSet +from pymatgen.io.qchem.inputs import QCInput +from pymatgen.io.qchem.utils import lower_and_check_unique + +if TYPE_CHECKING: + from pymatgen.core.structure import Molecule + +__author__ = "Alex Ganose, Ryan Kingsbury, Rishabh D Guha" +__copyright__ = "Copyright 2018-2022, The Materials Project" +__version__ = "0.1" + +# _BASE_QCHEM_SET = +# loadfn(resource_filename("atomate2.qchem.sets", "BaseQchemSet.yaml")) + + +class QCInputSet(InputSet): + """ + A class to represent a QChem input file as a QChem InputSet. + + Parameters + ---------- + qcinput + A QCInput object + optional_files + Any other optional input files supplied as a dict of ``{filename: object}``. + The objects should follow standard pymatgen conventions in + implementing an ``as_dict()`` and ``from_dict()`` method. + """ + + def __init__( + self, + qcinput: QCInput, + optional_files: dict | None = None, + ) -> None: + self.qcinput = qcinput + self.optional_files = {} if optional_files is None else optional_files + + def write_input( + self, + directory: str | Path, + overwrite: bool = True, + ) -> None: + """Write QChem input file to directory. + + Parameters + ---------- + directory + Directory to write input files to. + overwrite + Whether to overwrite an input file if it already exists. + """ + os.makedirs(directory, exist_ok=True) + directory = Path(directory) + + inputs = {"Input_Dict": self.qcinput} + inputs.update(self.optional_files) + + for key, val in inputs.items(): + if val is not None and (overwrite or not (directory / key).exists()): + with zopen(directory / key, "wt") as file: + file.write(str(val)) + elif not overwrite and (directory / key).exists(): + raise FileExistsError(f"{directory / key} already exists.") + + @staticmethod + def from_directory( + directory: str | Path, optional_files: dict = None + ) -> QCInputSet: + """Load a set of QChem inputs from a directory. + + Parameters + ---------- + directory + Directory to read QChem inputs from. + optional_files + Optional files to read in as well as a dict of {filename: Object class}. + Object class must have a static/class method from_file + """ + directory = Path(directory) + objs = {"Input_Dict": QCInput} + + inputs = {} + for name, obj in objs.items(): + if (directory / name).exists(): + inputs[name.lower()] = obj.from_file(directory / name) + + optional_inputs = {} + if optional_files is not None: + for name, obj in optional_files.items(): + optional_inputs[name] = obj.from_file(directory / name) + + return QCInputSet(inputs["input_dict"], optional_files=optional_inputs) + + # Todo + # Implement is_valid property + + +@dataclass +class QCInputGenerator(InputGenerator): + """ + A dataclass to generate QChem input set. + + Parameters + ---------- + job_type : str + QChem job type to run. Valid options are "opt" for optimization, + "sp" for single point, "freq" for frequency calculation, or "force" for + force evaluation. + + basis_set : str + Basis set to use. For example, "def2-tzvpd". + + scf_algorithm : str + Algorithm to use for converging the SCF. Recommended choices are + "DIIS", "GDM", and "DIIS_GDM". Other algorithms supported by Qchem's + GEN_SCFMAN module will also likely perform well. + Refer to the QChem manual for further details. + + dft_rung : int + Select the DFT functional among 5 recommended levels of theory, + in order of increasing accuracy/cost. 1 = SPW92, 2 = B97-D3(BJ), 3 = B97M-V, + 4 = ฯ‰B97M-V, 5 = ฯ‰B97M-(2). (Default: 4) + To set a functional not given by one of the above, set the overwrite_inputs + argument to {"method":""} + **Note that the "rungs" in this argument do NOT correspond to rungs on "Jacob's + Ladder of Density Functional Approximations"** + + pcm_dielectric : float + Dielectric constant to use for PCM implicit solvation model. (Default: None) + + smd_solvent : str + Solvent to use for SMD implicit solvation model. (Default: None) + Examples include "water", "ethanol", "methanol", and "acetonitrile". + Refer to the QChem manual for a complete list of solvents available. + To define a custom solvent, set this argument to "custom" and + populate custom_smd with the necessary parameters. + + **Note that only one of smd_solvent and pcm_dielectric may be set.** + + custom_smd : str + List of parameters to define a custom solvent in SMD. (Default: None) + Must be given as a string of seven comma separated values + in the following order: + "dielectric, refractive index, acidity, basicity, + surface tension, aromaticity, electronegative halogenicity" + Refer to the QChem manual for further details. + + opt_dict : dict + A dictionary of opt sections, where each opt section is a key + and the corresponding values are a list of strings. Strings must be formatted + as instructed by the QChem manual. + The different opt sections are: CONSTRAINT, FIXED, DUMMY, and CONNECT. + Ex. + opt = + {"CONSTRAINT": ["tors 2 3 4 5 25.0", "tors 2 5 7 9 80.0"], "FIXED": ["2 XY"]} + + scan_dict : dict + A dictionary of scan variables. Because two constraints of the + same type are allowed (for instance, two torsions or two bond stretches), + each TYPE of variable (stre, bend, tors) should be its own key in the dict, + rather than each variable. Note that the total number of variable + (sum of lengths of all lists) CANNOT be more than two. + Ex. scan_variables = + {"stre": ["3 6 1.5 1.9 0.1"], "tors": ["1 2 3 4 -180 180 15"]} + + max_scf_cycles : int + Maximum number of SCF iterations. (Default: 100) + + geom_opt_max_cycles : int + Maximum number of geometry optimization iterations. (Default: 200) + + plot_cubes : bool + Whether to write CUBE files of the electron density. (Default: False) + + nbo_params : dict + A dict containing the desired NBO params. Note that a key:value pair of + "version":7 will trigger NBO7 analysis. + Otherwise, NBO5 analysis will be performed, + including if an empty dict is passed. + Besides a key of "version", all other key:value pairs + will be written into the $nbo section of the QChem input file. (Default: False) + + new_geom_opt : dict + A dict containing parameters for the $geom_opt section of the QChem + input file, which control the new geometry optimizer + available starting in version 5.4.2. + Further note that even passing an empty dictionary + will trigger the new optimizer. + (Default: False) + + overwrite_inputs : dict + Dictionary of QChem input sections to add or overwrite variables. + The currently available sections (keys) are rem, pcm, solvent, smx, opt, + scan, van_der_waals, and plots. The value of each key is a dictionary + of key value pairs relevant to that section. + For example, to add a new variable to the rem section that sets + symmetry to false, use + overwrite_inputs = {"rem": {"symmetry": "false"}} + **Note that if something like basis is added to the rem dict it will overwrite + the default basis.** + **Note that supplying a van_der_waals section here will automatically modify + the PCM "radii" setting to "read".** + **Note that all keys must be given as strings, even when they are numbers!** + + vdw_mode : str + Method of specifying custom van der Waals radii. + Either "atomic" (default) or "sequential". + In "atomic" mode, dict keys represent the atomic number + associated with each radius (e.g., 12 = carbon). + In "sequential" mode, dict keys represent the sequential position + of a single specific atom in the input structure. + + """ + + job_type: str = field(default=None) + basis_set: str = field(default=None) + scf_algorithm: str = field(default=None) + dft_rung: int = field(default=4) + pcm_dielectric: float = field(default=None) + smd_solvent: str = field(default=None) + custom_smd: str = field(default=None) + opt_dict: dict[str, Any] = field(default_factory=dict) + scan_dict: dict[str, Any] = field(default_factory=dict) + max_scf_cycles: int = field(default=100) + geom_opt_max_cycles: int = field(default=200) + plot_cubes: bool = field(default=False) + nbo_params: dict[str, Any] = field(default_factory=dict) + new_geom_opt: dict[str, Any] = field(default_factory=dict) + overwrite_inputs: dict[str, str] = field(default_factory=dict) + vdw_mode: Literal["atomic", "sequential"] = field(default="atomic") + rem_dict: dict[str, Any] = field(default_factory=dict) + vdw_dict: dict[str, float] = field(default_factory=dict) + pcm_dict: dict[str, Any] = field(default_factory=dict) + solv_dict: dict[str, Any] = field(default_factory=dict) + smx_dict: dict[str, Any] = field(default_factory=dict) + plots_dict: dict[str, Any] = field(default_factory=dict) + + def __post_init__(self) -> None: + """Post init formatting of arguments.""" + self.rem_dict = { + "job_type": self.job_type, + "basis": self.basis_set, + "max_scf_cycles": str(self.max_scf_cycles), + "gen_scfman": "true", + "xc_grid": "3", + "thresh": "14", + "s2thresh": "16", + "scf_algorithm": self.scf_algorithm, + "resp_charges": "true", + "symmetry": "false", + "sym_ignore": "true", + } + + rung_2_func = ["spw92", "b97d3", "b97mv", "wb97mv", "wb97m(2)"] + qc_method = {i + 1: e for i, e in enumerate(rung_2_func)} + + if qc_method.get(self.dft_rung): + self.rem_dict["method"] = qc_method.get(self.dft_rung) + else: + raise ValueError("Provided DFT rung should be between 1 and 5!") + + if self.dft_rung == 2: + self.rem_dict["dft_D"] = "D3_BJ" + + if self.job_type.lower() in ["opt", "ts", "pes_scan"]: + self.rem_dict["geom_opt_max_cycles"] = str(self.geom_opt_max_cycles) + + if self.pcm_dielectric and self.smd_solvent: + raise ValueError( + "Only one of pcm or smd may be used as an implicit solvent. Not both!" + ) + + if self.pcm_dielectric: + pcm_defaults = { + "heavypoints": "194", + "hpoints": "194", + "radii": "uff", + "theory": "cpcm", + "vdwscale": "1.1", + } + + self.pcm_dict = pcm_defaults + self.solv_dict["dielectric"] = self.pcm_dielectric + self.rem_dict["solvent_method"] = "pcm" + + if self.smd_solvent: + if self.smd_solvent == "custom": + self.smx_dict["solvent"] = "other" + else: + self.smx_dict["solvent"] = self.smd_solvent + self.rem_dict["solvent_method"] = "smd" + self.rem_dict["ideriv"] = "1" + if self.smd_solvent in ("custom", "other") and self.custom_smd is None: + raise ValueError( + "A user-defined SMD requires passing custom_smd," + "a string of seven comma separated values in the following order: " + "dielectric, refractive index, acidity, basicity, surface tension," + "aromaticity, electronegative halogenicity" + ) + + if self.plot_cubes: + plots_defaults = {"grid_spacing": "0.05", "total_density": "0"} + self.plots_dict = plots_defaults + self.rem_dict["plots"] = "true" + self.rem_dict["make_cube_files"] = "true" + + if self.nbo_params: + self.rem_dict["nbo"] = "true" + nbo_params_copy = self.nbo_params.copy() + if "version" in nbo_params_copy: + if nbo_params_copy["version"] == 7: + self.rem_dict["nbo_external"] = "true" + else: + raise RuntimeError( + "nbo params version should only be set to 7! Exiting..." + ) + for key in nbo_params_copy: + if key == "version": + self.nbo_params.pop(key) + + if self.new_geom_opt: + self.rem_dict["geom_opt2"] = "3" + + if "maxiter" in self.new_geom_opt and self.new_geom_opt["maxiter"] != str( + self.geom_opt_max_cycles + ): + raise RuntimeError( + "Max # of optimization cycles must be the same! Exiting..." + ) + + def get_input_set(self, molecule: Molecule = None) -> QCInputSet: + """Get a QChem InputSet for a molecule. + + Parameters + ---------- + molecule: Molecule + Pymatgen representation of a molecule for which the QCInputSet + will be generated + + Returns + ------- + QchemInputSet + A QChem input set + """ + if self.overwrite_inputs: + for sub, sub_dict in self.overwrite_inputs.items(): + if sub == "rem": + temp_rem = lower_and_check_unique(sub_dict) + for k, v in temp_rem.items(): + self.rem_dict[k] = v + if sub == "pcm": + temp_pcm = lower_and_check_unique(sub_dict) + for k, v in temp_pcm.items(): + self.pcm_dict[k] = v + if sub == "solvent": + temp_solvent = lower_and_check_unique(sub_dict) + for k, v in temp_solvent.items(): + self.solv_dict[k] = v + if sub == "smx": + temp_smx = lower_and_check_unique(sub_dict) + for k, v in temp_smx.items(): + self.smx_dict[k] = v + if sub == "scan": + temp_scan = lower_and_check_unique(sub_dict) + for k, v in temp_scan.items(): + self.scan_dict[k] = v + if sub == "van_der_waals": + temp_vdw = lower_and_check_unique(sub_dict) + for k, v in temp_vdw.items(): + self.vdw_dict[k] = v + # set the PCM section to read custom radii + self.pcm_dict["radii"] = "read" + if sub == "plots": + temp_plots = lower_and_check_unique(sub_dict) + for k, v in temp_plots.items(): + self.plots_dict[k] = v + if sub == "nbo": + if self.nbo_dict is None: + raise RuntimeError( + "Can't overwrite nbo params when NBO" + "is not being run! Exiting..." + ) + temp_nbo = lower_and_check_unique(sub_dict) + for k, v in temp_nbo.items(): + self.nbo_dict[k] = v + if sub == "geom_opt": + if self.geom_opt_dict is None: + raise RuntimeError( + "Can't overwrite geom_opt params when" + "not using the new optimizer! Exiting..." + ) + temp_geomopt = lower_and_check_unique(sub_dict) + for k, v in temp_geomopt.items(): + self.geom_opt_dict[k] = v + if sub == "opt": + temp_opts = lower_and_check_unique(sub_dict) + for k, v in temp_opts.items(): + self.opt_dict[k] = v + + return QCInputSet( + qcinput=QCInput( + molecule, + rem=self.rem_dict, + opt=self.opt_dict, + pcm=self.pcm_dict, + solvent=self.solv_dict, + smx=self.smx_dict, + scan=self.scan_dict, + van_der_waals=self.vdw_dict, + vdw_mode=self.vdw_mode, + plots=self.plots_dict, + nbo=self.nbo_params, + geom_opt=self.new_geom_opt, + ) + ) diff --git a/src/atomate2/qchem/sets/core.py b/src/atomate2/qchem/sets/core.py new file mode 100644 index 0000000000..df92554f46 --- /dev/null +++ b/src/atomate2/qchem/sets/core.py @@ -0,0 +1,64 @@ +"""Module defining core QChem input set generators.""" + +from __future__ import annotations + +import logging +from dataclasses import dataclass + +from atomate2.qchem.sets.base import QCInputGenerator + +logger = logging.getLogger(__name__) + + +@dataclass +class SinglePointSetGenerator(QCInputGenerator): + """Generate QChem Single Point input sets.""" + + job_type: str = "sp" + scf_algorithm: str = "diis" + basis_set: str = "def2-tzvppd" + + +@dataclass +class OptSetGenerator(QCInputGenerator): + """Generate QChem Optimization input sets.""" + + job_type: str = "opt" + scf_algorithm: str = "diis" + basis_set: str = "def2-tzvppd" + + +@dataclass +class TransitionStateSetGenerator(QCInputGenerator): + """Generate QChem Transition State calculation input sets.""" + + job_type: str = "ts" + scf_algorithm: str = "diis" + basis_set: str = "def2-tzvppd" + + +@dataclass +class ForceSetGenerator(QCInputGenerator): + """Generate QChem force input sets.""" + + job_type: str = "force" + scf_algorithm: str = "diis" + basis_set: str = "def2-tzvppd" + + +@dataclass +class FreqSetGenerator(QCInputGenerator): + """Generate QChem frequency calculation input sets.""" + + job_type: str = "freq" + scf_algorithm: str = "diis" + basis_set: str = "def2-tzvppd" + + +@dataclass +class PESScanSetGenerator(QCInputGenerator): + """Generate QChem PES scan input sets.""" + + job_type: str = "pes_scan" + scf_algorithm: str = "diis" + basis_set: str = "def2-tzvppd" diff --git a/src/atomate2/settings.py b/src/atomate2/settings.py index 8d21c8931f..317f496e57 100644 --- a/src/atomate2/settings.py +++ b/src/atomate2/settings.py @@ -1,14 +1,16 @@ """Settings for atomate2.""" + from __future__ import annotations import warnings from pathlib import Path -from typing import Literal, Optional, Union +from typing import Any, Literal, Optional, Union from pydantic import Field, model_validator from pydantic_settings import BaseSettings, SettingsConfigDict _DEFAULT_CONFIG_FILE_PATH = "~/.atomate2.yaml" +_ENV_PREFIX = "atomate2_" class Atomate2Settings(BaseSettings): @@ -84,6 +86,18 @@ class Atomate2Settings(BaseSettings): description="Whether to run the Bader program when parsing VASP calculations." "Requires the bader executable to be on the path.", ) + VASP_RUN_DDEC6: bool = Field( + default=False, + description="Whether to run the DDEC6 program when parsing VASP calculations." + "Requires the chargemol executable to be on the path.", + ) + DDEC6_ATOMIC_DENSITIES_DIR: Optional[str] = Field( + default=None, + description="Directory where the atomic densities are stored.", + # TODO uncomment below once that functionality is actually implemented + # If not set, pymatgen tries to auto-download the densities and extract them + # into ~/.cache/pymatgen/ddec + ) VASP_ZIP_FILES: Union[bool, Literal["atomate"]] = Field( "atomate", @@ -92,7 +106,7 @@ class Atomate2Settings(BaseSettings): "to the simulation will be compressed. If False no file is compressed.", ) VASP_INHERIT_INCAR: bool = Field( - default=True, + default=False, description="Whether to inherit INCAR settings from previous calculation. " "This might be useful to port Custodian fixes to child jobs but can also be " "dangerous e.g. when switching from GGA to meta-GGA or relax to static jobs." @@ -162,6 +176,11 @@ class Atomate2Settings(BaseSettings): "to the simulation will be compressed. If False no file is compressed.", ) + # FHI-aims settings + AIMS_CMD: str = Field( + "aims.x > aims.out", description="The default command used run FHI-aims" + ) + # Elastic constant settings ELASTIC_FITTING_METHOD: str = Field( "finite_difference", description="Elastic constant fitting method" @@ -172,13 +191,59 @@ class Atomate2Settings(BaseSettings): None, description="Additional settings applied to AMSET settings file." ) - model_config = SettingsConfigDict(env_prefix="atomate2_") + # ABINIT settings + ABINIT_MPIRUN_CMD: Optional[str] = Field(None, description="Mpirun command.") + ABINIT_CMD: str = Field("abinit", description="Abinit command.") + ABINIT_MRGDDB_CMD: str = Field("mrgddb", description="Mrgddb command.") + ABINIT_ANADDB_CMD: str = Field("anaddb", description="Anaddb command.") + ABINIT_COPY_DEPS: bool = Field( + default=False, + description="Copy (True) or link file dependencies between jobs.", + ) + ABINIT_AUTOPARAL: bool = Field( + default=False, + description="Use autoparal to determine optimal parallel configuration.", + ) + ABINIT_ABIPY_MANAGER_FILE: Optional[str] = Field( + None, + description="Config file for task manager of abipy.", + ) + ABINIT_MAX_RESTARTS: int = Field( + 5, description="Maximum number of restarts of a job." + ) + + model_config = SettingsConfigDict(env_prefix=_ENV_PREFIX) + + # QChem specific settings + + QCHEM_CMD: str = Field( + "qchem_std", description="Command to run standard version of qchem." + ) + + QCHEM_CUSTODIAN_MAX_ERRORS: int = Field( + 5, description="Maximum number of errors to correct before custodian gives up" + ) + + QCHEM_MAX_CORES: int = Field(4, description="Maximum number of cores for QCJob") + + QCHEM_HANDLE_UNSUCCESSFUL: Union[str, bool] = Field( + "fizzle", + description="Three-way toggle on what to do if the job looks OK but is actually" + " unconverged (either electronic or ionic). - True: mark job as COMPLETED, but " + "stop children. - False: do nothing, continue with workflow as normal. 'error':" + " throw an error", + ) + + QCHEM_STORE_ADDITIONAL_JSON: bool = Field( + default=True, + description="Ingest any additional JSON data present into database when " + "parsing QChem directories useful for storing duplicate of FW.json", + ) @model_validator(mode="before") @classmethod - def load_default_settings(cls, values) -> dict: - """ - Load settings from file or environment variables. + def load_default_settings(cls, values: dict[str, Any]) -> dict[str, Any]: + """Load settings from file or environment variables. Loads settings from a root file if available and uses that as defaults in place of built-in defaults. @@ -187,14 +252,15 @@ def load_default_settings(cls, values) -> dict: """ from monty.serialization import loadfn - config_file_path = values.get("CONFIG_FILE", _DEFAULT_CONFIG_FILE_PATH) + config_file_path = values.get(key := "CONFIG_FILE", _DEFAULT_CONFIG_FILE_PATH) + env_var_name = f"{_ENV_PREFIX.upper()}{key}" config_file_path = Path(config_file_path).expanduser() new_values = {} if config_file_path.exists(): if config_file_path.stat().st_size == 0: warnings.warn( - f"Using atomate2 config file at {config_file_path} but it's empty", + f"Using {env_var_name} at {config_file_path} but it's empty", stacklevel=2, ) else: @@ -202,7 +268,12 @@ def load_default_settings(cls, values) -> dict: new_values.update(loadfn(config_file_path)) except ValueError: raise SyntaxError( - f"atomate2 config file at {config_file_path} is unparsable" + f"{env_var_name} at {config_file_path} is unparsable" ) from None + # warn if config path is not the default but file doesn't exist + elif config_file_path != Path(_DEFAULT_CONFIG_FILE_PATH).expanduser(): + warnings.warn( + f"{env_var_name} at {config_file_path} does not exist", stacklevel=2 + ) return {**new_values, **values} diff --git a/src/atomate2/utils/datetime.py b/src/atomate2/utils/datetime.py index 61ae600577..cdb9977d4a 100644 --- a/src/atomate2/utils/datetime.py +++ b/src/atomate2/utils/datetime.py @@ -2,7 +2,7 @@ from __future__ import annotations -from datetime import datetime +from datetime import datetime, timezone def datetime_str() -> str: @@ -14,4 +14,4 @@ def datetime_str() -> str: str The current time. """ - return str(datetime.utcnow()) + return str(datetime.now(tz=timezone.utc)) diff --git a/src/atomate2/utils/file_client.py b/src/atomate2/utils/file_client.py index 7529feb408..0e77aa4c13 100644 --- a/src/atomate2/utils/file_client.py +++ b/src/atomate2/utils/file_client.py @@ -1,8 +1,9 @@ """Tools for remote file IO using paramiko.""" - from __future__ import annotations +import errno +import os import shutil import stat import warnings @@ -10,12 +11,15 @@ from glob import glob from gzip import GzipFile from pathlib import Path -from typing import Any, Callable +from typing import TYPE_CHECKING, Any, Callable import paramiko from monty.io import zopen from paramiko import SFTPClient, SSHClient +if TYPE_CHECKING: + from types import TracebackType + class FileClient: """ @@ -74,8 +78,7 @@ def connect(self, host: str) -> None: self.connections[host] = {"ssh": ssh, "sftp": ssh.open_sftp()} def get_ssh(self, host: str) -> SSHClient: - """ - Get an SSH connection to a host. + """Get an SSH connection to a host. Parameters ---------- @@ -95,8 +98,7 @@ def get_ssh(self, host: str) -> SSHClient: return self.connections[host]["ssh"] def get_sftp(self, host: str) -> SFTPClient: - """ - Get an SFTP connection to a host. + """Get an SFTP connection to a host. Parameters ---------- @@ -136,13 +138,12 @@ def exists(self, path: str | Path, host: str | None = None) -> bool: path = str(self.abspath(path, host=host)) try: self.get_sftp(host).stat(path) - return True except FileNotFoundError: return False + return True def is_file(self, path: str | Path, host: str | None = None) -> bool: - """ - Whether a path is a file. + """Whether a path is a file. Parameters ---------- @@ -165,8 +166,7 @@ def is_file(self, path: str | Path, host: str | None = None) -> bool: return False def is_dir(self, path: str | Path, host: str | None = None) -> bool: - """ - Whether a path is a directory. + """Whether a path is a directory. Parameters ---------- @@ -189,8 +189,7 @@ def is_dir(self, path: str | Path, host: str | None = None) -> bool: return False def listdir(self, path: str | Path, host: str | None = None) -> list[Path]: - """ - Get the directory listing. + """Get the directory listing. Parameters ---------- @@ -257,6 +256,30 @@ def copy( "Copying between two different remote hosts is not supported." ) + def link( + self, + src_filename: str | Path, + dest_filename: str | Path, + ) -> None: + """ + Link a file from source to destination. + + Parameters + ---------- + src_filename : str or Path + Full path to source file. + dest_filename : str or Path + Full path to destination file. + """ + try: + os.symlink(src_filename, dest_filename) + except OSError as exc: + if exc.errno == errno.EEXIST: + os.remove(dest_filename) + os.symlink(src_filename, dest_filename) + else: + raise + def remove(self, path: str | Path, host: str | None = None) -> None: """ Remove a file (does not work on directories). @@ -300,8 +323,7 @@ def rename( self.get_sftp(host).rename(old_path, new_path) def abspath(self, path: str | Path, host: str | None = None) -> Path: - """ - Get the absolute path. + """Get the absolute path. Parameters ---------- @@ -400,15 +422,16 @@ def gzip( ) if host is None: - with open(path, "rb") as f_in, GzipFile( - path_gz, "wb", compresslevel=compresslevel - ) as f_out: + with ( + open(path, "rb") as f_in, + GzipFile(path_gz, "wb", compresslevel=compresslevel) as f_out, + ): shutil.copyfileobj(f_in, f_out) shutil.copystat(path, path_gz) path.unlink() else: ssh = self.get_ssh(host) - _, stdout, _ = ssh.exec_command(f"gzip -f {path!s}") + _, _stdout, _ = ssh.exec_command(f"gzip -f {path!s}") def gunzip( self, @@ -462,7 +485,7 @@ def gunzip( path.unlink() else: ssh = self.get_ssh(host) - _, stdout, _ = ssh.exec_command(f"gunzip -f {path!s}") + _stdin, _stdout, _stderr = ssh.exec_command(f"gunzip -f {path!s}") def close(self) -> None: """Close all connections.""" @@ -471,11 +494,16 @@ def close(self) -> None: connection["sftp"].close() self.connections = {} - def __enter__(self): + def __enter__(self) -> FileClient: # noqa: PYI034 """Support for "with" context.""" return self - def __exit__(self, exc_type, exc_val, exc_tb) -> None: + def __exit__( + self, + exc_type: type[BaseException] | None, + exc_val: BaseException | None, + exc_tb: TracebackType | None, + ) -> None: """Support for "with" context.""" self.close() @@ -518,9 +546,9 @@ def get_ssh_connection( ssh_config = paramiko.SSHConfig().from_path(str(config_filename)) host_config = ssh_config.lookup(hostname) # type: ignore[attr-defined] - for k in ("hostname", "user", "port"): - if k in host_config: - config[k.replace("user", "username")] = host_config[k] + for key in ("hostname", "user", "port"): + if key in host_config: + config[key.replace("user", "username")] = host_config[key] if "proxycommand" in host_config: config["sock"] = paramiko.ProxyCommand(host_config["proxycommand"]) @@ -531,7 +559,7 @@ def get_ssh_connection( return client -def auto_fileclient(method: Callable | None = None): +def auto_fileclient(method: Callable | None = None) -> Callable: """ Automatically pass a FileClient to the function if not already present in kwargs. @@ -547,9 +575,9 @@ def auto_fileclient(method: Callable | None = None): by the decorator. """ - def decorator(func): + def decorator(func: Callable) -> Callable: @wraps(func) - def gen_fileclient(*args, **kwargs): + def gen_file_client(*args, **kwargs) -> Any: file_client = kwargs.get("file_client") if file_client is None: with FileClient() as file_client: @@ -558,7 +586,7 @@ def gen_fileclient(*args, **kwargs): else: return func(*args, **kwargs) - return gen_fileclient + return gen_file_client # See if we're being called as @auto_fileclient or @auto_fileclient(). if method is None: diff --git a/src/atomate2/vasp/builders/elastic.py b/src/atomate2/vasp/builders/elastic.py index ae1b38ff81..2e9eae92c7 100644 --- a/src/atomate2/vasp/builders/elastic.py +++ b/src/atomate2/vasp/builders/elastic.py @@ -63,7 +63,7 @@ def __init__( ) -> None: self.tasks = tasks self.elasticity = elasticity - self.query = query if query else {} + self.query = query or {} self.kwargs = kwargs self.symprec = symprec self.fitting_method = fitting_method @@ -79,8 +79,7 @@ def ensure_indexes(self) -> None: self.elasticity.ensure_index("last_updated") def get_items(self) -> Generator: - """ - Get all items to process into elastic documents. + """Get all items to process into elastic documents. Yields ------ diff --git a/src/atomate2/vasp/drones.py b/src/atomate2/vasp/drones.py index 27bcd649bf..f0124d5333 100644 --- a/src/atomate2/vasp/drones.py +++ b/src/atomate2/vasp/drones.py @@ -39,21 +39,21 @@ def assimilate(self, path: str | Path | None = None) -> TaskDoc: TaskDoc A VASP task document. """ - if path is None: - path = Path.cwd() + path = path or Path.cwd() try: doc = TaskDoc.from_directory(path, **self.task_document_kwargs) except Exception: import traceback - logger.error(f"Error in {Path(path).absolute()}\n{traceback.format_exc()}") + logger.exception( + f"Error in {Path(path).absolute()}\n{traceback.format_exc()}" + ) raise return doc def get_valid_paths(self, path: tuple[str, list[str], list[str]]) -> list[str]: - """ - Get valid paths to assimilate. + """Get valid paths to assimilate. There are some restrictions on the valid directory structures: diff --git a/src/atomate2/vasp/files.py b/src/atomate2/vasp/files.py index 70f710b909..2cc2374d35 100644 --- a/src/atomate2/vasp/files.py +++ b/src/atomate2/vasp/files.py @@ -37,7 +37,7 @@ def copy_vasp_outputs( For folders containing multiple calculations (e.g., suffixed with relax1, relax2, etc), this function will only copy the files with the highest numbered suffix and - the suffix will be removed. Additional vasp files will be also be copied with the + the suffix will be removed. Additional vasp files will be also be copied with the same suffix applied. Lastly, this function will gunzip any gzipped files. Parameters @@ -77,7 +77,7 @@ def copy_vasp_outputs( # find optional files; do not fail if KPOINTS is missing, this might be KSPACING # note: POTCAR files never have the relax extension, whereas KPOINTS files should optional_files = [] - for file in ["POTCAR", "POTCAR.spec", "KPOINTS" + relax_ext]: + for file in ("POTCAR", "POTCAR.spec", "KPOINTS" + relax_ext): found_file = get_zfile(directory_listing, file, allow_missing=True) if found_file is not None: optional_files.append(found_file) @@ -104,8 +104,10 @@ def copy_vasp_outputs( if relax_ext: all_files = optional_files + required_files files_to_rename = { - k.name.replace(".gz", ""): k.name.replace(relax_ext, "").replace(".gz", "") - for k in all_files + file.name.replace(".gz", ""): file.name.replace(relax_ext, "").replace( + ".gz", "" + ) + for file in all_files } rename_files(files_to_rename, allow_missing=True, file_client=file_client) @@ -148,7 +150,7 @@ def get_largest_relax_extension( return "" numbers = [re.search(r".relax(\d+)", file.name).group(1) for file in relax_files] - max_relax = max(numbers, key=lambda x: int(x)) + max_relax = max(numbers, key=int) return f".relax{max_relax}" diff --git a/src/atomate2/vasp/flows/amset.py b/src/atomate2/vasp/flows/amset.py index 30a21864cb..fd1c140a22 100644 --- a/src/atomate2/vasp/flows/amset.py +++ b/src/atomate2/vasp/flows/amset.py @@ -86,26 +86,23 @@ class DeformationPotentialMaker(Maker): def make( self, structure: Structure, - prev_vasp_dir: str | Path | None = None, + prev_dir: str | Path | None = None, ibands: tuple[list[int], list[int]] = None, ) -> Flow: - """ - Make flow to calculate acoustic deformation potentials. + """Make flow to calculate acoustic deformation potentials. Parameters ---------- structure : .Structure A pymatgen structure. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous vasp calculation directory to use for copying outputs. ibands : tuple of list of int Which bands to include in the deformation.h5 file. Given as a tuple of one or two lists (one for each spin channel). The bands indices are zero indexed. """ - bulk = self.static_deformation_maker.make( - structure, prev_vasp_dir=prev_vasp_dir - ) + bulk = self.static_deformation_maker.make(structure, prev_dir=prev_dir) bulk.append_name("bulk ", prepend=True) # all deformation calculations need to be on the same k-point mesh, to achieve @@ -118,7 +115,7 @@ def make( vasp_deformation_calcs = run_amset_deformations( bulk.output.structure, symprec=self.symprec, - prev_vasp_dir=bulk.output.dir_name, + prev_dir=bulk.output.dir_name, static_deformation_maker=self.static_deformation_maker, ) @@ -156,7 +153,7 @@ class VaspAmsetMaker(Maker): temperatures : tuple of float Temperatures at which to calculate transport properties. use_hse_gap : bool - Whether to perform a HSE06 calculation to calculate the band gap for use in + Whether to perform an HSE06 calculation to calculate the band gap for use in AMSET. This can impact the results for small band gap materials. relax_maker : .BaseVaspMaker A maker to perform a tight relaxation on the bulk. Set to ``None`` to skip the @@ -205,32 +202,31 @@ class VaspAmsetMaker(Maker): def make( self, structure: Structure, - prev_vasp_dir: str | Path | None = None, + prev_dir: str | Path | None = None, ) -> Flow: - """ - Make flow to calculate electronic transport properties using AMSET and VASP. + """Make flow to calculate electronic transport properties using AMSET and VASP. Parameters ---------- structure : .Structure A pymatgen structure. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous vasp calculation directory to use for copying outputs. """ jobs = [] if self.relax_maker is not None: # optionally relax the structure - bulk = self.relax_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + bulk = self.relax_maker.make(structure, prev_dir=prev_dir) jobs.append(bulk) structure = bulk.output.structure - prev_vasp_dir = bulk.output.dir_name + prev_dir = bulk.output.dir_name - static = self.static_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + static = self.static_maker.make(structure, prev_dir=prev_dir) # dense band structure for eigenvalues and wave functions dense_bs = self.dense_uniform_maker.make( - static.output.structure, prev_vasp_dir=static.output.dir_name + static.output.structure, prev_dir=static.output.dir_name ) # elastic constant @@ -242,7 +238,7 @@ def make( # dielectric constant dielectric = self.dielectric_maker.make( - static.output.structure, prev_vasp_dir=static.output.dir_name + static.output.structure, prev_dir=static.output.dir_name ) # polar phonon frequency @@ -259,7 +255,7 @@ def make( # deformation potentials deformation = self.deformation_potential_maker.make( static.output.structure, - prev_vasp_dir=static.output.dir_name, + prev_dir=static.output.dir_name, ibands=wavefunction.output["ibands"], ) @@ -303,7 +299,7 @@ def make( if self.use_hse_gap and "bandgap" not in self.amset_settings: gap = self.hse_gap_maker.make( dense_bs.output.structure, - prev_vasp_dir=dense_bs.output.dir_name, + prev_dir=dense_bs.output.dir_name, mode="gap", ) settings["bandgap"] = gap.output.output.bandgap @@ -387,32 +383,31 @@ class HSEVaspAmsetMaker(Maker): def make( self, structure: Structure, - prev_vasp_dir: str | Path | None = None, + prev_dir: str | Path | None = None, ) -> Flow: - """ - Make flow to calculate electronic transport properties using AMSET and VASP. + """Make flow to calculate electronic transport properties using AMSET and VASP. Parameters ---------- structure : Structure A pymatgen structure. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous vasp calculation directory to use for copying outputs. """ jobs = [] if self.relax_maker is not None: # optionally relax the structure - bulk = self.relax_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + bulk = self.relax_maker.make(structure, prev_dir=prev_dir) jobs.append(bulk) structure = bulk.output.structure - prev_vasp_dir = bulk.output.dir_name + prev_dir = bulk.output.dir_name - static = self.static_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + static = self.static_maker.make(structure, prev_dir=prev_dir) # dense band structure for eigenvalues and wave functions dense_bs = self.dense_uniform_maker.make( - static.output.structure, prev_vasp_dir=static.output.dir_name + static.output.structure, prev_dir=static.output.dir_name ) # elastic constant @@ -424,7 +419,7 @@ def make( # dielectric constant dielectric = self.dielectric_maker.make( - static.output.structure, prev_vasp_dir=static.output.dir_name + static.output.structure, prev_dir=static.output.dir_name ) # polar phonon frequency @@ -441,7 +436,7 @@ def make( # deformation potentials deformation = self.deformation_potential_maker.make( static.output.structure, - prev_vasp_dir=static.output.dir_name, + prev_dir=static.output.dir_name, ibands=wavefunction.output["ibands"], ) diff --git a/src/atomate2/vasp/flows/core.py b/src/atomate2/vasp/flows/core.py index 7c6b02dc1e..aa25490f6e 100644 --- a/src/atomate2/vasp/flows/core.py +++ b/src/atomate2/vasp/flows/core.py @@ -23,6 +23,7 @@ from jobflow import Job from pymatgen.core.structure import Structure + from typing_extensions import Self from atomate2.vasp.jobs.base import BaseVaspMaker @@ -46,17 +47,14 @@ class DoubleRelaxMaker(Maker): relax_maker1: BaseVaspMaker | None = field(default_factory=RelaxMaker) relax_maker2: BaseVaspMaker = field(default_factory=RelaxMaker) - def make( - self, structure: Structure, prev_vasp_dir: str | Path | None = None - ) -> Flow: - """ - Create a flow with two chained relaxations. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Create a flow with two chained relaxations. Parameters ---------- structure : .Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns @@ -67,20 +65,20 @@ def make( jobs: list[Job] = [] if self.relax_maker1: # Run a pre-relaxation - relax1 = self.relax_maker1.make(structure, prev_vasp_dir=prev_vasp_dir) + relax1 = self.relax_maker1.make(structure, prev_dir=prev_dir) relax1.name += " 1" jobs += [relax1] structure = relax1.output.structure - prev_vasp_dir = relax1.output.dir_name + prev_dir = relax1.output.dir_name - relax2 = self.relax_maker2.make(structure, prev_vasp_dir=prev_vasp_dir) + relax2 = self.relax_maker2.make(structure, prev_dir=prev_dir) relax2.name += " 2" jobs += [relax2] return Flow(jobs, output=relax2.output, name=self.name) @classmethod - def from_relax_maker(cls, relax_maker: BaseVaspMaker) -> DoubleRelaxMaker: + def from_relax_maker(cls, relax_maker: BaseVaspMaker) -> Self: """ Instantiate the DoubleRelaxMaker with two relax makers of the same type. @@ -119,17 +117,14 @@ class BandStructureMaker(Maker): static_maker: BaseVaspMaker = field(default_factory=StaticMaker) bs_maker: BaseVaspMaker = field(default_factory=NonSCFMaker) - def make( - self, structure: Structure, prev_vasp_dir: str | Path | None = None - ) -> Flow: - """ - Create a band structure flow. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Create a band structure flow. Parameters ---------- structure : Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns @@ -137,7 +132,7 @@ def make( Flow A band structure flow. """ - static_job = self.static_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + static_job = self.static_maker.make(structure, prev_dir=prev_dir) jobs = [static_job] outputs = {} @@ -145,7 +140,7 @@ def make( if bandstructure_type in ("both", "uniform"): uniform_job = self.bs_maker.make( static_job.output.structure, - prev_vasp_dir=static_job.output.dir_name, + prev_dir=static_job.output.dir_name, mode="uniform", ) uniform_job.name += " uniform" @@ -159,7 +154,7 @@ def make( if bandstructure_type in ("both", "line"): line_job = self.bs_maker.make( static_job.output.structure, - prev_vasp_dir=static_job.output.dir_name, + prev_dir=static_job.output.dir_name, mode="line", ) line_job.name += " line" @@ -198,17 +193,14 @@ class UniformBandStructureMaker(Maker): static_maker: BaseVaspMaker = field(default_factory=StaticMaker) bs_maker: BaseVaspMaker = field(default_factory=NonSCFMaker) - def make( - self, structure: Structure, prev_vasp_dir: str | Path | None = None - ) -> Flow: - """ - Create a uniform band structure flow. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Create a uniform band structure flow. Parameters ---------- structure : Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns @@ -216,10 +208,10 @@ def make( Flow A uniform band structure flow. """ - static_job = self.static_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + static_job = self.static_maker.make(structure, prev_dir=prev_dir) uniform_job = self.bs_maker.make( static_job.output.structure, - prev_vasp_dir=static_job.output.dir_name, + prev_dir=static_job.output.dir_name, mode="uniform", ) uniform_job.name += " uniform" @@ -249,17 +241,14 @@ class LineModeBandStructureMaker(Maker): static_maker: BaseVaspMaker = field(default_factory=StaticMaker) bs_maker: BaseVaspMaker = field(default_factory=NonSCFMaker) - def make( - self, structure: Structure, prev_vasp_dir: str | Path | None = None - ) -> Flow: - """ - Create a line mode band structure flow. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Create a line mode band structure flow. Parameters ---------- structure : Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns @@ -267,10 +256,10 @@ def make( Flow A line mode band structure flow. """ - static_job = self.static_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + static_job = self.static_maker.make(structure, prev_dir=prev_dir) line_job = self.bs_maker.make( static_job.output.structure, - prev_vasp_dir=static_job.output.dir_name, + prev_dir=static_job.output.dir_name, mode="line", ) line_job.name += " line" @@ -283,7 +272,7 @@ class HSEBandStructureMaker(BandStructureMaker): """ Maker to generate VASP HSE band structures. - This is a HSE06 static calculation followed by one HSE06 uniform calculation and + This is an HSE06 static calculation followed by one HSE06 uniform calculation and one HSE06 line mode calculation. Parameters @@ -309,7 +298,7 @@ class HSEUniformBandStructureMaker(UniformBandStructureMaker): """ Maker to generate VASP HSE uniform band structures. - This is a HSE06 static calculation followed by a HSE06 uniform calculation. + This is an HSE06 static calculation followed by an HSE06 uniform calculation. Parameters ---------- @@ -331,7 +320,7 @@ class HSELineModeBandStructureMaker(LineModeBandStructureMaker): """ Maker to generate VASP HSE line mode band structures. - This is a HSE06 static calculation followed by a HSE06 line mode calculation. + This is an HSE06 static calculation followed by an HSE06 line mode calculation. Parameters ---------- @@ -369,17 +358,14 @@ class RelaxBandStructureMaker(Maker): relax_maker: BaseVaspMaker = field(default_factory=DoubleRelaxMaker) band_structure_maker: BaseVaspMaker = field(default_factory=BandStructureMaker) - def make( - self, structure: Structure, prev_vasp_dir: str | Path | None = None - ) -> Flow: - """ - Run a relaxation and then calculate the uniform and line mode band structures. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Run a relaxation, then calculate the uniform and line mode band structures. Parameters ---------- structure: .Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns @@ -387,9 +373,9 @@ def make( Flow A relax and band structure flow. """ - relax_job = self.relax_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + relax_job = self.relax_maker.make(structure, prev_dir=prev_dir) bs_flow = self.band_structure_maker.make( - relax_job.output.structure, prev_vasp_dir=relax_job.output.dir_name + relax_job.output.structure, prev_dir=relax_job.output.dir_name ) return Flow([relax_job, bs_flow], bs_flow.output, name=self.name) @@ -429,17 +415,14 @@ class OpticsMaker(Maker): ) ) - def make( - self, structure: Structure, prev_vasp_dir: str | Path | None = None - ) -> Flow: - """ - Run a static and then a non-scf optics calculation. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Run a static and then a non-scf optics calculation. Parameters ---------- structure: .Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns @@ -447,9 +430,9 @@ def make( Flow A static and nscf with optics flow. """ - static_job = self.static_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + static_job = self.static_maker.make(structure, prev_dir=prev_dir) nscf_job = self.band_structure_maker.make( - static_job.output.structure, prev_vasp_dir=static_job.output.dir_name + static_job.output.structure, prev_dir=static_job.output.dir_name ) return Flow([static_job, nscf_job], nscf_job.output, name=self.name) @@ -488,17 +471,14 @@ class HSEOpticsMaker(Maker): ) ) - def make( - self, structure: Structure, prev_vasp_dir: str | Path | None = None - ) -> Flow: - """ - Run a static and then a non-scf optics calculation. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Run a static and then a non-scf optics calculation. Parameters ---------- structure: .Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns @@ -506,8 +486,8 @@ def make( Flow A static and nscf with optics flow. """ - static_job = self.static_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + static_job = self.static_maker.make(structure, prev_dir=prev_dir) bs_job = self.band_structure_maker.make( - static_job.output.structure, prev_vasp_dir=static_job.output.dir_name + static_job.output.structure, prev_dir=static_job.output.dir_name ) return Flow([static_job, bs_job], bs_job.output, name=self.name) diff --git a/src/atomate2/vasp/flows/defect.py b/src/atomate2/vasp/flows/defect.py index e60918dc2e..55c58afb7c 100644 --- a/src/atomate2/vasp/flows/defect.py +++ b/src/atomate2/vasp/flows/defect.py @@ -4,16 +4,13 @@ import logging from dataclasses import dataclass, field -from pathlib import Path from typing import TYPE_CHECKING +from emmet.core.tasks import TaskDoc from jobflow import Flow, Maker, OutputReference from jobflow.core.maker import recursive_call -from pymatgen.io.vasp.outputs import Vasprun -from atomate2.common.files import get_zfile from atomate2.common.flows import defect as defect_flows -from atomate2.utils.file_client import FileClient from atomate2.vasp.flows.core import DoubleRelaxMaker from atomate2.vasp.jobs.core import RelaxMaker, StaticMaker from atomate2.vasp.jobs.defect import calculate_finite_diff @@ -26,6 +23,7 @@ if TYPE_CHECKING: from pymatgen.core.structure import Structure + from pymatgen.entries.computed_entries import ComputedStructureEntry from atomate2.common.schemas.defects import CCDDocument from atomate2.vasp.jobs.base import BaseVaspMaker @@ -87,7 +85,7 @@ class FormationEnergyMaker(defect_flows.FormationEnergyMaker): A maker to perform a atomic-position-only relaxation on the defect charge states. Since these calculations are expensive and the settings might get messy, it is recommended for each implementation of this maker to check - some of the most important settings in the `relax_maker`. Please see + some of the most important settings in the `relax_maker`. Please see `FormationEnergyMaker.validate_maker` for more details. bulk_relax_maker: Maker @@ -131,7 +129,7 @@ class FormationEnergyMaker(defect_flows.FormationEnergyMaker): .. note:: Once we remove the requirement for explicit bulk supercell calculations, - this setting will be removed. It is only needed because the bulk supercell + this setting will be removed. It is only needed because the bulk supercell locpot is currently needed for the finite-size correction calculation. Output format for the DefectEntry data: @@ -169,7 +167,9 @@ class FormationEnergyMaker(defect_flows.FormationEnergyMaker): bulk_relax_maker: BaseVaspMaker | None = None name: str = "formation energy" - def structure_from_prv(self, previous_dir: str) -> Structure: + def sc_entry_and_locpot_from_prv( + self, previous_dir: str + ) -> tuple[ComputedStructureEntry, dict]: """Copy the output structure from previous directory. Read the vasprun.xml file from the previous directory @@ -182,15 +182,14 @@ def structure_from_prv(self, previous_dir: str) -> Structure: Returns ------- - structure: Structure + ComputedStructureEntry """ - fc = FileClient() - # strip off the `hostname:` prefix - previous_dir = previous_dir.split(":")[-1] - files = fc.listdir(previous_dir) - vasprun_file = Path(previous_dir) / get_zfile(files, "vasprun.xml") - vasprun = Vasprun(vasprun_file) - return vasprun.final_structure + task_doc = TaskDoc.from_directory(previous_dir) + return task_doc.structure_entry, task_doc.calcs_reversed[0].output.locpot + + def get_planar_locpot(self, task_doc: TaskDoc) -> dict: + """Get the planar-averaged electrostatic potential.""" + return task_doc.calcs_reversed[0].output.locpot def validate_maker(self) -> None: """Check some key settings in the relax maker. diff --git a/src/atomate2/vasp/flows/elastic.py b/src/atomate2/vasp/flows/elastic.py index 800e565eb6..a8ffa7ab12 100644 --- a/src/atomate2/vasp/flows/elastic.py +++ b/src/atomate2/vasp/flows/elastic.py @@ -49,6 +49,11 @@ class ElasticMaker(BaseElasticMaker): bulk relaxation. elastic_relax_maker : .BaseVaspMaker Maker used to generate elastic relaxations. + max_failed_deformations: int or float + Maximum number of deformations allowed to fail to proceed with the fitting + of the elastic tensor. If an int the absolute number of deformations. If + a float between 0 an 1 the maximum fraction of deformations. If None any + number of deformations allowed. generate_elastic_deformations_kwargs : dict Keyword arguments passed to :obj:`generate_elastic_deformations`. fit_elastic_tensor_kwargs : dict @@ -65,12 +70,13 @@ class ElasticMaker(BaseElasticMaker): default_factory=lambda: DoubleRelaxMaker.from_relax_maker(TightRelaxMaker()) ) elastic_relax_maker: BaseVaspMaker = field(default_factory=ElasticRelaxMaker) + max_failed_deformations: int | float | None = None generate_elastic_deformations_kwargs: dict = field(default_factory=dict) fit_elastic_tensor_kwargs: dict = field(default_factory=dict) task_document_kwargs: dict = field(default_factory=dict) @property - def prev_calc_dir_argname(self): + def prev_calc_dir_argname(self) -> str: """Name of argument informing static maker of previous calculation directory. As this differs between different DFT codes (e.g., VASP, CP2K), it @@ -79,4 +85,4 @@ def prev_calc_dir_argname(self): Note: this is only applicable if a relax_maker is specified; i.e., two calculations are performed for each ordering (relax -> static) """ - return "prev_vasp_dir" + return "prev_dir" diff --git a/src/atomate2/vasp/flows/electrode.py b/src/atomate2/vasp/flows/electrode.py new file mode 100644 index 0000000000..b416a02722 --- /dev/null +++ b/src/atomate2/vasp/flows/electrode.py @@ -0,0 +1,83 @@ +"""Flow for electrode analysis with specific VASP implementations.""" + +from __future__ import annotations + +import logging +from pathlib import Path +from typing import TYPE_CHECKING + +from pymatgen.io.vasp.outputs import Chgcar + +from atomate2.common.flows import electrode as electrode_flows +from atomate2.utils.path import strip_hostname + +if TYPE_CHECKING: + from pymatgen.io.vasp.outputs import VolumetricData + +logger = logging.getLogger(__name__) + + +class ElectrodeInsertionMaker(electrode_flows.ElectrodeInsertionMaker): + """Attempt ion insertion into a structure. + + The basic unit for cation insertion is: + [get_stable_inserted_structure]: + (static) -> (chgcar analysis) -> + N x (relax) -> (return best structure) + + The workflow is: + [relax structure] + [get_stable_inserted_structure] + [get_stable_inserted_structure] + [get_stable_inserted_structure] + ... until the insertion is no longer topotactic. + + If you use this workflow please cite the following paper: + Shen, J.-X., Horton, M., & Persson, K. A. (2020). + A charge-density-based general cation insertion algorithm for + generating new Li-ion cathode materials. + npj Computational Materials, 6(161), 1โ€”7. + doi: 10.1038/s41524-020-00422-3 + + + Attributes + ---------- + name: str + The name of the flow created by this maker. + relax_maker: RelaxMaker + A maker to perform relaxation calculations. + bulk_relax_maker: Maker + A separate maker to perform the first bulk relaxation calculation. + If None, the relax_maker will be used. + static_maker: Maker + A maker to perform static calculations. + structure_matcher: StructureMatcher + The structure matcher to use to determine if additional insertion is needed. + """ + + def get_charge_density(self, prev_dir: Path | str) -> VolumetricData: + """Get the charge density of a structure. + + Parameters + ---------- + prev_dir: + The previous directory where the static calculation was performed. + + Returns + ------- + The charge density. + """ + prev_dir = Path(strip_hostname(prev_dir)) + aeccar0 = Chgcar.from_file(prev_dir / "AECCAR0.gz") + aeccar2 = Chgcar.from_file(prev_dir / "AECCAR2.gz") + return aeccar0 + aeccar2 + + def update_static_maker(self) -> None: + """Ensure that the static maker will store the desired data.""" + store_volumetric_data = list( + self.static_maker.task_document_kwargs.get("store_volumetric_data", []) + ) + store_volumetric_data.extend(["aeccar0", "aeccar2"]) + self.static_maker.task_document_kwargs["store_volumetric_data"] = ( + store_volumetric_data + ) diff --git a/src/atomate2/vasp/flows/elph.py b/src/atomate2/vasp/flows/elph.py index 977b89184b..6f553984f1 100644 --- a/src/atomate2/vasp/flows/elph.py +++ b/src/atomate2/vasp/flows/elph.py @@ -123,17 +123,14 @@ class ElectronPhononMaker(Maker): ) ) - def make( - self, structure: Structure, prev_vasp_dir: str | Path | None = None - ) -> Flow: - """ - Create a electron-phonon coupling workflow. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Create a electron-phonon coupling workflow. Parameters ---------- structure: .Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns @@ -145,27 +142,25 @@ def make( if self.relax_maker is not None: # optionally relax the structure - relax = self.relax_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + relax = self.relax_maker.make(structure, prev_dir=prev_dir) jobs.append(relax) structure = relax.output.structure - prev_vasp_dir = relax.output.dir_name + prev_dir = relax.output.dir_name - static = self.static_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + static = self.static_maker.make(structure, prev_dir=prev_dir) # update temperatures and supercell size for elph maker but make sure to not # overwrite original maker elph_maker = deepcopy(self.elph_displacement_maker) elph_maker.temperatures = self.temperatures elph_maker.min_supercell_length = self.min_supercell_length - elph = elph_maker.make( - static.output.structure, prev_vasp_dir=static.output.dir_name - ) + elph = elph_maker.make(static.output.structure, prev_dir=static.output.dir_name) # use static as prev_dir so we don't inherit elph settings; using a prev # directory is useful as we can turn off magnetism if necessary which gives a # reasonable speedup supercell_dos = self.uniform_maker.make( - elph.output.structure, prev_vasp_dir=static.output.dir_name + elph.output.structure, prev_dir=static.output.dir_name ) supercell_dos.append_name(" bulk supercell") @@ -173,7 +168,7 @@ def make( elph.output.calcs_reversed[0].output.elph_displaced_structures.temperatures, elph.output.calcs_reversed[0].output.elph_displaced_structures.structures, self.uniform_maker, - prev_vasp_dir=static.output.dir_name, + prev_dir=static.output.dir_name, original_structure=static.output.structure, supercell_structure=elph.output.structure, ) diff --git a/src/atomate2/vasp/flows/eos.py b/src/atomate2/vasp/flows/eos.py new file mode 100644 index 0000000000..269412b2eb --- /dev/null +++ b/src/atomate2/vasp/flows/eos.py @@ -0,0 +1,323 @@ +""" +Module defining equation of state workflows. + +Modeled on the atomate bulk_modulus workflows. + +Prefixes are also defined in atomate2.sets.eos and atomate2.jobs.eos: +- No prefix (EosDoubleRelaxMaker and EosMaker): atomate2 default parameters +- MPLegacy: legacy MP PBE-GGA-compatible parameters (very high k-point density) +- MPGGA: MP PBE-GGA compatible parameters +- MPMetaGGA: MP r2SCAN-meta-GGA compatible parameters +""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +from atomate2.common.flows.eos import CommonEosMaker +from atomate2.vasp.flows.core import DoubleRelaxMaker +from atomate2.vasp.jobs.eos import ( + EosRelaxMaker, + MPGGAEosRelaxMaker, + MPGGAEosStaticMaker, + MPLegacyEosRelaxMaker, + MPLegacyEosStaticMaker, + MPMetaGGAEosPreRelaxMaker, + MPMetaGGAEosRelaxMaker, + MPMetaGGAEosStaticMaker, +) +from atomate2.vasp.sets.eos import ( + EosSetGenerator, + MPGGAEosRelaxSetGenerator, + MPLegacyEosRelaxSetGenerator, + MPMetaGGAEosRelaxSetGenerator, +) + +if TYPE_CHECKING: + from jobflow import Maker + + from atomate2.vasp.jobs.base import BaseVaspMaker + +# No prefix, atomate2 base parameters + + +@dataclass +class EosDoubleRelaxMaker(DoubleRelaxMaker): + """ + Workflow to generate initial double relaxation for EOS fitting. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + relax_maker1 : .BaseVaspMaker + Maker to use to generate the first relaxation. + relax_maker2 : .BaseVaspMaker + Maker to use to generate the second relaxation. + + NB: WAVECARs are copied over to speed up calculation + """ + + name: str = "EOS double relax" + relax_maker1: BaseVaspMaker | None = field(default_factory=EosRelaxMaker) + relax_maker2: BaseVaspMaker = field(default_factory=EosRelaxMaker) + + +@dataclass +class EosMaker(CommonEosMaker): + """ + Generate equation of state data with default atomate2 parameters. + + First relax a structure using relax_maker. + Then perform a series of deformations on the relaxed structure, and + evaluate single-point energies with static_maker. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + initial_relax_maker : .Maker | None + Maker to relax the input structure, defaults to None (no initial relaxation). + eos_relax_maker : .Maker + Maker to relax deformationed structures for the EOS fit. + static_maker : .Maker | None + Maker to generate statics after each relaxation, defaults to None. + strain : tuple[float] + Percentage linear strain to apply as a deformation, default = -5% to 5%. + number_of_frames : int + Number of strain calculations to do for EOS fit, default = 6. + postprocessor : .atomate2.common.jobs.EOSPostProcessor + Optional postprocessing step, defaults to + `atomate2.common.jobs.PostProcessEosEnergy`. + _store_transformation_information : .bool = False + Whether to store the information about transformations. Unfortunately + needed at present to handle issues with emmet and pydantic validation + TODO: remove this when clash is fixed + """ + + name: str = "EOS Maker" + initial_relax_maker: Maker = field(default_factory=EosDoubleRelaxMaker) + eos_relax_maker: Maker | None = field( + default_factory=lambda: EosRelaxMaker( + input_set_generator=EosSetGenerator( + user_incar_settings={"ISIF": 2}, + ) + ) + ) + + +# MPLegacy prefix: legacy MP PBE-GGA + + +@dataclass +class MPLegacyEosDoubleRelaxMaker(DoubleRelaxMaker): + """ + Workflow to generate initial MP legacy PBE-GGA double relaxation. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + relax_maker1 : .BaseVaspMaker + Maker to use to generate the first relaxation. + relax_maker2 : .BaseVaspMaker + Maker to use to generate the second relaxation. + + NB: WAVECARs are copied over to speed up calculation + """ + + name: str = "MP Legacy EOS double relax" + relax_maker1: BaseVaspMaker | None = field(default_factory=MPLegacyEosRelaxMaker) + relax_maker2: BaseVaspMaker = field(default_factory=MPLegacyEosRelaxMaker) + + +@dataclass +class MPLegacyEosMaker(CommonEosMaker): + """ + Generate equation of state data with MP legacy PBE-GGA parameters. + + First relax a structure using relax_maker. + Then perform a series of deformations on the relaxed structure, and + evaluate single-point energies with static_maker. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + initial_relax_maker : .Maker | None + Maker to relax the input structure, defaults to None (no initial relaxation). + eos_relax_maker : .Maker + Maker to relax deformationed structures for the EOS fit. + static_maker : .Maker | None + Maker to generate statics after each relaxation, defaults to None. + strain : tuple[float] + Percentage linear strain to apply as a deformation, default = -5% to 5%. + number_of_frames : int + Number of strain calculations to do for EOS fit, default = 6. + postprocessor : .atomate2.common.jobs.EOSPostProcessor + Optional postprocessing step, defaults to + `atomate2.common.jobs.PostProcessEosEnergy`. + _store_transformation_information : .bool = False + Whether to store the information about transformations. Unfortunately + needed at present to handle issues with emmet and pydantic validation + TODO: remove this when clash is fixed + """ + + name: str = "MP Legacy GGA EOS Maker" + initial_relax_maker: Maker | None = field( + default_factory=MPLegacyEosDoubleRelaxMaker + ) + eos_relax_maker: Maker | None = field( + default_factory=lambda: MPLegacyEosRelaxMaker( + input_set_generator=MPLegacyEosRelaxSetGenerator( + user_incar_settings={"ISIF": 2}, + ) + ) + ) + static_maker: Maker | None = field(default_factory=MPLegacyEosStaticMaker) + + +# MPGGA prefix: MP PBE-GGA compatible + + +@dataclass +class MPGGAEosDoubleRelaxMaker(DoubleRelaxMaker): + """ + Workflow to generate initial MP PBE-GGA double relaxation for EOS fitting. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + relax_maker1 : .BaseVaspMaker + Maker to use to generate the first relaxation. + relax_maker2 : .BaseVaspMaker + Maker to use to generate the second relaxation. + + NB: WAVECARs are copied over to speed up calculation + """ + + name: str = "MP GGA EOS double relax" + relax_maker1: BaseVaspMaker | None = field( + default_factory=lambda: MPGGAEosRelaxMaker( + input_set_generator=MPGGAEosRelaxSetGenerator( + user_incar_settings={"EDIFFG": -0.05} + ) + ) + ) + relax_maker2: BaseVaspMaker = field(default_factory=MPGGAEosRelaxMaker) + + +@dataclass +class MPGGAEosMaker(CommonEosMaker): + """ + Generate equation of state data with MP PBE-GGA parameters. + + First relax a structure using relax_maker. + Then perform a series of deformations on the relaxed structure, and + evaluate single-point energies with static_maker. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + initial_relax_maker : .Maker | None + Maker to relax the input structure, defaults to None (no initial relaxation). + eos_relax_maker : .Maker + Maker to relax deformationed structures for the EOS fit. + static_maker : .Maker | None + Maker to generate statics after each relaxation, defaults to None. + strain : tuple[float] + Percentage linear strain to apply as a deformation, default = -5% to 5%. + number_of_frames : int + Number of strain calculations to do for EOS fit, default = 6. + postprocessor : .atomate2.common.jobs.EOSPostProcessor + Optional postprocessing step, defaults to + `atomate2.common.jobs.PostProcessEosEnergy`. + _store_transformation_information : .bool = False + Whether to store the information about transformations. Unfortunately + needed at present to handle issues with emmet and pydantic validation + TODO: remove this when clash is fixed + """ + + name: str = "MP GGA EOS Maker" + initial_relax_maker: Maker | None = field(default_factory=MPGGAEosDoubleRelaxMaker) + eos_relax_maker: Maker | None = field( + default_factory=lambda: MPGGAEosRelaxMaker( + input_set_generator=MPGGAEosRelaxSetGenerator( + user_incar_settings={"ISIF": 2} + ) + ) + ) + static_maker: Maker | None = field(default_factory=MPGGAEosStaticMaker) + + +@dataclass +class MPMetaGGAEosDoubleRelaxMaker(DoubleRelaxMaker): + """ + Workflow to generate initial MP r2SCAN Meta-GGA double relaxation for EOS fitting. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + relax_maker1 : .BaseVaspMaker + Maker to use to generate the first relaxation. + relax_maker2 : .BaseVaspMaker + Maker to use to generate the second relaxation. + + NB: WAVECARs are copied over to speed up calculation + """ + + name: str = "MP Meta-GGA EOS double relax" + relax_maker1: BaseVaspMaker | None = field( + default_factory=MPMetaGGAEosPreRelaxMaker + ) + relax_maker2: BaseVaspMaker = field(default_factory=MPMetaGGAEosRelaxMaker) + + +@dataclass +class MPMetaGGAEosMaker(CommonEosMaker): + """ + Generate equation of state data with MP r2SCAN-meta-GGA parameters. + + First relax a structure using relax_maker. + Then perform a series of deformations on the relaxed structure, and + evaluate single-point energies with static_maker. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + initial_relax_maker : .Maker | None + Maker to relax the input structure, defaults to None (no initial relaxation). + eos_relax_maker : .Maker + Maker to relax deformationed structures for the EOS fit. + static_maker : .Maker | None + Maker to generate statics after each relaxation, defaults to None. + strain : tuple[float] + Percentage linear strain to apply as a deformation, default = -5% to 5%. + number_of_frames : int + Number of strain calculations to do for EOS fit, default = 6. + postprocessor : .atomate2.common.jobs.EOSPostProcessor + Optional postprocessing step, defaults to + `atomate2.common.jobs.PostProcessEosEnergy`. + _store_transformation_information : .bool = False + Whether to store the information about transformations. Unfortunately + needed at present to handle issues with emmet and pydantic validation + TODO: remove this when clash is fixed + """ + + name: str = "MP Meta-GGA EOS Maker" + initial_relax_maker: Maker | None = field( + default_factory=MPMetaGGAEosDoubleRelaxMaker + ) + eos_relax_maker: Maker | None = field( + default_factory=lambda: MPMetaGGAEosRelaxMaker( + input_set_generator=MPMetaGGAEosRelaxSetGenerator( + user_incar_settings={"ISIF": 2} + ) + ) + ) + static_maker: Maker | None = field(default_factory=MPMetaGGAEosStaticMaker) diff --git a/src/atomate2/vasp/flows/lobster.py b/src/atomate2/vasp/flows/lobster.py index 71a16452f9..6498f2e1df 100644 --- a/src/atomate2/vasp/flows/lobster.py +++ b/src/atomate2/vasp/flows/lobster.py @@ -6,6 +6,7 @@ from typing import TYPE_CHECKING from jobflow import Flow, Maker +from monty.dev import requires from atomate2.lobster.jobs import LobsterMaker from atomate2.vasp.flows.core import DoubleRelaxMaker, UniformBandStructureMaker @@ -18,6 +19,15 @@ ) from atomate2.vasp.sets.core import NonSCFSetGenerator, StaticSetGenerator +try: + import ijson + from lobsterpy.cohp.analyze import Analysis + from lobsterpy.cohp.describe import Description +except ImportError: + ijson = None + Analysis = None + Description = None + if TYPE_CHECKING: from pathlib import Path @@ -96,18 +106,22 @@ class VaspLobsterMaker(Maker): lobster_static_maker: BaseVaspMaker = field( default_factory=lambda: LOBSTER_UNIFORM_MAKER ) - lobster_maker: LobsterMaker | None = field(default_factory=lambda: LobsterMaker()) + lobster_maker: LobsterMaker | None = field(default_factory=LobsterMaker) delete_wavecars: bool = True address_min_basis: str | None = None address_max_basis: str | None = None + @requires( + Analysis, + "This flow requires lobsterpy and ijson to function properly. " + "Please reinstall atomate2 using atomate2[lobster]", + ) def make( self, structure: Structure, - prev_vasp_dir: str | Path | None = None, + prev_dir: str | Path | None = None, ) -> Flow: - """ - Make flow to calculate bonding properties. + """Make flow to calculate bonding properties. Parameters ---------- @@ -115,7 +129,7 @@ def make( A pymatgen structure. Please start with a structure that is nearly fully optimized as the internal optimizers have very strict settings! - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous vasp calculation directory to use for copying outputs. """ jobs = [] @@ -124,12 +138,12 @@ def make( optimization_dir = None optimization_uuid = None if self.relax_maker is not None: - optimization = self.relax_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + optimization = self.relax_maker.make(structure, prev_dir=prev_dir) jobs.append(optimization) structure = optimization.output.structure optimization_dir = optimization.output.dir_name optimization_uuid = optimization.output.uuid - prev_vasp_dir = optimization_dir + prev_dir = optimization_dir # Information about the basis is collected basis_infos = get_basis_infos( @@ -146,7 +160,7 @@ def make( self.lobster_static_maker, basis_infos.output["nbands"], structure, - prev_vasp_dir, + prev_dir, ) jobs.append(lobster_static) lobster_static_dir = lobster_static.output.dir_name diff --git a/src/atomate2/vasp/flows/matpes.py b/src/atomate2/vasp/flows/matpes.py index fcc747abea..4af71768fe 100644 --- a/src/atomate2/vasp/flows/matpes.py +++ b/src/atomate2/vasp/flows/matpes.py @@ -13,6 +13,7 @@ from jobflow import Flow, Maker from atomate2.vasp.jobs.matpes import MatPesGGAStaticMaker, MatPesMetaGGAStaticMaker +from atomate2.vasp.sets.matpes import MatPesGGAStaticSetGenerator if TYPE_CHECKING: from pathlib import Path @@ -21,7 +22,7 @@ @dataclass -class MatPesGGAPlusMetaGGAStaticMaker(Maker): +class MatPesStaticFlowMaker(Maker): """MatPES flow doing a GGA static followed by meta-GGA static. Uses the GGA WAVECAR to speed up electronic convergence on the meta-GGA static. @@ -34,35 +35,77 @@ class MatPesGGAPlusMetaGGAStaticMaker(Maker): Maker to generate the first VASP static. static2 : .BaseVaspMaker Maker to generate the second VASP static. + static3 : .BaseVaspMaker or None + Maker to generate the optional third VASP static. Defaults to GGA static with + +U corrections if structure contains elements with +U corrections, else to None. """ - name: str = "MatPES GGA plus meta-GGA static" - static1: Maker | None = field(default_factory=MatPesGGAStaticMaker) + name: str = "MatPES static flow" + static1: Maker | None = field( + default_factory=lambda: MatPesGGAStaticMaker( + input_set_generator=MatPesGGAStaticSetGenerator( + # write WAVECAR so we can use as pre-conditioned starting point for + # static2/3 + user_incar_settings={"LWAVE": True} + ), + ) + ) static2: Maker = field( default_factory=lambda: MatPesMetaGGAStaticMaker( - # could copy CHGCAR from GGA to meta-GGA directory too but is redundant - # since VASP can reconstruct it from WAVECAR + # start from pre-conditioned WAVECAR from static1 to speed up convergence + # could copy CHGCAR too but is redundant since VASP can reconstruct it from + # WAVECAR copy_vasp_kwargs={"additional_vasp_files": ("WAVECAR",)} ) ) + # optional 3rd PBE+U static in case structure contains elements with +U corrections + static3: Maker | None = field( + default_factory=lambda: MatPesGGAStaticMaker( + name="MatPES GGA+U static", + input_set_generator=MatPesGGAStaticSetGenerator( + user_incar_settings={"LDAU:": True}, # enable +U corrections + ), + copy_vasp_kwargs={"additional_vasp_files": ("WAVECAR",)}, + ) + ) - def make(self, structure: Structure, prev_vasp_dir: str | Path | None = None): - """ - Create a flow with two chained statics. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Create a flow with MatPES statics. + + By default, a PBE static is followed by an r2SCAN static and optionally a PBE+U + static if the structure contains elements with +U corrections. The PBE static is + run with LWAVE=True so its WAVECAR can be passed as a pre-conditioned starting + point to both the r2SCAN static and the PBE+U static. Parameters ---------- structure : .Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns ------- Flow - A flow containing two statics. + A flow containing 2 or 3 statics. """ - static1 = self.static1.make(structure, prev_vasp_dir=prev_vasp_dir) - static2 = self.static2.make(structure, prev_vasp_dir=static1.output.dir_name) + static1 = self.static1.make(structure, prev_dir=prev_dir) + static2 = self.static2.make(structure, prev_dir=static1.output.dir_name) output = {"static1": static1.output, "static2": static2.output} - return Flow([static1, static2], output=output, name=self.name) + jobs = [static1, static2] + + # only run 3rd static if set generator not None and structure contains at least + # one element with Hubbard +U corrections + if self.static3 is not None: + static3_config = self.static3.input_set_generator.config_dict + u_corrections = static3_config.get("INCAR", {}).get("LDAUU", {}) + elems = set(map(str, structure.elements)) + if self.static3 and any( + anion in elems and elems & {*cations} + for anion, cations in u_corrections.items() + ): + static3 = self.static3.make(structure, prev_dir=static1.output.dir_name) + output["static3"] = static3.output + jobs += [static3] + + return Flow(jobs=jobs, output=output, name=self.name) diff --git a/src/atomate2/vasp/flows/md.py b/src/atomate2/vasp/flows/md.py new file mode 100644 index 0000000000..a6109a2abe --- /dev/null +++ b/src/atomate2/vasp/flows/md.py @@ -0,0 +1,164 @@ +"""Flows for running molecular dynamics simulations.""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +from jobflow import Flow, Maker, OutputReference + +from atomate2.vasp.jobs.md import MDMaker, md_output +from atomate2.vasp.sets.core import MDSetGenerator + +if TYPE_CHECKING: + from pathlib import Path + + from pymatgen.core import Structure + from typing_extensions import Self + + from atomate2.vasp.jobs.base import BaseVaspMaker + + +@dataclass +class MultiMDMaker(Maker): + """ + Maker to perform an MD run split in several steps. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + md_makers : .BaseVaspMaker + Maker to use to generate the first relaxation. + """ + + name: str = "multi md" + md_makers: list[BaseVaspMaker] = field(default_factory=lambda: [MDMaker()]) + + def make( + self, + structure: Structure, + prev_dir: str | Path | None = None, + prev_traj_ids: list[str] | None = None, + ) -> Flow: + """Create a flow with several chained MD runs. + + Parameters + ---------- + structure : .Structure + A pymatgen structure object. + prev_dir : str or Path or None + A previous VASP calculation directory to copy output files from. + prev_traj_ids: a list of ids of job identifying previous steps of the + MD trajectory. + + Returns + ------- + Flow + A flow containing n_runs MD calculations. + """ + md_job = None + md_jobs = [] + md_structure = structure + md_prev_dir = prev_dir + + for idx, maker in enumerate(self.md_makers, start=1): + if md_job is not None: + md_structure = md_job.output.structure + md_prev_dir = md_job.output.dir_name + md_job = maker.make(md_structure, prev_dir=md_prev_dir) + md_job.name += f" {idx}" + md_jobs.append(md_job) + + output_job = md_output( + structure=md_jobs[-1].output.structure, + vasp_dir=md_jobs[-1].output.dir_name, + traj_ids=[j.uuid for j in md_jobs], + prev_traj_ids=prev_traj_ids, + ) + output_job.name = "molecular dynamics output" + + md_jobs.append(output_job) + + return Flow(md_jobs, output_job.output, name=self.name) + + def restart_from_uuid(self, md_ref: str | OutputReference) -> Flow: + """Create a flow from the output reference of another MultiMDMaker. + + The last output will be used as the starting point and the reference to + all the previous steps will be included in the final document. + + Parameters + ---------- + md_ref: str or OutputReference + The reference to the output of another MultiMDMaker + + Returns + ------- + A flow containing n_runs MD calculations. + """ + if isinstance(md_ref, str): + md_ref = OutputReference(md_ref) + + return self.make( + structure=md_ref.structure, + prev_dir=md_ref.vasp_dir, + prev_traj_ids=md_ref.full_traj_ids, + ) + + @classmethod + def from_parameters( + cls, + nsteps: int, + time_step: float, + n_runs: int, + ensemble: str, + start_temp: float, + end_temp: float | None = None, + **kwargs, + ) -> Self: + """Create an instance of the Maker based on the standard parameters. + + Set values in the Flow maker, the Job Maker and the VaspInputGenerator, + using them to create the final instance of the Maker. + + Parameters + ---------- + nsteps: int + Number of time steps for simulations. The VASP `NSW` parameter. + time_step: float + The time step (in femtosecond) for the simulation. The VASP + `POTIM` parameter. + n_runs : int + Number of MD runs in the flow. + ensemble: str + Molecular dynamics ensemble to run. Options include `nvt`, `nve`, and `npt`. + start_temp: float + Starting temperature. The VASP `TEBEG` parameter. + end_temp: float or None + Final temperature. The VASP `TEEND` parameter. If None the same + as start_temp. + kwargs: + Other parameters passed + + Returns + ------- + A MultiMDMaker + """ + if end_temp is None: + end_temp = start_temp + md_makers = [] + start_temp_i = start_temp + increment = (end_temp - start_temp) / n_runs + for _ in range(n_runs): + end_temp_i = start_temp_i + increment + generator = MDSetGenerator( + nsteps=nsteps, + time_step=time_step, + ensemble=ensemble, + start_temp=start_temp_i, + end_temp=end_temp_i, + ) + md_makers.append(MDMaker(input_set_generator=generator)) + start_temp_i = end_temp_i + return cls(md_makers=md_makers, **kwargs) diff --git a/src/atomate2/vasp/flows/mp.py b/src/atomate2/vasp/flows/mp.py index 8d82968718..c56d94be49 100644 --- a/src/atomate2/vasp/flows/mp.py +++ b/src/atomate2/vasp/flows/mp.py @@ -8,12 +8,15 @@ from __future__ import annotations +import logging from dataclasses import dataclass, field from typing import TYPE_CHECKING from jobflow import Flow, Maker +from atomate2.lobster.jobs import LobsterMaker from atomate2.vasp.flows.core import DoubleRelaxMaker +from atomate2.vasp.flows.lobster import VaspLobsterMaker from atomate2.vasp.jobs.mp import ( MPGGARelaxMaker, MPGGAStaticMaker, @@ -21,13 +24,17 @@ MPMetaGGAStaticMaker, MPPreRelaxMaker, ) +from atomate2.vasp.sets.mp import MPGGAStaticSetGenerator + +logger = logging.getLogger(__name__) if TYPE_CHECKING: from pathlib import Path - from jobflow import Job from pymatgen.core.structure import Structure + from atomate2.vasp.jobs.base import BaseVaspMaker + @dataclass class MPGGADoubleRelaxMaker(DoubleRelaxMaker): @@ -100,9 +107,7 @@ class MPGGADoubleRelaxStaticMaker(Maker): ) ) - def make( - self, structure: Structure, prev_vasp_dir: str | Path | None = None - ) -> Flow: + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: """ 1, 2 or 3-step flow with optional pre-relax and final static jobs. @@ -110,7 +115,7 @@ def make( ---------- structure : .Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns @@ -118,18 +123,14 @@ def make( Flow A flow containing the MP relaxation workflow. """ - jobs: list[Job] = [] - - relax_flow = self.relax_maker.make( - structure=structure, prev_vasp_dir=prev_vasp_dir - ) + relax_flow = self.relax_maker.make(structure=structure, prev_dir=prev_dir) output = relax_flow.output - jobs += [relax_flow] + jobs = [relax_flow] if self.static_maker: # Run a static calculation static_job = self.static_maker.make( - structure=output.structure, prev_vasp_dir=output.dir_name + structure=output.structure, prev_dir=output.dir_name ) output = static_job.output jobs += [static_job] @@ -162,11 +163,8 @@ class MPMetaGGADoubleRelaxStaticMaker(MPGGADoubleRelaxMaker): ) ) - def make( - self, structure: Structure, prev_vasp_dir: str | Path | None = None - ) -> Flow: - """ - Create a 2-step flow with a cheap pre-relaxation followed by a high-quality one. + def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow: + """Make a 2-step flow with a cheap pre-relaxation, then a high-quality one. An optional static calculation can be performed before the relaxation. @@ -174,7 +172,7 @@ def make( ---------- structure : .Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns @@ -182,19 +180,79 @@ def make( Flow A flow containing the MP relaxation workflow. """ - jobs: list[Job] = [] - - relax_flow = self.relax_maker.make( - structure=structure, prev_vasp_dir=prev_vasp_dir - ) + relax_flow = self.relax_maker.make(structure=structure, prev_dir=prev_dir) output = relax_flow.output - jobs += [relax_flow] + jobs = [relax_flow] if self.static_maker: # Run a static calculation (typically r2SCAN) static_job = self.static_maker.make( - structure=output.structure, prev_vasp_dir=output.dir_name + structure=output.structure, prev_dir=output.dir_name ) output = static_job.output jobs += [static_job] return Flow(jobs=jobs, output=output, name=self.name) + + +# update potcars to 54, use correct W potcar +# use staticmaker for compatibility +@dataclass +class MPVaspLobsterMaker(VaspLobsterMaker): + """ + Maker to perform a Lobster computation. + + The calculations performed are: + + 1. Optional optimization. + 2. Static calculation with ISYM=0. + 3. Several Lobster computations testing several basis sets are performed. + + .. Note:: + + The basis sets can only be changed with yaml files. + + Parameters + ---------- + name : str + Name of the flows produced by this maker. + relax_maker : .BaseVaspMaker or None + A maker to perform a relaxation on the bulk. Set to ``None`` to skip the + bulk relaxation. + lobster_static_maker : .BaseVaspMaker + A maker to perform the computation of the wavefunction before the static + run. Cannot be skipped. It can be LOBSTERUNIFORM or LobsterStaticMaker() + lobster_maker : .LobsterMaker + A maker to perform the Lobster run. + delete_wavecars : bool + If true, all WAVECARs will be deleted after the run. + address_min_basis : str + A path to a yaml file including basis set information. + address_max_basis : str + A path to a yaml file including basis set information. + """ + + name: str = "lobster" + relax_maker: BaseVaspMaker | None = field(default_factory=MPGGADoubleRelaxMaker) + lobster_static_maker: BaseVaspMaker = field( + default_factory=lambda: MPGGAStaticMaker( + input_set_generator=MPGGAStaticSetGenerator( + user_potcar_functional="PBE_54", + user_potcar_settings={"W": "W_sv"}, + user_kpoints_settings={"reciprocal_density": 310}, + user_incar_settings={ + "EDIFF": 1e-6, + "NSW": 0, + "LWAVE": True, + "ISYM": 0, + "IBRION": -1, + "ISMEAR": -5, + "LORBIT": 11, + "ALGO": "Normal", + }, + ) + ) + ) + lobster_maker: LobsterMaker | None = field(default_factory=LobsterMaker) + delete_wavecars: bool = True + address_min_basis: str | None = None + address_max_basis: str | None = None diff --git a/src/atomate2/vasp/flows/phonons.py b/src/atomate2/vasp/flows/phonons.py index b6e50c55e2..e07748db61 100644 --- a/src/atomate2/vasp/flows/phonons.py +++ b/src/atomate2/vasp/flows/phonons.py @@ -1,36 +1,22 @@ -"""Flows for calculating phonons.""" +"""Define the VASP PhononMaker.""" from __future__ import annotations from dataclasses import dataclass, field from typing import TYPE_CHECKING -from jobflow import Flow, Maker - -from atomate2.common.jobs.phonons import ( - PhononDisplacementMaker, - generate_frequencies_eigenvectors, - generate_phonon_displacements, - get_supercell_size, - get_total_energy_per_cell, - run_phonon_displacements, -) -from atomate2.common.jobs.utils import structure_to_conventional, structure_to_primitive +from atomate2.common.flows.phonons import BasePhononMaker from atomate2.vasp.flows.core import DoubleRelaxMaker from atomate2.vasp.jobs.core import DielectricMaker, StaticMaker, TightRelaxMaker +from atomate2.vasp.jobs.phonons import PhononDisplacementMaker from atomate2.vasp.sets.core import StaticSetGenerator if TYPE_CHECKING: - from pathlib import Path - - from emmet.core.math import Matrix3D - from pymatgen.core.structure import Structure - from atomate2.vasp.jobs.base import BaseVaspMaker @dataclass -class PhononMaker(Maker): +class PhononMaker(BasePhononMaker): """ Maker to calculate harmonic phonons with VASP and Phonopy. @@ -40,7 +26,7 @@ class PhononMaker(Maker): forces are computed for these structures. With the help of phonopy, these forces are then converted into a dynamical matrix. To correct for polarization effects, a correction of the dynamical matrix based on BORN charges can - be performed. Finally, phonon densities of states, phonon band structures + be performed. Finally, phonon densities of states, phonon band structures and thermodynamic properties are computed. .. Note:: @@ -53,25 +39,25 @@ class PhononMaker(Maker): Parameters ---------- - name : str + name : str = "phonon" Name of the flows produced by this maker. - sym_reduce : bool + sym_reduce : bool = True Whether to reduce the number of deformations using symmetry. - symprec : float + symprec : float = 1e-4 Symmetry precision to use in the reduction of symmetry to find the primitive/conventional cell (use_primitive_standard_structure, use_conventional_standard_structure) and to handle all symmetry-related tasks in phonopy - displacement: float + displacement: float = 0.01 displacement distance for phonons - min_length: float + min_length: float = 20.0 min length of the supercell that will be built - prefer_90_degrees: bool + prefer_90_degrees: bool = True if set to True, supercell algorithm will first try to find a supercell with 3 90 degree angles - get_supercell_size_kwargs: dict + get_supercell_size_kwargs: dict = {} kwargs that will be passed to get_supercell_size to determine supercell size - use_symmetrized_structure: str + use_symmetrized_structure: str or None = None allowed strings: "primitive", "conventional", None - "primitive" will enforce to start the phonon computation @@ -106,7 +92,7 @@ class PhononMaker(Maker): Keyword arguments passed to :obj:`generate_frequencies_eigenvectors`. create_thermal_displacements: bool Bool that determines if thermal_displacement_matrices are computed - kpath_scheme: str + kpath_scheme: str = "seekpath" scheme to generate kpoints. Please be aware that you can only use seekpath with any kind of cell Otherwise, please use the standard primitive structure @@ -116,12 +102,14 @@ class PhononMaker(Maker): seekpath can be used with any kind of unit cell as it relies on phonopy to handle the relationship to the primitive cell and not pymatgen - code: str - determines the dft code. currently only vasp is implemented. + code: str = "vasp" + determines the DFT code. currently only vasp is implemented. This keyword might enable the implementation of other codes in the future store_force_constants: bool if True, force constants will be stored + socket: bool + If True, use the socket for the calculation """ name: str = "phonon" @@ -132,6 +120,12 @@ class PhononMaker(Maker): prefer_90_degrees: bool = True get_supercell_size_kwargs: dict = field(default_factory=dict) use_symmetrized_structure: str | None = None + create_thermal_displacements: bool = True + generate_frequencies_eigenvectors_kwargs: dict = field(default_factory=dict) + kpath_scheme: str = "seekpath" + store_force_constants: bool = True + socket: bool = False + code: str = "vasp" bulk_relax_maker: BaseVaspMaker | None = field( default_factory=lambda: DoubleRelaxMaker.from_relax_maker(TightRelaxMaker()) ) @@ -144,198 +138,15 @@ class PhononMaker(Maker): phonon_displacement_maker: BaseVaspMaker = field( default_factory=PhononDisplacementMaker ) - create_thermal_displacements: bool = True - generate_frequencies_eigenvectors_kwargs: dict = field(default_factory=dict) - kpath_scheme: str = "seekpath" - code: str = "vasp" - store_force_constants: bool = True - def make( - self, - structure: Structure, - prev_vasp_dir: str | Path | None = None, - born: list[Matrix3D] | None = None, - epsilon_static: Matrix3D | None = None, - total_dft_energy_per_formula_unit: float | None = None, - supercell_matrix: Matrix3D | None = None, - ) -> Flow: - """ - Make flow to calculate the phonon properties. + @property + def prev_calc_dir_argname(self) -> str: + """Name of argument informing static maker of previous calculation directory. - Parameters - ---------- - structure : .Structure - A pymatgen structure. Please start with a structure that is nearly fully - optimized as the internal optimizers have very strict settings! - prev_vasp_dir : str or Path or None - A previous vasp calculation directory to use for copying outputs. - born: Matrix3D - Instead of recomputing born charges and epsilon, these values can also be - provided manually. If born and epsilon_static are provided, the born run - will be skipped it can be provided in the VASP convention with information - for every atom in unit cell. Please be careful when converting structures - within in this workflow as this could lead to errors - epsilon_static: Matrix3D - The high-frequency dielectric constant to use instead of recomputing born - charges and epsilon. If born, epsilon_static are provided, the born run - will be skipped - total_dft_energy_per_formula_unit: float - It has to be given per formula unit (as a result in corresponding Doc). - Instead of recomputing the energy of the bulk structure every time, this - value can also be provided in eV. If it is provided, the static run will be - skipped. This energy is the typical output dft energy of the dft workflow. - No conversion needed. - supercell_matrix: list - Instead of min_length, also a supercell_matrix can be given, e.g. - [[1.0,0.0,0.0],[0.0,1.0,0.0],[0.0,0.0,1.0] - """ - if self.use_symmetrized_structure not in [None, "primitive", "conventional"]: - raise ValueError( - "use_symmetrized_structure can only be primitive, conventional, None" - ) - - if ( - not self.use_symmetrized_structure == "primitive" - and self.kpath_scheme != "seekpath" - ): - raise ValueError( - "You can only use other kpath schemes with the primitive standard " - "structure" - ) - - if self.kpath_scheme not in [ - "seekpath", - "hinuma", - "setyawan_curtarolo", - "latimer_munro", - ]: - raise ValueError("kpath scheme is not implemented") - - jobs = [] - - # TODO: should this be after or before structural optimization as the - # optimization could change the symmetry we could add a tutorial and point out - # that the structure should be nearly optimized before the phonon workflow - if self.use_symmetrized_structure == "primitive": - # These structures are compatible with many - # of the kpath algorithms that are used for Materials Project - prim_job = structure_to_primitive(structure, self.symprec) - jobs.append(prim_job) - structure = prim_job.output - elif self.use_symmetrized_structure == "conventional": - # it could be beneficial to use conventional standard structures to arrive - # faster at supercells with right angles - conv_job = structure_to_conventional(structure, self.symprec) - jobs.append(conv_job) - structure = conv_job.output + As this differs between different DFT codes (e.g., VASP, CP2K), it + has been left as a property to be implemented by the inheriting class. - optimization_run_job_dir = None - optimization_run_uuid = None - if self.bulk_relax_maker is not None: - # optionally relax the structure - bulk = self.bulk_relax_maker.make(structure, prev_vasp_dir=prev_vasp_dir) - jobs.append(bulk) - structure = bulk.output.structure - prev_vasp_dir = bulk.output.dir_name - optimization_run_job_dir = bulk.output.dir_name - optimization_run_uuid = bulk.output.uuid - - # if supercell_matrix is None, supercell size will be determined after relax - # maker to ensure that cell lengths are really larger than threshold - if supercell_matrix is None: - supercell_job = get_supercell_size( - structure, - self.min_length, - self.prefer_90_degrees, - **self.get_supercell_size_kwargs, - ) - jobs.append(supercell_job) - supercell_matrix = supercell_job.output - - # Computation of static energy - total_dft_energy = None - static_run_job_dir = None - static_run_uuid = None - if (self.static_energy_maker is not None) and ( - total_dft_energy_per_formula_unit is None - ): - static_job = self.static_energy_maker.make( - structure=structure, prev_vasp_dir=prev_vasp_dir - ) - jobs.append(static_job) - total_dft_energy = static_job.output.output.energy - static_run_job_dir = static_job.output.dir_name - static_run_uuid = static_job.output.uuid - prev_vasp_dir = static_job.output.dir_name - elif total_dft_energy_per_formula_unit is not None: - # to make sure that one can reuse results from Doc - compute_total_energy_job = get_total_energy_per_cell( - total_dft_energy_per_formula_unit, structure - ) - jobs.append(compute_total_energy_job) - total_dft_energy = compute_total_energy_job.output - - # get a phonon object from phonopy - displacements = generate_phonon_displacements( - structure=structure, - supercell_matrix=supercell_matrix, - displacement=self.displacement, - sym_reduce=self.sym_reduce, - symprec=self.symprec, - use_symmetrized_structure=self.use_symmetrized_structure, - kpath_scheme=self.kpath_scheme, - code=self.code, - ) - jobs.append(displacements) - - # perform the phonon displacement calculations - vasp_displacement_calcs = run_phonon_displacements( - displacements=displacements.output, - structure=structure, - supercell_matrix=supercell_matrix, - phonon_maker=self.phonon_displacement_maker, - prev_vasp_dir=prev_vasp_dir, - ) - jobs.append(vasp_displacement_calcs) - - # Computation of BORN charges - born_run_job_dir = None - born_run_uuid = None - if self.born_maker is not None and (born is None or epsilon_static is None): - born_job = self.born_maker.make(structure, prev_vasp_dir=prev_vasp_dir) - jobs.append(born_job) - - # I am not happy how we currently access "born" charges - # This is very vasp specific code - epsilon_static = born_job.output.calcs_reversed[0].output.epsilon_static - born = born_job.output.calcs_reversed[0].output.outcar["born"] - born_run_job_dir = born_job.output.dir_name - born_run_uuid = born_job.output.uuid - - phonon_collect = generate_frequencies_eigenvectors( - supercell_matrix=supercell_matrix, - displacement=self.displacement, - sym_reduce=self.sym_reduce, - symprec=self.symprec, - use_symmetrized_structure=self.use_symmetrized_structure, - kpath_scheme=self.kpath_scheme, - code=self.code, - structure=structure, - displacement_data=vasp_displacement_calcs.output, - epsilon_static=epsilon_static, - born=born, - total_dft_energy=total_dft_energy, - static_run_job_dir=static_run_job_dir, - static_run_uuid=static_run_uuid, - born_run_job_dir=born_run_job_dir, - born_run_uuid=born_run_uuid, - optimization_run_job_dir=optimization_run_job_dir, - optimization_run_uuid=optimization_run_uuid, - create_thermal_displacements=self.create_thermal_displacements, - store_force_constants=self.store_force_constants, - **self.generate_frequencies_eigenvectors_kwargs, - ) - jobs.append(phonon_collect) - - # create a flow including all jobs for a phonon computation - return Flow(jobs, phonon_collect.output) + Note: this is only applicable if a relax_maker is specified; i.e., two + calculations are performed for each ordering (relax -> static) + """ + return "prev_dir" diff --git a/src/atomate2/vasp/jobs/amset.py b/src/atomate2/vasp/jobs/amset.py index c9b15bac74..b2a8d469e6 100644 --- a/src/atomate2/vasp/jobs/amset.py +++ b/src/atomate2/vasp/jobs/amset.py @@ -118,7 +118,7 @@ class StaticDeformationMaker(BaseVaspMaker): @dataclass class HSEStaticDeformationMaker(BaseVaspMaker): """ - Maker to perform a HSE06 static calculations on structural deformations. + Maker to perform an HSE06 static calculations on structural deformations. The main difference to a normal HSE06 static calculation is that this will write an explicit KPOINTS file, rather than using KSPACING. This is because all deformations @@ -200,7 +200,7 @@ class HSEDenseUniformMaker(HSEBSMaker): def run_amset_deformations( structure: Structure, symprec: float = SETTINGS.SYMPREC, - prev_vasp_dir: str | Path | None = None, + prev_dir: str | Path | None = None, static_deformation_maker: BaseVaspMaker | None = None, ) -> Response: """ @@ -216,7 +216,7 @@ def run_amset_deformations( symprec : float Symmetry precision used to reduce the number of deformations. Set to None for no symmetry reduction. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP directory to use for copying VASP outputs. static_deformation_maker : .BaseVaspMaker or None A VaspMaker to use to generate the static deformation jobs. @@ -237,16 +237,16 @@ def run_amset_deformations( statics = [] outputs = [] - for i, deformation in enumerate(deformations): + for idx, deformation in enumerate(deformations): # deform the structure dst = DeformStructureTransformation(deformation=deformation) deformed_structure = dst.apply_transformation(structure) # create the job static_job = static_deformation_maker.make( - deformed_structure, prev_vasp_dir=prev_vasp_dir + deformed_structure, prev_dir=prev_dir ) - static_job.append_name(f" {i + 1}/{len(deformations)}") + static_job.append_name(f" {idx + 1}/{len(deformations)}") statics.append(static_job) # extract the outputs we want (only the dir name) @@ -298,7 +298,7 @@ def calculate_deformation_potentials( # as zero indexed symprec_str = "N" if symprec is None else str(symprec) - # TODO: Handle hostnames properly + # TODO: Handle host names properly bulk_dir = strip_hostname(bulk_dir) deformation_dirs = [strip_hostname(d) for d in deformation_dirs] args = [ @@ -307,7 +307,9 @@ def calculate_deformation_potentials( f"--symprec={symprec_str}", ] if ibands is not None: - bands_str = ".".join(",".join([str(idx + 1) for idx in b]) for b in ibands) + bands_str = ".".join( + ",".join([str(idx + 1) for idx in band_ids]) for band_ids in ibands + ) args.append(f"--bands={bands_str}") runner = CliRunner() diff --git a/src/atomate2/vasp/jobs/base.py b/src/atomate2/vasp/jobs/base.py index 3122803e62..c41b16a390 100644 --- a/src/atomate2/vasp/jobs/base.py +++ b/src/atomate2/vasp/jobs/base.py @@ -2,6 +2,7 @@ from __future__ import annotations +import warnings from dataclasses import dataclass, field from pathlib import Path from shutil import which @@ -29,6 +30,12 @@ _BADER_EXE_EXISTS = bool(which("bader") or which("bader.exe")) +_CHARGEMOL_EXE_EXISTS = bool( + which("Chargemol_09_26_2017_linux_parallel") + or which("Chargemol_09_26_2017_linux_serial") + or which("chargemol") +) + _DATA_OBJECTS = [ BandStructure, BandStructureSymmLine, @@ -41,6 +48,7 @@ Trajectory, "force_constants", "normalmode_eigenvecs", + "bandstructure", # FIX: BandStructure is not currently MSONable ] # Input files. Partially from https://www.vasp.at/wiki/index.php/Category:Input_files @@ -182,16 +190,15 @@ class BaseVaspMaker(Maker): @vasp_job def make( - self, structure: Structure, prev_vasp_dir: str | Path | None = None + self, structure: Structure, prev_dir: str | Path | None = None ) -> Response: - """ - Run a VASP calculation. + """Run a VASP calculation. Parameters ---------- structure : Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. Returns @@ -200,9 +207,9 @@ def make( commands of the VASP run. """ # copy previous inputs - from_prev = prev_vasp_dir is not None - if prev_vasp_dir is not None: - copy_vasp_outputs(prev_vasp_dir, **self.copy_vasp_kwargs) + from_prev = prev_dir is not None + if prev_dir is not None: + copy_vasp_outputs(prev_dir, **self.copy_vasp_kwargs) self.write_input_set_kwargs.setdefault("from_prev", from_prev) @@ -239,10 +246,7 @@ def make( ) -def get_vasp_task_document( - path: Path | str, - **kwargs, -) -> TaskDoc: +def get_vasp_task_document(path: Path | str, **kwargs) -> TaskDoc: """Get VASP Task Document using atomate2 settings.""" kwargs.setdefault("store_additional_json", SETTINGS.VASP_STORE_ADDITIONAL_JSON) @@ -250,7 +254,37 @@ def get_vasp_task_document( "volume_change_warning_tol", SETTINGS.VASP_VOLUME_CHANGE_WARNING_TOL ) - kwargs.setdefault("run_bader", SETTINGS.VASP_RUN_BADER and _BADER_EXE_EXISTS) + if SETTINGS.VASP_RUN_BADER: + kwargs.setdefault("run_bader", _BADER_EXE_EXISTS) + if not _BADER_EXE_EXISTS: + warnings.warn( + f"{SETTINGS.VASP_RUN_BADER=} but bader executable not found on path", + stacklevel=1, + ) + if SETTINGS.VASP_RUN_DDEC6: + # if VASP_RUN_DDEC6 is True but _CHARGEMOL_EXE_EXISTS is False, just silently + # skip running DDEC6 + run_ddec6: bool | str = _CHARGEMOL_EXE_EXISTS + if run_ddec6 and isinstance(SETTINGS.DDEC6_ATOMIC_DENSITIES_DIR, str): + # if DDEC6_ATOMIC_DENSITIES_DIR is a string and directory at that path + # exists, use as path to the atomic densities + if Path(SETTINGS.DDEC6_ATOMIC_DENSITIES_DIR).is_dir(): + run_ddec6 = SETTINGS.DDEC6_ATOMIC_DENSITIES_DIR + else: + # if the directory doesn't exist, warn the user and skip running DDEC6 + warnings.warn( + f"{SETTINGS.DDEC6_ATOMIC_DENSITIES_DIR=} does not exist, skipping " + "DDEC6", + stacklevel=1, + ) + kwargs.setdefault("run_ddec6", run_ddec6) + + if not _CHARGEMOL_EXE_EXISTS: + warnings.warn( + f"{SETTINGS.VASP_RUN_DDEC6=} but chargemol executable not found on " + "path", + stacklevel=1, + ) kwargs.setdefault("store_volumetric_data", SETTINGS.VASP_STORE_VOLUMETRIC_DATA) diff --git a/src/atomate2/vasp/jobs/core.py b/src/atomate2/vasp/jobs/core.py index 027b17e918..07f467e3c3 100644 --- a/src/atomate2/vasp/jobs/core.py +++ b/src/atomate2/vasp/jobs/core.py @@ -4,17 +4,8 @@ import logging from dataclasses import dataclass, field -from typing import TYPE_CHECKING - -from custodian.vasp.handlers import ( - FrozenJobErrorHandler, - IncorrectSmearingHandler, - LargeSigmaHandler, - MeshSymmetryErrorHandler, - PositiveEnergyErrorHandler, - StdErrHandler, - VaspErrorHandler, -) +from typing import TYPE_CHECKING, Literal + from pymatgen.alchemy.materials import TransformedStructure from pymatgen.alchemy.transmuters import StandardTransmuter @@ -25,7 +16,6 @@ HSERelaxSetGenerator, HSEStaticSetGenerator, HSETightRelaxSetGenerator, - MDSetGenerator, NonSCFSetGenerator, RelaxSetGenerator, StaticSetGenerator, @@ -181,17 +171,16 @@ class NonSCFMaker(BaseVaspMaker): def make( self, structure: Structure, - prev_vasp_dir: str | Path | None, + prev_dir: str | Path | None, mode: str = "uniform", ) -> Response: - """ - Run a non-scf VASP job. + """Run a non-scf VASP job. Parameters ---------- structure : .Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. mode : str Type of band structure calculation. Options are: @@ -206,7 +195,7 @@ def make( # copy previous inputs self.copy_vasp_kwargs.setdefault("additional_vasp_files", ("CHGCAR",)) - return super().make.original(self, structure, prev_vasp_dir) + return super().make.original(self, structure, prev_dir) @dataclass @@ -355,19 +344,18 @@ class HSEBSMaker(BaseVaspMaker): def make( self, structure: Structure, - prev_vasp_dir: str | Path | None = None, - mode="uniform", + prev_dir: str | Path | None = None, + mode: Literal["line", "uniform", "gap"] = "uniform", ) -> Response: - """ - Run a HSE06 band structure VASP job. + """Run an HSE06 band structure VASP job. Parameters ---------- structure : .Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. - mode : str + mode : str = "uniform" Type of band structure calculation. Options are: - "line": Full band structure along symmetry lines. - "uniform": Uniform mesh band structure. @@ -375,7 +363,7 @@ def make( """ self.input_set_generator.mode = mode - if mode == "gap" and prev_vasp_dir is None: + if mode == "gap" and prev_dir is None: logger.warning( "HSE band structure in 'gap' mode requires a previous VASP calculation " "directory from which to extract the VBM and CBM k-points. This " @@ -390,10 +378,10 @@ def make( self.task_document_kwargs.setdefault("parse_bandstructure", parse_bandstructure) # copy previous inputs - if prev_vasp_dir is not None: + if prev_dir is not None: self.copy_vasp_kwargs.setdefault("additional_vasp_files", ("CHGCAR",)) - return super().make.original(self, structure, prev_vasp_dir) + return super().make.original(self, structure, prev_dir) @dataclass @@ -487,16 +475,15 @@ class TransmuterMaker(BaseVaspMaker): def make( self, structure: Structure, - prev_vasp_dir: str | Path | None = None, + prev_dir: str | Path | None = None, ) -> Response: - """ - Run a transmuter VASP job. + """Run a transmuter VASP job. Parameters ---------- structure : Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. """ transformations = get_transformations( @@ -510,60 +497,4 @@ def make( tjson = transmuter.transformed_structures[-1] self.write_additional_data.setdefault("transformations:json", tjson) - return super().make.original(self, structure, prev_vasp_dir) - - -@dataclass -class MDMaker(BaseVaspMaker): - """ - Maker to create VASP molecular dynamics jobs. - - Parameters - ---------- - name : str - The job name. - input_set_generator : .VaspInputSetGenerator - A generator used to make the input set. - write_input_set_kwargs : dict - Keyword arguments that will get passed to :obj:`.write_vasp_input_set`. - copy_vasp_kwargs : dict - Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`. - run_vasp_kwargs : dict - Keyword arguments that will get passed to :obj:`.run_vasp`. - task_document_kwargs : dict - Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. - stop_children_kwargs : dict - Keyword arguments that will get passed to :obj:`.should_stop_children`. - write_additional_data : dict - Additional data to write to the current directory. Given as a dict of - {filename: data}. Note that if using FireWorks, dictionary keys cannot contain - the "." character which is typically used to denote file extensions. To avoid - this, use the ":" character, which will automatically be converted to ".". E.g. - ``{"my_file:txt": "contents of the file"}``. - """ - - name: str = "molecular dynamics" - - input_set_generator: VaspInputGenerator = field(default_factory=MDSetGenerator) - - # Explicitly pass the handlers to not use the default ones. Some default handlers - # such as PotimErrorHandler do not apply to MD runs. - run_vasp_kwargs: dict = field( - default_factory=lambda: { - "handlers": ( - VaspErrorHandler(), - MeshSymmetryErrorHandler(), - PositiveEnergyErrorHandler(), - FrozenJobErrorHandler(), - StdErrHandler(), - LargeSigmaHandler(), - IncorrectSmearingHandler(), - ) - } - ) - - # Store ionic steps info in a pymatgen Trajectory object instead of in the output - # document. - task_document_kwargs: dict = field( - default_factory=lambda: {"store_trajectory": True} - ) + return super().make.original(self, structure, prev_dir) diff --git a/src/atomate2/vasp/jobs/defect.py b/src/atomate2/vasp/jobs/defect.py index 175cedf183..33b00aff45 100644 --- a/src/atomate2/vasp/jobs/defect.py +++ b/src/atomate2/vasp/jobs/defect.py @@ -57,19 +57,19 @@ def calculate_finite_diff( # Update the INCAR for the WSWQ calculation incar = Incar.from_file("INCAR") - incar.update({"ALGO": "None", "NSW": 0, "LWAVE": False, "LWSWQ": True}) + incar.update(ALGO="None", NSW=0, LWAVE=False, LWSWQ=True) incar.write_file("INCAR") d_dir_names = [strip_hostname(d) for d in distorted_calc_dirs] - for i, dir_name in enumerate(d_dir_names): + for idx, dir_name in enumerate(d_dir_names): # Copy a distorted WAVECAR to WAVECAR.qqq copy_files(dir_name, include_files=["WAVECAR.gz"], prefix="qqq.") gunzip_files(include_files="qqq.WAVECAR*", allow_missing=True) rename_files({"qqq.WAVECAR": "WAVECAR.qqq"}) run_vasp(**run_vasp_kwargs) - fc.copy("WSWQ", f"WSWQ.{i}") + fc.copy("WSWQ", f"WSWQ.{idx}") fd_doc = FiniteDifferenceDocument.from_directory( ".", ref_dir=ref_calc_dir, distorted_dirs=d_dir_names diff --git a/src/atomate2/vasp/jobs/elastic.py b/src/atomate2/vasp/jobs/elastic.py index a83041d5c4..7888ab305f 100644 --- a/src/atomate2/vasp/jobs/elastic.py +++ b/src/atomate2/vasp/jobs/elastic.py @@ -51,7 +51,7 @@ class ElasticRelaxMaker(BaseVaspMaker): name: str = "elastic relax" input_set_generator: VaspInputGenerator = field( default_factory=lambda: StaticSetGenerator( - user_kpoints_settings={"grid_density": 7000}, + user_kpoints_settings={"grid_density": 7_000}, user_incar_settings={ "IBRION": 2, "ISIF": 2, diff --git a/src/atomate2/vasp/jobs/elph.py b/src/atomate2/vasp/jobs/elph.py index a774f222d3..1cc05fbc4c 100644 --- a/src/atomate2/vasp/jobs/elph.py +++ b/src/atomate2/vasp/jobs/elph.py @@ -89,16 +89,15 @@ class SupercellElectronPhononDisplacedStructureMaker(TransmuterMaker): def make( self, structure: Structure, - prev_vasp_dir: str | Path | None = None, + prev_dir: str | Path | None = None, ) -> Response: - """ - Run a transmuter VASP job. + """Run a transmuter VASP job. Parameters ---------- structure : Structure A pymatgen structure object. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP calculation directory to copy output files from. """ dim = self.min_supercell_length / np.array(structure.lattice.abc) @@ -110,7 +109,7 @@ def make( # update temperatures self.input_set_generator.temperatures = self.temperatures - return super().make.original(self, structure, prev_vasp_dir) + return super().make.original(self, structure, prev_dir) @job @@ -118,7 +117,7 @@ def run_elph_displacements( temperatures: list[float], structures: list[Structure], vasp_maker: BaseVaspMaker, - prev_vasp_dir: str | Path | None = None, + prev_dir: str | Path | None = None, original_structure: Structure = None, supercell_structure: Structure = None, ) -> Response: @@ -135,7 +134,7 @@ def run_elph_displacements( Electron phonon displaced structures for each temperature. vasp_maker : BaseVaspMaker A maker to generate VASP calculations on the displaced structures. - prev_vasp_dir : str or Path or None + prev_dir : str or Path or None A previous VASP directory to use for copying VASP outputs. original_structure : Structure The original structure before supercell is made and before electron phonon @@ -157,7 +156,7 @@ def run_elph_displacements( } for temp, structure in zip(temperatures, structures): # create the job - elph_job = vasp_maker.make(structure, prev_vasp_dir=prev_vasp_dir) + elph_job = vasp_maker.make(structure, prev_dir=prev_dir) elph_job.append_name(f" T={temp}") # write details of the electron phonon temperature and structure elph_info.json @@ -241,7 +240,7 @@ def calculate_electron_phonon_renormalisation( ) # filter band structures that are None (i.e., the displacement calculation failed) - keep = [i for i, b in enumerate(displacement_band_structures) if b is not None] + keep = [idx for idx, b in enumerate(displacement_band_structures) if b is not None] temperatures = [temperatures[i] for i in keep] displacement_band_structures = [displacement_band_structures[i] for i in keep] displacement_structures = [displacement_structures[i] for i in keep] diff --git a/src/atomate2/vasp/jobs/eos.py b/src/atomate2/vasp/jobs/eos.py new file mode 100644 index 0000000000..ab2ea6b828 --- /dev/null +++ b/src/atomate2/vasp/jobs/eos.py @@ -0,0 +1,344 @@ +""" +Module to define EOS jobs using the default atomate2 parameters. + +Some jobs have prefixes to indicate their purpose: +- MPLegacy: for consistency with the atomate 1 implementation, or +[LDMWP] K. Latimer, S. Dwaraknath, K. Mathew, D. Winston, and K.A. Persson, +npj Comput. Materials 4, 40 (2018), +DOI: 10.1038/s41524-018-0091-x + +Also see the original atomate workflows + +- atomate.vasp.workflows.base.wf_bulk_modulus: +https://github.com/hackingmaterials/atomate/blob/main/atomate/vasp/workflows/presets/core.py#L564 +- atomate.vasp.workflows.base.bulk_modulus.get_wf_bulk_modulus: +https://github.com/hackingmaterials/atomate/blob/main/atomate/vasp/workflows/base/bulk_modulus.py#L21 + +These WFs are interesting that the k-point density is **extremely** high +despite the convergence tests in the SI of the Latimer et al. paper not +showing strong sensitivity when + "number of k-points per reciprocal atom" >= 3,000 + +- MPGGA: MP-compatible PBE-GGA jobs +- MPMetaGGA: MP-compatible r2SCAN meta-GGA jobs + +MPGGA and MPMetaGGA jobs use the highest k-point density in standard MP jobs, +KSPACING = 0.22, which is comparable to +KPPRA = k-points per reciprocal atom = 3000 + +This is justified by the SI of [LDMWP], which shows in Fig. S12 +that all EOS parameters (E0, V0, B0, B1) do not deviate by more than 1.5%, +and typically less than 0.1%, from a well-converged value when KPPRA = 3,000. +""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +from atomate2.vasp.jobs.base import BaseVaspMaker +from atomate2.vasp.sets.eos import ( + EosSetGenerator, + MPGGAEosRelaxSetGenerator, + MPGGAEosStaticSetGenerator, + MPLegacyEosRelaxSetGenerator, + MPLegacyEosStaticSetGenerator, + MPMetaGGAEosPreRelaxSetGenerator, + MPMetaGGAEosRelaxSetGenerator, + MPMetaGGAEosStaticSetGenerator, +) + +if TYPE_CHECKING: + from atomate2.vasp.sets.base import VaspInputGenerator + + +copy_wavecar = lambda: {"additional_vasp_files": ("WAVECAR",)} # noqa: E731 + + +# No prefix, base atomate 2 parameters +@dataclass +class EosRelaxMaker(BaseVaspMaker): + """ + Maker to create VASP relaxation job using EOS parameters. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .VaspInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_vasp_input_set`. + copy_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`. + run_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_vasp`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "EOS GGA relax" + input_set_generator: VaspInputGenerator = field(default_factory=EosSetGenerator) + copy_vasp_kwargs: dict = field(default_factory=copy_wavecar) + + +# MPLegacy prefix, legacy MP PBE-GGA +@dataclass +class MPLegacyEosRelaxMaker(BaseVaspMaker): + """ + Maker to create MP atomate1-compatible GGA relax job in VASP. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .VaspInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_vasp_input_set`. + copy_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`. + run_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_vasp`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "EOS MP legacy GGA relax" + input_set_generator: VaspInputGenerator = field( + default_factory=MPLegacyEosRelaxSetGenerator + ) + copy_vasp_kwargs: dict = field(default_factory=copy_wavecar) + + +@dataclass +class MPLegacyEosStaticMaker(BaseVaspMaker): + """ + Maker to create MP atomate1-compatible GGA static job in VASP. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .VaspInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_vasp_input_set`. + copy_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`. + run_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_vasp`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "EOS MP legacy GGA static" + input_set_generator: VaspInputGenerator = field( + default_factory=MPLegacyEosStaticSetGenerator + ) + copy_vasp_kwargs: dict = field(default_factory=copy_wavecar) + + +# MPGGA prefix, MP PBE-GGA compatible parameters +@dataclass +class MPGGAEosRelaxMaker(BaseVaspMaker): + """ + Maker to create MP-compatible GGA relax job in VASP using EOS parameters. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .VaspInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_vasp_input_set`. + copy_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`. + run_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_vasp`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "EOS MP GGA relax" + input_set_generator: VaspInputGenerator = field( + default_factory=MPGGAEosRelaxSetGenerator + ) + copy_vasp_kwargs: dict = field(default_factory=copy_wavecar) + + +@dataclass +class MPGGAEosStaticMaker(BaseVaspMaker): + """ + Maker to create MP-compatible GGA static job in VASP using EOS parameters. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .VaspInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_vasp_input_set`. + copy_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`. + run_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_vasp`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "EOS MP GGA static" + input_set_generator: VaspInputGenerator = field( + default_factory=MPGGAEosStaticSetGenerator + ) + copy_vasp_kwargs: dict = field(default_factory=copy_wavecar) + + +# MPMetaGGA prefix, MP r2SCAN-meta-GGA compatible +@dataclass +class MPMetaGGAEosPreRelaxMaker(BaseVaspMaker): + """ + Maker to create MP-compatible r2SCAN relax job in VASP using EOS parameters. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .VaspInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_vasp_input_set`. + copy_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`. + run_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_vasp`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "EOS MP meta-GGA pre-relax" + input_set_generator: VaspInputGenerator = field( + default_factory=MPMetaGGAEosPreRelaxSetGenerator + ) + + +@dataclass +class MPMetaGGAEosRelaxMaker(BaseVaspMaker): + """ + Maker to create MP-compatible r2SCAN relax job in VASP using EOS parameters. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .VaspInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_vasp_input_set`. + copy_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`. + run_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_vasp`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "EOS MP meta-GGA relax" + input_set_generator: VaspInputGenerator = field( + default_factory=MPMetaGGAEosRelaxSetGenerator + ) + copy_vasp_kwargs: dict = field(default_factory=copy_wavecar) + + +@dataclass +class MPMetaGGAEosStaticMaker(BaseVaspMaker): + """ + Maker to create MP-compatible meta-GGA static job in VASP using EOS parameters. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .VaspInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_vasp_input_set`. + copy_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`. + run_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_vasp`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "EOS MP meta-GGA static" + input_set_generator: VaspInputGenerator = field( + default_factory=MPMetaGGAEosStaticSetGenerator + ) + copy_vasp_kwargs: dict = field(default_factory=copy_wavecar) diff --git a/src/atomate2/vasp/jobs/lobster.py b/src/atomate2/vasp/jobs/lobster.py index 1a730874aa..3061742104 100644 --- a/src/atomate2/vasp/jobs/lobster.py +++ b/src/atomate2/vasp/jobs/lobster.py @@ -103,12 +103,12 @@ def get_basis_infos( """ # this logic enables handling of a flow or a simple maker try: - potcar_symbols = vasp_maker.static_maker.input_set_generator._get_potcar( + potcar_symbols = vasp_maker.static_maker.input_set_generator._get_potcar( # noqa: SLF001 structure=structure, potcar_spec=True ) except AttributeError: - potcar_symbols = vasp_maker.input_set_generator._get_potcar( + potcar_symbols = vasp_maker.input_set_generator._get_potcar( # noqa: SLF001 structure=structure, potcar_spec=True ) @@ -120,14 +120,14 @@ def get_basis_infos( address_basis_file_min=address_min_basis, ) - nband_list = [] + n_band_list: list[int] = [] for dict_for_basis in list_basis_dict: basis = [f"{key} {value}" for key, value in dict_for_basis.items()] lobsterin = Lobsterin(settingsdict={"basisfunctions": basis}) - nbands = lobsterin._get_nbands(structure=structure) - nband_list.append(nbands) + n_bands = lobsterin._get_nbands(structure=structure) # noqa: SLF001 + n_band_list.append(n_bands) - return {"nbands": max(nband_list), "basis_dict": list_basis_dict} + return {"nbands": max(n_band_list), "basis_dict": list_basis_dict} @job @@ -135,7 +135,7 @@ def update_user_incar_settings_maker( vasp_maker: BaseVaspMaker, nbands: int, structure: Structure, - prev_vasp_dir: Path | str, + prev_dir: Path | str, ) -> Response: """ Update the INCAR settings of a maker. @@ -143,13 +143,13 @@ def update_user_incar_settings_maker( Parameters ---------- vasp_maker : .BaseVaspMaker - A maker for the static run with all parammeters + A maker for the static run with all parameters relevant for Lobster. nbands : int integer indicating the correct number of bands structure : .Structure Structure object. - prev_vasp_dir : Path or str + prev_dir : Path or str Path or string to vasp files. Returns @@ -158,13 +158,13 @@ def update_user_incar_settings_maker( LobsterStaticMaker with correct number of bands. """ vasp_maker = update_user_incar_settings(vasp_maker, {"NBANDS": nbands}) - vasp_job = vasp_maker.make(structure=structure, prev_vasp_dir=prev_vasp_dir) + vasp_job = vasp_maker.make(structure=structure, prev_dir=prev_dir) return Response(replace=vasp_job) @job def get_lobster_jobs( - lobster_maker: LobsterMaker, + lobster_maker: LobsterMaker | None, basis_dict: dict, optimization_dir: Path | str, optimization_uuid: str, @@ -176,7 +176,7 @@ def get_lobster_jobs( Parameters ---------- - lobster_maker : .LobsterMaker + lobster_maker : .LobsterMaker or None maker for the Lobster jobs basis_dict : dict dict including basis set information. @@ -205,16 +205,15 @@ def get_lobster_jobs( "lobster_task_documents": [], } - if lobster_maker is None: - lobster_maker = LobsterMaker() + lobster_maker = lobster_maker or LobsterMaker() - for i, basis in enumerate(basis_dict): - lobsterjob = lobster_maker.make(wavefunction_dir=static_dir, basis_dict=basis) - lobsterjob.append_name(f"_run_{i}") - outputs["lobster_uuids"].append(lobsterjob.output.uuid) - outputs["lobster_dirs"].append(lobsterjob.output.dir_name) - outputs["lobster_task_documents"].append(lobsterjob.output) - jobs.append(lobsterjob) + for idx, basis in enumerate(basis_dict): + lobster_job = lobster_maker.make(wavefunction_dir=static_dir, basis_dict=basis) + lobster_job.append_name(f"_run_{idx}") + outputs["lobster_uuids"].append(lobster_job.output.uuid) + outputs["lobster_dirs"].append(lobster_job.output.dir_name) + outputs["lobster_task_documents"].append(lobster_job.output) + jobs.append(lobster_job) flow = Flow(jobs, output=outputs) return Response(replace=flow) diff --git a/src/atomate2/vasp/jobs/matpes.py b/src/atomate2/vasp/jobs/matpes.py index 0031c675ac..d22d7f7f44 100644 --- a/src/atomate2/vasp/jobs/matpes.py +++ b/src/atomate2/vasp/jobs/matpes.py @@ -22,7 +22,7 @@ @dataclass class MatPesGGAStaticMaker(BaseVaspMaker): """ - Maker to create VASP static job using r2SCAN by default. + Maker to create VASP static job using PBE by default. Parameters ---------- @@ -52,7 +52,6 @@ class MatPesGGAStaticMaker(BaseVaspMaker): input_set_generator: VaspInputGenerator = field( default_factory=MatPesGGAStaticSetGenerator ) - inherit_incar: bool = False @dataclass @@ -88,4 +87,3 @@ class MatPesMetaGGAStaticMaker(BaseVaspMaker): input_set_generator: VaspInputGenerator = field( default_factory=MatPesMetaGGAStaticSetGenerator ) - inherit_incar: bool = False diff --git a/src/atomate2/vasp/jobs/md.py b/src/atomate2/vasp/jobs/md.py new file mode 100644 index 0000000000..aa3aae99e6 --- /dev/null +++ b/src/atomate2/vasp/jobs/md.py @@ -0,0 +1,128 @@ +"""Module defining molecular dynamics jobs.""" + +from __future__ import annotations + +import logging +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +from custodian.vasp.handlers import ( + FrozenJobErrorHandler, + IncorrectSmearingHandler, + LargeSigmaHandler, + MeshSymmetryErrorHandler, + PositiveEnergyErrorHandler, + StdErrHandler, + VaspErrorHandler, +) +from emmet.core.vasp.calculation import StoreTrajectoryOption +from jobflow import Response, job + +from atomate2.vasp.jobs.base import BaseVaspMaker +from atomate2.vasp.schemas.md import MultiMDOutput +from atomate2.vasp.sets.core import MDSetGenerator + +if TYPE_CHECKING: + from pathlib import Path + + from pymatgen.core import Structure + + from atomate2.vasp.sets.base import VaspInputGenerator + + +logger = logging.getLogger(__name__) + + +@dataclass +class MDMaker(BaseVaspMaker): + """ + Maker to create VASP molecular dynamics jobs. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .VaspInputSetGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_vasp_input_set`. + copy_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`. + run_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_vasp`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "molecular dynamics" + + input_set_generator: VaspInputGenerator = field(default_factory=MDSetGenerator) + + # Explicitly pass the handlers to not use the default ones. Some default handlers + # such as PotimErrorHandler do not apply to MD runs. + run_vasp_kwargs: dict = field( + default_factory=lambda: { + "handlers": ( + VaspErrorHandler(), + MeshSymmetryErrorHandler(), + PositiveEnergyErrorHandler(), + FrozenJobErrorHandler(), + StdErrHandler(), + LargeSigmaHandler(), + IncorrectSmearingHandler(), + ) + } + ) + + # Store ionic steps info in a pymatgen Trajectory object instead of in the output + # document. + task_document_kwargs: dict = field( + default_factory=lambda: {"store_trajectory": StoreTrajectoryOption.PARTIAL} + ) + + +@job(output_schema=MultiMDOutput) +def md_output( + structure: Structure, + vasp_dir: str | Path, + traj_ids: list[str], + prev_traj_ids: list[str] | None, +) -> Response: + """ + Collect output references of a multistep MD flow. + + Parameters + ---------- + structure: .Structure + The final structure to be stored. + vasp_dir: str or Path + The path to the folder containing the last calculation of a MultiMDMaker. + traj_ids: list of str + List of the uuids of the jobs that will compose the trajectory. + prev_traj_ids: list of str + List of the uuids of the jobs coming from previous flow that will be + added to the trajectory. + + Returns + ------- + The output dictionary. + """ + full_traj_ids = list(traj_ids) + if prev_traj_ids: + full_traj_ids = prev_traj_ids + full_traj_ids + output = MultiMDOutput.from_structure( + structure=structure, + meta_structure=structure, + vasp_dir=str(vasp_dir), + traj_ids=traj_ids, + full_traj_ids=full_traj_ids, + ) + return Response(output=output) diff --git a/src/atomate2/vasp/jobs/phonons.py b/src/atomate2/vasp/jobs/phonons.py new file mode 100644 index 0000000000..8b8a169560 --- /dev/null +++ b/src/atomate2/vasp/jobs/phonons.py @@ -0,0 +1,60 @@ +"""Define the PhononDisplacementMaker for VASP.""" + +from dataclasses import dataclass, field + +from atomate2.vasp.jobs.base import BaseVaspMaker +from atomate2.vasp.sets.base import VaspInputGenerator +from atomate2.vasp.sets.core import StaticSetGenerator + + +@dataclass +class PhononDisplacementMaker(BaseVaspMaker): + """ + Maker to perform a static calculation as a part of the finite displacement method. + + The input set is for a static run with tighter convergence parameters. + Both the k-point mesh density and convergence parameters + are stricter than a normal relaxation. + + Parameters + ---------- + name : str + The job name. + input_set_generator : .VaspInputGenerator + A generator used to make the input set. + write_input_set_kwargs : dict + Keyword arguments that will get passed to :obj:`.write_vasp_input_set`. + copy_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`. + run_vasp_kwargs : dict + Keyword arguments that will get passed to :obj:`.run_vasp`. + task_document_kwargs : dict + Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`. + stop_children_kwargs : dict + Keyword arguments that will get passed to :obj:`.should_stop_children`. + write_additional_data : dict + Additional data to write to the current directory. Given as a dict of + {filename: data}. Note that if using FireWorks, dictionary keys cannot contain + the "." character which is typically used to denote file extensions. To avoid + this, use the ":" character, which will automatically be converted to ".". E.g. + ``{"my_file:txt": "contents of the file"}``. + """ + + name: str = "phonon static" + input_set_generator: VaspInputGenerator = field( + default_factory=lambda: StaticSetGenerator( + user_kpoints_settings={"reciprocal_density": 100}, + user_incar_settings={ + "IBRION": 2, + "ISIF": 3, + "ENCUT": 700, + "EDIFF": 1e-7, + "LAECHG": False, + "LREAL": False, + "ALGO": "Normal", + "NSW": 0, + "LCHARG": False, + }, + auto_ispin=True, + ) + ) diff --git a/src/atomate2/vasp/powerups.py b/src/atomate2/vasp/powerups.py index a050654628..c73813bbbb 100644 --- a/src/atomate2/vasp/powerups.py +++ b/src/atomate2/vasp/powerups.py @@ -8,6 +8,8 @@ from jobflow import Flow, Job, Maker from pymatgen.io.vasp import Kpoints +from atomate2.common.powerups import add_metadata_to_flow as base_add_metadata_to_flow +from atomate2.common.powerups import update_custodian_handlers as base_custodian_handler from atomate2.vasp.jobs.base import BaseVaspMaker @@ -277,3 +279,58 @@ def use_auto_ispin( name_filter=name_filter, class_filter=class_filter, ) + + +def add_metadata_to_flow( + flow: Flow, additional_fields: dict, class_filter: Maker = BaseVaspMaker +) -> Flow: + """ + Return the VASP flow with additional field(metadata) to the task doc. + + This allows adding metadata to the task-docs, could be useful + to query results from DB. + + Parameters + ---------- + flow : Flow + The flow to which to add metadata. + additional_fields : dict + A dict with metadata. + class_filter: .BaseVaspMaker + The Maker to which additional metadata needs to be added + + Returns + ------- + Flow + Flow with added metadata to the task-doc. + """ + return base_add_metadata_to_flow( + flow=flow, class_filter=class_filter, additional_fields=additional_fields + ) + + +def update_vasp_custodian_handlers( + flow: Flow, custom_handlers: tuple, class_filter: Maker = BaseVaspMaker +) -> Flow: + """ + Return the flow with custom custodian handlers for VASP jobs. + + This allows user to selectively set error correcting handlers for VASP jobs + or completely unset error handlers. + + Parameters + ---------- + flow: + custom_handlers : tuple + A tuple with custodian handlers. + class_filter: .Maker + The Maker to which custom custodian handler needs to be added + + Returns + ------- + Flow + Flow with modified custodian handlers. + """ + return base_custodian_handler( + flow=flow, custom_handlers=custom_handlers, class_filter=class_filter + ) diff --git a/src/atomate2/vasp/run.py b/src/atomate2/vasp/run.py index 0553980700..23741a960f 100644 --- a/src/atomate2/vasp/run.py +++ b/src/atomate2/vasp/run.py @@ -18,6 +18,7 @@ from custodian.vasp.handlers import ( FrozenJobErrorHandler, IncorrectSmearingHandler, + KspacingMetalHandler, LargeSigmaHandler, MeshSymmetryErrorHandler, NonConvergingErrorHandler, @@ -41,7 +42,7 @@ from emmet.core.tasks import TaskDoc -_DEFAULT_HANDLERS = ( +DEFAULT_HANDLERS = ( VaspErrorHandler(), MeshSymmetryErrorHandler(), UnconvergedErrorHandler(), @@ -52,6 +53,7 @@ StdErrHandler(), LargeSigmaHandler(), IncorrectSmearingHandler(), + KspacingMetalHandler(), ) _DEFAULT_VALIDATORS = (VasprunXMLValidator(), VaspFilesValidator()) @@ -85,7 +87,7 @@ def run_vasp( vasp_gamma_cmd: str = SETTINGS.VASP_GAMMA_CMD, max_errors: int = SETTINGS.VASP_CUSTODIAN_MAX_ERRORS, scratch_dir: str = SETTINGS.CUSTODIAN_SCRATCH_DIR, - handlers: Sequence[ErrorHandler] = _DEFAULT_HANDLERS, + handlers: Sequence[ErrorHandler] = DEFAULT_HANDLERS, validators: Sequence[Validator] = _DEFAULT_VALIDATORS, wall_time: int | None = None, vasp_job_kwargs: dict[str, Any] = None, @@ -134,7 +136,7 @@ def run_vasp( if job_type == JobType.DIRECT: logger.info(f"Running command: {vasp_cmd}") - return_code = subprocess.call(vasp_cmd, shell=True) + return_code = subprocess.call(vasp_cmd, shell=True) # noqa: S602 logger.info(f"{vasp_cmd} finished running with returncode: {return_code}") return diff --git a/src/atomate2/vasp/schemas/defect.py b/src/atomate2/vasp/schemas/defect.py index 07cb590402..f6f5a18795 100644 --- a/src/atomate2/vasp/schemas/defect.py +++ b/src/atomate2/vasp/schemas/defect.py @@ -6,6 +6,7 @@ from pydantic import BaseModel, Field from pymatgen.io.vasp.outputs import WSWQ +from typing_extensions import Self logger = logging.getLogger(__name__) @@ -36,9 +37,8 @@ def from_directory( directory: Union[str, Path], ref_dir: Optional[Union[str, Path]] = None, distorted_dirs: Optional[list[str]] = None, - ) -> "FiniteDifferenceDocument": - """ - Read the FiniteDiff file. + ) -> Self: + """Read the FiniteDiff file. Parameters ---------- diff --git a/src/atomate2/vasp/schemas/elph.py b/src/atomate2/vasp/schemas/elph.py index 3b3751bc6d..9c990dfa05 100644 --- a/src/atomate2/vasp/schemas/elph.py +++ b/src/atomate2/vasp/schemas/elph.py @@ -8,6 +8,7 @@ from pymatgen.core import Structure from pymatgen.electronic_structure.bandstructure import BandStructure from pymatgen.electronic_structure.core import Spin +from typing_extensions import Self logger = logging.getLogger(__name__) @@ -116,7 +117,7 @@ def from_band_structures( elph_uuid: str, elph_dir: str, original_structure: Structure, - ) -> "ElectronPhononRenormalisationDoc": + ) -> Self: """ Calculate an electron-phonon renormalisation document from band structures. @@ -162,7 +163,7 @@ def from_band_structures( "renormalisation" ) - if len({b.is_spin_polarized for b in displacement_band_structures}) != 1: + if len({band.is_spin_polarized for band in displacement_band_structures}) != 1: raise ValueError( "Some displacement bands structures are spin polarized and some are " "spin paired. Cannot continue." @@ -180,17 +181,20 @@ def from_band_structures( # discard metallic displacement calculations and log the issue keep = [] - for i, band_structure in enumerate(displacement_band_structures): + for idx, band_structure in enumerate(displacement_band_structures): if band_structure.is_metal(): - logger.warning("T = {} K band structure is metallic... skipping") + temp = temperatures[idx] + logger.warning(f"T = {temp} K band structure is metallic... skipping") else: - keep.append(i) + keep.append(idx) - temperatures = [temperatures[i] for i in keep] - displacement_band_structures = [displacement_band_structures[i] for i in keep] - displacement_structures = [displacement_structures[i] for i in keep] - displacement_dirs = [displacement_dirs[i] for i in keep] - displacement_uuids = [displacement_uuids[i] for i in keep] + temperatures = [temperatures[idx] for idx in keep] + displacement_band_structures = [ + displacement_band_structures[idx] for idx in keep + ] + displacement_structures = [displacement_structures[idx] for idx in keep] + displacement_dirs = [displacement_dirs[idx] for idx in keep] + displacement_uuids = [displacement_uuids[idx] for idx in keep] vbm_band_indices, cbm_band_indices = _get_band_edge_indices(bulk_band_structure) bulk_vbm = bulk_band_structure.get_vbm()["energy"] diff --git a/src/atomate2/vasp/schemas/md.py b/src/atomate2/vasp/schemas/md.py new file mode 100644 index 0000000000..c3b6364fb9 --- /dev/null +++ b/src/atomate2/vasp/schemas/md.py @@ -0,0 +1,16 @@ +"""Schemas for MD documents.""" + +from emmet.core.structure import StructureMetadata +from pydantic import Field +from pymatgen.core import Structure + + +class MultiMDOutput(StructureMetadata): + """Output of a MultiMD Flow.""" + + structure: Structure = Field("Final structure of the last step of the flow") + vasp_dir: str = Field("Path to the last vasp folder of the flow") + traj_ids: list[str] = Field("List of uuids of the MD calculations in the flow") + full_traj_ids: list[str] = Field( + "List of uuids of the MD calculations in the flow and in previous linked flows" + ) diff --git a/src/atomate2/vasp/sets/base.py b/src/atomate2/vasp/sets/base.py index 692367fe04..89b3e3dd19 100644 --- a/src/atomate2/vasp/sets/base.py +++ b/src/atomate2/vasp/sets/base.py @@ -7,6 +7,7 @@ import warnings from copy import deepcopy from dataclasses import dataclass, field +from importlib.resources import files as get_mod_path from itertools import groupby from pathlib import Path from typing import TYPE_CHECKING, Any @@ -14,7 +15,6 @@ import numpy as np from monty.io import zopen from monty.serialization import loadfn -from pkg_resources import resource_filename from pymatgen.electronic_structure.core import Magmom from pymatgen.io.core import InputGenerator, InputSet from pymatgen.io.vasp import Incar, Kpoints, Outcar, Poscar, Potcar, Vasprun @@ -33,8 +33,7 @@ from pymatgen.core import Structure - -_BASE_VASP_SET = loadfn(resource_filename("atomate2.vasp.sets", "BaseVaspSet.yaml")) +_BASE_VASP_SET = loadfn(get_mod_path("atomate2.vasp.sets") / "BaseVaspSet.yaml") class VaspInputSet(InputSet): @@ -78,8 +77,7 @@ def write_input( overwrite: bool = True, potcar_spec: bool = False, ) -> None: - """ - Write VASP input files to a directory. + """Write VASP input files to a directory. Parameters ---------- @@ -94,11 +92,7 @@ def write_input( if make_dir: os.makedirs(directory, exist_ok=True) - inputs = { - "INCAR": self.incar, - "KPOINTS": self.kpoints, - "POSCAR": self.poscar, - } + inputs = {"INCAR": self.incar, "KPOINTS": self.kpoints, "POSCAR": self.poscar} inputs.update(self.optional_files) if isinstance(self.potcar, Potcar): @@ -106,23 +100,22 @@ def write_input( else: inputs["POTCAR.spec"] = "\n".join(self.potcar) - for k, v in inputs.items(): - if v is not None and (overwrite or not (directory / k).exists()): - with zopen(directory / k, "wt") as f: - if isinstance(v, Poscar): + for key, val in inputs.items(): + if val is not None and (overwrite or not (directory / key).exists()): + with zopen(directory / key, mode="wt") as file: + if isinstance(val, Poscar): # write POSCAR with more significant figures - f.write(v.get_string(significant_figures=16)) + file.write(val.get_str(significant_figures=16)) else: - f.write(v.__str__()) - elif not overwrite and (directory / k).exists(): - raise FileExistsError(f"{directory / k} already exists.") + file.write(str(val)) + elif not overwrite and (directory / key).exists(): + raise FileExistsError(f"{directory / key} already exists.") @staticmethod def from_directory( directory: str | Path, optional_files: dict = None ) -> VaspInputSet: - """ - Load a set of VASP inputs from a directory. + """Load a set of VASP inputs from a directory. Note that only the standard INCAR, POSCAR, POTCAR and KPOINTS files are read unless optional_filenames is specified. @@ -155,14 +148,7 @@ def from_directory( @property def is_valid(self) -> bool: - """ - Whether the input set is valid. - - Returns - ------- - bool - Whether the input set is valid. - """ + """Whether the input set is valid.""" if self.incar.get("KSPACING", 0) > 0.5 and self.incar.get("ISMEAR", 0) == -5: warnings.warn( "Large KSPACING value detected with ISMEAR=-5. Ensure that VASP " @@ -171,38 +157,41 @@ def is_valid(self) -> bool: stacklevel=1, ) + ismear = self.incar.get("ISMEAR", 1) + sigma = self.incar.get("SIGMA", 0.2) if ( - all(k.is_metal for k in self.poscar.structure.composition) + all(elem.is_metal for elem in self.poscar.structure.composition) and self.incar.get("NSW", 0) > 0 - and self.incar.get("ISMEAR", 1) < 1 + and (ismear < 0 or (ismear == 0 and sigma > 0.05)) ): + ismear_docs = "https://www.vasp.at/wiki/index.php/ISMEAR" + msg = "" + if ismear < 0: + msg = f"Relaxation of likely metal with ISMEAR < 0 ({ismear})." + elif ismear == 0 and sigma > 0.05: + msg = f"ISMEAR = 0 with a small SIGMA ({sigma}) detected." warnings.warn( - "Relaxation of likely metal with ISMEAR < 1 detected. Please see VASP " - "recommendations on ISMEAR for metals.", + f"{msg} See VASP recommendations on ISMEAR for metals ({ismear_docs}).", BadInputSetWarning, stacklevel=1, ) - if self.incar.get("LHFCALC", False) is True and self.incar.get( - "ALGO", "Normal" - ) not in ["Normal", "All", "Damped"]: + algo = self.incar.get("ALGO", "Normal") + if self.incar.get("LHFCALC") and algo not in ("Normal", "All", "Damped"): warnings.warn( "Hybrid functionals only support Algo = All, Damped, or Normal.", BadInputSetWarning, stacklevel=1, ) - if not self.incar.get("LASPH", False) and ( + if not self.incar.get("LASPH") and ( self.incar.get("METAGGA") - or self.incar.get("LHFCALC", False) - or self.incar.get("LDAU", False) - or self.incar.get("LUSE_VDW", False) + or self.incar.get("LHFCALC") + or self.incar.get("LDAU") + or self.incar.get("LUSE_VDW") ): - warnings.warn( - "LASPH = True should be set for +U, meta-GGAs, hybrids, and vdW-DFT", - BadInputSetWarning, - stacklevel=1, - ) + msg = "LASPH = True should be set for +U, meta-GGAs, hybrids, and vdW-DFT" + warnings.warn(msg, BadInputSetWarning, stacklevel=1) return True @@ -234,8 +223,9 @@ class VaspInputGenerator(InputGenerator): so these keys can be defined in one of two ways, e.g. either {"LDAUU":{"O":{"Fe":5}}} to set LDAUU for Fe to 5 in an oxide, or {"LDAUU":{"Fe":5}} to set LDAUU to 5 regardless of the input structure. - To set magmoms, pass a dict mapping element symbols to magnetic moments, e.g. - {"MAGMOM": {"Co": 1}}. + To set magmoms, pass a dict mapping the strings of species to magnetic + moments, e.g. {"MAGMOM": {"Co": 1}} or {"MAGMOM": {"Fe2+,spin=4": 3.7}} in the + case of a site with Species("Fe2+", spin=4). If None is given, that key is unset. For example, {"ENCUT": None} will remove ENCUT from the incar settings. user_kpoints_settings @@ -245,8 +235,8 @@ class VaspInputGenerator(InputGenerator): Allow user to override POTCARs. E.g., {"Gd": "Gd_3"}. user_potcar_functional Functional to use. Default is to use the functional in the config dictionary. - Valid values: "PBE", "PBE_52", "PBE_54", "LDA", "LDA_52", "LDA_54", "PW91", - "LDA_US", "PW91_US". + Valid values: "PBE", "PBE_52", "PBE_54", "PBE_64", "LDA", "LDA_52", "LDA_54", + "LDA_64", "PW91", "LDA_US", "PW91_US". auto_ismear If true, the values for ISMEAR and SIGMA will be set automatically depending on the bandgap of the system. If the bandgap is not known (e.g., there is no @@ -267,7 +257,7 @@ class VaspInputGenerator(InputGenerator): auto_kspacing If true, automatically use the VASP recommended KSPACING based on bandgap, i.e. higher kpoint spacing for insulators than metals. Can be boolean or float. - If float, then the value will interpreted as the bandgap in eV to use for the + If a float, the value will be interpreted as the bandgap in eV to use for the KSPACING calculation. constrain_total_magmom Whether to constrain the total magmom (NUPDOWN in INCAR) to be the sum of the @@ -276,7 +266,7 @@ class VaspInputGenerator(InputGenerator): Ensure that missing magmom values are filled in with the default value of 1.0. use_structure_charge If set to True, then the overall charge of the structure (``structure.charge``) - is used to set NELECT. + is used to set NELECT. sort_structure Whether to sort the structure (using the default sort order of electronegativity) before generating input files. Defaults to True, the behavior @@ -389,8 +379,7 @@ def get_input_set( prev_dir: str | Path = None, potcar_spec: bool = False, ) -> VaspInputSet: - """ - Get a VASP input set. + """Get a VASP input set. Note, if both ``structure`` and ``prev_dir`` are set, then the structure specified will be preferred over the final structure from the last VASP run. @@ -436,10 +425,20 @@ def get_input_set( bandgap=bandgap, ispin=ispin, ) + site_properties = structure.site_properties + poscar = Poscar( + structure, + velocities=site_properties.get("velocities"), + predictor_corrector=site_properties.get("predictor_corrector"), + predictor_corrector_preamble=structure.properties.get( + "predictor_corrector_preamble" + ), + lattice_velocities=structure.properties.get("lattice_velocities"), + ) return VaspInputSet( incar=incar, kpoints=kpoints, - poscar=Poscar(structure), + poscar=poscar, potcar=self._get_potcar(structure, potcar_spec=potcar_spec), ) @@ -451,8 +450,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for this calculation type. + """Get updates to the INCAR for this calculation type. Parameters ---------- @@ -482,8 +480,7 @@ def get_kpoints_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the kpoints configuration for this calculation type. + """Get updates to the kpoints configuration for this calculation type. Note, these updates will be ignored if the user has set user_kpoint_settings. @@ -508,8 +505,7 @@ def get_kpoints_updates( return {} def get_nelect(self, structure: Structure) -> float: - """ - Get the default number of electrons for a given structure. + """Get the default number of electrons for a given structure. Parameters ---------- @@ -535,7 +531,7 @@ def _get_previous( ) -> tuple: """Load previous calculation outputs and decide which structure to use.""" if structure is None and prev_dir is None: - raise ValueError("Either structure or prev_dir must be set.") + raise ValueError("Either structure or prev_dir must be set") prev_incar = {} prev_structure = None @@ -550,13 +546,13 @@ def _get_previous( # CONTCAR is already renamed POSCAR contcars = list(glob.glob(str(path_prev_dir / "POSCAR*"))) - contcarfile_fullpath = str(path_prev_dir / "POSCAR") - contcarfile = ( - contcarfile_fullpath - if contcarfile_fullpath in contcars - else sorted(contcars)[-1] + contcar_file_fullpath = str(path_prev_dir / "POSCAR") + contcar_file = ( + contcar_file_fullpath + if contcar_file_fullpath in contcars + else max(contcars) ) - contcar = Poscar.from_file(contcarfile) + contcar = Poscar.from_file(contcar_file) if vasprun.efermi is None: # VASP doesn't output efermi in vasprun if IBRION = 1 @@ -639,19 +635,21 @@ def _get_incar( # generate incar incar = Incar() - for k, v in incar_settings.items(): - if k == "MAGMOM": - incar[k] = _get_magmoms( + for key, val in incar_settings.items(): + if key == "MAGMOM": + incar[key] = get_magmoms( structure, - magmoms=self.user_incar_settings.get("MAGMOMS", {}), + magmoms=self.user_incar_settings.get("MAGMOM", {}), config_magmoms=config_magmoms, ) - elif k in ("LDAUU", "LDAUJ", "LDAUL") and incar_settings.get("LDAU", False): - incar[k] = _get_u_param(k, v, structure) - elif k.startswith("EDIFF") and k != "EDIFFG": - incar["EDIFF"] = _get_ediff(k, v, structure, incar_settings) + elif key in ("LDAUU", "LDAUJ", "LDAUL") and incar_settings.get( + "LDAU", False + ): + incar[key] = _get_u_param(key, val, structure) + elif key.startswith("EDIFF") and key != "EDIFFG": + incar["EDIFF"] = _get_ediff(key, val, structure, incar_settings) else: - incar[k] = v + incar[key] = val _set_u_params(incar, incar_settings, structure) # apply previous incar settings, be careful not to override user_incar_settings @@ -714,7 +712,9 @@ def _get_incar( # Finally, re-apply `self.user_incar_settings` to make sure any accidentally # overwritten settings are changed back to the intended values. - _apply_incar_updates(incar, self.user_incar_settings) + # skip dictionary parameters to avoid dictionaries appearing in the INCAR + skip = ["LDAUU", "LDAUJ", "LDAUL", "MAGMOM"] + _apply_incar_updates(incar, self.user_incar_settings, skip=skip) return incar @@ -877,18 +877,15 @@ def _get_kpoints( return _combine_kpoints(base_kpoints, zero_weighted_kpoints, added_kpoints) - def _kspacing(self, incar_updates) -> float | None: + def _kspacing(self, incar_updates: dict[str, Any]) -> float | None: """Get KSPACING value based on the config dict, updates and user settings.""" - if "KSPACING" in self.user_incar_settings: - return self.user_incar_settings["KSPACING"] - if "KSPACING" in incar_updates: - return incar_updates["KSPACING"] - if "KSPACING" in self.config_dict["INCAR"]: - return self.config_dict["INCAR"]["KSPACING"] - return None + key = "KSPACING" + return self.user_incar_settings.get( + key, incar_updates.get(key, self.config_dict["INCAR"].get(key)) + ) -def _get_magmoms( +def get_magmoms( structure: Structure, magmoms: dict[str, float] = None, config_magmoms: dict[str, float] = None, @@ -928,7 +925,9 @@ def _get_magmoms( return mag -def _get_u_param(lda_param, lda_config, structure: Structure) -> list[float]: +def _get_u_param( + lda_param: str, lda_config: dict[str, Any], structure: Structure +) -> list[float]: """Get U parameters.""" comp = structure.composition elements = sorted((el for el in comp.elements if comp[el] > 0), key=lambda e: e.X) @@ -949,14 +948,18 @@ def _get_u_param(lda_param, lda_config, structure: Structure) -> list[float]: ] -def _get_ediff(param, value, structure: Structure, incar_settings) -> float: +def _get_ediff( + param: str, value: str | float, structure: Structure, incar_settings: dict[str, Any] +) -> float: """Get EDIFF.""" if incar_settings.get("EDIFF") is None and param == "EDIFF_PER_ATOM": return float(value) * structure.num_sites return float(incar_settings["EDIFF"]) -def _set_u_params(incar: Incar, incar_settings, structure: Structure) -> None: +def _set_u_params( + incar: Incar, incar_settings: dict[str, Any], structure: Structure +) -> None: """Modify INCAR for use with U parameters.""" has_u = incar_settings.get("LDAU") and sum(incar["LDAUU"]) > 0 @@ -978,7 +981,9 @@ def _set_u_params(incar: Incar, incar_settings, structure: Structure) -> None: incar.setdefault("LMAXMIX", 4) -def _apply_incar_updates(incar, updates, skip: Sequence[str] = ()) -> None: +def _apply_incar_updates( + incar: dict[str, Any], updates: dict[str, Any], skip: Sequence[str] = () +) -> None: """ Apply updates to an INCAR file. @@ -991,17 +996,19 @@ def _apply_incar_updates(incar, updates, skip: Sequence[str] = ()) -> None: skip Keys to skip. """ - for k, v in updates.items(): - if k in skip: + for key, val in updates.items(): + if key in skip: continue - if v is None: - incar.pop(k, None) + if val is None: + incar.pop(key, None) else: - incar[k] = v + incar[key] = val -def _remove_unused_incar_params(incar, skip: Sequence[str] = ()) -> None: +def _remove_unused_incar_params( + incar: dict[str, Any], skip: Sequence[str] = () +) -> None: """ Remove INCAR parameters that are not actively used by VASP. @@ -1024,8 +1031,8 @@ def _remove_unused_incar_params(incar, skip: Sequence[str] = ()) -> None: incar.pop("MAGMOM", None) # Turn off +U flags if +U is not even used - ldau_flags = ["LDAUU", "LDAUJ", "LDAUL", "LDAUTYPE"] - if incar.get("LDAU", False) is False: + ldau_flags = ("LDAUU", "LDAUJ", "LDAUL", "LDAUTYPE") + if not incar.get("LDAU"): for ldau_flag in ldau_flags: if ldau_flag not in skip: incar.pop(ldau_flag, None) @@ -1033,19 +1040,16 @@ def _remove_unused_incar_params(incar, skip: Sequence[str] = ()) -> None: def _combine_kpoints(*kpoints_objects: Kpoints) -> Kpoints: """Combine k-points files together.""" - labels = [] - kpoints = [] - weights = [] + labels, kpoints, weights = [], [], [] + recip_mode = Kpoints.supported_modes.Reciprocal for kpoints_object in filter(None, kpoints_objects): - if kpoints_object.style != Kpoints.supported_modes.Reciprocal: + if kpoints_object.style != recip_mode: raise ValueError( - "Can only combine kpoints with style=Kpoints.supported_modes.Reciprocal" + f"Can only combine kpoints with style {recip_mode}, " + f"got {kpoints_object.style}" ) - if kpoints_object.labels is None: - labels.append([""] * len(kpoints_object.kpts)) - else: - labels.append(kpoints_object.labels) + labels.append(kpoints_object.labels or [""] * len(kpoints_object.kpts)) weights.append(kpoints_object.kpts_weights) kpoints.append(kpoints_object.kpts) @@ -1055,7 +1059,7 @@ def _combine_kpoints(*kpoints_objects: Kpoints) -> Kpoints: kpoints = np.concatenate(kpoints) return Kpoints( comment="Combined k-points", - style=Kpoints.supported_modes.Reciprocal, + style=recip_mode, num_kpts=len(kpoints), kpts=kpoints, labels=labels, diff --git a/src/atomate2/vasp/sets/core.py b/src/atomate2/vasp/sets/core.py index a405eb9fd0..1ce14b4f84 100644 --- a/src/atomate2/vasp/sets/core.py +++ b/src/atomate2/vasp/sets/core.py @@ -33,8 +33,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for a relaxation job. + """Get updates to the INCAR for a relaxation job. Parameters ---------- @@ -69,8 +68,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for a tight relaxation job. + """Get updates to the INCAR for a tight relaxation job. Parameters ---------- @@ -131,8 +129,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for a static VASP job. + """Get updates to the INCAR for a static VASP job. Parameters ---------- @@ -157,7 +154,7 @@ def get_incar_updates( # LPEAD=T: numerical evaluation of overlap integral prevents LRF_COMMUTATOR # errors and can lead to better expt. agreement but produces slightly # different results - updates.update({"IBRION": 8, "LEPSILON": True, "LPEAD": True, "NSW": 1}) + updates.update(IBRION=8, LEPSILON=True, LPEAD=True, NSW=1) if self.lcalcpol: updates["LCALCPOL"] = True @@ -217,8 +214,7 @@ def get_kpoints_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the kpoints configuration for a non-self consistent VASP job. + """Get updates to the kpoints configuration for a non-self consistent VASP job. Note, these updates will be ignored if the user has set user_kpoint_settings. @@ -259,8 +255,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for a non-self-consistent field VASP job. + """Get updates to the INCAR for a non-self-consistent field VASP job. Parameters ---------- @@ -300,14 +295,14 @@ def get_incar_updates( n_edos = _get_nedos(vasprun, self.dedos) # use tetrahedron method for DOS and optics calculations - updates.update({"ISMEAR": -5, "ISYM": 2, "NEDOS": n_edos}) + updates.update(ISMEAR=-5, ISYM=2, NEDOS=n_edos) elif self.mode in ("line", "boltztrap"): # if line mode or explicit k-points (boltztrap) can't use ISMEAR=-5 # use small sigma to avoid partial occupancies for small band gap materials # use a larger sigma if the material is a metal sigma = 0.2 if bandgap == 0 else 0.01 - updates.update({"ISMEAR": 0, "SIGMA": sigma}) + updates.update(ISMEAR=0, SIGMA=sigma) if self.optics: # LREAL not supported with LOPTICS = True; automatic NEDOS usually @@ -339,8 +334,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for a VASP HSE06 relaxation job. + """Get updates to the INCAR for a VASP HSE06 relaxation job. Parameters ---------- @@ -392,8 +386,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for a HSE tight relaxation job. + """Get updates to the INCAR for an HSE tight relaxation job. Parameters ---------- @@ -451,8 +444,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for a VASP HSE06 static job. + """Get updates to the INCAR for a VASP HSE06 static job. Parameters ---------- @@ -567,8 +559,7 @@ def get_kpoints_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the kpoints configuration for a VASP HSE06 band structure job. + """Get updates to the kpoints configuration for a VASP HSE06 band structure job. Note, these updates will be ignored if the user has set user_kpoint_settings. @@ -597,9 +588,9 @@ def get_kpoints_updates( kpoints["zero_weighted_line_density"] = self.line_density elif self.mode == "uniform_dense": - kpoints[ - "zero_weighted_reciprocal_density" - ] = self.zero_weighted_reciprocal_density + kpoints["zero_weighted_reciprocal_density"] = ( + self.zero_weighted_reciprocal_density + ) added_kpoints = deepcopy(self.added_kpoints) if vasprun is not None and self.mode == "gap": @@ -620,8 +611,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for a VASP HSE06 band structure job. + """Get updates to the INCAR for a VASP HSE06 band structure job. Parameters ---------- @@ -661,12 +651,12 @@ def get_incar_updates( nedos = _get_nedos(vasprun, self.dedos) # use tetrahedron method for DOS and optics calculations - updates.update({"ISMEAR": -5, "NEDOS": nedos}) + updates.update(ISMEAR=-5, NEDOS=nedos) else: # if line mode or explicit k-points (gap) can't use ISMEAR=-5 # use small sigma to avoid partial occupancies for small band gap materials - updates.update({"ISMEAR": 0, "SIGMA": 0.01}) + updates.update(ISMEAR=0, SIGMA=0.01) if vasprun is not None: # set nbands @@ -675,7 +665,7 @@ def get_incar_updates( if self.optics: # LREAL not supported with LOPTICS - updates.update({"LOPTICS": True, "LREAL": False, "CSHIFT": 1e-5}) + updates.update(LOPTICS=True, LREAL=False, CSHIFT=1e-5) updates["MAGMOM"] = None @@ -723,8 +713,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for a static VASP job. + """Get updates to the INCAR for a static VASP job. Parameters ---------- @@ -772,8 +761,7 @@ def get_kpoints_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the kpoints configuration for a non-self consistent VASP job. + """Get updates to the kpoints configuration for a non-self consistent VASP job. Note, these updates will be ignored if the user has set user_kpoint_settings. @@ -823,7 +811,7 @@ class MDSetGenerator(VaspInputGenerator): start_temp: float = 300 end_temp: float = 300 nsteps: int = 1000 - time_step: int = 2 + time_step: float = 2 auto_ispin: bool = True def get_incar_updates( @@ -834,8 +822,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for a molecular dynamics job. + """Get updates to the INCAR for a molecular dynamics job. Parameters ---------- @@ -859,27 +846,25 @@ def get_incar_updates( # Based on pymatgen.io.vasp.sets.MPMDSet. updates.update( - { - "ENCUT": 520, - "TEBEG": self.start_temp, - "TEEND": self.end_temp, - "NSW": self.nsteps, - "POTIM": self.time_step, - "LCHARG": False, - "NELMIN": 4, - "MAXMIX": 20, - "NELM": 500, - "ISYM": 0, - "IBRION": 0, - "KBLOCK": 100, - "PREC": "Normal", - } + ENCUT=520, + TEBEG=self.start_temp, + TEEND=self.end_temp, + NSW=self.nsteps, + POTIM=self.time_step, + LCHARG=False, + NELMIN=4, + MAXMIX=20, + NELM=500, + ISYM=0, + IBRION=0, + KBLOCK=100, + PREC="Normal", ) if Element("H") in structure.species and updates["POTIM"] > 0.5: logger.warning( f"Molecular dynamics time step is {updates['POTIM']}, which is " - "typically too large for a structure containing H. Consider set it " + "typically too large for a structure containing H. Consider setting it " "to a value of 0.5 or smaller." ) diff --git a/src/atomate2/vasp/sets/eos.py b/src/atomate2/vasp/sets/eos.py new file mode 100644 index 0000000000..fa632bd44c --- /dev/null +++ b/src/atomate2/vasp/sets/eos.py @@ -0,0 +1,505 @@ +""" +Module defining equation of state (EOS) parameter sets. + +Three families of sets: default atomate2 params, +MP GGA compatible, and MP meta-GGA compatible +""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from importlib.resources import files as import_files +from typing import TYPE_CHECKING + +from monty.serialization import loadfn + +from atomate2.vasp.sets.base import VaspInputGenerator + +if TYPE_CHECKING: + from pymatgen.core import Structure + from pymatgen.io.vasp import Outcar, Vasprun + + +_BASE_MP_GGA_RELAX_SET = loadfn( + import_files("atomate2.vasp.sets") / "BaseMPGGASet.yaml" +) +_BASE_MP_R2SCAN_RELAX_SET = loadfn( + import_files("atomate2.vasp.sets") / "BaseMPR2SCANRelaxSet.yaml" +) + + +@dataclass +class EosSetGenerator(VaspInputGenerator): + """Class to generate VASP EOS deformation + relax input sets.""" + + force_gamma: bool = True + auto_ismear: bool = False + auto_kspacing: bool = False + inherit_incar: bool = False + + def get_incar_updates( + self, + structure: Structure, + prev_incar: dict = None, + bandgap: float = None, + vasprun: Vasprun = None, + outcar: Outcar = None, + ) -> dict: + """Get updates to the INCAR for a relaxation job. + + Parameters + ---------- + structure + A structure. + prev_incar + An incar from a previous calculation. + bandgap + The band gap. + vasprun + A vasprun from a previous calculation. + outcar + An outcar from a previous calculation. + + Returns + ------- + dict + A dictionary of updates to apply. + """ + return { + "NSW": 99, + "LCHARG": False, + "ISIF": 3, + "IBRION": 2, + "EDIFF": 1e-6, + "ENCUT": 680, + "ENAUG": 1360, + "LREAL": False, + "LWAVE": True, + "ISMEAR": 0, + "SIGMA": 0.05, + "KSPACING": 0.22, + } + + +# MPLegacy prefix = MP PBE-GGA compatible with atomate implementation +@dataclass +class MPLegacyEosRelaxSetGenerator(VaspInputGenerator): + """Class to generate atomate1-MP-compatible VASP GGA EOS relax input sets.""" + + config_dict: dict = field(default_factory=lambda: _BASE_MP_GGA_RELAX_SET) + auto_ismear: bool = False + auto_kspacing: bool = False + inherit_incar: bool = False + + def get_incar_updates( + self, + structure: Structure, + prev_incar: dict = None, + bandgap: float = None, + vasprun: Vasprun = None, + outcar: Outcar = None, + ) -> dict: + """Get updates to the INCAR for a relaxation job. + + Parameters + ---------- + structure + A structure. + prev_incar + An incar from a previous calculation. + bandgap + The band gap. + vasprun + A vasprun from a previous calculation. + outcar + An outcar from a previous calculation. + + Returns + ------- + dict + A dictionary of updates to apply. + """ + return { + "NSW": 99, + "LCHARG": False, + "ISIF": 3, + "IBRION": 2, + "EDIFF": 1e-6, + "ENCUT": 600, + "LREAL": False, + "LWAVE": True, + } + + def get_kpoints_updates( + self, + structure: Structure, + prev_incar: dict = None, + bandgap: float = 0.0, + vasprun: Vasprun = None, + outcar: Outcar = None, + ) -> dict: + """Get updates to the kpoints configuration for a non-self consistent VASP job. + + Note, these updates will be ignored if the user has set user_kpoint_settings. + + Parameters + ---------- + structure + A structure. + prev_incar + An incar from a previous calculation. + bandgap + The band gap. + vasprun + A vasprun from a previous calculation. + outcar + An outcar from a previous calculation. + + Returns + ------- + dict + A dictionary of updates to apply to the KPOINTS config. + """ + return {"grid_density": 7000} + + +@dataclass +class MPLegacyEosStaticSetGenerator(EosSetGenerator): + """Class to generate atomate1-MP-compatible VASP GGA EOS relax input sets.""" + + config_dict: dict = field(default_factory=lambda: _BASE_MP_GGA_RELAX_SET) + auto_ismear: bool = False + auto_kspacing: bool = False + inherit_incar: bool = False + + def get_incar_updates( + self, + structure: Structure, + prev_incar: dict = None, + bandgap: float = None, + vasprun: Vasprun = None, + outcar: Outcar = None, + ) -> dict: + """Get updates to the INCAR for a relaxation job. + + Parameters + ---------- + structure + A structure. + prev_incar + An incar from a previous calculation. + bandgap + The band gap. + vasprun + A vasprun from a previous calculation. + outcar + An outcar from a previous calculation. + + Returns + ------- + dict + A dictionary of updates to apply. + """ + # Original atomate wf_bulk_modulus had 600 eV cutoff + # and k-point grid_density = 7,000 + return { + "NSW": 0, + "LCHARG": False, + "EDIFF": 1e-6, + "ENCUT": 600, + "LREAL": False, + "LWAVE": False, + "IBRION": -1, + "ISMEAR": -5, + "LORBIT": 11, + "ALGO": "Normal", + } + + +# MPGGA prefix = MP GGA compatible +@dataclass +class MPGGAEosRelaxSetGenerator(VaspInputGenerator): + """Class to generate MP-compatible VASP GGA EOS relax input sets.""" + + config_dict: dict = field(default_factory=lambda: _BASE_MP_R2SCAN_RELAX_SET) + auto_ismear: bool = False + auto_kspacing: bool = False + inherit_incar: bool = False + + def get_incar_updates( + self, + structure: Structure, + prev_incar: dict = None, + bandgap: float = None, + vasprun: Vasprun = None, + outcar: Outcar = None, + ) -> dict: + """Get updates to the INCAR for a relaxation job. + + Parameters + ---------- + structure + A structure. + prev_incar + An incar from a previous calculation. + bandgap + The band gap. + vasprun + A vasprun from a previous calculation. + outcar + An outcar from a previous calculation. + + Returns + ------- + dict + A dictionary of updates to apply. + """ + return { + "NSW": 99, + "LCHARG": False, + "ISIF": 3, + "IBRION": 2, + "EDIFF": 1e-6, + "ALGO": "FAST", + "LREAL": False, + "LWAVE": True, + "ISMEAR": 0, + "SIGMA": 0.05, + "LMAXMIX": 6, + "KSPACING": 0.22, + "METAGGA": None, + } + + +@dataclass +class MPGGAEosStaticSetGenerator(EosSetGenerator): + """Class to generate MP-compatible VASP GGA EOS relax input sets.""" + + config_dict: dict = field(default_factory=lambda: _BASE_MP_R2SCAN_RELAX_SET) + auto_ismear: bool = False + auto_kspacing: bool = False + inherit_incar: bool = False + + def get_incar_updates( + self, + structure: Structure, + prev_incar: dict = None, + bandgap: float = None, + vasprun: Vasprun = None, + outcar: Outcar = None, + ) -> dict: + """Get updates to the INCAR for a relaxation job. + + Parameters + ---------- + structure + A structure. + prev_incar + An incar from a previous calculation. + bandgap + The band gap. + vasprun + A vasprun from a previous calculation. + outcar + An outcar from a previous calculation. + + Returns + ------- + dict + A dictionary of updates to apply. + """ + return { + "NSW": 0, + "LCHARG": False, + "IBRION": -1, + "EDIFF": 1e-6, + "ALGO": "NORMAL", + "LREAL": False, + "LWAVE": False, + "ISMEAR": -5, + "LMAXMIX": 6, + "KSPACING": 0.22, + "METAGGA": None, + } + + +# MPMetaGGA prefix = MP r2SCAN meta-GGA compatible +@dataclass +class MPMetaGGAEosStaticSetGenerator(VaspInputGenerator): + """Class to generate MP-compatible VASP Meta-GGA static input sets.""" + + config_dict: dict = field(default_factory=lambda: _BASE_MP_R2SCAN_RELAX_SET) + auto_ismear: bool = False + auto_kspacing: bool = False + inherit_incar: bool = False + + def get_incar_updates( + self, + structure: Structure, + prev_incar: dict = None, + bandgap: float = None, + vasprun: Vasprun = None, + outcar: Outcar = None, + ) -> dict: + """Get updates to the INCAR for this calculation type. + + Parameters + ---------- + structure + A structure. + prev_incar + An incar from a previous calculation. + bandgap + The band gap. + vasprun + A vasprun from a previous calculation. + outcar + An outcar from a previous calculation. + + Returns + ------- + dict + A dictionary of updates to apply. + """ + return { + "EDIFF": 1e-6, + "ALGO": "NORMAL", + "GGA": None, # unset GGA, shouldn't be set anyway but best be sure + "NSW": 0, + "LCHARG": True, + "LWAVE": False, + "LREAL": False, + "ISMEAR": -5, + "IBRION": -1, + "LMAXMIX": 6, + "KSPACING": 0.22, + } + + +@dataclass +class MPMetaGGAEosRelaxSetGenerator(VaspInputGenerator): + """Class to generate MP-compatible VASP meta-GGA relaxation input sets. + + Parameters + ---------- + config_dict: dict + The config dict. + bandgap_tol: float + Tolerance for metallic bandgap. If bandgap < bandgap_tol, KSPACING will be 0.22, + otherwise it will increase with bandgap up to a max of 0.44. + """ + + config_dict: dict = field(default_factory=lambda: _BASE_MP_R2SCAN_RELAX_SET) + bandgap_tol: float = 1e-4 + auto_ismear: bool = False + auto_kspacing: bool = False + inherit_incar: bool = False + + def get_incar_updates( + self, + structure: Structure, + prev_incar: dict = None, + bandgap: float = None, + vasprun: Vasprun = None, + outcar: Outcar = None, + ) -> dict: + """Get updates to the INCAR for this calculation type. + + Parameters + ---------- + structure + A structure. + prev_incar + An incar from a previous calculation. + bandgap + The band gap. + vasprun + A vasprun from a previous calculation. + outcar + An outcar from a previous calculation. + + Returns + ------- + dict + A dictionary of updates to apply. + """ + # unset GGA, shouldn't be set anyway but doesn't hurt to be sure + return { + "LCHARG": True, + "LWAVE": True, + "GGA": None, + "LMAXMIX": 6, + "KSPACING": 0.22, + "NSW": 99, + "ISIF": 3, + "IBRION": 2, + "EDIFF": 1e-6, + "LREAL": False, + "ISMEAR": 0, + "SIGMA": 0.05, + } + + +@dataclass +class MPMetaGGAEosPreRelaxSetGenerator(VaspInputGenerator): + """Class to generate MP-compatible VASP meta-GGA pre-relaxation input sets. + + Parameters + ---------- + config_dict: dict + The config dict. + bandgap_tol: float + Tolerance for metallic bandgap. If bandgap < bandgap_tol, KSPACING will be 0.22, + otherwise it will increase with bandgap up to a max of 0.44. + """ + + config_dict: dict = field(default_factory=lambda: _BASE_MP_R2SCAN_RELAX_SET) + bandgap_tol: float = 1e-4 + auto_ismear: bool = False + auto_kspacing: bool = False + inherit_incar: bool = False + + def get_incar_updates( + self, + structure: Structure, + prev_incar: dict = None, + bandgap: float = None, + vasprun: Vasprun = None, + outcar: Outcar = None, + ) -> dict: + """Get updates to the INCAR for this calculation type. + + Parameters + ---------- + structure + A structure. + prev_incar + An incar from a previous calculation. + bandgap + The band gap. + vasprun + A vasprun from a previous calculation. + outcar + An outcar from a previous calculation. + + Returns + ------- + dict + A dictionary of updates to apply. + """ + # unset METAGGA, shouldn't be set anyway but doesn't hurt to be sure + return { + "LCHARG": True, + "LWAVE": True, + "GGA": "PS", + "METAGGA": None, + "NSW": 99, + "ISIF": 3, + "IBRION": 2, + "EDIFF": 1e-6, + "EDIFFG": -0.05, + "LREAL": False, + "ISMEAR": 0, + "SIGMA": 0.05, + "KSPACING": 0.22, + } diff --git a/src/atomate2/vasp/sets/matpes.py b/src/atomate2/vasp/sets/matpes.py index 19bfdc5ee3..75bc3c6514 100644 --- a/src/atomate2/vasp/sets/matpes.py +++ b/src/atomate2/vasp/sets/matpes.py @@ -7,10 +7,10 @@ from __future__ import annotations from dataclasses import dataclass, field +from importlib.resources import files as get_mod_path from typing import TYPE_CHECKING from monty.serialization import loadfn -from pkg_resources import resource_filename from atomate2.vasp.sets.base import VaspInputGenerator @@ -21,13 +21,11 @@ # POTCAR section comes from PARENT but atomate2 does not support inheritance yet _BASE_MATPES_PBE_STATIC_SET_NO_POTCAR = loadfn( - resource_filename("pymatgen.io.vasp", "MatPESStaticSet.yaml") + get_mod_path("pymatgen.io.vasp") / "MatPESStaticSet.yaml" ) -_BASE_PBE54_SET = loadfn(resource_filename("pymatgen.io.vasp", "PBE54Base.yaml")) -_BASE_MATPES_PBE_STATIC_SET = { - **_BASE_PBE54_SET, - **_BASE_MATPES_PBE_STATIC_SET_NO_POTCAR, -} +_POTCAR_BASE_FILE = f"{_BASE_MATPES_PBE_STATIC_SET_NO_POTCAR['PARENT']}.yaml" +_POTCAR_SET = loadfn(get_mod_path("pymatgen.io.vasp") / _POTCAR_BASE_FILE) +_BASE_MATPES_PBE_STATIC_SET = {**_POTCAR_SET, **_BASE_MATPES_PBE_STATIC_SET_NO_POTCAR} @dataclass @@ -46,8 +44,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for this calculation type. + """Get updates to the INCAR for this calculation type. Parameters ---------- @@ -72,7 +69,7 @@ def get_incar_updates( @dataclass class MatPesMetaGGAStaticSetGenerator(MatPesGGAStaticSetGenerator): - """Class to generate MP-compatible VASP GGA static input sets.""" + """Class to generate MP-compatible VASP meta-GGA static input sets.""" def get_incar_updates( self, @@ -82,8 +79,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for this calculation type. + """Get updates to the INCAR for this calculation type. Parameters ---------- diff --git a/src/atomate2/vasp/sets/mp.py b/src/atomate2/vasp/sets/mp.py index 63ecbe9186..5b28b59b46 100644 --- a/src/atomate2/vasp/sets/mp.py +++ b/src/atomate2/vasp/sets/mp.py @@ -9,10 +9,10 @@ from __future__ import annotations from dataclasses import dataclass, field +from importlib.resources import files as get_mod_path from typing import TYPE_CHECKING from monty.serialization import loadfn -from pkg_resources import resource_filename from atomate2.vasp.sets.core import RelaxSetGenerator, StaticSetGenerator @@ -21,10 +21,10 @@ from pymatgen.io.vasp import Outcar, Vasprun _BASE_MP_GGA_RELAX_SET = loadfn( - resource_filename("atomate2.vasp.sets", "BaseMPGGASet.yaml") + get_mod_path("atomate2.vasp.sets") / "BaseMPGGASet.yaml" ) _BASE_MP_R2SCAN_RELAX_SET = loadfn( - resource_filename("atomate2.vasp.sets", "BaseMPR2SCANRelaxSet.yaml") + get_mod_path("atomate2.vasp.sets") / "BaseMPR2SCANRelaxSet.yaml" ) @@ -33,8 +33,9 @@ class MPGGARelaxSetGenerator(RelaxSetGenerator): """Class to generate MP-compatible VASP GGA relaxation input sets.""" config_dict: dict = field(default_factory=lambda: _BASE_MP_GGA_RELAX_SET) + auto_ismear: bool = False auto_kspacing: bool = True - inherit_incar: bool = False + inherit_incar: bool | None = False @dataclass @@ -42,8 +43,9 @@ class MPGGAStaticSetGenerator(StaticSetGenerator): """Class to generate MP-compatible VASP GGA static input sets.""" config_dict: dict = field(default_factory=lambda: _BASE_MP_GGA_RELAX_SET) + auto_ismear: bool = False auto_kspacing: bool = True - inherit_incar: bool = False + inherit_incar: bool | None = False def get_incar_updates( self, @@ -53,8 +55,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for this calculation type. + """Get updates to the INCAR for this calculation type. Parameters ---------- @@ -89,8 +90,10 @@ class MPMetaGGAStaticSetGenerator(StaticSetGenerator): """Class to generate MP-compatible VASP GGA static input sets.""" config_dict: dict = field(default_factory=lambda: _BASE_MP_R2SCAN_RELAX_SET) + auto_ismear: bool = False auto_kspacing: bool = True - inherit_incar: bool = False + bandgap_tol: float = 1e-4 + inherit_incar: bool | None = False def get_incar_updates( self, @@ -100,8 +103,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for this calculation type. + """Get updates to the INCAR for this calculation type. Parameters ---------- @@ -147,8 +149,9 @@ class MPMetaGGARelaxSetGenerator(RelaxSetGenerator): config_dict: dict = field(default_factory=lambda: _BASE_MP_R2SCAN_RELAX_SET) bandgap_tol: float = 1e-4 + auto_ismear: bool = False auto_kspacing: bool = True - inherit_incar: bool = False + inherit_incar: bool | None = False def get_incar_updates( self, @@ -158,8 +161,7 @@ def get_incar_updates( vasprun: Vasprun = None, outcar: Outcar = None, ) -> dict: - """ - Get updates to the INCAR for this calculation type. + """Get updates to the INCAR for this calculation type. Parameters ---------- diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/std_err.txt b/tests/abinit/__init__.py similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/std_err.txt rename to tests/abinit/__init__.py diff --git a/tests/abinit/conftest.py b/tests/abinit/conftest.py new file mode 100644 index 0000000000..b431c8a389 --- /dev/null +++ b/tests/abinit/conftest.py @@ -0,0 +1,172 @@ +from __future__ import annotations + +import logging +from pathlib import Path +from typing import TYPE_CHECKING, Literal + +import pytest + +if TYPE_CHECKING: + from collections.abc import Sequence + + +logger = logging.getLogger("atomate2") + +_REF_PATHS = {} +_ABINIT_FILES = ("run.abi", "abinit_input.json") +_FAKE_RUN_ABINIT_KWARGS = {} + + +@pytest.fixture(scope="session") +def abinit_test_dir(test_dir): + return test_dir / "abinit" + + +@pytest.fixture(scope="session") +def abinit_integration_tests(pytestconfig): + return pytestconfig.getoption("abinit_integration") + + +@pytest.fixture() +def mock_abinit(mocker, abinit_test_dir, abinit_integration_tests): + """ + This fixture allows one to mock running ABINIT. + + It works by monkeypatching (replacing) calls to run_abinit. + + The primary idea is that instead of running ABINIT to generate the output files, + reference files will be copied into the directory instead. + """ + import atomate2.abinit.files + import atomate2.abinit.jobs.base + import atomate2.abinit.run + + # Wrap the write_abinit_input_set so that we can check inputs after calling it + def wrapped_write_abinit_input_set(*args, **kwargs): + from jobflow import CURRENT_JOB + + name = CURRENT_JOB.job.name + index = CURRENT_JOB.job.index + ref_path = abinit_test_dir / _REF_PATHS[name][str(index)] + + atomate2.abinit.files.write_abinit_input_set(*args, **kwargs) + check_abinit_inputs(ref_path) + + mocker.patch.object( + atomate2.abinit.jobs.base, + "write_abinit_input_set", + wrapped_write_abinit_input_set, + ) + + if not abinit_integration_tests: + # Mock abinit run (i.e. this will copy reference files) + def mock_run_abinit(wall_time=None, start_time=None): + from jobflow import CURRENT_JOB + + name = CURRENT_JOB.job.name + index = CURRENT_JOB.job.index + ref_path = abinit_test_dir / _REF_PATHS[name][str(index)] + check_abinit_inputs(ref_path) + fake_run_abinit(ref_path) + + mocker.patch.object(atomate2.abinit.run, "run_abinit", mock_run_abinit) + mocker.patch.object(atomate2.abinit.jobs.base, "run_abinit", mock_run_abinit) + + def _run(ref_paths, fake_run_abinit_kwargs=None): + if fake_run_abinit_kwargs is None: + fake_run_abinit_kwargs = {} + _REF_PATHS.update(ref_paths) + _FAKE_RUN_ABINIT_KWARGS.update(fake_run_abinit_kwargs) + + yield _run + + mocker.stopall() + _REF_PATHS.clear() + _FAKE_RUN_ABINIT_KWARGS.clear() + + +def fake_run_abinit(ref_path: str | Path): + """ + Emulate running ABINIT. + + Parameters + ---------- + ref_path + Path to reference directory with ABINIT input files in the folder named 'inputs' + and output files in the folder named 'outputs'. + """ + logger.info("Running fake ABINIT.") + + ref_path = Path(ref_path) + + copy_abinit_outputs(ref_path) + + # pretend to run ABINIT by copying pre-generated outputs from reference dir + logger.info("Generated fake ABINIT outputs") + + +def check_abinit_inputs( + ref_path: str | Path, + check_inputs: Sequence[Literal["run.abi"]] = _ABINIT_FILES, +): + ref_path = Path(ref_path) + + if "run.abi" in check_inputs: + check_run_abi(ref_path) + + if "abinit_input.json" in check_inputs: + check_abinit_input_json(ref_path) + + logger.info("Verified inputs successfully") + + +def check_run_abi(ref_path: str | Path): + from abipy.abio.abivars import AbinitInputFile + from monty.io import zopen + + user = AbinitInputFile.from_file("run.abi") + assert user.ndtset == 1, f"'run.abi' has multiple datasets (ndtset={user.ndtset})." + with zopen(ref_path / "inputs" / "run.abi.gz") as file: + ref_str = file.read() + ref = AbinitInputFile.from_string(ref_str.decode("utf-8")) + # Ignore the pseudos as the directory depends on the pseudo root directory + diffs = user.get_differences(ref, ignore_vars=["pseudos"]) + # TODO: should we still add some check on the pseudos here ? + assert diffs == [], "'run.abi' is different from reference." + + +def check_abinit_input_json(ref_path: str | Path): + from abipy.abio.inputs import AbinitInput + from monty.serialization import loadfn + + user = loadfn("abinit_input.json") + assert isinstance(user, AbinitInput) + ref = loadfn(ref_path / "inputs" / "abinit_input.json.gz") + assert user.structure == ref.structure + assert user.runlevel == ref.runlevel + + +def clear_abinit_files(): + for abinit_file in ("run.abo",): + if Path(abinit_file).exists(): + Path(abinit_file).unlink() + logger.info("Cleared abinit files.") + + +def copy_abinit_outputs(ref_path: str | Path): + import shutil + + from monty.shutil import decompress_file + + ref_path = Path(ref_path) + output_path = ref_path / "outputs" + for output_file in output_path.iterdir(): + if output_file.is_file(): + shutil.copy(output_file, ".") + decompress_file(output_file.name) + for data_dir in ("indata", "outdata", "tmpdata"): + ref_data_dir = output_path / data_dir + for file in ref_data_dir.iterdir(): + if file.is_file(): + shutil.copy(file, data_dir) + decompress_file(str(Path(data_dir, file.name))) diff --git a/tests/abinit/flows/test_core.py b/tests/abinit/flows/test_core.py new file mode 100644 index 0000000000..bb8f92a0fb --- /dev/null +++ b/tests/abinit/flows/test_core.py @@ -0,0 +1,62 @@ +def test_band_structure_run_silicon(mock_abinit, abinit_test_dir, clean_dir): + from jobflow import run_locally + from monty.serialization import loadfn + from pymatgen.core.structure import Structure + + # load the initial structure, the maker and the ref_paths from the test_dir + test_dir = abinit_test_dir / "flows" / "core" / "BandStructureMaker" / "silicon" + structure = Structure.from_file(test_dir / "initial_structure.json.gz") + maker_info = loadfn(test_dir / "maker.json.gz") + maker = maker_info["maker"] + ref_paths = loadfn(test_dir / "ref_paths.json.gz") + + mock_abinit(ref_paths) + + # make the flow or job, run it and ensure that it finished running successfully + flow_or_job = maker.make(structure) + responses = run_locally(flow_or_job, create_folders=True, ensure_success=True) + + # validation the outputs of the flow or job + assert len(responses) == 3 + for job, _parents in flow_or_job.iterflow(): + assert len(responses[job.uuid]) == 1 + + +def test_relax_run_silicon_standard(mock_abinit, abinit_test_dir, clean_dir): + from jobflow import run_locally + from monty.serialization import loadfn + from pymatgen.core.structure import Structure + + # load the initial structure, the maker and the ref_paths from the test_dir + test_dir = ( + abinit_test_dir / "flows" / "core" / "RelaxFlowMaker" / "silicon_standard" + ) + structure = Structure.from_file(test_dir / "initial_structure.json.gz") + maker_info = loadfn(test_dir / "maker.json.gz") + maker = maker_info["maker"] + ref_paths = loadfn(test_dir / "ref_paths.json.gz") + + mock_abinit(ref_paths) + + # make the flow or job, run it and ensure that it finished running successfully + flow_or_job = maker.make(structure) + responses = run_locally(flow_or_job, create_folders=True, ensure_success=True) + + # validation the outputs of the flow or job + assert len(responses) == 2 + for job, _parents in flow_or_job.iterflow(): + assert len(responses[job.uuid]) == 1 + + +def test_relax_ion_ioncell_relaxation(): + from atomate2.abinit.flows.core import RelaxFlowMaker + + settings = {"nband": 100} + maker = RelaxFlowMaker.ion_ioncell_relaxation(user_abinit_settings=settings) + assert len(maker.relaxation_makers) == 2 + assert ( + maker.relaxation_makers[0].input_set_generator.user_abinit_settings == settings + ) + assert ( + maker.relaxation_makers[1].input_set_generator.user_abinit_settings == settings + ) diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/std_err.txt b/tests/abinit/jobs/__init__.py similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/std_err.txt rename to tests/abinit/jobs/__init__.py diff --git a/tests/abinit/jobs/test_base.py b/tests/abinit/jobs/test_base.py new file mode 100644 index 0000000000..7e4c5e7af2 --- /dev/null +++ b/tests/abinit/jobs/test_base.py @@ -0,0 +1,68 @@ +from __future__ import annotations + +from dataclasses import dataclass, field + +from abipy.abio.input_tags import SCF +from abipy.abio.inputs import AbinitInput + +from atomate2.abinit.jobs.base import BaseAbinitMaker +from atomate2.abinit.sets.base import AbinitInputGenerator, as_pseudo_table + + +@dataclass +class SomeAISG1(AbinitInputGenerator): + calc_type: str = "some_calc1" + + param1: int = 1 + param2: float | None = None + param3: list[int] = field(default_factory=list) + param4: str = "test_string1" + + user_abinit_settings: dict = field( + default_factory=lambda: {"extra1": 1, "extra2": 2} + ) + + restart_from_deps: tuple = (f"{SCF}:WFK|DEN",) + + def get_abinit_input( + self, structure=None, pseudos=None, prev_outputs=None, **kwargs + ): + return AbinitInput( + structure=structure, + pseudos=as_pseudo_table(AbinitInputGenerator.pseudos), + ) + + +@dataclass +class SomeAISG2(AbinitInputGenerator): + calc_type: str = "some_calc2" + + param1: int = 2 + # param2: Optional[float] = None + param3: list[int] = field(default_factory=list) + param4: str = "test_string2" + param5: dict[int, str] = field(default_factory=lambda: {1: "1"}) + + user_abinit_settings: dict = field(default_factory=dict) + + restart_from_deps: tuple = (f"{SCF}:WFK|DEN",) + + def get_abinit_input( + self, structure=None, pseudos=None, prev_outputs=None, **kwargs + ): + return AbinitInput( + structure=structure, + pseudos=as_pseudo_table(AbinitInputGenerator.pseudos), + ) + + +@dataclass +class SomeMaker1(BaseAbinitMaker): + name: str = "SomeMaker1 calculation" + input_set_generator: SomeAISG1 = field(default_factory=SomeAISG1) + + +@dataclass +class SomeMaker2(BaseAbinitMaker): + name: str = "SomeMaker2 calculation" + input_set_generator: SomeAISG2 = field(default_factory=SomeAISG2) diff --git a/tests/abinit/jobs/test_core.py b/tests/abinit/jobs/test_core.py new file mode 100644 index 0000000000..dc909cd6cb --- /dev/null +++ b/tests/abinit/jobs/test_core.py @@ -0,0 +1,116 @@ +from typing import TYPE_CHECKING + +if TYPE_CHECKING: + from jobflow import Maker + + +def test_static_run_silicon_standard(mock_abinit, abinit_test_dir, clean_dir): + from jobflow import run_locally + from monty.serialization import loadfn + from pymatgen.core.structure import Structure + + from atomate2.abinit.schemas.task import AbinitTaskDoc as AbinitTaskDocument + + # load the initial structure, the maker and the ref_paths from the test_dir + test_dir = abinit_test_dir / "jobs" / "core" / "StaticMaker" / "silicon_standard" + structure = Structure.from_file(test_dir / "initial_structure.json.gz") + maker: Maker = loadfn(test_dir / "maker.json.gz")["maker"] + ref_paths = loadfn(test_dir / "ref_paths.json.gz") + + mock_abinit(ref_paths) + + # make the job, run it and ensure that it finished running successfully + job = maker.make(structure) + responses = run_locally(job, create_folders=True, ensure_success=True) + + # validation the outputs of the job + output1 = responses[job.uuid][1].output + assert isinstance(output1, AbinitTaskDocument) + # assert output1.run_number == 1 + + +def test_static_run_silicon_restarts(mock_abinit, abinit_test_dir, clean_dir): + from jobflow import run_locally + from monty.serialization import loadfn + from pymatgen.core.structure import Structure + + from atomate2.abinit.schemas.task import AbinitTaskDoc as AbinitTaskDocument + + # load the initial structure, the maker and the ref_paths from the test_dir + test_dir = abinit_test_dir / "jobs" / "core" / "StaticMaker" / "silicon_restarts" + structure = Structure.from_file(test_dir / "initial_structure.json.gz") + maker: Maker = loadfn(test_dir / "maker.json.gz")["maker"] + ref_paths = loadfn(test_dir / "ref_paths.json.gz") + + mock_abinit(ref_paths) + + # make the job, run it and ensure that it finished running successfully + job = maker.make(structure) + responses = run_locally(job, create_folders=True, ensure_success=True) + + # validation the outputs of the job + output1 = responses[job.uuid][1].output + assert isinstance(output1, AbinitTaskDocument) + # assert output1.run_number == 1 + # TODO 2024-04-25: figure out why responses[job.uuid][2] causes KeyError + # output2 = responses[job.uuid][2].output + # assert isinstance(output2, AbinitTaskDocument) + # assert output2.run_number == 2 + + +def test_relax_run_silicon_scaled1p2_standard(mock_abinit, abinit_test_dir, clean_dir): + from jobflow import run_locally + from monty.serialization import loadfn + from pymatgen.core.structure import Structure + + from atomate2.abinit.schemas.task import AbinitTaskDoc as AbinitTaskDocument + + # load the initial structure, the maker and the ref_paths from the test_dir + test_dir = ( + abinit_test_dir / "jobs" / "core" / "RelaxMaker" / "silicon_scaled1p2_standard" + ) + structure = Structure.from_file(test_dir / "initial_structure.json.gz") + maker: Maker = loadfn(test_dir / "maker.json.gz")["maker"] + ref_paths = loadfn(test_dir / "ref_paths.json.gz") + + mock_abinit(ref_paths) + + # make the flow or job, run it and ensure that it finished running successfully + job = maker.make(structure) + responses = run_locally(job, create_folders=True, ensure_success=True) + + # validation the outputs of the flow or job + output1 = responses[job.uuid][1].output + assert isinstance(output1, AbinitTaskDocument) + # assert output1.run_number == 1 + + +def test_relax_run_silicon_scaled1p2_restart(mock_abinit, abinit_test_dir, clean_dir): + from jobflow import run_locally + from monty.serialization import loadfn + from pymatgen.core.structure import Structure + + from atomate2.abinit.schemas.task import AbinitTaskDoc as AbinitTaskDocument + + # load the initial structure, the maker and the ref_paths from the test_dir + test_dir = ( + abinit_test_dir / "jobs" / "core" / "RelaxMaker" / "silicon_scaled1p2_restart" + ) + structure = Structure.from_file(test_dir / "initial_structure.json.gz") + maker: Maker = loadfn(test_dir / "maker.json.gz")["maker"] + ref_paths = loadfn(test_dir / "ref_paths.json.gz") + + mock_abinit(ref_paths) + + # make the flow or job, run it and ensure that it finished running successfully + job = maker.make(structure) + responses = run_locally(job, create_folders=True, ensure_success=True) + + # validation the outputs of the flow or job + output1 = responses[job.uuid][1].output + assert isinstance(output1, AbinitTaskDocument) + # assert output1.run_number == 1 + # TODO 2024-04-25: figure out why responses[job.uuid][2] causes KeyError + # output2 = responses[job.uuid][2].output + # assert isinstance(output2, AbinitTaskDocument) + # assert output2.run_number == 2 diff --git a/tests/abinit/sets/__init__.py b/tests/abinit/sets/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/abinit/sets/test_base.py b/tests/abinit/sets/test_base.py new file mode 100644 index 0000000000..a101cbf7bb --- /dev/null +++ b/tests/abinit/sets/test_base.py @@ -0,0 +1,375 @@ +from __future__ import annotations + +import os +from dataclasses import dataclass, field +from pathlib import Path + +import numpy as np +import pytest +from abipy.abio.input_tags import SCF +from abipy.abio.inputs import AbinitInput +from monty.os import makedirs_p +from monty.tempfile import ScratchDir + +import atomate2 +from atomate2.abinit.files import load_abinit_input +from atomate2.abinit.sets.base import ( + AbinitInputGenerator, + AbinitInputSet, + as_pseudo_table, +) +from atomate2.abinit.utils.common import INDIR_NAME, OUTDIR_NAME, InitializationError + + +def mocked_factory(structure, pseudos): + from abipy.abio.inputs import AbinitInput + + return AbinitInput(structure, pseudos) + + +def test_abinit_input_set_init(abinit_test_dir): + abinit_input = load_abinit_input( + os.path.join(abinit_test_dir, "abinit_inputs"), fname="abinit_input_Si.json" + ) + ais = AbinitInputSet(abinit_input=abinit_input) + assert set(ais.inputs.keys()) == {"run.abi", "abinit_input.json"} + assert ais.inputs["run.abi"] == abinit_input + assert '"@class": "AbinitInput"' in ais.inputs["abinit_input.json"] + assert ais.input_files is None + assert ais.link_files is True + assert ais.validate() is True + ais = AbinitInputSet( + abinit_input=abinit_input, + input_files=[ + ("/some/input/file", "file"), + ("/some/other/input/file", "other_file"), + ], + link_files=False, + ) + assert ais.input_files == [ + ("/some/input/file", "file"), + ("/some/other/input/file", "other_file"), + ] + assert ais.link_files is False + assert ais.validate() is False + + +def test_abinit_input_set_set_workdir(): + with ScratchDir(".") as tmp: + indir, outdir, tmpdir = AbinitInputSet.set_workdir("someworkdir") + indata = os.path.join("someworkdir", "indata") + outdata = os.path.join("someworkdir", "outdata") + tmpdata = os.path.join("someworkdir", "tmpdata") + assert os.path.exists(indata) + assert os.path.exists(outdata) + assert os.path.exists(tmpdata) + assert indir.path == os.path.join(tmp, indata) + assert outdir.path == os.path.join(tmp, outdata) + assert tmpdir.path == os.path.join(tmp, tmpdata) + + +def test_abinit_input_set_write_input(abinit_test_dir): + abinit_input = load_abinit_input( + os.path.join(abinit_test_dir, "abinit_inputs"), fname="abinit_input_Si.json" + ) + with ScratchDir("."): + ais = AbinitInputSet(abinit_input=abinit_input) + assert ais.validate() is True + ais.write_input("testdir") + assert os.path.exists("testdir") + dirlist = os.listdir("testdir") + assert len(dirlist) == 5 + assert "indata" in dirlist + assert "outdata" in dirlist + assert "tmpdata" in dirlist + assert os.path.isdir("testdir/indata") + assert os.path.isdir("testdir/outdata") + assert os.path.isdir("testdir/tmpdata") + assert "run.abi" in dirlist + assert "abinit_input.json" in dirlist + with open("testdir/run.abi") as file: + abistr = file.read() + assert "ecut" in abistr + with open("testdir/abinit_input.json") as file: + abijsonstr = file.read() + assert "@module" in abijsonstr + with pytest.raises(FileExistsError): + ais.write_input("testdir", overwrite=False) + + with ScratchDir(".") as tmpdir: + prev_output_dir = os.path.join(tmpdir, "prev_output") + prev_outdata = os.path.join(prev_output_dir, OUTDIR_NAME) + makedirs_p(prev_outdata) + out_den = Path(os.path.join(prev_outdata, "out_DEN")) + out_den.touch() + ais = AbinitInputSet( + abinit_input=abinit_input, input_files=[(out_den, "in_DEN")] + ) + assert "irdden" not in ais.abinit_input + assert ais.validate() is False + ais.write_input("testdir") + in_den = os.path.join("testdir", "indata", "in_DEN") + assert os.path.islink(in_den) + assert os.readlink(in_den) == str(out_den) + + with ScratchDir(".") as tmpdir: + prev_output_dir = os.path.join(tmpdir, "prev_output") + prev_outdata = os.path.join(prev_output_dir, OUTDIR_NAME) + makedirs_p(prev_outdata) + out_den = Path(os.path.join(prev_outdata, "out_DEN")) + out_den.touch() + ais = AbinitInputSet( + abinit_input=abinit_input, + input_files=[(out_den, "in_DEN")], + link_files=False, + ) + assert "irdden" not in ais.abinit_input + assert ais.validate() is False + ais.abinit_input["irdden"] = 1 + assert "irdden" in ais.abinit_input + assert ais.validate() is True + ais.write_input("testdir") + assert os.path.exists(in_den) + assert os.path.isfile(in_den) + assert not os.path.islink(in_den) + with open("testdir/run.abi") as file: + abistr = file.read() + assert "irdden 1" in abistr + del ais.abinit_input["irdden"] + + with ScratchDir(".") as tmpdir: + prev_output_dir = os.path.join(tmpdir, "prev_output") + prev_outdata = os.path.join(prev_output_dir, OUTDIR_NAME) + makedirs_p(prev_outdata) + Path(os.path.join(prev_outdata, "out_TIM1_DEN")).touch() + Path(os.path.join(prev_outdata, "out_TIM2_DEN")).touch() + out_den = Path(os.path.join(prev_outdata, "out_TIM15_DEN")) + out_den.touch() + abinit_input["irdden"] = 1 + ais = AbinitInputSet( + abinit_input=abinit_input, + input_files=[(str(out_den), "in_DEN")], + ) + ais.write_input("testdir") + in_den = os.path.join("testdir", INDIR_NAME, "in_DEN") + assert os.path.islink(in_den) + assert os.readlink(in_den) == str(out_den) + + +def test_abinit_input_set_set_remove_vars(abinit_test_dir): + abinit_input = load_abinit_input( + os.path.join(abinit_test_dir, "abinit_inputs"), fname="abinit_input_Si.json" + ) + ais = AbinitInputSet(abinit_input=abinit_input) + assert "ntime" not in ais.abinit_input + assert ais.abinit_input["nband"] == 5 + ais.set_vars(nband=10, ntime=5) + assert ais.abinit_input["nband"] == 10 + assert ais.abinit_input["ntime"] == 5 + assert "occopt" in ais.abinit_input + ais.remove_vars("occopt") + assert "occopt" not in ais.abinit_input + ais.remove_vars(["nband", "ntime"]) + assert "nband" not in ais.abinit_input + assert "ntime" not in ais.abinit_input + + +def test_abinit_input_set_runlevel(abinit_test_dir): + abinit_input = load_abinit_input( + os.path.join(abinit_test_dir, "abinit_inputs"), fname="abinit_input_Si.json" + ) + ais = AbinitInputSet(abinit_input=abinit_input) + assert ais.runlevel() == abinit_input.runlevel + + +def test_abinit_input_set_set_structure(abinit_test_dir): + abinit_input = load_abinit_input( + os.path.join(abinit_test_dir, "abinit_inputs"), fname="abinit_input_Si.json" + ) + ais = AbinitInputSet(abinit_input=abinit_input) + struct = abinit_input.structure + newstruct = struct.copy() + newstruct.scale_lattice(newstruct.volume * 1.2) + ais.set_structure(newstruct) + assert ais.abinit_input.structure == newstruct + + +@dataclass +class SomeAbinitInputSetGenerator(AbinitInputGenerator): + calc_type: str = "some_calc" + + param1: int = 1 + param2: float | None = None + param3: list[int] = field(default_factory=list) + param4: str = "test_string" + + user_abinit_settings: dict = field(default_factory=dict) + + restart_from_deps: tuple = (f"{SCF}:WFK|DEN",) + + def get_abinit_input( + self, structure=None, pseudos=None, prev_outputs=None, **kwargs + ): + return AbinitInput( + structure=structure, + pseudos=as_pseudo_table(AbinitInputGenerator.pseudos), + ) + + +def test_generator_check_format_prev_dirs(): + aisg = AbinitInputGenerator(factory=mocked_factory) + prev_outputs = aisg.check_format_prev_dirs(None) + assert prev_outputs is None + prev_outputs = aisg.check_format_prev_dirs("/some/path") + assert prev_outputs == ["/some/path"] + prev_outputs = aisg.check_format_prev_dirs(Path("/some/path")) + assert prev_outputs == ["/some/path"] + prev_outputs = aisg.check_format_prev_dirs(["/some/path", Path("/some/other/path")]) + assert prev_outputs == ["/some/path", "/some/other/path"] + + +def test_generator_resolve_dep(): + aisg = AbinitInputGenerator(factory=mocked_factory) + with ScratchDir(".") as tmpdir: + prev_output_dir = os.path.join(tmpdir, "prev_output") + prev_outdata = os.path.join(prev_output_dir, OUTDIR_NAME) + makedirs_p(prev_outdata) + Path(os.path.join(prev_outdata, "out_DEN")).touch() + irdvars, restart_file = aisg.resolve_dep_exts( + prev_output_dir, exts=("WFK", "DEN") + ) + assert irdvars == {"irdden": 1} + assert restart_file == [(os.path.join(prev_outdata, "out_DEN"), "in_DEN")] + Path(os.path.join(prev_outdata, "out_WFK")).touch() + irdvars, restart_file = aisg.resolve_dep_exts( + prev_output_dir, exts=("WFK", "DEN") + ) + assert irdvars == {"irdwfk": 1} + assert restart_file == [(os.path.join(prev_outdata, "out_WFK"), "in_WFK")] + irdvars, restart_file = aisg.resolve_dep_exts(prev_output_dir, exts=("DEN",)) + assert irdvars == {"irdden": 1} + assert restart_file == [(os.path.join(prev_outdata, "out_DEN"), "in_DEN")] + with ScratchDir(".") as tmpdir: + prev_output_dir = os.path.join(tmpdir, "prev_output") + prev_outdata = os.path.join(prev_output_dir, OUTDIR_NAME) + makedirs_p(prev_outdata) + Path(os.path.join(prev_outdata, "out_WFK")).touch() + irdvars, restart_file = aisg.resolve_dep_exts( + prev_output_dir, exts=("WFK", "DEN") + ) + assert irdvars == {"irdwfk": 1} + assert restart_file == [(os.path.join(prev_outdata, "out_WFK"), "in_WFK")] + with pytest.raises( + InitializationError, match=r"Cannot find DDB file to restart from." + ): + aisg.resolve_dep_exts(prev_output_dir, exts=("DDB",)) + with pytest.raises( + InitializationError, + match=r"Cannot find DDB or DVDB or DKK file to restart from.", + ): + aisg.resolve_dep_exts(prev_output_dir, exts=("DDB", "DVDB", "DKK")) + with ScratchDir(".") as tmpdir: + prev_output_dir = os.path.join(tmpdir, "prev_output") + prev_outdata = os.path.join(prev_output_dir, OUTDIR_NAME) + makedirs_p(prev_outdata) + Path(os.path.join(prev_outdata, "out_TIM1_DEN")).touch() + Path(os.path.join(prev_outdata, "out_TIM2_DEN")).touch() + Path(os.path.join(prev_outdata, "out_TIM15_DEN")).touch() + irdvars, restart_file = aisg.resolve_dep_exts(prev_output_dir, exts=("DEN",)) + assert irdvars == {"irdden": 1} + assert restart_file == [(os.path.join(prev_outdata, "out_TIM15_DEN"), "in_DEN")] + Path(os.path.join(prev_outdata, "out_DEN")).touch() + irdvars, restart_file = aisg.resolve_dep_exts(prev_output_dir, exts=("DEN",)) + assert irdvars == {"irdden": 1} + assert restart_file == [(os.path.join(prev_outdata, "out_DEN"), "in_DEN")] + + +def test_generator_resolve_deps(): + aisg = AbinitInputGenerator(factory=mocked_factory) + with ScratchDir(".") as tmpdir1: + prev_output_dir1 = os.path.join(tmpdir1, "prev_output") + prev_outdata1 = os.path.join(prev_output_dir1, OUTDIR_NAME) + makedirs_p(prev_outdata1) + den = Path(os.path.join(prev_outdata1, "out_DEN")) + den.touch() + with ScratchDir(".") as tmpdir2: + prev_output_dir2 = os.path.join(tmpdir2, "prev_output") + prev_outdata2 = os.path.join(prev_output_dir2, OUTDIR_NAME) + makedirs_p(prev_outdata2) + wfk = Path(os.path.join(prev_outdata2, "out_WFK")) + wfk.touch() + prev_outputs = [prev_output_dir1, prev_output_dir2] + irdvars, input_files = aisg.resolve_deps( + prev_outputs, deps=("any:WFK|DEN",), check_runlevel=False + ) + assert irdvars == {"irdden": 1, "irdwfk": 1} + assert (str(wfk), "in_WFK") in input_files + assert (str(den), "in_DEN") in input_files + assert len(input_files) == 2 + + +def test_generator_get_input_set(si_structure, mocker): + with ScratchDir(".") as tmpdir: + saisg = SomeAbinitInputSetGenerator(factory=mocked_factory) + abinit_input_set = saisg.get_input_set( + structure=si_structure, + ) + abinit_input_set.write_input("output1") + output1 = os.path.join(tmpdir, "output1") + + out_wfk1 = Path(os.path.join(output1, OUTDIR_NAME, "out_WFK")) + out_wfk1.touch() + out_den1 = Path(os.path.join(output1, OUTDIR_NAME, "out_DEN")) + out_den1.touch() + + abinit_input_set.write_input("output1b") + output1b = os.path.join(tmpdir, "output1b") + + out_den1b = Path(os.path.join(output1b, OUTDIR_NAME, "out_DEN")) + out_den1b.touch() + + mocker.patch.object( + atomate2.abinit.sets.base, + "get_final_structure", + return_value=si_structure, + ) + abinit_input_set = saisg.get_input_set( + structure=si_structure, + restart_from=output1, + ) + assert "irdwfk" in abinit_input_set.abinit_input + assert "irdden" not in abinit_input_set.abinit_input + assert abinit_input_set.abinit_input["irdwfk"] == 1 + assert abinit_input_set.validate() is True + abinit_input_set.write_input("output2") + output2 = os.path.join(tmpdir, "output2") + in_wfk2 = os.path.join(output2, INDIR_NAME, "in_WFK") + assert os.path.islink(in_wfk2) + assert os.readlink(in_wfk2) == str(out_wfk1) + + abinit_input_set = saisg.get_input_set( + structure=si_structure, + restart_from=output1b, + ) + assert "irdwfk" not in abinit_input_set.abinit_input + assert "irdden" in abinit_input_set.abinit_input + assert abinit_input_set.abinit_input["irdden"] == 1 + assert abinit_input_set.validate() is True + abinit_input_set.write_input("output2b") + output2b = os.path.join(tmpdir, "output2b") + in_den2b = os.path.join(output2b, INDIR_NAME, "in_DEN") + assert os.path.islink(in_den2b) + assert os.readlink(in_den2b) == str(out_den1b) + + +def test_generator_set_kpt_vars(abinit_test_dir): + aig = AbinitInputGenerator(factory=mocked_factory) + abinit_input = load_abinit_input( + os.path.join(abinit_test_dir, "abinit_inputs"), fname="abinit_input_Si.json" + ) + aig._set_kpt_vars(abinit_input, {"grid_density": 300}) # noqa: SLF001 + assert np.array_equal(abinit_input["ngkpt"], [5, 5, 5]) + + aig._set_kpt_vars(abinit_input, {"line_density": 10}) # noqa: SLF001 + assert abinit_input["nkpt"] == 92 + assert "ngkpt" not in abinit_input diff --git a/tests/abinit/sets/test_core.py b/tests/abinit/sets/test_core.py new file mode 100644 index 0000000000..ef5ac7cf48 --- /dev/null +++ b/tests/abinit/sets/test_core.py @@ -0,0 +1,118 @@ +import os + +import pytest +from abipy.abio.inputs import AbinitInput + +from atomate2.abinit.sets.base import AbinitInputSet +from atomate2.abinit.sets.core import StaticSetGenerator + + +def test_init_static_generator(): + StaticSetGenerator() + + +def test_static_generator_get_abinit_input(si_structure, abinit_test_dir): + ssg = StaticSetGenerator() + si_pseudo = os.path.join(abinit_test_dir, "pseudos", "14si.fhi") + abinit_input = ssg.get_abinit_input(structure=si_structure, pseudos=si_pseudo) + assert isinstance(abinit_input, AbinitInput) + with pytest.raises(RuntimeError, match=r"Structure is mandatory.*"): + ssg.get_abinit_input() + + with pytest.raises( + RuntimeError, + match=r"Previous outputs not allowed.*", + ): + ssg.get_abinit_input(structure=si_structure, prev_outputs="prev_fake_dir") + + +def test_static_generator_get_input_set(si_structure): + ssg = StaticSetGenerator() + input_set = ssg.get_input_set(structure=si_structure) + assert isinstance(input_set, AbinitInputSet) + + +# def test_static_generator_restart(si_structure): +# ssg1 = StaticSetGenerator(ecut=8.5, nband=13, smearing=None) +# ssg2 = StaticSetGenerator(nband=8, smearing=None) +# ssg3 = StaticSetGenerator() +# +# with ScratchDir(".") as tmpdir: +# input_set1 = ssg1.get_input_set( +# structure=si_structure, smearing="marzari5:0.5 eV" +# ) +# assert isinstance(input_set1, AbinitInputSet) +# assert input_set1.abinit_input["occopt"] == 5 +# input_set1.write_input("first_run") +# dirlist = os.listdir("first_run") +# assert len(dirlist) == 6 +# assert "abinit_input_set_generator.json" in dirlist +# assert "abinit_input.json" in dirlist +# with open("first_run/run.abi") as file: +# runabi1_str = file.read() +# assert "ecut 8.5" in runabi1_str +# assert "nband 13" in runabi1_str +# assert "occopt 5" in runabi1_str +# matched_tsmear_lines = [ +# line for line in runabi1_str.split("\n") if "tsmear" in line +# ] +# assert len(matched_tsmear_lines) == 1 +# _, tsmear, tsmear_unit = matched_tsmear_lines[0].split() +# assert float(tsmear) == pytest.approx(0.0183746610878275) +# assert tsmear_unit == "Ha" +# outdenpath = os.path.join( +# tmpdir, "first_run", OUTDIR_NAME, f"{OUTDATAFILE_PREFIX}_DEN" +# ) +# Path(outdenpath).touch() +# +# input_set2 = ssg2.get_input_set( +# structure=si_structure, +# charge=1.0, +# restart_from=os.path.join(tmpdir, "first_run"), +# ) +# input_set2.write_input("second_run") +# indenpath = os.path.join( +# tmpdir, "second_run", INDIR_NAME, f"{INDATAFILE_PREFIX}_DEN" +# ) +# assert os.path.islink(indenpath) +# assert os.readlink(indenpath) == outdenpath +# with open("second_run/run.abi") as file: +# runabi2_str = file.read() +# assert "ecut 8.5" in runabi2_str +# assert "nband 8" in runabi2_str +# assert "occopt" not in runabi2_str +# assert "tsmear" not in runabi2_str +# assert "charge 1.0" in runabi2_str +# assert "irdden 1" in runabi2_str +# +# outwfkpath = os.path.join( +# tmpdir, "first_run", OUTDIR_NAME, f"{OUTDATAFILE_PREFIX}_WFK" +# ) +# Path(outwfkpath).touch() +# input_set3 = ssg3.get_input_set( +# structure=si_structure, restart_from=os.path.join(tmpdir, "first_run") +# ) +# input_set3.write_input("second_run_bis") +# indenpath = os.path.join( +# tmpdir, "second_run_bis", INDIR_NAME, f"{INDATAFILE_PREFIX}_DEN" +# ) +# inwfkpath = os.path.join( +# tmpdir, "second_run_bis", INDIR_NAME, f"{INDATAFILE_PREFIX}_WFK" +# ) +# assert os.path.islink(inwfkpath) +# assert os.readlink(inwfkpath) == outwfkpath +# with open("second_run_bis/run.abi") as file: +# runabi3_str = file.read() +# assert "ecut 8.5" in runabi3_str +# assert "nband 13" in runabi3_str +# assert "occopt 5" in runabi3_str +# matched_tsmear_lines = [ +# line for line in runabi3_str.split("\n") if "tsmear" in line +# ] +# assert len(matched_tsmear_lines) == 1 +# _, tsmear, tsmear_unit = matched_tsmear_lines[0].split() +# assert float(tsmear) == pytest.approx(0.0183746610878275) +# assert tsmear_unit == "Ha" +# outdenpath = os.path.join( +# tmpdir, "first_run", OUTDIR_NAME, f"{OUTDATAFILE_PREFIX}_DEN" +# ) diff --git a/tests/abinit/test_powerups.py b/tests/abinit/test_powerups.py new file mode 100644 index 0000000000..98292f21c5 --- /dev/null +++ b/tests/abinit/test_powerups.py @@ -0,0 +1,123 @@ +import pytest + + +@pytest.mark.parametrize( + "powerup,attribute,settings", + [ + ("update_user_abinit_settings", "user_abinit_settings", {"ecut": 10}), + ( + "update_user_kpoints_settings", + "user_kpoints_settings", + {"reciprocal_density": 100}, + ), + ("update_factory_kwargs", "factory_kwargs", {"kppa": 100}), + ], +) +def test_update_user_settings(powerup, attribute, settings): + from atomate2.abinit import powerups + from atomate2.abinit.flows.core import RelaxFlowMaker + from atomate2.abinit.jobs.core import RelaxMaker + + powerup_func = getattr(powerups, powerup) + + # test job maker + rm = RelaxMaker() + rm = powerup_func(rm, settings) + assert getattr(rm.input_set_generator, attribute) == settings + + # test job + job = RelaxMaker().make(1) + job = powerup_func(job, settings) + assert getattr(job.function.__self__.input_set_generator, attribute) == settings + + # test flow maker + drm = RelaxFlowMaker() + drm = powerup_func(drm, settings) + for relax_maker_i in drm.relaxation_makers: + assert getattr(relax_maker_i.input_set_generator, attribute) == settings + + # test flow + drm = RelaxFlowMaker() + flow = drm.make(1) + flow = powerup_func(flow, settings) + assert ( + getattr(flow.jobs[0].function.__self__.input_set_generator, attribute) + == settings + ) + assert ( + getattr(flow.jobs[1].function.__self__.input_set_generator, attribute) + == settings + ) + + # test name filter + drm = RelaxFlowMaker() + flow = drm.make(1) + + flow = powerup_func( + flow, settings, name_filter="Relaxation calculation (ions only)" + ) + assert ( + getattr(flow.jobs[0].function.__self__.input_set_generator, attribute) + == settings + ) + assert ( + getattr(flow.jobs[1].function.__self__.input_set_generator, attribute) + != settings + ) + + +def test_update_generator_attributes(): + from atomate2.abinit.flows.core import RelaxFlowMaker + from atomate2.abinit.jobs.core import RelaxMaker + from atomate2.abinit.powerups import update_generator_attributes + + settings = {"pseudos": "ONCVPSP-PBE-SR-PDv0.3:standard"} + + # test job maker + rm = RelaxMaker() + rm = update_generator_attributes(rm, settings) + for attribute, value in settings.items(): + assert getattr(rm.input_set_generator, attribute) == value + + # test job + job = RelaxMaker().make(1) + job = update_generator_attributes(job, settings) + for attribute, value in settings.items(): + assert getattr(job.function.__self__.input_set_generator, attribute) == value + + # test flow maker + drm = RelaxFlowMaker() + drm = update_generator_attributes(drm, settings) + for attribute, value in settings.items(): + for relax_maker_i in drm.relaxation_makers: + assert getattr(relax_maker_i.input_set_generator, attribute) == value + + # test flow + drm = RelaxFlowMaker() + flow = drm.make(1) + flow = update_generator_attributes(flow, settings) + for attribute, value in settings.items(): + assert ( + getattr(flow.jobs[0].function.__self__.input_set_generator, attribute) + == value + ) + assert ( + getattr(flow.jobs[1].function.__self__.input_set_generator, attribute) + == value + ) + + # test name filter + drm = RelaxFlowMaker() + flow = drm.make(1) + flow = update_generator_attributes( + flow, settings, name_filter="Relaxation calculation (ions only)" + ) + for attribute, value in settings.items(): + assert ( + getattr(flow.jobs[0].function.__self__.input_set_generator, attribute) + == value + ) + assert ( + getattr(flow.jobs[1].function.__self__.input_set_generator, attribute) + != value + ) diff --git a/tests/aims/__init__.py b/tests/aims/__init__.py new file mode 100644 index 0000000000..332c3ccf52 --- /dev/null +++ b/tests/aims/__init__.py @@ -0,0 +1,35 @@ +"""Utils or testing""" + +import gzip +import json +from glob import glob +from pathlib import Path + + +def compare_files(test_name, work_dir, ref_dir): + for file in glob(f"{work_dir / test_name}/*in"): + with open(file) as test_file: + test_lines = [ + line.strip() + for line in test_file.readlines()[4:] + if len(line.strip()) > 0 + ] + + with gzip.open(f"{ref_dir / test_name / Path(file).name}.gz", "rt") as ref_file: + ref_lines = [ + line.strip() + for line in ref_file.readlines()[4:] + if len(line.strip()) > 0 + ] + + assert test_lines == ref_lines + + with open(f"{ref_dir / test_name}/parameters.json") as ref_file: + ref = json.load(ref_file) + ref.pop("species_dir", None) + + with open(f"{work_dir / test_name}/parameters.json") as check_file: + check = json.load(check_file) + check.pop("species_dir", None) + + assert ref == check diff --git a/tests/aims/conftest.py b/tests/aims/conftest.py new file mode 100644 index 0000000000..e27c28a7ce --- /dev/null +++ b/tests/aims/conftest.py @@ -0,0 +1,219 @@ +from __future__ import annotations + +import logging +import os +from pathlib import Path +from typing import TYPE_CHECKING, Literal + +import pytest +from pymatgen.core import Lattice, Molecule, Structure +from pymatgen.io.aims.sets.base import AimsInputGenerator + +import atomate2.aims.jobs.base +import atomate2.aims.run +from atomate2.common.files import gunzip_files + +if TYPE_CHECKING: + from collections.abc import Sequence + + +_REF_PATHS = {} +_FAKE_RUN_AIMS_KWARGS = {} +_VFILES = "control.in" + + +logger = logging.getLogger(__name__) + + +def pytest_addoption(parser): + parser.addoption( + "--generate-test-data", + action="store_true", + help="Runs FHI-aims to create test data;" + " runs tests against the created outputs", + ) + + +@pytest.fixture() +def si(): + return Structure( + lattice=Lattice( + [[0.0, 2.715, 2.715], [2.715, 0.0, 2.715], [2.715, 2.715, 0.0]] + ), + species=["Si", "Si"], + coords=[[0, 0, 0], [0.25, 0.25, 0.25]], + ) + + +@pytest.fixture() +def o2(): + return Molecule(species=["O", "O"], coords=[[0, 0, 0.622978], [0, 0, -0.622978]]) + + +@pytest.fixture(scope="session") +def species_dir(): + return Path(__file__).resolve().parent / "species_dir" + + +@pytest.fixture(scope="session") +def ref_path(): + from pathlib import Path + + module_dir = Path(__file__).resolve().parents[1] + test_dir = module_dir / "test_data/aims/" + return test_dir.resolve() + + +@pytest.fixture() +def should_mock_aims(request): + try: + return not request.config.getoption("--generate-test-data") + except ValueError: + return True + + +@pytest.fixture() +def mock_aims(monkeypatch, ref_path, should_mock_aims): + """ + This fixture allows one to mock (fake) running FHI-aims. + + To use the fixture successfully, the following steps must be followed: + 1. "mock_aims" should be included as an argument to any test that would like to use + its functionally. + 2. For each job in your workflow, you should prepare a reference directory + containing two folders "inputs" (containing the reference input files expected + to be produced by write_aims_input_set) and "outputs" (containing the expected + output files to be produced by run_aims). These files should reside in a + subdirectory of "tests/test_data/aims". + 3. Create a dictionary mapping each job name to its reference directory. Note that + you should supply the reference directory relative to the "tests/test_data/aims" + folder. For example, if your calculation has one job named "static" and the + reference files are present in "tests/test_data/aims/Si_static", the dictionary + would look like: ``{"static": "Si_static"}``. + 4. Optional (does not work yet): create a dictionary mapping each job name to + custom keyword arguments that will be supplied to fake_run_aims. + This way you can configure which control.in settings are expected for each job. + For example, if your calculation has one job named "static" and you wish to + validate that "xc" is set correctly in the control.in, your dictionary would + look like + ``{"static": {"input_settings": {"relativistic": "atomic_zora scalar"}}``. + 5. Inside the test function, call `mock_aims(ref_paths, fake_aims_kwargs)`, where + ref_paths is the dictionary created in step 3 and fake_aims_kwargs is the + dictionary created in step 4. + 6. Run your aims job after calling `mock_aims`. + + For examples, see the tests in tests/aims/jobs/core.py. + """ + + def mock_run_aims(*args, **kwargs): + from jobflow import CURRENT_JOB + + name = CURRENT_JOB.job.name + ref_dir = ref_path / _REF_PATHS[name] + fake_run_aims(ref_dir, **_FAKE_RUN_AIMS_KWARGS.get(name, {})) + + get_input_set_orig = AimsInputGenerator.get_input_set + + def generate_test_data(*args, **kwargs): + """A monkey patch for atomate2.aims.run.run_aims + + Runs the actual executable and copies inputs and outputs to the + test data directory + """ + import shutil + + from jobflow import CURRENT_JOB + + input_files = ["control.in", "geometry.in", "parameters.json"] + name = CURRENT_JOB.job.name + ref_dir = ref_path / _REF_PATHS[name] + # running aims + atomate2.aims.run.run_aims() + # copy output files + output_files = [f for f in Path.cwd().glob("*") if f.name not in input_files] + shutil.rmtree(ref_dir, ignore_errors=True) + os.makedirs(ref_dir / "inputs") + os.makedirs(ref_dir / "outputs") + for f in input_files: + shutil.copy(Path.cwd() / f, ref_dir / "inputs") + for f in output_files: + shutil.copy(f, ref_dir / "outputs") + + def mock_get_input_set(self, *args, **kwargs): + return get_input_set_orig(self, *args, **kwargs) + + if should_mock_aims: + monkeypatch.setattr(atomate2.aims.run, "run_aims", mock_run_aims) + monkeypatch.setattr(atomate2.aims.jobs.base, "run_aims", mock_run_aims) + monkeypatch.setattr(AimsInputGenerator, "get_input_set", mock_get_input_set) + else: + monkeypatch.setattr(atomate2.aims.jobs.base, "run_aims", generate_test_data) + + def _run(ref_paths, fake_run_aims_kwargs=None): + if fake_run_aims_kwargs is None: + fake_run_aims_kwargs = {} + + _REF_PATHS.update(ref_paths) + _FAKE_RUN_AIMS_KWARGS.update(fake_run_aims_kwargs) + + yield _run + + monkeypatch.undo() + _REF_PATHS.clear() + _FAKE_RUN_AIMS_KWARGS.clear() + + +def fake_run_aims( + ref_path: str | Path, + input_settings: Sequence[str] = (), + check_inputs: Sequence[Literal["control.in"]] = _VFILES, + clear_inputs: bool = False, +): + """ + Emulate running aims and validate aims input files. + + Parameters + ---------- + ref_path + Path to reference directory with aims input files in the folder named 'inputs' + and output files in the folder named 'outputs'. + input_settings + A list of input settings to check. + check_inputs + A list of aims input files to check. Supported options are "aims.inp" + clear_inputs + Whether to clear input files before copying in the reference aims outputs. + """ + logger.info("Running fake aims.") + + ref_path = Path(ref_path) + + logger.info("Verified inputs successfully") + + if clear_inputs: + clear_aims_inputs() + + copy_aims_outputs(ref_path) + gunzip_files( + include_files=list(Path.cwd().glob("*")), + allow_missing=True, + ) + + # pretend to run aims by copying pre-generated outputs from reference dir + logger.info("Generated fake aims outputs") + + +def clear_aims_inputs(): + for aims_file in ("control.in", "geometry.in", "parameters.json"): + if Path(aims_file).exists(): + Path(aims_file).unlink() + logger.info("Cleared aims inputs") + + +def copy_aims_outputs(ref_path: str | Path): + import shutil + + output_path = ref_path / "outputs" + for output_file in output_path.iterdir(): + if output_file.is_file(): + shutil.copy(output_file, ".") diff --git a/tests/aims/species_dir/light/01_H_default b/tests/aims/species_dir/light/01_H_default new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/aims/species_dir/light/08_O_default b/tests/aims/species_dir/light/08_O_default new file mode 100644 index 0000000000..9232a9aab7 --- /dev/null +++ b/tests/aims/species_dir/light/08_O_default @@ -0,0 +1,80 @@ +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for O atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species O +# global species definitions + nucleus 8 + mass 15.9994 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 36 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2659 50 + division 0.4451 110 + division 0.6052 194 + division 0.7543 302 +# division 0.8014 434 +# division 0.8507 590 +# division 0.8762 770 +# division 0.9023 974 +# division 1.2339 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 2 s 2. + valence 2 p 4. +# ion occupancy + ion_occ 2 s 1. + ion_occ 2 p 3. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A +# +################################################################################ +# "First tier" - improvements: -699.05 meV to -159.38 meV + hydro 2 p 1.8 + hydro 3 d 7.6 + hydro 3 s 6.4 +# "Second tier" - improvements: -49.91 meV to -5.39 meV +# hydro 4 f 11.6 +# hydro 3 p 6.2 +# hydro 3 d 5.6 +# hydro 5 g 17.6 +# hydro 1 s 0.75 +# "Third tier" - improvements: -2.83 meV to -0.50 meV +# ionic 2 p auto +# hydro 4 f 10.8 +# hydro 4 d 4.7 +# hydro 2 s 6.8 +# "Fourth tier" - improvements: -0.40 meV to -0.12 meV +# hydro 3 p 5 +# hydro 3 s 3.3 +# hydro 5 g 15.6 +# hydro 4 f 17.6 +# hydro 4 d 14 +# Further basis functions - -0.08 meV and below +# hydro 3 s 2.1 +# hydro 4 d 11.6 +# hydro 3 p 16 +# hydro 2 s 17.2 diff --git a/tests/aims/species_dir/light/14_Si_default b/tests/aims/species_dir/light/14_Si_default new file mode 100644 index 0000000000..83008b4edf --- /dev/null +++ b/tests/aims/species_dir/light/14_Si_default @@ -0,0 +1,87 @@ +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for Si atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +# 2020/09/08 Added f function to "light" after reinspection of Delta test outcomes. +# This was done for all of Al-Cl and is a tricky decision since it makes +# "light" calculations measurably more expensive for these elements. +# Nevertheless, outcomes for P, S, Cl (and to some extent, Si) appear +# to justify this choice. +# +################################################################################ + species Si +# global species definitions + nucleus 14 + mass 28.0855 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 42 5.0 + radial_multiplier 1 + angular_grids specified + division 0.5866 50 + division 0.9616 110 + division 1.2249 194 + division 1.3795 302 +# division 1.4810 434 +# division 1.5529 590 +# division 1.6284 770 +# division 1.7077 974 +# division 2.4068 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 3 s 2. + valence 3 p 2. +# ion occupancy + ion_occ 3 s 1. + ion_occ 3 p 1. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A +# +################################################################################ +# "First tier" - improvements: -571.96 meV to -37.03 meV + hydro 3 d 4.2 + hydro 2 p 1.4 + hydro 4 f 6.2 + ionic 3 s auto +# "Second tier" - improvements: -16.76 meV to -3.03 meV +# hydro 3 d 9 +# hydro 5 g 9.4 +# hydro 4 p 4 +# hydro 1 s 0.65 +# "Third tier" - improvements: -3.89 meV to -0.60 meV +# ionic 3 d auto +# hydro 3 s 2.6 +# hydro 4 f 8.4 +# hydro 3 d 3.4 +# hydro 3 p 7.8 +# "Fourth tier" - improvements: -0.33 meV to -0.11 meV +# hydro 2 p 1.6 +# hydro 5 g 10.8 +# hydro 5 f 11.2 +# hydro 3 d 1 +# hydro 4 s 4.5 +# Further basis functions that fell out of the optimization - noise +# level... < -0.08 meV +# hydro 4 d 6.6 +# hydro 5 g 16.4 +# hydro 4 d 9 diff --git a/tests/aims/species_dir/tight/08_O_default b/tests/aims/species_dir/tight/08_O_default new file mode 100644 index 0000000000..b6fd218468 --- /dev/null +++ b/tests/aims/species_dir/tight/08_O_default @@ -0,0 +1,90 @@ +################################################################################ +# +# FHI-aims code project +# Volker Blum, Fritz Haber Institute Berlin, 2009 +# +# Suggested "tight" defaults for O atom (to be pasted into control.in file) +# +################################################################################ + species O +# global species definitions + nucleus 8 + mass 15.9994 +# + l_hartree 6 +# + cut_pot 4.0 2.0 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 36 7.0 + radial_multiplier 2 + angular_grids specified + division 0.1817 50 + division 0.3417 110 + division 0.4949 194 + division 0.6251 302 + division 0.8014 434 +# division 0.8507 590 +# division 0.8762 770 +# division 0.9023 974 +# division 1.2339 1202 +# outer_grid 974 + outer_grid 434 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 2 s 2. + valence 2 p 4. +# ion occupancy + ion_occ 2 s 1. + ion_occ 2 p 3. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A +# +################################################################################ +# "First tier" - improvements: -699.05 meV to -159.38 meV + hydro 2 p 1.8 + hydro 3 d 7.6 + hydro 3 s 6.4 +# "Second tier" - improvements: -49.91 meV to -5.39 meV + hydro 4 f 11.6 + hydro 3 p 6.2 + hydro 3 d 5.6 + hydro 5 g 17.6 + hydro 1 s 0.75 +# "Third tier" - improvements: -2.83 meV to -0.50 meV +# ionic 2 p auto +# hydro 4 f 10.8 +# hydro 4 d 4.7 +# hydro 2 s 6.8 +# "Fourth tier" - improvements: -0.40 meV to -0.12 meV +# hydro 3 p 5 +# hydro 3 s 3.3 +# hydro 5 g 15.6 +# hydro 4 f 17.6 +# hydro 4 d 14 +# Further basis functions - -0.08 meV and below +# hydro 3 s 2.1 +# hydro 4 d 11.6 +# hydro 3 p 16 +# hydro 2 s 17.2 +################################################################################ +# +# For methods that use the localized form of the "resolution of identity" for +# the two-electron Coulomb operator (RI_method LVL), particularly Hartree-Fock and +# hybrid density functional calculations, the highest accuracy can be obtained by +# uncommenting the line beginning with "for_aux" below, thus adding an extra g radial +# function to the construction of the product basis set for the expansion. +# See Ref. New J. Phys. 17, 093020 (2015) for more information, particularly Figs. 1 and 6. +# +################################################################################ +# +# for_aux hydro 5 g 6.0 diff --git a/tests/aims/species_dir/tight/14_Si_default b/tests/aims/species_dir/tight/14_Si_default new file mode 100644 index 0000000000..7f503709f2 --- /dev/null +++ b/tests/aims/species_dir/tight/14_Si_default @@ -0,0 +1,94 @@ +################################################################################ +# +# FHI-aims code project +# Volker Blum, Fritz Haber Institute Berlin, 2009 +# +# Suggested "tight" defaults for Si atom (to be pasted into control.in file) +# +# Revised Jan 04, 2011, following tests (SiC) done by Lydia Nemec: +# d and g functions of tier 2 now enabled by default. +# +################################################################################ + species Si +# global species definitions + nucleus 14 + mass 28.0855 +# + l_hartree 6 +# + cut_pot 4.0 2.0 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 42 7.0 + radial_multiplier 2 + angular_grids specified + division 0.4121 50 + division 0.7665 110 + division 1.0603 194 + division 1.2846 302 + division 1.4125 434 +# division 1.4810 590 +# division 1.5529 770 +# division 1.6284 974 +# division 2.6016 1202 +# outer_grid 974 + outer_grid 434 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 3 s 2. + valence 3 p 2. +# ion occupancy + ion_occ 3 s 1. + ion_occ 3 p 1. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A +# +################################################################################ +# "First tier" - improvements: -571.96 meV to -37.03 meV + hydro 3 d 4.2 + hydro 2 p 1.4 + hydro 4 f 6.2 + ionic 3 s auto +# "Second tier" - improvements: -16.76 meV to -3.03 meV + hydro 3 d 9 + hydro 5 g 9.4 +# hydro 4 p 4 +# hydro 1 s 0.65 +# "Third tier" - improvements: -3.89 meV to -0.60 meV +# ionic 3 d auto +# hydro 3 s 2.6 +# hydro 4 f 8.4 +# hydro 3 d 3.4 +# hydro 3 p 7.8 +# "Fourth tier" - improvements: -0.33 meV to -0.11 meV +# hydro 2 p 1.6 +# hydro 5 g 10.8 +# hydro 5 f 11.2 +# hydro 3 d 1 +# hydro 4 s 4.5 +# Further basis functions that fell out of the optimization - noise +# level... < -0.08 meV +# hydro 4 d 6.6 +# hydro 5 g 16.4 +# hydro 4 d 9 +################################################################################ +# +# For methods that use the localized form of the "resolution of identity" for +# the two-electron Coulomb operator (RI_method LVL), particularly Hartree-Fock and +# hybrid density functional calculations, the highest accuracy can be obtained by +# uncommenting the line beginning with "for_aux" below, thus adding an extra g radial +# function to the construction of the product basis set for the expansion. +# See Ref. New J. Phys. 17, 093020 (2015) for more information, particularly Figs. 1 and 6. +# +################################################################################ +# +# for_aux hydro 5 g 6.0 diff --git a/tests/aims/test_files/__init__.py b/tests/aims/test_files/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/aims/test_files/outputs/D_spin_01_kpt_000001.csc b/tests/aims/test_files/outputs/D_spin_01_kpt_000001.csc new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/aims/test_files/outputs/D_spin_01_kpt_000002.csc b/tests/aims/test_files/outputs/D_spin_01_kpt_000002.csc new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/aims/test_files/outputs/aims.out b/tests/aims/test_files/outputs/aims.out new file mode 100644 index 0000000000..8939796de0 --- /dev/null +++ b/tests/aims/test_files/outputs/aims.out @@ -0,0 +1,5259 @@ +------------------------------------------------------------ + Invoking FHI-aims ... + + When using FHI-aims, please cite the following reference: + + Volker Blum, Ralf Gehrke, Felix Hanke, Paula Havu, + Ville Havu, Xinguo Ren, Karsten Reuter, and Matthias Scheffler, + 'Ab Initio Molecular Simulations with Numeric Atom-Centered Orbitals', + Computer Physics Communications 180, 2175-2196 (2009) + + In addition, many other developments in FHI-aims are likely important for + your particular application. A partial list of references is given at the end of + this file. Thank you for giving credit to the authors of these developments. + + For any questions about FHI-aims, please visit our slack channel at + + https://fhi-aims.slack.com + + and our main development and support site at + + https://aims-git.rz-berlin.mpg.de . + + The latter site, in particular, has a wiki to collect information, as well + as an issue tracker to log discussions, suggest improvements, and report issues + or bugs. https://aims-git.rz-berlin.mpg.de is also the main development site + of the project and all new and updated code versions can be obtained there. + Please send an email to aims-coordinators@fhi-berlin.mpg.de and we will add + you to these sites. They are for you and everyone is welcome there. + +------------------------------------------------------------ + + + + Date : 20230117, Time : 114544.660 + Time zero on CPU 1 : 0.474143400000000E+01 s. + Internal wall clock time zero : 443187944.660 s. + + FHI-aims created a unique identifier for this run for later identification + aims_uuid : 1842BF69-05B0-47B3-A510-68677842FECA + + Build configuration of the current instance of FHI-aims + ------------------------------------------------------- + FHI-aims version : 221103 + Commit number : cc62f3b89 + CMake host system : Linux-5.15.0-56-generic + CMake version : 3.22.1 + Fortran compiler : /opt/intel/oneapi/mpi/2021.8.0/bin/mpiifort (Intel) version 2021.8.0.20221119 + Fortran compiler flags: -O3 -ip -fp-model precise + C compiler : /opt/intel/oneapi/compiler/2023.0.0/linux/bin/intel64/icc (Intel) version 2021.8.0.20221119 + C compiler flags : -O3 -ip -fp-model precise -std=gnu99 -diag-disable=10441 + HIP compiler : + HIP compiler flags : + HIP GPU arch : + Using MPI + Using ScaLAPACK + Using LibXC + Using i-PI + Using RLSY + Linking against: /opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_intel_lp64.so + /opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_sequential.so + /opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.so + /opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_blacs_intelmpi_lp64.so + /opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_scalapack_lp64.so + + Using 8 parallel tasks. + Task 0 on host andrey-Latitude-5411 reporting. + Task 1 on host andrey-Latitude-5411 reporting. + Task 2 on host andrey-Latitude-5411 reporting. + Task 3 on host andrey-Latitude-5411 reporting. + Task 4 on host andrey-Latitude-5411 reporting. + Task 5 on host andrey-Latitude-5411 reporting. + Task 6 on host andrey-Latitude-5411 reporting. + Task 7 on host andrey-Latitude-5411 reporting. + + Obtaining array dimensions for all initial allocations: + + ----------------------------------------------------------------------- + Parsing control.in (first pass over file, find array dimensions only). + The contents of control.in will be repeated verbatim below + unless switched off by setting 'verbatim_writeout .false.' . + in the first line of control.in . + ----------------------------------------------------------------------- + + ######################################################################################### + # + # Volker Blum, FHI 2010 : Input file for FHI-aims + # + # + ######################################################################################### + # + # Physical model settings + # + xc hse06 0.11 # positive screening parameter omega + hse_unit b + charge 0. + spin none + # default_initial_moment 0.0 + # default_initial_moment 0.0 + # fixed_spin_moment 2.0 + relativistic atomic_zora scalar + include_spin_orbit + vdw_correction_hirshfeld + use_dipole_correction + # to evaluate work function of both surface of slab + evaluate_work_function + + # + # SCF convergence settings + # + occupation_type gaussian 0.01 + mixer pulay + n_max_pulay 6 + charge_mix_param 0.1 + ini_linear_mixing 10 + ini_linear_mix_param 0.05 + # preconditioner kerker 1.5 + # precondition_max_l 0 + # preconditioner turnoff charge 1e-4 + # preconditioner turnoff sum_ev 1e-1 + sc_accuracy_rho 1E-3 + sc_accuracy_eev 1E-2 + sc_accuracy_etot 1E-5 + sc_iter_limit 200 + # + elsi_restart read_and_write 10 + # + # For periodic boundary conditions + # + # here the k-mesh is given + k_grid 25 25 1 + output band 0.0 0.0 0.0 0.0 0.5 0.0 21 G M + output band 0.0 0.5 0.0 0.3333 0.3333 0.0 21 M K + output band 0.3333 0.3333 0.0 0.0 0.0 0.0 21 K G + output band 0.0 0.0 0.0 -0.3333 -0.3333 0.0 21 G Kp + + + output band_mulliken 0.0 0.0 0.0 0.0 0.5 0.0 21 G M + output band_mulliken 0.0 0.5 0.0 0.3333 0.3333 0.0 21 M K + output band_mulliken 0.3333 0.3333 0.0 0.0 0.0 0.0 21 K G + output band_mulliken 0.0 0.0 0.0 -0.3333 -0.3333 0.0 21 G Kp + + # Output options: + # k-path through which the band structure is calculated and plotted using the below setting + # output band kstart1 kstart1 kstart2 kstart3 kend1 kend2 kend3 n_points name_start name_end + exx_band_structure_version 1 + + + + # + # RI_method LVL_fast + # For relaxation: + # + # relax_geometry bfgs 5.e-3 + # relax_unit_cell full + # sc_accuracy_forces 5E-4 + + # + # Output options: + # pdos + output dos -20 20 1000 0.01 + # output species_proj_dos -20 20 1000 0.01 + output atom_proj_dos -20 20 1000 0.01 + + # linear response calculations + # The momentum matrix elements in the energy window [ VBM-(omega_max + 10.0 eV), + # CBM+(omega_max + 10.0 eV)] (in eV) relative to the internal zero will be summed + # compute_dielectric omega_max n_omega + # + compute_dielectric 10.0 1000 + # output dielectric lorentzian 0.05 x x + output dielectric gaussian 0.05 x x + + # output dielectric lorentzian 0.05 y y + output dielectric gaussian 0.05 y y + + # output dielectric lorentzian 0.05 z z + output dielectric gaussian 0.05 z z + + + compute_absorption 0.1 -20 20 0.005 10.0 1000 x .true. + compute_absorption 0.1 -20 20 0.005 10.0 1000 y .true. + compute_absorption 0.1 -20 30 0.005 10.0 1000 z .true. + # + # High-symmetry k-points for fcc band structure output, if requested. + # + # output l_proj_dos -20 30 1000 0.3 + # output band 0.25 0.50 0.75 0.5 0.5 0.5 100 W L + # output band 0.5 0.5 0.5 0.25 0.25 0.25 100 L Lambda + # output band 0.25 0.25 0.25 0 0 0 100 Lambda Gamma + # output band 0 0 0 0.00 0.25 0.25 100 Gamma Delta + # output band 0.00 0.25 0.25 0 0.5 0.5 100 Delta X + # output band 0 0.5 0.5 0.125 0.5 0.625 100 X Z + # output band 0.125 0.5 0.625 0.25 0.50 0.75 100 Z W + # output band 0.25 0.50 0.75 0.375 0.375 0.75 100 W K + ################################################################################ + # + # FHI-aims code project + # Volker Blum, Fritz Haber Institute Berlin, 2009 + # + # Suggested "tight" defaults for Mo atom (to be pasted into control.in file) + # + ################################################################################ + species Mo + # global species definitions + nucleus 42 + mass 95.94 + # + l_hartree 6 + # + cut_pot 4.0 2.0 1.0 + basis_dep_cutoff 1e-4 + # + radial_base 59 7.0 + radial_multiplier 2 + angular_grids specified + division 0.3117 50 + division 0.6750 110 + division 1.0351 194 + division 1.2073 302 + division 1.6402 434 + # division 1.9185 590 + # division 2.0237 770 + # division 2.0980 974 + # division 2.7972 1202 + # outer_grid 974 + outer_grid 434 + ################################################################################ + # + # Definition of "minimal" basis + # + ################################################################################ + # valence basis states + valence 5 s 1. + valence 4 p 6. + valence 4 d 5. + # ion occupancy + ion_occ 5 s 0. + ion_occ 4 p 6. + ion_occ 4 d 4. + ################################################################################ + # + # Suggested additional basis functions. For production calculations, + # uncomment them one after another (the most important basis functions are + # listed first). + # + # Constructed for dimers: 1.675 A, 1.9 A, 2.375 A, 3.00 A, 4.00 A + # + ################################################################################ + # "First tier" - max. impr. -711.23 meV, min. impr. -21.07 meV + hydro 4 f 8.4 + hydro 3 d 2.8 + ionic 5 p auto + hydro 5 g 12 + ionic 5 s auto + # "Second tier" - max. impr. -39.38 meV, min. impr. -2.68 meV + # hydro 4 f 12.4 + # hydro 3 d 3.3 + # hydro 6 h 17.2 + # hydro 4 f 7.6 + # hydro 3 p 3.0 + # hydro 1 s 0.65 + # "Third tier" - max. impr. -5.50 meV, min. impr. -0.47 meV + # hydro 4 f 29.2 + # hydro 5 g 11.2 + # hydro 3 d 6.8 + # hydro 6 h 14.8 + # hydro 2 p 2.3 + # hydro 4 s 3.8 + # "Fourth tier" - max. impr. -0.58 meV, min. impr. -0.19 meV + # hydro 5 f 6.8 + # hydro 5 d 14.8 + # hydro 6 s 7.8 + # hydro 5 g 20.8 + # hydro 5 d 10.4 + # hydro 5 p 9.8 + # Further functions - -0.17 meV and below + # hydro 5 d 3.2 + ################################################################################ + # + # FHI-aims code project + # Volker Blum, Fritz Haber Institute Berlin, 2009 + # + # Suggested "tight" defaults for Se atom (to be pasted into control.in file) + # + ################################################################################ + species Se + # global species definitions + nucleus 34 + mass 78.96 + # + l_hartree 6 + # + cut_pot 4.0 2.0 1.0 + basis_dep_cutoff 1e-4 + # + radial_base 55 7.0 + radial_multiplier 2 + angular_grids specified + division 0.0830 110 + division 0.1357 194 + division 0.7377 302 + division 0.8610 434 + # division 0.9640 590 + # division 1.0773 770 + # division 2.5539 974 + # outer_grid 974 + outer_grid 434 + ################################################################################ + # + # Definition of "minimal" basis + # + ################################################################################ + # valence basis states + valence 4 s 2. + valence 4 p 4. + valence 3 d 10. + # ion occupancy + ion_occ 4 s 1. + ion_occ 4 p 3. + ion_occ 3 d 10. + ################################################################################ + # + # Suggested additional basis functions. For production calculations, + # uncomment them one after another (the most important basis functions are + # listed first). + # + # Constructed for dimers: 1.85 A, 2.15 A, 2.50 A, 3.00 A, 4.00 A + # + ################################################################################ + # "First tier" - improvements: -336.21 meV to -36.85 meV + hydro 3 d 4.3 + hydro 2 p 1.6 + hydro 4 f 7.2 + ionic 4 s auto + # "Second tier" - improvements: -14.39 meV to -1.49 meV + # hydro 5 g 10.4 + # hydro 4 p 4.5 + # hydro 4 d 6.2 + # hydro 4 f 11.2 + # hydro 1 s 0.65 + # hydro 6 h 15.2 + # Third tier - improvements: -0.46 meV and below + # hydro 5 g 14.4 + # ionic 4 d auto + # hydro 4 f 22.4 + # hydro 5 f 7.4 + # hydro 5 p 8 + # hydro 5 s 9.4 + # Fourth tier - improvements: -0.12 meV and below + # hydro 5 d 11.6 + # hydro 6 h 18 + # hydro 4 p 4 + # hydro 5 f 16 + # hydro 4 s 3.9 + ################################################################################ + # + # FHI-aims code project + # Volker Blum, Fritz Haber Institute Berlin, 2009 + # + # Suggested "tight" defaults for S atom (to be pasted into control.in file) + # + # Revised Jan 04, 2011, following tests (SiC) done by Lydia Nemec: + # d and g functions of tier 2 now enabled by default. + # + ################################################################################ + species S + # global species definitions + nucleus 16 + mass 32.065 + # + l_hartree 6 + # + cut_pot 4.0 2.0 1.0 + basis_dep_cutoff 1e-4 + # + radial_base 44 7.0 + radial_multiplier 2 + angular_grids specified + division 0.4665 110 + division 0.5810 194 + division 0.7139 302 + division 0.8274 434 + # division 0.9105 590 + # division 1.0975 770 + # division 1.2028 974 + # outer_grid 974 + outer_grid 434 + ################################################################################ + # + # Definition of "minimal" basis + # + ################################################################################ + # valence basis states + valence 3 s 2. + valence 3 p 4. + # ion occupancy + ion_occ 3 s 1. + ion_occ 3 p 3. + ################################################################################ + # + # Suggested additional basis functions. For production calculations, + # uncomment them one after another (the most important basis functions are + # listed first). + # + # Constructed for dimers: 1.6 A, 1.9 A, 2.5 A, 3.25 A, 4.0 A + # + ################################################################################ + # "First tier" - improvements: -652.81 meV to -45.53 meV + ionic 3 d auto + hydro 2 p 1.8 + hydro 4 f 7 + ionic 3 s auto + # "Second tier" - improvements: -30.20 meV to -1.74 meV + hydro 4 d 6.2 + hydro 5 g 10.8 + # hydro 4 p 4.9 + # hydro 5 f 10 + # hydro 1 s 0.8 + # "Third tier" - improvements: -1.04 meV to -0.20 meV + # hydro 3 d 3.9 + # hydro 3 d 2.7 + # hydro 5 g 12 + # hydro 4 p 10.4 + # hydro 5 f 12.4 + # hydro 2 s 1.9 + # "Fourth tier" - improvements: -0.35 meV to -0.06 meV + # hydro 4 d 10.4 + # hydro 4 p 7.2 + # hydro 4 d 10 + # hydro 5 g 19.2 + # hydro 4 s 12 + + ################################################################################ + # + # For methods that use the localized form of the "resolution of identity" for + # the two-electron Coulomb operator (RI_method LVL), particularly Hartree-Fock and + # hybrid density functional calculations, the highest accuracy can be obtained by + # uncommenting the line beginning with "for_aux" below, thus adding an extra g radial + # function to the construction of the product basis set for the expansion. + # See Ref. New J. Phys. 17, 093020 (2015) for more information, particularly Figs. 1 and 6. + # + ################################################################################ + # + # for_aux hydro 5 g 6.0 + ################################################################################ + # + # FHI-aims code project + # Volker Blum, Fritz Haber Institute Berlin, 2009 + # + # Suggested "tight" defaults for W atom (to be pasted into control.in file) + # + ################################################################################ + species W + # global species definitions + nucleus 74 + mass 183.84 + # + l_hartree 6 + # + cut_pot 4.0 2.0 1.0 + basis_dep_cutoff 1e-4 + # + radial_base 71 7.0 + radial_multiplier 2 + angular_grids specified + division 0.2901 50 + division 0.6986 110 + division 1.0528 194 + division 1.2659 302 + division 1.5223 434 + # division 1.8111 590 + # division 2.0105 770 + # division 2.0413 974 + # division 2.8804 1202 + # outer_grid 974 + outer_grid 434 + ################################################################################ + # + # Definition of "minimal" basis + # + ################################################################################ + # valence basis states + valence 6 s 2. + valence 5 p 6. + valence 5 d 4. + valence 4 f 14. + # ion occupancy + ion_occ 6 s 1. + ion_occ 5 p 6. + ion_occ 5 d 3. + ion_occ 4 f 14. + ################################################################################ + # + # Suggested additional basis functions. For production calculations, + # uncomment them one after another (the most important basis functions are + # listed first). + # + # Constructed for dimers: 1.775, 1.99, 2.50, 3.25, 4.50 AA + # + ################################################################################ + # + # "First tier" - improvements: -603.77 meV to -28.99 meV + hydro 4 f 7.8 + hydro 4 d 5.8 + ionic 6 p auto + hydro 5 g 12.4 + ionic 6 s auto + # "Second tier" - improvements: -28.30 meV to -1.31 meV + # hydro 6 h 16.8 + # ionic 5 d auto + # hydro 4 f 8.6 + # hydro 5 g 16.8 + # hydro 5 d 8.4 + # hydro 3 p 3.3 + # hydro 1 s 0.55 + # "Third tier" - max. impr. -1.79 meV, min. impr. -0.26 meV + # hydro 5 f 10.8 + # hydro 5 g 34.4 + # hydro 6 h 20.8 + # hydro 5 g 12.8 + # hydro 2 p 1.6 + # hydro 4 s 4.7 + # hydro 6 d 18.4 + # "Fourth tier" -0.46 max. impr. - meV, min. impr. -0.09 meV + # hydro 6 h 21.6 + # hydro 5 f 22.4 + # hydro 4 f 4 + # hydro 5 p 9.6 + # hydro 6 d 17.2 + # hydro 3 p 5.2 + # hydro 5 g 4.7 + # hydro 6 s 7.6 + + ################################################################################ + # + # FHI-aims code project + # Volker Blum, Fritz Haber Institute Berlin, 2009 + # + # Suggested "tight" defaults for Te atom (to be pasted into control.in file) + # + # 2020/09/15 Added g function to "tight" settings, since this creates truly "tight" + # but not overly tight defaults. See "intermediate" settings for the past + # "tight" settings, which are still very reliable. Consider "intermediate" + # for hybrid functionals, for example. + # + ################################################################################ + species Te + # global species definitions + nucleus 52 + mass 127.60 + # + l_hartree 6 + # + cut_pot 4.0 2.0 1.0 + basis_dep_cutoff 1e-4 + # + radial_base 64 7.0 + radial_multiplier 2 + angular_grids specified + division 0.1259 110 + division 0.8959 194 + division 0.9864 302 + division 1.1196 434 + # division 1.1922 590 + # division 1.3098 770 + # division 2.9404 974 + # outer_grid 974 + outer_grid 434 + ################################################################################ + # + # Definition of "minimal" basis + # + ################################################################################ + # valence basis states + valence 5 s 2. + valence 5 p 4. + valence 4 d 10. + # ion occupancy + ion_occ 5 s 1. + ion_occ 5 p 3. + ion_occ 4 d 10. + ################################################################################ + # + # Suggested additional basis functions. For production calculations, + # uncomment them one after another (the most important basis functions are + # listed first). + # + # Constructed for dimers: 2.15 A, 2.55 A, 3.10 A, 3.60 A, 4.50 A + # + ################################################################################ + # "First tier" - max. impr. -217.34 meV, min. impr. -22.97 meV + hydro 3 d 3.7 + hydro 4 f 6 + hydro 3 p 2.7 + ionic 5 s auto + # "Second tier" - max. impr. -17.80 meV, min. impr. -0.57 meV + hydro 5 g 9 + # hydro 4 f 16.4 + # hydro 6 h 12 + # hydro 4 p 6.4 + # hydro 5 f 32.4 + # hydro 4 d 5 + # hydro 3 s 2.8 + # "Third tier" - max. impr. -0.51 meV, min. impr. -0.06 meV + # hydro 5 f 8.4 + # hydro 5 g 11.6 + # hydro 6 h 15.6 + # hydro 2 p 1.7 + # hydro 4 d 9.6 + # hydro 1 s 6.4 + # Further functions that fell out of the optimization: -0.17 meV and below + # hydro 4 f 33.6 + # hydro 5 d 6.8 + # hydro 5 f 16 + + + ----------------------------------------------------------------------- + Completed first pass over input file control.in . + ----------------------------------------------------------------------- + + + ----------------------------------------------------------------------- + Parsing geometry.in (first pass over file, find array dimensions only). + The contents of geometry.in will be repeated verbatim below + unless switched off by setting 'verbatim_writeout .false.' . + in the first line of geometry.in . + ----------------------------------------------------------------------- + + # + # This is the geometry file that corresponds to the current relaxation step. + # If you do not want this file to be written, set the "write_restart_geometry" flag to .false. + # aims_uuid : 30F25284-AA5C-43EF-ACEA-2542C5DCBEDB + # + set_vacuum_level 21.961371 + lattice_vector 3.40717493 0.00014206 0.00000000 + lattice_vector -1.70378822 2.95054058 0.00000000 + lattice_vector 0.00013496 0.00027045 30.69261765 + atom 0.02071770 0.02091759 2.79151492 Mo + atom -0.02140986 -0.01576611 10.18168839 W + atom 0.02054554 1.98843192 1.16989135 Se + atom 0.02081213 1.98757349 4.66407853 Te + atom -0.02140973 1.95099156 8.55192704 Se + atom -0.02178102 1.95181653 12.06464594 Te + + + ----------------------------------------------------------------------- + Completed first pass over input file geometry.in . + ----------------------------------------------------------------------- + + + Basic array size parameters: + | Number of species : 5 + | Number of atoms : 6 + | Number of lattice vectors : 3 + | Max. basis fn. angular momentum : 4 + | Max. atomic/ionic basis occupied n: 6 + | Max. number of basis fn. types : 3 + | Max. radial fns per species/type : 14 + | Max. logarithmic grid size : 1483 + | Max. radial integration grid size : 143 + | Max. angular integration grid size: 434 + | Max. angular grid division number : 8 + | Radial grid for Hartree potential : 1483 + | Number of spin channels : 1 + +------------------------------------------------------------ + Reading file control.in. +------------------------------------------------------------ + + XC: Using HSE-functional with OMEGA = 0.110000E+00 . + XC: For the actual units (bohr^-1 or Angstrom^-1), see below. + hse_unit: Unit for the HSE06 hybrid functional screening parameter set to bohr^(-1). + Charge = 0.000000E+00: Neutral system requested explicitly. + Spin treatment: No spin polarisation. + Scalar relativistic treatment of kinetic energy: on-site free-atom approximation to ZORA. + Calculating non-self-consistent second-variational spin-orbit coupling after scf-cycle + Using dipole correction. +Evaluating the work function. + Occupation type: Gaussian broadening, width = 0.100000E-01 eV. + Using pulay charge density mixing. + Pulay mixing - number of memorized iterations: 6 + Charge density mixing - mixing parameter: 0.1000 + Number of initial iterations with linear charge density mixing: 10 + Charge density mixing parameter for initial linear mixing: 0.50000E-01 + Convergence accuracy of self-consistent charge density: 0.1000E-02 + Convergence accuracy of sum of eigenvalues: 0.1000E-01 + Convergence accuracy of total energy: 0.1000E-04 + Maximum number of s.-c. iterations : 200 + Found k-point grid: 25 25 1 + + Plot band 1 + | begin 0.000000 0.000000 0.000000 + | end 0.000000 0.500000 0.000000 + | number of points: 21 + + Plot band 2 + | begin 0.000000 0.500000 0.000000 + | end 0.333300 0.333300 0.000000 + | number of points: 21 + + Plot band 3 + | begin 0.333300 0.333300 0.000000 + | end 0.000000 0.000000 0.000000 + | number of points: 21 + + Plot band 4 + | begin 0.000000 0.000000 0.000000 + | end -0.333300 -0.333300 0.000000 + | number of points: 21 + Mulliken analysis of all k points in band will be performed + + Plot band 5 + | begin 0.000000 0.000000 0.000000 + | end 0.000000 0.500000 0.000000 + | number of points: 21 + Mulliken analysis of all k points in band will be performed + + Plot band 6 + | begin 0.000000 0.500000 0.000000 + | end 0.333300 0.333300 0.000000 + | number of points: 21 + Mulliken analysis of all k points in band will be performed + + Plot band 7 + | begin 0.333300 0.333300 0.000000 + | end 0.000000 0.000000 0.000000 + | number of points: 21 + Mulliken analysis of all k points in band will be performed + + Plot band 8 + | begin 0.000000 0.000000 0.000000 + | end -0.333300 -0.333300 0.000000 + | number of points: 21 + Calculating density of states with + | energy interval :-20.000000 20.000000 + | points & broadening : 1000 0.010000 + Calculating atom-projected density of states with + | energy interval :-20.000000 20.000000 + | points & broadening : 1000 0.010000 + Compute Momentum Matrix. + + Plot dielectric direction 1 + + Plot dielectric direction 2 + + Plot dielectric direction 3 + Compute Absorption. + Compute Absorption. + Compute Absorption. + + Reading configuration options for species Mo . + | Found nuclear charge : 42.0000 + | Found atomic mass : 95.9400000000000 amu + | Found l_max for Hartree potential : 6 + | Found cutoff potl. onset [A], width [A], scale factor : 4.00000 2.00000 1.00000 + | Threshold for basis-dependent cutoff potential is 0.100000E-03 + | Found data for basic radial integration grid : 59 points, outermost radius = 7.000 A + | Found multiplier for basic radial grid : 2 + | Found angular grid specification: user-specified. + | Specified grid contains 6 separate shells. + | Check grid settings after all constraints further below. + | Found free-atom valence shell : 5 s 1.000 + | Found free-atom valence shell : 4 p 6.000 + | Found free-atom valence shell : 4 d 5.000 + | Found free-ion valence shell : 5 s 0.000 + | Found free-ion valence shell : 4 p 6.000 + | Found free-ion valence shell : 4 d 4.000 + | Found hydrogenic basis function : 4 f 8.400 + | Found hydrogenic basis function : 3 d 2.800 + | Found ionic basis function : 5 p , default cutoff radius. + | Found hydrogenic basis function : 5 g 12.000 + | Found ionic basis function : 5 s , default cutoff radius. + Species Mo : Missing cutoff potential type. + Defaulting to exp(1/x)/(1-x)^2 type cutoff potential. + Species Mo: No 'logarithmic' tag. Using default grid for free atom: + | Default logarithmic grid data [bohr] : 0.1000E-03 0.1000E+03 0.1012E+01 + | Will include ionic basis functions of 2.0-fold positive Mo ion. + Species Mo: On-site basis accuracy parameter (for Gram-Schmidt orthonormalisation) not specified. + Using default value basis_acc = 0.1000000E-03. + Species Mo : Using default innermost maximum threshold i_radial= 2 for radial functions. + Species Mo : Default cutoff onset for free atom density etc. : 0.40000000E+01 AA. + Species Mo : Basic radial grid will be enhanced according to radial_multiplier = 2, to contain 119 grid points. + + Reading configuration options for species Se . + | Found nuclear charge : 34.0000 + | Found atomic mass : 78.9600000000000 amu + | Found l_max for Hartree potential : 6 + | Found cutoff potl. onset [A], width [A], scale factor : 4.00000 2.00000 1.00000 + | Threshold for basis-dependent cutoff potential is 0.100000E-03 + | Found data for basic radial integration grid : 55 points, outermost radius = 7.000 A + | Found multiplier for basic radial grid : 2 + | Found angular grid specification: user-specified. + | Specified grid contains 5 separate shells. + | Check grid settings after all constraints further below. + | Found free-atom valence shell : 4 s 2.000 + | Found free-atom valence shell : 4 p 4.000 + | Found free-atom valence shell : 3 d 10.000 + | Found free-ion valence shell : 4 s 1.000 + | Found free-ion valence shell : 4 p 3.000 + | Found free-ion valence shell : 3 d 10.000 + | Found hydrogenic basis function : 3 d 4.300 + | Found hydrogenic basis function : 2 p 1.600 + | Found hydrogenic basis function : 4 f 7.200 + | Found ionic basis function : 4 s , default cutoff radius. + Species Se : Missing cutoff potential type. + Defaulting to exp(1/x)/(1-x)^2 type cutoff potential. + Species Se: No 'logarithmic' tag. Using default grid for free atom: + | Default logarithmic grid data [bohr] : 0.1000E-03 0.1000E+03 0.1012E+01 + | Will include ionic basis functions of 2.0-fold positive Se ion. + Species Se: On-site basis accuracy parameter (for Gram-Schmidt orthonormalisation) not specified. + Using default value basis_acc = 0.1000000E-03. + Species Se : Using default innermost maximum threshold i_radial= 2 for radial functions. + Species Se : Default cutoff onset for free atom density etc. : 0.40000000E+01 AA. + Species Se : Basic radial grid will be enhanced according to radial_multiplier = 2, to contain 111 grid points. + + Reading configuration options for species S . + | Found nuclear charge : 16.0000 + | Found atomic mass : 32.0650000000000 amu + | Found l_max for Hartree potential : 6 + | Found cutoff potl. onset [A], width [A], scale factor : 4.00000 2.00000 1.00000 + | Threshold for basis-dependent cutoff potential is 0.100000E-03 + | Found data for basic radial integration grid : 44 points, outermost radius = 7.000 A + | Found multiplier for basic radial grid : 2 + | Found angular grid specification: user-specified. + | Specified grid contains 5 separate shells. + | Check grid settings after all constraints further below. + | Found free-atom valence shell : 3 s 2.000 + | Found free-atom valence shell : 3 p 4.000 + | Found free-ion valence shell : 3 s 1.000 + | Found free-ion valence shell : 3 p 3.000 + | Found ionic basis function : 3 d , default cutoff radius. + | Found hydrogenic basis function : 2 p 1.800 + | Found hydrogenic basis function : 4 f 7.000 + | Found ionic basis function : 3 s , default cutoff radius. + | Found hydrogenic basis function : 4 d 6.200 + | Found hydrogenic basis function : 5 g 10.800 + Species S : Missing cutoff potential type. + Defaulting to exp(1/x)/(1-x)^2 type cutoff potential. + Species S : No 'logarithmic' tag. Using default grid for free atom: + | Default logarithmic grid data [bohr] : 0.1000E-03 0.1000E+03 0.1012E+01 + | Will include ionic basis functions of 2.0-fold positive S ion. + Species S : On-site basis accuracy parameter (for Gram-Schmidt orthonormalisation) not specified. + Using default value basis_acc = 0.1000000E-03. + Species S : Using default innermost maximum threshold i_radial= 2 for radial functions. + Species S : Default cutoff onset for free atom density etc. : 0.40000000E+01 AA. + Species S : Basic radial grid will be enhanced according to radial_multiplier = 2, to contain 89 grid points. + + Reading configuration options for species W . + | Found nuclear charge : 74.0000 + | Found atomic mass : 183.840000000000 amu + | Found l_max for Hartree potential : 6 + | Found cutoff potl. onset [A], width [A], scale factor : 4.00000 2.00000 1.00000 + | Threshold for basis-dependent cutoff potential is 0.100000E-03 + | Found data for basic radial integration grid : 71 points, outermost radius = 7.000 A + | Found multiplier for basic radial grid : 2 + | Found angular grid specification: user-specified. + | Specified grid contains 6 separate shells. + | Check grid settings after all constraints further below. + | Found free-atom valence shell : 6 s 2.000 + | Found free-atom valence shell : 5 p 6.000 + | Found free-atom valence shell : 5 d 4.000 + | Found free-atom valence shell : 4 f 14.000 + | Found free-ion valence shell : 6 s 1.000 + | Found free-ion valence shell : 5 p 6.000 + | Found free-ion valence shell : 5 d 3.000 + | Found free-ion valence shell : 4 f 14.000 + | Found hydrogenic basis function : 4 f 7.800 + | Found hydrogenic basis function : 4 d 5.800 + | Found ionic basis function : 6 p , default cutoff radius. + | Found hydrogenic basis function : 5 g 12.400 + | Found ionic basis function : 6 s , default cutoff radius. + Species W : Missing cutoff potential type. + Defaulting to exp(1/x)/(1-x)^2 type cutoff potential. + Species W : No 'logarithmic' tag. Using default grid for free atom: + | Default logarithmic grid data [bohr] : 0.1000E-03 0.1000E+03 0.1012E+01 + | Will include ionic basis functions of 2.0-fold positive W ion. + Species W : On-site basis accuracy parameter (for Gram-Schmidt orthonormalisation) not specified. + Using default value basis_acc = 0.1000000E-03. + Species W : Using default innermost maximum threshold i_radial= 2 for radial functions. + Species W : Default cutoff onset for free atom density etc. : 0.40000000E+01 AA. + Species W : Basic radial grid will be enhanced according to radial_multiplier = 2, to contain 143 grid points. + + Reading configuration options for species Te . + | Found nuclear charge : 52.0000 + | Found atomic mass : 127.600000000000 amu + | Found l_max for Hartree potential : 6 + | Found cutoff potl. onset [A], width [A], scale factor : 4.00000 2.00000 1.00000 + | Threshold for basis-dependent cutoff potential is 0.100000E-03 + | Found data for basic radial integration grid : 64 points, outermost radius = 7.000 A + | Found multiplier for basic radial grid : 2 + | Found angular grid specification: user-specified. + | Specified grid contains 5 separate shells. + | Check grid settings after all constraints further below. + | Found free-atom valence shell : 5 s 2.000 + | Found free-atom valence shell : 5 p 4.000 + | Found free-atom valence shell : 4 d 10.000 + | Found free-ion valence shell : 5 s 1.000 + | Found free-ion valence shell : 5 p 3.000 + | Found free-ion valence shell : 4 d 10.000 + | Found hydrogenic basis function : 3 d 3.700 + | Found hydrogenic basis function : 4 f 6.000 + | Found hydrogenic basis function : 3 p 2.700 + | Found ionic basis function : 5 s , default cutoff radius. + | Found hydrogenic basis function : 5 g 9.000 + Species Te : Missing cutoff potential type. + Defaulting to exp(1/x)/(1-x)^2 type cutoff potential. + Species Te: No 'logarithmic' tag. Using default grid for free atom: + | Default logarithmic grid data [bohr] : 0.1000E-03 0.1000E+03 0.1012E+01 + | Will include ionic basis functions of 2.0-fold positive Te ion. + Species Te: On-site basis accuracy parameter (for Gram-Schmidt orthonormalisation) not specified. + Using default value basis_acc = 0.1000000E-03. + Species Te : Using default innermost maximum threshold i_radial= 2 for radial functions. + Species Te : Default cutoff onset for free atom density etc. : 0.40000000E+01 AA. + Species Te : Basic radial grid will be enhanced according to radial_multiplier = 2, to contain 129 grid points. + + Finished reading input file 'control.in'. + +------------------------------------------------------------ + + +------------------------------------------------------------ + Reading geometry description geometry.in. +------------------------------------------------------------ + Vacuum level in z-axis : 0.219614E+02 + | The smallest distance between any two atoms is 2.54917855 AA. + | The first atom of this pair is atom number 1 . + | The second atom of this pair is atom number 3 . + | Wigner-Seitz cell of the first atom image 0 0 0 . + | (The Wigner-Seitz cell of the second atom is 0 0 0 by definition.) + + Symmetry information by spglib: + | Precision set to 0.1E-04 + | Number of Operations : 1 + | Space group : 1 + | International : P1 /op + | Schoenflies : C1^1 + Input structure read successfully. + The structure contains 6 atoms, and a total of 288.000 electrons. + + Input geometry: + | Unit cell: + | 3.40717493 0.00014206 0.00000000 + | -1.70378822 2.95054058 0.00000000 + | 0.00013496 0.00027045 30.69261765 + | Atomic structure: + | Atom x [A] y [A] z [A] + | 1: Species Mo 0.02071770 0.02091759 2.79151492 + | 2: Species W -0.02140986 -0.01576611 10.18168839 + | 3: Species Se 0.02054554 1.98843192 1.16989135 + | 4: Species Te 0.02081213 1.98757349 4.66407853 + | 5: Species Se -0.02140973 1.95099156 8.55192704 + | 6: Species Te -0.02178102 1.95181653 12.06464594 + + Lattice parameters for 3D lattice (in Angstroms) : 3.407175 3.407137 30.692618 + Angle(s) between unit vectors (in degrees) : 89.999689 89.999748 120.001876 + + + Quantities derived from the lattice vectors (in Angstrom^-1): + | Reciprocal lattice vector 1: 1.844060 1.064851 -0.000017 + | Reciprocal lattice vector 2: -0.000089 2.129452 -0.000019 + | Reciprocal lattice vector 3: 0.000000 -0.000000 0.204713 + | Unit cell volume : 0.308561E+03 Angstrom^3 + + Fractional coordinates: + L1 L2 L3 + atom_frac 0.00961773 0.00708061 0.09095070 Mo + atom_frac -0.00898393 -0.00537344 0.33173086 W + atom_frac 0.34301889 0.67390122 0.03811638 Se + atom_frac 0.34294192 0.67359984 0.15196092 Te + atom_frac 0.32433958 0.66119075 0.27863140 Se + atom_frac 0.32436064 0.66145985 0.39307973 Te + + + Finished reading input file 'geometry.in'. + + + + Consistency checks for stacksize environment parameter are next. + + | Maximum stacksize for task 0: unlimited + | Maximum stacksize for task 1: unlimited + | Maximum stacksize for task 2: unlimited + | Maximum stacksize for task 3: unlimited + | Maximum stacksize for task 4: unlimited + | Maximum stacksize for task 5: unlimited + | Maximum stacksize for task 6: unlimited + | Maximum stacksize for task 7: unlimited + | Current stacksize for task 0: unlimited + | Current stacksize for task 1: unlimited + | Current stacksize for task 2: unlimited + | Current stacksize for task 3: unlimited + | Current stacksize for task 4: unlimited + | Current stacksize for task 5: unlimited + | Current stacksize for task 6: unlimited + | Current stacksize for task 7: unlimited + + Consistency checks for the contents of control.in are next. + + HSE06 screening parameters: omega_HF = 0.11000000 bohr^-1, and + omega_PBE = 0.11000000 bohr^-1. + MPI_IN_PLACE appears to work with this MPI implementation. + | Keeping use_mpi_in_place .true. (see manual). + Explicit treatment of the Coulomb operator is needed, but the RI method is not specified. + Coulomb operator: Defaulting to 'LVL fast' resolution of identity - RI_type = LVL_fast + Species Mo: Using default value for prodbas_acc = 1.000000E-04. + Species Mo: Using default value max_l_prodbas = 20. + Species Se: Using default value for prodbas_acc = 1.000000E-04. + Species Se: Using default value max_l_prodbas = 20. + Species S: Using default value for prodbas_acc = 1.000000E-04. + Species S: Using default value max_l_prodbas = 20. + Species W: Using default value for prodbas_acc = 1.000000E-04. + Species W: Using default value max_l_prodbas = 20. + Species Te: Using default value for prodbas_acc = 1.000000E-04. + Species Te: Using default value max_l_prodbas = 20. + Target number of points in a grid batch is not set. Defaulting to 100 + Method for grid partitioning is not set. Defaulting to parallel hash+maxmin partitioning. + Batch size limit is not set. Defaulting to 200 + By default, will store active basis functions for each batch. + If in need of memory, prune_basis_once .false. can be used to disable this option. + communication_type for Hartree potential was not specified. + Defaulting to calc_hartree . + Work space size for distributed Hartree potential not set. + Defaulting to 0.200000E+03 MB. + Algorithm-dependent basis array size parameters: + | n_max_pulay : 6 + Presetting 1001 iterations before the initial mixing cycle + is restarted anyway using the sc_init_iter criterion / keyword. + Presetting a factor 1.000 between actual scf density residual + and density convergence criterion sc_accuracy_rho below which sc_init_iter + takes no effect. + Calculation of forces was not defined in control.in. No forces will be calculated. + Geometry relaxation not requested: no relaxation will be performed. + No accuracy limit for integral partition fn. given. Defaulting to 0.1000E-14. + No threshold value for u(r) in integrations given. Defaulting to 0.1000E-05. + No accuracy for occupation numbers given. Defaulting to 0.1000E-12. + No threshold value for occupation numbers given. Defaulting to 0.0000E+00. + No accuracy for fermi level given. Defaulting to 0.1000E-19. + Maximum # of iterations to find E_F not set. Defaulting to 200. + Preferred method for the eigenvalue solver ('KS_method') not specified in 'control.in'. + Defaulting to serial version, LAPACK (via ELSI), since more k-points than CPUs available. + Will not use alltoall communication since running on < 1024 CPUs. + Threshold for basis singularities not set. + Default threshold for basis singularities: 0.1000E-04 + partition_type (choice of integration weights) for integrals was not specified. + | Using a version of the partition function of Stratmann and coworkers ('stratmann_sparse'). + | At each grid point, the set of atoms used to build the partition table is smoothly restricted to + | only those atoms whose free-atom density would be non-zero at that grid point. + Partitioning for Hartree potential was not defined. Using partition_type for integrals. + | Adjusted default value of keyword multip_moments_threshold to: 0.10000000E-11 + | This value may affect high angular momentum components of the Hartree potential in periodic systems. + Threshold for auxiliary basis singularities not set. + Default threshold for auxiliary basis singularities: 0.1000E-04 + No q(lm)/r^(l+1) cutoff set for long-range Hartree potential. + | Using default value of 0.100000E-09 . + | Verify using the multipole_threshold keyword. + Defaulting to new monopole extrapolation. + Density update method: automatic selection selected. + Using density matrix based charge density update. + Using density matrix based charge density update. + Using packed matrix style: index . + * NOTE: You are attempting to run a periodic structure with an exchange treatment + * which requires a two-electron Coulomb operator (Hartree-Fock or a hybrid functional). + * The present implementation is reliable to our knowledge, but some things + * (like band structure output, or perhaps the auxilary basis set for small + * orbital basis sets - see the "for_aux" keyword) require extra care. + * Please let us know if you encounter any trouble. + Coulomb operator: Defaulting to screening threshold for four-center integrals: 0.100000E-06 + Coulomb operator: Defaulting to screening threshold for Coulomb matrix: 0.100000E-09 + Fock matrix calculation: Setting the screening threshold for overlap matrix to coul_mat_threshold: 0.100000E-09 + Coulomb operator: Defaulting to 'LVL_fast' resolution of identity - RI_type = LVL_fast + No other resolution of identity version is supported for periodic boundary conditions at present. + Coulomb operator: Defaulting to logarithmic spherical Bessel transform integrals (use_logsbt .true.). + HSE with LVL_fast: Also defaulting to logarithmic spherical Bessel transform integrals. + Defaulting to use time-reversal symmetry for k-point grid. + Charge integration errors on the 3D integration grid will be compensated + by explicit normalization and distribution of residual charges. + Use the "compensate_multipole_errors" flag to change this behaviour. + LVL not implemented with density matrix yet + -> switching to transformed overlap + LVL probably works better with logsbt + Default to 1D ("use_logsbt") integrations for auxiliary 2-center integrals. + Default onset of logarithmic r-grid for SBT is -38.000000000000 + Default onset of logarithmic k-grid for SBT is -25.000000000000 + Default range of logarithmic r- and k-grid for SBT is 45.000000000000 + Default number of logarithmic r- and k-grid for SBT is 4096 + * Use logSBT for radial HSE integration, too + * NOTE: Band structure and exact exchange are requested at the same time, + * and exx_band_structure_version is set to 1. + * exx_band_structure_version 1 is evaluated in a real-space formalism. It is fast + * and the preferred version. HOWEVER, it does require a sufficiently + * dense 'k_grid' to be used for the preceding s.c.f. cycle. + * If the 'k_grid used for s.c.f. is NOT dense enough, the real- + * space approach will produce bands that are OBVIOUSLY incorrect. + * You cannot miss this - they won't look 'slightly' correct. In + * that case, please try to increase the 'k_grid' parameters used + * for the s.c.f. cycle. In particular, please avoid k_grid dimensions + * of '1' (one) in any dimension. We apologize for this inconvenience. + * On the bright side, if you use exx_band_structure_version 1 + * correctly, it will give reliable results without much overhead. + * + * If your band structure does not look reasonable, increase the s.c.f. k-point + * grid density. Again, it is especially recommended that you avoid dimensions of 1 when + * specifying k_grid and using this option, even for large unit cells where a + * gamma-point-only k-grid would be sufficient to converge the accuracy of the + * calculation. + * + * Please test (e.g., by comparing results from different k_grid settings) when in any doubt. + Using the following vdw_convergence_threshold for supercell sums + over the Tkatchenko-Scheffler correction: 0.100000E-05 eV. + Set 'collect_eigenvectors' to be '.true.' for all serial calculations. This is mandatory. + Set 'collect_eigenvectors' to be '.true.' for KS_method lapack_fast and serial. + + Consistency checks for the contents of geometry.in are next. + + + Range separation radius for Ewald summation (hartree_convergence_parameter): 5.00000000 bohr. + Number of empty states per atom not set in control.in - providing a guess from actual geometry. + | Total number of empty states used during s.c.f. cycle: 37 + If you use a very high smearing, use empty_states (per atom!) in control.in to increase this value. + * Since a dielectric function calculation was requested, the number of empty states requested was INCREASED. + * Since a DOS, bandstructure or SOC calculation was requested, the number of empty states requested was INCREASED. + | Number of empty states (old): 373.00000 + | Number of empty states (new): 383.00000 + + Structure-dependent array size parameters: + | Maximum number of distinct radial functions : 73 + | Maximum number of basis functions : 286 + | Number of Kohn-Sham states (occupied + empty): 336 +------------------------------------------------------------ + Setting Coulomb cut-width to 1.091868692359 * rcut. + Setting Coulomb cutting radius rcut to 15.346308825744 A. + + Performing system and environment tests: + | Environment variable OMP_NUM_THREADS correctly set to 1. + | Checking for ScaLAPACK... + | Testing pdtran()... + | All pdtran() tests passed. + | Testing pzgemm()... + | All pzgemm() tests passed. + +------------------------------------------------------------ + Preparing all fixed parts of the calculation. +------------------------------------------------------------ + Determining machine precision: + 2.225073858507201E-308 + Setting up grids for atomic and cluster calculations. + + Creating wave function, potential, and density for free atoms. + Runtime choices for atomic solver: + | atomic solver xc : PBE + | compute density gradient: 1 + | compute kinetic density : F + + Species: Mo + + List of occupied orbitals and eigenvalues: + n l occ energy [Ha] energy [eV] + 1 0 2.0000 -745.344654 -20281.8600 + 2 0 2.0000 -103.288246 -2810.6162 + 3 0 2.0000 -17.516687 -476.6533 + 4 0 2.0000 -2.358559 -64.1796 + 5 0 1.0000 -0.145159 -3.9500 + 2 1 6.0000 -92.308627 -2511.8455 + 3 1 6.0000 -13.936005 -379.2180 + 4 1 6.0000 -1.408138 -38.3174 + 3 2 10.0000 -8.119011 -220.9295 + 4 2 5.0000 -0.132984 -3.6187 + + + Species: Se + + List of occupied orbitals and eigenvalues: + n l occ energy [Ha] energy [eV] + 1 0 2.0000 -466.337810 -12689.6975 + 2 0 2.0000 -59.202598 -1610.9847 + 3 0 2.0000 -7.847116 -213.5309 + 4 0 2.0000 -0.634372 -17.2621 + 2 1 6.0000 -52.061107 -1416.6548 + 3 1 6.0000 -5.620941 -152.9536 + 4 1 4.0000 -0.238469 -6.4891 + 3 2 10.0000 -1.951949 -53.1152 + + + Species: S + + List of occupied orbitals and eigenvalues: + n l occ energy [Ha] energy [eV] + 1 0 2.0000 -88.680731 -2413.1255 + 2 0 2.0000 -7.781719 -211.7513 + 3 0 2.0000 -0.633662 -17.2428 + 2 1 6.0000 -5.751976 -156.5192 + 3 1 4.0000 -0.257086 -6.9957 + + + Species: W + + List of occupied orbitals and eigenvalues: + n l occ energy [Ha] energy [eV] + 1 0 2.0000 -2764.899999 -75236.7570 + 2 0 2.0000 -447.822848 -12185.8797 + 3 0 2.0000 -101.923634 -2773.4832 + 4 0 2.0000 -20.945301 -569.9506 + 5 0 2.0000 -2.899582 -78.9016 + 6 0 2.0000 -0.207066 -5.6345 + 2 1 6.0000 -391.021390 -10640.2334 + 3 1 6.0000 -85.417793 -2324.3364 + 4 1 6.0000 -15.562838 -423.4864 + 5 1 6.0000 -1.582233 -43.0547 + 3 2 10.0000 -66.517936 -1810.0451 + 4 2 10.0000 -8.758436 -238.3292 + 5 2 4.0000 -0.161873 -4.4048 + 4 3 14.0000 -1.221948 -33.2509 + + + Species: Te + + List of occupied orbitals and eigenvalues: + n l occ energy [Ha] energy [eV] + 1 0 2.0000 -1205.196269 -32795.0591 + 2 0 2.0000 -179.435283 -4882.6825 + 3 0 2.0000 -35.515934 -966.4377 + 4 0 2.0000 -6.038599 -164.3187 + 5 0 2.0000 -0.553449 -15.0601 + 2 1 6.0000 -160.997293 -4380.9593 + 3 1 6.0000 -29.570439 -804.6526 + 4 1 6.0000 -4.201054 -114.3165 + 5 1 4.0000 -0.217175 -5.9096 + 3 2 10.0000 -20.601415 -560.5930 + 4 2 10.0000 -1.529160 -41.6105 + + + Adding cutoff potential to free-atom effective potential. + Creating fixed part of basis set: Ionic, confined, hydrogenic. + + Mo ion: + + List of free ionic orbitals and eigenvalues: + n l energy [Ha] energy [eV] + 1 0 -746.048685 -20301.0176 + 2 0 -103.980912 -2829.4646 + 3 0 -18.206601 -495.4268 + 4 0 -3.040545 -82.7374 + 2 1 -93.001013 -2530.6863 + 3 1 -14.625827 -397.9890 + 4 1 -2.084855 -56.7318 + 3 2 -8.808854 -239.7011 + 4 2 -0.765435 -20.8285 + + + List of ionic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 5 1 -0.465587 -12.6693 5.456393 + 5 0 -0.650331 -17.6964 5.390095 + + + Mo hydrogenic: + + List of hydrogenic basis orbitals: + n l effective z eigenvalue [eV] inner max. [A] outer max. [A] outer radius [A] + 4 3 8.400000 -60.0010 1.009788 1.009788 4.487018 + 3 2 2.800000 -11.8048 1.687401 1.687401 5.456393 + 5 4 12.000000 -78.3687 1.100005 1.100005 4.432498 + + + Se ion: + + List of free ionic orbitals and eigenvalues: + n l energy [Ha] energy [eV] + 1 0 -467.261007 -12714.8189 + 2 0 -60.104893 -1635.5374 + 3 0 -8.743714 -237.9286 + 4 0 -1.414053 -38.4783 + 2 1 -52.964156 -1441.2280 + 3 1 -6.516916 -177.3343 + 4 1 -0.961869 -26.1738 + 3 2 -2.844511 -77.4031 + + + List of ionic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 4 0 -1.414046 -38.4782 4.083166 + + + Se hydrogenic: + + List of hydrogenic basis orbitals: + n l effective z eigenvalue [eV] inner max. [A] outer max. [A] outer radius [A] + 3 2 4.300000 -27.9518 1.103845 1.103845 5.278265 + 2 1 1.600000 -8.6828 1.326010 1.326010 5.475439 + 4 3 7.200000 -44.0822 1.173422 1.173422 4.965294 + + + S ion: + + List of free ionic orbitals and eigenvalues: + n l energy [Ha] energy [eV] + 1 0 -89.703778 -2440.9640 + 2 0 -8.775428 -238.7916 + 3 0 -1.470343 -40.0101 + 2 1 -6.747660 -183.6132 + 3 1 -1.048627 -28.5346 + + + List of ionic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 3 2 -0.495605 -13.4861 5.386362 + 3 0 -1.470336 -40.0099 3.967934 + + + S hydrogenic: + + List of hydrogenic basis orbitals: + n l effective z eigenvalue [eV] inner max. [A] outer max. [A] outer radius [A] + 2 1 1.800000 -11.0118 1.168531 1.168531 5.452614 + 4 3 7.000000 -41.6672 1.212182 1.212182 5.066981 + 4 2 6.200000 -32.6848 0.582121 1.814567 5.386362 + 5 4 10.800000 -63.4785 1.227092 1.227092 4.766538 + + + W ion: + + List of free ionic orbitals and eigenvalues: + n l energy [Ha] energy [eV] + 1 0 -2765.664016 -75257.5469 + 2 0 -448.543169 -12205.4806 + 3 0 -102.635476 -2792.8534 + 4 0 -21.655379 -589.2728 + 5 0 -3.604872 -98.0936 + 6 0 -0.752243 -20.4696 + 2 1 -391.740682 -10659.8063 + 3 1 -86.129333 -2343.6984 + 4 1 -16.272893 -442.8080 + 5 1 -2.280103 -62.0448 + 3 2 -67.229405 -1829.4052 + 4 2 -9.468448 -257.6496 + 5 2 -0.806537 -21.9470 + 4 3 -1.931058 -52.5468 + + + List of ionic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 6 1 -0.508246 -13.8301 5.434360 + 6 0 -0.752227 -20.4691 5.368330 + + + W hydrogenic: + + List of hydrogenic basis orbitals: + n l effective z eigenvalue [eV] inner max. [A] outer max. [A] outer radius [A] + 4 3 7.800000 -51.7355 1.082252 1.082252 4.692859 + 4 2 5.800000 -28.5979 0.616741 1.946131 5.434360 + 5 4 12.400000 -83.6803 1.069102 1.069102 4.307971 + + + Te ion: + + List of free ionic orbitals and eigenvalues: + n l energy [Ha] energy [eV] + 1 0 -1206.001395 -32816.9677 + 2 0 -180.213456 -4903.8576 + 3 0 -36.289734 -987.4939 + 4 0 -6.806662 -185.2187 + 5 0 -1.230780 -33.4912 + 2 1 -161.775412 -4402.1329 + 3 1 -30.344117 -825.7054 + 4 1 -4.968097 -135.1888 + 5 1 -0.843350 -22.9487 + 3 2 -21.374869 -581.6398 + 4 2 -2.290936 -62.3395 + + + List of ionic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 5 0 -1.230774 -33.4911 4.407087 + + + Te hydrogenic: + + List of hydrogenic basis orbitals: + n l effective z eigenvalue [eV] inner max. [A] outer max. [A] outer radius [A] + 3 2 3.700000 -20.6934 1.282089 1.282089 5.425112 + 4 3 6.000000 -30.6116 1.413813 1.413813 5.359194 + 3 1 2.700000 -10.8497 0.586309 2.305482 5.491841 + 5 4 9.000000 -44.0820 1.466627 1.466627 5.359194 + + Creating atomic-like basis functions for current effective potential. + + Species Mo : + + List of atomic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 1 0 -745.344654 -20281.8600 0.247552 + 2 0 -103.288246 -2810.6162 0.682864 + 3 0 -17.516687 -476.6533 1.626637 + 4 0 -2.358559 -64.1796 4.220963 + 5 0 -0.145159 -3.9500 5.456393 + 2 1 -92.308627 -2511.8455 0.699766 + 3 1 -13.936005 -379.2180 1.793761 + 4 1 -1.408138 -38.3174 4.828511 + 3 2 -8.119011 -220.9295 2.181285 + 4 2 -0.132984 -3.6187 5.390095 + + + Species Se : + + List of atomic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 1 0 -466.337810 -12689.6975 0.309561 + 2 0 -59.202598 -1610.9847 0.885812 + 3 0 -7.847116 -213.5309 2.355489 + 4 0 -0.634372 -17.2621 5.214131 + 2 1 -52.061107 -1416.6548 0.907737 + 3 1 -5.620941 -152.9536 2.694529 + 4 1 -0.238469 -6.4891 5.408909 + 3 2 -1.951949 -53.1152 4.083166 + + + Species S : + + List of atomic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 1 0 -88.680731 -2413.1255 0.682391 + 2 0 -7.781719 -211.7513 2.289014 + 3 0 -0.633662 -17.2428 5.256262 + 2 1 -5.751976 -156.5192 2.555240 + 3 1 -0.257086 -6.9957 5.386362 + + + Species W : + + List of atomic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 1 0 -2764.899999 -75236.7570 0.130566 + 2 0 -447.822848 -12185.8797 0.342973 + 3 0 -101.923634 -2773.4832 0.722975 + 4 0 -20.945301 -569.9506 1.542753 + 5 0 -2.899582 -78.9016 3.859132 + 6 0 -0.207066 -5.6345 5.434360 + 2 1 -391.021390 -10640.2334 0.355785 + 3 1 -85.417793 -2324.3364 0.768545 + 4 1 -15.562838 -423.4864 1.722184 + 5 1 -1.582233 -43.0547 4.750581 + 3 2 -66.517936 -1810.0451 0.827037 + 4 2 -8.758436 -238.3292 2.172477 + 5 2 -0.161873 -4.4048 5.368330 + 4 3 -1.221948 -33.2509 4.579510 + + + Species Te : + + List of atomic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 1 0 -1205.196269 -32795.0591 0.195117 + 2 0 -179.435283 -4882.6825 0.531683 + 3 0 -35.515934 -966.4377 1.176937 + 4 0 -6.038599 -164.3187 2.735843 + 5 0 -0.553449 -15.0601 5.294077 + 2 1 -160.997293 -4380.9593 0.544843 + 3 1 -29.570439 -804.6526 1.266511 + 4 1 -4.201054 -114.3165 3.168123 + 5 1 -0.217175 -5.9096 5.425112 + 3 2 -20.601415 -560.5930 1.431203 + 4 2 -1.529160 -41.6105 4.627949 + + Assembling full basis from fixed parts. + | Species Mo : atomic orbital 1 s accepted. + | Species Mo : atomic orbital 2 s accepted. + | Species Mo : atomic orbital 3 s accepted. + | Species Mo : atomic orbital 4 s accepted. + | Species Mo : ionic orbital 5 s accepted. + | Species Mo : atomic orbital 5 s accepted. + | Species Mo : atomic orbital 2 p accepted. + | Species Mo : atomic orbital 3 p accepted. + | Species Mo : atomic orbital 4 p accepted. + | Species Mo : ionic orbital 5 p accepted. + | Species Mo : atomic orbital 3 d accepted. + | Species Mo : atomic orbital 4 d accepted. + | Species Mo : hydro orbital 3 d accepted. + | Species Mo : hydro orbital 4 f accepted. + | Species Mo : hydro orbital 5 g accepted. + | Species Se : atomic orbital 1 s accepted. + | Species Se : atomic orbital 2 s accepted. + | Species Se : atomic orbital 3 s accepted. + | Species Se : ionic orbital 4 s accepted. + | Species Se : atomic orbital 4 s accepted. + | Species Se : atomic orbital 2 p accepted. + | Species Se : atomic orbital 3 p accepted. + | Species Se : atomic orbital 4 p accepted. + | Species Se : hydro orbital 2 p accepted. + | Species Se : atomic orbital 3 d accepted. + | Species Se : hydro orbital 3 d accepted. + | Species Se : hydro orbital 4 f accepted. + | Species S : atomic orbital 1 s accepted. + | Species S : atomic orbital 2 s accepted. + | Species S : ionic orbital 3 s accepted. + | Species S : atomic orbital 3 s accepted. + | Species S : atomic orbital 2 p accepted. + | Species S : atomic orbital 3 p accepted. + | Species S : hydro orbital 2 p accepted. + | Species S : ionic orbital 3 d accepted. + | Species S : hydro orbital 4 d accepted. + | Species S : hydro orbital 4 f accepted. + | Species S : hydro orbital 5 g accepted. + | Species W : atomic orbital 1 s accepted. + | Species W : atomic orbital 2 s accepted. + | Species W : atomic orbital 3 s accepted. + | Species W : atomic orbital 4 s accepted. + | Species W : atomic orbital 5 s accepted. + | Species W : ionic orbital 6 s accepted. + | Species W : atomic orbital 6 s accepted. + | Species W : atomic orbital 2 p accepted. + | Species W : atomic orbital 3 p accepted. + | Species W : atomic orbital 4 p accepted. + | Species W : atomic orbital 5 p accepted. + | Species W : ionic orbital 6 p accepted. + | Species W : atomic orbital 3 d accepted. + | Species W : atomic orbital 4 d accepted. + | Species W : atomic orbital 5 d accepted. + | Species W : hydro orbital 4 d accepted. + | Species W : atomic orbital 4 f accepted. + | Species W : hydro orbital 4 f accepted. + | Species W : hydro orbital 5 g accepted. + | Species Te : atomic orbital 1 s accepted. + | Species Te : atomic orbital 2 s accepted. + | Species Te : atomic orbital 3 s accepted. + | Species Te : atomic orbital 4 s accepted. + | Species Te : ionic orbital 5 s accepted. + | Species Te : atomic orbital 5 s accepted. + | Species Te : atomic orbital 2 p accepted. + | Species Te : atomic orbital 3 p accepted. + | Species Te : atomic orbital 4 p accepted. + | Species Te : atomic orbital 5 p accepted. + | Species Te : hydro orbital 3 p accepted. + | Species Te : atomic orbital 3 d accepted. + | Species Te : atomic orbital 4 d accepted. + | Species Te : hydro orbital 3 d accepted. + | Species Te : hydro orbital 4 f accepted. + | Species Te : hydro orbital 5 g accepted. + Reducing total number of Kohn-Sham states to 286. + + Basis size parameters after reduction: + | Total number of radial functions: 73 + | Total number of basis functions : 286 + + Per-task memory consumption for arrays in subroutine allocate_ext: + | 27.726404MB. + Testing on-site integration grid accuracy. + | Species Function (log., in eV) (rad., in eV) + 1 1 -20281.8599610543 -20281.8584300616 + 1 2 -2810.6161812280 -2810.6161551921 + 1 3 -476.6533163555 -476.6533136395 + 1 4 -64.1796433667 -64.1796426456 + 1 5 -3.3691762756 -3.3691802887 + 1 6 4.4704608512 4.4699102345 + 1 7 -2511.8455406047 -2511.8455385741 + 1 8 -379.2179896350 -379.2179882338 + 1 9 -38.3173891619 -38.3173886619 + 1 10 0.2493245095 0.2492931069 + 1 11 -220.9295301098 -220.9295297081 + 1 12 -3.6195697699 -3.6195754704 + 1 13 7.1428000922 7.1426882355 + 1 14 23.3975871087 23.3975871819 + 1 15 50.2449608881 50.2449608586 + 2 16 -12689.6974611609 -12689.6967666984 + 2 17 -1610.9846578580 -1610.9846472470 + 2 18 -213.5308789869 -213.5308777267 + 2 19 -17.0464428502 -17.0464426496 + 2 20 6.7356859379 6.7356842047 + 2 21 -1416.6548010133 -1416.6548002108 + 2 22 -152.9535734377 -152.9535727493 + 2 23 -6.4896265677 -6.4896303794 + 2 24 5.2703037283 5.2701679583 + 2 25 -53.1152220964 -53.1152219035 + 2 26 7.6186674138 7.6186665630 + 2 27 23.1072799052 23.1072803137 + 3 28 -2413.1254568977 -2413.1254096663 + 3 29 -211.7513411281 -211.7513404762 + 3 30 -16.9725280787 -16.9725279206 + 3 31 7.6024436204 7.6024549059 + 3 32 -156.5192206929 -156.5192205451 + 3 33 -6.9959757887 -6.9959777655 + 3 34 6.8896462808 6.8895564741 + 3 35 6.0214250550 6.0214220200 + 3 36 19.6206468977 19.6206494558 + 3 37 24.7008710786 24.7008710738 + 3 38 47.5292252001 47.5292260486 + 4 39 -75236.7569897398 -75236.7398021816 + 4 40 -12185.8796968880 -12185.8793671389 + 4 41 -2773.4831911435 -2773.4831624928 + 4 42 -569.9506420417 -569.9506363235 + 4 43 -78.9016401752 -78.9016385968 + 4 44 -5.1691854984 -5.1691848358 + 4 45 4.5636857939 4.5638143912 + 4 46 -10640.2333851158 -10640.2333803363 + 4 47 -2324.3364165327 -2324.3364072919 + 4 48 -423.4863614587 -423.4863574859 + 4 49 -43.0547390741 -43.0547381500 + 4 50 -0.2794590886 -0.2794514857 + 4 51 -1810.0451240061 -1810.0451202456 + 4 52 -238.3291788477 -238.3291766726 + 4 53 -4.4054312547 -4.4054293963 + 4 54 8.2928303329 8.2928369211 + 4 55 -33.2508975442 -33.2508971531 + 4 56 21.3563540731 21.3563541107 + 4 57 49.8060668072 49.8060668107 + 5 58 -32795.0590846455 -32795.0556605232 + 5 59 -4882.6824813465 -4882.6824159868 + 5 60 -966.4377413866 -966.4377361228 + 5 61 -164.3186507888 -164.3186490966 + 5 62 -14.8855865446 -14.8855862180 + 5 63 5.2437428292 5.2437525172 + 5 64 -4380.9592556630 -4380.9592506320 + 5 65 -804.6525815679 -804.6525796130 + 5 66 -114.3164854912 -114.3164843738 + 5 67 -5.9109395843 -5.9109349312 + 5 68 4.8569390905 4.8570662328 + 5 69 -560.5930245701 -560.5930241259 + 5 70 -41.6105488448 -41.6105483746 + 5 71 5.2198476695 5.2198521163 + 5 72 13.1245618285 13.1245643331 + 5 73 29.0453900150 29.0453912086 + + Preparing densities etc. for the partition functions (integrals / Hartree potential). + + Preparations completed. + max(cpu_time) : 0.991 s. + Wall clock time (cpu1) : 0.996 s. +------------------------------------------------------------ + + Initializing index lists of integration centers etc. from given atomic structure: + Mapping all atomic coordinates to central unit cell. + + Initializing the k-points + Using symmetry for reducing the k-points + | k-points reduced from: 625 to 313 + | Number of k-points : 313 + | Consuming 3056 KiB for k_phase_exx. + The eigenvectors in the calculations are COMPLEX. + | K-points in task 0: 39 + | K-points in task 1: 40 + | K-points in task 2: 39 + | K-points in task 3: 39 + | K-points in task 4: 39 + | K-points in task 5: 39 + | K-points in task 6: 39 + | K-points in task 7: 39 + | Number of basis functions in the Hamiltonian integrals : 4449 + | Number of basis functions in a single unit cell : 286 + | Number of centers in hartree potential : 642 + | Number of centers in hartree multipole : 342 + | Number of centers in electron density summation: 264 + | Number of centers in basis integrals : 288 + | Number of centers in integrals : 153 + | Number of centers in hamiltonian : 264 + | Consuming 322 KiB for k_phase. + | Number of super-cells (origin) [n_cells] : 1125 + | Number of super-cells (after PM_index) [n_cells] : 66 + | Number of super-cells in hamiltonian [n_cells_in_hamiltonian]: 52 + | Size of matrix packed + index [n_hamiltonian_matrix_size] : 631566 + +------------------------------------------------------------ + Begin self-consistency loop: Initialization. + + Date : 20230117, Time : 114552.002 +------------------------------------------------------------ + | Estimated reciprocal-space cutoff momentum G_max: 1.90186217 bohr^-1 . + | Reciprocal lattice points for long-range Hartree potential: 208 + Partitioning the integration grid into batches with parallel hashing+maxmin method. + | Number of batches: 2360 + | Maximal batch size: 160 + | Minimal batch size: 37 + | Average batch size: 81.776 + | Standard deviation of batch sizes: 24.693 + + Integration load balanced across 8 MPI tasks. + Work distribution over tasks is as follows: + Task 0 has 24105 integration points. + Task 1 has 24104 integration points. + Task 2 has 24156 integration points. + Task 3 has 24139 integration points. + Task 4 has 24178 integration points. + Task 5 has 24118 integration points. + Task 6 has 24118 integration points. + Task 7 has 24074 integration points. + Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). + | initialize_grid_storage: Actual outermost partition radius vs. multipole_radius_free + | (-- VB: in principle, multipole_radius_free should be larger, hence this output) + | Species 1: Confinement radius = 6.000000000000000 AA, multipole_radius_free = 6.016994434057369 AA. + | Species 1: outer_partition_radius set to 6.016994434057369 AA . + | Species 2: Confinement radius = 6.000000000000000 AA, multipole_radius_free = 6.037996416842453 AA. + | Species 2: outer_partition_radius set to 6.037996416842453 AA . + | Species 3: Confinement radius = 6.000000000000000 AA, multipole_radius_free = 6.012827091137924 AA. + | Species 3: outer_partition_radius set to 6.012827091137924 AA . + | Species 4: Confinement radius = 6.000000000000000 AA, multipole_radius_free = 6.066407844853155 AA. + | Species 4: outer_partition_radius set to 6.066407844853155 AA . + | Species 5: Confinement radius = 6.000000000000000 AA, multipole_radius_free = 6.056084577048819 AA. + | Species 5: outer_partition_radius set to 6.056084577048819 AA . + | The sparse table of interatomic distances needs 698.55 kbyte instead of 663.55 kbyte of memory. + | Using the partition_type stratmann_smoother will reduce your memory usage. + | Net number of integration points: 192992 + | of which are non-zero points : 163724 + | Numerical average free-atom electrostatic potential : -9.05439813 eV + Renormalizing the initial density to the exact electron count on the 3D integration grid. + | Initial density: Formal number of electrons (from input files) : 288.0000000000 + | Integrated number of electrons on 3D grid : 287.9998104340 + | Charge integration error : -0.0001895660 + | Normalization factor for density and gradient : 1.0000006582 + Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 288.0000000000 + | Integrated number of electrons on 3D grid : 287.9998104340 + | Charge integration error : -0.0001895660 + | Normalization factor for density and gradient : 1.0000006582 + Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). + | Maximal number of non-zero basis functions: 1142 in task 0 + | Maximal number of non-zero basis functions: 1197 in task 1 + | Maximal number of non-zero basis functions: 1058 in task 2 + | Maximal number of non-zero basis functions: 1155 in task 3 + | Maximal number of non-zero basis functions: 1103 in task 4 + | Maximal number of non-zero basis functions: 1092 in task 5 + | Maximal number of non-zero basis functions: 1107 in task 6 + | Maximal number of non-zero basis functions: 1088 in task 7 + Allocating 48.676 MB for KS_eigenvector_complex + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 47.351 s, elapsed 53.185 s + Integrating overlap matrix. + Time summed over all CPUs for integration: real work 34.212 s, elapsed 38.875 s + Calculating total energy contributions from superposition of free atom densities. + + -------------------------------------------- + Constructing auxiliary basis (full product) ... + + Product basis: + | charge radius: extent of product basis function + | field radius: extent of its Coulomb potential + | Species l charge radius field radius + | Mo 0 1.729167 A 1.729167 A + | Mo 0 1.708156 A 1.708156 A + | Mo 0 2.889515 A 2.889515 A + | Mo 0 4.119012 A 4.119012 A + | Mo 0 4.828511 A 4.828511 A + | Mo 0 5.070493 A 5.070493 A + | Mo 0 5.195995 A 5.195995 A + | Mo 0 5.324602 A 11.931560 A + | Mo 0 5.390095 A 19.695916 A + | Mo 0 5.390095 A 22.530865 A + | Mo 0 5.456393 A 24.245621 A + | Mo 0 5.456393 A 25.151335 A + | Mo 0 5.456393 A 25.773864 A + | Mo 0 5.456393 A 25.460697 A + | Mo 1 1.587348 A 1.587348 A + | Mo 1 2.376168 A 2.376168 A + | Mo 1 3.346077 A 3.346077 A + | Mo 1 4.169676 A 4.169676 A + | Mo 1 4.887902 A 4.887902 A + | Mo 1 5.070493 A 5.070493 A + | Mo 1 5.195995 A 5.195995 A + | Mo 1 5.324602 A 14.868378 A + | Mo 1 5.390095 A 20.937383 A + | Mo 1 5.390095 A 23.088533 A + | Mo 1 5.456393 A 24.543843 A + | Mo 1 5.456393 A 25.460697 A + | Mo 1 5.456393 A 25.460697 A + | Mo 2 2.051947 A 2.051947 A + | Mo 2 3.109428 A 3.109428 A + | Mo 2 4.169676 A 4.169676 A + | Mo 2 4.828511 A 4.828511 A + | Mo 2 5.070493 A 5.070493 A + | Mo 2 5.259905 A 5.259905 A + | Mo 2 5.324602 A 7.406904 A + | Mo 2 5.390095 A 12.997563 A + | Mo 2 5.456393 A 20.682982 A + | Mo 2 5.456393 A 23.088533 A + | Mo 2 5.456393 A 24.543843 A + | Mo 2 5.523507 A 25.460697 A + | Mo 2 5.523507 A 25.773864 A + | Mo 3 2.620300 A 2.620300 A + | Mo 3 3.781189 A 3.781189 A + | Mo 3 4.654634 A 4.654634 A + | Mo 3 4.887902 A 4.887902 A + | Mo 3 5.132860 A 5.132860 A + | Mo 3 5.259905 A 5.259905 A + | Mo 3 5.324602 A 6.883056 A + | Mo 3 5.390095 A 15.805557 A + | Mo 3 5.390095 A 21.986666 A + | Mo 3 5.456393 A 23.951023 A + | Mo 3 5.456393 A 25.151335 A + | Mo 3 5.456393 A 25.773864 A + | Mo 4 3.305420 A 3.305420 A + | Mo 4 4.654634 A 4.654634 A + | Mo 4 4.948023 A 4.948023 A + | Mo 4 5.132860 A 5.132860 A + | Mo 4 5.132860 A 5.132860 A + | Mo 4 5.259905 A 6.967717 A + | Mo 4 5.390095 A 15.805557 A + | Mo 4 5.390095 A 19.938176 A + | Mo 4 5.390095 A 22.530865 A + | Mo 4 5.456393 A 24.543843 A + | Mo 4 5.456393 A 25.460697 A + | Mo 5 4.169676 A 4.169676 A + | Mo 5 4.487018 A 4.487018 A + | Mo 5 4.654634 A 4.654634 A + | Mo 5 4.654634 A 4.654634 A + | Mo 5 4.769842 A 14.332959 A + | Mo 5 4.828511 A 20.682982 A + | Mo 5 4.828511 A 22.807995 A + | Mo 5 4.887902 A 24.245621 A + | Mo 6 4.487018 A 4.487018 A + | Mo 6 4.711886 A 10.819901 A + | Mo 6 4.769842 A 16.597657 A + | Mo 6 4.711886 A 21.194913 A + | Mo 6 4.769842 A 23.372523 A + | Mo 7 4.487018 A 18.302935 A + | Mo 7 4.487018 A 20.937383 A + | Mo 8 4.378641 A 19.938176 A + | Se 0 2.443480 A 2.443480 A + | Se 0 3.841058 A 3.841058 A + | Se 0 4.786491 A 4.786491 A + | Se 0 4.965294 A 4.965294 A + | Se 0 5.150776 A 5.278265 A + | Se 0 5.214131 A 9.262247 A + | Se 0 5.278265 A 10.089765 A + | Se 0 5.343188 A 19.287278 A + | Se 0 5.408909 A 22.609507 A + | Se 0 5.475439 A 24.330249 A + | Se 0 5.475439 A 25.239125 A + | Se 0 5.475439 A 25.549566 A + | Se 0 5.475439 A 25.549566 A + | Se 1 2.110075 A 2.110075 A + | Se 1 3.569401 A 3.569401 A + | Se 1 4.614127 A 4.614127 A + | Se 1 5.026367 A 5.026367 A + | Se 1 5.150776 A 5.150776 A + | Se 1 5.150776 A 7.342446 A + | Se 1 5.278265 A 8.607180 A + | Se 1 5.408909 A 16.453215 A + | Se 1 5.475439 A 22.609507 A + | Se 1 5.475439 A 23.454103 A + | Se 1 5.408909 A 24.629512 A + | Se 1 5.475439 A 25.239125 A + | Se 1 5.475439 A 25.549566 A + | Se 2 2.829566 A 2.829566 A + | Se 2 3.794387 A 3.794387 A + | Se 2 4.965294 A 4.965294 A + | Se 2 5.150776 A 5.150776 A + | Se 2 5.214131 A 5.214131 A + | Se 2 5.150776 A 10.991216 A + | Se 2 5.343188 A 19.287278 A + | Se 2 5.408909 A 22.609507 A + | Se 2 5.475439 A 24.330249 A + | Se 2 5.475439 A 25.239125 A + | Se 2 5.475439 A 25.863826 A + | Se 3 3.794387 A 3.794387 A + | Se 3 4.786491 A 4.786491 A + | Se 3 5.088191 A 5.088191 A + | Se 3 5.150776 A 5.150776 A + | Se 3 5.150776 A 7.342446 A + | Se 3 5.343188 A 12.120477 A + | Se 3 5.343188 A 15.860726 A + | Se 3 5.343188 A 21.268893 A + | Se 3 5.408909 A 23.454103 A + | Se 3 5.408909 A 24.629512 A + | Se 3 5.475439 A 25.549566 A + | Se 4 4.965294 A 4.965294 A + | Se 4 5.150776 A 5.150776 A + | Se 4 5.278265 A 11.973206 A + | Se 4 5.343188 A 18.143653 A + | Se 4 5.343188 A 21.530501 A + | Se 4 5.343188 A 23.454103 A + | Se 4 5.343188 A 24.629512 A + | Se 5 5.088191 A 18.592732 A + | Se 5 5.150776 A 22.334789 A + | Se 5 5.150776 A 23.742589 A + | Se 6 4.965294 A 22.063409 A + | W 0 0.705513 A 4.052533 A + | W 0 1.178944 A 3.542623 A + | W 0 1.680587 A 3.212558 A + | W 0 2.281351 A 2.949078 A + | W 0 3.332566 A 3.332566 A + | W 0 4.203919 A 4.203919 A + | W 0 4.868164 A 4.868164 A + | W 0 5.112134 A 5.368330 A + | W 0 5.238666 A 6.066408 A + | W 0 5.303101 A 11.883380 A + | W 0 5.368330 A 19.378033 A + | W 0 5.434360 A 22.439884 A + | W 0 5.434360 A 24.147717 A + | W 0 5.434360 A 25.049773 A + | W 0 5.501203 A 25.669788 A + | W 0 5.434360 A 25.357886 A + | W 1 0.787568 A 0.787568 A + | W 1 1.122680 A 1.122680 A + | W 1 1.505490 A 1.505490 A + | W 1 1.994300 A 1.994300 A + | W 1 2.546686 A 2.546686 A + | W 1 3.542623 A 3.542623 A + | W 1 4.307971 A 4.307971 A + | W 1 4.868164 A 4.868164 A + | W 1 5.112134 A 5.112134 A + | W 1 5.238666 A 5.238666 A + | W 1 5.303101 A 7.024938 A + | W 1 5.368330 A 15.935357 A + | W 1 5.434360 A 21.631811 A + | W 1 5.434360 A 23.564465 A + | W 1 5.434360 A 24.745404 A + | W 1 5.501203 A 25.669788 A + | W 1 5.501203 A 25.669788 A + | W 2 0.993490 A 0.993490 A + | W 2 1.487198 A 1.487198 A + | W 2 2.337818 A 2.337818 A + | W 2 2.949078 A 2.949078 A + | W 2 3.954650 A 3.954650 A + | W 2 4.692859 A 4.692859 A + | W 2 4.988658 A 4.988658 A + | W 2 5.175013 A 5.175013 A + | W 2 5.303101 A 5.303101 A + | W 2 5.368330 A 12.787788 A + | W 2 5.368330 A 20.349169 A + | W 2 5.434360 A 22.995301 A + | W 2 5.434360 A 24.444734 A + | W 2 5.501203 A 25.357886 A + | W 2 5.501203 A 25.985527 A + | W 3 1.095564 A 1.095564 A + | W 3 1.899125 A 1.899125 A + | W 3 2.018830 A 2.018830 A + | W 3 3.332566 A 3.332566 A + | W 3 4.750581 A 4.750581 A + | W 3 4.988658 A 4.988658 A + | W 3 5.112134 A 5.112134 A + | W 3 5.238666 A 5.238666 A + | W 3 5.368330 A 9.081062 A + | W 3 5.434360 A 18.453244 A + | W 3 5.434360 A 21.631811 A + | W 3 5.368330 A 23.278144 A + | W 3 5.368330 A 24.444734 A + | W 3 5.434360 A 25.357886 A + | W 4 1.451277 A 48.473338 A + | W 4 2.120004 A 52.804098 A + | W 4 3.212558 A 52.804098 A + | W 4 4.360959 A 52.804098 A + | W 4 4.868164 A 52.804098 A + | W 4 5.112134 A 49.069561 A + | W 4 5.238666 A 5.238666 A + | W 4 5.303101 A 7.652568 A + | W 4 5.368330 A 16.329778 A + | W 4 5.434360 A 20.599464 A + | W 4 5.434360 A 22.995301 A + | W 4 5.434360 A 25.049773 A + | W 4 5.501203 A 25.669788 A + | W 5 3.252072 A 3.252072 A + | W 5 4.692859 A 4.692859 A + | W 5 4.868164 A 4.868164 A + | W 5 4.988658 A 4.988658 A + | W 5 5.175013 A 5.175013 A + | W 5 5.303101 A 11.178763 A + | W 5 5.303101 A 14.275082 A + | W 5 5.303101 A 21.109327 A + | W 5 5.368330 A 23.278144 A + | W 5 5.368330 A 24.444734 A + | W 6 4.152839 A 4.152839 A + | W 6 4.635838 A 4.635838 A + | W 6 4.692859 A 4.692859 A + | W 6 4.750581 A 9.536162 A + | W 6 4.809013 A 18.229027 A + | W 6 4.809013 A 21.631811 A + | W 6 4.809013 A 23.278144 A + | W 7 4.414599 A 10.776210 A + | W 7 4.468899 A 19.142579 A + | W 7 4.523866 A 21.897883 A + | W 8 4.307971 A 19.616383 A + | Te 0 1.266511 A 2.040184 A + | Te 0 1.379665 A 1.379665 A + | Te 0 2.511461 A 2.511461 A + | Te 0 3.409239 A 3.409239 A + | Te 0 4.095398 A 4.095398 A + | Te 0 4.742497 A 4.742497 A + | Te 0 5.041425 A 5.696993 A + | Te 0 5.229751 A 7.364442 A + | Te 0 5.359194 A 11.863158 A + | Te 0 5.359194 A 12.156786 A + | Te 0 5.359194 A 20.067707 A + | Te 0 5.425112 A 22.956170 A + | Te 0 5.425112 A 24.403136 A + | Te 0 5.491841 A 25.314734 A + | Te 0 5.491841 A 25.626106 A + | Te 0 5.491841 A 25.626106 A + | Te 1 1.134555 A 1.134555 A + | Te 1 1.783477 A 1.783477 A + | Te 1 2.480945 A 2.480945 A + | Te 1 3.409239 A 3.409239 A + | Te 1 4.407087 A 4.407087 A + | Te 1 4.919657 A 4.919657 A + | Te 1 5.103434 A 5.103434 A + | Te 1 5.229751 A 5.229751 A + | Te 1 5.294077 A 9.755565 A + | Te 1 5.359194 A 15.908240 A + | Te 1 5.425112 A 21.595000 A + | Te 1 5.425112 A 23.524365 A + | Te 1 5.491841 A 24.703295 A + | Te 1 5.491841 A 25.314734 A + | Te 1 5.491841 A 25.626106 A + | Te 2 1.637204 A 1.637204 A + | Te 2 2.421022 A 2.421022 A + | Te 2 3.899951 A 3.899951 A + | Te 2 4.980169 A 4.980169 A + | Te 2 5.041425 A 5.041425 A + | Te 2 5.166207 A 5.166207 A + | Te 2 5.229751 A 6.927772 A + | Te 2 5.359194 A 11.297005 A + | Te 2 5.425112 A 15.714946 A + | Te 2 5.425112 A 20.067707 A + | Te 2 5.425112 A 22.956170 A + | Te 2 5.425112 A 24.403136 A + | Te 2 5.491841 A 25.314734 A + | Te 2 5.491841 A 25.941307 A + | Te 3 1.942819 A 1.942819 A + | Te 3 3.054037 A 3.054037 A + | Te 3 3.899951 A 3.899951 A + | Te 3 4.407087 A 4.407087 A + | Te 3 4.684873 A 4.684873 A + | Te 3 4.980169 A 4.980169 A + | Te 3 5.229751 A 5.229751 A + | Te 3 5.294077 A 8.846642 A + | Te 3 5.425112 A 11.159740 A + | Te 3 5.359194 A 15.714946 A + | Te 3 5.425112 A 21.860619 A + | Te 3 5.425112 A 23.813715 A + | Te 3 5.491841 A 25.007146 A + | Te 3 5.491841 A 25.626106 A + | Te 4 2.391605 A 2.391605 A + | Te 4 3.624130 A 48.986058 A + | Te 4 4.196765 A 4.196765 A + | Te 4 4.919657 A 4.919657 A + | Te 4 5.103434 A 5.103434 A + | Te 4 5.229751 A 5.229751 A + | Te 4 5.294077 A 11.863158 A + | Te 4 5.359194 A 20.067707 A + | Te 4 5.425112 A 22.401698 A + | Te 4 5.425112 A 24.106624 A + | Te 4 5.425112 A 25.007146 A + | Te 5 4.300640 A 4.300640 A + | Te 5 5.041425 A 5.041425 A + | Te 5 5.166207 A 5.166207 A + | Te 5 5.294077 A 5.294077 A + | Te 5 5.359194 A 11.863158 A + | Te 5 5.425112 A 19.583002 A + | Te 5 5.425112 A 22.401698 A + | Te 5 5.491841 A 23.813715 A + | Te 5 5.491841 A 25.007146 A + | Te 6 5.229751 A 5.229751 A + | Te 6 5.294077 A 9.875558 A + | Te 6 5.294077 A 19.583002 A + | Te 6 5.425112 A 22.677239 A + | Te 6 5.425112 A 24.106624 A + | Te 7 5.359194 A 21.595000 A + | Te 7 5.425112 A 22.956170 A + | Te 8 5.359194 A 21.595000 A + + | Shrink_full_auxil_basis : there are 321 radial auxiliary wave functions + accepted and 775 rejected. + | Shrink_full_auxil_basis : there are totally 122540 partial auxiliary wave functions. + prodbas_tasks_distribution_pbc not up to date - distributing tasks. + + | Number of product basis functions per thread : 15318 + Parallel distribution of product basis not up to date - distributing tasks. + + | Number of product basis functions per thread : 349 + | Minimal requirement for computer memory : 0.912 Gbs + Minimal free memory per node on init_fm entry [GB]: 24.74 + ----------------------------------------- + --- Initializing Fock matrix calculations + ----------------------------------------- + screening_threshold (crit_val) = 0.000000100000 + coul_mat_threshold = 0.000000000100 + No atoms are split internally + Number of super-cells in X Y Z: 7 7 2 + Number of atoms pairs total: 1056 + Atom pair distribution: + Cell: -4 -2 0 atom pairs: 4 + Cell: -4 -1 0 atom pairs: 4 + Cell: -3 -3 0 atom pairs: 20 + Cell: -3 -2 0 atom pairs: 22 + Cell: -3 -1 0 atom pairs: 22 + Cell: -3 0 0 atom pairs: 18 + Cell: -3 1 0 atom pairs: 4 + Cell: -2 -4 0 atom pairs: 4 + Cell: -2 -3 0 atom pairs: 23 + Cell: -2 -2 0 atom pairs: 30 + Cell: -2 -1 0 atom pairs: 32 + Cell: -2 0 0 atom pairs: 32 + Cell: -2 1 0 atom pairs: 22 + Cell: -2 2 0 atom pairs: 5 + Cell: -1 -4 0 atom pairs: 4 + Cell: -1 -3 0 atom pairs: 22 + Cell: -1 -2 0 atom pairs: 32 + Cell: -1 -1 0 atom pairs: 34 + Cell: -1 0 0 atom pairs: 34 + Cell: -1 1 0 atom pairs: 32 + Cell: -1 2 0 atom pairs: 22 + Cell: -1 3 0 atom pairs: 4 + Cell: 0 -3 0 atom pairs: 18 + Cell: 0 -2 0 atom pairs: 32 + Cell: 0 -1 0 atom pairs: 34 + Cell: 0 0 0 atom pairs: 36 + Cell: 0 1 0 atom pairs: 34 + Cell: 0 2 0 atom pairs: 32 + Cell: 0 3 0 atom pairs: 18 + Cell: 1 -3 0 atom pairs: 4 + Cell: 1 -2 0 atom pairs: 22 + Cell: 1 -1 0 atom pairs: 32 + Cell: 1 0 0 atom pairs: 34 + Cell: 1 1 0 atom pairs: 34 + Cell: 1 2 0 atom pairs: 32 + Cell: 1 3 0 atom pairs: 22 + Cell: 1 4 0 atom pairs: 4 + Cell: 2 -2 0 atom pairs: 5 + Cell: 2 -1 0 atom pairs: 22 + Cell: 2 0 0 atom pairs: 32 + Cell: 2 1 0 atom pairs: 32 + Cell: 2 2 0 atom pairs: 30 + Cell: 2 3 0 atom pairs: 23 + Cell: 2 4 0 atom pairs: 4 + Cell: 3 -1 0 atom pairs: 4 + Cell: 3 0 0 atom pairs: 18 + Cell: 3 1 0 atom pairs: 22 + Cell: 3 2 0 atom pairs: 22 + Cell: 3 3 0 atom pairs: 20 + Cell: 4 1 0 atom pairs: 4 + Cell: 4 2 0 atom pairs: 4 + sparsity of pfbvk: 1.000000 + Number of atoms pairs in BvK cells: 1056 + Max. memory consumption per node for Pulay mixing [GB]: 3.37 + Minimal total memory per node [GB]: 32.46 + Minimal free memory per node [GB]: 21.44 + --- Initializing LVL triples, type HSE + | Storage requirements for basis-basbas products (processor-local): + | Species Mo: n_prodsfn: 2135; storage: 66.72 MiB. + | Species Se: n_prodsfn: 1151; storage: 35.97 MiB. + | Species S: n_prodsfn: 0; storage: 0.00 MiB. + | Species W: n_prodsfn: 3403; storage: 106.34 MiB. + | Species Te: n_prodsfn: 2494; storage: 77.94 MiB. + + --- Initializing Coulomb matrix calculations, type HSE + Preparing TB like auxiliary 2-center HSE-pot matrix + SBT integration errors (all should be 'small'): + large logFT aliasing -> increase N/lnrange + large SBT aliasing -> decrease lnk0 & increase lnk0+lnrange + large SBT ringing -> decrease lnr0 & increase lnr0+lnrange + | El't L: logFT-al. small-k large-k small-r large-r + | Need to store125748 splines of 288 points taking 284904 KiB. + | Spline reduction from 4096 to 288 points by (cutting and) 1 x coarsening gives error: 0.00E+00 + | Maximum value outside interaction range: 6.41E-13 + Finished with initialize_tb_auxmat/lvl_triples, time: 5.894 + --- Calculating Coulomb matrices + Upper limit for memory consumption per node [GB] for Coulomb matrices if no compression occurs: 0.088 + Upper limit for temporary arrays in Coulomb matrix initalization [GB]: 2.40 + Min./max. time for Coulomb matrix computation [s]: 39.48 98.78 + Max. memory consumption per node for global Coulomb matrix [GB]: 1.67 + Time to calculate Coulomb Matrices : 99.057 + Max. memory consumption per node for uncompressed ovlp3fn matrix [GB]: 9.573 + --- Calculating OVLP3FN + --- Done calculating OVLP3FN, time: 331.805 + Max. memory consumption per node for compressed global ovlp3fn matrix [GB]: 3.167 + Atomic logSBT for 2-center HSE-pot matrix : max(cpu_time) wall_clock(cpu1) + | TB initialization : 4.893 s 4.896 s + | TB usage : 48.219 s 48.350 s + + Atomic logSBT for LVL-triples : max(cpu_time) wall_clock(cpu1) + | Multiplication with kernel : 0.733 s 0.711 s + | Main matrix multiplication : 122.133 s 122.371 s + | Analytic angular integration : 0.671 s 0.675 s + | Kernel construction : 0.651 s 0.567 s + | Overall 2-center overlap time : 135.119 s 135.341 s + | 3-center preparation multiplications : 2.250 s 1.548 s + | 3-center preparation SBTs : 29.164 s 20.337 s + | 3-center combinations : 200.376 s 200.757 s + | Overal 3-center time : 222.455 s 222.848 s + | LVL initialization : 0.983 s 0.991 s + | Whole LVL-triples : 0.983 s 0.991 s + + Assumed free memory per node for Fock matrix prefactors [GB] 18.19 + Memory per instance for Coulomb / ovlp matrix [GB] 1.67 3.17 + Number of nodes, tasks per node 1 8 + Number of instances: 1 + ----------------------------------------------------- + Dividing atoms among tasks for exact exchange energy: + Atom: 1 Weight: 0.20135E+09 + Atom: 2 Weight: 0.35722E+09 + Atom: 3 Weight: 0.66925E+08 + Atom: 4 Weight: 0.26265E+09 + Atom: 5 Weight: 0.97677E+08 + Atom: 6 Weight: 0.21083E+09 + + Average weight per task: 0.14958E+09 + + Number of "big" (above average) atoms : 4 + Number of "small" (below average) atoms: 2 + + There are "big" and "small" atoms + Reserving 4 tasks for "big" atoms + Max. weight for big atoms: 0.35722E+09 small atoms: 0.97677E+08 + Trying 5 tasks for "big" atoms: + Max. weight for big atoms: 0.26265E+09 small atoms: 0.97677E+08 + => Atom 2 gets 2 tasks + Trying 6 tasks for "big" atoms: + Max. weight for big atoms: 0.21083E+09 small atoms: 0.97677E+08 + => Atom 4 gets 2 tasks + Trying 7 tasks for "big" atoms: + Max. weight for big atoms: 0.20135E+09 small atoms: 0.16460E+09 + => Atom 6 gets 2 tasks + Using 1 tasks for "small" atoms, 7 for "big" atoms + + Atom division among tasks: + Atom 1: (initial) task: 0, # of tasks: 1 + Atom 2: (initial) task: 1, # of tasks: 2 + Atom 3: (initial) task: 7, # of tasks: 1 + Atom 4: (initial) task: 3, # of tasks: 2 + Atom 5: (initial) task: 7, # of tasks: 1 + Atom 6: (initial) task: 5, # of tasks: 2 + + ----------------------------------------------------- + Task 0: my_n_atoms2: 1 my_atom_list: 1 + Task 1: my_n_atoms2: 1 my_atom_list: 2 + Task 2: my_n_atoms2: 1 my_atom_list: 2 + Task 3: my_n_atoms2: 1 my_atom_list: 4 + Task 4: my_n_atoms2: 1 my_atom_list: 4 + Task 5: my_n_atoms2: 1 my_atom_list: 6 + Task 6: my_n_atoms2: 1 my_atom_list: 6 + Task 7: my_n_atoms2: 2 my_atom_list: 3 5 + Task 0: my_n_atom_pairs: 179 + Task 1: my_n_atom_pairs: 91 + Task 2: my_n_atom_pairs: 90 + Task 3: my_n_atom_pairs: 101 + Task 4: my_n_atom_pairs: 100 + Task 5: my_n_atom_pairs: 74 + Task 6: my_n_atom_pairs: 74 + Task 7: my_n_atom_pairs: 347 + Transferring Coulomb matrix to final data layout + Coulomb matrix communicaton time [s] 0.39 + Max. memory per node for ovlp3fn matrices: 3.166 GB + Total memory for ovlp3fn matrices: 3.166 GB + --- Done getting norm of OVLP3FN, time: 0.002 + Sparsity of ovlp3fn matrix 888 1056 + --- time for get_ovlp3fn: 0.864 + Max. memory consumption per node for Hartree Fock matrix [GB] 3.37 + Blocksize for Fock matrix computation: 4 + Minimal free memory per node after Fock matrix initialization [GB]: 14.52 + Initialize hartree_potential_storage + Max. number of atoms included in rho_multipole: 6 + + End scf initialization - timings : max(cpu_time) wall_clock(cpu1) + | Time for scf. initialization : 453.633 s 454.344 s + | Boundary condition initialization : 6.282 s 6.282 s + | Integration : 11.529 s 11.535 s + | Grid partitioning : 0.366 s 0.364 s + | Preloading free-atom quantities on grid : 1.118 s 1.120 s + | Free-atom superposition energy : 0.195 s 0.195 s + | Product basis setup: Total time : 440.429 s 441.123 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 328.025 MB (on task 6) + | Maximum: 572.099 MB (on task 0) + | Average: 440.775 MB + | Peak value for overall tracked memory usage: + | Minimum: 1023.924 MB (on task 7 after allocating ovlp3fn2) + | Maximum: 2253.341 MB (on task 6 after allocating ovlp3fn_nosplit%m) + | Average: 1684.765 MB + | Largest tracked array allocation so far: + | Minimum: 510.595 MB (ovlp3fn_nosplit%dat on task 7) + | Maximum: 1608.479 MB (ovlp3fn_nosplit%dat on task 6) + | Average: 1141.214 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Evaluating new KS density using the density matrix + Evaluating density matrix + Finished reading density matrices from file + | Time : 0.190 s + + Time summed over all CPUs for getting density from density matrix: real work 101.938 s, elapsed 121.445 s + Integration grid: deviation in total charge ( - N_e) = -9.271162E-11 + + Time for density update prior : max(cpu_time) wall_clock(cpu1) + | self-consistency iterative process : 15.684 s 15.686 s + +------------------------------------------------------------ + Initial SCF-cycle to compute last known + density from restart information. + + Date : 20230117, Time : 115342.034 +------------------------------------------------------------ + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 288.0000000000 + | Integrated number of electrons on 3D grid : 287.9999999999 + | Charge integration error : -0.0000000001 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.186220E-12 + | Sum of charges compensated after spline to logarithmic grids = 0.612508E-07 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.186399E-12 + Summing up the Hartree potential. + Calculating dipole correction via potential gradient + | Dipole correction gradient : 0.05025020 eV/Angstrom + | Dipole correction potential jump : -1.54231010 eV + Time summed over all CPUs for potential: real work 27.293 s, elapsed 33.668 s + | RMS charge density error from multipole expansion : 0.600004E-02 + | Average real-space part of the electrostatic potential : -0.01380736 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 52.642 s, elapsed 61.632 s + Max. memory consumption per node for dm_cols [GB]: 0.65 + Max. memory consumption per node for fock_matrix [GB]: 0.40 + Finished reading density matrices from file + | Time : 0.246 s + + Calculating non-local Hartree-Fock exchange by two-center RI (RI-LVL). + screening_threshold (crit_val) = 0.000000100000 + Max. allocated memory per node for ovlp3fn_rcv [GB]: 0.28 + Max. allocated memory per node for fock_matrix_row [GB]: 0.05 + Max. memory consumption per node for m_ovlp_fact11 [GB]: 0.01 + Max. memory consumption per node for d_aux_mem [GB]: 0.01 + Max. memory consumption per node for dm_x_o3fn_aux [GB]: 0.08 + Max. allocated memory per node for tmp1/tmp2 [GB]: 9.09 + final impselect vector 2 3 6 1 + Time for autotuning: 30.1495707824506 + Exact exchange progress report - outermost block loop i_block: 1 .. 72 + | 1 2 3 4 5 6 7 8 9 10 + | 11 12 13 14 15 16 17 18 19 20 + | 21 22 23 24 25 26 27 28 29 30 + | 31 32 33 34 35 36 37 38 39 40 + | 41 42 43 44 45 46 47 48 49 50 + | 51 52 53 54 55 56 57 58 59 60 + | 61 62 63 64 65 66 67 68 69 70 + | 71 72 + Total ovlp3fn data transfer [GB] 5.36701221391559 + Full exact exchange energy: 25852.056449109368 eV. + Detailed communication and barrier times: + | Comm 0: 0.001 0.000 0.000 0.000 0.065 0.001 0.001 0.000 0.000 0.000 + | Comm 1: 0.001 0.000 0.000 5.944 0.065 0.001 0.001 0.000 0.000 6.386 + | Comm 2: 0.001 0.000 0.000 5.943 0.065 0.001 0.001 0.000 0.000 6.385 + | Comm 3: 0.001 0.000 0.000 3.487 0.064 0.001 0.001 0.000 0.000 4.453 + | Comm 4: 0.001 0.000 0.000 3.487 0.065 0.001 0.001 0.000 0.000 4.453 + | Comm 5: 0.001 0.000 0.000 2.748 0.064 0.001 0.001 0.000 0.000 4.799 + | Comm 6: 0.001 0.000 0.000 2.747 0.065 0.001 0.001 0.000 0.000 4.799 + | Comm 7: 0.001 0.000 0.000 0.000 0.064 0.001 0.001 0.000 0.000 0.000 + | Imbalance 0: 0.037 0.000 0.000 0.000 3.147 0.000 0.110 0.000 0.000 0.000 + | Imbalance 1: 0.013 0.000 0.000 0.002 51.284 0.000 0.140 0.000 0.000 15.513 + | Imbalance 2: 0.126 0.000 0.002 6.793 69.483 0.000 0.161 0.000 0.000 0.777 + | Imbalance 3: 0.044 0.000 0.000 0.012 117.552 0.000 0.232 0.000 0.000 0.001 + | Imbalance 4: 0.137 0.000 0.002 28.702 143.929 0.000 0.381 0.000 0.000 66.123 + | Imbalance 5: 0.070 0.000 0.001 0.163 292.944 0.000 0.450 0.000 0.000 14.675 + | Imbalance 6: 0.136 0.000 0.002 3.198 295.215 0.000 0.460 0.000 0.000 2.284 + | Imbalance 7: 0.058 0.000 0.000 0.000 114.433 0.000 0.275 0.000 0.000 0.000 + Times DM_x_o3fn CM_prod_1 CM_prod_2 tmp2_prod Sync Imbalance Other Total calc + | Times 0: 145.095 291.629 55.284 62.023 0.069 3.295 5.922 563.316 + | Times 1: 123.739 218.144 47.895 85.743 12.398 66.951 8.457 563.326 + | Times 2: 116.945 229.543 51.199 67.625 12.397 77.342 8.267 563.318 + | Times 3: 102.119 202.735 37.751 87.533 8.009 117.842 7.331 563.319 + | Times 4: 73.465 146.007 28.535 61.636 8.008 239.274 6.385 563.309 + | Times 5: 49.982 109.843 25.517 55.337 7.615 308.302 6.720 563.315 + | Times 6: 46.948 121.872 25.887 52.974 7.614 301.296 6.720 563.310 + | Times 7: 77.541 237.342 61.160 66.853 0.068 114.766 5.587 563.318 + | Times sum: 735.833 1557.114 333.228 539.724 56.176 1229.067 55.389 4506.532 + + Decomposition of Other based on code block (only on MPI task 0): + Times Block #1 Block #2 Block #3 Block #4 Block #5 Block #6 Block #7 Block #8 + | Times 0: 1.326 0.000 0.068 0.020 0.058 0.011 0.856 0.001 + + Times Block #9 Block #10 Block #11 Block #12 Block #13 Block #14 Block #15 Block #16 + | Times 0: 0.084 0.000 0.996 0.320 0.000 0.735 0.056 0.017 + + Times Block Sum Expected + | Times 0: 4.547 5.922 + Time for Fock matrix mixing 0.666982541664765 + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Singularity check in k-point 8, task 0 (analysis for other k-points/tasks may follow below): + Overlap matrix is not singular + | Lowest and highest eigenvalues : 0.6366E-03, 0.6411E+01 + Finished singularity check of overlap matrix + | Time : 0.021 s + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.004 s + Finished transformation to standard eigenproblem + | Time : 0.012 s + Finished solving standard eigenproblem + | Time : 0.035 s + Finished back-transformation of eigenvectors + | Time : 0.007 s + + Obtaining occupation numbers and electronic chemical potential using ELSI. + | Note that, for insulating systems, the printed 'chemical potential' value is not uniquely defined. + | It can be anywhere in the energy gap, as long as it correctly separates occupied and unoccupied states. + | In systems with a gap, the physically relevant chemical potential is the VBM or HOMO. + + | Chemical potential (Fermi level): -5.47044126 eV + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -2770.799162 -75397.28137 + 2 2.00000 -1208.925945 -32896.54871 + 3 2.00000 -1208.904417 -32895.96291 + 4 2.00000 -748.317796 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61.64031 + 274 0.00000 2.265445 61.64591 + 275 0.00000 2.276948 61.95889 + 276 0.00000 2.277093 61.96285 + 277 0.00000 2.332164 63.46141 + 278 0.00000 2.339426 63.65903 + 279 0.00000 2.339834 63.67012 + 280 0.00000 2.365138 64.35867 + 281 0.00000 2.398546 65.26777 + 282 0.00000 2.440476 66.40872 + 283 0.00000 2.440749 66.41616 + 284 0.00000 2.464848 67.07192 + 285 0.00000 2.465055 67.07757 + 286 0.00000 2.472210 67.27226 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.51016545 eV (relative to internal zero) + | Occupation number: 1.99999998 + | K-point: 152 at 0.320000 0.360000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.12786925 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 82 at 0.160000 0.640000 0.000000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 1.38229621 eV between HOMO at k-point 152 and LUMO at k-point 82 + | This appears to be an indirect band gap. + | Smallest direct gap : 1.43545018 eV for k_point 152 at 0.320000 0.360000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Writing energy levels: + | Potential vacuum level, "upper" slab surface: -1.12401807 eV + | Potential vacuum level, "lower" slab surface: 0.41829203 eV + | Work function ("upper" slab surface) : 4.34642319 eV + | Work function ("lower" slab surface) : 5.88873329 eV + *** Warning: band gap may exist, check the suitability to define work function using chemical potential. + | VBM (reference: upper vacuum level) : 4.38614739 eV + | CBM (reference: upper vacuum level) : 3.00385118 eV + + Total energy components: + | Sum of eigenvalues : -24401.22749183 Ha -663991.18355223 eV + | XC energy correction : -506.82228793 Ha -13791.33614996 eV + | XC potential correction : 968.45897369 Ha 26353.10950562 eV + | Free-atom electrostatic energy: -15462.20469666 Ha -420747.99721842 eV + | Hartree energy correction : -1.49487525 Ha -40.67762524 eV + | vdW energy correction : 0.00000000 Ha 0.00000000 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -39403.29037797 Ha -1072218.08504023 eV + | Total energy, T -> 0 : -39403.29037797 Ha -1072218.08504023 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -39403.29037797 Ha -1072218.08504023 eV + + Derived energy quantities: + | Kinetic energy : 42031.89370222 Ha 1143746.02079416 eV + | Electrostatic energy : -80453.33898462 Ha -2189246.74141939 eV + | Energy correction for multipole + | error in Hartree potential : -0.00057050 Ha -0.01552423 eV + | Sum of eigenvalues per atom : -110665.19725871 eV + | Total energy (T->0) per atom : -178703.01417337 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -178703.01417337 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 97.245 s, elapsed 116.199 s + Integration grid: deviation in total charge ( - N_e) = -1.824674E-10 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1604E+00 + | Change of unmixed KS density : 0.5943E+03 + | Change of sum of eigenvalues : -0.6640E+06 eV + | Change of total energy : -0.1072E+07 eV + + +------------------------------------------------------------ + End self-consistency iteration # 0 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 626.752 s 627.121 s + | Charge density update : 15.214 s 15.216 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.007 s 0.007 s + | Hartree multipole summation : 4.234 s 4.235 s + | Integration : 7.718 s 7.719 s + | Fock matrix evaluation : 593.754 s 594.142 s + | Solution of K.-S. eqns. : 5.789 s 5.790 s + | Total energy evaluation : 0.006 s 0.004 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 328.025 MB (on task 6) + | Maximum: 572.099 MB (on task 0) + | Average: 440.775 MB + | Peak value for overall tracked memory usage: + | Minimum: 1023.924 MB (on task 7 after allocating ovlp3fn2) + | Maximum: 2253.341 MB (on task 6 after allocating ovlp3fn_nosplit%m) + | Average: 1684.765 MB + | Largest tracked array allocation so far: + | Minimum: 510.595 MB (ovlp3fn_nosplit%dat on task 7) + | Maximum: 1608.479 MB (ovlp3fn_nosplit%dat on task 6) + | Average: 1141.214 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 1 + + Date : 20230117, Time : 120409.155 +------------------------------------------------------------ + Linear mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 288.0000000000 + | Integrated number of electrons on 3D grid : 288.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.329431E-12 + | Sum of charges compensated after spline to logarithmic grids = 0.612511E-07 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.329324E-12 + Summing up the Hartree potential. + Calculating dipole correction via potential gradient + | Dipole correction gradient : 0.05024983 eV/Angstrom + | Dipole correction potential jump : -1.54229885 eV + Time summed over all CPUs for potential: real work 25.718 s, elapsed 33.033 s + | RMS charge density error from multipole expansion : 0.600004E-02 + | Average real-space part of the electrostatic potential : -0.01380728 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 46.900 s, elapsed 53.880 s + Calculating non-local Hartree-Fock exchange by two-center RI (RI-LVL). + screening_threshold (crit_val) = 0.000000100000 + Exact exchange progress report - outermost block loop i_block: 1 .. 72 + | 1 2 3 4 5 6 7 8 9 10 + | 11 12 13 14 15 16 17 18 19 20 + | 21 22 23 24 25 26 27 28 29 30 + | 31 32 33 34 35 36 37 38 39 40 + | 41 42 43 44 45 46 47 48 49 50 + | 51 52 53 54 55 56 57 58 59 60 + | 61 62 63 64 65 66 67 68 69 70 + | 71 72 + Total ovlp3fn data transfer [GB] 5.14889938756824 + Full exact exchange energy: 25852.056611034077 eV. + Times DM_x_o3fn CM_prod_1 CM_prod_2 tmp2_prod Sync Imbalance Other Total calc + | Times 0: 142.791 -9525.904 52.602 60.580 0.084 3.493 5.483 -9260.872 + | Times 1: 120.720 -9594.887 44.160 83.129 11.848 66.098 8.039 -9260.892 + | Times 2: 113.892 -9583.487 47.046 65.372 11.837 76.607 7.845 -9260.887 + | Times 3: 99.723 191.963 -9765.921 84.416 7.702 114.420 6.826 -9260.871 + | Times 4: 73.517 139.920 27.062 59.153 7.708 -9574.267 6.013 -9260.893 + | Times 5: 47.040 105.542 24.560 54.929 7.529 -9506.783 6.287 -9260.897 + | Times 6: 46.080 115.958 24.388 52.501 7.528 -9513.668 6.297 -9260.915 + | Times 7: 76.517 -9572.553 58.088 65.208 0.096 106.567 5.190 -9260.887 + | Times sum: 720.282 -37723.448 -9488.014 525.288 54.331 -28227.533 51.980 -74087.114 + + Decomposition of Other based on code block (only on MPI task 0): + Times Block #1 Block #2 Block #3 Block #4 Block #5 Block #6 Block #7 Block #8 + | Times 0: 1.251 0.000 0.064 0.014 0.045 0.009 0.828 0.001 + + Times Block #9 Block #10 Block #11 Block #12 Block #13 Block #14 Block #15 Block #16 + | Times 0: 0.083 0.000 0.998 0.239 0.000 0.506 0.055 0.017 + + Times Block Sum Expected + | Times 0: 4.111 5.483 + Time for Fock matrix mixing 0.670616115200584 + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.005 s + Finished transformation to standard eigenproblem + | Time : 0.012 s + Finished solving standard eigenproblem + | Time : 0.034 s + Finished back-transformation of eigenvectors + | Time : 0.004 s + + Obtaining occupation numbers and electronic chemical potential using ELSI. + | Note that, for insulating systems, the printed 'chemical potential' value is not uniquely defined. + | It can be anywhere in the energy gap, as long as it correctly separates occupied and unoccupied states. + | In systems with a gap, the physically relevant chemical potential is the VBM or HOMO. + + | Chemical potential (Fermi level): -5.47044376 eV + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -2770.799161 -75397.28135 + 2 2.00000 -1208.925944 -32896.54870 + 3 2.00000 -1208.904417 -32895.96291 + 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0.00000 1.472399 40.06600 + 243 0.00000 1.513797 41.19251 + 244 0.00000 1.514870 41.22170 + 245 0.00000 1.515499 41.23883 + 246 0.00000 1.531215 41.66648 + 247 0.00000 1.531438 41.67254 + 248 0.00000 1.608326 43.76478 + 249 0.00000 1.608578 43.77163 + 250 0.00000 1.669809 45.43782 + 251 0.00000 1.670986 45.46984 + 252 0.00000 1.730939 47.10124 + 253 0.00000 1.749437 47.60460 + 254 0.00000 1.749786 47.61409 + 255 0.00000 1.766432 48.06705 + 256 0.00000 1.776230 48.33368 + 257 0.00000 1.777104 48.35746 + 258 0.00000 1.784557 48.56027 + 259 0.00000 1.806022 49.14437 + 260 0.00000 1.806822 49.16613 + 261 0.00000 1.807111 49.17399 + 262 0.00000 1.874770 51.01508 + 263 0.00000 1.875379 51.03166 + 264 0.00000 1.910035 51.97470 + 265 0.00000 2.125686 57.84286 + 266 0.00000 2.125799 57.84592 + 267 0.00000 2.142441 58.29877 + 268 0.00000 2.142696 58.30573 + 269 0.00000 2.172804 59.12501 + 270 0.00000 2.220334 60.41836 + 271 0.00000 2.220418 60.42064 + 272 0.00000 2.261528 61.53932 + 273 0.00000 2.265240 61.64031 + 274 0.00000 2.265445 61.64591 + 275 0.00000 2.276948 61.95891 + 276 0.00000 2.277093 61.96286 + 277 0.00000 2.332165 63.46143 + 278 0.00000 2.339426 63.65903 + 279 0.00000 2.339834 63.67012 + 280 0.00000 2.365138 64.35867 + 281 0.00000 2.398547 65.26778 + 282 0.00000 2.440476 66.40873 + 283 0.00000 2.440750 66.41618 + 284 0.00000 2.464848 67.07192 + 285 0.00000 2.465055 67.07757 + 286 0.00000 2.472210 67.27226 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.51016801 eV (relative to internal zero) + | Occupation number: 1.99999998 + | K-point: 152 at 0.320000 0.360000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.12785860 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 82 at 0.160000 0.640000 0.000000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 1.38230941 eV between HOMO at k-point 152 and LUMO at k-point 82 + | This appears to be an indirect band gap. + | Smallest direct gap : 1.43546694 eV for k_point 152 at 0.320000 0.360000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Writing energy levels: + | Potential vacuum level, "upper" slab surface: -1.11020741 eV + | Potential vacuum level, "lower" slab surface: 0.43209145 eV + | Work function ("upper" slab surface) : 4.36023635 eV + | Work function ("lower" slab surface) : 5.90253520 eV + *** Warning: band gap may exist, check the suitability to define work function using chemical potential. + | VBM (reference: upper vacuum level) : 4.39996061 eV + | CBM (reference: upper vacuum level) : 3.01765119 eV + + Total energy components: + | Sum of eigenvalues : -24401.22742107 Ha -663991.18162666 eV + | XC energy correction : -506.82228749 Ha -13791.33613793 eV + | XC potential correction : 968.45897407 Ha 26353.10951581 eV + | Free-atom electrostatic energy: -15462.20469666 Ha -420747.99721842 eV + | Hartree energy correction : -1.49494760 Ha -40.67959384 eV + | vdW energy correction : 0.00000000 Ha 0.00000000 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -39403.29037874 Ha -1072218.08506104 eV + | Total energy, T -> 0 : -39403.29037874 Ha -1072218.08506104 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -39403.29037874 Ha -1072218.08506104 eV + + Derived energy quantities: + | Kinetic energy : 42031.89370647 Ha 1143746.02090999 eV + | Electrostatic energy : -80453.33898864 Ha -2189246.74152874 eV + | Energy correction for multipole + | error in Hartree potential : -0.00057051 Ha -0.01552423 eV + | Sum of eigenvalues per atom : -110665.19693778 eV + | Total energy (T->0) per atom : -178703.01417684 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -178703.01417684 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Finished writing density matrices to file + | Time : 0.212 s + + Time summed over all CPUs for getting density from density matrix: real work 91.068 s, elapsed 105.098 s + Integration grid: deviation in total charge ( - N_e) = -1.823537E-10 + + Self-consistency convergence accuracy: + | Change of charge density : 0.3414E-05 + | Change of unmixed KS density : 0.3414E-05 + | Change of sum of eigenvalues : 0.1926E-02 eV + | Change of total energy : -0.2081E-04 eV + + +------------------------------------------------------------ + End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 568.105 s 3872.120 s + | Charge density update : 14.048 s 14.053 s + | Density mixing : 0.005 s 0.006 s + | Hartree multipole update : 0.007 s 0.006 s + | Hartree multipole summation : 4.154 s 4.155 s + | Integration : 6.749 s 6.749 s + | Fock matrix evaluation : 539.393 s 3843.435 s + | Solution of K.-S. eqns. : 3.708 s 3.709 s + | Total energy evaluation : 0.006 s 0.003 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 328.025 MB (on task 6) + | Maximum: 572.099 MB (on task 0) + | Average: 440.775 MB + | Peak value for overall tracked memory usage: + | Minimum: 1023.924 MB (on task 7 after allocating ovlp3fn2) + | Maximum: 2253.341 MB (on task 6 after allocating ovlp3fn_nosplit%m) + | Average: 1684.765 MB + | Largest tracked array allocation so far: + | Minimum: 510.595 MB (ovlp3fn_nosplit%dat on task 7) + | Maximum: 1608.479 MB (ovlp3fn_nosplit%dat on task 6) + | Average: 1141.214 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 2 + + Date : 20230117, Time : 130841.276 +------------------------------------------------------------ + Linear mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 288.0000000000 + | Integrated number of electrons on 3D grid : 288.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.394745E-12 + | Sum of charges compensated after spline to logarithmic grids = 0.612514E-07 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.394532E-12 + Summing up the Hartree potential. + Calculating dipole correction via potential gradient + | Dipole correction gradient : 0.05024959 eV/Angstrom + | Dipole correction potential jump : -1.54229149 eV + Time summed over all CPUs for potential: real work 15.265 s, elapsed 19.691 s + | RMS charge density error from multipole expansion : 0.600004E-02 + | Average real-space part of the electrostatic potential : -0.01380720 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 48.683 s, elapsed 55.764 s + Calculating non-local Hartree-Fock exchange by two-center RI (RI-LVL). + screening_threshold (crit_val) = 0.000000100000 + Exact exchange progress report - outermost block loop i_block: 1 .. 72 + | 1 2 3 4 5 6 7 8 9 10 + | 11 12 13 14 15 16 17 18 19 20 + | 21 22 23 24 25 26 27 28 29 30 + | 31 32 33 34 35 36 37 38 39 40 + | 41 42 43 44 45 46 47 48 49 50 + | 51 52 53 54 55 56 57 58 59 60 + | 61 62 63 64 65 66 67 68 69 70 + | 71 72 + Total ovlp3fn data transfer [GB] 5.14889938756824 + Full exact exchange energy: 25852.056606406633 eV. + Times DM_x_o3fn CM_prod_1 CM_prod_2 tmp2_prod Sync Imbalance Other Total calc + | Times 0: 174.956 343.235 62.722 68.324 0.072 2.405 6.143 657.858 + | Times 1: 140.465 246.681 55.204 102.518 13.964 89.807 9.229 657.868 + | Times 2: 131.487 260.207 58.741 82.689 13.963 101.854 8.918 657.857 + | Times 3: 116.719 229.256 44.365 98.862 9.213 151.647 7.798 657.859 + | Times 4: 90.710 171.384 36.530 73.407 9.210 269.625 6.982 657.848 + | Times 5: 60.721 133.756 32.250 65.344 9.011 349.403 7.371 657.856 + | Times 6: 60.428 147.774 32.064 62.705 9.010 338.538 7.338 657.857 + | Times 7: 96.202 299.494 77.446 77.944 0.072 100.791 5.912 657.860 + | Times sum: 871.688 1831.786 399.322 631.793 64.514 1404.070 59.690 5262.864 + + Decomposition of Other based on code block (only on MPI task 0): + Times Block #1 Block #2 Block #3 Block #4 Block #5 Block #6 Block #7 Block #8 + | Times 0: 1.169 0.000 0.074 0.014 0.036 0.008 0.975 0.001 + + Times Block #9 Block #10 Block #11 Block #12 Block #13 Block #14 Block #15 Block #16 + | Times 0: 0.092 0.000 1.108 0.186 0.000 0.796 0.065 0.019 + + Times Block Sum Expected + | Times 0: 4.543 6.143 + Time for Fock matrix mixing 0.861784353296343 + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.007 s + Finished transformation to standard eigenproblem + | Time : 0.014 s + Finished solving standard eigenproblem + | Time : 0.051 s + Finished back-transformation of eigenvectors + | Time : 0.008 s + + Obtaining occupation numbers and electronic chemical potential using ELSI. + | Note that, for insulating systems, the printed 'chemical potential' value is not uniquely defined. + | It can be anywhere in the energy gap, as long as it correctly separates occupied and unoccupied states. + | In systems with a gap, the physically relevant chemical potential is the VBM or HOMO. + + | Chemical potential (Fermi level): -5.47044379 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.51016805 eV (relative to internal zero) + | Occupation number: 1.99999998 + | K-point: 152 at 0.320000 0.360000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.12784864 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 82 at 0.160000 0.640000 0.000000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 1.38231941 eV between HOMO at k-point 152 and LUMO at k-point 82 + | This appears to be an indirect band gap. + | Smallest direct gap : 1.43548217 eV for k_point 152 at 0.320000 0.360000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Checking to see if s.c.f. parameters should be adjusted. + + Total energy components: + | Sum of eigenvalues : -24401.22735640 Ha -663991.17986680 eV + | XC energy correction : -506.82228793 Ha -13791.33615015 eV + | XC potential correction : 968.45897442 Ha 26353.10952534 eV + | Free-atom electrostatic energy: -15462.20469666 Ha -420747.99721842 eV + | Hartree energy correction : -1.49501235 Ha -40.68135598 eV + | vdW energy correction : 0.00000000 Ha 0.00000000 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -39403.29037892 Ha -1072218.08506601 eV + | Total energy, T -> 0 : -39403.29037892 Ha -1072218.08506601 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -39403.29037892 Ha -1072218.08506601 eV + + Derived energy quantities: + | Kinetic energy : 42031.89370992 Ha 1143746.02100380 eV + | Electrostatic energy : -80453.33899219 Ha -2189246.74162545 eV + | Energy correction for multipole + | error in Hartree potential : -0.00057051 Ha -0.01552423 eV + | Sum of eigenvalues per atom : -110665.19664447 eV + | Total energy (T->0) per atom : -178703.01417767 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -178703.01417767 eV + + Self-consistency convergence accuracy: + | Change of charge density : 0.3330E-05 + | Change of unmixed KS density : 0.2647E-06 + | Change of sum of eigenvalues : 0.1760E-02 eV + | Change of total energy : -0.4968E-05 eV + + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -2770.799161 -75397.28133 + 2 2.00000 -1208.925944 -32896.54870 + 3 2.00000 -1208.904417 -32895.96291 + 4 2.00000 -748.317796 -20362.76327 + 5 2.00000 -468.574206 -12750.55288 + 6 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-436.84841 + 62 2.00000 -16.053883 -436.84837 + 63 2.00000 -14.438786 -392.89935 + 64 2.00000 -14.437462 -392.86334 + 65 2.00000 -14.437461 -392.86330 + 66 2.00000 -9.121622 -248.21196 + 67 2.00000 -9.121620 -248.21192 + 68 2.00000 -9.121472 -248.20789 + 69 2.00000 -9.121315 -248.20362 + 70 2.00000 -9.121314 -248.20359 + 71 2.00000 -8.480758 -230.77318 + 72 2.00000 -8.480491 -230.76591 + 73 2.00000 -8.480490 -230.76589 + 74 2.00000 -8.479619 -230.74218 + 75 2.00000 -8.479619 -230.74218 + 76 2.00000 -8.189862 -222.85750 + 77 2.00000 -8.164336 -222.16289 + 78 2.00000 -6.332017 -172.30294 + 79 2.00000 -6.310220 -171.70982 + 80 2.00000 -5.893687 -160.37539 + 81 2.00000 -5.893686 -160.37536 + 82 2.00000 -5.892006 -160.32963 + 83 2.00000 -5.868296 -159.68445 + 84 2.00000 -5.868294 -159.68442 + 85 2.00000 -5.866121 -159.62527 + 86 2.00000 -4.438078 -120.76625 + 87 2.00000 -4.438077 -120.76621 + 88 2.00000 -4.435087 -120.68487 + 89 2.00000 -4.416313 -120.17399 + 90 2.00000 -4.416311 -120.17393 + 91 2.00000 -4.413018 -120.08434 + 92 2.00000 -3.077537 -83.74405 + 93 2.00000 -2.583476 -70.29995 + 94 2.00000 -2.106838 -57.32998 + 95 2.00000 -2.106837 -57.32995 + 96 2.00000 -2.105552 -57.29498 + 97 2.00000 -2.105551 -57.29496 + 98 2.00000 -2.104969 -57.27912 + 99 2.00000 -2.081500 -56.64051 + 100 2.00000 -2.081500 -56.64050 + 101 2.00000 -2.079803 -56.59431 + 102 2.00000 -2.079802 -56.59430 + 103 2.00000 -2.079095 -56.57506 + 104 2.00000 -1.713069 -46.61499 + 105 2.00000 -1.708466 -46.48973 + 106 2.00000 -1.708461 -46.48960 + 107 2.00000 -1.661305 -45.20640 + 108 2.00000 -1.661304 -45.20639 + 109 2.00000 -1.658219 -45.12242 + 110 2.00000 -1.658217 -45.12239 + 111 2.00000 -1.658110 -45.11946 + 112 2.00000 -1.639913 -44.62430 + 113 2.00000 -1.639911 -44.62426 + 114 2.00000 -1.636620 -44.53469 + 115 2.00000 -1.636618 -44.53464 + 116 2.00000 -1.635884 -44.51467 + 117 2.00000 -1.580956 -43.02000 + 118 2.00000 -1.573484 -42.81667 + 119 2.00000 -1.573479 -42.81655 + 120 2.00000 -1.416101 -38.53406 + 121 2.00000 -1.416098 -38.53399 + 122 2.00000 -1.415924 -38.52925 + 123 2.00000 -1.415759 -38.52475 + 124 2.00000 -1.415757 -38.52472 + 125 2.00000 -1.415594 -38.52027 + 126 2.00000 -1.415506 -38.51787 + 127 2.00000 -0.792882 -21.57540 + 128 2.00000 -0.753752 -20.51065 + 129 2.00000 -0.731593 -19.90765 + 130 2.00000 -0.702802 -19.12423 + 131 2.00000 -0.465496 -12.66678 + 132 2.00000 -0.417164 -11.35160 + 133 2.00000 -0.323162 -8.79369 + 134 2.00000 -0.313523 -8.53138 + 135 2.00000 -0.313512 -8.53111 + 136 2.00000 -0.286935 -7.80789 + 137 2.00000 -0.286905 -7.80708 + 138 2.00000 -0.285815 -7.77743 + 139 2.00000 -0.255096 -6.94152 + 140 2.00000 -0.255068 -6.94075 + 141 2.00000 -0.235879 -6.41859 + 142 2.00000 -0.235860 -6.41806 + 143 2.00000 -0.227811 -6.19906 + 144 2.00000 -0.208954 -5.68592 + 145 0.00000 -0.091704 -2.49538 + 146 0.00000 -0.091660 -2.49420 + 147 0.00000 -0.073757 -2.00702 + 148 0.00000 -0.073724 -2.00612 + 149 0.00000 -0.061600 -1.67622 + 150 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12.48413 + 182 0.00000 0.459232 12.49635 + 183 0.00000 0.491817 13.38302 + 184 0.00000 0.515851 14.03701 + 185 0.00000 0.537856 14.63581 + 186 0.00000 0.538216 14.64561 + 187 0.00000 0.550392 14.97694 + 188 0.00000 0.550797 14.98794 + 189 0.00000 0.553197 15.05326 + 190 0.00000 0.607384 16.52777 + 191 0.00000 0.645174 17.55608 + 192 0.00000 0.654002 17.79629 + 193 0.00000 0.654251 17.80308 + 194 0.00000 0.676597 18.41114 + 195 0.00000 0.677555 18.43720 + 196 0.00000 0.704751 19.17724 + 197 0.00000 0.755950 20.57044 + 198 0.00000 0.756878 20.59570 + 199 0.00000 0.766119 20.84717 + 200 0.00000 0.767013 20.87149 + 201 0.00000 0.789229 21.47602 + 202 0.00000 0.812771 22.11663 + 203 0.00000 0.857620 23.33703 + 204 0.00000 0.858321 23.35610 + 205 0.00000 0.881456 23.98565 + 206 0.00000 0.886545 24.12411 + 207 0.00000 0.888357 24.17342 + 208 0.00000 0.909208 24.74080 + 209 0.00000 1.010400 27.49438 + 210 0.00000 1.023135 27.84092 + 211 0.00000 1.036122 28.19432 + 212 0.00000 1.037229 28.22444 + 213 0.00000 1.042509 28.36811 + 214 0.00000 1.042857 28.37758 + 215 0.00000 1.054058 28.68238 + 216 0.00000 1.067153 29.03871 + 217 0.00000 1.131717 30.79559 + 218 0.00000 1.133662 30.84850 + 219 0.00000 1.140985 31.04779 + 220 0.00000 1.155431 31.44088 + 221 0.00000 1.157713 31.50296 + 222 0.00000 1.163356 31.65652 + 223 0.00000 1.173224 31.92506 + 224 0.00000 1.232421 33.53587 + 225 0.00000 1.260623 34.30331 + 226 0.00000 1.301633 35.41924 + 227 0.00000 1.302366 35.43917 + 228 0.00000 1.328494 36.15015 + 229 0.00000 1.329311 36.17238 + 230 0.00000 1.354680 36.86271 + 231 0.00000 1.377425 37.48163 + 232 0.00000 1.377522 37.48429 + 233 0.00000 1.404313 38.21329 + 234 0.00000 1.408885 38.33770 + 235 0.00000 1.408964 38.33986 + 236 0.00000 1.413168 38.45425 + 237 0.00000 1.420398 38.65099 + 238 0.00000 1.455753 39.61305 + 239 0.00000 1.456628 39.63688 + 240 0.00000 1.464465 39.85011 + 241 0.00000 1.465304 39.87296 + 242 0.00000 1.472399 40.06600 + 243 0.00000 1.513797 41.19252 + 244 0.00000 1.514870 41.22170 + 245 0.00000 1.515499 41.23883 + 246 0.00000 1.531215 41.66648 + 247 0.00000 1.531438 41.67254 + 248 0.00000 1.608326 43.76478 + 249 0.00000 1.608578 43.77164 + 250 0.00000 1.669809 45.43782 + 251 0.00000 1.670986 45.46984 + 252 0.00000 1.730939 47.10124 + 253 0.00000 1.749437 47.60460 + 254 0.00000 1.749785 47.61409 + 255 0.00000 1.766432 48.06705 + 256 0.00000 1.776230 48.33369 + 257 0.00000 1.777104 48.35747 + 258 0.00000 1.784558 48.56028 + 259 0.00000 1.806022 49.14437 + 260 0.00000 1.806822 49.16614 + 261 0.00000 1.807111 49.17400 + 262 0.00000 1.874770 51.01508 + 263 0.00000 1.875379 51.03166 + 264 0.00000 1.910035 51.97470 + 265 0.00000 2.125686 57.84287 + 266 0.00000 2.125799 57.84593 + 267 0.00000 2.142441 58.29877 + 268 0.00000 2.142696 58.30573 + 269 0.00000 2.172805 59.12503 + 270 0.00000 2.220334 60.41837 + 271 0.00000 2.220418 60.42065 + 272 0.00000 2.261528 61.53932 + 273 0.00000 2.265240 61.64031 + 274 0.00000 2.265445 61.64591 + 275 0.00000 2.276949 61.95892 + 276 0.00000 2.277094 61.96288 + 277 0.00000 2.332165 63.46144 + 278 0.00000 2.339426 63.65903 + 279 0.00000 2.339834 63.67012 + 280 0.00000 2.365138 64.35867 + 281 0.00000 2.398547 65.26780 + 282 0.00000 2.440476 66.40874 + 283 0.00000 2.440750 66.41619 + 284 0.00000 2.464848 67.07192 + 285 0.00000 2.465055 67.07757 + 286 0.00000 2.472210 67.27226 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.51016805 eV (relative to internal zero) + | Occupation number: 1.99999998 + | K-point: 152 at 0.320000 0.360000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.12784864 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 82 at 0.160000 0.640000 0.000000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 1.38231941 eV between HOMO at k-point 152 and LUMO at k-point 82 + | This appears to be an indirect band gap. + | Smallest direct gap : 1.43548217 eV for k_point 152 at 0.320000 0.360000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + | Chemical Potential : -5.47044379 eV + | Note that, for insulating systems, the printed 'chemical potential' value is not uniquely defined. + | It can be anywhere in the energy gap, as long as it correctly separates occupied and unoccupied states. + | In systems with a gap, the physically relevant chemical potential is the VBM or HOMO. + + Writing energy levels: + | Potential vacuum level, "upper" slab surface: -1.11020586 eV + | Potential vacuum level, "lower" slab surface: 0.43208563 eV + | Work function ("upper" slab surface) : 4.36023793 eV + | Work function ("lower" slab surface) : 5.90252942 eV + *** Warning: band gap may exist, check the suitability to define work function using chemical potential. + | VBM (reference: upper vacuum level) : 4.39996220 eV + | CBM (reference: upper vacuum level) : 3.01764278 eV + + Self-consistency cycle converged. + + Finished writing density matrices to file + | Time : 0.320 s + + +------------------------------------------------------------ + End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 673.084 s 674.749 s + | Charge density update : 0.000 s 0.000 s + | Density mixing : 0.008 s 0.008 s + | Hartree multipole update : 0.005 s 0.006 s + | Hartree multipole summation : 2.478 s 2.477 s + | Integration : 6.987 s 6.987 s + | Fock matrix evaluation : 657.232 s 658.729 s + | Solution of K.-S. eqns. : 5.691 s 5.693 s + | Total energy evaluation : 0.007 s 0.006 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 328.025 MB (on task 6) + | Maximum: 572.099 MB (on task 0) + | Average: 440.775 MB + | Peak value for overall tracked memory usage: + | Minimum: 1023.924 MB (on task 7 after allocating ovlp3fn2) + | Maximum: 2253.341 MB (on task 6 after allocating ovlp3fn_nosplit%m) + | Average: 1684.765 MB + | Largest tracked array allocation so far: + | Minimum: 510.595 MB (ovlp3fn_nosplit%dat on task 7) + | Maximum: 1608.479 MB (ovlp3fn_nosplit%dat on task 6) + | Average: 1141.214 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Obtaining max. number of non-zero basis functions in each batch . + Evaluating KS electron density on previously omitted grid points, using the density matrix. + Evaluating density matrix + Evaluating non-empirical van der Waals correction (Tkatchenko/Scheffler 2009). + Performing Hirshfeld analysis of fragment charges and moments. + ---------------------------------------------------------------------- + | Atom 1: Mo + | Hirshfeld charge : 0.14334549 + | Free atom volume : 161.44141347 + | Hirshfeld volume : 166.69870797 + | Hirshfeld dipole vector : 0.00001486 0.00000113 -0.02826154 + | Hirshfeld dipole moment : 0.02826154 + | Hirshfeld second moments: -0.14903398 -0.00002236 0.00002431 + | -0.00002236 -0.14933710 -0.00000332 + | 0.00002431 -0.00000332 -0.06503340 + ---------------------------------------------------------------------- + | Atom 2: W + | Hirshfeld charge : 0.03397108 + | Free atom volume : 183.26905631 + | Hirshfeld volume : 186.71300181 + | Hirshfeld dipole vector : -0.00000563 -0.00001985 -0.03408373 + | Hirshfeld dipole moment : 0.03408373 + | Hirshfeld second moments: -0.10212085 0.00000533 -0.00000843 + | 0.00000533 -0.10239772 0.00005836 + | -0.00000843 0.00005836 -0.06443174 + ---------------------------------------------------------------------- + | Atom 3: Se + | Hirshfeld charge : -0.09679955 + | Free atom volume : 103.35483164 + | Hirshfeld volume : 102.99374237 + | Hirshfeld dipole vector : -0.00000182 0.00002059 -0.16365042 + | Hirshfeld dipole moment : 0.16365042 + | Hirshfeld second moments: -0.00127560 0.00000424 -0.00000261 + | 0.00000424 -0.00127931 -0.00001042 + | -0.00000261 -0.00001042 -0.05927415 + ---------------------------------------------------------------------- + | Atom 4: Te + | Hirshfeld charge : -0.04246364 + | Free atom volume : 162.39794762 + | Hirshfeld volume : 162.54253923 + | Hirshfeld dipole vector : 0.00001606 0.00000810 0.17625494 + | Hirshfeld dipole moment : 0.17625495 + | Hirshfeld second moments: 0.00633079 0.00000603 0.00018705 + | 0.00000603 0.00631243 0.00011641 + | 0.00018705 0.00011641 -0.08793520 + ---------------------------------------------------------------------- + | Atom 5: Se + | Hirshfeld charge : -0.04403537 + | Free atom volume : 103.35483164 + | Hirshfeld volume : 101.75906502 + | Hirshfeld dipole vector : -0.00004613 -0.00004125 -0.11935505 + | Hirshfeld dipole moment : 0.11935507 + | Hirshfeld second moments: 0.03870993 -0.00004325 0.00018264 + | -0.00004325 0.03873151 0.00020737 + | 0.00018264 0.00020737 -0.02441430 + ---------------------------------------------------------------------- + | Atom 6: Te + | Hirshfeld charge : 0.00568900 + | Free atom volume : 162.39794762 + | Hirshfeld volume : 160.76768289 + | Hirshfeld dipole vector : -0.00001285 0.00002171 0.12611076 + | Hirshfeld dipole moment : 0.12611076 + | Hirshfeld second moments: 0.04941872 0.00000377 -0.00001726 + | 0.00000377 0.04947758 0.00004006 + | -0.00001726 0.00004006 -0.03562343 + ---------------------------------------------------------------------- + + Converging periodic supercell size for vdw calculation. + Convergence accuracy (and time!) can be adjusted using the vdw_convergence_threshold keyword. + | Shell number: 1 + | VDW energy change: -0.864496E+00 eV. + | Not converged. + | Shell number: 2 + | VDW energy change: -0.455753E+00 eV. + | Not converged. + | Shell number: 3 + | VDW energy change: -0.703525E-01 eV. + | Not converged. + | Shell number: 4 + | VDW energy change: -0.190625E-01 eV. + | Not converged. + | Shell number: 5 + | VDW energy change: -0.696535E-02 eV. + | Not converged. + | Shell number: 6 + | VDW energy change: -0.308094E-02 eV. + | Not converged. + | Shell number: 7 + | VDW energy change: -0.156047E-02 eV. + | Not converged. + | Shell number: 8 + | VDW energy change: -0.874347E-03 eV. + | Not converged. + | Shell number: 9 + | VDW energy change: -0.529219E-03 eV. + | Not converged. + | Shell number: 10 + | VDW energy change: -0.340128E-03 eV. + | Not converged. + | Shell number: 11 + | VDW energy change: -0.229201E-03 eV. + | Not converged. + | Shell number: 12 + | VDW energy change: -0.160432E-03 eV. + | Not converged. + | Shell number: 13 + | VDW energy change: -0.115834E-03 eV. + | Not converged. + | Shell number: 14 + | VDW energy change: -0.858156E-04 eV. + | Not converged. + | Shell number: 15 + | VDW energy change: -0.649739E-04 eV. + | Not converged. + | Shell number: 16 + | VDW energy change: -0.501186E-04 eV. + | Not converged. + | Shell number: 17 + | VDW energy change: -0.392896E-04 eV. + | Not converged. + | Shell number: 18 + | VDW energy change: -0.312402E-04 eV. + | Not converged. + | Shell number: 19 + | VDW energy change: -0.251540E-04 eV. + | Not converged. + | Shell number: 20 + | VDW energy change: -0.204820E-04 eV. + | Not converged. + | Shell number: 21 + | VDW energy change: -0.168470E-04 eV. + | Not converged. + | Shell number: 22 + | VDW energy change: -0.139842E-04 eV. + | Not converged. + | Shell number: 23 + | VDW energy change: -0.117047E-04 eV. + | Not converged. + | Shell number: 24 + | VDW energy change: -0.987147E-05 eV. + | Not converged. + | Shell number: 25 + | VDW energy change: -0.838357E-05 eV. + | Not converged. + | Shell number: 26 + | VDW energy change: -0.716579E-05 eV. + | Not converged. + | Shell number: 27 + | VDW energy change: -0.616133E-05 eV. + | Not converged. + | Shell number: 28 + | VDW energy change: -0.532688E-05 eV. + | Not converged. + | Shell number: 29 + | VDW energy change: -0.462905E-05 eV. + | Not converged. + | Shell number: 30 + | VDW energy change: -0.404184E-05 eV. + | Not converged. + | Shell number: 31 + | VDW energy change: -0.354487E-05 eV. + | Not converged. + | Shell number: 32 + | VDW energy change: -0.312199E-05 eV. + | Not converged. + | Shell number: 33 + | VDW energy change: -0.276033E-05 eV. + | Not converged. + | Shell number: 34 + | VDW energy change: -0.244956E-05 eV. + | Not converged. + | Shell number: 35 + | VDW energy change: -0.218132E-05 eV. + | Not converged. + | Shell number: 36 + | VDW energy change: -0.194882E-05 eV. + | Not converged. + | Shell number: 37 + | VDW energy change: -0.174648E-05 eV. + | Not converged. + | Shell number: 38 + | VDW energy change: -0.156974E-05 eV. + | Not converged. + | Shell number: 39 + | VDW energy change: -0.141480E-05 eV. + | Not converged. + | Shell number: 40 + | VDW energy change: -0.127851E-05 eV. + | Not converged. + | Shell number: 41 + | VDW energy change: -0.115825E-05 eV. + | Not converged. + | Shell number: 42 + | VDW energy change: -0.105180E-05 eV. + | Not converged. + | Shell number: 43 + | VDW energy change: -0.957306E-06 eV. + | Converged. + + Total energy components: + | Sum of eigenvalues : -24401.22735640 Ha -663991.17986680 eV + | XC energy correction : -506.82228793 Ha -13791.33615015 eV + | XC potential correction : 968.45897442 Ha 26353.10952534 eV + | Free-atom electrostatic energy: -15462.20469666 Ha -420747.99721842 eV + | Hartree energy correction : -1.49501235 Ha -40.68135598 eV + | vdW energy correction : -0.05374857 Ha -1.46257291 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -39403.34412749 Ha -1072219.54763892 eV + | Total energy, T -> 0 : -39403.34412749 Ha -1072219.54763892 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -39403.34412749 Ha -1072219.54763892 eV + + Derived energy quantities: + | Kinetic energy : 42031.89370992 Ha 1143746.02100380 eV + | Electrostatic energy : -80453.33899219 Ha -2189246.74162545 eV + | Energy correction for multipole + | error in Hartree potential : -0.00057051 Ha -0.01552423 eV + | Sum of eigenvalues per atom : -110665.19664447 eV + | Total energy (T->0) per atom : -178703.25793982 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -178703.25793982 eV + Timings for VdW correction (Tkatchenko-Scheffler 2009 or later): + | CPU time: 7.527 s, Wall clock time: 7.534 s. + + Energy and forces in a compact form: + | Total energy uncorrected : -0.107221954763892E+07 eV + | Total energy corrected : -0.107221954763892E+07 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -0.107221954763892E+07 eV + + Calculating total density of states ... + | Chemical potential is -5.470444 eV. + | writing DOS (shifted by electron chemical potential) to file KS_DOS_total.dat.no_soc + | writing DOS (raw data) to file KS_DOS_total_raw.dat.no_soc + | Note that, for insulating systems, the printed 'chemical potential' value is not uniquely defined. + | It can be anywhere in the energy gap, as long as it correctly separates occupied and unoccupied states. + | In systems with a gap, the physically relevant chemical potential is the VBM or HOMO. + ------------------------------------ + Start decomposition of the XC Energy + ------------------------------------ + X and C from original XC functional choice + Hartree-Fock Energy : -237.511404523 Ha -6463.014151602 eV + X Energy : -966.117942690 Ha -26289.406810876 eV + C Energy : -15.727154125 Ha -427.957637983 eV + XC Energy w/o HF : -744.333692292 Ha -20254.350297257 eV + Total XC Energy : -981.845096814 Ha -26717.364448858 eV + ------------------------------------ + LDA X and C from self-consistent density + X Energy LDA : -922.172898532 Ha -25093.601317430 eV + C Energy LDA : -27.738329925 Ha -754.798360983 eV + ------------------------------------ + End decomposition of the XC Energy + ------------------------------------ + +------------------------------------------------------------ + + | Chemical Potential : -5.47044379 eV + | Note that, for insulating systems, the printed 'chemical potential' value is not uniquely defined. + | It can be anywhere in the energy gap, as long as it correctly separates occupied and unoccupied states. + | In systems with a gap, the physically relevant chemical potential is the VBM or HOMO. + + Writing energy levels: + | Potential vacuum level, "upper" slab surface: -1.11020586 eV + | Potential vacuum level, "lower" slab surface: 0.43208563 eV + | Work function ("upper" slab surface) : 4.36023793 eV + | Work function ("lower" slab surface) : 5.90252942 eV + *** Warning: band gap may exist, check the suitability to define work function using chemical potential. + | VBM (reference: upper vacuum level) : 4.39996220 eV + | CBM (reference: upper vacuum level) : 3.01764278 eV + + ****************************************************************** + ** STARTING SECOND VARIATIONAL SOC CALCULATION ** + ****************************************************************** + + ****************************************************************** + ** Stable functionality: ** + ** Writes eigenvalues to stdout ** + ** Recalculates band gaps ** + ** Regular and interpolated DOSs ** + ** Band structures ** + ** Mulliken analysis ** + ** ELSI Support ** + ****************************************************************** + + ****************************************************************** + ** New/Experimental functionality: ** + ** use_local_index and load balancing support ** + ** Dielectric constant/absorption coefficents ** + ** Specifying restricted energy window ** + ** Cube files ** + ****************************************************************** + + ****************************************************************** + ** Known buggy functionality (in SOC code): ** + ** SOC-perturbed total energies are meaningless (DO NOT USE) ** + ****************************************************************** + + ****************************************************************** + ** Note: ** + ** You may see oscillations or blips in ** + ** high-lying conduction bands or slight sub-banding ** + ** in calculations. This is likely due to ** + ** to not enough empty bands being mixed into the ** + ** eigensolver, and you should increase ** + ** the keyword 'empty_states' until the behavior goes ** + ** away to fix it. ** + ** If you are feeling particularly paranoid, consider ** + ** setting the calculate_all_eigenstates flag in ** + ** control.in to calculate all empty states possible. ** + ** This is rarely needed. ** + ****************************************************************** + + ****************************************************************** + ** Future Developments: ** + ** Self-Consistency ** + ****************************************************************** + + Number of core states to omit from SOC : 0 + Number of high-lying states to omit from SOC : 0 + + Index of first SOC-perturbed state to save : 1 + Index of last SOC-perturbed state to save : 572 + + Allocating memory for main spin-orbit coupling matrices... + Allocating 4.992 MB for soc_ham + Allocating 4.992 MB for eigenvec_soc_wf_basis + Allocating 1.366 MB for KS_eigenvalue_soc_perturbed + Allocating 1.366 MB for occ_numbers_soc + Allocating 6.830 MB for spin_expectation + Allocating 0.004 MB for KS_eigenvalue_soc_perturbed_temp + Allocating 0.002 MB for sr_to_soc_idxmap + Allocating 0.022 MB for spin_expectation_temp + Allocating 194.705 MB for KS_eigenvector_soc_perturbed + Allocating 14.455 MB for soc_matrix + + Integrating SOC matrix: batch-based integration p2 version. + Allocating 0.187 MB for dist_tab + Allocating 0.187 MB for dist_tab_sq + Allocating 0.560 MB for dir_tab + Allocating 0.043 MB for i_basis_fns + Allocating 1.880 MB for i_basis_fns_inv + Allocating 0.043 MB for i_atom_fns + Allocating 4.182 MB for gradient_basis_wave + Allocating 0.008 MB for ylm_tab + Allocating 0.002 MB for radial_wave + Allocating 0.002 MB for radial_wave_deriv + Allocating 0.017 MB for i_basis + Allocating 9.950 MB for soc_shell + Allocating 0.023 MB for cartesians + Allocating 0.023 MB for sum_gradient + Allocating 0.047 MB for sum_hessian + Allocating 0.001 MB for potential_shell + + Largest matrix element of SOC matrix is 19.48826 + Sparsity of soc_matrix based on threshold of 0.19488E-13 is 0.43394 + + Determining occupation numbers for Kohn-Sham eigenstates using ELSI. + | Chemical potential (Fermi level) in eV : -.42420700E+01 + | Note that, for insulating systems, the printed 'chemical potential' value is not uniquely defined. + | It can be anywhere in the energy gap, as long as it correctly separates occupied and unoccupied states. + | In systems with a gap, the physically relevant chemical potential is the VBM or HOMO. + Writing SOC-perturbed Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Unperturbed Eigenvalue [eV] Eigenvalue [eV] Level Spacing [eV] + 1 1.00000 -75397.281329 -75397.281329 0.000000 + 2 1.00000 -75397.281329 -75397.281329 0.000000 + 3 1.00000 -32896.548696 -32896.548696 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59.156164 0.000000 + 539 0.00000 60.418372 60.278614 1.122450 + 540 0.00000 60.418372 60.278614 0.000000 + 541 0.00000 60.420652 60.706418 0.427804 + 542 0.00000 60.420652 60.706418 0.000000 + 543 0.00000 61.539316 61.373816 0.667398 + 544 0.00000 61.539316 61.373816 0.000000 + 545 0.00000 61.640310 61.543630 0.169814 + 546 0.00000 61.640310 61.543630 0.000000 + 547 0.00000 61.645907 61.952638 0.409008 + 548 0.00000 61.645907 61.952638 0.000000 + 549 0.00000 61.958923 61.967619 0.014981 + 550 0.00000 61.958923 61.967619 0.000000 + 551 0.00000 61.962875 62.117690 0.150071 + 552 0.00000 61.962875 62.117690 0.000000 + 553 0.00000 63.461437 63.483695 1.366005 + 554 0.00000 63.461437 63.483695 0.000000 + 555 0.00000 63.659025 63.658177 0.174482 + 556 0.00000 63.659025 63.658177 0.000000 + 557 0.00000 63.670115 63.676724 0.018547 + 558 0.00000 63.670115 63.676724 0.000000 + 559 0.00000 64.358671 64.362142 0.685418 + 560 0.00000 64.358671 64.362142 0.000000 + 561 0.00000 65.267798 65.267807 0.905666 + 562 0.00000 65.267798 65.267807 0.000000 + 563 0.00000 66.408740 66.083380 0.815573 + 564 0.00000 66.408740 66.083380 0.000000 + 565 0.00000 66.416187 66.825412 0.742032 + 566 0.00000 66.416187 66.825412 0.000000 + 567 0.00000 67.071917 66.997103 0.171691 + 568 0.00000 67.071917 66.997103 0.000000 + 569 0.00000 67.077572 67.272159 0.275055 + 570 0.00000 67.077572 67.272159 0.000000 + 571 0.00000 67.272261 67.529094 0.256936 + 572 0.00000 67.272261 67.529094 0.000000 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.40200629 eV (relative to internal zero) + | Occupation number: 1.00000000 + | K-point: 152 at 0.320000 0.360000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.20383680 eV (relative to internal zero) + | Occupation number: 0.00000003 + | K-point: 99 at 0.200000 0.600000 0.000000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 1.19816948 eV between HOMO at k-point 152 and LUMO at k-point 99 + | This appears to be an indirect band gap. + | Smallest direct gap : 1.27357279 eV for k_point 151 at 0.320000 0.320000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + | Potential vacuum level, "upper" slab surface: -1.11020586 eV + | Potential vacuum level, "lower" slab surface: 0.43208563 eV + | Work function ("upper" slab surface) : 3.13186418 eV + | Work function ("lower" slab surface) : 4.67415567 eV + *** Warning: band gap may exist, check the suitability to define work function using chemical potential. + | VBM (reference: upper vacuum level) : 4.29180043 eV + | CBM (reference: upper vacuum level) : 3.09363095 eV + Calculating total density of states ... + | Chemical potential is -4.242070 eV. + | writing DOS (shifted by electron chemical potential) to file KS_DOS_total.dat + | writing DOS (raw data) to file KS_DOS_total_raw.dat + | Note that, for insulating systems, the printed 'chemical potential' value is not uniquely defined. + | It can be anywhere in the energy gap, as long as it correctly separates occupied and unoccupied states. + | In systems with a gap, the physically relevant chemical potential is the VBM or HOMO. + + + Spin-orbit coupling : max(cpu_time) wall_clock(cpu1) + | Computing matrix elements for SOC operator : 69.968 73.172 + | Constructing second-variational Hamiltonian : 4.413 4.567 + | Diagonalizing second-variational Hamiltonian : 50.095 52.073 + | Constructing SOC-perturbed eigenvectors : 1.814 1.884 + | Syncing data and calculating occupations : 10.504 0.090 + | Writing out data, calculating band gaps, etc. : 0.687 0.693 + | Total SOC time : 132.154 132.499 + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 258.162 MB (on task 0) + | Maximum: 264.402 MB (on task 1) + | Average: 258.942 MB + | Peak value for overall tracked memory usage: + | Minimum: 1023.924 MB (on task 7 after allocating ovlp3fn2) + | Maximum: 2253.341 MB (on task 6 after allocating ovlp3fn_nosplit%m) + | Average: 1684.765 MB + | Largest tracked array allocation so far: + | Minimum: 510.595 MB (ovlp3fn_nosplit%dat on task 7) + | Maximum: 1608.479 MB (ovlp3fn_nosplit%dat on task 6) + | Average: 1141.214 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. + ------------------------------------------------------------ + Work function related results without post-SCF corrections: + ------------------------------------------------------------ + + | Chemical Potential : -5.47044379 eV + | Note that, for insulating systems, the printed 'chemical potential' value is not uniquely defined. + | It can be anywhere in the energy gap, as long as it correctly separates occupied and unoccupied states. + | In systems with a gap, the physically relevant chemical potential is the VBM or HOMO. + Writing energy levels: + | Potential vacuum level, "upper" slab surface: -1.11020586 eV + | Potential vacuum level, "lower" slab surface: 0.43208563 eV + | Work function ("upper" slab surface) : 4.36023793 eV + | Work function ("lower" slab surface) : 5.90252942 eV + *** Warning: band gap may exist, check the suitability to define work function using chemical potential. + | VBM (reference: upper vacuum level) : 4.39996220 eV + | CBM (reference: upper vacuum level) : 3.01764278 eV + ------------------------------------------------------------ + Work function related results including post-SCF second variational SOC corrections: + ------------------------------------------------------------ + + | Chemical Potential : -4.24207004 eV + | Note that, for insulating systems, the printed 'chemical potential' value is not uniquely defined. + | It can be anywhere in the energy gap, as long as it correctly separates occupied and unoccupied states. + | In systems with a gap, the physically relevant chemical potential is the VBM or HOMO. + Writing energy levels: + | Potential vacuum level, "upper" slab surface: -1.11020586 eV + | Potential vacuum level, "lower" slab surface: 0.43208563 eV + | Work function ("upper" slab surface) : 3.13186418 eV + | Work function ("lower" slab surface) : 4.67415567 eV + *** Warning: band gap may exist, check the suitability to define work function using chemical potential. + | VBM (reference: upper vacuum level) : 4.29180043 eV + | CBM (reference: upper vacuum level) : 3.09363095 eV + ------------------------------------------------------------ + + ------------------------------------------------------------ + Starting Mulliken Analysis + ------------------------------------------------------------ + + Performing scalar-relativistic Mulliken charge analysis on all atoms. + Full analysis (per state, per k-point, etc.) will NOT be written to separate file 'Mulliken.out.no_soc'. + This file can be requested by stating 'output mulliken' explicitly. + Summary of the per-atom charge analysis: + | + | atom electrons charge l=0 l=1 l=2 l=3 l=4 + | 1 41.923307 0.076693 8.220548 18.707886 14.918590 0.066796 0.009487 + | 2 73.889834 0.110166 10.400388 24.759551 24.631958 14.088523 0.009413 + | 3 34.028796 -0.028796 7.885998 15.935472 10.167724 0.039602 + | 4 52.046954 -0.046954 9.851300 21.780090 20.272277 0.119951 0.023335 + | 5 34.062137 -0.062137 7.874747 15.961790 10.184714 0.040885 + | 6 52.048972 -0.048972 9.846689 21.773367 20.283131 0.123032 0.022753 + | + | Total 288.000000 0.000000 + + + Calculating atom-projected density of states ... + | Chemical potential is -5.470444 eV. + | Note that, for insulating systems, the printed 'chemical potential' value is not uniquely defined. + | It can be anywhere in the energy gap, as long as it correctly separates occupied and unoccupied states. + | In systems with a gap, the physically relevant chemical potential is the VBM or HOMO. + | writing projected DOS (shifted by the chemical potential) for species Mo to file atom_proj_dos_Mo0001.dat.no_soc. + | writing projected DOS (raw data) for species Mo to file atom_proj_dos_Mo0001_raw.dat.no_soc. + | writing projected DOS (shifted by the chemical potential) for species W to file atom_proj_dos_W0002.dat.no_soc. + | writing projected DOS (raw data) for species W to file atom_proj_dos_W0002_raw.dat.no_soc. + | writing projected DOS (shifted by the chemical potential) for species Se to file atom_proj_dos_Se0003.dat.no_soc. + | writing projected DOS (raw data) for species Se to file atom_proj_dos_Se0003_raw.dat.no_soc. + | writing projected DOS (shifted by the chemical potential) for species Te to file atom_proj_dos_Te0004.dat.no_soc. + | writing projected DOS (raw data) for species Te to file atom_proj_dos_Te0004_raw.dat.no_soc. + | writing projected DOS (shifted by the chemical potential) for species Se to file atom_proj_dos_Se0005.dat.no_soc. + | writing projected DOS (raw data) for species Se to file atom_proj_dos_Se0005_raw.dat.no_soc. + | writing projected DOS (shifted by the chemical potential) for species Te to file atom_proj_dos_Te0006.dat.no_soc. + | writing projected DOS (raw data) for species Te to file atom_proj_dos_Te0006_raw.dat.no_soc. + + Performing spin-orbit-coupled Mulliken charge analysis on all atoms. +*** output_mulliken expected pure occ_numbers +*** sum(occ_numbers) = 4.5214000000032043E+04 instead of 2.8800000000000000E+02 + Full analysis (per state, per k-point, etc.) will NOT be written to separate file 'Mulliken.out.no_soc'. + This file can be requested by stating 'output mulliken' explicitly. + Summary of the per-atom charge analysis: + | + | atom electrons charge l=0 l=1 l=2 l=3 l=4 + | 1 41.934860 0.065140 8.218798 18.708571 14.931359 0.066696 0.009436 + | 2 73.909299 0.090701 10.397036 24.766484 24.648327 14.088232 0.009220 + | 3 34.026777 -0.026777 7.885897 15.933519 10.167754 0.039607 + | 4 52.037552 -0.037552 9.851215 21.770494 20.272792 0.119761 0.023290 + | 5 34.054451 -0.054451 7.872627 15.962431 10.180031 0.039362 + | 6 52.037060 -0.037060 9.845985 21.771713 20.277902 0.119876 0.021585 + | + | Total 288.000000 -0.000000 + + + Calculating atom-projected density of states ... + | Chemical potential is -4.242070 eV. + | Note that, for insulating systems, the printed 'chemical potential' value is not uniquely defined. + | It can be anywhere in the energy gap, as long as it correctly separates occupied and unoccupied states. + | In systems with a gap, the physically relevant chemical potential is the VBM or HOMO. + | writing projected DOS (shifted by the chemical potential) for species Mo to file atom_proj_dos_Mo0001.dat. + | writing projected DOS (raw data) for species Mo to file atom_proj_dos_Mo0001_raw.dat. + | writing projected DOS (shifted by the chemical potential) for species W to file atom_proj_dos_W0002.dat. + | writing projected DOS (raw data) for species W to file atom_proj_dos_W0002_raw.dat. + | writing projected DOS (shifted by the chemical potential) for species Se to file atom_proj_dos_Se0003.dat. + | writing projected DOS (raw data) for species Se to file atom_proj_dos_Se0003_raw.dat. + | writing projected DOS (shifted by the chemical potential) for species Te to file atom_proj_dos_Te0004.dat. + | writing projected DOS (raw data) for species Te to file atom_proj_dos_Te0004_raw.dat. + | writing projected DOS (shifted by the chemical potential) for species Se to file atom_proj_dos_Se0005.dat. + | writing projected DOS (raw data) for species Se to file atom_proj_dos_Se0005_raw.dat. + | writing projected DOS (shifted by the chemical potential) for species Te to file atom_proj_dos_Te0006.dat. + | writing projected DOS (raw data) for species Te to file atom_proj_dos_Te0006_raw.dat. + Mulliken analysis : max(cpu_time) wall_clock(cpu1) + | Time for Mulliken analysis (scalar relativistic) : 67.875 69.860 + | Time for Mulliken analysis (spin-orbit coupled) : 272.921 280.614 + | Total time for Mulliken analysis : 340.796 350.474 +------------------------------------------------------------ + ------------------------------------------------------------ + Starting Dielectric Calculations + ------------------------------------------------------------ + + Recalculating HOMO and LUMO levels to determine eigenstates needed for dielectric calculations... + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.40200629 eV (relative to internal zero) + | Occupation number: 1.00000000 + | K-point: 152 at 0.320000 0.360000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.20383680 eV (relative to internal zero) + | Occupation number: 0.00000003 + | K-point: 99 at 0.200000 0.600000 0.000000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 1.19816948 eV between HOMO at k-point 152 and LUMO at k-point 99 + | This appears to be an indirect band gap. + | Smallest direct gap : 1.27357279 eV for k_point 151 at 0.320000 0.320000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Index of first state to include in dielectric calculations : 253 + Index of last state to include in dielectric calculations : 378 + + Allocating memory for main dielectric-related matrices... + Allocating 0.000 MB for omega_plasma_sq + Allocating 0.046 MB for interband_polarizability + Allocating 0.046 MB for intraband_polarizability + Allocating 0.046 MB for dielectric + Allocating 0.023 MB for absorption_coeff + Allocating 4.818 MB for mommat_full_x_up + Allocating 4.818 MB for mommat_full_x_low + Allocating 4.818 MB for mommat_full_y_up + Allocating 4.818 MB for mommat_full_y_low + Allocating 4.818 MB for mommat_full_z_up + Allocating 4.818 MB for mommat_full_z_low + Allocating 0.366 MB for moment_TZ + + Calculating p_x matrix elements... + Integrating real-space momentum matrix: batch-based integration. + Time summed over all CPUs for integration: real work 164.131 s, elapsed 183.458 s + + Calculating p_y matrix elements... + Integrating real-space momentum matrix: batch-based integration. + Time summed over all CPUs for integration: real work 170.118 s, elapsed 189.178 s + + Calculating p_z matrix elements... + Integrating real-space momentum matrix: batch-based integration. + Time summed over all CPUs for integration: real work 160.675 s, elapsed 177.687 s + + Calculating dielectric tensor elements... + Performing Kramers-Kronig transform for interband contribution to dielectric component # 1 + Performing Kramers-Kronig transform for interband contribution to dielectric component # 2 + Performing Kramers-Kronig transform for interband contribution to dielectric component # 3 + + Summary for dielectric component # x_x + | Broadening parameters : 5.00000E-02 eV (Gaussian) + | Plasma frequency : 6.12519E-03 eV + | Minimum omega value : 5.00000E-03 eV + | Epsilon at minimum omega : 5.41864E+00 + + + Summary for dielectric component # y_y + | Broadening parameters : 5.00000E-02 eV (Gaussian) + | Plasma frequency : 6.56166E-03 eV + | Minimum omega value : 5.00000E-03 eV + | Epsilon at minimum omega : 5.41857E+00 + + + Summary for dielectric component # z_z + | Broadening parameters : 5.00000E-02 eV (Gaussian) + | Plasma frequency : 1.75279E-06 eV + | Minimum omega value : 5.00000E-03 eV + | Epsilon at minimum omega : 3.51307E+00 + + Dielectric calculations : max(cpu_time) wall_clock(cpu1) + | Time for real-space momentum matrix integration : 66.085 68.865 + | Time for calculating momentum matrix elements : 2.186 2.254 + | Time for plasma frequency and interband contributions : 95.749 98.262 + | Time for syncing and postprocessing : 0.178 0.182 + | Total time for dielectric calculations : 164.205 169.582 + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 258.162 MB (on task 0) + | Maximum: 264.402 MB (on task 1) + | Average: 258.942 MB + | Peak value for overall tracked memory usage: + | Minimum: 1023.924 MB (on task 7 after allocating ovlp3fn2) + | Maximum: 2253.341 MB (on task 6 after allocating ovlp3fn_nosplit%m) + | Average: 1684.765 MB + | Largest tracked array allocation so far: + | Minimum: 510.595 MB (ovlp3fn_nosplit%dat on task 7) + | Maximum: 1608.479 MB (ovlp3fn_nosplit%dat on task 6) + | Average: 1141.214 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Output mulliken decomposition of band k points for SOC in LAPACK + + ------------------------------------------------------------------- + Writing the requested band structure output (LAPACK version): + ------------------------------------------------------------------- + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 56.119 s, elapsed 65.124 s + Integrating SOC matrix: batch-based integration p2 version. + Allocating 0.187 MB for dist_tab + Allocating 0.187 MB for dist_tab_sq + Allocating 0.560 MB for dir_tab + Allocating 0.043 MB for i_basis_fns + Allocating 1.880 MB for i_basis_fns_inv + Allocating 0.043 MB for i_atom_fns + Allocating 4.182 MB for gradient_basis_wave + Allocating 0.008 MB for ylm_tab + Allocating 0.002 MB for radial_wave + Allocating 0.002 MB for radial_wave_deriv + Allocating 0.017 MB for i_basis + Allocating 9.950 MB for soc_shell + Allocating 0.023 MB for cartesians + Allocating 0.023 MB for sum_gradient + Allocating 0.047 MB for sum_hessian + Allocating 0.001 MB for potential_shell + No atoms are split internally + Number of super-cells in X Y Z: 7 7 2 + Number of atoms pairs total: 1056 + sparsity of pfbvk: 1.000000 + Number of atoms pairs in BvK cells: 1056 + Number of instances: 1 + ----------------------------------------------------- + Dividing atoms among tasks for exact exchange energy: + Atom: 1 Weight: 0.20135E+09 + Atom: 2 Weight: 0.35722E+09 + Atom: 3 Weight: 0.66925E+08 + Atom: 4 Weight: 0.26265E+09 + Atom: 5 Weight: 0.97677E+08 + Atom: 6 Weight: 0.21083E+09 + + Average weight per task: 0.14958E+09 + + Number of "big" (above average) atoms : 4 + Number of "small" (below average) atoms: 2 + + There are "big" and "small" atoms + Reserving 4 tasks for "big" atoms + Max. weight for big atoms: 0.35722E+09 small atoms: 0.97677E+08 + Trying 5 tasks for "big" atoms: + Max. weight for big atoms: 0.26265E+09 small atoms: 0.97677E+08 + => Atom 2 gets 2 tasks + Trying 6 tasks for "big" atoms: + Max. weight for big atoms: 0.21083E+09 small atoms: 0.97677E+08 + => Atom 4 gets 2 tasks + Trying 7 tasks for "big" atoms: + Max. weight for big atoms: 0.20135E+09 small atoms: 0.16460E+09 + => Atom 6 gets 2 tasks + Using 1 tasks for "small" atoms, 7 for "big" atoms + + Atom division among tasks: + Atom 1: (initial) task: 0, # of tasks: 1 + Atom 2: (initial) task: 1, # of tasks: 2 + Atom 3: (initial) task: 7, # of tasks: 1 + Atom 4: (initial) task: 3, # of tasks: 2 + Atom 5: (initial) task: 7, # of tasks: 1 + Atom 6: (initial) task: 5, # of tasks: 2 + + ----------------------------------------------------- + Task 0: my_n_atoms2: 1 my_atom_list: 1 + Task 1: my_n_atoms2: 1 my_atom_list: 2 + Task 2: my_n_atoms2: 1 my_atom_list: 2 + Task 3: my_n_atoms2: 1 my_atom_list: 4 + Task 4: my_n_atoms2: 1 my_atom_list: 4 + Task 5: my_n_atoms2: 1 my_atom_list: 6 + Task 6: my_n_atoms2: 1 my_atom_list: 6 + Task 7: my_n_atoms2: 2 my_atom_list: 3 5 + Task 0: my_n_atom_pairs: 179 + Task 1: my_n_atom_pairs: 91 + Task 2: my_n_atom_pairs: 90 + Task 3: my_n_atom_pairs: 101 + Task 4: my_n_atom_pairs: 100 + Task 5: my_n_atom_pairs: 74 + Task 6: my_n_atom_pairs: 74 + Task 7: my_n_atom_pairs: 347 + + Treating all 21 k-points in band plot segment # 1: + + Overlap matrix is not singular + | Lowest and highest eigenvalues : 0.1236E-02, 0.7973E+01 + Finished singularity check of overlap matrix + | Time : 0.024 s + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.006 s + Finished transformation to standard eigenproblem + | Time : 0.017 s + Finished solving standard eigenproblem + | Time : 0.044 s + Finished back-transformation of eigenvectors + | Time : 0.006 s + Scalar-relativistic "band gap" along reciprocal space direction number: 1 + | Lowest unoccupied state: -3.84285642 eV + | Highest occupied state : -5.68591882 eV + | Energy difference : 1.84306240 eV + + Performing spin-orbit-coupled Mulliken charge analysis on all atoms. + Allocating 1.923 MB for mulliken_decomp + Spin-orbit-coupled "band gap" along reciprocal space direction number: 1 + | Lowest unoccupied state: -3.90669843 eV + | Highest occupied state : -5.65142414 eV + | Energy difference : 1.74472571 eV + + + Treating all 21 k-points in band plot segment # 2: + + Scalar-relativistic "band gap" along reciprocal space direction number: 2 + | Lowest unoccupied state: -4.10029833 eV + | Highest occupied state : -5.49673488 eV + | Energy difference : 1.39643655 eV + + Performing spin-orbit-coupled Mulliken charge analysis on all atoms. + Allocating 1.923 MB for mulliken_decomp + Spin-orbit-coupled "band gap" along reciprocal space direction number: 2 + | Lowest unoccupied state: -4.14839893 eV + | Highest occupied state : -5.38762145 eV + | Energy difference : 1.23922252 eV + + + Treating all 21 k-points in band plot segment # 3: + + Scalar-relativistic "band gap" along reciprocal space direction number: 3 + | Lowest unoccupied state: -4.14183662 eV + | Highest occupied state : -5.49673488 eV + | Energy difference : 1.35489826 eV + + Performing spin-orbit-coupled Mulliken charge analysis on all atoms. + Allocating 1.923 MB for mulliken_decomp + Spin-orbit-coupled "band gap" along reciprocal space direction number: 3 + | Lowest unoccupied state: -4.20772232 eV + | Highest occupied state : -5.38762145 eV + | Energy difference : 1.17989913 eV + + + Treating all 21 k-points in band plot segment # 4: + + Scalar-relativistic "band gap" along reciprocal space direction number: 4 + | Lowest unoccupied state: -4.14183662 eV + | Highest occupied state : -5.49673488 eV + | Energy difference : 1.35489826 eV + + Performing spin-orbit-coupled Mulliken charge analysis on all atoms. + Allocating 1.923 MB for mulliken_decomp + Spin-orbit-coupled "band gap" along reciprocal space direction number: 4 + | Lowest unoccupied state: -4.20772232 eV + | Highest occupied state : -5.38762145 eV + | Energy difference : 1.17989913 eV + + + Treating all 21 k-points in band plot segment # 5: + + Scalar-relativistic "band gap" along reciprocal space direction number: 5 + | Lowest unoccupied state: -3.84285642 eV + | Highest occupied state : -5.68591882 eV + | Energy difference : 1.84306240 eV + + Performing spin-orbit-coupled Mulliken charge analysis on all atoms. + Allocating 1.923 MB for mulliken_decomp + Spin-orbit-coupled "band gap" along reciprocal space direction number: 5 + | Lowest unoccupied state: -3.90669843 eV + | Highest occupied state : -5.65142414 eV + | Energy difference : 1.74472571 eV + + + Treating all 21 k-points in band plot segment # 6: + + Scalar-relativistic "band gap" along reciprocal space direction number: 6 + | Lowest unoccupied state: -4.10029833 eV + | Highest occupied state : -5.49673488 eV + | Energy difference : 1.39643655 eV + + Performing spin-orbit-coupled Mulliken charge analysis on all atoms. + Allocating 1.923 MB for mulliken_decomp + Spin-orbit-coupled "band gap" along reciprocal space direction number: 6 + | Lowest unoccupied state: -4.14839893 eV + | Highest occupied state : -5.38762145 eV + | Energy difference : 1.23922252 eV + + + Treating all 21 k-points in band plot segment # 7: + + Scalar-relativistic "band gap" along reciprocal space direction number: 7 + | Lowest unoccupied state: -4.14183662 eV + | Highest occupied state : -5.49673488 eV + | Energy difference : 1.35489826 eV + + Performing spin-orbit-coupled Mulliken charge analysis on all atoms. + Allocating 1.923 MB for mulliken_decomp + Spin-orbit-coupled "band gap" along reciprocal space direction number: 7 + | Lowest unoccupied state: -4.20772232 eV + | Highest occupied state : -5.38762145 eV + | Energy difference : 1.17989913 eV + + + Treating all 21 k-points in band plot segment # 8: + + Scalar-relativistic "band gap" along reciprocal space direction number: 8 + | Lowest unoccupied state: -4.14183662 eV + | Highest occupied state : -5.49673488 eV + | Energy difference : 1.35489826 eV + + Performing spin-orbit-coupled Mulliken charge analysis on all atoms. + Allocating 1.923 MB for mulliken_decomp + Spin-orbit-coupled "band gap" along reciprocal space direction number: 8 + | Lowest unoccupied state: -4.20772232 eV + | Highest occupied state : -5.38762145 eV + | Energy difference : 1.17989913 eV + + Scalar-relativistic "band gap" of total set of bands: + | Lowest unoccupied state: -4.14183662 eV + | Highest occupied state : -5.49673488 eV + | Energy difference : 1.35489826 eV + + + Spin-orbit-coupled "band gap" of total set of bands: + | Lowest unoccupied state: -4.20772232 eV + | Highest occupied state : -5.38762145 eV + | Energy difference : 1.17989913 eV + + + + Band Structure : max(cpu_time) wall_clock(cpu1) + | Total Time : 162.471 168.103 +------------------------------------------------------------ + + ------------------------------------------------------------------- + Writing the requested band structure output (LAPACK version): + ------------------------------------------------------------------- + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 57.116 s, elapsed 66.806 s + Integrating SOC matrix: batch-based integration p2 version. + Allocating 0.187 MB for dist_tab + Allocating 0.187 MB for dist_tab_sq + Allocating 0.560 MB for dir_tab + Allocating 0.043 MB for i_basis_fns + Allocating 1.880 MB for i_basis_fns_inv + Allocating 0.043 MB for i_atom_fns + Allocating 4.182 MB for gradient_basis_wave + Allocating 0.008 MB for ylm_tab + Allocating 0.002 MB for radial_wave + Allocating 0.002 MB for radial_wave_deriv + Allocating 0.017 MB for i_basis + Allocating 9.950 MB for soc_shell + Allocating 0.023 MB for cartesians + Allocating 0.023 MB for sum_gradient + Allocating 0.047 MB for sum_hessian + Allocating 0.001 MB for potential_shell + No atoms are split internally + Number of super-cells in X Y Z: 7 7 2 + Number of atoms pairs total: 1056 + sparsity of pfbvk: 1.000000 + Number of atoms pairs in BvK cells: 1056 + Number of instances: 1 + ----------------------------------------------------- + Dividing atoms among tasks for exact exchange energy: + Atom: 1 Weight: 0.20135E+09 + Atom: 2 Weight: 0.35722E+09 + Atom: 3 Weight: 0.66925E+08 + Atom: 4 Weight: 0.26265E+09 + Atom: 5 Weight: 0.97677E+08 + Atom: 6 Weight: 0.21083E+09 + + Average weight per task: 0.14958E+09 + + Number of "big" (above average) atoms : 4 + Number of "small" (below average) atoms: 2 + + There are "big" and "small" atoms + Reserving 4 tasks for "big" atoms + Max. weight for big atoms: 0.35722E+09 small atoms: 0.97677E+08 + Trying 5 tasks for "big" atoms: + Max. weight for big atoms: 0.26265E+09 small atoms: 0.97677E+08 + => Atom 2 gets 2 tasks + Trying 6 tasks for "big" atoms: + Max. weight for big atoms: 0.21083E+09 small atoms: 0.97677E+08 + => Atom 4 gets 2 tasks + Trying 7 tasks for "big" atoms: + Max. weight for big atoms: 0.20135E+09 small atoms: 0.16460E+09 + => Atom 6 gets 2 tasks + Using 1 tasks for "small" atoms, 7 for "big" atoms + + Atom division among tasks: + Atom 1: (initial) task: 0, # of tasks: 1 + Atom 2: (initial) task: 1, # of tasks: 2 + Atom 3: (initial) task: 7, # of tasks: 1 + Atom 4: (initial) task: 3, # of tasks: 2 + Atom 5: (initial) task: 7, # of tasks: 1 + Atom 6: (initial) task: 5, # of tasks: 2 + + ----------------------------------------------------- + Task 0: my_n_atoms2: 1 my_atom_list: 1 + Task 1: my_n_atoms2: 1 my_atom_list: 2 + Task 2: my_n_atoms2: 1 my_atom_list: 2 + Task 3: my_n_atoms2: 1 my_atom_list: 4 + Task 4: my_n_atoms2: 1 my_atom_list: 4 + Task 5: my_n_atoms2: 1 my_atom_list: 6 + Task 6: my_n_atoms2: 1 my_atom_list: 6 + Task 7: my_n_atoms2: 2 my_atom_list: 3 5 + Task 0: my_n_atom_pairs: 179 + Task 1: my_n_atom_pairs: 91 + Task 2: my_n_atom_pairs: 90 + Task 3: my_n_atom_pairs: 101 + Task 4: my_n_atom_pairs: 100 + Task 5: my_n_atom_pairs: 74 + Task 6: my_n_atom_pairs: 74 + Task 7: my_n_atom_pairs: 347 + +=================================================================================== += BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES += RANK 1 PID 66572 RUNNING AT andrey-Latitude-5411 += KILLED BY SIGNAL: 9 (Killed) +=================================================================================== + +=================================================================================== += BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES += RANK 2 PID 66573 RUNNING AT andrey-Latitude-5411 += KILLED BY SIGNAL: 9 (Killed) +=================================================================================== diff --git a/tests/aims/test_files/outputs/geometry.in.next_step b/tests/aims/test_files/outputs/geometry.in.next_step new file mode 100644 index 0000000000..0bd6c26a61 --- /dev/null +++ b/tests/aims/test_files/outputs/geometry.in.next_step @@ -0,0 +1,17 @@ +# +# This is the geometry file that corresponds to the current relaxation step. +# If you do not want this file to be written, set the "write_restart_geometry" flag to .false. +# aims_uuid : 3538959A-A7AC-49B8-A692-B5D8E1478ABA +# +lattice_vector 2.83178921 0.00000000 0.00000000 +lattice_vector -0.00000000 2.83179074 -0.00000000 +lattice_vector -0.00000000 0.00000000 2.83179072 +atom_frac 0.49999995 0.50000004 0.49999998 Fe +atom_frac 0.00000005 -0.00000004 0.00000002 Fe +# +# What follows is the current estimated Hessian matrix constructed by the BFGS algorithm. +# This is NOT the true Hessian matrix of the system. +# If you do not want this information here, switch it off using the "hessian_to_restart_geometry" keyword. +# +trust_radius 0.2000000030 +hessian_file diff --git a/tests/aims/test_files/outputs/hessian.aims b/tests/aims/test_files/outputs/hessian.aims new file mode 100644 index 0000000000..31438994de Binary files /dev/null and b/tests/aims/test_files/outputs/hessian.aims differ diff --git a/tests/aims/test_files/test_files.py b/tests/aims/test_files/test_files.py new file mode 100644 index 0000000000..2316f635d6 --- /dev/null +++ b/tests/aims/test_files/test_files.py @@ -0,0 +1,35 @@ +"""Tests for file manipulation""" + +from pathlib import Path + +import pytest + +TEST_DIR = Path(__file__).parent + + +@pytest.fixture() +def tmp_dir(): + """Same as clean_dir but is fresh for every test""" + import os + import shutil + import tempfile + + old_cwd = os.getcwd() + newpath = tempfile.mkdtemp() + os.chdir(newpath) + yield + os.chdir(old_cwd) + shutil.rmtree(newpath) + + +def test_copy_aims_outputs(tmp_dir): + from atomate2.aims.files import copy_aims_outputs + + files = ["aims.out"] + restart_files = ["geometry.in.next_step", "D_spin_01_kpt_000001.csc"] + + path = TEST_DIR / "outputs" + copy_aims_outputs(src_dir=path, restart_to_input=True, additional_aims_files=files) + + for f in files + restart_files: + assert Path(f).exists() diff --git a/tests/aims/test_flows/test_core.py b/tests/aims/test_flows/test_core.py new file mode 100644 index 0000000000..4c467a39dc --- /dev/null +++ b/tests/aims/test_flows/test_core.py @@ -0,0 +1,49 @@ +"""Test core FHI-aims workflows""" + +import os + +import pytest + +cwd = os.getcwd() + + +def test_double_relax(mock_aims, tmp_path, si, species_dir): + """A test for the double relaxation flow""" + + from jobflow import run_locally + + from atomate2.aims.flows.core import DoubleRelaxMaker + from atomate2.aims.schemas.task import AimsTaskDoc + + # mapping from job name to directory containing test files + ref_paths = { + "Relaxation calculation 1": "double-relax-si/relax-1", + "Relaxation calculation 2": "double-relax-si/relax-2", + } + + parameters = { + "k_grid": [2, 2, 2], + "species_dir": (species_dir).as_posix(), + } + + # settings passed to fake_run_aims + fake_run_kwargs = {} + + # automatically use fake AIMS + mock_aims(ref_paths, fake_run_kwargs) + + # generate flow + flow = DoubleRelaxMaker.from_parameters(parameters).make(si) + + # Run the flow or job and ensure that it finished running successfully + os.chdir(tmp_path) + responses = run_locally(flow, create_folders=True, ensure_success=True) + os.chdir(cwd) + + # validate output + output1 = responses[flow.jobs[0].uuid][1].output + output2 = responses[flow.jobs[1].uuid][1].output + + assert isinstance(output1, AimsTaskDoc) + assert output1.output.energy == pytest.approx(-15800.22554) + assert output2.output.energy == pytest.approx(-15800.25855) diff --git a/tests/aims/test_flows/test_gw_convergence.py b/tests/aims/test_flows/test_gw_convergence.py new file mode 100644 index 0000000000..d3c5c0fb2e --- /dev/null +++ b/tests/aims/test_flows/test_gw_convergence.py @@ -0,0 +1,63 @@ +"""A test for GW workflows for FHI-aims.""" + +import pytest + +# from atomate2.aims.utils.msonable_atoms import MSONableAtoms + + +def test_gw_convergence(mock_aims, tmp_dir, o2, species_dir): + """A test for the GW convergence maker for molecule with respect to the basis set + size + """ + + from jobflow import run_locally + from pymatgen.io.aims.sets.bs import GWSetGenerator + + from atomate2.aims.flows.gw import GWConvergenceMaker + from atomate2.aims.jobs.core import GWMaker + from atomate2.aims.schemas.task import ConvergenceSummary + + # mapping from job name to directory containing test files + ref_paths = { + "GW 0": "basis-gw-convergence-o2/static-1", + "GW 1": "basis-gw-convergence-o2/static-2", + } + + input_set_parameters = {} + + parameters = { + "maker": GWMaker( + input_set_generator=GWSetGenerator(user_params=input_set_parameters) + ), + "criterion_name": "vbm", + "epsilon": 0.05, + "convergence_field": "species_dir", + "convergence_steps": [ + (species_dir / "light").as_posix(), + (species_dir / "tight").as_posix(), + ], + } + + # settings passed to fake_run_aims + fake_run_kwargs = {} + + # automatically use fake AIMS + mock_aims(ref_paths, fake_run_kwargs) + + # generate job + job = GWConvergenceMaker(**parameters).make(o2) + + # Run the job and ensure that it finished running successfully + responses = run_locally(job, create_folders=True, ensure_success=True) + + job_uuid = job.uuid + while responses[job_uuid][1].replace: + job_uuid = responses[job_uuid][1].replace.all_uuids[1] + + output = responses[job_uuid][1].output + + # validate output + assert isinstance(output, ConvergenceSummary) + assert output.converged + assert "tight" in output.convergence_field_value + assert output.actual_epsilon == pytest.approx(0.04594407) diff --git a/tests/aims/test_flows/test_phonon_workflow.py b/tests/aims/test_flows/test_phonon_workflow.py new file mode 100644 index 0000000000..1270905fb9 --- /dev/null +++ b/tests/aims/test_flows/test_phonon_workflow.py @@ -0,0 +1,346 @@ +"""Test various makers""" + +import json +import os + +import pytest + +cwd = os.getcwd() + + +def test_phonon_flow(si, tmp_path, mock_aims, species_dir): + import numpy as np + from jobflow import run_locally + from pymatgen.io.aims.sets.core import StaticSetGenerator + + from atomate2.aims.flows.phonons import PhononMaker + from atomate2.aims.jobs.core import RelaxMaker, StaticMaker + from atomate2.aims.jobs.phonons import PhononDisplacementMaker + + # mapping from job name to directory containing test files + ref_paths = { + "Relaxation calculation": "phonon-relax-si", + "phonon static aims 1/1": "phonon-disp-si", + "SCF Calculation": "phonon-energy-si", + } + + # settings passed to fake_run_aims; adjust these to check for certain input settings + fake_run_aims_kwargs = {} + + # automatically use fake FHI-aims + mock_aims(ref_paths, fake_run_aims_kwargs) + + parameters = { + "k_grid": [2, 2, 2], + "species_dir": (species_dir / "light").as_posix(), + } + # generate job + + parameters_phonon_disp = dict(compute_forces=True, **parameters) + maker = PhononMaker( + bulk_relax_maker=RelaxMaker.full_relaxation(user_params=parameters), + static_energy_maker=StaticMaker( + input_set_generator=StaticSetGenerator(user_params=parameters) + ), + use_symmetrized_structure="primitive", + phonon_displacement_maker=PhononDisplacementMaker( + input_set_generator=StaticSetGenerator( + user_params=parameters_phonon_disp, + user_kpoints_settings={"density": 5.0, "even": True}, + ) + ), + ) + maker.name = "phonons" + flow = maker.make( + si, + supercell_matrix=np.array([-1, 1, 1, 1, -1, 1, 1, 1, -1]).reshape((3, 3)), + ) + + # run the flow or job and ensure that it finished running successfully + os.chdir(tmp_path) + responses = run_locally(flow, create_folders=True, ensure_success=True) + os.chdir(cwd) + + # validation the outputs of the job + output = responses[flow.job_uuids[-1]][1].output + + phonopy_settings_schema = { + "description": "Collection to store computational settings for the " + "phonon computation.", + "properties": { + "npoints_band": { + "default": "number of points for band structure computation", + "title": "Npoints Band", + "type": "integer", + }, + "kpath_scheme": { + "default": "indicates the kpath scheme", + "title": "Kpath Scheme", + "type": "string", + }, + "kpoint_density_dos": { + "default": "number of points for computation of free energies and" + " densities of states", + "title": "Kpoint Density Dos", + "type": "integer", + }, + }, + "title": "PhononComputationalSettings", + "type": "object", + } + assert output.code == "aims" + assert output.born is None + assert not output.has_imaginary_modes + + assert output.temperatures == list(range(0, 500, 10)) + assert output.heat_capacities[0] == 0.0 + assert np.round(output.heat_capacities[-1], 2) == 23.06 + assert output.phonopy_settings.schema_json() == json.dumps(phonopy_settings_schema) + assert np.round(output.phonon_bandstructure.bands[-1, 0], 2) == 14.41 + + +@pytest.mark.skip(reason="Currently not mocked and needs FHI-aims binary") +def test_phonon_socket_flow(si, tmp_path, mock_aims, species_dir): + import numpy as np + from jobflow import run_locally + from pymatgen.io.aims.sets.core import StaticSetGenerator + + from atomate2.aims.flows.phonons import PhononMaker + from atomate2.aims.jobs.core import RelaxMaker, StaticMaker + from atomate2.aims.jobs.phonons import PhononDisplacementMakerSocket + + # mapping from job name to directory containing test files + ref_paths = { + "Relaxation calculation": "phonon-relax-si", + "phonon static aims 1/1": "phonon-disp-si", + "SCF Calculation": "phonon-energy-si", + } + + # settings passed to fake_run_aims; + fake_run_aims_kwargs = {} + + # automatically use fake FHI-aims + mock_aims(ref_paths, fake_run_aims_kwargs) + + parameters = { + "k_grid": [2, 2, 2], + "species_dir": (species_dir / "light/").as_posix(), + } + parameters_phonon_disp = dict( + compute_forces=True, use_pimd_wrapper=("localhost", 12345), **parameters + ) + + # generate job + + maker = PhononMaker( + bulk_relax_maker=RelaxMaker.full_relaxation(user_params=parameters), + static_energy_maker=StaticMaker( + input_set_generator=StaticSetGenerator(user_params=parameters) + ), + use_symmetrized_structure="primitive", + socket=True, + phonon_displacement_maker=PhononDisplacementMakerSocket( + input_set_generator=StaticSetGenerator( + user_params=parameters_phonon_disp, + user_kpoints_settings={"density": 5.0, "even": True}, + ) + ), + ) + maker.name = "phonons" + flow = maker.make( + si, + supercell_matrix=np.array([-1, 1, 1, 1, -1, 1, 1, 1, -1]).reshape((3, 3)), + ) + + # run the flow or job and ensure that it finished running successfully + # os.chdir(tmp_path) + responses = run_locally(flow, create_folders=True, ensure_success=True) + # os.chdir(cwd) + + # validation the outputs of the job + output = responses[flow.job_uuids[-1]][1].output + phonopy_settings_schema = { + "description": "Collection to store computational settings for the " + "phonon computation.", + "properties": { + "npoints_band": { + "default": "number of points for band structure computation", + "title": "Npoints Band", + "type": "integer", + }, + "kpath_scheme": { + "default": "indicates the kpath scheme", + "title": "Kpath Scheme", + "type": "string", + }, + "kpoint_density_dos": { + "default": "number of points for computation of free energies and" + " densities of states", + "title": "Kpoint Density Dos", + "type": "integer", + }, + }, + "title": "PhononComputationalSettings", + "type": "object", + } + assert output.code == "aims" + assert output.born is None + assert not output.has_imaginary_modes + + assert output.temperatures == list(range(0, 500, 10)) + assert output.heat_capacities[0] == 0.0 + assert np.round(output.heat_capacities[-1], 2) == 23.06 + assert output.phonopy_settings.schema_json() == json.dumps(phonopy_settings_schema) + assert np.round(output.phonon_bandstructure.bands[-1, 0], 2) == 14.41 + + +def test_phonon_default_flow(si, tmp_path, mock_aims, species_dir): + import numpy as np + from jobflow import run_locally + + from atomate2.aims.flows.phonons import PhononMaker + + # mapping from job name to directory containing test files + ref_paths = { + "Relaxation calculation": "phonon-relax-default-si", + "phonon static aims 1/1": "phonon-disp-default-si", + "SCF Calculation": "phonon-energy-default-si", + } + + # settings passed to fake_run_aims + fake_run_aims_kwargs = {} + + # automatically use fake FHI-aims + mock_aims(ref_paths, fake_run_aims_kwargs) + + aims_sd = os.environ.get("AIMS_SPECIES_DIR", None) + os.environ["AIMS_SPECIES_DIR"] = str(species_dir / "light") + + maker = PhononMaker() + maker.name = "phonons" + flow = maker.make( + si, + supercell_matrix=np.array([-1, 1, 1, 1, -1, 1, 1, 1, -1]).reshape((3, 3)), + ) + + # run the flow or job and ensure that it finished running successfully + os.chdir(tmp_path) + responses = run_locally(flow, create_folders=True, ensure_success=True) + os.chdir(cwd) + + # validation the outputs of the job + output = responses[flow.job_uuids[-1]][1].output + phonopy_settings_schema = { + "description": "Collection to store computational settings for " + "the phonon computation.", + "properties": { + "npoints_band": { + "default": "number of points for band structure computation", + "title": "Npoints Band", + "type": "integer", + }, + "kpath_scheme": { + "default": "indicates the kpath scheme", + "title": "Kpath Scheme", + "type": "string", + }, + "kpoint_density_dos": { + "default": "number of points for computation of free energies " + "and densities of states", + "title": "Kpoint Density Dos", + "type": "integer", + }, + }, + "title": "PhononComputationalSettings", + "type": "object", + } + assert output.code == "aims" + assert output.born is None + assert not output.has_imaginary_modes + + assert output.temperatures == list(range(0, 500, 10)) + assert output.heat_capacities[0] == 0.0 + assert np.round(output.heat_capacities[-1], 2) == 22.85 + assert output.phonopy_settings.schema_json() == json.dumps(phonopy_settings_schema) + assert np.round(output.phonon_bandstructure.bands[-1, 0], 2) == 15.02 + + if aims_sd is not None: + os.environ["AIMS_SPECIES_DIR"] = aims_sd + + +@pytest.mark.skip(reason="Currently not mocked and needs FHI-aims binary") +def test_phonon_default_socket_flow(si, tmp_path, mock_aims, species_dir): + import numpy as np + from jobflow import run_locally + + from atomate2.aims.flows.phonons import PhononMaker + + aims_sd = os.environ.get("AIMS_SPECIES_DIR", None) + os.environ["AIMS_SPECIES_DIR"] = str(species_dir / "light") + + # mapping from job name to directory containing test files + ref_paths = { + "Relaxation calculation": "phonon-relax-default-si", + "phonon static aims 1/1": "phonon-disp-default-si", + "SCF Calculation": "phonon-energy-default-si", + } + + # settings passed to fake_run_aims + fake_run_aims_kwargs = {} + + # automatically use fake FHI-aims + mock_aims(ref_paths, fake_run_aims_kwargs) + + # generate job + + maker = PhononMaker(socket=True) + maker.name = "phonons" + flow = maker.make( + si, + supercell_matrix=np.array([-1, 1, 1, 1, -1, 1, 1, 1, -1]).reshape((3, 3)), + ) + + # run the flow or job and ensure that it finished running successfully + os.chdir(tmp_path) + responses = run_locally(flow, create_folders=True, ensure_success=True) + os.chdir(cwd) + + # validation the outputs of the job + output = responses[flow.job_uuids[-1]][1].output + + phonopy_settings_schema = { + "description": "Collection to store computational settings for " + "the phonon computation.", + "properties": { + "npoints_band": { + "default": "number of points for band structure computation", + "title": "Npoints Band", + "type": "integer", + }, + "kpath_scheme": { + "default": "indicates the kpath scheme", + "title": "Kpath Scheme", + "type": "string", + }, + "kpoint_density_dos": { + "default": "number of points for computation of free energies " + "and densities of states", + "title": "Kpoint Density Dos", + "type": "integer", + }, + }, + "title": "PhononComputationalSettings", + "type": "object", + } + assert output.code == "aims" + assert output.born is None + assert not output.has_imaginary_modes + + assert output.temperatures == list(range(0, 500, 10)) + assert output.heat_capacities[0] == 0.0 + assert np.round(output.heat_capacities[-1], 2) == 22.85 + assert output.phonopy_settings.schema_json() == json.dumps(phonopy_settings_schema) + assert np.round(output.phonon_bandstructure.bands[-1, 0], 2) == 15.02 + + if aims_sd is not None: + os.environ["AIMS_SPECIES_DIR"] = aims_sd diff --git a/tests/aims/test_makers/test_convergence.py b/tests/aims/test_makers/test_convergence.py new file mode 100644 index 0000000000..be767eac49 --- /dev/null +++ b/tests/aims/test_makers/test_convergence.py @@ -0,0 +1,62 @@ +"""A test for AIMS convergence maker (used for GW, for instance)""" + +import os + +import pytest + +cwd = os.getcwd() + + +def test_convergence(mock_aims, tmp_path, si, species_dir): + """A test for the convergence maker""" + + from jobflow import run_locally + + from atomate2.aims.jobs.convergence import ConvergenceMaker + from atomate2.aims.jobs.core import StaticMaker, StaticSetGenerator + from atomate2.aims.schemas.task import ConvergenceSummary + + # mapping from job name to directory containing test files + ref_paths = { + "SCF Calculation 0": "k-grid-convergence-si/static-1", + "SCF Calculation 1": "k-grid-convergence-si/static-2", + "SCF Calculation 2": "k-grid-convergence-si/static-3", + } + + input_set_parameters = {"species_dir": (species_dir / "light").as_posix()} + + parameters = { + "maker": StaticMaker( + input_set_generator=StaticSetGenerator(user_params=input_set_parameters) + ), + "criterion_name": "energy_per_atom", + "epsilon": 0.2, + "convergence_field": "k_grid", + "convergence_steps": [[3, 3, 3], [4, 4, 4], [5, 5, 5], [6, 6, 6]], + } + + # settings passed to fake_run_aims + fake_run_kwargs = {} + + # automatically use fake AIMS + mock_aims(ref_paths, fake_run_kwargs) + + # generate job + job = ConvergenceMaker(**parameters).make(si) + + # Run the job and ensure that it finished running successfully + os.chdir(tmp_path) + responses = run_locally(job, create_folders=True, ensure_success=True) + os.chdir(cwd) + + job_uuid = job.uuid + while responses[job_uuid][1].replace: + job_uuid = responses[job_uuid][1].replace.all_uuids[1] + + output = responses[job_uuid][1].output + + # validate output + assert isinstance(output, ConvergenceSummary) + assert output.converged + assert output.convergence_field_value == [5, 5, 5] + assert output.actual_epsilon == pytest.approx(0.0614287) diff --git a/tests/aims/test_makers/test_gw.py b/tests/aims/test_makers/test_gw.py new file mode 100644 index 0000000000..8c2fad4300 --- /dev/null +++ b/tests/aims/test_makers/test_gw.py @@ -0,0 +1,36 @@ +"""A test for GW job maker.""" + +import pytest +from jobflow import run_locally +from pymatgen.io.aims.sets.bs import GWSetGenerator + +from atomate2.aims.jobs.core import GWMaker +from atomate2.aims.schemas.task import AimsTaskDoc + + +def test_gw_maker_molecule(tmp_dir, species_dir, mock_aims, o2): + # mapping from job name to directory containing test files + ref_paths = {"gw_o2": "gw-o2"} + + # settings passed to fake_run_aims; adjust these to check for certain input settings + fake_run_aims_kwargs = {} + + # automatically use fake FHI-aims + mock_aims(ref_paths, fake_run_aims_kwargs) + + parameters = { + "k_grid": [2, 2, 2], + "species_dir": (species_dir / "light").as_posix(), + } + # generate job + maker = GWMaker(input_set_generator=GWSetGenerator(user_params=parameters)) + maker.name = "gw_o2" + job = maker.make(o2) + + # run the flow or job and ensure that it finished running successfully + responses = run_locally(job, create_folders=True, ensure_success=True) + + # validation the outputs of the job (maybe add gw energy levels as well) + output1 = responses[job.uuid][1].output + assert isinstance(output1, AimsTaskDoc) + assert output1.output.energy == pytest.approx(-4092.0702534) diff --git a/tests/aims/test_makers/test_relax.py b/tests/aims/test_makers/test_relax.py new file mode 100644 index 0000000000..9dbc0c247e --- /dev/null +++ b/tests/aims/test_makers/test_relax.py @@ -0,0 +1,71 @@ +import os + +import pytest +from jobflow import run_locally + +from atomate2.aims.jobs.core import RelaxMaker +from atomate2.aims.schemas.task import AimsTaskDoc + +cwd = os.getcwd() + + +def test_base_maker(tmp_path, species_dir, mock_aims, si): + # mapping from job name to directory containing test files + ref_paths = {"relax_si": "relax-si"} + + # settings passed to fake_run_aims; adjust these to check for certain input settings + fake_run_aims_kwargs = {} + + # automatically use fake FHI-aims + mock_aims(ref_paths, fake_run_aims_kwargs) + + parameters = { + "k_grid": [2, 2, 2], + "species_dir": (species_dir / "light").as_posix(), + } + # generate job + maker = RelaxMaker.full_relaxation(user_params=parameters) + maker.name = "relax_si" + job = maker.make(si) + + # run the flow or job and ensure that it finished running successfully + os.chdir(tmp_path) + responses = run_locally(job, create_folders=True, ensure_success=True) + os.chdir(cwd) + + # validation the outputs of the job + output1 = responses[job.uuid][1].output + assert isinstance(output1, AimsTaskDoc) + assert output1.output.energy == pytest.approx(-15800.2255448846) + + +def test_relax_fixed_cell_maker(tmp_path, species_dir, mock_aims, si): + # mapping from job name to directory containing test files + ref_paths = {"relax_fixed_cell_si": "relax-fixed-cell-si"} + + # settings passed to fake_run_aims; adjust these to check for certain input settings + fake_run_aims_kwargs = {} + + # automatically use fake FHI-aims + mock_aims(ref_paths, fake_run_aims_kwargs) + + parameters = { + "k_grid": [2, 2, 2], + "species_dir": (species_dir / "light").as_posix(), + } + # generate job + maker = RelaxMaker.fixed_cell_relaxation(user_params=parameters) + maker.name = "relax_fixed_cell_si" + structure = si.copy() + structure.frac_coords[0, 0] += 0.25 + job = maker.make(structure) + + # run the flow or job and ensure that it finished running successfully + os.chdir(tmp_path) + responses = run_locally(job, create_folders=True, ensure_success=True) + os.chdir(cwd) + + # validation the outputs of the job + output1 = responses[job.uuid][1].output + assert isinstance(output1, AimsTaskDoc) + assert output1.output.energy == pytest.approx(-15800.099741042) diff --git a/tests/aims/test_makers/test_socket_calc.py b/tests/aims/test_makers/test_socket_calc.py new file mode 100644 index 0000000000..90dd6ac9da --- /dev/null +++ b/tests/aims/test_makers/test_socket_calc.py @@ -0,0 +1,59 @@ +import os + +import pytest + +cwd = os.getcwd() + + +@pytest.mark.skip(reason="Currently not mocked and needs FHI-aims binary") +def test_static_socket_maker(si, species_dir, mock_aims, tmp_path): + from jobflow import run_locally + from pymatgen.io.aims.sets.core import SocketIOSetGenerator + + from atomate2.aims.jobs.core import SocketIOStaticMaker + from atomate2.aims.schemas.task import AimsTaskDoc + + atoms = si + atoms_list = [atoms, atoms.copy(), atoms.copy()] + atoms_list[1].positions[0, 0] += 0.02 + atoms_list[2].cell[:, :] *= 1.02 + + # mapping from job name to directory containing test files + ref_paths = {"socket": "socket_tests"} + + # settings passed to fake_run_aims; adjust these to check for certain input settings + fake_run_aims_kwargs = {} + + # automatically use fake FHI-aims + mock_aims(ref_paths, fake_run_aims_kwargs) + + parameters = { + "k_grid": [2, 2, 2], + "species_dir": (species_dir / "light").as_posix(), + } + # generate job + maker = SocketIOStaticMaker( + input_set_generator=SocketIOSetGenerator(user_params=parameters) + ) + maker.name = "socket" + job = maker.make(atoms_list) + + # run the flow or job and ensure that it finished running successfully + os.chdir(tmp_path) + responses = run_locally(job, create_folders=True, ensure_success=True) + os.chdir(cwd) + + # validation the outputs of the job + outputs = responses[job.uuid][1].output + assert isinstance(outputs, AimsTaskDoc) + assert len(outputs.output.trajectory) == 3 + assert outputs.output.trajectory[0].get_potential_energy() == pytest.approx( + -15800.0997410132 + ) + assert outputs.output.trajectory[1].get_potential_energy() == pytest.approx( + -15800.0962356206 + ) + assert outputs.output.trajectory[2].get_potential_energy() == pytest.approx( + -15800.1847237514 + ) + # assert output1.output.energy == pytest.approx(-15800.099740991) diff --git a/tests/aims/test_makers/test_static.py b/tests/aims/test_makers/test_static.py new file mode 100644 index 0000000000..24a3c02ff1 --- /dev/null +++ b/tests/aims/test_makers/test_static.py @@ -0,0 +1,43 @@ +"""Test various makers""" + +import os + +import pytest + +cwd = os.getcwd() + + +def test_static_maker(si, tmp_path, mock_aims, species_dir): + from jobflow import run_locally + from pymatgen.io.aims.sets.core import StaticSetGenerator + + from atomate2.aims.jobs.core import StaticMaker + from atomate2.aims.schemas.task import AimsTaskDoc + + # mapping from job name to directory containing test files + ref_paths = {"base": "static-si"} + + # settings passed to fake_run_aims; adjust these to check for certain input settings + fake_run_aims_kwargs = {} + + # automatically use fake FHI-aims + mock_aims(ref_paths, fake_run_aims_kwargs) + + parameters = { + "k_grid": [2, 2, 2], + "species_dir": (species_dir / "light").as_posix(), + } + # generate job + maker = StaticMaker(input_set_generator=StaticSetGenerator(user_params=parameters)) + maker.name = "base" + job = maker.make(si) + + # run the flow or job and ensure that it finished running successfully + os.chdir(tmp_path) + responses = run_locally(job, create_folders=True, ensure_success=True) + os.chdir(cwd) + + # validation the outputs of the job + output1 = responses[job.uuid][1].output + assert isinstance(output1, AimsTaskDoc) + assert output1.output.energy == pytest.approx(-15800.099740991) diff --git a/tests/aims/test_parsers/test_chunks.py b/tests/aims/test_parsers/test_chunks.py new file mode 100644 index 0000000000..6080905473 --- /dev/null +++ b/tests/aims/test_parsers/test_chunks.py @@ -0,0 +1 @@ +"""Deprecating""" diff --git a/tests/common/jobs/test_elastic.py b/tests/common/jobs/test_elastic.py index b152bc6b0d..6f2362083e 100644 --- a/tests/common/jobs/test_elastic.py +++ b/tests/common/jobs/test_elastic.py @@ -5,8 +5,11 @@ from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from atomate2 import SETTINGS -from atomate2.common.jobs.elastic import generate_elastic_deformations -from atomate2.common.schemas.elastic import _expand_strains +from atomate2.common.jobs.elastic import ( + fit_elastic_tensor, + generate_elastic_deformations, +) +from atomate2.common.schemas.elastic import ElasticWarnings, expand_strains @pytest.mark.parametrize("conventional", [False, True]) @@ -25,7 +28,7 @@ def test_reduce_expand_strains(clean_dir, symmetry_structure, conventional): dummy_stresses = [Stress(np.zeros((3, 3)))] * len(reduced_strains) dummy = ["dummy"] * len(reduced_strains) - recovered_strains, _, _, _ = _expand_strains( + recovered_strains, _, _, _ = expand_strains( structure, reduced_strains, stresses=dummy_stresses, @@ -54,3 +57,137 @@ def _get_strains(structure, sym_reduce): deformations = response[job.uuid][1].output return [d.green_lagrange_strain for d in deformations] + + +def test_fit_elastic_tensor(clean_dir, si_structure, caplog): + conventional = SpacegroupAnalyzer( + si_structure + ).get_conventional_standard_structure() + + deformation_data = [ + { + "stress": [ + [15.73376749, 0.0, 0.0], + [0.0, 6.40261126, 0.0], + [0.0, 0.0, 6.40261126], + ], + "deformation": [ + [0.9899494936611666, 0.0, 0.0], + [0.0, 1.0, 0.0], + [0.0, 0.0, 1.0], + ], + "uuid": "b7715382-9130-409c-ae2d-32a01321a0d0", + "job_dir": "a", + }, + { + "stress": [ + [7.74111679, 0.0, 0.0], + [0.0, 3.05807413, -0.0], + [0.0, -0.0, 3.05807413], + ], + "deformation": [ + [0.99498743710662, 0.0, 0.0], + [0.0, 1.0, 0.0], + [0.0, 0.0, 1.0], + ], + "uuid": "6cd2688c-764b-4a08-80f8-5c3ed75b91b9", + "job_dir": "b", + }, + { + "stress": [ + [-7.9262828, 0.0, -0.0], + [0.0, -3.20998817, 0.0], + [0.0, 0.0, -3.20998817], + ], + "deformation": [ + [1.004987562112089, 0.0, 0.0], + [0.0, 1.0, 0.0], + [0.0, 0.0, 1.0], + ], + "uuid": "fc3405d7-4171-4fe6-ab1b-086378ae6d0f", + "job_dir": "c", + }, + { + "stress": [ + [-15.60955466, 0.0, -0.0], + [0.0, -6.14725418, 0.0], + [-0.0, 0.0, -6.14725418], + ], + "deformation": [ + [1.0099504938362078, 0.0, 0.0], + [0.0, 1.0, 0.0], + [0.0, 0.0, 1.0], + ], + "uuid": "013d1100-f5b7-493b-b4ac-894c85733c7e", + "job_dir": "d", + }, + { + "stress": [ + [-0.21994363, 0.0, 0.0], + [0.0, -0.1846297, 14.80836455], + [0.0, 14.80836455, 0.40782339], + ], + "deformation": [ + [1.0, 0.0, 0.0], + [0.0, 1.0, -0.02], + [0.0, 0.0, 0.999799979995999], + ], + "uuid": "ab2857a6-188b-49a5-a90f-adfc30f884a7", + "job_dir": "e", + }, + { + "stress": [ + [-0.17602242, 0.0, 0.0], + [0.0, -0.16580315, 7.40412018], + [0.0, 7.40412018, -0.01771334], + ], + "deformation": [ + [1.0, 0.0, 0.0], + [0.0, 1.0, -0.01], + [0.0, 0.0, 0.9999499987499375], + ], + "uuid": "6cee0242-2ff6-4c02-afe8-9c0e8c0e37b7", + "job_dir": "f", + }, + ] + + job = fit_elastic_tensor(conventional, deformation_data) + + response = run_locally(job, ensure_success=True) + + elastic_out = response[job.uuid][1].output + assert elastic_out.fitting_data.failed_uuids == [] + assert elastic_out.warnings is None + assert len(set(elastic_out.fitting_data.uuids)) == 6 + + # test failure + # remove one of the outputs + deformation_data[0]["stress"] = None + job = fit_elastic_tensor(conventional, deformation_data, max_failed_deformations=2) + + response = run_locally(job, ensure_success=True) + + elastic_out = response[job.uuid][1].output + assert elastic_out.fitting_data.failed_uuids == [deformation_data[0]["uuid"]] + assert elastic_out.warnings == [ElasticWarnings.FAILED_PERTURBATIONS.value] + assert len(set(elastic_out.fitting_data.uuids)) == 5 + + job = fit_elastic_tensor(conventional, deformation_data, max_failed_deformations=0) + + response = run_locally(job, ensure_success=False) + + assert job.uuid not in response + assert "1 deformation calculations have failed, maximum allowed: 0" in caplog.text + + caplog.clear() + job = fit_elastic_tensor( + conventional, deformation_data, max_failed_deformations=0.01 + ) + + response = run_locally(job, ensure_success=False) + + assert job.uuid not in response + assert ( + "666666 fraction of deformation calculations have failed, " + "maximum fraction allowed: 0.01" in caplog.text + ) diff --git a/tests/common/jobs/test_eos.py b/tests/common/jobs/test_eos.py new file mode 100644 index 0000000000..5cead9608e --- /dev/null +++ b/tests/common/jobs/test_eos.py @@ -0,0 +1,156 @@ +from __future__ import annotations + +from typing import TYPE_CHECKING + +import numpy as np +from jobflow import run_locally +from pytest import approx + +from atomate2.common.jobs.eos import ( + PostProcessEosEnergy, + PostProcessEosPressure, + apply_strain_to_structure, +) + +if TYPE_CHECKING: + from collections.abc import Sequence + +# random params that are not unreasonable +_eos_test_pars = {"e0": -1.25e2, "b0": 85.0, "b1": 4.46, "v0": 11.15} + + +def taylor_energy( + v: float | Sequence, e0: float, b0: float, b1: float, v0: float +) -> float | Sequence: + """ + Taylor series expansion of an equation of state about the E(V) minimum. + + Parameters + ---------- + v : float | Sequence + A volume or list of volumes to evaluate the EOS at + e0 : float + The EOS minimum energy, i.e., E(V0), where V0 is the + equilibrium volume + b0 : float + The bulk modulus at V0 + b1 : float + The pressure derivative of the bulk modulus at V0 + v0: float + The equilibrium volume + + Rigorously, the EOS allows one to express E(V) as a Taylor series + E(V) = E0 + B0 V0/2 (V/V0 - 1)**2 - (1 + B1) B0 V0/6 (V/V0 - 1)**3 + ... + """ + eta = v / v0 - 1.0 + return e0 + b0 * v0 * eta**2 / 2.0 - (1.0 + b1) * b0 * v0 * eta**3 / 6.0 + + +def taylor_pressure( + v: float | Sequence, b0: float, b1: float, v0: float +) -> float | Sequence: + """ + Taylor series expansion of an equation of state about the p(V) zero. + + Parameters + ---------- + v : float | Sequence + A volume or list of volumes to evaluate the EOS at + e0 : float + The EOS minimum energy, i.e., E(V0), where V0 is the + equilibrium volume + b0 : float + The bulk modulus at V0 + b1 : float + The pressure derivative of the bulk modulus at V0 + v0: float + The equilibrium volume + + Rigorously, the EOS allows one to express p(V) as a Taylor series + p(V) = - d E / dV + = - B0 (V/V0 - 1) + (1 + B1) B0 /2 (V/V0 - 1)**2 + ... + """ + eta = v / v0 - 1.0 + return -b0 * eta + (1.0 + b1) * b0 * eta**2 / 2.0 + + +def test_postprocess_eos(clean_dir): + volumes = _eos_test_pars["v0"] * np.linspace(0.95, 1.05, 11) + energies = taylor_energy( + volumes, *[_eos_test_pars[key] for key in ("e0", "b0", "b1", "v0")] + ) + e_v_dict = { + "relax": { + "E0": _eos_test_pars["e0"], + "V0": _eos_test_pars["v0"], + "energy": list(energies), + "volume": list(volumes), + } + } + + # analysis_job = postprocess_eos(e_v_dict) + analysis_job = PostProcessEosEnergy().make(e_v_dict) + response = run_locally(analysis_job, create_folders=False, ensure_success=True) + job_output = response[analysis_job.uuid][1].output + assert set(job_output["relax"]) == {"E0", "V0", "energy", "volume", "EOS"} + assert set(job_output["relax"]["EOS"]) == { + "murnaghan", + "birch", + "birch_murnaghan", + "pourier_tarantola", + "vinet", + } + + # Testing that percent errors are less than 5%. Makes sense for + # testing EOS close to minimum, where Taylor series applies + for eos in job_output["relax"]["EOS"]: + assert all( + abs(job_output["relax"]["EOS"][eos][par] / _eos_test_pars[par] - 1.0) < 0.05 + for par in _eos_test_pars + ) + + +def test_postprocess_eos_pressure(clean_dir): + volumes = _eos_test_pars["v0"] * np.linspace(0.95, 1.05, 3) + pressures = taylor_pressure( + volumes, *[_eos_test_pars[key] for key in ("b0", "b1", "v0")] + ) + energies = taylor_energy( + volumes, *[_eos_test_pars[key] for key in ("e0", "b0", "b1", "v0")] + ) + + e_v_dict = { + "relax": { + "energy": list(energies), + "pressure": list(pressures), + "volume": list(volumes), + } + } + + analysis_job = PostProcessEosPressure().make(e_v_dict) + response = run_locally(analysis_job, create_folders=False, ensure_success=True) + job_output = response[analysis_job.uuid][1].output + assert set(job_output["relax"]) == {"energy", "volume", "pressure", "EOS"} + + # Testing that percent errors are less than 5%. Makes sense for + # testing EOS close to minimum, where Taylor series applies + assert all( + abs(job_output["relax"]["EOS"][par] / _eos_test_pars[par] - 1.0) < 0.05 + for par in ("b0", "b1", "v0") + ) + + +def test_apply_strain_to_structure(clean_dir, si_structure): + strains = [1.0 + eps for eps in (-0.05, 0.0, 0.05)] + + expected_volumes = [strain**3 * si_structure.volume for strain in strains] + deformations = [strain * np.identity(3) for strain in strains] + + job = apply_strain_to_structure(si_structure, deformations) + response = run_locally(job) + transformations = response[job.uuid][1].output + + assert all( + transformations[i].final_structure.volume == approx(expected) + for i, expected in enumerate(expected_volumes) + ) diff --git a/tests/common/jobs/test_phonon.py b/tests/common/jobs/test_phonon.py new file mode 100644 index 0000000000..c8b9ed86ac --- /dev/null +++ b/tests/common/jobs/test_phonon.py @@ -0,0 +1,14 @@ +from jobflow import run_locally +from numpy.testing import assert_allclose +from pymatgen.core.structure import Structure + +from atomate2.common.jobs.phonons import get_supercell_size + + +def test_phonon_get_supercell_size(clean_dir, si_structure: Structure): + job = get_supercell_size(si_structure, min_length=18, prefer_90_degrees=True) + + # run the flow or job and ensure that it finished running successfully + responses = run_locally(job, create_folders=True, ensure_success=True) + + assert_allclose(responses[job.uuid][1].output, [[6, -2, 0], [0, 6, 0], [-3, -2, 5]]) diff --git a/tests/common/schemas/test_cclib.py b/tests/common/schemas/test_cclib.py index 2561316ad2..bb34fd84bf 100644 --- a/tests/common/schemas/test_cclib.py +++ b/tests/common/schemas/test_cclib.py @@ -1,8 +1,12 @@ import gzip +import json import os import shutil import pytest +from monty.json import MontyDecoder, MontyEncoder, jsanitize + +from atomate2.common.schemas.cclib import TaskDocument try: import cclib @@ -12,10 +16,6 @@ @pytest.mark.skipif(cclib is None, reason="requires cclib to be installed") def test_cclib_taskdoc(test_dir): - from monty.json import MontyDecoder, jsanitize - - from atomate2.common.schemas.cclib import TaskDocument - p = test_dir / "schemas" # Plain parsing of task doc. We do not check all cclib entries @@ -36,24 +36,23 @@ def test_cclib_taskdoc(test_dir): assert doc["molecule"][0].coords == pytest.approx([0.397382, 0.0, 0.0]) assert doc["last_updated"] is not None assert doc["attributes"]["homo_energies"] == pytest.approx( - [-7.054007346511501, -11.618445074798501] + [-7.05400734, -11.61844507] ) assert doc["attributes"]["lumo_energies"] == pytest.approx( - [4.2384453353880005, -3.9423854660440005] + [4.23844533, -3.94238546] ) assert doc["attributes"]["homo_lumo_gaps"] == pytest.approx( - [11.292452681899501, 7.6760596087545006] + [11.29245268, 7.67605960] ) - assert doc["attributes"]["min_homo_lumo_gap"] == pytest.approx(7.6760596087545006) + assert doc["attributes"]["min_homo_lumo_gap"] == pytest.approx(7.67605960) # Now we will try two possible extensions, but we will make sure that # it fails because the newest log file (.txt) is not valid - with open(p / "test.txt", "w") as f: - f.write("I am a dummy log file") - with pytest.raises(Exception) as e: + with open(p / "test.txt", "w") as file: + file.write("I am a dummy log file") + with pytest.raises(ValueError, match="Could not parse"): doc = TaskDocument.from_logfile(p, [".log", ".txt"]).dict() os.remove(p / "test.txt") - assert "Could not parse" in str(e.value) # Test a population analysis doc = TaskDocument.from_logfile(p, "psi_test.out", analysis="MBO").dict() @@ -73,9 +72,10 @@ def test_cclib_taskdoc(test_dir): # Let's try a volumetric analysis # We'll gunzip the .cube.gz file because cclib can't read cube.gz files yet. # Can remove the gzip part when https://github.com/cclib/cclib/issues/108 is closed. - with gzip.open(p / "psi_test.cube.gz", "r") as f_in, open( - p / "psi_test.cube", "wb" - ) as f_out: + with ( + gzip.open(p / "psi_test.cube.gz", "r") as f_in, + open(p / "psi_test.cube", "wb") as f_out, + ): shutil.copyfileobj(f_in, f_out) doc = TaskDocument.from_logfile(p, "psi_test.out", analysis=["Bader"]).dict() os.remove(p / "psi_test.cube") @@ -101,3 +101,7 @@ def test_cclib_taskdoc(test_dir): # and decoded json_str = MontyDecoder().process_decoded(dct) assert "builder_meta=EmmetMeta" in json_str + + +def test_model_validate(): + TaskDocument.model_validate_json(json.dumps(TaskDocument(), cls=MontyEncoder)) diff --git a/tests/common/schemas/test_defect.py b/tests/common/schemas/test_defect.py index 931b3319db..4728e9dbd4 100644 --- a/tests/common/schemas/test_defect.py +++ b/tests/common/schemas/test_defect.py @@ -1,19 +1,44 @@ +import json + +import numpy as np +import pytest +from monty.json import MontyEncoder + +from atomate2.common.schemas.defects import ( + CCDDocument, + FormationEnergyDiagramDocument, + sort_pos_dist, +) + + def test_sort_pos_dist(): """ Test the sorting algorithm with a list of 2D positions. The algorithm should sort the list into a straight line depending on the direction of s1 and s2 """ - import numpy as np - - from atomate2.common.schemas.defects import sort_pos_dist def abs_d(s1, s2): return np.linalg.norm(np.array(s1) - np.array(s2)) points_on_line_2d = [(1, 1), (-2, -2), (0, 0), (2, 2), (-1, -1)] - r, d = sort_pos_dist(points_on_line_2d, s1=(0, 0), s2=(1.5, 1.5), dist=abs_d) - assert r == [(-2, -2), (-1, -1), (0, 0), (1, 1), (2, 2)] + sorted_pts, dists = sort_pos_dist( + points_on_line_2d, s1=(0, 0), s2=(1.5, 1.5), dist=abs_d + ) + assert sorted_pts == [(-2, -2), (-1, -1), (0, 0), (1, 1), (2, 2)] + assert dists == pytest.approx([-2.8284271, -1.4142135, 0, 1.41421356, 2.82842712]) + + sorted_pts, dists = sort_pos_dist( + points_on_line_2d, s1=(0, 0), s2=(-2.5, -2.5), dist=abs_d + ) + assert sorted_pts == [(2, 2), (1, 1), (0, 0), (-1, -1), (-2, -2)] + assert dists == pytest.approx([-2.8284271, -1.4142135, 0, 1.41421356, 2.82842712]) + - r, d = sort_pos_dist(points_on_line_2d, s1=(0, 0), s2=(-2.5, -2.5), dist=abs_d) - assert r == [(2, 2), (1, 1), (0, 0), (-1, -1), (-2, -2)] +# schemas where all fields have default values +@pytest.mark.parametrize( + "model_cls", + [FormationEnergyDiagramDocument, CCDDocument], +) +def test_model_validate(model_cls): + model_cls.model_validate_json(json.dumps(model_cls(), cls=MontyEncoder)) diff --git a/tests/common/schemas/test_elastic.py b/tests/common/schemas/test_elastic.py index c5b469fae6..f218e83034 100644 --- a/tests/common/schemas/test_elastic.py +++ b/tests/common/schemas/test_elastic.py @@ -1,10 +1,29 @@ -from atomate2.common.schemas.elastic import ElasticDocument +import json +import pytest +from monty.json import MontyEncoder + +from atomate2.common.schemas.elastic import ( + DerivedProperties, + ElasticDocument, + ElasticTensorDocument, + FittingData, +) -def test_elastic_document(test_dir): - import json +def test_elastic_document(test_dir): schema_path = test_dir / "schemas" / "elastic.json" schema_ref = json.loads(schema_path.read_text()) - ElasticDocument(**schema_ref) + doc = ElasticDocument(**schema_ref) + validated = ElasticDocument.model_validate_json(json.dumps(doc, cls=MontyEncoder)) + assert isinstance(validated, ElasticDocument) + + +# schemas where all fields have default values +@pytest.mark.parametrize( + "model_cls", + [ElasticDocument, ElasticTensorDocument, DerivedProperties, FittingData], +) +def test_model_validate(model_cls): + model_cls.model_validate_json(json.dumps(model_cls(), cls=MontyEncoder)) diff --git a/tests/common/schemas/test_phonons.py b/tests/common/schemas/test_phonons.py new file mode 100644 index 0000000000..649aa28c23 --- /dev/null +++ b/tests/common/schemas/test_phonons.py @@ -0,0 +1,60 @@ +import json + +import numpy as np +import pytest +from monty.json import MontyEncoder +from pydantic import ValidationError + +from atomate2.common.schemas.phonons import ( + PhononBSDOSDoc, + PhononComputationalSettings, + PhononJobDirs, + PhononUUIDs, + ThermalDisplacementData, +) + + +def test_thermal_displacement_data(): + doc = ThermalDisplacementData(freq_min_thermal_displacements=0.0) + validated = ThermalDisplacementData.model_validate_json( + json.dumps(doc, cls=MontyEncoder) + ) + assert isinstance(validated, ThermalDisplacementData) + + +def test_phonon_bs_dos_doc(): + kwargs = dict( + total_dft_energy=None, + supercell_matrix=np.eye(3), + primitive_matrix=np.eye(3), + code="test", + phonopy_settings=PhononComputationalSettings( + npoints_band=1, kpath_scheme="test", kpoint_density_dos=1 + ), + thermal_displacement_data=None, + jobdirs=None, + uuids=None, + ) + doc = PhononBSDOSDoc(**kwargs) + # check validation raises no errors + validated = PhononBSDOSDoc.model_validate_json(json.dumps(doc, cls=MontyEncoder)) + assert isinstance(validated, PhononBSDOSDoc) + + # test invalid supercell_matrix type fails + with pytest.raises(ValidationError): + doc = PhononBSDOSDoc(**kwargs | {"supercell_matrix": (1, 1, 1)}) + + # test optional material_id + doc = PhononBSDOSDoc(**kwargs | {"material_id": 1234}) + assert doc.material_id == 1234 + + # test extra="allow" option + doc = PhononBSDOSDoc(**kwargs | {"extra_field": "test"}) + assert doc.extra_field == "test" + + +# schemas where all fields have default values +@pytest.mark.parametrize("model_cls", [PhononJobDirs, PhononUUIDs]) +def test_model_validate(model_cls): + validated = model_cls.model_validate_json(json.dumps(model_cls(), cls=MontyEncoder)) + assert isinstance(validated, model_cls) diff --git a/tests/common/test_files.py b/tests/common/test_files.py index 2df1e4ce96..a3173ed1de 100644 --- a/tests/common/test_files.py +++ b/tests/common/test_files.py @@ -1,6 +1,9 @@ -def test_gunzip_force_overwrites(tmp_path): - from atomate2.common.files import gunzip_files, gzip_files +from pathlib import Path + +from atomate2.common.files import gunzip_files, gzip_files, gzip_output_folder + +def test_gunzip_force_overwrites(tmp_path): files = ["file1", "file2", "file3"] for fname in files: f = tmp_path / fname @@ -31,11 +34,7 @@ def test_gunzip_force_overwrites(tmp_path): def test_zip_outputs(tmp_dir): - from pathlib import Path - - from atomate2.common.files import gzip_output_folder - - for file_name in ["a", "b"]: + for file_name in ("a", "b"): (Path.cwd() / file_name).touch() gzip_output_folder(directory=Path.cwd(), setting=False, files_list=["a"]) diff --git a/tests/common/test_jobs.py b/tests/common/test_jobs.py index 08e4a40ab0..e860b4f065 100644 --- a/tests/common/test_jobs.py +++ b/tests/common/test_jobs.py @@ -1,13 +1,18 @@ import os +from datetime import datetime, timezone +from jobflow import run_locally +from pymatgen.core import Structure from pytest import approx, mark +from atomate2.common.jobs.utils import ( + retrieve_structure_from_materials_project, + structure_to_conventional, + structure_to_primitive, +) -def test_structure_to_primitive(si_structure): - from jobflow import run_locally - - from atomate2.common.jobs.utils import structure_to_primitive +def test_structure_to_primitive(si_structure): job = structure_to_primitive(si_structure) responses = run_locally(job) @@ -17,10 +22,6 @@ def test_structure_to_primitive(si_structure): def test_structure_to_conventional(si_structure): - from jobflow import run_locally - - from atomate2.common.jobs.utils import structure_to_conventional - job = structure_to_conventional(si_structure) responses = run_locally(job) @@ -34,13 +35,6 @@ def test_structure_to_conventional(si_structure): reason="Materials Project API key not set in environment.", ) def test_retrieve_structure_from_materials_project(): - from datetime import datetime - - from jobflow import run_locally - from pymatgen.core import Structure - - from atomate2.common.jobs.utils import retrieve_structure_from_materials_project - job = retrieve_structure_from_materials_project("mp-149") responses = run_locally(job) @@ -50,7 +44,9 @@ def test_retrieve_structure_from_materials_project(): assert isinstance(output, Structure) # test stored data is in expected format - datetime.strptime(stored_data["database_version"], "%Y.%m.%d") + datetime.strptime(stored_data["database_version"], "%Y.%m.%d").replace( + tzinfo=timezone.utc + ) assert stored_data["task_id"].startswith("mp-") job = retrieve_structure_from_materials_project( diff --git a/tests/common/test_settings.py b/tests/common/test_settings.py index 004adbdacc..40bc598ed8 100644 --- a/tests/common/test_settings.py +++ b/tests/common/test_settings.py @@ -1,35 +1,49 @@ +from pathlib import Path + import pytest from pydantic import ValidationError +from atomate2.settings import _DEFAULT_CONFIG_FILE_PATH, _ENV_PREFIX, Atomate2Settings -def test_empty_and_invalid_config_file(clean_dir): - import os - from pathlib import Path - from atomate2.settings import Atomate2Settings +def test_empty_and_invalid_config_file( + clean_dir, monkeypatch: pytest.MonkeyPatch, capsys: pytest.CaptureFixture[str] +): + # test no warning if config path is default and file does not exist + env_var_name = f"{_ENV_PREFIX.upper()}CONFIG_FILE" + monkeypatch.delenv(env_var_name, raising=False) + settings = Atomate2Settings() + assert settings.CONFIG_FILE == _DEFAULT_CONFIG_FILE_PATH + stdout, stderr = capsys.readouterr() + assert stdout == "" + assert stderr == "" - # set path to load settings from though ATOMATE2_CONFIG_FILE env variable + # set path to load settings from with ATOMATE2_CONFIG_FILE env variable config_file_path = Path.cwd() / "test-atomate2-config.yaml" - os.environ["ATOMATE2_CONFIG_FILE"] = str(config_file_path) + monkeypatch.setenv(env_var_name, str(config_file_path)) + + settings = Atomate2Settings() + assert str(config_file_path) == settings.CONFIG_FILE + assert settings.SYMPREC == 0.1 + assert settings.BANDGAP_TOL == 1e-4 + assert settings.VASP_RUN_BADER is False + assert settings.VASP_RUN_DDEC6 is False + assert settings.DDEC6_ATOMIC_DENSITIES_DIR is None - # test warning if config file is empty + # test warning if config file exists but is empty config_file_path.touch() - with pytest.warns( - UserWarning, match="Using atomate2 config file at .+ but it's empty" - ): + with pytest.warns(UserWarning, match=f"Using {env_var_name} at .+ but it's empty"): Atomate2Settings() # test error if the file exists and contains invalid YAML with open(config_file_path, "w") as file: file.write("invalid yaml") - - with pytest.raises(SyntaxError, match="atomate2 config file at"): + with pytest.raises(SyntaxError, match=f"{env_var_name} at"): Atomate2Settings() # test error if the file exists and contains invalid settings with open(config_file_path, "w") as file: file.write("VASP_CMD: 42") - with pytest.raises( ValidationError, match="1 validation error for Atomate2Settings\nVASP_CMD\n " @@ -37,12 +51,17 @@ def test_empty_and_invalid_config_file(clean_dir): ): Atomate2Settings() + # another invalid setting with open(config_file_path, "w") as file: file.write("BANDGAP_TOL: invalid") - with pytest.raises( ValidationError, match="1 validation error for Atomate2Settings\nBANDGAP_TOL\n " "Input should be a valid number", ): Atomate2Settings() + + # test warning if config path is non-default and file does not exist + config_file_path.unlink() + with pytest.warns(UserWarning, match=f"{env_var_name} at .+ does not exist"): + Atomate2Settings() diff --git a/tests/conftest.py b/tests/conftest.py index 85951de8af..66115a3a27 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,11 +1,24 @@ +import logging +import os +import shutil +import sys +import tempfile +from pathlib import Path +from unittest import mock + import pytest +from fireworks import LaunchPad +from jobflow import JobStore +from jobflow.settings import JobflowSettings +from maggma.stores import MemoryStore from monty.serialization import loadfn +from pymatgen.core import Structure + +from atomate2.utils.log import initialize_logger @pytest.fixture(scope="session") def test_dir(): - from pathlib import Path - module_dir = Path(__file__).resolve().parent test_dir = module_dir / "test_data" return test_dir.resolve() @@ -13,9 +26,6 @@ def test_dir(): @pytest.fixture(scope="session") def log_to_stdout(): - import logging - import sys - # Set Logging root = logging.getLogger() root.setLevel(logging.DEBUG) @@ -29,16 +39,12 @@ def log_to_stdout(): @pytest.fixture(scope="session") def clean_dir(debug_mode): - import os - import shutil - import tempfile - old_cwd = os.getcwd() new_path = tempfile.mkdtemp() os.chdir(new_path) yield if debug_mode: - print(f"Tests ran in {new_path}") + print(f"Tests ran in {new_path}") # noqa: T201 else: os.chdir(old_cwd) shutil.rmtree(new_path) @@ -47,9 +53,6 @@ def clean_dir(debug_mode): @pytest.fixture() def tmp_dir(): """Same as clean_dir but is fresh for every test""" - import os - import shutil - import tempfile old_cwd = os.getcwd() new_path = tempfile.mkdtemp() @@ -66,8 +69,6 @@ def debug_mode(): @pytest.fixture(scope="session") def lpad(database, debug_mode): - from fireworks import LaunchPad - lpad = LaunchPad(name=database) lpad.reset("", require_password=False) yield lpad @@ -80,9 +81,6 @@ def lpad(database, debug_mode): @pytest.fixture() def memory_jobstore(): - from jobflow import JobStore - from maggma.stores import MemoryStore - store = JobStore(MemoryStore(), additional_stores={"data": MemoryStore()}) store.connect() @@ -91,24 +89,27 @@ def memory_jobstore(): @pytest.fixture(scope="session", autouse=True) def log_to_stdout_auto_use(): - from atomate2.utils.log import initialize_logger - initialize_logger() @pytest.fixture() def si_structure(test_dir): - from pymatgen.core import Structure - return Structure.from_file(test_dir / "structures" / "Si.cif") +@pytest.fixture() +def sr_ti_o3_structure(test_dir): + return Structure.from_file(test_dir / "structures" / "SrTiO3.cif") + + +@pytest.fixture() +def ba_ti_o3_structure(test_dir): + return Structure.from_file(test_dir / "structures" / "BaTiO3.cif") + + @pytest.fixture(autouse=True) def mock_jobflow_settings(memory_jobstore): """Mock the jobflow settings to use our specific jobstore (with data store).""" - from unittest import mock - - from jobflow.settings import JobflowSettings settings = JobflowSettings(JOB_STORE=memory_jobstore) @@ -154,3 +155,13 @@ def symmetry_structure(test_dir, request): See https://github.com/hackingmaterials/amset/blob/main/tests/conftest.py """ return loadfn(test_dir / "symmetry_structures" / f"{request.param}.json.gz") + + +def pytest_addoption(parser): + parser.addoption( + "--abinit-integration", + action="store_true", + default=False, + help="Run abinit integration tests. " + "This basically runs the same tests but without the mocking.", + ) diff --git a/tests/cp2k/conftest.py b/tests/cp2k/conftest.py index 734b18aa8e..cb6403ff91 100644 --- a/tests/cp2k/conftest.py +++ b/tests/cp2k/conftest.py @@ -135,7 +135,7 @@ def fake_run_cp2k( input_settings: Sequence[str] = (), check_inputs: Sequence[Literal["cp2k.inp"]] = _VFILES, clear_inputs: bool = True, -): +) -> None: """ Emulate running CP2K and validate CP2K input files. @@ -171,16 +171,16 @@ def fake_run_cp2k( @pytest.fixture() def check_input(): - def _check_input(ref_path, user_input): - from pymatgen.io.cp2k.inputs import Cp2kInput + from pymatgen.io.cp2k.inputs import Cp2kInput - ref = Cp2kInput.from_file(ref_path / "inputs" / "cp2k.inp") + def _check_input(ref_path, user_input: Cp2kInput): + ref_input = Cp2kInput.from_file(ref_path / "inputs" / "cp2k.inp") user_input.verbosity(verbosity=False) - ref.verbosity(verbosity=False) - user_string = " ".join(user_input.get_string().lower().split()) + ref_input.verbosity(verbosity=False) + user_string = " ".join(user_input.get_str().lower().split()) user_hash = md5(user_string.encode("utf-8")).hexdigest() - ref_string = " ".join(ref.get_string().lower().split()) + ref_string = " ".join(ref_input.get_str().lower().split()) ref_hash = md5(ref_string.encode("utf-8")).hexdigest() if ref_hash != user_hash: @@ -190,10 +190,7 @@ def _check_input(ref_path, user_input): def clear_cp2k_inputs(): - for cp2k_file in ( - "cp2k.inp", - "cp2k.out", - ): + for cp2k_file in ("cp2k.inp", "cp2k.out"): if Path(cp2k_file).exists(): Path(cp2k_file).unlink() logger.info("Cleared cp2k inputs") diff --git a/tests/cp2k/jobs/test_core.py b/tests/cp2k/jobs/test_core.py index c7afa23e05..c3b6139d05 100644 --- a/tests/cp2k/jobs/test_core.py +++ b/tests/cp2k/jobs/test_core.py @@ -32,7 +32,7 @@ def test_static_maker(tmp_path, mock_cp2k, si_structure, basis_and_potential): # validate job outputs output1 = responses[job.uuid][1].output assert isinstance(output1, TaskDocument) - assert output1.output.energy == approx(-214.23651374775685) + assert output1.output.energy == approx(-214.23651374) def test_relax_maker(tmp_path, mock_cp2k, basis_and_potential, si_structure): @@ -66,7 +66,7 @@ def test_relax_maker(tmp_path, mock_cp2k, basis_and_potential, si_structure): # validate job outputs output1 = responses[job.uuid][1].output assert isinstance(output1, TaskDocument) - assert output1.output.energy == approx(-193.39161102270234) + assert output1.output.energy == approx(-193.39161102) assert len(output1.calcs_reversed[0].output.ionic_steps) == 1 assert output1.calcs_reversed[0].output.structure.lattice.abc == approx( si_structure.lattice.abc @@ -106,7 +106,7 @@ def test_transmuter(tmp_path, mock_cp2k, basis_and_potential, si_structure): # validate outputs output1 = responses[job.uuid][1].output assert isinstance(output1, TaskDocument) - assert output1.output.energy == approx(-404.0823179177859) + assert output1.output.energy == approx(-404.08231791) assert output1.transformations["history"][0]["scaling_matrix"] == [ [1, 0, 0], [0, 1, 0], diff --git a/tests/cp2k/sets/test_base.py b/tests/cp2k/sets/test_base.py index d2d4aece6a..05fe0a8953 100644 --- a/tests/cp2k/sets/test_base.py +++ b/tests/cp2k/sets/test_base.py @@ -9,9 +9,9 @@ def test_cp2k_input_set(cp2k_test_dir, cp2k_test_inputs): def test_recursive_update(): from atomate2.cp2k.sets.base import recursive_update - d = {"activate_hybrid": {"hybrid_functional": "HSE06"}} - u = {"activate_hybrid": {"cutoff_radius": 8}} - dnew = recursive_update(d, u) + in_dict = {"activate_hybrid": {"hybrid_functional": "HSE06"}} + update_dict = {"activate_hybrid": {"cutoff_radius": 8}} + actual = recursive_update(in_dict, update_dict) - assert dnew["activate_hybrid"]["hybrid_functional"] == "HSE06" - assert dnew["activate_hybrid"]["cutoff_radius"] == 8 + expected = {"activate_hybrid": {"hybrid_functional": "HSE06", "cutoff_radius": 8}} + assert actual == expected diff --git a/tests/cp2k/sets/test_core.py b/tests/cp2k/sets/test_core.py index 42aca1baa6..48a5de33a3 100644 --- a/tests/cp2k/sets/test_core.py +++ b/tests/cp2k/sets/test_core.py @@ -13,18 +13,18 @@ def test_input_generators(si_structure, basis_and_potential): StaticSetGenerator, ) - for gen in [ + for gen in ( StaticSetGenerator(user_input_settings=basis_and_potential), HybridStaticSetGenerator(user_input_settings=basis_and_potential), - ]: + ): input_set = gen.get_input_set(si_structure) assert input_set.cp2k_input["GLOBAL"]["RUN_TYPE"].values[0] == "ENERGY_FORCE" assert input_set.cp2k_input.check("FORCE_EVAL/DFT/KPOINTS") - for gen in [ + for gen in ( RelaxSetGenerator(user_input_settings=basis_and_potential), HybridRelaxSetGenerator(user_input_settings=basis_and_potential), - ]: + ): input_set = gen.get_input_set(si_structure) assert input_set.cp2k_input["GLOBAL"]["RUN_TYPE"].values[0] == "GEO_OPT" assert input_set.cp2k_input.get("MOTION") @@ -32,10 +32,10 @@ def test_input_generators(si_structure, basis_and_potential): 0 ] == pytest.approx(0.1) - for gen in [ + for gen in ( CellOptSetGenerator(user_input_settings=basis_and_potential), HybridCellOptSetGenerator(user_input_settings=basis_and_potential), - ]: + ): input_set = gen.get_input_set(si_structure) assert input_set.cp2k_input["GLOBAL"]["RUN_TYPE"].values[0] == "CELL_OPT" diff --git a/tests/cp2k/test_powerups.py b/tests/cp2k/test_powerups.py index e3b74bb819..587bff8e8d 100644 --- a/tests/cp2k/test_powerups.py +++ b/tests/cp2k/test_powerups.py @@ -60,3 +60,43 @@ def test_update_user_settings(powerup, attribute, settings): getattr(flow.jobs[1].function.__self__.input_set_generator, attribute) != settings ) + + +@pytest.mark.parametrize( + "powerup,settings", + [ + ("add_metadata_to_flow", {"mp-id": "mp-xxx"}), + ("add_metadata_to_flow", {"mp-id": "mp-170", "composition": "NaCl"}), + ], +) +def test_add_metadata_to_flow(powerup, settings): + from atomate2.cp2k import powerups + from atomate2.cp2k.flows.core import DoubleRelaxMaker + + powerup_func = getattr(powerups, powerup) + + # test flow + drm = DoubleRelaxMaker() + flow = drm.make(1) + flow = powerup_func(flow, settings) + assert ( + flow.jobs[0].function.__self__.task_document_kwargs["additional_fields"] + == settings + ) + + +@pytest.mark.parametrize( + "powerup, settings", + [("update_cp2k_custodian_handlers", ())], +) +def test_update_cp2k_custodian_handlers(powerup, settings): + from atomate2.cp2k import powerups + from atomate2.cp2k.flows.core import DoubleRelaxMaker + + powerup_func = getattr(powerups, powerup) + + # test flow + drm = DoubleRelaxMaker() + flow = drm.make(1) + flow = powerup_func(flow, settings) + assert flow.jobs[0].function.__self__.run_cp2k_kwargs["handlers"] == settings diff --git a/tests/forcefields/flows/test_elastic.py b/tests/forcefields/flows/test_elastic.py index bd4c29848c..dea097eb95 100644 --- a/tests/forcefields/flows/test_elastic.py +++ b/tests/forcefields/flows/test_elastic.py @@ -1,30 +1,33 @@ -def test_elastic_wf(clean_dir, si_structure): - from jobflow import run_locally - from numpy.testing import assert_allclose - from pymatgen.symmetry.analyzer import SpacegroupAnalyzer +import pytest +from jobflow import run_locally +from pymatgen.symmetry.analyzer import SpacegroupAnalyzer - from atomate2.common.schemas.elastic import ElasticDocument - from atomate2.forcefields.flows.elastic import ElasticMaker - from atomate2.forcefields.jobs import M3GNetRelaxMaker +from atomate2.common.schemas.elastic import ElasticDocument +from atomate2.forcefields.flows.elastic import ElasticMaker +from atomate2.forcefields.jobs import MACERelaxMaker + +def test_elastic_wf_with_mace(clean_dir, si_structure, test_dir): si_prim = SpacegroupAnalyzer(si_structure).get_primitive_standard_structure() + model_path = f"{test_dir}/forcefields/mace/MACE.model" + common_kwds = dict( + calculator_kwargs={"model": model_path, "default_dtype": "float64"}, + relax_kwargs={"fmax": 0.00001}, + ) - # !!! Generate job - job = ElasticMaker( - bulk_relax_maker=M3GNetRelaxMaker( - relax_cell=True, relax_kwargs={"fmax": 0.00001} - ), - elastic_relax_maker=M3GNetRelaxMaker( - relax_cell=False, relax_kwargs={"fmax": 0.00001} - ), + flow = ElasticMaker( + bulk_relax_maker=MACERelaxMaker(**common_kwds, relax_cell=True), + elastic_relax_maker=MACERelaxMaker(**common_kwds, relax_cell=False), ).make(si_prim) # run the flow or job and ensure that it finished running successfully - responses = run_locally(job, create_folders=True, ensure_success=True) - elastic_output = responses[job.jobs[-1].uuid][1].output + responses = run_locally(flow, create_folders=True, ensure_success=True) + elastic_output = responses[flow[-1].uuid][1].output assert isinstance(elastic_output, ElasticDocument) - assert_allclose(elastic_output.derived_properties.k_voigt, 118.26914, atol=1e-1) - assert_allclose( - elastic_output.derived_properties.g_voigt, 17.327374125417816, atol=1e-1 + assert elastic_output.derived_properties.k_voigt == pytest.approx( + 9.7005429, abs=0.01 + ) + assert elastic_output.derived_properties.g_voigt == pytest.approx( + 0.002005039, abs=0.01 ) assert elastic_output.chemsys == "Si" diff --git a/tests/forcefields/flows/test_eos.py b/tests/forcefields/flows/test_eos.py new file mode 100644 index 0000000000..ef7f565663 --- /dev/null +++ b/tests/forcefields/flows/test_eos.py @@ -0,0 +1,35 @@ +import pytest +import torch +from jobflow import run_locally +from monty.serialization import loadfn + +from atomate2.forcefields.flows.eos import CHGNetEosMaker, M3GNetEosMaker, MACEEosMaker + +_mlff_to_maker = { + "CHGNet": CHGNetEosMaker, + "M3GNet": M3GNetEosMaker, + "MACE": MACEEosMaker, +} + + +@pytest.mark.parametrize("mlff", list(_mlff_to_maker)) +def test_ml_ff_eos_makers(mlff: str, si_structure, clean_dir, test_dir): + # MACE changes the default dtype, ensure consistent dtype here + torch.set_default_dtype(torch.float32) + + job = _mlff_to_maker[mlff]().make(si_structure) + job_to_uuid = {job.name: job.uuid for job in job.jobs} + postprocess_uuid = job_to_uuid[f"{mlff} EOS Maker postprocessing"] + response = run_locally(job, ensure_success=True) + output = response[postprocess_uuid][1].output + + ref_data = loadfn(f"{test_dir}/forcefields/eos/{mlff}_Si_eos.json.gz") + + for key in ref_data["relax"]: + if isinstance(key, float): + assert output["relax"][key] == pytest.approx(ref_data["relax"][key]) + elif isinstance(key, list): + assert all( + output["relax"][key][i] == pytest.approx(value) + for i, value in ref_data["relax"][key].items() + ) diff --git a/tests/forcefields/flows/test_phonon.py b/tests/forcefields/flows/test_phonon.py index c18cb86622..b1eea9462e 100644 --- a/tests/forcefields/flows/test_phonon.py +++ b/tests/forcefields/flows/test_phonon.py @@ -1,3 +1,8 @@ +import os +from pathlib import Path + +import torch +from jobflow import run_locally from numpy.testing import assert_allclose from pymatgen.core.structure import Structure from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine @@ -12,89 +17,79 @@ from atomate2.forcefields.flows.phonons import PhononMaker -def test_phonon_wf(clean_dir): - from jobflow import run_locally - - structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) +def test_phonon_wf_force_field(clean_dir, si_structure: Structure, tmp_path: Path): + # TODO brittle due to inability to adjust dtypes in CHGNetRelaxMaker + torch.set_default_dtype(torch.float32) - job = PhononMaker( + flow = PhononMaker( use_symmetrized_structure="conventional", create_thermal_displacements=False, store_force_constants=False, prefer_90_degrees=False, - generate_frequencies_eigenvectors_kwargs={"tstep": 100}, - ).make(structure) + generate_frequencies_eigenvectors_kwargs={ + "tstep": 100, + "filename_bs": (filename_bs := f"{tmp_path}/phonon_bs_test.png"), + "filename_dos": (filename_dos := f"{tmp_path}/phonon_dos_test.pdf"), + }, + ).make(si_structure) # run the flow or job and ensure that it finished running successfully - responses = run_locally(job, create_folders=True, ensure_success=True) + responses = run_locally(flow, create_folders=True, ensure_success=True) # validate the outputs - assert isinstance(responses[job.jobs[-1].uuid][1].output, PhononBSDOSDoc) + ph_bs_dos_doc = responses[flow[-1].uuid][1].output + assert isinstance(ph_bs_dos_doc, PhononBSDOSDoc) assert_allclose( - responses[job.jobs[-1].uuid][1].output.free_energies, + ph_bs_dos_doc.free_energies, [5058.4521752, 4907.4957516, 3966.5493299, 2157.8178928, -357.5054580], - rtol=0.08, + atol=1000, ) - assert isinstance( - responses[job.jobs[-1].uuid][1].output.phonon_bandstructure, - PhononBandStructureSymmLine, - ) - assert isinstance(responses[job.jobs[-1].uuid][1].output.phonon_dos, PhononDos) - assert responses[job.jobs[-1].uuid][1].output.thermal_displacement_data is None - assert isinstance(responses[job.jobs[-1].uuid][1].output.structure, Structure) - assert_allclose( - responses[job.jobs[-1].uuid][1].output.temperatures, [0, 100, 200, 300, 400] - ) - assert responses[job.jobs[-1].uuid][1].output.force_constants is None - assert isinstance(responses[job.jobs[-1].uuid][1].output.jobdirs, PhononJobDirs) - assert isinstance(responses[job.jobs[-1].uuid][1].output.uuids, PhononUUIDs) - assert_allclose( - responses[job.jobs[-1].uuid][1].output.total_dft_energy, -5.372457981109619, 4 - ) - assert responses[job.jobs[-1].uuid][1].output.born is None - assert responses[job.jobs[-1].uuid][1].output.epsilon_static is None + ph_band_struct = ph_bs_dos_doc.phonon_bandstructure + assert isinstance(ph_band_struct, PhononBandStructureSymmLine) + + ph_dos = ph_bs_dos_doc.phonon_dos + assert isinstance(ph_dos, PhononDos) + assert ph_bs_dos_doc.thermal_displacement_data is None + assert isinstance(ph_bs_dos_doc.structure, Structure) + assert_allclose(ph_bs_dos_doc.temperatures, [0, 100, 200, 300, 400]) + assert ph_bs_dos_doc.force_constants is None + assert isinstance(ph_bs_dos_doc.jobdirs, PhononJobDirs) + assert isinstance(ph_bs_dos_doc.uuids, PhononUUIDs) + assert_allclose(ph_bs_dos_doc.total_dft_energy, -5.37245798, 4) + assert ph_bs_dos_doc.born is None + assert ph_bs_dos_doc.epsilon_static is None assert_allclose( - responses[job.jobs[-1].uuid][1].output.supercell_matrix, + ph_bs_dos_doc.supercell_matrix, [[4.0, 0.0, 0.0], [0.0, 4.0, 0.0], [0.0, 0.0, 4.0]], ) assert_allclose( - responses[job.jobs[-1].uuid][1].output.primitive_matrix, + ph_bs_dos_doc.primitive_matrix, ((0, 0.5, 0.5), (0.5, 0.0, 0.5), (0.5, 0.5, 0.0)), atol=1e-8, ) - assert responses[job.jobs[-1].uuid][1].output.code == "vasp" - assert isinstance( - responses[job.jobs[-1].uuid][1].output.phonopy_settings, - PhononComputationalSettings, - ) - assert responses[job.jobs[-1].uuid][1].output.phonopy_settings.npoints_band == 101 - assert ( - responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpath_scheme - == "seekpath" - ) - assert ( - responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpoint_density_dos - == 7000 - ) + assert ph_bs_dos_doc.code == "forcefields" + assert isinstance(ph_bs_dos_doc.phonopy_settings, PhononComputationalSettings) + assert ph_bs_dos_doc.phonopy_settings.npoints_band == 101 + assert ph_bs_dos_doc.phonopy_settings.kpath_scheme == "seekpath" + assert ph_bs_dos_doc.phonopy_settings.kpoint_density_dos == 7_000 assert_allclose( - responses[job.jobs[-1].uuid][1].output.entropies, - [0.0, 4.7839398173, 13.993186953, 21.886413347, 28.191106671], - rtol=0.05, + ph_bs_dos_doc.entropies, + [0.0, 4.78393981, 13.99318695, 21.88641334, 28.19110667], + atol=2, ) assert_allclose( - responses[job.jobs[-1].uuid][1].output.heat_capacities, - [0.0, 8.8606058656, 17.557589434, 21.089039169, 22.625872713], - rtol=0.05, + ph_bs_dos_doc.heat_capacities, + [0.0, 8.86060586, 17.55758943, 21.08903916, 22.62587271], + atol=2, ) - assert_allclose( - responses[job.jobs[-1].uuid][1].output.internal_energies, + ph_bs_dos_doc.internal_energies, [5058.44158791, 5385.88058579, 6765.19854165, 8723.78588089, 10919.0199409], - rtol=0.05, + atol=1000, ) + + # check phonon plots exist + assert os.path.isfile(filename_bs) + assert os.path.isfile(filename_dos) diff --git a/tests/forcefields/test_jobs.py b/tests/forcefields/test_jobs.py index f78bd3a9d2..310a9132ca 100644 --- a/tests/forcefields/test_jobs.py +++ b/tests/forcefields/test_jobs.py @@ -1,14 +1,28 @@ +from importlib.metadata import version as get_imported_version +from pathlib import Path + +import pytest +from jobflow import run_locally +from pymatgen.core import Structure +from pymatgen.symmetry.analyzer import SpacegroupAnalyzer from pytest import approx, importorskip -importorskip("quippy") +from atomate2.forcefields.jobs import ( + CHGNetRelaxMaker, + CHGNetStaticMaker, + GAPRelaxMaker, + GAPStaticMaker, + M3GNetRelaxMaker, + M3GNetStaticMaker, + MACERelaxMaker, + MACEStaticMaker, + NequipRelaxMaker, + NequipStaticMaker, +) +from atomate2.forcefields.schemas import ForceFieldTaskDocument def test_chgnet_static_maker(si_structure): - from jobflow import run_locally - - from atomate2.forcefields.jobs import CHGNetStaticMaker - from atomate2.forcefields.schemas import ForceFieldTaskDocument - task_doc_kwargs = {"ionic_step_data": ("structure", "energy")} # generate job @@ -20,22 +34,52 @@ def test_chgnet_static_maker(si_structure): # validate job outputs output1 = responses[job.uuid][1].output assert isinstance(output1, ForceFieldTaskDocument) - assert output1.output.energy == approx(-10.7452, rel=1e-4) + assert output1.output.energy == approx(-10.6275062, rel=1e-4) assert output1.output.ionic_steps[-1].magmoms is None assert output1.output.n_steps == 1 - -def test_chgnet_relax_maker(si_structure): - from jobflow import run_locally - - from atomate2.forcefields.jobs import CHGNetRelaxMaker - from atomate2.forcefields.schemas import ForceFieldTaskDocument - + assert output1.forcefield_version == get_imported_version("chgnet") + + +@pytest.mark.parametrize( + "fix_symmetry, symprec", [(True, 1e-2), (False, 1e-2), (True, 1e-1)] +) +def test_chgnet_relax_maker_fix_symmetry( + ba_ti_o3_structure: Structure, + fix_symmetry: bool, + symprec: float, +): + # translate one atom to break symmetry but stay below symprec threshold + ba_ti_o3_structure.translate_sites(1, [symprec / 10.0, 0, 0]) + job = CHGNetRelaxMaker( + relax_kwargs={"fmax": 0.01}, + fix_symmetry=fix_symmetry, + symprec=symprec, + ).make(ba_ti_o3_structure) + # get space group number of input structure + initial_space_group = SpacegroupAnalyzer( + ba_ti_o3_structure, symprec=symprec + ).get_space_group_number() + responses = run_locally(job, ensure_success=True) + output1 = responses[job.uuid][1].output + assert output1.is_force_converged + final_space_group = SpacegroupAnalyzer( + output1.output.structure, symprec=symprec + ).get_space_group_number() + if fix_symmetry: + assert initial_space_group == final_space_group + else: + assert initial_space_group != final_space_group + + +@pytest.mark.parametrize("relax_cell", [True, False]) +def test_chgnet_relax_maker(si_structure: Structure, relax_cell: bool): # translate one atom to ensure a small number of relaxation steps are taken si_structure.translate_sites(0, [0, 0, 0.1]) + max_step = 25 # generate job - job = CHGNetRelaxMaker(steps=25).make(si_structure) + job = CHGNetRelaxMaker(steps=max_step, relax_cell=relax_cell).make(si_structure) # run the flow or job and ensure that it finished running successfully responses = run_locally(job, ensure_success=True) @@ -43,17 +87,22 @@ def test_chgnet_relax_maker(si_structure): # validate job outputs output1 = responses[job.uuid][1].output assert isinstance(output1, ForceFieldTaskDocument) - assert output1.output.energy == approx(-10.74523544, rel=1e-4) - assert output1.output.ionic_steps[-1].magmoms[0] == approx(0.00211287, rel=1e-4) - assert output1.output.n_steps == 12 + if relax_cell: + assert not output1.is_force_converged + assert output1.output.n_steps == max_step + 2 + assert output1.output.energy == approx(-10.62461, abs=1e-2) + assert output1.output.ionic_steps[-1].magmoms[0] == approx(0.00251674, rel=1e-1) + else: + assert output1.is_force_converged + assert output1.output.n_steps == 13 + assert output1.output.energy == approx(-10.6274, rel=1e-2) + assert output1.output.ionic_steps[-1].magmoms[0] == approx(0.00303572, rel=1e-2) + # check the force_field_task_doc attributes + assert Path(responses[job.uuid][1].output.dir_name).exists() -def test_m3gnet_static_maker(si_structure): - from jobflow import run_locally - - from atomate2.forcefields.jobs import M3GNetStaticMaker - from atomate2.forcefields.schemas import ForceFieldTaskDocument +def test_m3gnet_static_maker(si_structure): task_doc_kwargs = {"ionic_step_data": ("structure", "energy")} # generate job @@ -68,18 +117,16 @@ def test_m3gnet_static_maker(si_structure): assert output1.output.energy == approx(-10.8, abs=0.2) assert output1.output.n_steps == 1 + assert output1.forcefield_version == get_imported_version("matgl") -def test_m3gnet_relax_maker(si_structure): - from jobflow import run_locally - - from atomate2.forcefields.jobs import M3GNetRelaxMaker - from atomate2.forcefields.schemas import ForceFieldTaskDocument +def test_m3gnet_relax_maker(si_structure): # translate one atom to ensure a small number of relaxation steps are taken si_structure.translate_sites(0, [0, 0, 0.1]) # generate job - job = M3GNetRelaxMaker(steps=25).make(si_structure) + max_step = 25 + job = M3GNetRelaxMaker(steps=max_step).make(si_structure) # run the flow or job and ensure that it finished running successfully responses = run_locally(job, ensure_success=True) @@ -87,25 +134,153 @@ def test_m3gnet_relax_maker(si_structure): # validate job outputs output1 = responses[job.uuid][1].output assert isinstance(output1, ForceFieldTaskDocument) + assert output1.is_force_converged assert output1.output.energy == approx(-10.8, abs=0.2) - assert output1.output.n_steps == 14 + assert output1.output.n_steps == 24 + + +mace_paths = pytest.mark.parametrize( + "model", + [ + # None, # TODO uncomment once https://github.com/ACEsuit/mace/pull/230 is merged + # to test loading MACE checkpoint on the fly from figshare + f"{Path(__file__).parent.parent}/test_data/forcefields/mace/MACE.model", + ], +) + + +@mace_paths +def test_mace_static_maker(si_structure: Structure, test_dir: Path, model): + task_doc_kwargs = {"ionic_step_data": ("structure", "energy")} + + # generate job + # NOTE the test model is not trained on Si, so the energy is not accurate + job = MACEStaticMaker( + calculator_kwargs={"model": model}, task_document_kwargs=task_doc_kwargs + ).make(si_structure) + + # run the flow or job and ensure that it finished running successfully + responses = run_locally(job, ensure_success=True) + + # validation the outputs of the job + output1 = responses[job.uuid][1].output + assert isinstance(output1, ForceFieldTaskDocument) + assert output1.output.energy == approx(-0.068231, rel=1e-4) + assert output1.output.n_steps == 1 + assert output1.forcefield_version == get_imported_version("mace-torch") + + +@pytest.mark.parametrize( + "fix_symmetry, symprec", [(True, 1e-2), (False, 1e-2), (True, 1e-1)] +) +def test_mace_relax_maker_fix_symmetry( + ba_ti_o3_structure: Structure, + fix_symmetry: bool, + symprec: float, +): + # translate one atom to break symmetry but stay below symprec threshold + ba_ti_o3_structure.translate_sites(1, [symprec / 10.0, 0, 0]) + job = MACERelaxMaker( + relax_kwargs={"fmax": 0.02}, + fix_symmetry=fix_symmetry, + symprec=symprec, + ).make(ba_ti_o3_structure) + # get space group number of input structure + initial_space_group = SpacegroupAnalyzer( + ba_ti_o3_structure, symprec=symprec + ).get_space_group_number() + responses = run_locally(job, ensure_success=True) + output1 = responses[job.uuid][1].output + assert output1.is_force_converged + final_space_group = SpacegroupAnalyzer( + output1.output.structure, symprec=symprec + ).get_space_group_number() + if fix_symmetry: + assert initial_space_group == final_space_group + else: + assert initial_space_group != final_space_group + + +@pytest.mark.parametrize( + "fix_symmetry, symprec", [(True, 1e-2), (False, 1e-2), (True, 1e-1)] +) +@pytest.mark.parametrize("relax_cell", [True, False]) +@mace_paths +def test_mace_relax_maker( + si_structure: Structure, + model, + relax_cell: bool, + fix_symmetry: bool, + symprec: float, +): + from ase.spacegroup.symmetrize import check_symmetry, is_subgroup + + _, init_spg_num = si_structure.get_space_group_info() + assert init_spg_num == 227 + + # translate one atom to ensure a small number of relaxation steps are taken + si_structure.translate_sites(0, [0, 0, 0.1]) + + _, init_spg_num = si_structure.get_space_group_info() + assert init_spg_num == 12 + + # generate job + # NOTE the test model is not trained on Si, so the energy is not accurate + job = MACERelaxMaker( + calculator_kwargs={"model": model}, + steps=25, + optimizer_kwargs={"optimizer": "BFGSLineSearch"}, + relax_cell=relax_cell, + fix_symmetry=fix_symmetry, + symprec=symprec, + relax_kwargs={"fmax": 0.04}, + ).make(si_structure) + + # run the flow or job and ensure that it finished running successfully + responses = run_locally(job, ensure_success=True) + + # validating the outputs of the job + output1 = responses[job.uuid][1].output + assert output1.is_force_converged + assert isinstance(output1, ForceFieldTaskDocument) + + si_atoms = si_structure.to_ase_atoms() + symmetry_ops_init = check_symmetry(si_atoms, symprec=1.0e-3) + si_atoms_final = output1.output.structure.to_ase_atoms() + symmetry_ops_final = check_symmetry(si_atoms_final, symprec=1.0e-3) + # get space group number of input structure + _, final_spg_num = output1.output.structure.get_space_group_info() + if relax_cell: + assert final_spg_num == 12 + else: + assert final_spg_num == 74 -def test_gap_static_maker(si_structure, test_dir): - from jobflow import run_locally + if fix_symmetry: # if symmetry is fixed, the symmetry should be the same or higher + assert is_subgroup(symmetry_ops_init, symmetry_ops_final) + else: # if symmetry is not fixed, it can both increase or decrease + assert not is_subgroup(symmetry_ops_init, symmetry_ops_final) - from atomate2.forcefields.jobs import GAPStaticMaker - from atomate2.forcefields.schemas import ForceFieldTaskDocument + if relax_cell: + assert output1.output.energy == approx(-0.071117445, rel=1e-1) + assert output1.output.n_steps >= 4 + else: + assert output1.output.energy == approx(-0.06772976, rel=1e-4) + assert output1.output.n_steps == 7 + + +def test_gap_static_maker(si_structure: Structure, test_dir): + importorskip("quippy") task_doc_kwargs = {"ionic_step_data": ("structure", "energy")} # generate job - # Test files have been provided by Yuanbin Liu (University of Oxford) + # Test files have been provided by @YuanbinLiu (University of Oxford) job = GAPStaticMaker( - potential_args_str="IP GAP", - potential_param_file_name=str( - test_dir / "forcefields" / "gap" / "gap_file.xml" - ), + calculator_kwargs={ + "args_str": "IP GAP", + "param_filename": str(test_dir / "forcefields" / "gap" / "gap_file.xml"), + }, task_document_kwargs=task_doc_kwargs, ).make(si_structure) @@ -117,22 +292,93 @@ def test_gap_static_maker(si_structure, test_dir): assert isinstance(output1, ForceFieldTaskDocument) assert output1.output.energy == approx(-10.8523, rel=1e-4) assert output1.output.n_steps == 1 + assert output1.forcefield_version == get_imported_version("quippy-ase") + + +def test_nequip_static_maker(sr_ti_o3_structure: Structure, test_dir: Path): + importorskip("nequip") + task_doc_kwargs = {"ionic_step_data": ("structure", "energy")} + + # generate job + # NOTE the test model is not trained on Si, so the energy is not accurate + job = NequipStaticMaker( + task_document_kwargs=task_doc_kwargs, + calculator_kwargs={ + "model_path": test_dir / "forcefields" / "nequip" / "nequip_ff_sr_ti_o3.pth" + }, + ).make(sr_ti_o3_structure) + + # run the flow or job and ensure that it finished running successfully + responses = run_locally(job, ensure_success=True) + + # validation the outputs of the job + output1 = responses[job.uuid][1].output + assert isinstance(output1, ForceFieldTaskDocument) + assert output1.output.energy == approx(-44.40017, rel=1e-4) + assert output1.output.n_steps == 1 + assert output1.forcefield_version == get_imported_version("nequip") + + +@pytest.mark.parametrize( + ("relax_cell", "fix_symmetry"), + [(True, False), (False, True)], +) +def test_nequip_relax_maker( + sr_ti_o3_structure: Structure, + test_dir: Path, + relax_cell: bool, + fix_symmetry: bool, +): + importorskip("nequip") + # translate one atom to ensure a small number of relaxation steps are taken + sr_ti_o3_structure.translate_sites(0, [0, 0, 0.2]) + # generate job + job = NequipRelaxMaker( + steps=25, + optimizer_kwargs={"optimizer": "BFGSLineSearch"}, + relax_cell=relax_cell, + fix_symmetry=fix_symmetry, + calculator_kwargs={ + "model_path": test_dir / "forcefields" / "nequip" / "nequip_ff_sr_ti_o3.pth" + }, + ).make(sr_ti_o3_structure) + # run the flow or job and ensure that it finished running successfully + responses = run_locally(job, ensure_success=True) -def test_gap_relax_maker(si_structure, test_dir): - from jobflow import run_locally + # validation the outputs of the job + output1 = responses[job.uuid][1].output + assert isinstance(output1, ForceFieldTaskDocument) + if relax_cell: + assert output1.output.energy == approx(-44.407, rel=1e-3) + assert output1.output.n_steps == 5 + else: + assert output1.output.energy == approx(-44.40015, rel=1e-4) + assert output1.output.n_steps == 5 - from atomate2.forcefields.jobs import GAPRelaxMaker - from atomate2.forcefields.schemas import ForceFieldTaskDocument + # fix_symmetry makes no difference for this structure relaxer combo + # just testing that passing fix_symmetry doesn't break + final_spg_num = output1.output.structure.get_space_group_info()[1] + assert final_spg_num == 99 + + +@pytest.mark.parametrize("relax_cell", [True, False]) +def test_gap_relax_maker(si_structure: Structure, test_dir: Path, relax_cell: bool): + importorskip("quippy") # translate one atom to ensure a small number of relaxation steps are taken si_structure.translate_sites(0, [0, 0, 0.1]) # generate job - # Test files have been provided by Yuanbin Liu (University of Oxford) + # Test files have been provided by @YuanbinLiu (University of Oxford) + max_step = 25 job = GAPRelaxMaker( - potential_param_file_name=test_dir / "forcefields" / "gap" / "gap_file.xml", - steps=25, + calculator_kwargs={ + "args_str": "IP GAP", + "param_filename": str(test_dir / "forcefields" / "gap" / "gap_file.xml"), + }, + steps=max_step, + relax_cell=relax_cell, ).make(si_structure) # run the flow or job and ensure that it finished running successfully @@ -141,5 +387,11 @@ def test_gap_relax_maker(si_structure, test_dir): # validating the outputs of the job output1 = responses[job.uuid][1].output assert isinstance(output1, ForceFieldTaskDocument) - assert output1.output.energy == approx(-10.8523, rel=1e-4) - assert output1.output.n_steps == 17 + if relax_cell: + assert not output1.is_force_converged + assert output1.output.energy == approx(-13.08492, rel=1e-2) + assert output1.output.n_steps == max_step + 2 + else: + assert output1.is_force_converged + assert output1.output.energy == approx(-10.8523, rel=1e-4) + assert output1.output.n_steps == 17 diff --git a/tests/forcefields/test_md.py b/tests/forcefields/test_md.py new file mode 100644 index 0000000000..d47736a4ab --- /dev/null +++ b/tests/forcefields/test_md.py @@ -0,0 +1,267 @@ +"""Tests for forcefield MD flows.""" + +from pathlib import Path + +import numpy as np +import pytest +from ase import units +from ase.io import Trajectory +from ase.md.verlet import VelocityVerlet +from jobflow import run_locally +from monty.serialization import loadfn +from pymatgen.analysis.structure_matcher import StructureMatcher +from pymatgen.core import Structure + +from atomate2.forcefields.md import ( + CHGNetMDMaker, + GAPMDMaker, + M3GNetMDMaker, + MACEMDMaker, + NequipMDMaker, +) + +name_to_maker = { + "CHGNet": CHGNetMDMaker, + "M3GNet": M3GNetMDMaker, + "MACE": MACEMDMaker, + "GAP": GAPMDMaker, + "Nequip": NequipMDMaker, +} + + +@pytest.mark.parametrize( + "ff_name", + ["CHGNet", "M3GNet", "MACE", "GAP", "Nequip"], +) +def test_ml_ff_md_maker(ff_name, si_structure, sr_ti_o3_structure, test_dir, clean_dir): + n_steps = 5 + + ref_energies_per_atom = { + "CHGNet": -5.280157089233398, + "M3GNet": -5.387282371520996, + "MACE": -5.311369895935059, + "GAP": -5.391255755606209, + "Nequip": -8.84670181274414, + } + + # ASE can slightly change tolerances on structure positions + matcher = StructureMatcher() + + calculator_kwargs = {} + unit_cell_structure = si_structure.copy() + if ff_name == "GAP": + calculator_kwargs = { + "args_str": "IP GAP", + "param_filename": str(test_dir / "forcefields" / "gap" / "gap_file.xml"), + } + elif ff_name == "Nequip": + calculator_kwargs = { + "model_path": test_dir / "forcefields" / "nequip" / "nequip_ff_sr_ti_o3.pth" + } + unit_cell_structure = sr_ti_o3_structure.copy() + + structure = unit_cell_structure.to_conventional() * (2, 2, 2) + + job = name_to_maker[ff_name]( + n_steps=n_steps, + traj_file="md_traj.json.gz", + traj_file_fmt="pmg", + task_document_kwargs={"store_trajectory": "partial"}, + calculator_kwargs=calculator_kwargs, + ).make(structure) + response = run_locally(job, ensure_success=True) + task_doc = response[next(iter(response))][1].output + + # Check that energies are reasonably close to reference values + assert task_doc.output.energy / len(structure) == pytest.approx( + ref_energies_per_atom[ff_name], abs=0.1 + ) + + # Check that we have the right number of MD steps + # ASE logs the initial structure energy, and doesn't count this as an MD step + assert matcher.fit(task_doc.output.ionic_steps[0].structure, structure) + assert len(task_doc.output.ionic_steps) == n_steps + 1 + + # Check that the ionic steps have the expected physical properties + assert all( + key in step.model_dump() + for key in ("energy", "forces", "stress", "structure") + for step in task_doc.output.ionic_steps + ) + + # Check that the trajectory has expected physical properties + assert task_doc.included_objects == ["trajectory"] + assert len(task_doc.forcefield_objects["trajectory"]) == n_steps + 1 + assert all( + key in step + for key in ("energy", "forces", "stress", "velocities", "temperature") + for step in task_doc.forcefield_objects["trajectory"].frame_properties + ) + + +@pytest.mark.parametrize("traj_file", ["trajectory.json.gz", "atoms.traj"]) +def test_traj_file(traj_file, si_structure, clean_dir, ff_name="CHGNet"): + n_steps = 5 + + # Check that traj file written to disk is consistent with trajectory + # stored to the task document + + if ".json.gz" in traj_file: + traj_file_fmt = "pmg" + traj_file_loader = loadfn + else: + traj_file_fmt = "ase" + traj_file_loader = Trajectory + + structure = si_structure.to_conventional() * (2, 2, 2) + job = name_to_maker[ff_name]( + n_steps=n_steps, + traj_file=traj_file, + traj_file_fmt=traj_file_fmt, + ).make(structure) + response = run_locally(job, ensure_success=True) + task_doc = response[next(iter(response))][1].output + + traj_from_file = traj_file_loader(traj_file) + + assert len(traj_from_file) == n_steps + 1 + + if traj_file_fmt == "pmg": + assert all( + np.all( + traj_from_file.frame_properties[idx][key] + == task_doc.forcefield_objects["trajectory"] + .frame_properties[idx] + .get(key) + ) + for key in ("energy", "temperature", "forces", "velocities") + for idx in range(n_steps + 1) + ) + elif traj_file_fmt == "ase": + traj_as_dict = [ + { + "energy": traj_from_file[idx].get_potential_energy(), + "temperature": traj_from_file[idx].get_temperature(), + "forces": traj_from_file[idx].get_forces(), + "velocities": traj_from_file[idx].get_velocities(), + } + for idx in range(1, n_steps + 1) + ] + assert all( + np.all( + traj_as_dict[idx - 1][key] + == task_doc.forcefield_objects["trajectory"] + .frame_properties[idx] + .get(key) + ) + for key in ("energy", "temperature", "forces", "velocities") + for idx in range(1, n_steps + 1) + ) + + +def test_nve_and_dynamics_obj(si_structure: Structure, test_dir: Path): + # This test serves two purposes: + # 1. Test the NVE calculator + # 2. Test specifying the `dynamics` kwarg of the `MDMaker` as a str + # vs. as an ase.md.md.MolecularDynamics object + + output = {} + for key in ("from_str", "from_dyn"): + if key == "from_str": + dyn = "velocityverlet" + elif key == "from_dyn": + dyn = VelocityVerlet + + job = CHGNetMDMaker( + ensemble="nve", + dynamics=dyn, + n_steps=50, + traj_file=None, + ).make(si_structure) + + response = run_locally(job, ensure_success=True) + output[key] = response[next(iter(response))][1].output + + # check that energy and volume are constants + assert output["from_str"].output.energy == pytest.approx(-10.6, abs=0.1) + assert output["from_str"].output.structure.volume == pytest.approx( + output["from_str"].input.structure.volume + ) + assert all( + step.energy == pytest.approx(-10.6, abs=0.1) + for step in output["from_str"].output.ionic_steps + ) + + # ensure that output is consistent if molecular dynamics object is specified + # as str or as MolecularDynamics object + for attr in ("energy", "forces", "stress", "structure"): + vals = { + key: getattr(output[key].output, attr) for key in ("from_str", "from_dyn") + } + if isinstance(vals["from_str"], float): + assert vals["from_str"] == pytest.approx(vals["from_dyn"]) + elif isinstance(vals["from_str"], Structure): + assert vals["from_str"] == vals["from_dyn"] + else: + assert all( + vals["from_str"][i][j] == pytest.approx(vals["from_dyn"][i][j]) + for i in range(len(vals["from_str"])) + for j in range(len(vals["from_str"][i])) + ) + + +@pytest.mark.parametrize("ff_name", ["CHGNet"]) +def test_temp_schedule(ff_name, si_structure, clean_dir): + n_steps = 50 + temp_schedule = [300, 3000] + + structure = si_structure.to_conventional() * (2, 2, 2) + + job = name_to_maker[ff_name]( + n_steps=n_steps, + traj_file=None, + dynamics="nose-hoover", + temperature=temp_schedule, + ase_md_kwargs=dict(ttime=50.0 * units.fs, pfactor=None), + ).make(structure) + response = run_locally(job, ensure_success=True) + task_doc = response[next(iter(response))][1].output + + temp_history = [ + step["temperature"] + for step in task_doc.forcefield_objects["trajectory"].frame_properties + ] + + assert temp_history[-1] > temp_schedule[0] + + +@pytest.mark.parametrize("ff_name", ["CHGNet"]) +def test_press_schedule(ff_name, si_structure, clean_dir): + n_steps = 20 + press_schedule = [0, 10] # kBar + + structure = si_structure.to_conventional() * (3, 3, 3) + + job = name_to_maker[ff_name]( + ensemble="npt", + n_steps=n_steps, + traj_file="md_traj.json.gz", + traj_file_fmt="pmg", + dynamics="nose-hoover", + pressure=press_schedule, + ase_md_kwargs=dict( + ttime=50.0 * units.fs, + pfactor=(75.0 * units.fs) ** 2 * units.GPa, + ), + ).make(structure) + run_locally(job, ensure_success=True) + # task_doc = response[next(iter(response))][1].output + + traj_from_file = loadfn("md_traj.json.gz") + + stress_history = [ + sum(traj_from_file.frame_properties[idx]["stress"][:3]) / 3.0 + for idx in range(len(traj_from_file)) + ] + + assert stress_history[-1] < stress_history[0] diff --git a/tests/forcefields/test_utils.py b/tests/forcefields/test_utils.py new file mode 100644 index 0000000000..9b4b6417f5 --- /dev/null +++ b/tests/forcefields/test_utils.py @@ -0,0 +1,165 @@ +import os + +import pytest +from ase.build import bulk +from ase.calculators.lj import LennardJones +from ase.optimize import BFGS +from ase.spacegroup.symmetrize import check_symmetry +from numpy.testing import assert_allclose +from pymatgen.core import Structure + +from atomate2.forcefields import MLFF +from atomate2.forcefields.utils import ( + FrechetCellFilter, + Relaxer, + TrajectoryObserver, + ase_calculator, +) + + +def test_safe_import(): + assert FrechetCellFilter is None or FrechetCellFilter.__module__ == "ase.filters" + + +def test_trajectory_observer(si_structure: Structure, test_dir, tmp_dir): + atoms = si_structure.to_ase_atoms() + atoms.set_calculator(LennardJones()) + + traj = TrajectoryObserver(atoms) + + expected_energy = -0.06830751105 + assert traj.compute_energy() == pytest.approx(expected_energy) + + traj() + # NB: always 3 Cartesian components to each interatomic force, + # and only 6 unique elements of the flattened stress tensor + assert traj.energies[0] == pytest.approx(expected_energy) + + expected_forces = [ + [8.32667268e-17, 4.16333634e-17, 7.31069641e-17], + [-8.32667268e-17, -4.16333634e-17, -7.31069641e-17], + ] + assert_allclose(traj.forces[0], expected_forces, atol=1e-8) + expected_stresses = [ + 4.38808e-03, + 4.38808e-03, + 4.38808e-03, + -9.47784e-19, + -1.24675e-18, + -1.76448e-18, + ] + assert_allclose(traj.stresses[0], expected_stresses, atol=1e-8) + + save_file_name = "log_file.traj" + traj.save(save_file_name) + assert os.path.isfile(save_file_name) + + +@pytest.mark.parametrize( + ("optimizer", "traj_file"), + [("BFGS", None), (None, None), (BFGS, "log_file.traj")], +) +def test_relaxer(si_structure, test_dir, tmp_dir, optimizer, traj_file): + if FrechetCellFilter: + expected_lattice = { + "a": 3.866974, + "b": 3.866974, + "c": 3.866974, + "volume": 40.888292, + } + expected_forces = [ + [8.32667268e-17, 4.16333634e-17, 7.31069641e-17], + [-8.32667268e-17, -4.16333634e-17, -7.31069641e-17], + ] + expected_energy = -0.0683075110 + expected_stresses = [ + 4.38808588e-03, + 4.38808588e-03, + 4.38808588e-03, + -9.74728670e-19, + -1.31340626e-18, + -1.60482883e-18, + ] + else: + expected_lattice = { + "a": 1.77102507, + "b": 1.77102507, + "c": 1.77102507, + "volume": 3.927888, + } + expected_forces = [ + [-5.95083358e-12, -1.65202964e-12, 2.84683735e-13], + [5.92662724e-12, 1.65667133e-12, -2.77979812e-13], + ] + expected_energy = -5.846762493 + expected_stresses = [ + -1.27190530e-03, + -1.27190530e-03, + -1.27190530e-03, + -2.31413557e-14, + -3.26060788e-14, + 5.09222979e-13, + ] + + if optimizer is None: + with pytest.raises(ValueError, match="Optimizer cannot be None"): + Relaxer(calculator=LennardJones(), optimizer=optimizer) + return + + relaxer = Relaxer(calculator=LennardJones(), optimizer=optimizer) + + try: + relax_output = relaxer.relax(atoms=si_structure, traj_file=traj_file) + except TypeError: + return + + assert { + key: getattr(relax_output["final_structure"].lattice, key) + for key in expected_lattice + } == pytest.approx(expected_lattice) + + assert relax_output["trajectory"].frame_properties[-1]["energy"] == pytest.approx( + expected_energy + ) + + assert_allclose( + relax_output["trajectory"].frame_properties[-1]["forces"], expected_forces + ) + + assert_allclose( + relax_output["trajectory"].frame_properties[-1]["stress"], expected_stresses + ) + + if traj_file: + assert os.path.isfile(traj_file) + + +@pytest.mark.parametrize(("force_field"), ["CHGNet", "MACE"]) +def test_ext_load(force_field: str): + decode_dict = { + "CHGNet": {"@module": "chgnet.model.dynamics", "@callable": "CHGNetCalculator"}, + "MACE": {"@module": "mace.calculators", "@callable": "mace_mp"}, + }[force_field] + calc_from_decode = ase_calculator(decode_dict) + calc_from_preset = ase_calculator(str(MLFF(force_field))) + assert type(calc_from_decode) == type(calc_from_preset) + assert calc_from_decode.name == calc_from_preset.name + assert calc_from_decode.parameters == calc_from_preset.parameters == {} + + +@pytest.mark.parametrize(("fix_symmetry"), [True, False]) +def test_fix_symmetry(fix_symmetry): + # adapted from the example at https://wiki.fysik.dtu.dk/ase/ase/constraints.html#the-fixsymmetry-class + relaxer = Relaxer( + calculator=LennardJones(), relax_cell=True, fix_symmetry=fix_symmetry + ) + atoms_al = bulk("Al", "bcc", a=2 / 3**0.5, cubic=True) + atoms_al = atoms_al * (2, 2, 2) + atoms_al.positions[0, 0] += 1e-7 + symmetry_init = check_symmetry(atoms_al, 1e-6) + final_struct: Structure = relaxer.relax(atoms=atoms_al, steps=1)["final_structure"] + symmetry_final = check_symmetry(final_struct.to_ase_atoms(), 1e-6) + if fix_symmetry: + assert symmetry_init["number"] == symmetry_final["number"] == 229 + else: + assert symmetry_init["number"] != symmetry_final["number"] == 99 diff --git a/tests/qchem/conftest.py b/tests/qchem/conftest.py new file mode 100644 index 0000000000..229680b734 --- /dev/null +++ b/tests/qchem/conftest.py @@ -0,0 +1,200 @@ +from __future__ import annotations + +import logging +import shutil +from pathlib import Path +from typing import TYPE_CHECKING, Any, Callable, Final, Literal + +import pytest +from jobflow import CURRENT_JOB +from pymatgen.io.qchem.inputs import QCInput +from pytest import MonkeyPatch + +import atomate2.qchem.jobs.base +import atomate2.qchem.jobs.core +import atomate2.qchem.run +from atomate2.qchem.sets.base import QCInputGenerator + +if TYPE_CHECKING: + from collections.abc import Generator, Sequence + + +logger = logging.getLogger("atomate2") + +_QFILES: Final = "mol.qin.gz" +_REF_PATHS: dict[str, str | Path] = {} +_FAKE_RUN_QCHEM_KWARGS: dict[str, dict] = {} + + +@pytest.fixture(scope="session") +def qchem_test_dir(test_dir): + return test_dir / "qchem" + + +@pytest.fixture() +def mock_qchem( + monkeypatch: MonkeyPatch, qchem_test_dir: Path +) -> Generator[Callable[[Any, Any], Any], None, None]: + """ + This fixture allows one to mock (fake) running qchem. + + It works by monkeypatching (replacing) calls to run_qchem and + QCInputSet.write_inputs with versions that will work when the + Qchem executables are not present. + + The primary idea is that instead of running QChem to generate the output files, + reference files will be copied into the directory instead. As we do not want to + test whether QChem is giving the correct output rather that the calculation inputs + are generated correctly and that the outputs are parsed properly, this should be + sufficient for our needs. + + To use the fixture successfully, the following steps must be followed: + 1. "mock_qchem" should be included as an argument to any test that would like to use + its functionally. + 2. For each job in your workflow, you should prepare a reference directory + containing two folders "inputs" (containing the reference input files expected + to be produced by write_qchem_input_set) and "outputs" (containing the expected + output files to be produced by run_qchem). These files should reside in a + subdirectory of "tests/test_data/qchem". + 3. Create a dictionary mapping each job name to its reference directory. Note that + you should supply the reference directory relative to the "tests/test_data/qchem" + folder. For example, if your calculation has one job named "single_point" + and the reference files are present in + "tests/test_data/qchem/single_point", the dictionary + would look like: ``{"single_point": "single_point"}``. + 4. Optional: create a dictionary mapping each job name to + custom keyword arguments that will be supplied to fake_run_qchem. + This way you can configure which rem settings are expected for each job. + For example, if your calculation has one job named "single_point" and + you wish to validate that "BASIS" is set correctly in the qin, + your dictionary would look like ``{"single_point": {"rem": {"BASIS": "6-31G"}}``. + 5. Inside the test function, call `mock_qchem(ref_paths, fake_qchem_kwargs)`, where + ref_paths is the dictionary created in step 3 and fake_qchem_kwargs is the + dictionary created in step 4. + 6. Run your qchem job after calling `mock_qchem`. + + For examples, see the tests in tests/qchem/makers/core.py. + """ + + # print(f"qchem_test directory is {qchem_test_dir}") + def mock_run_qchem(*args, **kwargs): + name = CURRENT_JOB.job.name + try: + ref_path = qchem_test_dir / _REF_PATHS[name] + except KeyError: + raise ValueError( + f"no reference directory found for job {name!r}; " + f"reference paths received={_REF_PATHS}" + ) from None + + fake_run_qchem(ref_path, **_FAKE_RUN_QCHEM_KWARGS.get(name, {})) + + get_input_set_orig = QCInputGenerator.get_input_set + + def mock_get_input_set(self, *args, **kwargs): + return get_input_set_orig(self, *args, **kwargs) + + monkeypatch.setattr(atomate2.qchem.run, "run_qchem", mock_run_qchem) + monkeypatch.setattr(atomate2.qchem.jobs.base, "run_qchem", mock_run_qchem) + monkeypatch.setattr(QCInputGenerator, "get_input_set", mock_get_input_set) + # monkeypatch.setattr(QCInputGenerator, "get_nelect", mock_get_nelect) + + def _run(ref_paths, fake_run_qchem_kwargs=None): + _REF_PATHS.update(ref_paths) + _FAKE_RUN_QCHEM_KWARGS.update(fake_run_qchem_kwargs or {}) + + yield _run + + monkeypatch.undo() + _REF_PATHS.clear() + _FAKE_RUN_QCHEM_KWARGS.clear() + + +def fake_run_qchem( + ref_path: Path, + input_settings: Sequence[str] = None, + input_exclude: Sequence[str] = None, + check_inputs: Sequence[Literal["qin"]] = _QFILES, + clear_inputs: bool = True, +): + """ + Emulate running QChem and validate QChem input files. + + Parameters + ---------- + ref_path + Path to reference directory with QChem input files in the folder named 'inputs' + and output files in the folder named 'outputs'. + input_settings + A list of input settings to check. Defaults to None which checks all settings. + Empty list or tuple means no settings will be checked. + input_exclude + A list of input settings to exclude from checking. Defaults to None, meaning + no settings will be excluded. + check_inputs + A list of qchem input files to check. In case of qchem, it is "qin". + clear_inputs + Whether to clear input files before copying in the reference QChem outputs. + """ + logger.info("Running fake QChem.") + + if "mol.qin.gz" in check_inputs: + check_qin(ref_path, input_settings, input_exclude) + + # This is useful to check if the WAVECAR has been copied + logger.info("Verified inputs successfully") + + if clear_inputs: + clear_qchem_inputs() + + copy_qchem_outputs(ref_path) + + # pretend to run VASP by copying pre-generated outputs from reference dir + logger.info("Generated fake qchem outputs") + + +def check_qin( + ref_path: Path, qin_settings: Sequence[str], qin_exclude: Sequence[str] +) -> None: + # user_qin = QCInput.from_file("mol.qin.gz") + ref_qin_path = ref_path / "inputs" / "mol.qin.gz" + ref_qin = QCInput.from_file(ref_qin_path) + script_directory = Path(__file__).resolve().parent + # print(f"The job name is {job_name}") + # defaults = {"sym_ignore": True, "symmetry": False, "xc_grid": 3} + job_name = ref_path.stem + if job_name == "water_single_point": + user_qin_path = script_directory / "sp.qin.gz" + elif job_name == "water_optimization": + user_qin_path = script_directory / "opt.qin.gz" + elif job_name == "water_frequency": + user_qin_path = script_directory / "freq.qin.gz" + user_qin = QCInput.from_file(user_qin_path) + + keys_to_check = ( + set(user_qin.as_dict()) if qin_settings is None else set(qin_settings) + ) - set(qin_exclude or []) + user_dict = user_qin.as_dict() + ref_dict = ref_qin.as_dict() + for key in keys_to_check: + user_val = user_dict[key] + ref_val = ref_dict[key] + if user_val != ref_val: + raise ValueError( + f"\n\nQCInput value of {key} is inconsistent: expected {ref_val}, " + f"got {user_val} \nin ref file {ref_qin_path}" + ) + + +def clear_qchem_inputs(): + for qchem_file in ("mol.qin.gz", "mol.qin.orig.gz"): + if Path(qchem_file).exists(): + Path(qchem_file).unlink() + logger.info("Cleared qchem inputs") + + +def copy_qchem_outputs(ref_path: Path): + output_path = ref_path / "outputs" + for output_file in output_path.iterdir(): + if output_file.is_file(): + shutil.copy(output_file, ".") diff --git a/tests/qchem/freq.qin.gz b/tests/qchem/freq.qin.gz new file mode 100644 index 0000000000..e56db71ea0 Binary files /dev/null and b/tests/qchem/freq.qin.gz differ diff --git a/tests/qchem/jobs/H2O.xyz b/tests/qchem/jobs/H2O.xyz new file mode 100644 index 0000000000..212ca2ea8f --- /dev/null +++ b/tests/qchem/jobs/H2O.xyz @@ -0,0 +1,5 @@ +3 + +O 0.00000 0.00000 0.12124 +H -0.78304 -0.00000 -0.48495 +H 0.78304 0.00000 -0.48495 diff --git a/tests/qchem/jobs/test_core.py b/tests/qchem/jobs/test_core.py new file mode 100644 index 0000000000..75b5907cf5 --- /dev/null +++ b/tests/qchem/jobs/test_core.py @@ -0,0 +1,97 @@ +from pathlib import Path + +from emmet.core.qc_tasks import TaskDoc +from jobflow import run_locally +from pymatgen.core.structure import Molecule +from pytest import approx + +from atomate2.qchem.jobs.core import FreqMaker, OptMaker, SinglePointMaker + +current_directory = Path(__file__).resolve().parent +file_name = current_directory / "H2O.xyz" + +H2O = Molecule.from_file(file_name) + + +def test_single_point_maker(mock_qchem, clean_dir): + # mapping from job name to directory containing test files + ref_paths = {"single point": "water_single_point"} + + # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings + # fake_run_qchem_kwargs = {"single_point": {"qin_settings": None}} + fake_run_qchem_kwargs = {} + + # automatically use fake qchem during the test + mock_qchem(ref_paths, fake_run_qchem_kwargs) + + # generate job + job = SinglePointMaker().make(H2O) + + # run the flow or job and ensure that it finished running successfully + responses = run_locally(job, create_folders=True, ensure_success=True) + + # validate job outputs + output1 = responses[job.uuid][1].output + assert isinstance(output1, TaskDoc) + assert output1.output.final_energy == approx(-76.4451488262) + + +def test_opt_maker(mock_qchem, clean_dir): + ref_paths = {"optimization": "water_optimization"} + fake_run_qchem_kwargs = {} + mock_qchem(ref_paths, fake_run_qchem_kwargs) + + job = OptMaker().make(H2O) + + responses = run_locally(job, create_folders=True, ensure_success=True) + opt_geometry = { + "@module": "pymatgen.core.structure", + "@class": "Molecule", + "charge": 0, + "spin_multiplicity": 1, + "sites": [ + { + "name": "O", + "species": [{"element": "O", "occu": 1}], + "xyz": [-0.8001136722, 2.2241304324, -0.0128020517], + "properties": {}, + "label": "O", + }, + { + "name": "H", + "species": [{"element": "H", "occu": 1}], + "xyz": [0.1605037895, 2.195300528, 0.0211059581], + "properties": {}, + "label": "H", + }, + { + "name": "H", + "species": [{"element": "H", "occu": 1}], + "xyz": [-1.0782701173, 1.6278690395, 0.6883760935], + "properties": {}, + "label": "H", + }, + ], + "properties": {}, + } + + output1 = responses[job.uuid][1].output + assert isinstance(output1, TaskDoc) + assert sorted(opt_geometry.items()) == sorted( + output1.output.optimized_molecule.as_dict().items() + ) + assert output1.output.final_energy == approx(-76.450849061819) + + +def test_freq(mock_qchem, clean_dir): + ref_paths = {"frequency": "water_frequency"} + fake_run_qchem_kwargs = {} + mock_qchem(ref_paths, fake_run_qchem_kwargs) + + job = FreqMaker().make(H2O) + + responses = run_locally(job, create_folders=True, ensure_success=True) + ref_freqs = [1643.03, 3446.82, 3524.32] + output1 = responses[job.uuid][1].output + assert output1.calcs_reversed[0].output.frequencies == ref_freqs + assert output1.output.final_energy == approx(-76.449405011) diff --git a/tests/qchem/opt.qin.gz b/tests/qchem/opt.qin.gz new file mode 100644 index 0000000000..bad1fee842 Binary files /dev/null and b/tests/qchem/opt.qin.gz differ diff --git a/tests/qchem/sets/test_core.py b/tests/qchem/sets/test_core.py new file mode 100644 index 0000000000..2d02f797c5 --- /dev/null +++ b/tests/qchem/sets/test_core.py @@ -0,0 +1,160 @@ +import pytest + +from atomate2.qchem.sets.base import QCInputGenerator +from atomate2.qchem.sets.core import ( + ForceSetGenerator, + FreqSetGenerator, + OptSetGenerator, + PESScanSetGenerator, + SinglePointSetGenerator, + TransitionStateSetGenerator, +) + + +@pytest.mark.parametrize( + "set_generator, expected_job_type", + [ + (SinglePointSetGenerator, "sp"), + (OptSetGenerator, "opt"), + (TransitionStateSetGenerator, "ts"), + (ForceSetGenerator, "force"), + (FreqSetGenerator, "freq"), + (PESScanSetGenerator, "pes_scan"), + ], +) +def test_qc_sets(set_generator: QCInputGenerator, expected_job_type: str) -> None: + qc_set: QCInputGenerator = set_generator() + assert {*qc_set.__dict__} >= { + "job_type", + "basis_set", + "scf_algorithm", + "dft_rung", + "pcm_dielectric", + "smd_solvent", + "custom_smd", + "opt_dict", + "scan_dict", + "max_scf_cycles", + "geom_opt_max_cycles", + "plot_cubes", + "nbo_params", + "new_geom_opt", + "overwrite_inputs", + "vdw_mode", + "rem_dict", + "pcm_dict", + "solv_dict", + "smx_dict", + "vdw_dict", + "plots_dict", + } + assert qc_set.scf_algorithm == "diis" + assert qc_set.job_type == expected_job_type + assert qc_set.basis_set == "def2-tzvppd" + assert isinstance(qc_set.rem_dict, dict) + + +@pytest.mark.parametrize( + "set_generator_pcm_d3, expected_job_type", + [ + (SinglePointSetGenerator, "sp"), + (OptSetGenerator, "opt"), + (TransitionStateSetGenerator, "ts"), + (ForceSetGenerator, "force"), + (FreqSetGenerator, "freq"), + (PESScanSetGenerator, "pes_scan"), + ], +) +def test_extra_params_pcm( + set_generator_pcm_d3: QCInputGenerator, expected_job_type: str +) -> None: + qc_set: QCInputGenerator = set_generator_pcm_d3(dft_rung=2, pcm_dielectric=78.39) + assert qc_set.rem_dict["dft_D"] == "D3_BJ" + assert qc_set.rem_dict["solvent_method"] == "pcm" + + pcm_defaults = { + "heavypoints": "194", + "hpoints": "194", + "radii": "uff", + "theory": "cpcm", + "vdwscale": "1.1", + } + + assert qc_set.pcm_dict == pcm_defaults + assert qc_set.solv_dict["dielectric"] == qc_set.pcm_dielectric + assert qc_set.scf_algorithm == "diis" + assert qc_set.job_type == expected_job_type + assert qc_set.basis_set == "def2-tzvppd" + assert isinstance(qc_set.rem_dict, dict) + + +@pytest.mark.parametrize( + "set_generator_smd, expected_job_type", + [ + (SinglePointSetGenerator, "sp"), + (OptSetGenerator, "opt"), + (TransitionStateSetGenerator, "ts"), + (ForceSetGenerator, "force"), + (FreqSetGenerator, "freq"), + (PESScanSetGenerator, "pes_scan"), + ], +) +def test_extra_params_smd( + set_generator_smd: QCInputGenerator, expected_job_type: str +) -> None: + qc_set: QCInputGenerator = set_generator_smd(smd_solvent="water") + assert qc_set.rem_dict["solvent_method"] == "smd" + assert qc_set.rem_dict["ideriv"] == "1" + assert qc_set.smx_dict["solvent"] == "water" + assert qc_set.scf_algorithm == "diis" + assert qc_set.job_type == expected_job_type + assert qc_set.basis_set == "def2-tzvppd" + assert isinstance(qc_set.rem_dict, dict) + + +@pytest.mark.parametrize( + "set_generator_plots, expected_job_type", + [ + (SinglePointSetGenerator, "sp"), + (OptSetGenerator, "opt"), + (TransitionStateSetGenerator, "ts"), + (ForceSetGenerator, "force"), + (FreqSetGenerator, "freq"), + (PESScanSetGenerator, "pes_scan"), + ], +) +def test_extra_params_plots( + set_generator_plots: QCInputGenerator, expected_job_type: str +) -> None: + qc_set: QCInputGenerator = set_generator_plots(plot_cubes=True) + assert qc_set.plots_dict == {"grid_spacing": "0.05", "total_density": "0"} + assert qc_set.rem_dict["plots"] == "true" + assert qc_set.rem_dict["make_cube_files"] == "true" + assert qc_set.scf_algorithm == "diis" + assert qc_set.job_type == expected_job_type + assert qc_set.basis_set == "def2-tzvppd" + + +@pytest.mark.parametrize( + "set_generator_nbo, expected_job_type", + [ + (SinglePointSetGenerator, "sp"), + (OptSetGenerator, "opt"), + (TransitionStateSetGenerator, "ts"), + (ForceSetGenerator, "force"), + (FreqSetGenerator, "freq"), + (PESScanSetGenerator, "pes_scan"), + ], +) +def test_extra_params_nbo( + set_generator_nbo: QCInputGenerator, expected_job_type: str +) -> None: + qc_set: QCInputGenerator = set_generator_nbo( + nbo_params={"version": 7, "plots": "PLOT"} + ) + + assert qc_set.rem_dict["nbo"] == "true" + assert qc_set.rem_dict["nbo_external"] == "true" + assert qc_set.scf_algorithm == "diis" + assert qc_set.job_type == expected_job_type + assert qc_set.basis_set == "def2-tzvppd" diff --git a/tests/qchem/sp.qin.gz b/tests/qchem/sp.qin.gz new file mode 100644 index 0000000000..bb34b43366 Binary files /dev/null and b/tests/qchem/sp.qin.gz differ diff --git a/tests/qchem/test_drones.py b/tests/qchem/test_drones.py new file mode 100644 index 0000000000..31dcffb1ac --- /dev/null +++ b/tests/qchem/test_drones.py @@ -0,0 +1,19 @@ +from atomate2.qchem.drones import QChemDrone + + +def test_structure_optimization(qchem_test_dir): + drone = QChemDrone() + doc = drone.assimilate(qchem_test_dir / "water_single_point" / "outputs") + assert doc + + +def test_valid_paths(qchem_test_dir): + drone = QChemDrone() + valid_paths = drone.get_valid_paths( + [ + str(qchem_test_dir) + "/water_frequency", + ["inputs/", "outputs/"], + ["mol.in", "mol.out"], + ] + ) + assert valid_paths diff --git a/tests/qchem/test_files.py b/tests/qchem/test_files.py new file mode 100644 index 0000000000..d504b61757 --- /dev/null +++ b/tests/qchem/test_files.py @@ -0,0 +1,39 @@ +from pathlib import Path + +import pytest + +from atomate2.qchem.files import copy_qchem_outputs, get_largest_opt_extension + + +@pytest.mark.parametrize( + "files", + [("custodian.json.gz", "FW.json.gz")], +) +def test_copy_qchem_outputs_sp(qchem_test_dir, tmp_dir, files): + path = qchem_test_dir / "water_single_point" / "outputs" + copy_qchem_outputs(src_dir=path, additional_qchem_files=files) + + for file in files: + assert Path(path / file).exists() + + +@pytest.mark.parametrize( + "files", + [("custodian.json.gz", "FW.json.gz")], +) +def test_copy_qchem_outputs_freq(qchem_test_dir, tmp_dir, files): + path = qchem_test_dir / "water_frequency" / "outputs" + copy_qchem_outputs(src_dir=path, additional_qchem_files=files) + + for file in files: + assert Path(path / file).exists() + + +def test_get_largest_opt_extension(qchem_test_dir): + path = qchem_test_dir / "double_opt_test" / "outputs" + extension = get_largest_opt_extension(directory=path) + assert extension == ".opt_2" + + path = qchem_test_dir / "water_single_point" / "static" / "outputs" + extension = get_largest_opt_extension(directory=path) + assert extension == "" diff --git a/tests/qchem/test_run.py b/tests/qchem/test_run.py new file mode 100644 index 0000000000..325b244b48 --- /dev/null +++ b/tests/qchem/test_run.py @@ -0,0 +1,36 @@ +import pytest + +from atomate2.qchem.drones import QChemDrone +from atomate2.qchem.run import should_stop_children + + +def test_stop_children_val_td(qchem_test_dir): + drone = QChemDrone() + task_doc = drone.assimilate(qchem_test_dir / "water_single_point" / "outputs") + chk_stop_children = should_stop_children( + task_document=task_doc, handle_unsuccessful=False + ) + + assert isinstance(chk_stop_children, bool) + with pytest.raises(RuntimeError) as exc_info: + should_stop_children(task_document=task_doc, handle_unsuccessful="error") + + error_message = "Job was successful but children jobs need to be stopped!" + + assert str(exc_info.value) == error_message + + +def test_stop_children_inval_td(qchem_test_dir): + drone = QChemDrone() + task_doc = drone.assimilate(qchem_test_dir / "failed_qchem_task_dir" / "outputs") + + with pytest.raises(RuntimeError) as exc_info: + should_stop_children(task_document=task_doc, handle_unsuccessful="error") + + error_message = ( + "Job was not successful " + "(perhaps your job did not converge within the " + "limit of electronic/ionic iterations)!" + ) + + assert str(exc_info.value) == error_message diff --git a/tests/qchem/test_sets.py b/tests/qchem/test_sets.py new file mode 100644 index 0000000000..8aa2d21d32 --- /dev/null +++ b/tests/qchem/test_sets.py @@ -0,0 +1,106 @@ +import os + +import pytest +from pymatgen.core.structure import Molecule +from pymatgen.io.qchem.inputs import QCInput + +from atomate2.qchem.sets.base import QCInputSet +from atomate2.qchem.sets.core import SinglePointSetGenerator + + +@pytest.fixture(scope="module") +def water_mol() -> Molecule: + """Dummy molecular structure for water as a test molecule.""" + return Molecule( + ["O", "H", "H"], + [[0.0, 0.0, 0.121], [-0.783, 0.0, -0.485], [0.783, 0.0, -0.485]], + ) + + +@pytest.mark.parametrize( + "molecule,overwrite_inputs", + [ + ("water_mol", {"rem": {"ideriv": 1, "method": "B97-D3", "dft_d": "D3_BJ"}}), + ("water_mol", {"opt": {"CONSTRAINT": ["stre 1 2 0.96"]}}), + ( + "water_mol", + { + "rem": {"solvent_method": "pcm"}, + "pcm": {"theory": "cpcm", "hpoints": "194"}, + "solvent": {"dielectric": "78.39"}, + }, + ), + ("water_mol", {"rem": {"solvent_method": "smd"}, "smx": {"solvent": "water"}}), + ("water_mol", {"scan": {"stre": ["1 2 0.95 1.35 0.1"]}}), + ], +) +def test_overwrite(molecule, overwrite_inputs, request) -> None: + """ + Test for ensuring whether overwrite_inputs correctly + changes the default input_set parameters. + + Here, we use the StaticSetGenerator as an example, + but any input generator that has a passed overwrite_inputs + dict as an input argument could be used. + """ + molecule = request.getfixturevalue(molecule) + + input_gen = SinglePointSetGenerator() + input_gen.overwrite_inputs = overwrite_inputs + in_set = input_gen.get_input_set(molecule) + in_set_rem = {} + in_set_opt = {} + in_set_pcm = {} + in_set_smx = {} + in_set_solvent = {} + in_set_scan = {} + if overwrite_inputs.keys() == "rem": + in_set_rem = in_set.qcinput.as_dict()["rem"] + elif overwrite_inputs.keys() == "opt": + in_set_opt = in_set.qcinput.as_dict()["opt"] + elif overwrite_inputs.keys() == ["rem", "pcm", "solvent"]: + in_set_rem = in_set.qcinput.as_dict()["rem"] + in_set_pcm = in_set.qcinput.as_dict()["pcm"] + in_set_solvent = in_set.qcinput.as_dict()["solvent"] + elif overwrite_inputs.keys() == ["rem", "smx"]: + in_set_rem = in_set.qcinput.as_dict()["rem"] + in_set_smx = in_set.qcinput.as_dict()["smx"] + + if in_set_rem: # case 1 + assert in_set_rem["method"] == "b97-d3" + assert in_set_rem["dft_d"] == "d3_bj" + elif in_set_opt: # case 2 + assert in_set_opt["constraint"] == ["stre 1 2 0.96"] + elif in_set_rem and in_set_pcm and in_set_solvent: + assert in_set_rem["solvent_method"] == "pcm" + assert in_set_pcm["theory"] == "cpcm" + assert in_set_pcm["hpoints"] == "194" + assert in_set_solvent["dielectric"] == "78.39" + elif in_set_rem and in_set_smx: + assert in_set_rem["solvent_method"] == "smd" + assert in_set_smx["solvent"] == "water" + elif in_set_scan: + assert in_set_scan["stre"] == ["1 2 0.95 1.35 0.1"] + + +@pytest.mark.parametrize( + "molecule", + [("water_mol")], +) +def test_write_set(molecule, clean_dir, request) -> None: + """ + Test for ensuring whether overwrite_inputs correctly + changes the default input_set parameters. + + Here, we use the StaticSetGenerator as an example, + but any input generator that has a passed overwrite_inputs + dict as an input argument could be used. + """ + molecule = request.getfixturevalue(molecule) + + input_gen = SinglePointSetGenerator() + in_set = input_gen.get_input_set(molecule) + in_set.write_input(directory="./inset_write", overwrite=True) + chk_input_set = QCInputSet.from_directory(directory="./inset_write") + assert os.path.isdir("./inset_write") + assert isinstance(chk_input_set.qcinput, QCInput) diff --git a/tests/test_data/abinit/abinit_inputs/abinit_input_Si.json b/tests/test_data/abinit/abinit_inputs/abinit_input_Si.json new file mode 100644 index 0000000000..10632e5423 --- /dev/null +++ b/tests/test_data/abinit/abinit_inputs/abinit_input_Si.json @@ -0,0 +1 @@ +{"structure": {"@module": "abipy.core.structure", "@class": "Structure", "charge": 0, "lattice": {"matrix": [[3.8401979337, 0.0, 0.0], [1.9200989668, 3.3257101909, 0.0], [0.0, -2.2171384943, 3.1355090603]], "a": 3.8401979337, "b": 3.840198994344244, "c": 3.8401979337177736, "alpha": 119.99999086398421, "beta": 90.0, "gamma": 60.00000913732221, "volume": 40.04479464425159}, "sites": [{"species": [{"element": "Si", "occu": 1}], "abc": [0.0, 0.0, 0.0], "xyz": [0.0, 0.0, 0.0], "label": "Si", "properties": {}}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.5, 0.75], "xyz": [3.8401979336749994, 1.2247250003039056e-06, 2.351631795225], "label": "Si", "properties": {}}]}, "pseudos": [{"basename": "Si.psp8", "type": "NcAbinitPseudo", "symbol": "Si", "Z": 14, "Z_val": 4.0, "l_max": 2, "md5": "45c393525680abc7b25445b8ec62bf83", "filepath": "@ONCVPSP-PBE-SR-PDv0.4/Si/Si.psp8", "@module": 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0.0000000000000D+00 +598 5.9700000000000D+00 2.0546497534330D-03 2.0546181970209D-03 0.0000000000000D+00 +599 5.9800000000000D+00 2.0297912476985D-03 2.0297598698469D-03 0.0000000000000D+00 +600 5.9900000000000D+00 2.0052475140738D-03 2.0052163147879D-03 0.0000000000000D+00 + +# +#ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) +#scalar-relativistic version 3.2.3 08/16/2016 +# +#While it is not required under the terms of the GNU GPL, it is +#suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) +#in any publication utilizing these pseudopotentials. +# +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile +Al 13.00 1 4 4 psp8 +# +# n l f +1 0 2.00 +2 0 2.00 +2 1 6.00 +3 0 2.00 +3 1 1.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax +2 +# +# l, rc, ep, ncon, nbas, qcut +0 1.40000 -3.97500 4 8 8.60000 +1 1.60000 -2.55934 4 8 9.00000 +2 1.80000 0.15000 4 8 8.60000 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 +4 5 1.00000 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl +0 2 3.69008 +1 2 2.45967 +2 2 2.50000 +# +# MODEL CORE CHARGE +# icmod, fcfact, rcfact +0 0.00000 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh +-12.00 12.00 0.02 +# +# OUTPUT GRID +# rlmax, drl +6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf +0 +# nvcnf +# n l f + diff --git a/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Al/Al.psp8 b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Al/Al.psp8 new file mode 100644 index 0000000000..8abb352b60 --- /dev/null +++ b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Al/Al.psp8 @@ -0,0 +1,3667 @@ +Al ONCVPSP-3.2.3.1 r_core= 1.76802 1.76802 1.70587 +13.0000 3.0000 170504 zatom,zion,pspd +8 11 2 4 600 0 pspcod,pspxc,lmax,lloc,mmax,r2well +5.99000000 5.00000000 0.00000000 rchrg fchrg qchrg +2 2 2 0 0 nproj +1 1 extension_switch +0 5.1266666014246D+00 7.2829148183016D-01 +1 0.0000000000000D+00 -1.5381676765625D-09 3.4042463917250D-09 +2 1.0000000000000D-02 2.2298172446312D-02 -7.7006378468391D-03 +3 2.0000000000000D-02 4.4482909181753D-02 -1.5144395297959D-02 +4 3.0000000000000D-02 6.6442672061522D-02 -2.2078637794878D-02 +5 4.0000000000000D-02 8.8069689883742D-02 -2.8259159999525D-02 +6 5.0000000000000D-02 1.0926177178604D-01 -3.3454245150594D-02 +7 6.0000000000000D-02 1.2992403766179D-01 -3.7448540570734D-02 +8 7.0000000000000D-02 1.4997053976839D-01 -4.0046692097503D-02 +9 8.0000000000000D-02 1.6932575123847D-01 -4.1076683615210D-02 +10 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4.6247898212315D-11 +593 5.9200000000000D+00 2.1837715873293D-03 2.1837820873544D-03 4.4069021201509D-11 +594 5.9300000000000D+00 2.1572747894848D-03 2.1572850035994D-03 4.1992996895487D-11 +595 5.9400000000000D+00 2.1311145953268D-03 2.1311245288794D-03 4.0014960536193D-11 +596 5.9500000000000D+00 2.1052865140641D-03 2.1052961723145D-03 3.8130277748013D-11 +597 5.9600000000000D+00 2.0797861175372D-03 2.0797955056586D-03 3.6334533585968D-11 +598 5.9700000000000D+00 2.0546090393178D-03 2.0546181623974D-03 3.4623521375087D-11 +599 5.9800000000000D+00 2.0297509738129D-03 2.0297598368537D-03 3.2993228660048D-11 +600 5.9900000000000D+00 2.0052076754260D-03 2.0052162833481D-03 3.1439846031973D-11 + +# +#ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) +#scalar-relativistic version 3.2.3 08/16/2016 +# +#While it is not required under the terms of the GNU GPL, it is +#suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) +#in any publication utilizing these pseudopotentials. +# +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile +Al 13.00 3 2 4 psp8 +# +# n l f +1 0 2.00 +2 0 2.00 +2 1 6.00 +3 0 2.00 +3 1 1.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax +2 +# +# l, rc, ep, ncon, nbas, qcut +0 1.75000 -0.28491 4 9 6.00000 +1 1.75000 -0.09967 4 9 6.40000 +2 1.70000 0.05000 4 9 6.50000 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 +4 5 1.40000 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl +0 2 2.80000 +1 2 2.80000 +2 2 1.50000 +# +# MODEL CORE CHARGE +# icmod, fcfact, rcfact +3 5.00000 1.30000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh +-12.00 12.00 0.02 +# +# OUTPUT GRID +# rlmax, drl +6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf +0 +# nvcnf +# n l f + diff --git a/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Fe/Fe-sp-high.psp8 b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Fe/Fe-sp-high.psp8 new file mode 100644 index 0000000000..5c3b5c68a4 --- /dev/null +++ b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Fe/Fe-sp-high.psp8 @@ -0,0 +1,3669 @@ +Fe ONCVPSP-3.2.3.1 r_core= 1.10889 1.10889 1.35818 +26.0000 16.0000 170704 zatom,zion,pspd +8 11 2 4 600 0 pspcod,pspxc,lmax,lloc,mmax,r2well +5.99000000 3.00000000 0.00000000 rchrg fchrg qchrg +2 2 2 0 0 nproj +1 1 extension_switch +0 1.5648626166267D+01 1.8397090434400D+00 +1 0.0000000000000D+00 -8.4068640937573D-10 3.0892698954510D-09 +2 1.0000000000000D-02 1.1362330467551D-01 -3.9760870308131D-02 +3 2.0000000000000D-02 2.2678967711727D-01 -7.9046661890144D-02 +4 3.0000000000000D-02 3.3904470182639D-01 -1.1738686764604D-01 +5 4.0000000000000D-02 4.4993897712054D-01 -1.5432006803273D-01 +6 5.0000000000000D-02 5.5903057312656D-01 -1.8939833640605D-01 +7 6.0000000000000D-02 6.6588743167992D-01 -2.2219148047286D-01 +8 7.0000000000000D-02 7.7008968976738D-01 -2.5229106891003D-01 +9 8.0000000000000D-02 8.7123190898980D-01 -2.7931419529673D-01 +10 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0.0000000000000D+00 +595 5.9400000000000D+00 1.5346738551555D-03 1.5346963027919D-03 0.0000000000000D+00 +596 5.9500000000000D+00 1.5130578731594D-03 1.5130793290999D-03 0.0000000000000D+00 +597 5.9600000000000D+00 1.4917458596277D-03 1.4917663483260D-03 0.0000000000000D+00 +598 5.9700000000000D+00 1.4707335364983D-03 1.4707530818998D-03 0.0000000000000D+00 +599 5.9800000000000D+00 1.4500166862567D-03 1.4500353118081D-03 0.0000000000000D+00 +600 5.9900000000000D+00 1.4295911510400D-03 1.4296088796992D-03 0.0000000000000D+00 + +# +#ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) +#scalar-relativistic version 3.2.3 08/16/2016 +# +#While it is not required under the terms of the GNU GPL, it is +#suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) +#in any publication utilizing these pseudopotentials. +# +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile +Fe 26.00 3 4 4 psp8 +# +# n l f +1 0 2.00 +2 0 2.00 +2 1 6.00 +3 0 2.00 +3 1 6.00 +3 2 6.00 +4 0 2.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax +2 +# +# l, rc, ep, ncon, nbas, qcut +0 1.10000 -3.45509 3 7 10.30000 +1 1.10000 -2.20653 3 7 9.20000 +2 1.35000 -0.27580 3 7 10.80000 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 +4 5 1.10000 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl +0 2 3.26061 +1 2 2.15783 +2 2 0.80000 +# +# MODEL CORE CHARGE +# icmod, fcfact, rcfact +3 3.00000 1.70000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh +-24.00 12.00 0.02 +# +# OUTPUT GRID +# rlmax, drl +6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf +0 +# nvcnf +# n l f + diff --git a/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Fe/Fe-sp.psp8 b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Fe/Fe-sp.psp8 new file mode 100644 index 0000000000..ce22ed10e1 --- /dev/null +++ b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Fe/Fe-sp.psp8 @@ -0,0 +1,3669 @@ +Fe ONCVPSP-3.2.3.1 r_core= 1.26437 1.20546 1.56719 +26.0000 16.0000 170429 zatom,zion,pspd +8 11 2 4 600 0 pspcod,pspxc,lmax,lloc,mmax,r2well +5.99000000 3.00000000 0.00000000 rchrg fchrg qchrg +2 2 2 0 0 nproj +1 1 extension_switch +0 1.0165788498768D+01 1.4646150645517D+00 +1 0.0000000000000D+00 6.2816418733291D-13 2.2306656521920D-10 +2 1.0000000000000D-02 9.5003991480818D-02 -2.8504563550008D-02 +3 2.0000000000000D-02 1.8971990861746D-01 -5.6755390037992D-02 +4 3.0000000000000D-02 2.8386067209299D-01 -8.4500162491699D-02 +5 4.0000000000000D-02 3.7714118962101D-01 -1.1148939569032D-01 +6 5.0000000000000D-02 4.6927934190068D-01 -1.3747783102662D-01 +7 6.0000000000000D-02 5.5999695949758D-01 -1.6222580631087D-01 +8 7.0000000000000D-02 6.4902078762378D-01 -1.8550059242653D-01 +9 8.0000000000000D-02 7.3608343578961D-01 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0.0000000000000D+00 +594 5.9300000000000D+00 1.5566249221074D-03 1.5566216093700D-03 0.0000000000000D+00 +595 5.9400000000000D+00 1.5347001358133D-03 1.5346963027919D-03 0.0000000000000D+00 +596 5.9500000000000D+00 1.5130836664802D-03 1.5130793290999D-03 0.0000000000000D+00 +597 5.9600000000000D+00 1.4917711744941D-03 1.4917663483260D-03 0.0000000000000D+00 +598 5.9700000000000D+00 1.4707583816320D-03 1.4707530818998D-03 0.0000000000000D+00 +599 5.9800000000000D+00 1.4500410702211D-03 1.4500353118081D-03 0.0000000000000D+00 +600 5.9900000000000D+00 1.4296150822434D-03 1.4296088796992D-03 0.0000000000000D+00 + +# +#ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) +#scalar-relativistic version 3.2.3 08/16/2016 +# +#While it is not required under the terms of the GNU GPL, it is +#suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) +#in any publication utilizing these pseudopotentials. +# +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile +Fe 26.00 3 4 4 psp8 +# +# n l f +1 0 2.00 +2 0 2.00 +2 1 6.00 +3 0 2.00 +3 1 6.00 +3 2 6.00 +4 0 2.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax +2 +# +# l, rc, ep, ncon, nbas, qcut +0 1.25000 -3.45509 3 7 9.40000 +1 1.20000 -2.20653 3 7 9.40000 +2 1.55000 -0.27580 3 7 9.40000 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 +4 5 1.10000 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl +0 2 3.26061 +1 2 2.15783 +2 2 0.80000 +# +# MODEL CORE CHARGE +# icmod, fcfact, rcfact +3 3.00000 1.70000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh +-24.00 12.00 0.02 +# +# OUTPUT GRID +# rlmax, drl +6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf +0 +# nvcnf +# n l f + diff --git a/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/O/O-high.psp8 b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/O/O-high.psp8 new file mode 100644 index 0000000000..3a59c21430 --- /dev/null +++ b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/O/O-high.psp8 @@ -0,0 +1,3665 @@ +O ONCVPSP-3.2.3.1 r_core= 1.26150 1.35509 1.26150 +8.0000 6.0000 170504 zatom,zion,pspd +8 11 2 4 600 0 pspcod,pspxc,lmax,lloc,mmax,r2well +5.99000000 4.00000000 0.00000000 rchrg fchrg qchrg +2 2 1 0 0 nproj +1 1 extension_switch +0 7.2366985471894D+00 9.9768859532965D-01 +1 0.0000000000000D+00 -7.2644567028490D-09 1.8444153426778D-08 +2 1.0000000000000D-02 1.0665027785755D-01 -4.8085246035022D-02 +3 2.0000000000000D-02 2.1276571663443D-01 -9.5367746531287D-02 +4 3.0000000000000D-02 3.1781743822719D-01 -1.4105812652336D-01 +5 4.0000000000000D-02 4.2128838529094D-01 -1.8439350077069D-01 +6 5.0000000000000D-02 5.2267898053461D-01 -2.2465009490497D-01 +7 6.0000000000000D-02 6.2151249001462D-01 -2.6115513157727D-01 +8 7.0000000000000D-02 7.1734000048432D-01 -2.9329775875911D-01 +9 8.0000000000000D-02 8.0974492812082D-01 -3.2053881579560D-01 +10 9.0000000000000D-02 8.9834698476875D-01 -3.4241925519412D-01 +11 1.0000000000000D-01 9.8280553804507D-01 -3.5856706403073D-01 +12 1.1000000000000D-01 1.0628223130450D+00 -3.6870255777321D-01 +13 1.2000000000000D-01 1.1381433957600D+00 -3.7264195070140D-01 +14 1.3000000000000D-01 1.2085605114313D+00 -3.7029914035087D-01 +15 1.4000000000000D-01 1.2739115646607D+00 -3.6168567787708D-01 +16 1.5000000000000D-01 1.3340804419334D+00 -3.4690893127352D-01 +17 1.6000000000000D-01 1.3889960910046D+00 -3.2616848330437D-01 +18 1.7000000000000D-01 1.4386309051009D+00 -2.9975084015792D-01 +19 1.8000000000000D-01 1.4829984528333D+00 -2.6802255953254D-01 +20 1.9000000000000D-01 1.5221506068575D+00 -2.3142193750010D-01 +21 2.0000000000000D-01 1.5561741354224D+00 -1.9044942145815D-01 +22 2.1000000000000D-01 1.5851868307998D+00 -1.4565694123779D-01 +23 2.2000000000000D-01 1.6093332570006D+00 -9.7636371494331D-02 +24 2.3000000000000D-01 1.6287802059905D+00 -4.7007355458611D-02 +25 2.4000000000000D-01 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0.0000000000000D+00 +596 5.9500000000000D+00 4.8195683785881D-05 4.8201345986656D-05 0.0000000000000D+00 +597 5.9600000000000D+00 4.7248751048558D-05 4.7254308404713D-05 0.0000000000000D+00 +598 5.9700000000000D+00 4.6320665555318D-05 4.6326120034714D-05 0.0000000000000D+00 +599 5.9800000000000D+00 4.5411046775429D-05 4.5416400308397D-05 0.0000000000000D+00 +600 5.9900000000000D+00 4.4519521984744D-05 4.4524776464809D-05 0.0000000000000D+00 + +# +#ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) +#scalar-relativistic version 3.2.3 08/16/2016 +# +#While it is not required under the terms of the GNU GPL, it is +#suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) +#in any publication utilizing these pseudopotentials. +# +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile +O 8.00 1 2 4 psp8 +# +# n l f +1 0 2.00 +2 0 2.00 +2 1 4.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax +2 +# +# l, rc, ep, ncon, nbas, qcut +0 1.25000 -0.88057 4 8 8.50000 +1 1.35000 -0.33187 4 8 9.40000 +2 1.25000 0.10000 4 8 6.00000 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 +4 5 1.20000 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl +0 2 1.00000 +1 2 1.00000 +2 1 1.00000 +# +# MODEL CORE CHARGE +# icmod, fcfact, rcfact +3 4.00000 1.50000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh +-12.00 12.00 0.02 +# +# OUTPUT GRID +# rlmax, drl +6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf +0 +# nvcnf +# n l f + diff --git a/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/O/O.psp8 b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/O/O.psp8 new file mode 100644 index 0000000000..81715615c6 --- /dev/null +++ b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/O/O.psp8 @@ -0,0 +1,3665 @@ +O ONCVPSP-3.2.3.1 r_core= 1.35509 1.45563 1.26150 +8.0000 6.0000 170504 zatom,zion,pspd +8 11 2 4 600 0 pspcod,pspxc,lmax,lloc,mmax,r2well +5.99000000 4.00000000 0.00000000 rchrg fchrg qchrg +2 2 1 0 0 nproj +1 1 extension_switch +0 6.0567354683862D+00 8.2402409647555D-01 +1 0.0000000000000D+00 -2.2498329865783D-09 5.6883400767482D-09 +2 1.0000000000000D-02 9.6628298964105D-02 -3.8338277531244D-02 +3 2.0000000000000D-02 1.9288513881170D-01 -7.6200750970053D-02 +4 3.0000000000000D-02 2.8840191058960D-01 -1.1311751295130D-01 +5 4.0000000000000D-02 3.8281566855271D-01 -1.4863035920204D-01 +6 5.0000000000000D-02 4.7577186955815D-01 -1.8229841566382D-01 +7 6.0000000000000D-02 5.6692700343876D-01 -2.1370350043310D-01 +8 7.0000000000000D-02 6.5595108070714D-01 -2.4245513893020D-01 +9 8.0000000000000D-02 7.4252994619030D-01 -2.6819515639574D-01 +10 9.0000000000000D-02 8.2636738993799D-01 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5.9500000000000D+00 4.8195440415896D-05 4.8201345986656D-05 0.0000000000000D+00 +597 5.9600000000000D+00 4.7248511721169D-05 4.7254308404713D-05 0.0000000000000D+00 +598 5.9700000000000D+00 4.6320430204661D-05 4.6326120034714D-05 0.0000000000000D+00 +599 5.9800000000000D+00 4.5410815336679D-05 4.5416400308397D-05 0.0000000000000D+00 +600 5.9900000000000D+00 4.4519294394098D-05 4.4524776464809D-05 0.0000000000000D+00 + +# +#ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) +#scalar-relativistic version 3.2.3 08/16/2016 +# +#While it is not required under the terms of the GNU GPL, it is +#suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) +#in any publication utilizing these pseudopotentials. +# +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile +O 8.00 1 2 4 psp8 +# +# n l f +1 0 2.00 +2 0 2.00 +2 1 4.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax +2 +# +# l, rc, ep, ncon, nbas, qcut +0 1.35000 -0.88057 4 8 8.40000 +1 1.45000 -0.33187 4 8 9.30000 +2 1.25000 0.10000 4 8 6.00000 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 +4 5 1.20000 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl +0 2 1.00000 +1 2 1.00000 +2 1 1.00000 +# +# MODEL CORE CHARGE +# icmod, fcfact, rcfact +3 4.00000 1.50000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh +-12.00 12.00 0.02 +# +# OUTPUT GRID +# rlmax, drl +6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf +0 +# nvcnf +# n l f + diff --git a/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/P/P-sp.psp8 b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/P/P-sp.psp8 new file mode 100644 index 0000000000..514fb68296 --- /dev/null +++ b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/P/P-sp.psp8 @@ -0,0 +1,3067 @@ +P ONCVPSP-3.2.3.1 r_core= 1.40954 1.60717 1.81079 +15.0000 13.0000 170429 zatom,zion,pspd +8 11 2 4 600 0 pspcod,pspxc,lmax,lloc,mmax,r2well +5.99000000 0.00000000 0.00000000 rchrg fchrg qchrg +2 2 2 0 0 nproj +1 1 extension_switch +0 -4.8633398957102D+00 -7.3620122738006D-01 +1 0.0000000000000D+00 -2.6608937275796D-11 6.8446409651202D-10 +2 1.0000000000000D-02 7.2150944408062D-02 -5.6037238981900D-02 +3 2.0000000000000D-02 1.4414807595758D-01 -1.1179283562417D-01 +4 3.0000000000000D-02 2.1583801442269D-01 -1.6698668985829D-01 +5 4.0000000000000D-02 2.8706824344572D-01 -2.2134177269628D-01 +6 5.0000000000000D-02 3.5768753898517D-01 -2.7458562829447D-01 +7 6.0000000000000D-02 4.2754639359955D-01 -3.2645183634093D-01 +8 7.0000000000000D-02 4.9649743521046D-01 -3.7668142235834D-01 +9 8.0000000000000D-02 5.6439583901524D-01 -4.2502420419889D-01 +10 9.0000000000000D-02 6.3109973125186D-01 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1.1116625363170D-03 0.0000000000000D+00 +579 5.7800000000000D+00 1.0943101392092D-03 1.0943260071503D-03 0.0000000000000D+00 +580 5.7900000000000D+00 1.0772484620166D-03 1.0772640805197D-03 0.0000000000000D+00 +581 5.8000000000000D+00 1.0604569428792D-03 1.0604723160145D-03 0.0000000000000D+00 +582 5.8100000000000D+00 1.0439312152742D-03 1.0439463470429D-03 0.0000000000000D+00 +583 5.8200000000000D+00 1.0276669852252D-03 1.0276818795612D-03 0.0000000000000D+00 +584 5.8300000000000D+00 1.0116600300473D-03 1.0116746908180D-03 0.0000000000000D+00 +585 5.8400000000000D+00 9.9590619710434D-04 9.9592062811201D-04 0.0000000000000D+00 +586 5.8500000000000D+00 9.8040140270128D-04 9.8041560768395D-04 0.0000000000000D+00 +587 5.8600000000000D+00 9.6514163079087D-04 9.6515561342364D-04 0.0000000000000D+00 +588 5.8700000000000D+00 9.5012293184846D-04 9.5013669574455D-04 0.0000000000000D+00 +589 5.8800000000000D+00 9.3534142173097D-04 9.3535497044278D-04 0.0000000000000D+00 +590 5.8900000000000D+00 9.2079328055631D-04 9.2080661757648D-04 0.0000000000000D+00 +591 5.9000000000000D+00 9.0647475159653D-04 9.0648788035899D-04 0.0000000000000D+00 +592 5.9100000000000D+00 8.9238214018278D-04 8.9239506406375D-04 0.0000000000000D+00 +593 5.9200000000000D+00 8.7851181273351D-04 8.7852453505250D-04 0.0000000000000D+00 +594 5.9300000000000D+00 8.6486019560833D-04 8.6487271962911D-04 0.0000000000000D+00 +595 5.9400000000000D+00 8.5142377411806D-04 8.5143610304967D-04 0.0000000000000D+00 +596 5.9500000000000D+00 8.3819909151873D-04 8.3821122851640D-04 0.0000000000000D+00 +597 5.9600000000000D+00 8.2518274802351D-04 8.2519469618956D-04 0.0000000000000D+00 +598 5.9700000000000D+00 8.1237139982919D-04 8.1238316221400D-04 0.0000000000000D+00 +599 5.9800000000000D+00 7.9976175813684D-04 7.9977333773970D-04 0.0000000000000D+00 +600 5.9900000000000D+00 7.8735058831934D-04 7.8736198808938D-04 0.0000000000000D+00 + +# +#ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) +#scalar-relativistic version 3.2.3 08/16/2016 +# +#While it is not required under the terms of the GNU GPL, it is +#suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) +#in any publication utilizing these pseudopotentials. +# +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile +P 15.00 1 4 4 psp8 +# +# n l f +1 0 2.00 +2 0 2.00 +2 1 6.00 +3 0 2.00 +3 1 3.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax +2 +# +# l, rc, ep, ncon, nbas, qcut +0 1.40000 -6.39406 4 8 9.40000 +1 1.60000 -4.57505 4 8 9.00000 +2 1.80000 0.15000 4 8 9.00000 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 +4 5 1.20000 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl +0 2 5.88070 +1 2 4.37268 +2 2 2.50000 +# +# MODEL CORE CHARGE +# icmod, fcfact, rcfact +0 0.00000 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh +-12.00 12.00 0.02 +# +# OUTPUT GRID +# rlmax, drl +6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf +0 +# nvcnf +# n l f + diff --git a/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/P/P.psp8 b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/P/P.psp8 new file mode 100644 index 0000000000..a3fd8f204b --- /dev/null +++ b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/P/P.psp8 @@ -0,0 +1,3667 @@ +P ONCVPSP-3.2.3.1 r_core= 1.46089 1.55067 1.70594 +15.0000 5.0000 170429 zatom,zion,pspd +8 11 2 4 600 0 pspcod,pspxc,lmax,lloc,mmax,r2well +5.99000000 5.00000000 0.00000000 rchrg fchrg qchrg +2 2 2 0 0 nproj +1 1 extension_switch +0 6.5987217472880D+00 1.0523413858461D+00 +1 0.0000000000000D+00 -1.7843262922757D-08 4.3303683749940D-08 +2 1.0000000000000D-02 5.6646201283736D-02 -5.2493920729883D-02 +3 2.0000000000000D-02 1.1274394998422D-01 -1.0371210656417D-01 +4 3.0000000000000D-02 1.6775599342775D-01 -1.5240594702909D-01 +5 4.0000000000000D-02 2.2116724732778D-01 -1.9738051924477D-01 +6 5.0000000000000D-02 2.7249530609086D-01 -2.3752003998614D-01 +7 6.0000000000000D-02 3.2130027750217D-01 -2.7181167931989D-01 +8 7.0000000000000D-02 3.6719373804603D-01 -2.9936724176394D-01 +9 8.0000000000000D-02 4.0984662295975D-01 -3.1944226421926D-01 +10 9.0000000000000D-02 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1.1292781835174D-03 2.7537149450984D-14 +578 5.7700000000000D+00 1.1116326256261D-03 1.1116625362911D-03 2.5836178198383D-14 +579 5.7800000000000D+00 1.0942965968999D-03 1.0943260071260D-03 2.4240405045757D-14 +580 5.7900000000000D+00 1.0772351621275D-03 1.0772640804970D-03 2.2743317995266D-14 +581 5.8000000000000D+00 1.0604438810487D-03 1.0604723159931D-03 2.1338807964379D-14 +582 5.8100000000000D+00 1.0439183872203D-03 1.0439463470229D-03 2.0021143622128D-14 +583 5.8200000000000D+00 1.0276543867436D-03 1.0276818795425D-03 1.8784947900698D-14 +584 5.8300000000000D+00 1.0116476570101D-03 1.0116746908004D-03 1.7625171649610D-14 +585 5.8400000000000D+00 9.9589404545882D-04 9.9592062809548D-04 1.6537062284236D-14 +586 5.8500000000000D+00 9.8038946846823D-04 9.8041560766843D-04 1.5516209318247D-14 +587 5.8600000000000D+00 9.6512991006338D-04 9.6515561340908D-04 1.4558452043872D-14 +588 5.8700000000000D+00 9.5011142079055D-04 9.5013669573089D-04 1.3659886983234D-14 +589 5.8800000000000D+00 9.3533011657630D-04 9.3535497042996D-04 1.2816851834786D-14 +590 5.8900000000000D+00 9.2078217760687D-04 9.2080661756446D-04 1.2025910489825D-14 +591 5.9000000000000D+00 9.0646384722141D-04 9.0648788034771D-04 1.1283835863062D-14 +592 5.9100000000000D+00 8.9237143081689D-04 8.9239506405316D-04 1.0587589761016D-14 +593 5.9200000000000D+00 8.7850129487642D-04 8.7852453504256D-04 9.9343547455303D-15 +594 5.9300000000000D+00 8.6484986582303D-04 8.6487271961979D-04 9.3214716520889D-15 +595 5.9400000000000D+00 8.5141362902982D-04 8.5143610304092D-04 8.7464455958051D-15 +596 5.9500000000000D+00 8.3818912781397D-04 8.3821122850819D-04 8.2069357224736D-15 +597 5.9600000000000D+00 8.2517296244861D-04 8.2519469618186D-04 7.7007456432102D-15 +598 5.9700000000000D+00 8.1236178918948D-04 8.1238316220678D-04 7.2258134197139D-15 +599 5.9800000000000D+00 7.9975231929542D-04 7.9977333773292D-04 6.7801938001720D-15 +600 5.9900000000000D+00 7.8734131819609D-04 7.8736198808302D-04 6.3620875896047D-15 + +# +#ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) +#scalar-relativistic version 3.2.3 08/16/2016 +# +#While it is not required under the terms of the GNU GPL, it is +#suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) +#in any publication utilizing these pseudopotentials. +# +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile +P 15.00 3 2 4 psp8 +# +# n l f +1 0 2.00 +2 0 2.00 +2 1 6.00 +3 0 2.00 +3 1 3.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax +2 +# +# l, rc, ep, ncon, nbas, qcut +0 1.45000 -0.51336 4 9 6.20000 +1 1.55000 -0.20237 4 9 6.60000 +2 1.70000 0.05000 4 9 6.60000 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 +4 5 1.45000 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl +0 2 3.00000 +1 2 2.50000 +2 2 2.00000 +# +# MODEL CORE CHARGE +# icmod, fcfact, rcfact +3 5.00000 1.10000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh +-12.00 12.00 0.02 +# +# OUTPUT GRID +# rlmax, drl +6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf +0 +# nvcnf +# n l f + diff --git a/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Si/Si-sp.psp8 b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Si/Si-sp.psp8 new file mode 100644 index 0000000000..4cf0fccea5 --- /dev/null +++ b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Si/Si-sp.psp8 @@ -0,0 +1,3067 @@ +Si ONCVPSP-3.2.3.1 r_core= 1.40591 1.60303 1.80612 +14.0000 12.0000 170510 zatom,zion,pspd +8 11 2 4 600 0 pspcod,pspxc,lmax,lloc,mmax,r2well +5.99000000 0.00000000 0.00000000 rchrg fchrg qchrg +2 2 2 0 0 nproj +1 1 extension_switch +0 1.8360502489818D+00 -1.6640355119901D+00 +1 0.0000000000000D+00 -1.4562797634454D-09 2.2523943821184D-10 +2 1.0000000000000D-02 1.3612856380636D-01 4.3769627133219D-02 +3 2.0000000000000D-02 2.7142247219746D-01 8.7545530854770D-02 +4 3.0000000000000D-02 4.0505283069588D-01 1.3133342199120D-01 +5 4.0000000000000D-02 5.3620222249892D-01 1.7513788582009D-01 +6 5.0000000000000D-02 6.6407033718586D-01 2.1896183417434D-01 +7 6.0000000000000D-02 7.8787946830904D-01 2.6280597523998D-01 +8 7.0000000000000D-02 9.0687983788597D-01 3.0666830667848D-01 +9 8.0000000000000D-02 1.0203547072664D+00 3.5054363747952D-01 +10 9.0000000000000D-02 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0.0000000000000D+00 +590 5.8900000000000D+00 1.5798394495417D-03 1.5798282920150D-03 0.0000000000000D+00 +591 5.9000000000000D+00 1.5581363543903D-03 1.5581252358608D-03 0.0000000000000D+00 +592 5.9100000000000D+00 1.5367388881221D-03 1.5367278097151D-03 0.0000000000000D+00 +593 5.9200000000000D+00 1.5156426045559D-03 1.5156315673560D-03 0.0000000000000D+00 +594 5.9300000000000D+00 1.4948431248072D-03 1.4948321298595D-03 0.0000000000000D+00 +595 5.9400000000000D+00 1.4743361362257D-03 1.4743251845366D-03 0.0000000000000D+00 +596 5.9500000000000D+00 1.4541173913500D-03 1.4541064838883D-03 0.0000000000000D+00 +597 5.9600000000000D+00 1.4341827068613D-03 1.4341718445590D-03 0.0000000000000D+00 +598 5.9700000000000D+00 1.4145279626182D-03 1.4145171463712D-03 0.0000000000000D+00 +599 5.9800000000000D+00 1.3951491006413D-03 1.3951383313104D-03 0.0000000000000D+00 +600 5.9900000000000D+00 1.3760421241156D-03 1.3760314025275D-03 0.0000000000000D+00 + +# +#ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) +#scalar-relativistic version 3.2.3 08/16/2016 +# +#While it is not required under the terms of the GNU GPL, it is +#suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) +#in any publication utilizing these pseudopotentials. +# +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile +Si 14.00 1 4 4 psp8 +# +# n l f +1 0 2.00 +2 0 2.00 +2 1 6.00 +3 0 2.00 +3 1 2.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax +2 +# +# l, rc, ep, ncon, nbas, qcut +0 1.40000 -5.12655 4 8 9.20000 +1 1.60000 -3.51174 4 8 9.00000 +2 1.80000 0.15000 4 8 8.60000 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 +4 5 1.00000 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl +0 2 4.72918 +1 2 3.36175 +2 2 2.50000 +# +# MODEL CORE CHARGE +# icmod, fcfact, rcfact +0 0.00000 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh +-12.00 12.00 0.02 +# +# OUTPUT GRID +# rlmax, drl +6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf +0 +# nvcnf +# n l f + diff --git a/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Si/Si.psp8 b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Si/Si.psp8 new file mode 100644 index 0000000000..094d0c2fe5 --- /dev/null +++ b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/Si/Si.psp8 @@ -0,0 +1,3667 @@ +Si ONCVPSP-3.2.3.1 r_core= 1.60303 1.72197 1.91712 +14.0000 4.0000 170510 zatom,zion,pspd +8 11 2 4 600 0 pspcod,pspxc,lmax,lloc,mmax,r2well +5.99000000 4.00000000 0.00000000 rchrg fchrg qchrg +2 2 2 0 0 nproj +1 1 extension_switch +0 5.1689652486091D+00 8.2988268871509D-01 +1 0.0000000000000D+00 -5.6328875175371D-09 1.2523277137522D-08 +2 1.0000000000000D-02 3.1595742774954D-02 -7.8297391246428D-03 +3 2.0000000000000D-02 6.2932621167537D-02 -1.5104637953209D-02 +4 3.0000000000000D-02 9.3756650477386D-02 -2.1280726187726D-02 +5 4.0000000000000D-02 1.2382351921221D-01 -2.5835581967505D-02 +6 5.0000000000000D-02 1.5290321177103D-01 -2.8278630456707D-02 +7 6.0000000000000D-02 1.8078437851144D-01 -2.8160880765399D-02 +8 7.0000000000000D-02 2.0727837573680D-01 -2.5083928969944D-02 +9 8.0000000000000D-02 2.3222290377250D-01 -1.8708067521868D-02 +10 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6.1205173707996D-13 +595 5.9400000000000D+00 1.4743030258904D-03 1.4743251839580D-03 5.7866317005956D-13 +596 5.9500000000000D+00 1.4540846979142D-03 1.4541064833412D-03 5.4709872882254D-13 +597 5.9600000000000D+00 1.4341504249860D-03 1.4341718440417D-03 5.1725835188627D-13 +598 5.9700000000000D+00 1.4144960870346D-03 1.4145171458821D-03 4.8904778609947D-13 +599 5.9800000000000D+00 1.3951176261493D-03 1.3951383308480D-03 4.6237802796975D-13 +600 5.9900000000000D+00 1.3760110455835D-03 1.3760314020903D-03 4.3716480956818D-13 + +# +#ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) +#scalar-relativistic version 3.2.3 08/16/2016 +# +#While it is not required under the terms of the GNU GPL, it is +#suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) +#in any publication utilizing these pseudopotentials. +# +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile +Si 14.00 3 2 4 psp8 +# +# n l f +1 0 2.00 +2 0 2.00 +2 1 6.00 +3 0 2.00 +3 1 2.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax +2 +# +# l, rc, ep, ncon, nbas, qcut +0 1.60000 -0.39736 4 9 6.40000 +1 1.71000 -0.14998 4 9 6.40000 +2 1.90000 0.05000 4 9 6.40000 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 +4 5 1.60000 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl +0 2 2.50000 +1 2 2.50000 +2 2 1.50000 +# +# MODEL CORE CHARGE +# icmod, fcfact, rcfact +3 4.00000 1.30000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh +-12.00 12.00 0.02 +# +# OUTPUT GRID +# rlmax, drl +6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf +0 +# nvcnf +# n l f + diff --git a/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/standard.djson b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/standard.djson new file mode 100644 index 0000000000..599a75d8f5 --- /dev/null +++ b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/standard.djson @@ -0,0 +1,122 @@ +{ + "dojo_info": { + "pp_type": "NC", + "description": "Standard table designed for GS applications (Small set of elements for testing purposes: Si, O, P, Al, Fe)", + "xc_name": "PBE", + "references": ["Dojo paper"], + "authors": ["M. J. van Setten", "M. Giantomassi"], + "dojo_dir": "ONCVPSP-PBE-PDv0.4" + }, + "pseudos_metadata": { + "O": { + "basename": "O.psp8", + "Z_val": 6.0, + "l_max": 2, + "md5": "abbcf0645b4a6d69360cd16bcad3e730", + "dfact_meV": 2.0239038146491146, + "dfactprime_meV": 6.525523051760969, + "tags": [ + "GW" + ], + "hints": { + "high": { + "ecut": 48.0 + }, + "low": { + "ecut": 36.0 + }, + "normal": { + "ecut": 42.0 + } + } + }, + "Al": { + "basename": "Al.psp8", + "Z_val": 3.0, + "l_max": 2, + "md5": "57224185a50eb565dff7432e4aa35376", + "dfact_meV": 0.5415764904603724, + "dfactprime_meV": 1.2693657960935043, + "tags": [ + " " + ], + "hints": { + "high": { + "ecut": 26.0 + }, + "low": { + "ecut": 16.0 + }, + "normal": { + "ecut": 20.0 + } + } + }, + "Si": { + "basename": "Si.psp8", + "Z_val": 4.0, + "l_max": 2, + "md5": "45c393525680abc7b25445b8ec62bf83", + "dfact_meV": 0.14564468100850006, + "dfactprime_meV": 0.24230171913924484, + "tags": [ + " " + ], + "hints": { + "high": { + "ecut": 24.0 + }, + "low": { + "ecut": 14.0 + }, + "normal": { + "ecut": 18.0 + } + } + }, + "P": { + "basename": "P.psp8", + "Z_val": 5.0, + "l_max": 2, + "md5": "35592df3bc13b6b759c1537803003316", + "dfact_meV": 0.14214001236980747, + "dfactprime_meV": 0.29291384117786673, + "tags": [ + " " + ], + "hints": { + "high": { + "ecut": 28.0 + }, + "low": { + "ecut": 18.0 + }, + "normal": { + "ecut": 22.0 + } + } + }, + "Fe": { + "basename": "Fe-sp.psp8", + "Z_val": 16.0, + "l_max": 2, + "md5": "b1a6c6085aee6d23d80253cdcecbb587", + "dfact_meV": 5.599087963470159, + "dfactprime_meV": 9.21433064020024, + "tags": [ + " GW" + ], + "hints": { + "high": { + "ecut": 53.0 + }, + "low": { + "ecut": 41.0 + }, + "normal": { + "ecut": 45.0 + } + } + } + } +} diff --git a/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/stringent.djson b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/stringent.djson new file mode 100644 index 0000000000..7c518a4685 --- /dev/null +++ b/tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4/stringent.djson @@ -0,0 +1,122 @@ +{ + "dojo_info": { + "pp_type": "NC", + "description": "Stringent table designed for GS applications (Small set of elements for testing purposes: Si, O, P, Al, Fe)", + "xc_name": "PBE", + "references": ["Dojo paper"], + "authors": ["M. J. van Setten", "M. Giantomassi"], + "dojo_dir": "ONCVPSP-PBE-PDv0.4" + }, + "pseudos_metadata": { + "O": { + "basename": "O-high.psp8", + "Z_val": 6.0, + "l_max": 2, + "md5": "0809a764092335b3e47855c0f93d8a2b", + "dfact_meV": 1.2560607157786003, + "dfactprime_meV": 4.040285582324057, + "tags": [ + "GW" + ], + "hints": { + "high": { + "ecut": 52.0 + }, + "low": { + "ecut": 42.0 + }, + "normal": { + "ecut": 46.0 + } + } + }, + "Al": { + "basename": "Al.psp8", + "Z_val": 3.0, + "l_max": 2, + "md5": "57224185a50eb565dff7432e4aa35376", + "dfact_meV": 0.5415764904603724, + "dfactprime_meV": 1.2693657960935043, + "tags": [ + " " + ], + "hints": { + "high": { + "ecut": 26.0 + }, + "low": { + "ecut": 16.0 + }, + "normal": { + "ecut": 20.0 + } + } + }, + "Si": { + "basename": "Si.psp8", + "Z_val": 4.0, + "l_max": 2, + "md5": "45c393525680abc7b25445b8ec62bf83", + "dfact_meV": 0.14564468100850006, + "dfactprime_meV": 0.24230171913924484, + "tags": [ + " " + ], + "hints": { + "high": { + "ecut": 24.0 + }, + "low": { + "ecut": 14.0 + }, + "normal": { + "ecut": 18.0 + } + } + }, + "P": { + "basename": "P.psp8", + "Z_val": 5.0, + "l_max": 2, + "md5": "35592df3bc13b6b759c1537803003316", + "dfact_meV": 0.14214001236980747, + "dfactprime_meV": 0.29291384117786673, + "tags": [ + " " + ], + "hints": { + "high": { + "ecut": 28.0 + }, + "low": { + "ecut": 18.0 + }, + "normal": { + "ecut": 22.0 + } + } + }, + "Fe": { + "basename": "Fe-sp-high.psp8", + "Z_val": 16.0, + "l_max": 2, + "md5": "f2747631c0e1355c32e3434d3bcc8f2b", + "dfact_meV": 2.09212558024094, + "dfactprime_meV": 3.0559749725257976, + "tags": [ + " GW" + ], + "hints": { + "high": { + "ecut": 65.0 + }, + "low": { + "ecut": 55.0 + }, + "normal": { + "ecut": 59.0 + } + } + } + } +} diff --git a/tests/test_data/aims/basis-gw-convergence-o2/static-1/inputs/control.in.gz b/tests/test_data/aims/basis-gw-convergence-o2/static-1/inputs/control.in.gz new file mode 100644 index 0000000000..8e85e66e67 Binary files /dev/null and b/tests/test_data/aims/basis-gw-convergence-o2/static-1/inputs/control.in.gz differ diff --git a/tests/test_data/aims/basis-gw-convergence-o2/static-1/inputs/geometry.in.gz b/tests/test_data/aims/basis-gw-convergence-o2/static-1/inputs/geometry.in.gz new file mode 100644 index 0000000000..34e58f0b17 Binary files /dev/null and b/tests/test_data/aims/basis-gw-convergence-o2/static-1/inputs/geometry.in.gz differ diff --git a/tests/test_data/aims/basis-gw-convergence-o2/static-1/inputs/parameters.json b/tests/test_data/aims/basis-gw-convergence-o2/static-1/inputs/parameters.json new file mode 100644 index 0000000000..d7804d91eb --- /dev/null +++ b/tests/test_data/aims/basis-gw-convergence-o2/static-1/inputs/parameters.json @@ -0,0 +1,7 @@ +{ + "xc": "pbe", + "relativistic": "atomic_zora scalar", + "anacon_type": "two-pole", + "qpe_calc": "gw", + "species_dir": "/home/andrey/workspace/atomate2/tests/aims/species_dir/light" +} diff --git a/tests/test_data/aims/basis-gw-convergence-o2/static-1/outputs/aims.out.gz b/tests/test_data/aims/basis-gw-convergence-o2/static-1/outputs/aims.out.gz new file mode 100644 index 0000000000..9a45302ba8 Binary files /dev/null and b/tests/test_data/aims/basis-gw-convergence-o2/static-1/outputs/aims.out.gz differ diff --git a/tests/test_data/aims/basis-gw-convergence-o2/static-1/outputs/convergence.json b/tests/test_data/aims/basis-gw-convergence-o2/static-1/outputs/convergence.json new file mode 100644 index 0000000000..8d7209bd81 --- /dev/null +++ b/tests/test_data/aims/basis-gw-convergence-o2/static-1/outputs/convergence.json @@ -0,0 +1 @@ +{"criterion_name": "vbm", "criterion_values": [-6.09530754], "convergence_field_name": "species_dir", "convergence_field_values": ["/home/andrey/workspace/atomate2/tests/aims/species_dir/light"], "converged": false, "idx": 0} diff --git a/tests/test_data/aims/basis-gw-convergence-o2/static-2/inputs/control.in.gz b/tests/test_data/aims/basis-gw-convergence-o2/static-2/inputs/control.in.gz new file mode 100644 index 0000000000..ee0c4686ba Binary files /dev/null and b/tests/test_data/aims/basis-gw-convergence-o2/static-2/inputs/control.in.gz differ diff --git a/tests/test_data/aims/basis-gw-convergence-o2/static-2/inputs/geometry.in.gz b/tests/test_data/aims/basis-gw-convergence-o2/static-2/inputs/geometry.in.gz new file mode 100644 index 0000000000..2b91e33fa9 Binary files /dev/null and b/tests/test_data/aims/basis-gw-convergence-o2/static-2/inputs/geometry.in.gz differ diff --git a/tests/test_data/aims/basis-gw-convergence-o2/static-2/inputs/parameters.json b/tests/test_data/aims/basis-gw-convergence-o2/static-2/inputs/parameters.json new file mode 100644 index 0000000000..d535ab4a86 --- /dev/null +++ b/tests/test_data/aims/basis-gw-convergence-o2/static-2/inputs/parameters.json @@ -0,0 +1,7 @@ +{ + "xc": "pbe", + "relativistic": "atomic_zora scalar", + "anacon_type": "two-pole", + "qpe_calc": "gw", + "species_dir": "/home/andrey/workspace/atomate2/tests/aims/species_dir/tight" +} diff --git a/tests/test_data/aims/basis-gw-convergence-o2/static-2/outputs/aims.out.gz b/tests/test_data/aims/basis-gw-convergence-o2/static-2/outputs/aims.out.gz new file mode 100644 index 0000000000..16e9258e8a Binary files /dev/null and b/tests/test_data/aims/basis-gw-convergence-o2/static-2/outputs/aims.out.gz differ diff --git a/tests/test_data/aims/basis-gw-convergence-o2/static-2/outputs/convergence.json b/tests/test_data/aims/basis-gw-convergence-o2/static-2/outputs/convergence.json new file mode 100644 index 0000000000..d3abc388b5 --- /dev/null +++ b/tests/test_data/aims/basis-gw-convergence-o2/static-2/outputs/convergence.json @@ -0,0 +1 @@ +{"criterion_name": "vbm", "criterion_values": [-6.09530754, -6.14125161], "convergence_field_name": "species_dir", "convergence_field_values": ["/home/andrey/workspace/atomate2/tests/aims/species_dir/light", "/home/andrey/workspace/atomate2/tests/aims/species_dir/tight"], "converged": true, "idx": 1} diff --git a/tests/test_data/aims/double-relax-si/relax-1/inputs/control.in.gz b/tests/test_data/aims/double-relax-si/relax-1/inputs/control.in.gz new file mode 100644 index 0000000000..d9c370ef9a Binary files /dev/null and b/tests/test_data/aims/double-relax-si/relax-1/inputs/control.in.gz differ diff --git a/tests/test_data/aims/double-relax-si/relax-1/inputs/geometry.in.gz b/tests/test_data/aims/double-relax-si/relax-1/inputs/geometry.in.gz new file mode 100644 index 0000000000..112e2e9ee5 Binary files /dev/null and b/tests/test_data/aims/double-relax-si/relax-1/inputs/geometry.in.gz differ diff --git a/tests/test_data/aims/double-relax-si/relax-1/inputs/parameters.json b/tests/test_data/aims/double-relax-si/relax-1/inputs/parameters.json new file mode 100644 index 0000000000..df77f0481f --- /dev/null +++ b/tests/test_data/aims/double-relax-si/relax-1/inputs/parameters.json @@ -0,0 +1,12 @@ +{ + "xc": "pbe", + "relativistic": "atomic_zora scalar", + "relax_geometry": "trm 1.000000e-03", + "relax_unit_cell": "full", + "k_grid": [ + 2, + 2, + 2 + ], + "species_dir": "/home/andrey/workspace/atomate2-fhi-aims/tests/species_dir/light" +} diff --git a/tests/test_data/aims/double-relax-si/relax-1/outputs/aims.out.gz b/tests/test_data/aims/double-relax-si/relax-1/outputs/aims.out.gz new file mode 100644 index 0000000000..dadedac8f8 Binary files /dev/null and b/tests/test_data/aims/double-relax-si/relax-1/outputs/aims.out.gz differ diff --git a/tests/test_data/aims/double-relax-si/relax-1/outputs/geometry.in.next_step.gz b/tests/test_data/aims/double-relax-si/relax-1/outputs/geometry.in.next_step.gz new file mode 100644 index 0000000000..877d725bd2 Binary files /dev/null and b/tests/test_data/aims/double-relax-si/relax-1/outputs/geometry.in.next_step.gz differ diff --git a/tests/test_data/aims/double-relax-si/relax-1/outputs/hessian.aims.gz b/tests/test_data/aims/double-relax-si/relax-1/outputs/hessian.aims.gz new file mode 100644 index 0000000000..cf260ff15e Binary files /dev/null and b/tests/test_data/aims/double-relax-si/relax-1/outputs/hessian.aims.gz differ diff --git a/tests/test_data/aims/double-relax-si/relax-1/outputs/parameters.json b/tests/test_data/aims/double-relax-si/relax-1/outputs/parameters.json new file mode 100644 index 0000000000..df77f0481f --- /dev/null +++ b/tests/test_data/aims/double-relax-si/relax-1/outputs/parameters.json @@ -0,0 +1,12 @@ +{ + "xc": "pbe", + "relativistic": "atomic_zora scalar", + "relax_geometry": "trm 1.000000e-03", + "relax_unit_cell": "full", + "k_grid": [ + 2, + 2, + 2 + ], + "species_dir": "/home/andrey/workspace/atomate2-fhi-aims/tests/species_dir/light" +} diff --git a/tests/test_data/aims/double-relax-si/relax-2/inputs/control.in.gz b/tests/test_data/aims/double-relax-si/relax-2/inputs/control.in.gz new file mode 100644 index 0000000000..491e8d6174 Binary files 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b/tests/test_data/qchem/water_single_point/outputs/mol.qin.gz new file mode 100644 index 0000000000..bb34b43366 Binary files /dev/null and b/tests/test_data/qchem/water_single_point/outputs/mol.qin.gz differ diff --git a/tests/test_data/qchem/water_single_point/outputs/mol.qin.orig.gz b/tests/test_data/qchem/water_single_point/outputs/mol.qin.orig.gz new file mode 100644 index 0000000000..43b8eee336 Binary files /dev/null and b/tests/test_data/qchem/water_single_point/outputs/mol.qin.orig.gz differ diff --git a/tests/test_data/qchem/water_single_point/outputs/mol.qout.gz b/tests/test_data/qchem/water_single_point/outputs/mol.qout.gz new file mode 100644 index 0000000000..edc4ea953b Binary files /dev/null and b/tests/test_data/qchem/water_single_point/outputs/mol.qout.gz differ diff --git a/tests/test_data/structures/BaTiO3.cif b/tests/test_data/structures/BaTiO3.cif new file mode 100644 index 0000000000..df0e6eee84 --- /dev/null +++ b/tests/test_data/structures/BaTiO3.cif @@ -0,0 +1,37 @@ +# generated using pymatgen +data_BaTiO3 +_symmetry_space_group_name_H-M 'P 1' +_cell_length_a 4.00768164 +_cell_length_b 4.00768164 +_cell_length_c 4.00768164 +_cell_angle_alpha 90.00000000 +_cell_angle_beta 90.00000000 +_cell_angle_gamma 90.00000000 +_symmetry_Int_Tables_number 1 +_chemical_formula_structural BaTiO3 +_chemical_formula_sum 'Ba1 Ti1 O3' +_cell_volume 64.36942706 +_cell_formula_units_Z 1 +loop_ + _symmetry_equiv_pos_site_id + _symmetry_equiv_pos_as_xyz + 1 'x, y, z' +loop_ + _atom_type_symbol + _atom_type_oxidation_number + Ba2+ 2.0 + Ti4+ 4.0 + O2- -2.0 +loop_ + _atom_site_type_symbol + _atom_site_label + _atom_site_symmetry_multiplicity + _atom_site_fract_x + _atom_site_fract_y + _atom_site_fract_z + _atom_site_occupancy + Ba2+ Ba0 1 0.50000000 0.50000000 0.50000000 1 + Ti4+ Ti1 1 0.00000000 0.00000000 0.00000000 1 + O2- O2 1 0.50000000 0.00000000 0.00000000 1 + O2- O3 1 0.00000000 0.50000000 0.00000000 1 + O2- O4 1 0.00000000 0.00000000 0.50000000 1 diff --git a/tests/test_data/structures/SrTiO3.cif b/tests/test_data/structures/SrTiO3.cif new file mode 100644 index 0000000000..2b76c6f1d1 --- /dev/null +++ b/tests/test_data/structures/SrTiO3.cif @@ -0,0 +1,81 @@ +# generated using pymatgen +data_SrTiO3 +_symmetry_space_group_name_H-M Pm-3m +_cell_length_a 3.91270131 +_cell_length_b 3.91270131 +_cell_length_c 3.91270131 +_cell_angle_alpha 90.00000000 +_cell_angle_beta 90.00000000 +_cell_angle_gamma 90.00000000 +_symmetry_Int_Tables_number 221 +_chemical_formula_structural SrTiO3 +_chemical_formula_sum 'Sr1 Ti1 O3' +_cell_volume 59.90045031 +_cell_formula_units_Z 1 +loop_ + _symmetry_equiv_pos_site_id + _symmetry_equiv_pos_as_xyz + 1 'x, y, z' + 2 '-x, -y, -z' + 3 '-y, x, z' + 4 'y, -x, -z' + 5 '-x, -y, z' + 6 'x, y, -z' + 7 'y, -x, z' + 8 '-y, x, -z' + 9 'x, -y, -z' + 10 '-x, y, z' + 11 '-y, -x, -z' + 12 'y, x, z' + 13 '-x, y, -z' + 14 'x, -y, z' + 15 'y, x, -z' + 16 '-y, -x, z' + 17 'z, x, y' + 18 '-z, -x, -y' + 19 'z, -y, x' + 20 '-z, y, -x' + 21 'z, -x, -y' + 22 '-z, x, y' + 23 'z, y, -x' + 24 '-z, -y, x' + 25 '-z, x, -y' + 26 'z, -x, y' + 27 '-z, -y, -x' + 28 'z, y, x' + 29 '-z, -x, y' + 30 'z, x, -y' + 31 '-z, y, x' + 32 'z, -y, -x' + 33 'y, z, x' + 34 '-y, -z, -x' + 35 'x, z, -y' + 36 '-x, -z, y' + 37 '-y, z, -x' + 38 'y, -z, x' + 39 '-x, z, y' + 40 'x, -z, -y' + 41 '-y, -z, x' + 42 'y, z, -x' + 43 '-x, -z, -y' + 44 'x, z, y' + 45 'y, -z, -x' + 46 '-y, z, x' + 47 'x, -z, y' + 48 '-x, z, -y' +loop_ + _atom_type_symbol + Sr + Ti + O2 +loop_ + _atom_site_type_symbol + _atom_site_label + _atom_site_symmetry_multiplicity + _atom_site_fract_x + _atom_site_fract_y + _atom_site_fract_z + _atom_site_occupancy + Sr Sr 1 0.00000000 0.00000000 0.00000000 1 + Ti Ti 1 0.50000000 0.50000000 0.50000000 1 + O O 3 0.00000000 0.50000000 0.50000000 1 diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/INCAR b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/INCAR new file mode 100644 index 0000000000..500fbd2d78 --- /dev/null +++ b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/INCAR @@ -0,0 +1,18 @@ +ALGO = Fast +EDIFF = 0.0001 +ENCUT = 520 +IBRION = 2 +ISIF = 3 +ISMEAR = -5 +ISPIN = 2 +LASPH = True +LCHARG = False +LMAXMIX = 4 +LORBIT = 11 +LREAL = Auto +LWAVE = False +MAGMOM = 2*2.758 +NELM = 100 +NSW = 99 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/KPOINTS b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/KPOINTS new file mode 100644 index 0000000000..bc596ffe8c --- /dev/null +++ b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 211 / number of atoms +0 +Gamma +5 5 3 diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/POSCAR b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/POSCAR new file mode 100644 index 0000000000..e10a1b50b1 --- /dev/null +++ b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/POSCAR @@ -0,0 +1,10 @@ +Fe2 +1.0 + 2.3361450900000000 0.0001116700000000 -0.8258229300000000 + -1.1680779800000001 2.0230472399999999 -0.8260822000000000 + 1.1700738700000000 2.0273050000000001 3.3103279600000000 +Fe +2 +direct + 0.5000000200000000 0.5000000800000000 0.4999999900000000 Fe + 0.9999999800000000 0.9999999200000000 0.0000000100000000 Fe diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/POTCAR.spec b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/POTCAR.spec new file mode 100644 index 0000000000..012adc2642 --- /dev/null +++ b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/POTCAR.spec @@ -0,0 +1 @@ +Fe_pv diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/outputs/CHGCAR.gz b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/outputs/CHGCAR.gz new file mode 100644 index 0000000000..748fdae87b Binary files /dev/null and b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/outputs/CHGCAR.gz differ diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/outputs/CONTCAR.gz 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--git a/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/outputs/custodian.json.gz b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/outputs/custodian.json.gz new file mode 100644 index 0000000000..deb0136a5e Binary files /dev/null and b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/outputs/vasprun.xml.gz b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..ce617d5edf Binary files /dev/null and b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/INCAR b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/INCAR new file mode 100644 index 0000000000..f372b1bb55 --- /dev/null +++ b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/INCAR @@ -0,0 +1,18 @@ +ALGO = Fast +EDIFF = 0.0001 +ENCUT = 520 +IBRION = 2 +ISIF = 3 +ISMEAR = -5 +ISPIN = 2 +LASPH = True +LCHARG = False +LMAXMIX = 4 +LORBIT = 11 +LREAL = Auto +LWAVE = False +MAGMOM = 1*2.106 1*2.107 +NELM = 100 +NSW = 99 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/KPOINTS b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/KPOINTS new file mode 100644 index 0000000000..5490d2f1ea --- /dev/null +++ b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 220 / number of atoms +0 +Gamma +5 5 3 diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/POSCAR b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/POSCAR new file mode 100644 index 0000000000..7f93a19b59 --- /dev/null +++ b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/POSCAR @@ -0,0 +1,10 @@ +Fe2 +1.0 + 2.3247697431142709 0.0011158394059855 -0.8224083286119700 + -1.1615226345878924 2.0137000999124477 -0.8226732920954348 + 1.1372826593766157 1.9704788611038830 3.2175225091681869 +Fe 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file mode 100644 index 0000000000..a1a185998f Binary files /dev/null and b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/outputs/vasprun.xml.gz b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..4d0f722ef3 Binary files /dev/null and b/tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/INCAR b/tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/INCAR new file mode 100644 index 0000000000..e5188468d2 --- /dev/null +++ b/tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/INCAR @@ -0,0 +1,19 @@ +ALGO = Normal +EDIFF = 1e-06 +ENCUT = 520 +IBRION = -1 +ISMEAR = -5 +ISPIN = 2 +ISYM = 0 +LASPH = True +LCHARG = True +LMAXMIX = 4 +LORBIT = 11 +LREAL = False +LWAVE = True +MAGMOM = 2*2.105 +NBANDS = 18 +NELM = 100 +NSW = 0 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/KPOINTS b/tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/KPOINTS new file mode 100644 index 0000000000..9deeb56b33 --- /dev/null +++ b/tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 221 / number of atoms +0 +Gamma +5 5 3 diff --git a/tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/POSCAR b/tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/POSCAR new file mode 100644 index 0000000000..0cfb8d7ad3 --- /dev/null +++ b/tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/POSCAR @@ -0,0 +1,10 @@ +Fe2 +1.0 + 2.3191222174320663 0.0022375575036685 -0.8210990887096972 + -1.1577271585521238 2.0093705129625041 -0.8213633337288552 + 1.1366928212633334 1.9694568925378289 3.2158537811988110 +Fe +2 +direct + 0.4999999975681035 0.5000000220874199 0.5000000028567015 Fe + 0.0000000024318965 0.9999999779125801 0.9999999971432985 Fe diff --git 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b/tests/test_data/vasp/H_Graphite/relax_1_(0)/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/H_Graphite/relax_1_(1)/inputs/INCAR b/tests/test_data/vasp/H_Graphite/relax_1_(1)/inputs/INCAR new file mode 100644 index 0000000000..6157886906 --- /dev/null +++ b/tests/test_data/vasp/H_Graphite/relax_1_(1)/inputs/INCAR @@ -0,0 +1,28 @@ +ALGO = All +EDIFF = 1e-05 +EDIFFG = -0.1 +ENAUG = 1360 +ENCUT = 680 +IBRION = 2 +ISIF = 2 +ISMEAR = 0 +ISPIN = 2 +LAECHG = True +LASPH = True +LCHARG = True +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = Auto +LVTOT = True +LWAVE = True +MAGMOM = 6*0.6 +METAGGA = R2scan +NCORE = 12 +NELM = 200 +NGX = 18 +NGY = 18 +NGZ = 60 +NSW = 99 +PREC = Accurate +SIGMA = 0.2 diff --git a/tests/test_data/vasp/H_Graphite/relax_1_(1)/inputs/KPOINTS b/tests/test_data/vasp/H_Graphite/relax_1_(1)/inputs/KPOINTS new file mode 100644 index 0000000000..9bcad4fb60 --- /dev/null +++ b/tests/test_data/vasp/H_Graphite/relax_1_(1)/inputs/KPOINTS @@ -0,0 +1,4 @@ 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+ISPIN = 2 +LAECHG = True +LASPH = True +LCHARG = True +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = Auto +LVTOT = True +LWAVE = True +MAGMOM = 6*0.6 +METAGGA = R2scan +NCORE = 12 +NELM = 200 +NGX = 18 +NGY = 18 +NGZ = 60 +NSW = 99 +PREC = Accurate +SIGMA = 0.2 diff --git a/tests/test_data/vasp/H_Graphite/relax_1_(2)/inputs/KPOINTS b/tests/test_data/vasp/H_Graphite/relax_1_(2)/inputs/KPOINTS new file mode 100644 index 0000000000..9bcad4fb60 --- /dev/null +++ b/tests/test_data/vasp/H_Graphite/relax_1_(2)/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 88 / number of atoms +0 +Gamma +3 3 1 diff --git a/tests/test_data/vasp/H_Graphite/relax_1_(2)/inputs/POSCAR b/tests/test_data/vasp/H_Graphite/relax_1_(2)/inputs/POSCAR new file mode 100644 index 0000000000..e2b2d38465 --- /dev/null +++ b/tests/test_data/vasp/H_Graphite/relax_1_(2)/inputs/POSCAR @@ -0,0 +1,14 @@ +H2 C4 +1.0 + 1.2338620000000000 -2.1371120000000001 0.0000000000000000 + 1.2338620000000000 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b/tests/test_data/vasp/H_Graphite/static_0/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 88 / number of atoms +0 +Gamma +4 4 1 diff --git a/tests/test_data/vasp/H_Graphite/static_0/inputs/POSCAR b/tests/test_data/vasp/H_Graphite/static_0/inputs/POSCAR new file mode 100644 index 0000000000..3a506ad1da --- /dev/null +++ b/tests/test_data/vasp/H_Graphite/static_0/inputs/POSCAR @@ -0,0 +1,12 @@ +C4 +1.0 + 1.2338620000000000 -2.1371120000000001 0.0000000000000000 + 1.2338620000000000 2.1371120000000001 0.0000000000000000 + 0.0000000000000000 0.0000000000000000 8.6850380000000005 +C +4 +direct + 0.0000000000000000 0.0000000000000000 0.7500000000000000 C + 0.0000000000000000 0.0000000000000000 0.2500000000000000 C + 0.3333330000000032 0.6666669999999968 0.7500000000000000 C + 0.6666669999999968 0.3333330000000032 0.2500000000000000 C diff --git a/tests/test_data/vasp/H_Graphite/static_0/inputs/POTCAR.spec b/tests/test_data/vasp/H_Graphite/static_0/inputs/POTCAR.spec new file 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mode 100644 index 0000000000..7958558086 --- /dev/null +++ b/tests/test_data/vasp/H_Graphite/static_1/inputs/INCAR @@ -0,0 +1,27 @@ +ALGO = Fast +EDIFF = 1e-05 +EDIFFG = -0.1 +ENAUG = 1360 +ENCUT = 680 +ISIF = 2 +ISMEAR = -5 +ISPIN = 2 +LAECHG = True +LASPH = True +LCHARG = True +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 1*-0.331 2*-0.215 2*0.21 +METAGGA = R2scan +NCORE = 12 +NELM = 200 +NGX = 18 +NGY = 18 +NGZ = 60 +NSW = 0 +PREC = Accurate +SIGMA = 0.2 diff --git a/tests/test_data/vasp/H_Graphite/static_1/inputs/KPOINTS b/tests/test_data/vasp/H_Graphite/static_1/inputs/KPOINTS new file mode 100644 index 0000000000..9bcad4fb60 --- /dev/null +++ b/tests/test_data/vasp/H_Graphite/static_1/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 88 / number of atoms +0 +Gamma +3 3 1 diff --git a/tests/test_data/vasp/H_Graphite/static_1/inputs/POSCAR b/tests/test_data/vasp/H_Graphite/static_1/inputs/POSCAR new file mode 100644 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index 0000000000..35025b8b16 --- /dev/null +++ b/tests/test_data/vasp/H_Graphite/static_1/outputs/POTCAR.spec @@ -0,0 +1,2 @@ +H +C diff --git a/tests/test_data/vasp/H_Graphite/static_1/outputs/custodian.json.gz b/tests/test_data/vasp/H_Graphite/static_1/outputs/custodian.json.gz new file mode 100644 index 0000000000..100362efd0 Binary files /dev/null and b/tests/test_data/vasp/H_Graphite/static_1/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/H_Graphite/static_1/outputs/vasprun.xml.gz b/tests/test_data/vasp/H_Graphite/static_1/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..ea65a1a889 Binary files /dev/null and b/tests/test_data/vasp/H_Graphite/static_1/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/inputs/INCAR b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/inputs/INCAR new file mode 100644 index 0000000000..3ff6f8ad37 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/inputs/INCAR @@ -0,0 +1,31 @@ +ALGO = Fast +EDIFF = 1e-05 +EDIFFG = -0.02 +ENAUG = 1360 +ENCUT = 680 +GGA = Ps +IBRION = 2 +ISIF = 3 +ISMEAR = 0 +ISPIN = 2 +LAECHG = True +LASPH = True +LCHARG = False +LDAU = True +LDAUJ = 0 0 0 +LDAUL = 0 2 0 +LDAUPRINT = 1 +LDAUTYPE = 2 +LDAUU = 0 3.9 0 +LELF = False +LMAXMIX = 4 +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 2*0.0 4*5.0 8*0.0 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.2 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/inputs/KPOINTS b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/inputs/KPOINTS new file mode 100644 index 0000000000..5d460a8102 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 1454 / number of atoms +0 +Gamma +4 4 4 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/inputs/POSCAR b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/inputs/POSCAR new file mode 100644 index 0000000000..0afb7ac348 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/inputs/POSCAR @@ -0,0 +1,22 @@ +Mg2 Mn4 O8 +1.0 + 5.0688234300000001 0.0001248800000000 -2.6611016699999999 + -1.3970423400000000 4.8724991099999997 -2.6611020299999999 + 0.0098609100000000 0.0130852800000000 6.1764935899999998 +Mg Mn O +2 4 8 +direct + 0.3748972600000000 0.6251027400000000 0.7500000200000000 Mg,spin=0 + 0.6251027400000000 0.3748972600000000 0.2499999800000000 Mg,spin=0 + -0.0000000000000000 -0.0000000000000000 0.5000000000000000 Mn,spin=5 + -0.0000000000000000 0.5000000000000000 0.0000000000000000 Mn,spin=5 + 0.5000000000000000 -0.0000000000000000 0.5000000000000000 Mn,spin=5 + -0.0000000000000000 -0.0000000000000000 0.0000000000000000 Mn,spin=5 + 0.7540230900000000 0.7782675000000000 0.5080588200000000 O,spin=0 + 0.7702028500000000 0.2459477900000000 0.9919131600000000 O,spin=0 + 0.2217325400000000 0.2459768900000000 0.9919411600000000 O,spin=0 + 0.2459769100000000 0.2217325000000000 0.4919411800000000 O,spin=0 + 0.2459476500000000 0.7702028800000000 0.4919131300000000 O,spin=0 + 0.2297971500000000 0.7540522100000000 0.0080868400000000 O,spin=0 + 0.7540523500000000 0.2297971200000000 0.5080868700000000 O,spin=0 + 0.7782674600000000 0.7540231100000000 0.0080588400000000 O,spin=0 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/inputs/POTCAR.spec b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/inputs/POTCAR.spec new file mode 100644 index 0000000000..abc18fffd7 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/inputs/POTCAR.spec @@ -0,0 +1,3 @@ +Mg +Mn_pv +O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/CONTCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/CONTCAR.gz new file mode 100644 index 0000000000..d7016f52ab Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/CONTCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/INCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/INCAR.gz new file mode 100644 index 0000000000..b2c311e2d4 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/INCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/INCAR.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/INCAR.orig.gz new file mode 100644 index 0000000000..69dae9936d Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/INCAR.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/KPOINTS.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/KPOINTS.gz new file mode 100644 index 0000000000..3af00a47de Binary files /dev/null and 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b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/POSCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/POSCAR.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/POSCAR.orig.gz new file mode 100644 index 0000000000..0d652e79ae Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/POTCAR.spec b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/POTCAR.spec new file mode 100644 index 0000000000..abc18fffd7 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/POTCAR.spec @@ -0,0 +1,3 @@ +Mg +Mn_pv +O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/custodian.json.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/custodian.json.gz new file mode 100644 index 0000000000..1997906c3f Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/vasprun.xml.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..15eb1c2b7a Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_1_3_(fm)/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/inputs/INCAR b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/inputs/INCAR new file mode 100644 index 0000000000..57a194a5bf --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/inputs/INCAR @@ -0,0 +1,31 @@ +ALGO = Fast +EDIFF = 1e-05 +EDIFFG = -0.02 +ENAUG = 1360 +ENCUT = 680 +GGA = Ps +IBRION = 2 +ISIF = 3 +ISMEAR = 0 +ISPIN = 2 +LAECHG = True +LASPH = True +LCHARG = False +LDAU = True +LDAUJ = 0 0 0 +LDAUL = 0 2 0 +LDAUPRINT = 1 +LDAUTYPE = 2 +LDAUU = 0 3.9 0 +LELF = False +LMAXMIX = 4 +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 2*0.6 2*-5.0 2*5.0 8*0.6 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.2 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/inputs/KPOINTS b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/inputs/KPOINTS new file mode 100644 index 0000000000..5d460a8102 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 1454 / number of atoms +0 +Gamma +4 4 4 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/inputs/POSCAR b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/inputs/POSCAR new file mode 100644 index 0000000000..7f5034e8ab --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/inputs/POSCAR @@ -0,0 +1,22 @@ +Mg2 Mn4 O8 +1.0 + -1.3970423400000000 4.8724991099999997 -2.6611020299999999 + 0.0098609100000000 0.0130852800000000 6.1764935899999998 + 5.0688234300000001 0.0001248800000000 -2.6611016699999999 +Mg Mn O +2 4 8 +direct + 0.6251027400000000 0.7500000200000000 0.3748972600000000 Mg + 0.3748972600000001 0.2499999800000000 0.6251027400000001 Mg + 0.5000000000000000 0.0000000000000000 0.0000000000000000 Mn,spin=-5 + 0.0000000000000000 0.0000000000000000 0.0000000000000000 Mn,spin=-5 + 0.0000000000000000 0.5000000000000000 0.0000000000000000 Mn,spin=5 + 0.0000000000000000 0.5000000000000000 0.5000000000000001 Mn,spin=5 + 0.7782674999999999 0.5080588200000000 0.7540230899999999 O + 0.2459477899999999 0.9919131600000001 0.7702028500000001 O + 0.2459768900000000 0.9919411600000000 0.2217325400000000 O + 0.2217324999999999 0.4919411800000000 0.2459769100000000 O + 0.7702028800000001 0.4919131300000000 0.2459476500000000 O + 0.7540522100000001 0.0080868400000000 0.2297971500000000 O + 0.2297971200000000 0.5080868700000000 0.7540523500000001 O + 0.7540231100000001 0.0080588400000000 0.7782674600000002 O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/inputs/POTCAR.spec b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/inputs/POTCAR.spec new file mode 100644 index 0000000000..abc18fffd7 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/inputs/POTCAR.spec @@ -0,0 +1,3 @@ +Mg +Mn_pv +O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/CONTCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/CONTCAR.gz new file mode 100644 index 0000000000..93f0ee2a6a Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/CONTCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/INCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/INCAR.gz new file mode 100644 index 0000000000..e39022f335 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/INCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/INCAR.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/INCAR.orig.gz new file mode 100644 index 0000000000..4745a48f91 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/INCAR.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/KPOINTS.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/KPOINTS.gz new file mode 100644 index 0000000000..b6adb244f6 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/KPOINTS.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/KPOINTS.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/KPOINTS.orig.gz new file mode 100644 index 0000000000..6fe6a1487b Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/KPOINTS.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/OUTCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/OUTCAR.gz new file mode 100644 index 0000000000..f9db520b2e Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/OUTCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/POSCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/POSCAR.gz new file mode 100644 index 0000000000..9e014b020e Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/POSCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/POSCAR.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/POSCAR.orig.gz new file mode 100644 index 0000000000..5daa642727 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/POTCAR.spec b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/POTCAR.spec new file mode 100644 index 0000000000..abc18fffd7 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/POTCAR.spec @@ -0,0 +1,3 @@ +Mg +Mn_pv +O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/custodian.json.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/custodian.json.gz new file mode 100644 index 0000000000..9cf4da6fe0 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/vasprun.xml.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..4e0d970850 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_2_3_(afm)/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/inputs/INCAR b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/inputs/INCAR new file mode 100644 index 0000000000..57a194a5bf --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/inputs/INCAR @@ -0,0 +1,31 @@ +ALGO = Fast +EDIFF = 1e-05 +EDIFFG = -0.02 +ENAUG = 1360 +ENCUT = 680 +GGA = Ps +IBRION = 2 +ISIF = 3 +ISMEAR = 0 +ISPIN = 2 +LAECHG = True +LASPH = True +LCHARG = False +LDAU = True +LDAUJ = 0 0 0 +LDAUL = 0 2 0 +LDAUPRINT = 1 +LDAUTYPE = 2 +LDAUU = 0 3.9 0 +LELF = False +LMAXMIX = 4 +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 2*0.6 2*-5.0 2*5.0 8*0.6 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.2 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/inputs/KPOINTS b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/inputs/KPOINTS new file mode 100644 index 0000000000..5d460a8102 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 1454 / number of atoms +0 +Gamma +4 4 4 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/inputs/POSCAR b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/inputs/POSCAR new file mode 100644 index 0000000000..e57ef3bf90 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/inputs/POSCAR @@ -0,0 +1,22 @@ +Mg2 Mn4 O8 +1.0 + -1.3970423400000000 4.8724991099999997 -2.6611020299999999 + 0.0098609100000000 0.0130852800000000 6.1764935899999998 + 5.0688234300000001 0.0001248800000000 -2.6611016699999999 +Mg Mn O +2 4 8 +direct + 0.6251027400000000 0.7500000200000000 0.3748972600000000 Mg + 0.3748972600000001 0.2499999800000000 0.6251027400000001 Mg + 0.0000000000000000 0.5000000000000000 0.5000000000000001 Mn,spin=-5 + 0.0000000000000000 0.0000000000000000 0.0000000000000000 Mn,spin=-5 + 0.0000000000000000 0.5000000000000000 0.0000000000000000 Mn,spin=5 + 0.5000000000000000 0.0000000000000000 0.0000000000000000 Mn,spin=5 + 0.7782674999999999 0.5080588200000000 0.7540230899999999 O + 0.2459477899999999 0.9919131600000001 0.7702028500000001 O + 0.2459768900000000 0.9919411600000000 0.2217325400000000 O + 0.2217324999999999 0.4919411800000000 0.2459769100000000 O + 0.7702028800000001 0.4919131300000000 0.2459476500000000 O + 0.7540522100000001 0.0080868400000000 0.2297971500000000 O + 0.2297971200000000 0.5080868700000000 0.7540523500000001 O + 0.7540231100000001 0.0080588400000000 0.7782674600000002 O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/inputs/POTCAR.spec b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/inputs/POTCAR.spec new file mode 100644 index 0000000000..abc18fffd7 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/inputs/POTCAR.spec @@ -0,0 +1,3 @@ +Mg +Mn_pv +O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/CONTCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/CONTCAR.gz new file mode 100644 index 0000000000..be3a51630b Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/CONTCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/INCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/INCAR.gz new file mode 100644 index 0000000000..8704a3c8db Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/INCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/INCAR.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/INCAR.orig.gz new file mode 100644 index 0000000000..d97e9002eb Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/INCAR.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/KPOINTS.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/KPOINTS.gz new file mode 100644 index 0000000000..23a44345bf Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/KPOINTS.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/KPOINTS.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/KPOINTS.orig.gz new file mode 100644 index 0000000000..0066254a72 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/KPOINTS.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/OUTCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/OUTCAR.gz new file mode 100644 index 0000000000..57c2baa813 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/OUTCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/POSCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/POSCAR.gz new file mode 100644 index 0000000000..31e55796bd Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/POSCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/POSCAR.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/POSCAR.orig.gz new file mode 100644 index 0000000000..cf8a05eb7f Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/POTCAR.spec b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/POTCAR.spec new file mode 100644 index 0000000000..abc18fffd7 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/POTCAR.spec @@ -0,0 +1,3 @@ +Mg +Mn_pv +O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/custodian.json.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/custodian.json.gz new file mode 100644 index 0000000000..213c354218 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/vasprun.xml.gz b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..af7b63abca Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/relax_3_3_(afm)/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/inputs/INCAR b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/inputs/INCAR new file mode 100644 index 0000000000..3a2e8e36fd --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/inputs/INCAR @@ -0,0 +1,28 @@ +ALGO = Fast +EDIFF = 1e-07 +ENAUG = 1360.0 +ENCUT = 680.0 +GGA = Ps +ISMEAR = -5 +ISPIN = 2 +LAECHG = True +LASPH = True +LCHARG = True +LDAU = True +LDAUJ = 0 0 0 +LDAUL = 0 2 0 +LDAUPRINT = 1 +LDAUTYPE = 2 +LDAUU = 0 3.9 0 +LELF = False +LMAXMIX = 4 +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 2*0.012 4*3.845 8*0.011 +NELM = 200 +NSW = 0 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/inputs/KPOINTS b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/inputs/KPOINTS new file mode 100644 index 0000000000..cfd4680134 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 1451 / number of atoms +0 +Gamma +4 4 4 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/inputs/POSCAR b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/inputs/POSCAR new file mode 100644 index 0000000000..dc6d7e9b05 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/inputs/POSCAR @@ -0,0 +1,22 @@ +Mg2 Mn4 O8 +1.0 + 5.0909545033140473 -0.0002218252672384 -2.6730180200002640 + -1.4034757878391055 4.8936772984975505 -2.6730183811819406 + -0.0110415142627305 -0.0146532080215893 6.1642541333076988 +Mg Mn O +2 4 8 +direct + 0.3750023476599546 0.6249976523400166 0.7500000199999994 Mg + 0.6249976523400455 0.3750023476599835 0.2499999800000005 Mg + 0.0000000000000000 -0.0000000000000000 0.5000000000000000 Mn + 0.0000000000000000 0.5000000000000000 -0.0000000000000000 Mn + 0.5000000000000000 -0.0000000000000000 0.5000000000000000 Mn + 0.0000000000000000 -0.0000000000000000 -0.0000000000000000 Mn + 0.7548982924496653 0.7784120911231091 0.5097750754479139 O + 0.7686508801896794 0.2450739539794833 0.9901696416152010 O + 0.2215879488760922 0.2451016875503940 0.9902249045520171 O + 0.2451017075503346 0.2215879088768909 0.4902249245520861 O + 0.2450738139793351 0.7686509101891128 0.4901696116151258 O + 0.2313491198103206 0.7549260460205168 0.0098303583847989 O + 0.7549261860206650 0.2313490898108872 0.5098303883848740 O + 0.7784120511239078 0.7548983124496059 0.0097750954479829 O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/inputs/POTCAR.spec b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/inputs/POTCAR.spec new file mode 100644 index 0000000000..abc18fffd7 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/inputs/POTCAR.spec @@ -0,0 +1,3 @@ +Mg +Mn_pv +O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/CONTCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/CONTCAR.gz new file mode 100644 index 0000000000..9f92db1838 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/CONTCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/INCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/INCAR.gz new file mode 100644 index 0000000000..afd227144a Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/INCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/INCAR.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/INCAR.orig.gz new file mode 100644 index 0000000000..351aa904a6 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/INCAR.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/KPOINTS.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/KPOINTS.gz new file mode 100644 index 0000000000..7222a7562e Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/KPOINTS.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/KPOINTS.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/KPOINTS.orig.gz new file mode 100644 index 0000000000..97ed59cb9a Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/KPOINTS.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/OUTCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/OUTCAR.gz new file mode 100644 index 0000000000..b2d9ba3a34 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/OUTCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/POSCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/POSCAR.gz new file mode 100644 index 0000000000..5508c5263c Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/POSCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/POSCAR.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/POSCAR.orig.gz new file mode 100644 index 0000000000..4db0699e8f Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/POTCAR.spec b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/POTCAR.spec new file mode 100644 index 0000000000..abc18fffd7 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/POTCAR.spec @@ -0,0 +1,3 @@ +Mg +Mn_pv +O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/custodian.json.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/custodian.json.gz new file mode 100644 index 0000000000..f4aa3d38e5 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/vasprun.xml.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..72d05c47b5 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_1_3_(fm)/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/inputs/INCAR b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/inputs/INCAR new file mode 100644 index 0000000000..d0ca6df76f --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/inputs/INCAR @@ -0,0 +1,28 @@ +ALGO = Fast +EDIFF = 1e-07 +ENAUG = 1360.0 +ENCUT = 680.0 +GGA = Ps +ISMEAR = -5 +ISPIN = 2 +LAECHG = True +LASPH = True +LCHARG = True +LDAU = True +LDAUJ = 0 0 0 +LDAUL = 0 2 0 +LDAUPRINT = 1 +LDAUTYPE = 2 +LDAUU = 0 3.9 0 +LELF = False +LMAXMIX = 4 +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 2*0.0 2*-3.823 2*3.823 1*-0.063 2*0.063 2*-0.063 1*0.063 1*-0.063 1*0.063 +NELM = 200 +NSW = 0 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/inputs/KPOINTS b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/inputs/KPOINTS new file mode 100644 index 0000000000..5d460a8102 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 1454 / number of atoms +0 +Gamma +4 4 4 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/inputs/POSCAR b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/inputs/POSCAR new file mode 100644 index 0000000000..d27fa00adf --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/inputs/POSCAR @@ -0,0 +1,22 @@ +Mg2 Mn4 O8 +1.0 + -1.4013627584047403 4.8863814616147661 -2.6690096428701415 + -0.0069000597693647 -0.0091579237479205 6.1628646215114546 + 5.0833568514662772 -0.0002027328146935 -2.6690078035749418 +Mg Mn O +2 4 8 +direct + 0.6250046392730044 0.7499993302874581 0.3749946584820302 Mg + 0.3749953607269955 0.2500006697125421 0.6250053415179697 Mg + 0.5000000000000000 -0.0000000000000000 0.0000000000000000 Mn + -0.0000000000000000 -0.0000000000000000 0.0000000000000000 Mn + -0.0000000000000000 0.5000000000000000 0.0000000000000000 Mn + -0.0000000000000000 0.5000000000000000 0.5000000000000000 Mn + 0.7780112445054692 0.5089096009337630 0.7544642856563863 O + 0.2455072748279359 0.9910362520651074 0.7691151397739133 O + 0.2455355743036234 0.9910903117108990 0.2219884378819191 O + 0.2219887554945306 0.4910903990662371 0.2455357143436137 O + 0.7691149643992734 0.4910363370673025 0.2455072946161888 O + 0.7544927251720641 0.0089637479348926 0.2308848602260867 O + 0.2308850356007265 0.5089636629326975 0.7544927053838113 O + 0.7544644256963766 0.0089096882891011 0.7780115621180809 O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/inputs/POTCAR.spec b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/inputs/POTCAR.spec new file mode 100644 index 0000000000..abc18fffd7 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/inputs/POTCAR.spec @@ -0,0 +1,3 @@ +Mg +Mn_pv +O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/CONTCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/CONTCAR.gz new file mode 100644 index 0000000000..bd646342bb Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/CONTCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/INCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/INCAR.gz new file mode 100644 index 0000000000..91244ef560 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/INCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/INCAR.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/INCAR.orig.gz new file mode 100644 index 0000000000..3d65e32e84 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/INCAR.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/KPOINTS.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/KPOINTS.gz new file mode 100644 index 0000000000..bfc92286d7 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/KPOINTS.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/KPOINTS.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/KPOINTS.orig.gz new file mode 100644 index 0000000000..6c1c7c5b59 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/KPOINTS.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/OUTCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/OUTCAR.gz new file mode 100644 index 0000000000..cbf27d9c43 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/OUTCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/POSCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/POSCAR.gz new file mode 100644 index 0000000000..2425c358a6 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/POSCAR.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/POSCAR.orig.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/POSCAR.orig.gz new file mode 100644 index 0000000000..92a3fba325 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/POTCAR.spec b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/POTCAR.spec new file mode 100644 index 0000000000..abc18fffd7 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/POTCAR.spec @@ -0,0 +1,3 @@ +Mg +Mn_pv +O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/custodian.json.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/custodian.json.gz new file mode 100644 index 0000000000..3958ac51d1 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/vasprun.xml.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..94fe6d0f64 Binary files /dev/null and b/tests/test_data/vasp/MgMn2O4_magnetic/static_2_3_(afm)/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/inputs/INCAR b/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/inputs/INCAR new file mode 100644 index 0000000000..d8fb501816 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/inputs/INCAR @@ -0,0 +1,28 @@ +ALGO = Fast +EDIFF = 1e-07 +ENAUG = 1360.0 +ENCUT = 680.0 +GGA = Ps +ISMEAR = -5 +ISPIN = 2 +LAECHG = True +LASPH = True +LCHARG = True +LDAU = True +LDAUJ = 0 0 0 +LDAUL = 0 2 0 +LDAUPRINT = 1 +LDAUTYPE = 2 +LDAUU = 0 3.9 0 +LELF = False +LMAXMIX = 4 +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 2*-0.0 2*-3.806 2*3.806 2*-0.039 1*0.039 1*-0.039 1*0.039 1*-0.039 2*0.039 +NELM = 200 +NSW = 0 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/inputs/KPOINTS b/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/inputs/KPOINTS new file mode 100644 index 0000000000..d81d334f72 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 1457 / number of atoms +0 +Gamma +4 4 4 diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/inputs/POSCAR b/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/inputs/POSCAR new file mode 100644 index 0000000000..82cc4edc59 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/inputs/POSCAR @@ -0,0 +1,22 @@ +Mg2 Mn4 O8 +1.0 + -1.4134749544772500 4.8851318875074039 -2.6615688416227865 + -0.0049004986004434 -0.0064997088868317 6.1494648899885469 + 5.0854959019673869 -0.0121921293214673 -2.6615702914822061 +Mg Mn O +2 4 8 +direct + 0.6250177427242132 0.7499998952804642 0.3749818770097100 Mg + 0.3749822572757868 0.2500001047195358 0.6250181229902900 Mg + -0.0000000000000000 0.5000000000000000 0.5000000000000000 Mn + -0.0000000000000000 -0.0000000000000000 0.0000000000000000 Mn + -0.0000000000000000 0.5000000000000000 0.0000000000000000 Mn + 0.5000000000000000 -0.0000000000000000 0.0000000000000000 Mn + 0.7783487146233745 0.5095421654445897 0.7548271973998141 O + 0.2452555980671230 0.9904261541048694 0.7687992902150146 O + 0.2451729015097585 0.9904581224981112 0.2216514877768520 O + 0.2216512853766253 0.4904578345554103 0.2451728026001859 O + 0.7687992353080364 0.4904259676412834 0.2452554534283477 O + 0.7547444019328770 0.0095738458951307 0.2312007097849854 O + 0.2312007646919633 0.5095740323587166 0.7547445465716525 O + 0.7548270984902415 0.0095418775018887 0.7783485122231479 O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/inputs/POTCAR.spec b/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/inputs/POTCAR.spec new file mode 100644 index 0000000000..abc18fffd7 --- /dev/null +++ b/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/inputs/POTCAR.spec @@ -0,0 +1,3 @@ +Mg +Mn_pv +O diff --git a/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/outputs/CONTCAR.gz b/tests/test_data/vasp/MgMn2O4_magnetic/static_3_3_(afm)/outputs/CONTCAR.gz new file mode 100644 index 0000000000..c1862d9726 Binary files /dev/null and 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b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_0/inputs/INCAR @@ -0,0 +1,27 @@ +ALGO = Fast +EDIFF = 1e-06 +EDIFFG = -0.02 +ENAUG = 1360 +ENCUT = 680 +IBRION = 2 +ISIF = 2 +ISMEAR = 0 +ISPIN = 2 +KPAR = 2 +KSPACING = 0.22 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMAXMIX = 6 +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = False +LWAVE = True +MAGMOM = 2*0.0 +NCORE = 16 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_0/inputs/POSCAR b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_0/inputs/POSCAR new file mode 100644 index 0000000000..6bd2360833 --- /dev/null +++ b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_0/inputs/POSCAR @@ -0,0 +1,10 @@ +Si2 +1.0 + 3.1814727567389238 0.0000000000000000 1.8368238935270336 + 1.0604909189129750 2.9995224698857785 1.8368238935270336 + 0.0000000000000000 0.0000000000000000 3.6736477870540671 +Si +2 +direct + 0.8750000000000000 0.8750000000000000 0.8750000000000000 Si + 0.1250000000000000 0.1250000000000000 0.1250000000000000 Si diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/inputs/POTCAR.spec b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_0/inputs/POTCAR.spec similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/inputs/POTCAR.spec rename to tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_0/inputs/POTCAR.spec diff --git a/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_0/outputs/CHG.gz b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_0/outputs/CHG.gz new file mode 100644 index 0000000000..17aa32f879 Binary files /dev/null and b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_0/outputs/CHG.gz differ diff --git a/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_0/outputs/CHGCAR.gz 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@@ +ALGO = Fast +EDIFF = 1e-06 +EDIFFG = -0.02 +ENAUG = 1360 +ENCUT = 680 +IBRION = 2 +ISIF = 2 +ISMEAR = 0 +ISPIN = 2 +KPAR = 2 +KSPACING = 0.22 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMAXMIX = 6 +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = False +LWAVE = True +MAGMOM = 2*0.0 +NCORE = 16 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_1/inputs/POSCAR b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_1/inputs/POSCAR new file mode 100644 index 0000000000..61aff50833 --- /dev/null +++ b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Deformation_Relax_1/inputs/POSCAR @@ -0,0 +1,10 @@ +Si2 +1.0 + 3.5163646258693375 0.0000000000000000 2.0301737770561954 + 1.1721215419564459 3.3152616772421761 2.0301737770561954 + 0.0000000000000000 0.0000000000000000 4.0603475541123908 +Si +2 +direct + 0.8750000000000000 0.8750000000000000 0.8750000000000000 Si + 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+EDIFF = 1e-06 +EDIFFG = -0.05 +ENAUG = 1360 +ENCUT = 680 +IBRION = 2 +ISIF = 3 +ISMEAR = 0 +ISPIN = 2 +KPAR = 2 +KSPACING = 0.22 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMAXMIX = 6 +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = False +LWAVE = True +MAGMOM = 2*-0.0 +NCORE = 16 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_MP_GGA_relax_1/inputs/POSCAR b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_MP_GGA_relax_1/inputs/POSCAR new file mode 100644 index 0000000000..fcb5af8c91 --- /dev/null +++ b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_MP_GGA_relax_1/inputs/POSCAR @@ -0,0 +1,10 @@ +Si2 +1.0 + 3.3335729999999999 0.0000000000000000 1.9246390000000000 + 1.1111910000000000 3.1429239999999998 1.9246390000000000 + 0.0000000000000000 0.0000000000000000 3.8492780000000000 +Si +2 +direct + 0.8750000000000000 0.8750000000000000 0.8750000000000000 Si + 0.1250000000000000 0.1250000000000000 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a/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_MP_GGA_relax_2/inputs/POSCAR b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_MP_GGA_relax_2/inputs/POSCAR new file mode 100644 index 0000000000..8812f4b58f --- /dev/null +++ b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_MP_GGA_relax_2/inputs/POSCAR @@ -0,0 +1,10 @@ +Si2 +1.0 + 3.3489186913041307 -0.0000000000000000 1.9334988352916145 + 1.1163062304347104 3.1573920735639773 1.9334988352916145 + 0.0000000000000000 0.0000000000000000 3.8669976705832290 +Si +2 +direct + 0.8750000000000000 0.8750000000000000 0.8750000000000000 Si + 0.1250000000000000 0.1250000000000000 0.1250000000000000 Si diff --git a/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_MP_GGA_relax_2/inputs/POTCAR.spec b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_MP_GGA_relax_2/inputs/POTCAR.spec new file mode 100644 index 0000000000..e267321d2c --- /dev/null +++ b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_MP_GGA_relax_2/inputs/POTCAR.spec @@ -0,0 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file mode 100644 index 0000000000..692243f78c --- /dev/null +++ b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Static_0/inputs/INCAR @@ -0,0 +1,24 @@ +ALGO = Normal +EDIFF = 1e-06 +ENAUG = 1360 +ENCUT = 680 +ISMEAR = -5 +ISPIN = 2 +KPAR = 2 +KSPACING = 0.22 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMAXMIX = 6 +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = False +LWAVE = False +MAGMOM = 2*0.0 +NCORE = 16 +NELM = 200 +NSW = 0 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Static_0/inputs/POSCAR b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Static_0/inputs/POSCAR new file mode 100644 index 0000000000..6bd2360833 --- /dev/null +++ b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Static_0/inputs/POSCAR @@ -0,0 +1,10 @@ +Si2 +1.0 + 3.1814727567389238 0.0000000000000000 1.8368238935270336 + 1.0604909189129750 2.9995224698857785 1.8368238935270336 + 0.0000000000000000 0.0000000000000000 3.6736477870540671 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file mode 100644 index 0000000000..692243f78c --- /dev/null +++ b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Static_1/inputs/INCAR @@ -0,0 +1,24 @@ +ALGO = Normal +EDIFF = 1e-06 +ENAUG = 1360 +ENCUT = 680 +ISMEAR = -5 +ISPIN = 2 +KPAR = 2 +KSPACING = 0.22 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMAXMIX = 6 +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = False +LWAVE = False +MAGMOM = 2*0.0 +NCORE = 16 +NELM = 200 +NSW = 0 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Static_1/inputs/POSCAR b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Static_1/inputs/POSCAR new file mode 100644 index 0000000000..61aff50833 --- /dev/null +++ b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_Static_1/inputs/POSCAR @@ -0,0 +1,10 @@ +Si2 +1.0 + 3.5163646258693375 0.0000000000000000 2.0301737770561954 + 1.1721215419564459 3.3152616772421761 2.0301737770561954 + 0.0000000000000000 0.0000000000000000 4.0603475541123908 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b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_equilibrium_static/inputs/INCAR new file mode 100644 index 0000000000..692243f78c --- /dev/null +++ b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_equilibrium_static/inputs/INCAR @@ -0,0 +1,24 @@ +ALGO = Normal +EDIFF = 1e-06 +ENAUG = 1360 +ENCUT = 680 +ISMEAR = -5 +ISPIN = 2 +KPAR = 2 +KSPACING = 0.22 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMAXMIX = 6 +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = False +LWAVE = False +MAGMOM = 2*0.0 +NCORE = 16 +NELM = 200 +NSW = 0 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_equilibrium_static/inputs/POSCAR b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_equilibrium_static/inputs/POSCAR new file mode 100644 index 0000000000..8812f4b58f --- /dev/null +++ b/tests/test_data/vasp/Si_EOS_MP_GGA/mp-149-PBE-EOS_equilibrium_static/inputs/POSCAR @@ -0,0 +1,10 @@ +Si2 +1.0 + 3.3489186913041307 -0.0000000000000000 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b/tests/test_data/vasp/Si_elastic/elastic_relax_1_6/inputs/INCAR @@ -1,24 +1,24 @@ ALGO = Normal EDIFF = 1e-07 EDIFFG = -0.001 -ENAUG = 1360.0 -ENCUT = 700.0 +ENAUG = 1360 +ENCUT = 700 +GGA = Ps IBRION = 2 ISIF = 2 ISMEAR = -5 ISPIN = 2 -KSPACING = 0.2925287784072645 LAECHG = False LASPH = True -LCHARG = True -LELF = True +LCHARG = False +LELF = False LMIXTAU = True LORBIT = 11 LREAL = False LVTOT = True LWAVE = False -MAGMOM = 2*-0.0 +MAGMOM = 8*-0.0 NELM = 200 NSW = 99 PREC = Accurate -SIGMA = 0.05 +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_1_6/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic/elastic_relax_1_6/inputs/KPOINTS index 093abbe92b..5a195a0bf8 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_1_6/inputs/KPOINTS +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_1_6/inputs/KPOINTS @@ -1,4 +1,4 @@ -pymatgen with grid density = 100 / number of atoms +pymatgen with grid density = 7000 / number of atoms 0 Gamma -3 3 3 +9 9 9 diff --git 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{"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0.0, "lattice": {"matrix": [[5.436386043653454, -0.0, 3e-16], [-3e-16, 5.436386043653453, 3e-16], [0.0, -0.0, 5.436386043653453]], "pbc": [true, true, true], "a": 5.436386043653454, "b": 5.436386043653453, "c": 5.436386043653453, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 160.66854716749313}, "properties": {}, "sites": [{"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.25, 0.75], "xyz": [1.3590965109133635, 1.3590965109133633, 4.07728953274009], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, -0.0, -0.0], "xyz": [2.718193021826727, 0.0, 1.5e-16], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.75, 0.25], "xyz": [1.3590965109133633, 4.07728953274009, 1.3590965109133635], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, 0.5, 0.5], "xyz": [2.718193021826727, 2.7181930218267265, 2.718193021826727], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.25, 0.25], "xyz": [4.077289532740091, 1.3590965109133633, 1.3590965109133635], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.0, -0.0, 0.5], "xyz": [0.0, 0.0, 2.7181930218267265], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.75, 0.75], "xyz": [4.077289532740091, 4.07728953274009, 4.077289532740091], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [-0.0, 0.5, 0.0], "xyz": [-1.5e-16, 2.7181930218267265, 1.5e-16], "properties": {"magmom": -0.0}, "label": "Si"}]}, "output_parameters": {}}], "last_modified": "2024-02-09 22:21:52.163462", "other_parameters": {}, "@version": null} diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_1_6/outputs/transformations.json.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_1_6/outputs/transformations.json.gz deleted file mode 100644 index 5b648c8094..0000000000 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_1_6/outputs/transformations.json.gz and /dev/null differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_1_6/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_1_6/outputs/vasprun.xml.gz index 990e334b60..4c9574bec2 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_1_6/outputs/vasprun.xml.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_1_6/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/inputs/INCAR b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/inputs/INCAR index 9527e3c3e9..82499cb770 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/inputs/INCAR +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/inputs/INCAR @@ -1,24 +1,24 @@ ALGO = Normal EDIFF = 1e-07 EDIFFG = -0.001 -ENAUG = 1360.0 -ENCUT = 700.0 +ENAUG = 1360 +ENCUT = 700 +GGA = Ps IBRION = 2 ISIF = 2 ISMEAR = -5 ISPIN = 2 -KSPACING = 0.2925287784072645 LAECHG = False LASPH = True -LCHARG = True -LELF = True +LCHARG = False +LELF = False LMIXTAU = True LORBIT = 11 LREAL = False LVTOT = True LWAVE = False -MAGMOM = 2*-0.0 +MAGMOM = 8*-0.0 NELM = 200 NSW = 99 PREC = Accurate -SIGMA = 0.05 +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/inputs/KPOINTS index 093abbe92b..5a195a0bf8 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/inputs/KPOINTS +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/inputs/KPOINTS @@ -1,4 +1,4 @@ -pymatgen with grid density = 100 / number of atoms +pymatgen with grid density = 7000 / number of atoms 0 Gamma -3 3 3 +9 9 9 diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/inputs/POSCAR b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/inputs/POSCAR index 8611e314c7..b079e79e2d 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/inputs/POSCAR +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/inputs/POSCAR @@ -1,10 +1,16 @@ -Si2 +Si8 1.0 -0.000000 2.752777 2.752777 -2.738979 0.000000 2.752777 -2.738979 2.752777 0.000000 + 5.4091358166969474 0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4363860436534530 0.0000000000000003 + 0.0000000000000000 0.0000000000000000 5.4363860436534530 Si -2 +8 direct -0.750000 0.750000 0.750000 Si -0.500000 0.500000 0.500000 Si + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 -0.0000000000000000 -0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 -0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + -0.0000000000000000 0.5000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/CONTCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/CONTCAR.gz index c1138d4d43..74a4395b91 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/CONTCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/CONTCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/INCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/INCAR.gz index b0349f5fba..138f675d50 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/INCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/INCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/INCAR.orig.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/INCAR.orig.gz index d08d2b1e7e..1e47f39064 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/INCAR.orig.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/INCAR.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/KPOINTS.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/KPOINTS.gz index 8109e2acdf..7ff67a157a 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/KPOINTS.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/KPOINTS.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/KPOINTS.orig.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/KPOINTS.orig.gz index 9438648af3..3da9136614 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/KPOINTS.orig.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/KPOINTS.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/OUTCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/OUTCAR.gz index 655b38a03d..5b05df0869 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/OUTCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/OUTCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/POSCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/POSCAR.gz index a00cb81df8..6785ac3edb 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/POSCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/POSCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/POSCAR.orig.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/POSCAR.orig.gz index f8ff8d08fc..3b4e8fa041 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/POSCAR.orig.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/custodian.json.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/custodian.json.gz index fbb12a7d77..1caa502289 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/custodian.json.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/transformations.json b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/transformations.json new file mode 100644 index 0000000000..6fe80303b8 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/transformations.json @@ -0,0 +1 @@ +{"@module": "pymatgen.alchemy.materials", "@class": "TransformedStructure", "charge": 0.0, "lattice": {"matrix": [[5.409135816696947, 0.0, 3e-16], [-2.9849623113198597e-16, 5.436386043653453, 3e-16], [0.0, 0.0, 5.436386043653453]], "pbc": [true, true, true], "a": 5.409135816696947, "b": 5.436386043653453, "c": 5.436386043653453, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 159.86318596982807}, "properties": {}, "sites": [{"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.25, 0.75], "xyz": [1.3522839541742369, 1.3590965109133633, 4.07728953274009], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, -0.0, -0.0], "xyz": [2.7045679083484737, 0.0, 1.5e-16], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.75, 0.25], "xyz": [1.3522839541742366, 4.07728953274009, 1.3590965109133635], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, 0.5, 0.5], "xyz": [2.7045679083484737, 2.7181930218267265, 2.718193021826727], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.25, 0.25], "xyz": [4.05685186252271, 1.3590965109133633, 1.3590965109133635], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.0, -0.0, 0.5], "xyz": [0.0, 0.0, 2.7181930218267265], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.75, 0.75], "xyz": [4.05685186252271, 4.07728953274009, 4.077289532740091], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [-0.0, 0.5, 0.0], "xyz": [-1.4924811556599299e-16, 2.7181930218267265, 1.5e-16], "properties": {"magmom": -0.0}, "label": "Si"}], "history": [{"@module": "pymatgen.transformations.standard_transformations", "@class": "DeformStructureTransformation", "@version": null, "deformation": [[0.99498743710662, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], "input_structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0.0, "lattice": {"matrix": [[5.436386043653454, -0.0, 3e-16], [-3e-16, 5.436386043653453, 3e-16], [0.0, -0.0, 5.436386043653453]], "pbc": [true, true, true], "a": 5.436386043653454, "b": 5.436386043653453, "c": 5.436386043653453, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 160.66854716749313}, "properties": {}, "sites": [{"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.25, 0.75], "xyz": [1.3590965109133635, 1.3590965109133633, 4.07728953274009], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, -0.0, -0.0], "xyz": [2.718193021826727, 0.0, 1.5e-16], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.75, 0.25], "xyz": [1.3590965109133633, 4.07728953274009, 1.3590965109133635], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, 0.5, 0.5], "xyz": [2.718193021826727, 2.7181930218267265, 2.718193021826727], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.25, 0.25], "xyz": [4.077289532740091, 1.3590965109133633, 1.3590965109133635], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.0, -0.0, 0.5], "xyz": [0.0, 0.0, 2.7181930218267265], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.75, 0.75], "xyz": [4.077289532740091, 4.07728953274009, 4.077289532740091], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [-0.0, 0.5, 0.0], "xyz": [-1.5e-16, 2.7181930218267265, 1.5e-16], "properties": {"magmom": -0.0}, "label": "Si"}]}, "output_parameters": {}}], "last_modified": "2024-02-09 22:23:18.407207", "other_parameters": {}, "@version": null} diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/transformations.json.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/transformations.json.gz deleted file mode 100644 index 9645ef9ab9..0000000000 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/transformations.json.gz and /dev/null differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/vasprun.xml.gz index ec1bc31406..39395dddc5 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/vasprun.xml.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_2_6/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/inputs/INCAR b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/inputs/INCAR index 9527e3c3e9..82499cb770 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/inputs/INCAR +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/inputs/INCAR @@ -1,24 +1,24 @@ ALGO = Normal EDIFF = 1e-07 EDIFFG = -0.001 -ENAUG = 1360.0 -ENCUT = 700.0 +ENAUG = 1360 +ENCUT = 700 +GGA = Ps IBRION = 2 ISIF = 2 ISMEAR = -5 ISPIN = 2 -KSPACING = 0.2925287784072645 LAECHG = False LASPH = True -LCHARG = True -LELF = True +LCHARG = False +LELF = False LMIXTAU = True LORBIT = 11 LREAL = False LVTOT = True LWAVE = False -MAGMOM = 2*-0.0 +MAGMOM = 8*-0.0 NELM = 200 NSW = 99 PREC = Accurate -SIGMA = 0.05 +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/inputs/KPOINTS index 093abbe92b..5a195a0bf8 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/inputs/KPOINTS +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/inputs/KPOINTS @@ -1,4 +1,4 @@ -pymatgen with grid density = 100 / number of atoms +pymatgen with grid density = 7000 / number of atoms 0 Gamma -3 3 3 +9 9 9 diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/inputs/POSCAR b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/inputs/POSCAR index 6e30d19874..979cc8d8b4 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/inputs/POSCAR +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/inputs/POSCAR @@ -1,10 +1,16 @@ -Si2 +Si8 1.0 -0.000000 2.752777 2.752777 -2.766507 0.000000 2.752777 -2.766507 2.752777 0.000000 + 5.4635003567114691 0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4363860436534530 0.0000000000000003 + 0.0000000000000000 0.0000000000000000 5.4363860436534530 Si -2 +8 direct -0.750000 0.750000 0.750000 Si -0.500000 0.500000 0.500000 Si + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 -0.0000000000000000 -0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 -0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + -0.0000000000000000 0.5000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/CONTCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/CONTCAR.gz index c44e7f9052..8f59e1b22d 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/CONTCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/CONTCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/INCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/INCAR.gz index 82b0680f86..05a55b1814 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/INCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/INCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/INCAR.orig.gz 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a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/POSCAR.orig.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/custodian.json.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/custodian.json.gz index b9409121ae..2a937a7f88 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/custodian.json.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/transformations.json b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/transformations.json new file mode 100644 index 0000000000..a13fd96552 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/transformations.json @@ -0,0 +1 @@ +{"@module": "pymatgen.alchemy.materials", "@class": "TransformedStructure", "charge": 0.0, "lattice": {"matrix": [[5.463500356711469, 0.0, 3e-16], [-3.014962686336267e-16, 5.436386043653453, 3e-16], [0.0, 0.0, 5.436386043653453]], "pbc": [true, true, true], "a": 5.463500356711469, "b": 5.436386043653453, "c": 5.436386043653453, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 161.4698915259501}, "properties": {}, "sites": [{"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.25, 0.75], "xyz": [1.3658750891778673, 1.3590965109133633, 4.07728953274009], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, -0.0, -0.0], "xyz": [2.7317501783557345, 0.0, 1.5e-16], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.75, 0.25], "xyz": [1.365875089177867, 4.07728953274009, 1.3590965109133635], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, 0.5, 0.5], "xyz": [2.7317501783557345, 2.7181930218267265, 2.718193021826727], "properties": 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a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/transformations.json.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/transformations.json.gz deleted file mode 100644 index 41f0001fc9..0000000000 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/transformations.json.gz and /dev/null differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/vasprun.xml.gz index 333442ec23..8b6a2daf82 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/vasprun.xml.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_3_6/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/inputs/INCAR b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/inputs/INCAR index 9527e3c3e9..82499cb770 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/inputs/INCAR +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/inputs/INCAR @@ -1,24 +1,24 @@ ALGO = Normal EDIFF = 1e-07 EDIFFG = -0.001 -ENAUG = 1360.0 -ENCUT = 700.0 +ENAUG = 1360 +ENCUT = 700 +GGA = Ps IBRION = 2 ISIF = 2 ISMEAR = -5 ISPIN = 2 -KSPACING = 0.2925287784072645 LAECHG = False LASPH = True -LCHARG = True -LELF = True +LCHARG = False +LELF = False LMIXTAU = True LORBIT = 11 LREAL = False LVTOT = True LWAVE = False -MAGMOM = 2*-0.0 +MAGMOM = 8*-0.0 NELM = 200 NSW = 99 PREC = Accurate -SIGMA = 0.05 +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/inputs/KPOINTS index 093abbe92b..5a195a0bf8 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/inputs/KPOINTS +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/inputs/KPOINTS @@ -1,4 +1,4 @@ -pymatgen with grid density = 100 / number of atoms +pymatgen with grid density = 7000 / number of atoms 0 Gamma -3 3 3 +9 9 9 diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/inputs/POSCAR b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/inputs/POSCAR index 2bc21ac936..0b048e8908 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/inputs/POSCAR +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/inputs/POSCAR @@ -1,10 +1,16 @@ -Si2 +Si8 1.0 -0.000000 2.752777 2.752777 -2.780168 0.000000 2.752777 -2.780168 2.752777 0.000000 + 5.4904807694720743 0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4363860436534530 0.0000000000000003 + 0.0000000000000000 0.0000000000000000 5.4363860436534530 Si -2 +8 direct -0.750000 0.750000 0.750000 Si -0.500000 0.500000 0.500000 Si + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 -0.0000000000000000 -0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 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a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/POSCAR.orig.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/custodian.json.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/custodian.json.gz index 84b06d5cad..9462ff7f17 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/custodian.json.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/transformations.json b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/transformations.json new file mode 100644 index 0000000000..99e97f332f --- /dev/null +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/transformations.json @@ -0,0 +1 @@ +{"@module": "pymatgen.alchemy.materials", "@class": "TransformedStructure", "charge": 0.0, "lattice": {"matrix": 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0.5], "xyz": [2.718193021826727, 2.7181930218267265, 2.718193021826727], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.25, 0.25], "xyz": [4.077289532740091, 1.3590965109133633, 1.3590965109133635], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.0, -0.0, 0.5], "xyz": [0.0, 0.0, 2.7181930218267265], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.75, 0.75], "xyz": [4.077289532740091, 4.07728953274009, 4.077289532740091], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [-0.0, 0.5, 0.0], "xyz": [-1.5e-16, 2.7181930218267265, 1.5e-16], "properties": {"magmom": -0.0}, "label": "Si"}]}, "output_parameters": {}}], "last_modified": "2024-02-09 22:26:10.986675", "other_parameters": {}, "@version": null} diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/transformations.json.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/transformations.json.gz deleted file mode 100644 index de8d86ac20..0000000000 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/transformations.json.gz and /dev/null differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/vasprun.xml.gz index 81cd68973a..6467e36348 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/vasprun.xml.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_4_6/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/inputs/INCAR b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/inputs/INCAR index 9527e3c3e9..82499cb770 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/inputs/INCAR +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/inputs/INCAR @@ -1,24 +1,24 @@ ALGO = Normal EDIFF = 1e-07 EDIFFG = -0.001 -ENAUG = 1360.0 -ENCUT = 700.0 +ENAUG = 1360 +ENCUT = 700 +GGA = Ps IBRION = 2 ISIF = 2 ISMEAR = -5 ISPIN = 2 -KSPACING = 0.2925287784072645 LAECHG = False LASPH = True -LCHARG = True -LELF = True +LCHARG = False +LELF = False LMIXTAU = True LORBIT = 11 LREAL = False LVTOT = True LWAVE = False -MAGMOM = 2*-0.0 +MAGMOM = 8*-0.0 NELM = 200 NSW = 99 PREC = Accurate -SIGMA = 0.05 +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/inputs/KPOINTS index 093abbe92b..5a195a0bf8 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/inputs/KPOINTS +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/inputs/KPOINTS @@ -1,4 +1,4 @@ -pymatgen with grid density = 100 / number of atoms +pymatgen with grid density = 7000 / number of atoms 0 Gamma -3 3 3 +9 9 9 diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/inputs/POSCAR b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/inputs/POSCAR index 6622bc6767..215fdad1e6 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/inputs/POSCAR +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/inputs/POSCAR @@ -1,10 +1,16 @@ -Si2 +Si8 1.0 -0.000000 2.697721 2.752226 -2.752777 -0.055056 2.752226 -2.752777 2.752777 0.000000 + 5.4363860436534539 -0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4363860436534530 0.0000000000000003 + 0.0000000000000000 -0.1087277208730691 5.4352986576952507 Si -2 +8 direct -0.750000 0.750000 0.750000 Si -0.500000 0.500000 0.500000 Si + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 -0.0000000000000000 -0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 -0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + -0.0000000000000000 0.5000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/CONTCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/CONTCAR.gz index d852620fa3..a11619312e 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/CONTCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/CONTCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/INCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/INCAR.gz index 0e11e46f1b..cb3d141a49 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/INCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/INCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/INCAR.orig.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/INCAR.orig.gz index d49ac7d772..059dbedd1d 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/INCAR.orig.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/INCAR.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/KPOINTS.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/KPOINTS.gz index f25452832b..7240210872 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/KPOINTS.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/KPOINTS.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/KPOINTS.orig.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/KPOINTS.orig.gz index 243d51ff75..5841a5692e 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/KPOINTS.orig.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/KPOINTS.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/OUTCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/OUTCAR.gz index 0b9ad386f2..690bad4fb1 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/OUTCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/OUTCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/POSCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/POSCAR.gz index 7897fc6d02..5dd2d2dca0 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/POSCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/POSCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/POSCAR.orig.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/POSCAR.orig.gz index d1fdf70b39..3b5edfbca0 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/POSCAR.orig.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/custodian.json.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/custodian.json.gz index bf925bb6b8..bff0efbb93 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/custodian.json.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/transformations.json b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/transformations.json new file mode 100644 index 0000000000..f2de9bdfd0 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/transformations.json @@ -0,0 +1 @@ +{"@module": "pymatgen.alchemy.materials", "@class": "TransformedStructure", "charge": 0.0, "lattice": {"matrix": [[5.436386043653454, -6e-18, 2.999399939987997e-16], [-3e-16, 5.436386043653453, 2.999399939987997e-16], [0.0, -0.10872772087306906, 5.435298657695251]], "pbc": [true, true, true], "a": 5.436386043653454, "b": 5.436386043653453, "c": 5.436386043653453, "alpha": 91.14599199838858, "beta": 90.0, "gamma": 90.0, "volume": 160.63641024404583}, "properties": {}, "sites": [{"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.25, 0.75], "xyz": [1.3590965109133635, 1.2775507202585614, 4.0764739932714384], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, -0.0, -0.0], "xyz": [2.718193021826727, -3e-18, 1.4996999699939984e-16], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.75, 0.25], "xyz": [1.3590965109133633, 4.050107602521822, 1.358824664423813], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, 0.5, 0.5], "xyz": [2.718193021826727, 2.663829161390192, 2.717649328847626], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.25, 0.25], "xyz": [4.077289532740091, 1.331914580695096, 1.358824664423813], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.0, -0.0, 0.5], "xyz": [0.0, -0.05436386043653453, 2.7176493288476253], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.75, 0.75], "xyz": [4.07728953274009, 3.995743742085288, 4.0764739932714384], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [-0.0, 0.5, 0.0], "xyz": [-1.5e-16, 2.7181930218267265, 1.4996999699939984e-16], "properties": {"magmom": -0.0}, "label": "Si"}], "history": [{"@module": "pymatgen.transformations.standard_transformations", "@class": "DeformStructureTransformation", "@version": null, "deformation": [[1.0, 0.0, 0.0], [0.0, 1.0, -0.02], [0.0, 0.0, 0.999799979995999]], "input_structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0.0, "lattice": {"matrix": [[5.436386043653454, -0.0, 3e-16], [-3e-16, 5.436386043653453, 3e-16], [0.0, -0.0, 5.436386043653453]], "pbc": [true, true, true], "a": 5.436386043653454, "b": 5.436386043653453, "c": 5.436386043653453, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 160.66854716749313}, "properties": {}, "sites": [{"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.25, 0.75], "xyz": [1.3590965109133635, 1.3590965109133633, 4.07728953274009], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, -0.0, -0.0], "xyz": [2.718193021826727, 0.0, 1.5e-16], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.75, 0.25], "xyz": [1.3590965109133633, 4.07728953274009, 1.3590965109133635], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, 0.5, 0.5], "xyz": [2.718193021826727, 2.7181930218267265, 2.718193021826727], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.25, 0.25], "xyz": [4.077289532740091, 1.3590965109133633, 1.3590965109133635], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.0, -0.0, 0.5], "xyz": [0.0, 0.0, 2.7181930218267265], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.75, 0.75], "xyz": [4.077289532740091, 4.07728953274009, 4.077289532740091], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [-0.0, 0.5, 0.0], "xyz": [-1.5e-16, 2.7181930218267265, 1.5e-16], "properties": {"magmom": -0.0}, "label": "Si"}]}, "output_parameters": {}}], "last_modified": "2024-02-09 22:27:37.213422", "other_parameters": {}, "@version": null} diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/transformations.json.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/transformations.json.gz deleted file mode 100644 index cfd5812ba5..0000000000 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/transformations.json.gz and /dev/null differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/vasprun.xml.gz index e438b32846..0138ca3eb0 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/vasprun.xml.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_5_6/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/inputs/INCAR b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/inputs/INCAR index 9527e3c3e9..82499cb770 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/inputs/INCAR +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/inputs/INCAR @@ -1,24 +1,24 @@ ALGO = Normal EDIFF = 1e-07 EDIFFG = -0.001 -ENAUG = 1360.0 -ENCUT = 700.0 +ENAUG = 1360 +ENCUT = 700 +GGA = Ps IBRION = 2 ISIF = 2 ISMEAR = -5 ISPIN = 2 -KSPACING = 0.2925287784072645 LAECHG = False LASPH = True -LCHARG = True -LELF = True +LCHARG = False +LELF = False LMIXTAU = True LORBIT = 11 LREAL = False LVTOT = True LWAVE = False -MAGMOM = 2*-0.0 +MAGMOM = 8*-0.0 NELM = 200 NSW = 99 PREC = Accurate -SIGMA = 0.05 +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/inputs/KPOINTS index 093abbe92b..5a195a0bf8 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/inputs/KPOINTS +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/inputs/KPOINTS @@ -1,4 +1,4 @@ -pymatgen with grid density = 100 / number of atoms +pymatgen with grid density = 7000 / number of atoms 0 Gamma -3 3 3 +9 9 9 diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/inputs/POSCAR b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/inputs/POSCAR index fb79ae9d1b..6f75f7e62a 100644 --- a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/inputs/POSCAR +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/inputs/POSCAR @@ -1,10 +1,16 @@ -Si2 +Si8 1.0 -0.000000 2.725249 2.752639 -2.752777 -0.027528 2.752639 -2.752777 2.752777 0.000000 + 5.4363860436534539 -0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4363860436534530 0.0000000000000003 + 0.0000000000000000 -0.0543638604365345 5.4361142175554482 Si -2 +8 direct -0.750000 0.750000 0.750000 Si -0.500000 0.500000 0.500000 Si + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 -0.0000000000000000 -0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 -0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + -0.0000000000000000 0.5000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/CONTCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/CONTCAR.gz index e3617ca68f..9396e4e14b 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/CONTCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/CONTCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/INCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/INCAR.gz index 7847850b83..788578a996 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/INCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/INCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/INCAR.orig.gz 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b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/KPOINTS.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/OUTCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/OUTCAR.gz index ab25274eb7..191cc15d07 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/OUTCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/OUTCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/POSCAR.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/POSCAR.gz index 23b559f02c..a386ef963b 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/POSCAR.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/POSCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/POSCAR.orig.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/POSCAR.orig.gz index f96559ca62..0abfd0aa3c 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/POSCAR.orig.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/custodian.json.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/custodian.json.gz index bb06d4176d..39c714762c 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/custodian.json.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/transformations.json b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/transformations.json new file mode 100644 index 0000000000..b62ebfa4da --- /dev/null +++ b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/transformations.json @@ -0,0 +1 @@ +{"@module": "pymatgen.alchemy.materials", "@class": "TransformedStructure", "charge": 0.0, "lattice": {"matrix": [[5.436386043653454, -3e-18, 2.9998499962498123e-16], [-3e-16, 5.436386043653453, 2.9998499962498123e-16], [0.0, -0.05436386043653453, 5.436114217555448]], "pbc": [true, true, true], "a": 5.436386043653454, "b": 5.436386043653453, "c": 5.436386043653453, "alpha": 90.57296734485716, "beta": 90.0, "gamma": 90.0, "volume": 160.660513539289}, "properties": {}, "sites": [{"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.25, 0.75], "xyz": [1.3590965109133635, 1.3183236155859623, 4.077085663166586], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, -0.0, -0.0], "xyz": [2.718193021826727, -1.5e-18, 1.4999249981249061e-16], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.75, 0.25], "xyz": [1.3590965109133633, 4.063698567630956, 1.3590285543888623], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, 0.5, 0.5], "xyz": [2.718193021826727, 2.691011091608459, 2.7180571087777246], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.25, 0.25], "xyz": [4.077289532740091, 1.3455055458042295, 1.3590285543888623], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.0, -0.0, 0.5], "xyz": [0.0, -0.027181930218267265, 2.718057108777724], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.75, 0.75], "xyz": [4.07728953274009, 4.036516637412689, 4.077085663166587], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [-0.0, 0.5, 0.0], "xyz": [-1.5e-16, 2.7181930218267265, 1.4999249981249061e-16], "properties": {"magmom": -0.0}, "label": "Si"}], "history": [{"@module": "pymatgen.transformations.standard_transformations", "@class": "DeformStructureTransformation", "@version": null, "deformation": [[1.0, 0.0, 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"@version": null} diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/transformations.json.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/transformations.json.gz deleted file mode 100644 index b4608bde14..0000000000 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/transformations.json.gz and /dev/null differ diff --git a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/vasprun.xml.gz index 8acade9475..6b00f8abe2 100644 Binary files a/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/vasprun.xml.gz and b/tests/test_data/vasp/Si_elastic/elastic_relax_6_6/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_1/inputs/INCAR b/tests/test_data/vasp/Si_elastic/tight_relax_1/inputs/INCAR index d7811c02f9..c030cd7e24 100644 --- a/tests/test_data/vasp/Si_elastic/tight_relax_1/inputs/INCAR +++ b/tests/test_data/vasp/Si_elastic/tight_relax_1/inputs/INCAR @@ -1,8 +1,9 @@ -ALGO = Normal +ALGO = Fast EDIFF = 1e-07 EDIFFG = -0.001 ENAUG = 1360 ENCUT = 700 +GGA = Ps IBRION = 2 ISIF = 3 ISMEAR = 0 @@ -10,14 +11,14 @@ ISPIN = 2 LAECHG = False LASPH = True LCHARG = False -LELF = True +LELF = False LMIXTAU = True LORBIT = 11 LREAL = False LVTOT = True LWAVE = False -MAGMOM = 2*0.6 +MAGMOM = 8*0.6 NELM = 200 NSW = 99 PREC = Accurate -SIGMA = 0.05 +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_1/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic/tight_relax_1/inputs/KPOINTS index 093abbe92b..f37c0a02a2 100644 --- a/tests/test_data/vasp/Si_elastic/tight_relax_1/inputs/KPOINTS +++ b/tests/test_data/vasp/Si_elastic/tight_relax_1/inputs/KPOINTS @@ -1,4 +1,4 @@ -pymatgen with grid density = 100 / number of atoms +pymatgen with grid density = 777 / number of atoms 0 Gamma -3 3 3 +4 4 4 diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_1/inputs/POSCAR b/tests/test_data/vasp/Si_elastic/tight_relax_1/inputs/POSCAR index 6ce1d60136..4235d2a689 100644 --- a/tests/test_data/vasp/Si_elastic/tight_relax_1/inputs/POSCAR +++ b/tests/test_data/vasp/Si_elastic/tight_relax_1/inputs/POSCAR @@ -1,10 +1,16 @@ -Si2 +Si8 1.0 --0.000000 2.734364 2.734364 -2.734364 0.000000 2.734364 -2.734364 2.734364 0.000000 + 5.4687279953829524 0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4687279953829524 0.0000000000000003 + 0.0000000000000000 0.0000000000000000 5.4687279953829524 Si -2 +8 direct -0.750000 0.750000 0.750000 Si -0.500000 0.500000 0.500000 Si + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 0.0000000000000000 0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + 0.0000000000000000 0.5000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/CONTCAR.gz b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/CONTCAR.gz index e7512e13a5..7907c8afeb 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/CONTCAR.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/CONTCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/INCAR.gz b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/INCAR.gz index 16bf29b49d..6b7428e713 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/INCAR.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/INCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/INCAR.orig.gz b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/INCAR.orig.gz index b1db06842d..77521ab404 100644 Binary files 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41517a498a..24f3b5c848 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/OUTCAR.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/OUTCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/POSCAR.gz b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/POSCAR.gz index f66fe88218..ac93551636 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/POSCAR.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/POSCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/POSCAR.orig.gz b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/POSCAR.orig.gz index 15014feaee..a43906e2ee 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/POSCAR.orig.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/custodian.json.gz b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/custodian.json.gz index 7e4c78581a..a66adf0bd9 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/custodian.json.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/vasprun.xml.gz index 3b4143217b..52a6bd9030 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/vasprun.xml.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_1/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/inputs/INCAR b/tests/test_data/vasp/Si_elastic/tight_relax_2/inputs/INCAR index d8a35653fd..473d3fa10f 100644 --- a/tests/test_data/vasp/Si_elastic/tight_relax_2/inputs/INCAR +++ b/tests/test_data/vasp/Si_elastic/tight_relax_2/inputs/INCAR @@ -1,8 +1,9 @@ -ALGO = Normal +ALGO = Fast EDIFF = 1e-07 EDIFFG = -0.001 -ENAUG = 1360.0 +ENAUG = 1360 ENCUT = 700 +GGA = Ps IBRION = 2 ISIF = 3 ISMEAR = -5 @@ -10,13 +11,13 @@ ISPIN = 2 LAECHG = False LASPH = True LCHARG = False -LELF = True +LELF = False LMIXTAU = True LORBIT = 11 LREAL = False LVTOT = True LWAVE = False -MAGMOM = 2*-0.0 +MAGMOM = 8*0.0 NELM = 200 NSW = 99 PREC = Accurate diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic/tight_relax_2/inputs/KPOINTS index 093abbe92b..fb8e7ffacc 100644 --- a/tests/test_data/vasp/Si_elastic/tight_relax_2/inputs/KPOINTS +++ b/tests/test_data/vasp/Si_elastic/tight_relax_2/inputs/KPOINTS @@ -1,4 +1,4 @@ -pymatgen with grid density = 100 / number of atoms +pymatgen with grid density = 791 / number of atoms 0 Gamma -3 3 3 +4 4 4 diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/inputs/POSCAR b/tests/test_data/vasp/Si_elastic/tight_relax_2/inputs/POSCAR index 125daeab82..c3cc56d351 100644 --- a/tests/test_data/vasp/Si_elastic/tight_relax_2/inputs/POSCAR +++ b/tests/test_data/vasp/Si_elastic/tight_relax_2/inputs/POSCAR @@ -1,10 +1,16 @@ -Si2 +Si8 1.0 -0.000000 2.752777 2.752777 -2.752777 -0.000000 2.752777 -2.752777 2.752777 0.000000 + 5.4360111679571759 0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4360111679571759 0.0000000000000003 + -0.0000000000000000 -0.0000000000000000 5.4360111679571759 Si -2 +8 direct -0.750000 0.750000 0.750000 Si -0.500000 0.500000 0.500000 Si + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 0.0000000000000000 0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + -0.0000000000000000 0.5000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/CONTCAR.gz b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/CONTCAR.gz index 1405f3be86..64b791782f 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/CONTCAR.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/CONTCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/INCAR.gz b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/INCAR.gz index e88afa3316..4f7f67e261 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/INCAR.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/INCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/INCAR.orig.gz b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/INCAR.orig.gz index 1ca34a43eb..cfc7c50694 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/INCAR.orig.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/INCAR.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/KPOINTS.gz b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/KPOINTS.gz index 9eff2a9188..532b60d960 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/KPOINTS.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/KPOINTS.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/KPOINTS.orig.gz b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/KPOINTS.orig.gz index 89db07b535..56bdce9e17 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/KPOINTS.orig.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/KPOINTS.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/OUTCAR.gz b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/OUTCAR.gz index a001ce445c..cf66b72c81 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/OUTCAR.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/OUTCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/POSCAR.gz b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/POSCAR.gz index efba016678..7922ac8544 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/POSCAR.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/POSCAR.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/POSCAR.orig.gz b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/POSCAR.orig.gz index 35fe145ba3..76e2a5761e 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/POSCAR.orig.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/custodian.json.gz b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/custodian.json.gz index 54b0420d67..5072b77960 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/custodian.json.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/vasprun.xml.gz index 9747fed937..7507775d0f 100644 Binary files a/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/vasprun.xml.gz and b/tests/test_data/vasp/Si_elastic/tight_relax_2/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/inputs/INCAR b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/inputs/INCAR new file mode 100644 index 0000000000..e65ff99d9f --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/inputs/INCAR @@ -0,0 +1,24 @@ +ALGO = Normal +EDIFF = 1e-07 +EDIFFG = -0.001 +ENAUG = 1360 +ENCUT = 300 +GGA = Ps +IBRION = 2 +ISIF = 2 +ISMEAR = -5 +ISPIN = 2 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 8*-0.0 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/inputs/KPOINTS new file mode 100644 index 0000000000..f6f3064e20 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 100 / number of atoms +0 +Gamma +2 2 2 diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/inputs/POSCAR b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/inputs/POSCAR new file mode 100644 index 0000000000..419d602615 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/inputs/POSCAR @@ -0,0 +1,16 @@ +Si8 +1.0 + 5.4229442218237667 0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4502640129743263 0.0000000000000003 + 0.0000000000000000 0.0000000000000000 5.4502640129743263 +Si +8 +direct + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 0.0000000000000000 0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + 0.0000000000000000 0.5000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/inputs/POTCAR.spec b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/inputs/POTCAR.spec new file mode 100644 index 0000000000..e267321d2c --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/inputs/POTCAR.spec @@ -0,0 +1 @@ +Si diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/outputs/CONTCAR.gz 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b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/outputs/custodian.json.gz new file mode 100644 index 0000000000..7938bee946 Binary files /dev/null and b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/outputs/transformations.json b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/outputs/transformations.json new file mode 100644 index 0000000000..6527745afe --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_2_6/outputs/transformations.json @@ -0,0 +1 @@ +{"@module": "pymatgen.alchemy.materials", "@class": "TransformedStructure", "charge": 0.0, "lattice": {"matrix": [[5.422944221823767, 0.0, 3e-16], [-2.9849623113198597e-16, 5.450264012974326, 3e-16], [0.0, 0.0, 5.450264012974326]], "pbc": [true, true, true], "a": 5.422944221823767, "b": 5.450264012974326, "c": 5.450264012974326, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 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a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/inputs/INCAR b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/inputs/INCAR new file mode 100644 index 0000000000..e65ff99d9f --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/inputs/INCAR @@ -0,0 +1,24 @@ +ALGO = Normal +EDIFF = 1e-07 +EDIFFG = -0.001 +ENAUG = 1360 +ENCUT = 300 +GGA = Ps +IBRION = 2 +ISIF = 2 +ISMEAR = -5 +ISPIN = 2 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 8*-0.0 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/inputs/KPOINTS new file mode 100644 index 0000000000..f6f3064e20 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 100 / number of atoms +0 +Gamma +2 2 2 diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/inputs/POSCAR b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/inputs/POSCAR new file mode 100644 index 0000000000..da0af71c4d --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/inputs/POSCAR @@ -0,0 +1,16 @@ +Si8 +1.0 + 5.4774475432663188 0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4502640129743263 0.0000000000000003 + 0.0000000000000000 0.0000000000000000 5.4502640129743263 +Si +8 +direct + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 0.0000000000000000 0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + 0.0000000000000000 0.5000000000000000 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a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/outputs/POTCAR.spec b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/outputs/POTCAR.spec new file mode 100644 index 0000000000..e267321d2c --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/outputs/POTCAR.spec @@ -0,0 +1 @@ +Si diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/outputs/custodian.json.gz b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/outputs/custodian.json.gz new file mode 100644 index 0000000000..cbe306152d Binary files /dev/null and b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/outputs/transformations.json b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/outputs/transformations.json new file mode 100644 index 0000000000..edbf7fd3fc --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/outputs/transformations.json @@ -0,0 +1 @@ +{"@module": "pymatgen.alchemy.materials", "@class": "TransformedStructure", "charge": 0.0, "lattice": {"matrix": [[5.477447543266319, 0.0, 3e-16], [-3.014962686336267e-16, 5.450264012974326, 3e-16], [0.0, 0.0, 5.450264012974326]], "pbc": [true, true, true], "a": 5.477447543266319, "b": 5.450264012974326, "c": 5.450264012974326, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 162.70964871333354}, "properties": {}, "sites": [{"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.25, 0.75], "xyz": [1.3693618858165797, 1.3625660032435816, 4.087698009730745], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.5, 0.0, 0.0], "xyz": [2.7387237716331594, 0.0, 1.5e-16], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.75, 0.25], "xyz": [1.3693618858165795, 4.087698009730745, 1.3625660032435818], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": 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12:41:30.220539+00:00", "other_parameters": {}, "@version": null} diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..dbb5a6cdd1 Binary files /dev/null and b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_3_6/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/inputs/INCAR b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/inputs/INCAR new file mode 100644 index 0000000000..e65ff99d9f --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/inputs/INCAR @@ -0,0 +1,24 @@ +ALGO = Normal +EDIFF = 1e-07 +EDIFFG = -0.001 +ENAUG = 1360 +ENCUT = 300 +GGA = Ps +IBRION = 2 +ISIF = 2 +ISMEAR = -5 +ISPIN = 2 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 8*-0.0 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/inputs/KPOINTS new file mode 100644 index 0000000000..f6f3064e20 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 100 / number of atoms +0 +Gamma +2 2 2 diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/inputs/POSCAR b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/inputs/POSCAR new file mode 100644 index 0000000000..d076c8f331 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/inputs/POSCAR @@ -0,0 +1,16 @@ +Si8 +1.0 + 5.5044968314411324 0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4502640129743263 0.0000000000000003 + 0.0000000000000000 0.0000000000000000 5.4502640129743263 +Si +8 +direct + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 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b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/outputs/transformations.json b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/outputs/transformations.json new file mode 100644 index 0000000000..5f8c560241 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/outputs/transformations.json @@ -0,0 +1 @@ +{"@module": "pymatgen.alchemy.materials", "@class": "TransformedStructure", "charge": 0.0, "lattice": {"matrix": [[5.504496831441132, 0.0, 3e-16], [-3.0298514815086237e-16, 5.450264012974326, 3e-16], [0.0, 0.0, 5.450264012974326]], "pbc": [true, true, true], "a": 5.504496831441132, "b": 5.450264012974326, "c": 5.450264012974326, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 163.5131580380883}, "properties": {}, "sites": [{"species": [{"element": "Si", "occu": 1}], "abc": [0.25, 0.25, 0.75], "xyz": [1.376124207860283, 1.3625660032435816, 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{"species": [{"element": "Si", "occu": 1}], "abc": [0.75, 0.75, 0.75], "xyz": [4.087698009730745, 4.087698009730745, 4.087698009730746], "properties": {"magmom": -0.0}, "label": "Si"}, {"species": [{"element": "Si", "occu": 1}], "abc": [0.0, 0.5, 0.0], "xyz": [-1.5e-16, 2.725132006487163, 1.5e-16], "properties": {"magmom": -0.0}, "label": "Si"}]}, "output_parameters": {}}], "last_modified": "2024-05-29 12:41:41.262479+00:00", "other_parameters": {}, "@version": null} diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..b363d19a63 Binary files /dev/null and b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_4_6/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/inputs/INCAR b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/inputs/INCAR new file mode 100644 index 0000000000..e65ff99d9f --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/inputs/INCAR @@ -0,0 +1,24 @@ +ALGO = Normal +EDIFF = 1e-07 +EDIFFG = -0.001 +ENAUG = 1360 +ENCUT = 300 +GGA = Ps +IBRION = 2 +ISIF = 2 +ISMEAR = -5 +ISPIN = 2 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 8*-0.0 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/inputs/KPOINTS new file mode 100644 index 0000000000..f6f3064e20 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 100 / number of atoms +0 +Gamma +2 2 2 diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/inputs/POSCAR b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/inputs/POSCAR new file mode 100644 index 0000000000..7e0f5a6a9f --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/inputs/POSCAR @@ -0,0 +1,16 @@ +Si8 +1.0 + 5.4502640129743263 -0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4502640129743263 0.0000000000000003 + 0.0000000000000000 -0.1090052802594865 5.4491738511446446 +Si +8 +direct + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 0.0000000000000000 0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + 0.0000000000000000 0.5000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/inputs/POTCAR.spec 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"last_modified": "2024-05-29 12:41:52.399134+00:00", "other_parameters": {}, "@version": null} diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..79a7b9be94 Binary files /dev/null and b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_5_6/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/inputs/INCAR b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/inputs/INCAR new file mode 100644 index 0000000000..e65ff99d9f --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/inputs/INCAR @@ -0,0 +1,24 @@ +ALGO = Normal +EDIFF = 1e-07 +EDIFFG = -0.001 +ENAUG = 1360 +ENCUT = 300 +GGA = Ps +IBRION = 2 +ISIF = 2 +ISMEAR = -5 +ISPIN = 2 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 8*-0.0 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/inputs/KPOINTS new file mode 100644 index 0000000000..f6f3064e20 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 100 / number of atoms +0 +Gamma +2 2 2 diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/inputs/POSCAR b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/inputs/POSCAR new file mode 100644 index 0000000000..f5ba0ad10d --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/inputs/POSCAR @@ -0,0 +1,16 @@ +Si8 +1.0 + 5.4502640129743263 -0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4502640129743263 0.0000000000000003 + 0.0000000000000000 -0.0545026401297433 5.4499914929605069 +Si +8 +direct + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 0.0000000000000000 0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + 0.0000000000000000 0.5000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/inputs/POTCAR.spec b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/inputs/POTCAR.spec new file mode 100644 index 0000000000..e267321d2c --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/inputs/POTCAR.spec @@ -0,0 +1 @@ +Si diff --git a/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/outputs/CONTCAR.gz b/tests/test_data/vasp/Si_elastic_fail/elastic_relax_6_6/outputs/CONTCAR.gz new file mode 100644 index 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b/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/inputs/INCAR new file mode 100644 index 0000000000..99189bac55 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/inputs/INCAR @@ -0,0 +1,24 @@ +ALGO = Fast +EDIFF = 1e-07 +EDIFFG = -0.001 +ENAUG = 1360 +ENCUT = 300 +GGA = Ps +IBRION = 2 +ISIF = 3 +ISMEAR = 0 +ISPIN = 2 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 8*0.6 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.2 diff --git a/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/inputs/KPOINTS new file mode 100644 index 0000000000..f6f3064e20 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 100 / number of atoms +0 +Gamma +2 2 2 diff --git a/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/inputs/POSCAR b/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/inputs/POSCAR new file mode 100644 index 0000000000..4235d2a689 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/inputs/POSCAR @@ -0,0 +1,16 @@ +Si8 +1.0 + 5.4687279953829524 0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4687279953829524 0.0000000000000003 + 0.0000000000000000 0.0000000000000000 5.4687279953829524 +Si +8 +direct + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 0.0000000000000000 0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + 0.0000000000000000 0.5000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/inputs/POTCAR.spec 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b/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/outputs/POTCAR.spec new file mode 100644 index 0000000000..e267321d2c --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/outputs/POTCAR.spec @@ -0,0 +1 @@ +Si diff --git a/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/outputs/custodian.json.gz b/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/outputs/custodian.json.gz new file mode 100644 index 0000000000..43ac7a7274 Binary files /dev/null and b/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..020114611e Binary files /dev/null and b/tests/test_data/vasp/Si_elastic_fail/tight_relax_1/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/inputs/INCAR b/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/inputs/INCAR new file mode 100644 index 0000000000..23359c16b9 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/inputs/INCAR @@ -0,0 +1,24 @@ +ALGO = Fast +EDIFF = 1e-07 +EDIFFG = -0.001 +ENAUG = 1360 +ENCUT = 300 +GGA = Ps +IBRION = 2 +ISIF = 3 +ISMEAR = -5 +ISPIN = 2 +LAECHG = False +LASPH = True +LCHARG = False +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 8*-0.0 +NELM = 200 +NSW = 99 +PREC = Accurate +SIGMA = 0.05 diff --git a/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/inputs/KPOINTS b/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/inputs/KPOINTS new file mode 100644 index 0000000000..f6f3064e20 --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 100 / number of atoms +0 +Gamma +2 2 2 diff --git a/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/inputs/POSCAR b/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/inputs/POSCAR new file mode 100644 index 0000000000..b4783ec5ab --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/inputs/POSCAR @@ -0,0 +1,16 @@ +Si8 +1.0 + 5.4495306439927775 0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4495306439927775 0.0000000000000003 + -0.0000000000000000 -0.0000000000000000 5.4495306439927775 +Si +8 +direct + 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si + 0.5000000000000000 -0.0000000000000000 -0.0000000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si + 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 -0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + 0.0000000000000000 0.5000000000000000 -0.0000000000000000 Si diff --git 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a/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/outputs/POTCAR.spec b/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/outputs/POTCAR.spec new file mode 100644 index 0000000000..e267321d2c --- /dev/null +++ b/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/outputs/POTCAR.spec @@ -0,0 +1 @@ +Si diff --git a/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/outputs/custodian.json.gz b/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/outputs/custodian.json.gz new file mode 100644 index 0000000000..1a1df4a5d4 Binary files /dev/null and b/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..04629302f5 Binary files /dev/null and b/tests/test_data/vasp/Si_elastic_fail/tight_relax_2/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_hse_optics/hse_optics/inputs/INCAR b/tests/test_data/vasp/Si_hse_optics/hse_optics/inputs/INCAR index 9ac70e3177..d7abd3ccae 100644 --- a/tests/test_data/vasp/Si_hse_optics/hse_optics/inputs/INCAR +++ b/tests/test_data/vasp/Si_hse_optics/hse_optics/inputs/INCAR @@ -10,7 +10,7 @@ KSPACING = 0.5 LAECHG = True LASPH = True LCHARG = False -LELF = True +LELF = False LHFCALC = True LMIXTAU = True LOPTICS = True diff --git a/tests/test_data/vasp/Si_lobster/relax_1/inputs/POSCAR b/tests/test_data/vasp/Si_lobster/relax_1/inputs/POSCAR index 88ce0792fe..41a38bcf0c 100644 --- a/tests/test_data/vasp/Si_lobster/relax_1/inputs/POSCAR +++ b/tests/test_data/vasp/Si_lobster/relax_1/inputs/POSCAR @@ -1,10 +1,10 @@ Si2 1.0 - 0.0000000000000000 2.7300000000000000 2.7300000000000000 - 2.7300000000000000 0.0000000000000000 2.7300000000000000 - 2.7300000000000000 2.7300000000000000 0.0000000000000000 + 3.3488982826904379 0.0000000000000000 1.9334873250000004 + 1.1162994275634794 3.1573715802591895 1.9334873250000004 + 0.0000000000000000 0.0000000000000000 3.8669746500000000 Si 2 direct - 0.0000000000000000 0.0000000000000000 0.0000000000000000 Si 0.2500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 0.0000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_lobster/relax_2/inputs/POSCAR b/tests/test_data/vasp/Si_lobster/relax_2/inputs/POSCAR index 3151c58051..5f1debf8dc 100644 --- a/tests/test_data/vasp/Si_lobster/relax_2/inputs/POSCAR +++ b/tests/test_data/vasp/Si_lobster/relax_2/inputs/POSCAR @@ -8,6 +8,3 @@ Si direct 0.0000000000000000 -0.0000000000000000 -0.0000000000000000 Si 0.2500000000000000 0.2500000000000000 0.2500000000000000 Si - - 0.0000000000000000 0.0000000000000000 0.0000000000000000 - 0.0000000000000000 0.0000000000000000 0.0000000000000000 diff --git a/tests/test_data/vasp/Si_lobster/static_run/inputs/POSCAR b/tests/test_data/vasp/Si_lobster/static_run/inputs/POSCAR index 5e306546bf..c2e242254a 100644 --- a/tests/test_data/vasp/Si_lobster/static_run/inputs/POSCAR +++ b/tests/test_data/vasp/Si_lobster/static_run/inputs/POSCAR @@ -8,6 +8,3 @@ Si direct 0.0000000000000000 0.0000000000000000 0.0000000000000000 Si 0.2500000000000000 0.2500000000000000 0.2500000000000000 Si - - 0.0000000000000000 0.0000000000000000 0.0000000000000000 - 0.0000000000000000 0.0000000000000000 0.0000000000000000 diff --git a/tests/test_data/vasp/Si_lobster_uniform/non-scf_uniform/inputs/POSCAR b/tests/test_data/vasp/Si_lobster_uniform/non-scf_uniform/inputs/POSCAR index 57a66e36d8..41a38bcf0c 100644 --- a/tests/test_data/vasp/Si_lobster_uniform/non-scf_uniform/inputs/POSCAR +++ b/tests/test_data/vasp/Si_lobster_uniform/non-scf_uniform/inputs/POSCAR @@ -1,13 +1,10 @@ Si2 1.0 - -0.0000000000000000 2.7180346595296876 2.7180346595296876 - 2.7180346595296876 -0.0000000000000000 2.7180346595296876 - 2.7180346595296876 2.7180346595296876 -0.0000000000000000 + 3.3488982826904379 0.0000000000000000 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b/tests/test_data/vasp/Si_mp_gga_relax/GGA_Relax_1/inputs/INCAR index 8368b4e030..6e1fbb6731 100644 --- a/tests/test_data/vasp/Si_mp_gga_relax/GGA_Relax_1/inputs/INCAR +++ b/tests/test_data/vasp/Si_mp_gga_relax/GGA_Relax_1/inputs/INCAR @@ -3,7 +3,7 @@ EDIFF = 0.0001 ENCUT = 520 IBRION = 2 ISIF = 3 -ISMEAR = 0 +ISMEAR = -5 ISPIN = 2 LASPH = True LORBIT = 11 @@ -14,4 +14,4 @@ MAGMOM = 2*0.6 NELM = 100 NSW = 99 PREC = Accurate -SIGMA = 0.2 +SIGMA = 0.05 diff --git a/tests/test_data/vasp/Si_mp_meta_gga_relax/pbesol_pre_relax/inputs/INCAR b/tests/test_data/vasp/Si_mp_meta_gga_relax/pbesol_pre_relax/inputs/INCAR index f682301652..189d6d470f 100644 --- a/tests/test_data/vasp/Si_mp_meta_gga_relax/pbesol_pre_relax/inputs/INCAR +++ b/tests/test_data/vasp/Si_mp_meta_gga_relax/pbesol_pre_relax/inputs/INCAR @@ -22,4 +22,4 @@ MAGMOM = 2*0.6 NELM = 200 NSW = 99 PREC = Accurate -SIGMA = 0.2 +SIGMA = 0.05 diff --git a/tests/test_data/vasp/Si_mp_meta_gga_relax/r2scan_relax/inputs/INCAR b/tests/test_data/vasp/Si_mp_meta_gga_relax/r2scan_relax/inputs/INCAR index 7a2c6583db..70878e6b66 100644 --- a/tests/test_data/vasp/Si_mp_meta_gga_relax/r2scan_relax/inputs/INCAR +++ b/tests/test_data/vasp/Si_mp_meta_gga_relax/r2scan_relax/inputs/INCAR @@ -5,7 +5,7 @@ ENAUG = 1360.0 ENCUT = 680.0 IBRION = 2 ISIF = 3 -ISMEAR = -5 +ISMEAR = 0 ISPIN = 2 KSPACING = 0.28253269576667883 LAECHG = True diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_1/inputs/INCAR b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_1/inputs/INCAR new file mode 100644 index 0000000000..5385f3acb2 --- /dev/null +++ b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_1/inputs/INCAR @@ -0,0 +1,33 @@ +ALGO = Fast +EDIFF = 1e-05 +EDIFFG = -0.02 +ENAUG = 1360 +ENCUT = 520 +GGA = Ps +IBRION = 0 +ISIF = 2 +ISMEAR = 0 +ISPIN = 2 +ISYM = 0 +KBLOCK = 100 +LAECHG = True +LASPH = True +LCHARG = False +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAGMOM = 2*0.6 +MAXMIX = 20 +MDALGO = 2 +NELM = 500 +NELMIN = 4 +NSW = 3 +POTIM = 1 +PREC = Normal +SIGMA = 0.2 +SMASS = 0 +TEBEG = 300 +TEEND = 300.0 diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_1/inputs/KPOINTS b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_1/inputs/KPOINTS new file mode 100644 index 0000000000..093abbe92b --- /dev/null +++ b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_1/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 100 / number of atoms +0 +Gamma +3 3 3 diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_1/inputs/POSCAR b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_1/inputs/POSCAR new file mode 100644 index 0000000000..3c72d993a0 --- /dev/null +++ b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_1/inputs/POSCAR @@ -0,0 +1,10 @@ +Si2 +1.0 + 3.3488980000000002 0.0000000000000000 1.9334870000000000 + 1.1162989999999999 3.1573720000000001 1.9334870000000000 + 0.0000000000000000 0.0000000000000000 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b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_1/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/inputs/INCAR b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/inputs/INCAR new file mode 100644 index 0000000000..a6eced0c4a --- /dev/null +++ b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/inputs/INCAR @@ -0,0 +1,32 @@ +ALGO = Fast +EDIFF = 1e-05 +EDIFFG = -0.02 +ENAUG = 1360 +ENCUT = 520 +GGA = Ps +IBRION = 0 +ISIF = 2 +ISMEAR = -5 +ISPIN = 1 +ISYM = 0 +KBLOCK = 100 +LAECHG = True +LASPH = True +LCHARG = False +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAXMIX = 20 +MDALGO = 2 +NELM = 500 +NELMIN = 4 +NSW = 3 +POTIM = 1 +PREC = Normal +SIGMA = 0.05 +SMASS = 0 +TEBEG = 300.0 +TEEND = 300.0 diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/inputs/KPOINTS b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/inputs/KPOINTS new file mode 100644 index 0000000000..093abbe92b --- /dev/null +++ b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 100 / number of atoms +0 +Gamma +3 3 3 diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/inputs/POSCAR b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/inputs/POSCAR new file mode 100644 index 0000000000..d5f7bc1ac2 --- /dev/null +++ b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/inputs/POSCAR @@ -0,0 +1,23 @@ +Si2 +1.0 + 3.3488980000000002 0.0000000000000000 1.9334870000000000 + 1.1162989999999999 3.1573720000000001 1.9334870000000000 + 0.0000000000000000 0.0000000000000000 3.8669750000000001 +Si +2 +direct + 0.2509246999416777 0.2479629372437218 0.2497071651391614 Si + -0.0009246999416777 0.0020370627562782 0.0002928348608386 Si + + 0.0004025256800000 -0.0031480439000000 -0.0016045943000000 + -0.0004025256800000 0.0031480439000000 0.0016045943000000 + +1 + 1.0000000000000000 + -0.63509263E-03 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b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/POSCAR.gz differ diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/POSCAR.orig.gz b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/POSCAR.orig.gz new file mode 100644 index 0000000000..e8cffe8eb7 Binary files /dev/null and b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/POSCAR.orig.gz differ diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/POTCAR.spec b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/POTCAR.spec new file mode 100644 index 0000000000..e267321d2c --- /dev/null +++ b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/POTCAR.spec @@ -0,0 +1 @@ +Si diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/custodian.json.gz b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/custodian.json.gz new file mode 100644 index 0000000000..e1b6808bb3 Binary files /dev/null and b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..9ed080c665 Binary files /dev/null and b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_2/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/inputs/INCAR b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/inputs/INCAR new file mode 100644 index 0000000000..f1fb2a1630 --- /dev/null +++ b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/inputs/INCAR @@ -0,0 +1,32 @@ +ALGO = Fast +EDIFF = 1e-05 +EDIFFG = -0.02 +ENAUG = 1360 +ENCUT = 520 +GGA = Ps +IBRION = 0 +ISIF = 2 +ISMEAR = -5 +ISPIN = 1 +ISYM = 0 +KBLOCK = 100 +LAECHG = True +LASPH = True +LCHARG = False +LELF = False +LMIXTAU = True +LORBIT = 11 +LREAL = False +LVTOT = True +LWAVE = False +MAXMIX = 20 +MDALGO = 2 +NELM = 500 +NELMIN = 4 +NSW = 3 +POTIM = 1 +PREC = Normal +SIGMA = 0.05 +SMASS = 0 +TEBEG = 300 +TEEND = 300.0 diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/inputs/KPOINTS b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/inputs/KPOINTS new file mode 100644 index 0000000000..093abbe92b --- /dev/null +++ b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/inputs/KPOINTS @@ -0,0 +1,4 @@ +pymatgen with grid density = 100 / number of atoms +0 +Gamma +3 3 3 diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/inputs/POSCAR b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/inputs/POSCAR new file mode 100644 index 0000000000..5428183e57 --- /dev/null +++ b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/inputs/POSCAR @@ -0,0 +1,23 @@ +Si2 +1.0 + 3.3488980000000002 0.0000000000000000 1.9334870000000000 + 1.1162989999999999 3.1573720000000001 1.9334870000000000 + 0.0000000000000000 0.0000000000000000 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b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/outputs/POTCAR.spec @@ -0,0 +1 @@ +Si diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/outputs/custodian.json.gz b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/outputs/custodian.json.gz new file mode 100644 index 0000000000..8d4c906334 Binary files /dev/null and b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/outputs/custodian.json.gz differ diff --git a/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/outputs/vasprun.xml.gz b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/outputs/vasprun.xml.gz new file mode 100644 index 0000000000..e202d02ca1 Binary files /dev/null and b/tests/test_data/vasp/Si_multi_md/molecular_dynamics_3/outputs/vasprun.xml.gz differ diff --git a/tests/test_data/vasp/Si_phonons_1/phonon_static_1_1/inputs/POSCAR b/tests/test_data/vasp/Si_phonons_1/phonon_static_1_1/inputs/POSCAR index 69527787e6..73da6374a3 100644 --- a/tests/test_data/vasp/Si_phonons_1/phonon_static_1_1/inputs/POSCAR +++ b/tests/test_data/vasp/Si_phonons_1/phonon_static_1_1/inputs/POSCAR @@ -1,16 +1,16 @@ Si8 1.0 - 5.4600000000000000 0.0000000000000001 0.0000000000000005 - -0.0000000000000003 5.4599999999999991 0.0000000000000002 - -0.0000000000000001 -0.0000000000000001 5.4599999999999991 + 5.4687279953829524 -0.0000000000000002 0.0000000000000002 + -0.0000000000000002 5.4687279953829524 0.0000000000000005 + -0.0000000000000003 0.0000000000000002 5.4687279953829524 Si 8 direct - 0.5018315018315017 0.4999999999999999 0.5000000000000000 Si - 0.4999999999999999 0.0000000000000000 0.0000000000000000 Si + 0.7518285787862264 0.7500000000000001 0.7500000000000001 Si + 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.2500000000000000 0.7500000000000001 0.2500000000000000 Si + 0.2500000000000000 0.2500000000000001 0.7499999999999999 Si + 0.4999999999999999 0.4999999999999999 0.5000000000000000 Si + 0.4999999999999999 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0.2500000000000001 Si + 0.0000000000000000 0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000001 Si + 0.0000000000000000 0.5000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_phonons_2/static/inputs/POSCAR b/tests/test_data/vasp/Si_phonons_2/static/inputs/POSCAR index d4356a81ad..4235d2a689 100644 --- a/tests/test_data/vasp/Si_phonons_2/static/inputs/POSCAR +++ b/tests/test_data/vasp/Si_phonons_2/static/inputs/POSCAR @@ -1,16 +1,16 @@ Si8 1.0 - 5.4600000000000000 0.0000000000000000 0.0000000000000003 - -0.0000000000000003 5.4600000000000000 0.0000000000000003 - 0.0000000000000000 0.0000000000000000 5.4600000000000000 + 5.4687279953829524 0.0000000000000000 0.0000000000000003 + -0.0000000000000003 5.4687279953829524 0.0000000000000003 + 0.0000000000000000 0.0000000000000000 5.4687279953829524 Si 8 direct - 0.0000000000000000 0.0000000000000000 0.5000000000000000 Si - 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si - 0.0000000000000000 0.5000000000000000 0.0000000000000000 Si 0.2500000000000000 0.2500000000000000 0.7500000000000000 Si 0.5000000000000000 0.0000000000000000 0.0000000000000000 Si - 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + 0.2500000000000000 0.7500000000000000 0.2500000000000000 Si 0.5000000000000000 0.5000000000000000 0.5000000000000000 Si 0.7500000000000000 0.2500000000000000 0.2500000000000000 Si + 0.0000000000000000 0.0000000000000000 0.5000000000000000 Si + 0.7500000000000000 0.7500000000000000 0.7500000000000000 Si + 0.0000000000000000 0.5000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_phonons_3/phonon_static_1_1/inputs/POSCAR b/tests/test_data/vasp/Si_phonons_3/phonon_static_1_1/inputs/POSCAR index 04fd80b2b8..f9ffa694d7 100644 --- a/tests/test_data/vasp/Si_phonons_3/phonon_static_1_1/inputs/POSCAR +++ b/tests/test_data/vasp/Si_phonons_3/phonon_static_1_1/inputs/POSCAR @@ -1,16 +1,10 @@ -Si8 +Si2 1.0 - 5.4599999999999991 0.0000000000000001 0.0000000000000001 - 0.0000000000000001 5.4599999999999991 -0.0000000000000001 - -0.0000000000000001 -0.0000000000000001 5.4599999999999991 + 3.3488982826904379 0.0000000000000000 1.9334873250000004 + 1.1162994275634794 3.1573715802591895 1.9334873250000004 + 0.0000000000000000 0.0000000000000000 3.8669746500000000 Si -8 +2 direct - 0.0018315018315018 -0.0000000000000000 -0.0000000000000000 Si - 1.0000000000000000 0.5000000000000000 0.5000000000000000 Si - 0.5000000000000000 -0.0000000000000000 0.5000000000000000 Si - 0.4999999999999999 0.5000000000000000 0.0000000000000000 Si - 0.2500000000000000 0.2500000000000000 0.2500000000000000 Si - 0.2500000000000000 0.7500000000000001 0.7500000000000000 Si - 0.7500000000000000 0.2500000000000000 0.7500000000000001 Si - 0.7500000000000000 0.7500000000000001 0.2500000000000000 Si + 0.2525860009193493 0.2500000000000000 0.2499999999999999 Si + 0.0000000000000000 0.0000000000000000 0.0000000000000000 Si diff --git a/tests/test_data/vasp/Si_phonons_3/static/inputs/POSCAR b/tests/test_data/vasp/Si_phonons_3/static/inputs/POSCAR index 88ce0792fe..6bcf115f94 100644 --- a/tests/test_data/vasp/Si_phonons_3/static/inputs/POSCAR +++ b/tests/test_data/vasp/Si_phonons_3/static/inputs/POSCAR @@ -1,10 +1,10 @@ Si2 1.0 - 0.0000000000000000 2.7300000000000000 2.7300000000000000 - 2.7300000000000000 0.0000000000000000 2.7300000000000000 - 2.7300000000000000 2.7300000000000000 0.0000000000000000 +3.348898 0.000000 1.933487 +1.116299 3.157372 1.933487 +0.000000 0.000000 3.866975 Si 2 direct - 0.0000000000000000 0.0000000000000000 0.0000000000000000 Si - 0.2500000000000000 0.2500000000000000 0.2500000000000000 Si +0.250000 0.250000 0.250000 Si +0.000000 0.000000 0.000000 Si diff --git a/tests/test_data/vasp/Si_phonons_4/tight_relax_1/inputs/POSCAR b/tests/test_data/vasp/Si_phonons_4/tight_relax_1/inputs/POSCAR index 88ce0792fe..6bcf115f94 100644 --- a/tests/test_data/vasp/Si_phonons_4/tight_relax_1/inputs/POSCAR +++ b/tests/test_data/vasp/Si_phonons_4/tight_relax_1/inputs/POSCAR @@ -1,10 +1,10 @@ Si2 1.0 - 0.0000000000000000 2.7300000000000000 2.7300000000000000 - 2.7300000000000000 0.0000000000000000 2.7300000000000000 - 2.7300000000000000 2.7300000000000000 0.0000000000000000 +3.348898 0.000000 1.933487 +1.116299 3.157372 1.933487 +0.000000 0.000000 3.866975 Si 2 direct - 0.0000000000000000 0.0000000000000000 0.0000000000000000 Si - 0.2500000000000000 0.2500000000000000 0.2500000000000000 Si +0.250000 0.250000 0.250000 Si +0.000000 0.000000 0.000000 Si diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/inputs/INCAR b/tests/test_data/vasp/matpes_static_flow/pbe_static/inputs/INCAR similarity index 94% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/inputs/INCAR rename to tests/test_data/vasp/matpes_static_flow/pbe_static/inputs/INCAR index fc405a62d1..ca8fe85a58 100644 --- a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/inputs/INCAR +++ b/tests/test_data/vasp/matpes_static_flow/pbe_static/inputs/INCAR @@ -13,7 +13,7 @@ LMAXMIX = 6 LMIXTAU = True LORBIT = 11 LREAL = False -LWAVE = False +LWAVE = True NELM = 200 NSW = 0 PREC = Accurate diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/inputs/POSCAR b/tests/test_data/vasp/matpes_static_flow/pbe_static/inputs/POSCAR similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/inputs/POSCAR rename to tests/test_data/vasp/matpes_static_flow/pbe_static/inputs/POSCAR diff --git a/tests/test_data/vasp/matpes_static_flow/pbe_static/inputs/POTCAR.spec b/tests/test_data/vasp/matpes_static_flow/pbe_static/inputs/POTCAR.spec new file mode 100644 index 0000000000..e267321d2c --- /dev/null +++ b/tests/test_data/vasp/matpes_static_flow/pbe_static/inputs/POTCAR.spec @@ -0,0 +1 @@ +Si diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/CONTCAR.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/CONTCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/CONTCAR.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/CONTCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/DOSCAR.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/DOSCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/DOSCAR.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/DOSCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/EIGENVAL.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/EIGENVAL.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/EIGENVAL.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/EIGENVAL.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/IBZKPT.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/IBZKPT.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/IBZKPT.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/IBZKPT.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/INCAR.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/INCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/INCAR.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/INCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/INCAR.orig.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/INCAR.orig.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/INCAR.orig.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/INCAR.orig.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/OSZICAR.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/OSZICAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/OSZICAR.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/OSZICAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/OUTCAR.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/OUTCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/OUTCAR.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/OUTCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/PCDAT.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/PCDAT.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/PCDAT.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/PCDAT.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/POSCAR.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/POSCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/POSCAR.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/POSCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/POSCAR.orig.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/POSCAR.orig.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/POSCAR.orig.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/POSCAR.orig.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/PROCAR.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/PROCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/PROCAR.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/PROCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/REPORT.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/REPORT.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/REPORT.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/REPORT.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/WAVECAR.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/WAVECAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/WAVECAR.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/WAVECAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/XDATCAR.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/XDATCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/XDATCAR.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/XDATCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/custodian.json.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/custodian.json.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/custodian.json.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/custodian.json.gz diff --git a/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/std_err.txt b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/std_err.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/vasp.out.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/vasp.out.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/vasp.out.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/vasp.out.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/vasprun.xml.gz b/tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/vasprun.xml.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/outputs/vasprun.xml.gz rename to tests/test_data/vasp/matpes_static_flow/pbe_static/outputs/vasprun.xml.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/inputs/INCAR b/tests/test_data/vasp/matpes_static_flow/r2scan_static/inputs/INCAR similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/inputs/INCAR rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/inputs/INCAR diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/inputs/POSCAR b/tests/test_data/vasp/matpes_static_flow/r2scan_static/inputs/POSCAR similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/inputs/POSCAR rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/inputs/POSCAR diff --git a/tests/test_data/vasp/matpes_static_flow/r2scan_static/inputs/POTCAR.spec b/tests/test_data/vasp/matpes_static_flow/r2scan_static/inputs/POTCAR.spec new file mode 100644 index 0000000000..e267321d2c --- /dev/null +++ b/tests/test_data/vasp/matpes_static_flow/r2scan_static/inputs/POTCAR.spec @@ -0,0 +1 @@ +Si diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/CONTCAR.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/CONTCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/CONTCAR.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/CONTCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/DOSCAR.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/DOSCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/DOSCAR.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/DOSCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/EIGENVAL.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/EIGENVAL.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/EIGENVAL.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/EIGENVAL.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/IBZKPT.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/IBZKPT.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/IBZKPT.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/IBZKPT.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/INCAR.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/INCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/INCAR.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/INCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/INCAR.orig.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/INCAR.orig.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/INCAR.orig.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/INCAR.orig.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/OSZICAR.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/OSZICAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/OSZICAR.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/OSZICAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/OUTCAR.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/OUTCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/OUTCAR.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/OUTCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/PCDAT.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/PCDAT.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/PCDAT.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/PCDAT.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/POSCAR.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/POSCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/POSCAR.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/POSCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/POSCAR.orig.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/POSCAR.orig.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/POSCAR.orig.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/POSCAR.orig.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/PROCAR.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/PROCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/PROCAR.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/PROCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/REPORT.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/REPORT.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/REPORT.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/REPORT.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/WAVECAR.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/WAVECAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/WAVECAR.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/WAVECAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/XDATCAR.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/XDATCAR.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/XDATCAR.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/XDATCAR.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/custodian.json.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/custodian.json.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/custodian.json.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/custodian.json.gz diff --git a/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/std_err.txt b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/std_err.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/vasp.out.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/vasp.out.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/vasp.out.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/vasp.out.gz diff --git a/tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/vasprun.xml.gz b/tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/vasprun.xml.gz similarity index 100% rename from tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/outputs/vasprun.xml.gz rename to tests/test_data/vasp/matpes_static_flow/r2scan_static/outputs/vasprun.xml.gz diff --git a/tests/vasp/conftest.py b/tests/vasp/conftest.py index 37d6d39a32..b8e665c640 100644 --- a/tests/vasp/conftest.py +++ b/tests/vasp/conftest.py @@ -1,15 +1,26 @@ from __future__ import annotations import logging +import shutil from pathlib import Path from typing import TYPE_CHECKING, Any, Callable, Final, Literal +import numpy as np import pytest +from jobflow import CURRENT_JOB +from pymatgen.io.vasp import Incar, Kpoints, Poscar, Potcar +from pymatgen.util.coord import pbc_diff from pytest import MonkeyPatch +import atomate2.vasp.jobs.base +import atomate2.vasp.jobs.defect +import atomate2.vasp.run +from atomate2.vasp.sets.base import VaspInputGenerator + if TYPE_CHECKING: from collections.abc import Generator, Sequence + logger = logging.getLogger("atomate2") _VFILES: Final = ("incar", "kpoints", "potcar", "poscar") @@ -73,14 +84,8 @@ def mock_vasp( For examples, see the tests in tests/vasp/makers/core.py. """ - import atomate2.vasp.jobs.base - import atomate2.vasp.jobs.defect - import atomate2.vasp.run - from atomate2.vasp.sets.base import VaspInputGenerator def mock_run_vasp(*args, **kwargs): - from jobflow import CURRENT_JOB - name = CURRENT_JOB.job.name try: ref_path = vasp_test_dir / _REF_PATHS[name] @@ -121,6 +126,7 @@ def _run(ref_paths, fake_run_vasp_kwargs=None): def fake_run_vasp( ref_path: Path, incar_settings: Sequence[str] = None, + incar_exclude: Sequence[str] = None, check_inputs: Sequence[Literal["incar", "kpoints", "poscar", "potcar"]] = _VFILES, clear_inputs: bool = True, ): @@ -135,6 +141,9 @@ def fake_run_vasp( incar_settings A list of INCAR settings to check. Defaults to None which checks all settings. Empty list or tuple means no settings will be checked. + incar_exclude + A list of INCAR settings to exclude from checking. Defaults to None, meaning + no settings will be excluded. check_inputs A list of vasp input files to check. Supported options are "incar", "kpoints", "poscar", "potcar", "wavecar". @@ -144,7 +153,7 @@ def fake_run_vasp( logger.info("Running fake VASP.") if "incar" in check_inputs: - check_incar(ref_path, incar_settings) + check_incar(ref_path, incar_settings, incar_exclude) if "kpoints" in check_inputs: check_kpoints(ref_path) @@ -170,14 +179,18 @@ def fake_run_vasp( logger.info("Generated fake vasp outputs") -def check_incar(ref_path: Path, incar_settings: Sequence[str]): - from pymatgen.io.vasp import Incar - +def check_incar( + ref_path: Path, incar_settings: Sequence[str], incar_exclude: Sequence[str] +) -> None: user_incar = Incar.from_file("INCAR") ref_incar_path = ref_path / "inputs" / "INCAR" ref_incar = Incar.from_file(ref_incar_path) defaults = {"ISPIN": 1, "ISMEAR": 1, "SIGMA": 0.2} - for key in list(user_incar) if incar_settings is None else incar_settings: + + keys_to_check = ( + set(user_incar) if incar_settings is None else set(incar_settings) + ) - set(incar_exclude or []) + for key in keys_to_check: user_val = user_incar.get(key, defaults.get(key)) ref_val = ref_incar.get(key, defaults.get(key)) if user_val != ref_val: @@ -188,8 +201,6 @@ def check_incar(ref_path: Path, incar_settings: Sequence[str]): def check_kpoints(ref_path: Path): - from pymatgen.io.vasp import Incar, Kpoints - user_kpoints_exists = Path("KPOINTS").exists() ref_kpoints_exists = Path(ref_path / "inputs" / "KPOINTS").exists() @@ -228,10 +239,6 @@ def check_kpoints(ref_path: Path): def check_poscar(ref_path: Path): - import numpy as np - from pymatgen.io.vasp import Poscar - from pymatgen.util.coord import pbc_diff - user_poscar = Poscar.from_file("POSCAR") ref_poscar = Poscar.from_file(ref_path / "inputs" / "POSCAR") @@ -251,8 +258,6 @@ def check_poscar(ref_path: Path): def check_potcar(ref_path: Path): - from pymatgen.io.vasp import Potcar - if Path(ref_path / "inputs" / "POTCAR").exists(): ref_potcar = Potcar.from_file(ref_path / "inputs" / "POTCAR").symbols elif Path(ref_path / "inputs" / "POTCAR.spec").exists(): @@ -292,8 +297,6 @@ def clear_vasp_inputs(): def copy_vasp_outputs(ref_path: Path): - import shutil - output_path = ref_path / "outputs" for output_file in output_path.iterdir(): if output_file.is_file(): diff --git a/tests/vasp/flows/test_core.py b/tests/vasp/flows/test_core.py index e73790e103..dcebd64ac0 100644 --- a/tests/vasp/flows/test_core.py +++ b/tests/vasp/flows/test_core.py @@ -1,14 +1,28 @@ import pytest +from emmet.core.tasks import TaskDoc +from emmet.core.vasp.calculation import VaspObject +from jobflow import run_locally +from pymatgen.electronic_structure.bandstructure import ( + BandStructure, + BandStructureSymmLine, +) + +from atomate2.vasp.flows.core import ( + BandStructureMaker, + DoubleRelaxMaker, + HSEBandStructureMaker, + HSELineModeBandStructureMaker, + HSEOpticsMaker, + HSEUniformBandStructureMaker, + LineModeBandStructureMaker, + OpticsMaker, + UniformBandStructureMaker, +) +from atomate2.vasp.jobs.core import RelaxMaker +from atomate2.vasp.sets.core import RelaxSetGenerator def test_double_relax(mock_vasp, clean_dir, si_structure): - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - from atomate2.vasp.flows.core import DoubleRelaxMaker - from atomate2.vasp.jobs.core import RelaxMaker - from atomate2.vasp.sets.core import RelaxSetGenerator - # mapping from job name to directory containing test files ref_paths = { "relax 1": "Si_double_relax/relax_1", @@ -75,15 +89,6 @@ def test_double_relax(mock_vasp, clean_dir, si_structure): def test_band_structure(mock_vasp, clean_dir, si_structure): - from emmet.core.vasp.calculation import VaspObject - from jobflow import run_locally - from pymatgen.electronic_structure.bandstructure import ( - BandStructure, - BandStructureSymmLine, - ) - - from atomate2.vasp.flows.core import BandStructureMaker - # mapping from job name to directory containing test files ref_paths = { "non-scf line": "Si_band_structure/non-scf_line", @@ -128,12 +133,6 @@ def test_band_structure(mock_vasp, clean_dir, si_structure): def test_uniform_band_structure(mock_vasp, clean_dir, si_structure): - from emmet.core.vasp.calculation import VaspObject - from jobflow import run_locally - from pymatgen.electronic_structure.bandstructure import BandStructure - - from atomate2.vasp.flows.core import UniformBandStructureMaker - # mapping from job name to directory containing test files ref_paths = { "non-scf uniform": "Si_band_structure/non-scf_uniform", @@ -171,12 +170,6 @@ def test_uniform_band_structure(mock_vasp, clean_dir, si_structure): def test_line_mode_band_structure(mock_vasp, clean_dir, si_structure): - from emmet.core.vasp.calculation import VaspObject - from jobflow import run_locally - from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine - - from atomate2.vasp.flows.core import LineModeBandStructureMaker - # mapping from job name to directory containing test files ref_paths = { "non-scf line": "Si_band_structure/non-scf_line", @@ -210,15 +203,6 @@ def test_line_mode_band_structure(mock_vasp, clean_dir, si_structure): def test_hse_band_structure(mock_vasp, clean_dir, si_structure): - from emmet.core.vasp.calculation import VaspObject - from jobflow import run_locally - from pymatgen.electronic_structure.bandstructure import ( - BandStructure, - BandStructureSymmLine, - ) - - from atomate2.vasp.flows.core import HSEBandStructureMaker - # mapping from job name to directory containing test files ref_paths = { "hse band structure line": "Si_hse_band_structure/hse_band_structure_line", @@ -265,12 +249,6 @@ def test_hse_band_structure(mock_vasp, clean_dir, si_structure): def test_hse_uniform_band_structure(mock_vasp, clean_dir, si_structure): - from emmet.core.vasp.calculation import VaspObject - from jobflow import run_locally - from pymatgen.electronic_structure.bandstructure import BandStructure - - from atomate2.vasp.flows.core import HSEUniformBandStructureMaker - # mapping from job name to directory containing test files ref_paths = { "hse band structure uniform": "Si_hse_band_structure/" @@ -310,12 +288,6 @@ def test_hse_uniform_band_structure(mock_vasp, clean_dir, si_structure): def test_hse_line_mode_band_structure(mock_vasp, clean_dir, si_structure): - from emmet.core.vasp.calculation import VaspObject - from jobflow import run_locally - from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine - - from atomate2.vasp.flows.core import HSELineModeBandStructureMaker - # mapping from job name to directory containing test files ref_paths = { "hse band structure line": "Si_hse_band_structure/hse_band_structure_line", @@ -350,11 +322,6 @@ def test_hse_line_mode_band_structure(mock_vasp, clean_dir, si_structure): def test_optics(mock_vasp, clean_dir, si_structure): - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - from atomate2.vasp.flows.core import OpticsMaker - # mapping from job name to directory containing test files ref_paths = {"optics": "Si_optics/optics", "static": "Si_optics/static"} @@ -390,11 +357,6 @@ def test_optics(mock_vasp, clean_dir, si_structure): def test_hse_optics(mock_vasp, clean_dir, si_structure): - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - from atomate2.vasp.flows.core import HSEOpticsMaker - # mapping from job name to directory containing test files ref_paths = { "hse optics": "Si_hse_optics/hse_optics", diff --git a/tests/vasp/flows/test_defect.py b/tests/vasp/flows/test_defect.py index a78fe897db..cb18af69c2 100644 --- a/tests/vasp/flows/test_defect.py +++ b/tests/vasp/flows/test_defect.py @@ -1,16 +1,24 @@ from typing import TYPE_CHECKING +import numpy as np +from jobflow import JobStore, run_locally +from maggma.stores.mongolike import MemoryStore +from pymatgen.analysis.defects.generators import SubstitutionGenerator +from pymatgen.core import Structure +from pymatgen.io.vasp.outputs import WSWQ + +from atomate2.vasp.flows.defect import ( + ConfigurationCoordinateMaker, + FormationEnergyMaker, + NonRadiativeMaker, +) + if TYPE_CHECKING: from atomate2.common.schemas.defects import CCDDocument from atomate2.vasp.schemas.defect import FiniteDifferenceDocument def test_ccd_maker(mock_vasp, clean_dir, test_dir): - from jobflow import run_locally - from pymatgen.core import Structure - - from atomate2.vasp.flows.defect import ConfigurationCoordinateMaker - # mapping from job name to directory containing test files # mapping from job name to directory containing test files ref_paths = { @@ -29,7 +37,7 @@ def test_ccd_maker(mock_vasp, clean_dir, test_dir): "finite diff q1": "Si_config_coord/finite_diff_q1", "finite diff q2": "Si_config_coord/finite_diff_q2", } - fake_run_vasp_kwargs = {k: {"incar_settings": ["ISIF"]} for k in ref_paths} + fake_run_vasp_kwargs = {path: {"incar_settings": ["ISIF"]} for path in ref_paths} # automatically use fake VASP and write POTCAR.spec during the test mock_vasp(ref_paths, fake_run_vasp_kwargs) @@ -57,17 +65,6 @@ def test_ccd_maker(mock_vasp, clean_dir, test_dir): def test_nonrad_maker(mock_vasp, clean_dir, test_dir, monkeypatch): - import numpy as np - from jobflow import JobStore, run_locally - from maggma.stores.mongolike import MemoryStore - from pymatgen.core import Structure - from pymatgen.io.vasp.outputs import WSWQ - - from atomate2.vasp.flows.defect import ( - ConfigurationCoordinateMaker, - NonRadiativeMaker, - ) - # mapping from job name to directory containing test files ref_paths = { "relax q1": "Si_config_coord/relax_q1", @@ -85,7 +82,7 @@ def test_nonrad_maker(mock_vasp, clean_dir, test_dir, monkeypatch): "finite diff q1": "Si_config_coord/finite_diff_q1", "finite diff q2": "Si_config_coord/finite_diff_q2", } - fake_run_vasp_kwargs = {k: {"incar_settings": ["ISIF"]} for k in ref_paths} + fake_run_vasp_kwargs = {path: {"incar_settings": ["ISIF"]} for path in ref_paths} # automatically use fake VASP and write POTCAR.spec during the test mock_vasp(ref_paths, fake_run_vasp_kwargs) @@ -132,10 +129,6 @@ def test_nonrad_maker(mock_vasp, clean_dir, test_dir, monkeypatch): def test_formation_energy_maker(mock_vasp, clean_dir, test_dir, monkeypatch): from jobflow import SETTINGS, run_locally - from pymatgen.analysis.defects.generators import SubstitutionGenerator - from pymatgen.core import Structure - - from atomate2.vasp.flows.defect import FormationEnergyMaker # mapping from job name to directory containing test files ref_paths = { @@ -147,20 +140,20 @@ def test_formation_energy_maker(mock_vasp, clean_dir, test_dir, monkeypatch): } fake_run_vasp_kwargs = { - k: {"incar_settings": ["ISIF"], "check_inputs": ["incar"]} for k in ref_paths + path: {"incar_settings": ["ISIF"], "check_inputs": ["incar"]} + for path in ref_paths } # automatically use fake VASP and write POTCAR.spec during the test mock_vasp(ref_paths, fake_run_vasp_kwargs) - struct_GaN = Structure.from_file(test_dir / "structures" / "GaN.cif") + struct = Structure.from_file(test_dir / "structures" / "GaN.cif") defects = list( SubstitutionGenerator().get_defects( - structure=struct_GaN, substitution={"Ga": ["Mg"]} + structure=struct, substitution={"Ga": ["Mg"]} ) ) - # rmaker = RelaxMaker(input_set_generator=ChargeStateRelaxSetGenerator()) maker = FormationEnergyMaker( relax_radius="auto", perturb=0.1, @@ -185,5 +178,10 @@ def _check_plnr_locpot(name): plnr_locpot = job["output"]["calcs_reversed"][0]["output"]["locpot"] assert set(plnr_locpot) == {"0", "1", "2"} - for k in ref_paths: - _check_plnr_locpot(k) + for path in ref_paths: + _check_plnr_locpot(path) + + # make sure the the you can restart the calculation from prv + prv_dir = test_dir / "vasp/GaN_Mg_defect/bulk_relax/outputs" + flow2 = maker.make(defects[0], bulk_supercell_dir=prv_dir, defect_index=0) + _ = run_locally(flow2, create_folders=True, ensure_success=True) diff --git a/tests/vasp/flows/test_elastic.py b/tests/vasp/flows/test_elastic.py index 1a3448b8d4..16604ab14a 100644 --- a/tests/vasp/flows/test_elastic.py +++ b/tests/vasp/flows/test_elastic.py @@ -1,15 +1,18 @@ -def test_elastic(mock_vasp, clean_dir, si_structure): - from jobflow import run_locally - from numpy.testing import assert_allclose - from pymatgen.symmetry.analyzer import SpacegroupAnalyzer - - from atomate2.common.schemas.elastic import ElasticDocument - from atomate2.vasp.flows.elastic import ElasticMaker - from atomate2.vasp.powerups import ( - update_user_incar_settings, - update_user_kpoints_settings, - ) +import pytest +from jobflow import run_locally +from numpy.testing import assert_allclose +from pymatgen.symmetry.analyzer import SpacegroupAnalyzer + +from atomate2.common.schemas.elastic import ElasticDocument +from atomate2.vasp.flows.elastic import ElasticMaker +from atomate2.vasp.powerups import ( + update_user_incar_settings, + update_user_kpoints_settings, +) + +@pytest.mark.parametrize("conventional", [False, True]) +def test_elastic(mock_vasp, clean_dir, si_structure, conventional): # mapping from job name to directory containing test files ref_paths = { "elastic relax 1/6": "Si_elastic/elastic_relax_1_6", @@ -38,8 +41,8 @@ def test_elastic(mock_vasp, clean_dir, si_structure): mock_vasp(ref_paths, fake_run_vasp_kwargs) # generate flow - si_prim = SpacegroupAnalyzer(si_structure).get_primitive_standard_structure() - flow = ElasticMaker().make(si_prim) + si = SpacegroupAnalyzer(si_structure).get_conventional_standard_structure() + flow = ElasticMaker().make(si, conventional=conventional) flow = update_user_kpoints_settings( flow, {"grid_density": 100}, name_filter="relax" ) @@ -51,16 +54,67 @@ def test_elastic(mock_vasp, clean_dir, si_structure): # validation on the outputs elastic_output = responses[flow.jobs[-1].uuid][1].output assert isinstance(elastic_output, ElasticDocument) + assert_allclose( elastic_output.elastic_tensor.ieee_format, [ - [155.7923, 54.8871, 54.8871, 0.0, 0.0, 0.0], - [54.8871, 155.7923, 54.8871, 0.0, 0.0, 0.0], - [54.8871, 54.8871, 155.7923, 0.0, 0.0, 0.0], - [0.0, 0.0, 0.0, 94.6712, 0.0, 0.0], - [0.0, 0.0, 0.0, 0.0, 94.6712, 0.0], - [0.0, 0.0, 0.0, 0.0, 0.0, 94.6712], + [156.175, 62.1577, 62.1577, 0.0, 0.0, 0.0], + [62.1577, 156.175, 62.1577, 0.0, 0.0, 0.0], + [62.1577, 62.1577, 156.175, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.0, 73.8819, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 73.8819, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0, 73.8819], ], atol=1e-3, ) assert elastic_output.chemsys == "Si" + + +def test_elastic_fail(mock_vasp, clean_dir, si_structure, caplog): + """ + Test the Elastic flow in case one of the deformation fails. + + The failure has been generated by killing the vasp process during + the execution of the Job. max_failed_deformations is set to 0, + so that the Flow will not completely. The default value of + max_failed_deformations (None), would instead allow to complete the fit. + """ + from jobflow import run_locally + + # mapping from job name to directory containing test files + ref_paths = { + "elastic relax 2/6": "Si_elastic_fail/elastic_relax_2_6", + "elastic relax 3/6": "Si_elastic_fail/elastic_relax_3_6", + "elastic relax 4/6": "Si_elastic_fail/elastic_relax_4_6", + "elastic relax 5/6": "Si_elastic_fail/elastic_relax_5_6", + "elastic relax 6/6": "Si_elastic_fail/elastic_relax_6_6", + "tight relax 1": "Si_elastic_fail/tight_relax_1", + "tight relax 2": "Si_elastic_fail/tight_relax_2", + } + + # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings + fake_run_vasp_kwargs = { + "elastic relax 2/6": {"incar_settings": ["NSW", "ISMEAR"]}, + "elastic relax 3/6": {"incar_settings": ["NSW", "ISMEAR"]}, + "elastic relax 4/6": {"incar_settings": ["NSW", "ISMEAR"]}, + "elastic relax 5/6": {"incar_settings": ["NSW", "ISMEAR"]}, + "elastic relax 6/6": {"incar_settings": ["NSW", "ISMEAR"]}, + "tight relax 1": {"incar_settings": ["NSW", "ISMEAR"]}, + "tight relax 2": {"incar_settings": ["NSW", "ISMEAR"]}, + } + + # automatically use fake VASP and write POTCAR.spec during the test + mock_vasp(ref_paths, fake_run_vasp_kwargs) + + si = SpacegroupAnalyzer(si_structure).get_conventional_standard_structure() + + flow = ElasticMaker(max_failed_deformations=0).make(si) + flow = update_user_kpoints_settings(flow, {"grid_density": 100}) + flow = update_user_incar_settings(flow, {"ENCUT": 300}) + + # run the flow or job and ensure that it finished running successfully + responses = run_locally(flow, create_folders=True, ensure_success=False) + + assert flow[-2].uuid in responses + assert flow[-1].uuid not in responses + assert "1 deformation calculations have failed, maximum allowed: 0" in caplog.text diff --git a/tests/vasp/flows/test_electrode.py b/tests/vasp/flows/test_electrode.py new file mode 100644 index 0000000000..49c18ec005 --- /dev/null +++ b/tests/vasp/flows/test_electrode.py @@ -0,0 +1,122 @@ +from __future__ import annotations + +from unittest import mock + +import pytest +from jobflow.settings import JobflowSettings + + +@pytest.fixture() +def mock_jobflow_settings(memory_jobstore): + """Set the UID_TYPE to "ulid" to make sure the documents can be sorted. + + See: https://github.com/materialsproject/jobflow/issues/519#issuecomment-1906850096 + """ + + settings = JobflowSettings(JOB_STORE=memory_jobstore, UID_TYPE="ulid") + + with mock.patch("jobflow.SETTINGS", settings): + yield + + +def test_electrode_makers(mock_vasp, clean_dir, test_dir, mock_jobflow_settings): + from emmet.core.electrode import InsertionElectrodeDoc + from jobflow import OutputReference, run_locally + from monty.serialization import loadfn + from pymatgen.core import Structure + + from atomate2.vasp.flows.core import RelaxMaker, StaticMaker + from atomate2.vasp.flows.electrode import ElectrodeInsertionMaker + from atomate2.vasp.powerups import ( + update_user_incar_settings, + update_user_kpoints_settings, + ) + from atomate2.vasp.sets.mp import ( + MPMetaGGARelaxSetGenerator, + MPMetaGGAStaticSetGenerator, + ) + # mock the default setting + + # mapping from job name to directory containing test files + ref_paths = { + "relax": "H_Graphite/relax", + "relax 0 (0)": "H_Graphite/relax_0_(0)", + "relax 1 (0)": "H_Graphite/relax_1_(0)", + "relax 1 (1)": "H_Graphite/relax_1_(1)", + "relax 1 (2)": "H_Graphite/relax_1_(2)", + "static 0": "H_Graphite/static_0", + "static 1": "H_Graphite/static_1", + } + + fake_run_vasp_kwargs = { + "relax": { + "incar_settings": ["NSW", "ISIF"], + "check_inputs": ["incar", "poscar"], + }, + "relax 0 (0)": {"incar_settings": ["NSW"], "check_inputs": ["incar"]}, + "relax 1 (0)": {"incar_settings": ["NSW"], "check_inputs": ["incar"]}, + "relax 1 (1)": {"incar_settings": ["NSW"], "check_inputs": ["incar"]}, + "relax 1 (2)": {"incar_settings": ["NSW"], "check_inputs": ["incar"]}, + "static 0": {"incar_settings": ["NSW"], "check_inputs": ["incar"]}, + "static 1": {"incar_settings": ["NSW"], "check_inputs": ["incar"]}, + } + + # automatically use fake VASP and write POTCAR.spec during the test + mock_vasp(ref_paths, fake_run_vasp_kwargs) + + # create the workflow + struct = Structure.from_file(test_dir / "vasp/H_Graphite/C4.vasp") + h_entry = loadfn(test_dir / "vasp/H_Graphite/H_entry.json") + single_relax_maker = RelaxMaker(input_set_generator=MPMetaGGARelaxSetGenerator()) + static_maker = StaticMaker( + input_set_generator=MPMetaGGAStaticSetGenerator(), task_document_kwargs={} + ) + + maker = ElectrodeInsertionMaker( + relax_maker=single_relax_maker, static_maker=static_maker + ) + flow = maker.make( + struct, inserted_element="H", n_steps=2, working_ion_entry=h_entry + ) + + flow = update_user_kpoints_settings(flow, {"grid_density": 88}) + flow = update_user_incar_settings( + flow, {"NGX": 18, "NGY": 18, "NGZ": 60, "ISIF": 2, "EDIFFG": -0.1} + ) + + # run the flow or job and ensure that it finished running successfully + responses = run_locally( + flow, create_folders=True, ensure_success=True, raise_immediately=True + ) + + inserted_formulas = [] + ie_doc = None + for res in responses.values(): + for r in res.values(): + if not isinstance(r.output, OutputReference) and hasattr( + r.output, "formula_pretty" + ): + inserted_formulas.append( + f"{r.output.formula_pretty}-{r.output.task_label.split()[0]}" + ) + if isinstance(r.output, InsertionElectrodeDoc): + ie_doc = r.output + + inserted_formulas.sort() + + # C-relax, C-static + # HC4-relax (1x first insertion) + # HC4-static + # HC2-relax, (3x second insertion) + assert inserted_formulas == [ + "C-relax", + "C-static", + "HC2-relax", + "HC2-relax", + "HC2-relax", + "HC4-relax", + "HC4-static", + ] + + # None of the secondary insertions were topotactic + assert len(ie_doc.adj_pairs) == 1 diff --git a/tests/vasp/flows/test_elph.py b/tests/vasp/flows/test_elph.py index 9273cc7124..32c44d1f56 100644 --- a/tests/vasp/flows/test_elph.py +++ b/tests/vasp/flows/test_elph.py @@ -1,12 +1,11 @@ import pytest +from jobflow import run_locally +from atomate2.vasp.flows.elph import ElectronPhononMaker +from atomate2.vasp.schemas.elph import ElectronPhononRenormalisationDoc -def test_elph_renormalisation(mock_vasp, clean_dir, si_structure): - from jobflow import run_locally - - from atomate2.vasp.flows.elph import ElectronPhononMaker - from atomate2.vasp.schemas.elph import ElectronPhononRenormalisationDoc +def test_elph_renormalisation(mock_vasp, clean_dir, si_structure): # map job name to directory containing test files ref_paths = { "non-scf uniform T=0.0": "Si_elph_renorm/non-scf_uniform_T=0.0", @@ -43,24 +42,11 @@ def test_elph_renormalisation(mock_vasp, clean_dir, si_structure): flow = ElectronPhononMaker( min_supercell_length=3, temperatures=(0, 100), relax_maker=None ).make(si_structure) - flow.update_maker_kwargs( - { - "_set": { - "input_set_generator->user_kpoints_settings->reciprocal_density": 50 - } - }, - name_filter="static", - dict_mod=True, - ) - flow.update_maker_kwargs( - { - "_set": { - "input_set_generator->user_kpoints_settings->reciprocal_density": 50 - } - }, - name_filter="non-scf", - dict_mod=True, - ) + set_op = { + "_set": {"input_set_generator->user_kpoints_settings->reciprocal_density": 50} + } + flow.update_maker_kwargs(set_op, name_filter="static", dict_mod=True) + flow.update_maker_kwargs(set_op, name_filter="non-scf", dict_mod=True) # run the flow and ensure that it finished running successfully responses = run_locally(flow, create_folders=True, ensure_success=True) diff --git a/tests/vasp/flows/test_eos.py b/tests/vasp/flows/test_eos.py new file mode 100644 index 0000000000..d8524d20df --- /dev/null +++ b/tests/vasp/flows/test_eos.py @@ -0,0 +1,184 @@ +import pytest +from emmet.core.tasks import TaskDoc +from jobflow import Flow, run_locally +from monty.serialization import loadfn +from pymatgen.core import Structure +from pytest import approx + +from atomate2.common.jobs.eos import PostProcessEosPressure +from atomate2.vasp.flows.eos import MPGGAEosDoubleRelaxMaker, MPGGAEosMaker +from atomate2.vasp.jobs.eos import MPGGAEosStaticMaker + +expected_incar_relax = { + "ISIF": 3, + "IBRION": 2, + "EDIFF": 1e-6, + "ISMEAR": 0, + "SIGMA": 0.05, + "LMAXMIX": 6, + "KSPACING": 0.22, +} + +expected_incar_relax_1 = { + **expected_incar_relax, + "EDIFFG": -0.05, +} + +expected_incar_deform = {**expected_incar_relax, "ISIF": 2} + +expected_incar_static = {**expected_incar_relax, "NSW": 0, "IBRION": -1, "ISMEAR": -5} +expected_incar_static.pop("ISIF") + + +def structure_equality(struct1: Structure, struct2: Structure): + structs = [struct1, struct2] + for struct in structs: + for site_prop in struct.site_properties: + struct.remove_site_property(site_prop) + return structs[0] == structs[1] + + +def test_mp_eos_double_relax_maker(mock_vasp, clean_dir, vasp_test_dir): + ref_paths = { + "EOS MP GGA relax 1": "Si_EOS_MP_GGA/mp-149-PBE-EOS_MP_GGA_relax_1", + "EOS MP GGA relax 2": "Si_EOS_MP_GGA/mp-149-PBE-EOS_MP_GGA_relax_2", + } + + structure = Structure.from_file( + f"{vasp_test_dir}/{ref_paths['EOS MP GGA relax 1']}/inputs/POSCAR" + ) + + # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings + fake_run_vasp_kwargs = { + key: {"incar_settings": list(expected_incar_relax)} for key in ref_paths + } + mock_vasp(ref_paths, fake_run_vasp_kwargs) + + flow = MPGGAEosDoubleRelaxMaker().make(structure) + # ensure flow runs successfully + responses = run_locally(flow, create_folders=True, ensure_success=True) + + for uuid in responses: + assert isinstance(responses[uuid][1].output, TaskDoc) + + task_docs = [responses[uuid][1].output for uuid in responses] + + # ensure that output structure of first relaxation is fed to second + assert structure_equality( + task_docs[1].input.structure, task_docs[0].output.structure + ) + + assert len(responses) == len(ref_paths) + + +@pytest.mark.parametrize("do_statics", [False, True]) +def test_mp_eos_maker( + do_statics: bool, + mock_vasp, + clean_dir, + vasp_test_dir, + n_frames: int = 2, + linear_strain: tuple = (-0.05, 0.05), +): + base_ref_path = "Si_EOS_MP_GGA/" + ref_paths = {} + expected_incars = { + "EOS MP GGA relax 1": expected_incar_relax_1, + "EOS MP GGA relax 2": expected_incar_relax, + } + + for idx in range(2): + ref_paths[f"EOS MP GGA relax {idx + 1}"] = ( + f"mp-149-PBE-EOS_MP_GGA_relax_{idx + 1}" + ) + + for idx in range(n_frames): + ref_paths[f"EOS MP GGA relax deformation {idx}"] = ( + f"mp-149-PBE-EOS_Deformation_Relax_{idx}" + ) + expected_incars[f"EOS MP GGA relax deformation {idx}"] = expected_incar_deform + + if do_statics: + ref_paths[f"EOS MP GGA static {idx}"] = f"mp-149-PBE-EOS_Static_{idx}" + expected_incars[f"EOS MP GGA static {idx}"] = expected_incar_static + + if do_statics: + ref_paths["EOS equilibrium static"] = "mp-149-PBE-EOS_equilibrium_static" + expected_incars["EOS equilibrium static"] = expected_incar_static + + ref_paths = {job: base_ref_path + ref_paths[job] for job in ref_paths} + + fake_run_vasp_kwargs = { + key: {"incar_settings": list(expected_incars[key])} for key in ref_paths + } + + mock_vasp(ref_paths, fake_run_vasp_kwargs) + + static_maker = None + if do_statics: + static_maker = MPGGAEosStaticMaker( + copy_vasp_kwargs={"additional_vasp_files": ("WAVECAR",)} + ) + + structure = Structure.from_file( + f"{vasp_test_dir}/{ref_paths['EOS MP GGA relax 1']}/inputs/POSCAR" + ) + + # cannot perform least-squares fit for four parameters with only 3 data points + flow = MPGGAEosMaker( + static_maker=static_maker, + number_of_frames=n_frames, + linear_strain=linear_strain, + postprocessor=PostProcessEosPressure(), + _store_transformation_information=False, + ).make(structure) + + # ensure flow runs successfully + responses = run_locally(flow, create_folders=True, ensure_success=True) + + jobs = [] + for job in flow: + if isinstance(job, Flow): + jobs.extend(list(job.jobs)) + else: + jobs.append(job) + + postprocess_uuid = next( + job.uuid for job in jobs if job.name == "MP GGA EOS Maker postprocessing" + ) + flow_output = responses[postprocess_uuid][1].output + + jobs = {job.name: job.uuid for job in jobs if job.name in ref_paths} + job_output = { + job_name: responses[uuid][1].output for job_name, uuid in jobs.items() + } + + # deformation jobs not included in this + assert len(job_output) == len(ref_paths) + + ref_energies = {"EOS MP GGA relax 1": -10.849349, "EOS MP GGA relax 2": -10.849357} + if do_statics: + ref_energies["EOS equilibrium static"] = -10.849357 + + # check that TaskDoc energies agree + assert all( + approx(ref_energies[key]) == job_output[key].calcs_reversed[0].output.energy + for key in ref_energies + ) + + ref_eos_fit = loadfn(f"{vasp_test_dir}/{base_ref_path}/Si_pressure_EOS_fit.json.gz") + job_types_to_check = ("relax", "static") if do_statics else ("relax",) + for job_type in job_types_to_check: + for key in ("energy", "volume", "EOS"): + data = flow_output[job_type][key] + if isinstance(data, list): + assert all( + approx(ref_eos_fit[job_type][key][i]) == data[i] + for i in range(len(data)) + ) + elif isinstance(data, dict): + assert all( + approx(v) == data[k] for k, v in ref_eos_fit[job_type][key].items() + ) + elif isinstance(data, (float, int)): + assert approx(ref_eos_fit[job_type][key]) == data diff --git a/tests/vasp/flows/test_magnetism.py b/tests/vasp/flows/test_magnetism.py new file mode 100644 index 0000000000..b45d8ecdbc --- /dev/null +++ b/tests/vasp/flows/test_magnetism.py @@ -0,0 +1,50 @@ +from __future__ import annotations + +import pytest +from jobflow import run_locally +from pymatgen.analysis.magnetism.analyzer import Ordering +from pymatgen.core import Structure + +from atomate2.common.flows.magnetism import MagneticOrderingsMaker +from atomate2.common.schemas.magnetism import MagneticOrderingsDocument + + +def test_magnetic_orderings(mock_vasp, clean_dir, test_dir): + structure = Structure.from_file( + test_dir / "vasp" / "MgMn2O4_magnetic" / "relax_1_3_(fm)" / "inputs" / "POSCAR" + ) + + ref_paths = { + "relax 1/3 (fm)": "MgMn2O4_magnetic/relax_1_3_(fm)", + "relax 2/3 (afm)": "MgMn2O4_magnetic/relax_2_3_(afm)", + "relax 3/3 (afm)": "MgMn2O4_magnetic/relax_3_3_(afm)", + "static 1/3 (fm)": "MgMn2O4_magnetic/static_1_3_(fm)", + "static 2/3 (afm)": "MgMn2O4_magnetic/static_2_3_(afm)", + "static 3/3 (afm)": "MgMn2O4_magnetic/static_3_3_(afm)", + } + + fake_run_vasp_kwargs = { + "relax 1/3 (fm)": {"incar_settings": ["NSW", "ISMEAR"]}, + "relax 2/3 (afm)": {"incar_settings": ["NSW", "ISMEAR"]}, + "relax 3/3 (afm)": {"incar_settings": ["NSW", "ISMEAR"]}, + "static 1/3 (fm)": {"incar_settings": ["NSW", "ISMEAR"]}, + "static 2/3 (afm)": {"incar_settings": ["NSW", "ISMEAR"]}, + "static 3/3 (afm)": {"incar_settings": ["NSW", "ISMEAR"]}, + } + + mock_vasp(ref_paths, fake_run_vasp_kwargs) + + flow = MagneticOrderingsMaker().make(structure) + + responses = run_locally(flow, create_folders=True, ensure_success=True) + + final_output = responses[flow.jobs[-1].uuid][1].output + assert isinstance(final_output, MagneticOrderingsDocument) + assert len(final_output.outputs) == 3 + assert ( + final_output.ground_state_uuid + == min(final_output.outputs, key=lambda doc: doc.energy_per_atom).uuid + ) + assert final_output.ground_state_ordering == Ordering.AFM + assert final_output.ground_state_energy == pytest.approx(-104.29910777) + assert final_output.ground_state_energy_per_atom == pytest.approx(-7.44993626929) diff --git a/tests/vasp/flows/test_matpes.py b/tests/vasp/flows/test_matpes.py index 0df8f100d8..f6b98d8eb0 100644 --- a/tests/vasp/flows/test_matpes.py +++ b/tests/vasp/flows/test_matpes.py @@ -5,40 +5,44 @@ from jobflow import run_locally from pymatgen.core import Structure -from atomate2.vasp.flows.matpes import MatPesGGAPlusMetaGGAStaticMaker +from atomate2.vasp.flows.matpes import MatPesStaticFlowMaker -def test_matpes_gga_plus_meta_gga_static_maker(mock_vasp, clean_dir, vasp_test_dir): - # map from job name to directory containing reference output files - pre_relax_dir = "matpes_pbe_r2scan_flow/pbe_static" +def test_matpes_static_flow_maker(mock_vasp, clean_dir, vasp_test_dir): + # map from job name to directory containing reference input/output files + pre_relax_dir = "matpes_static_flow/pbe_static" ref_paths = { "MatPES GGA static": pre_relax_dir, - "MatPES meta-GGA static": "matpes_pbe_r2scan_flow/r2scan_static", + "MatPES meta-GGA static": "matpes_static_flow/r2scan_static", } si_struct = Structure.from_file(f"{vasp_test_dir}/{pre_relax_dir}/inputs/POSCAR") mock_vasp(ref_paths) # generate flow - flow = MatPesGGAPlusMetaGGAStaticMaker().make(si_struct) + flow = MatPesStaticFlowMaker().make(si_struct) - assert flow.name == "MatPES GGA plus meta-GGA static" + assert flow.name == "MatPES static flow" assert len(flow) == 2 assert [job.name for job in flow] == list(ref_paths) + # make sure first static has LWAVE=True so we can pass its WAVECAR to second static + # as pre-conditioned starting point + assert flow[0].maker.input_set_generator.user_incar_settings["LWAVE"] is True + # ensure flow runs successfully responses = run_locally(flow, create_folders=True, ensure_success=True) # validate output pbe_doc = responses[flow.jobs[0].uuid][1].output + assert isinstance(pbe_doc, TaskDoc) + assert pbe_doc.output.energy == pytest.approx(-10.84940729) + assert pbe_doc.output.bandgap == pytest.approx(0.6172, abs=1e-3) + r2scan_doc = responses[flow.jobs[-1].uuid][1].output assert isinstance(r2scan_doc, TaskDoc) assert r2scan_doc.output.energy == pytest.approx(-17.53895666) assert r2scan_doc.output.bandgap == pytest.approx(0.8087999) - assert isinstance(pbe_doc, TaskDoc) - assert pbe_doc.output.energy == pytest.approx(-10.84940729) - assert pbe_doc.output.bandgap == pytest.approx(0.6172, abs=1e-3) - assert isinstance(flow.output, dict) assert {*flow.output} == {"static1", "static2"} diff --git a/tests/vasp/flows/test_md.py b/tests/vasp/flows/test_md.py new file mode 100644 index 0000000000..61478740dc --- /dev/null +++ b/tests/vasp/flows/test_md.py @@ -0,0 +1,70 @@ +from emmet.core.vasp.calculation import VaspObject +from jobflow import Flow + +from atomate2.vasp.flows.md import MultiMDMaker +from atomate2.vasp.powerups import update_user_kpoints_settings +from atomate2.vasp.schemas.md import MultiMDOutput + + +def test_multi_md_flow(mock_vasp, clean_dir, si_structure): + from emmet.core.tasks import TaskDoc + from jobflow import run_locally + + # mapping from job name to directory containing test files + ref_paths = { + "molecular dynamics 1": "Si_multi_md/molecular_dynamics_1", + "molecular dynamics 2": "Si_multi_md/molecular_dynamics_2", + "molecular dynamics 3": "Si_multi_md/molecular_dynamics_3", + } + + # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings + fake_run_vasp_kwargs = { + "molecular dynamics 1": {"incar_settings": ["NSW", "ISMEAR"]}, + "molecular dynamics 2": {"incar_settings": ["NSW", "ISMEAR"]}, + "molecular dynamics 3": {"incar_settings": ["NSW", "ISMEAR"]}, + } + + # automatically use fake VASP and write POTCAR.spec during the test + mock_vasp(ref_paths, fake_run_vasp_kwargs) + + mdflow1 = MultiMDMaker.from_parameters( + nsteps=3, time_step=1, n_runs=2, ensemble="nvt", start_temp=300 + ).make(si_structure) + mdflow2 = MultiMDMaker.from_parameters( + nsteps=3, time_step=1, n_runs=1, ensemble="nvt", start_temp=300 + ).restart_from_uuid(mdflow1.jobs[-1].output) + # set the name of the continuation MD Job, otherwise the folders for + # files will conflict + mdflow2.jobs[0].name = "molecular dynamics 3" + + flow = Flow([mdflow1, mdflow2]) + flow = update_user_kpoints_settings( + flow, {"grid_density": 100}, name_filter="molecular dynamics" + ) + + # run the flow or job and ensure that it finished running successfully + responses = run_locally(flow, create_folders=True, ensure_success=True) + + # validate the outputs + output_md_1 = responses[flow.jobs[0].jobs[0].uuid][1].output + traj = output_md_1.vasp_objects[VaspObject.TRAJECTORY] + assert len(traj.frame_properties) == 3 + assert isinstance(output_md_1, TaskDoc) + + output_recap_1 = responses[flow.jobs[0].jobs[2].uuid][1].output + assert len(output_recap_1.traj_ids) == 2 + assert len(output_recap_1.full_traj_ids) == 2 + assert isinstance(output_recap_1, MultiMDOutput) + + output_recap_2 = responses[flow.jobs[1].jobs[1].uuid][1].output + assert len(output_recap_2.traj_ids) == 1 + assert len(output_recap_2.full_traj_ids) == 3 + assert isinstance(output_recap_1, MultiMDOutput) + + +def test_multi_md_flow_restart_from_uuid(): + # check that the correct reference is used if a string is passed + ref_id = "475bf8ab-06ec-4222-8bad-6f9f3979f2ea" + flow = MultiMDMaker().restart_from_uuid(ref_id) + + assert flow.jobs[0].function_kwargs["prev_dir"].uuid == ref_id diff --git a/tests/vasp/flows/test_mp.py b/tests/vasp/flows/test_mp.py index 8741959937..930c83cad1 100644 --- a/tests/vasp/flows/test_mp.py +++ b/tests/vasp/flows/test_mp.py @@ -1,19 +1,18 @@ from __future__ import annotations -from typing import TYPE_CHECKING - import pytest +from emmet.core.tasks import TaskDoc +from jobflow import Maker, run_locally from pymatgen.core import Structure -from atomate2.vasp.jobs.mp import ( - MPMetaGGARelaxMaker, - MPPreRelaxMaker, +from atomate2.vasp.flows.mp import ( + MPGGADoubleRelaxMaker, + MPGGADoubleRelaxStaticMaker, + MPMetaGGADoubleRelaxStaticMaker, ) +from atomate2.vasp.jobs.mp import MPMetaGGARelaxMaker, MPPreRelaxMaker from atomate2.vasp.sets.mp import MPMetaGGARelaxSetGenerator -if TYPE_CHECKING: - from jobflow import Maker - @pytest.mark.parametrize("name", ["test", None]) @pytest.mark.parametrize( @@ -28,8 +27,6 @@ def test_mp_meta_gga_relax_custom_values( name: str, relax_maker: Maker | None, static_maker: Maker | None ): - from atomate2.vasp.flows.mp import MPMetaGGADoubleRelaxStaticMaker - kwargs = {} if name: kwargs["name"] = name @@ -48,12 +45,7 @@ def test_mp_meta_gga_relax_custom_values( def test_mp_meta_gga_double_relax_static(mock_vasp, clean_dir, vasp_test_dir): - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - from atomate2.vasp.flows.mp import MPMetaGGADoubleRelaxStaticMaker - - # map from job name to directory containing reference output files + # map from job name to directory containing reference input/output files pre_relax_dir = "Si_mp_meta_gga_relax/pbesol_pre_relax" ref_paths = { "MP pre-relax 1": pre_relax_dir, @@ -83,12 +75,7 @@ def test_mp_meta_gga_double_relax_static(mock_vasp, clean_dir, vasp_test_dir): def test_mp_gga_double_relax_static(mock_vasp, clean_dir, vasp_test_dir): - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - from atomate2.vasp.flows.mp import MPGGADoubleRelaxStaticMaker - - # map from job name to directory containing reference output files + # map from job name to directory containing reference input/output files pre_relax_dir = "Si_mp_gga_relax/GGA_Relax_1" ref_paths = { "MP GGA relax 1": pre_relax_dir, @@ -112,12 +99,7 @@ def test_mp_gga_double_relax_static(mock_vasp, clean_dir, vasp_test_dir): def test_mp_gga_double_relax(mock_vasp, clean_dir, vasp_test_dir): - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - from atomate2.vasp.flows.mp import MPGGADoubleRelaxMaker - - # map from job name to directory containing reference output files + # map from job name to directory containing reference input/output files pre_relax_dir = "Si_mp_gga_relax/GGA_Relax_1" ref_paths = { "MP GGA relax 1": pre_relax_dir, diff --git a/tests/vasp/flows/test_phonons.py b/tests/vasp/flows/test_phonons.py index 1c794cc89f..687e5eff3d 100644 --- a/tests/vasp/flows/test_phonons.py +++ b/tests/vasp/flows/test_phonons.py @@ -1,5 +1,6 @@ import numpy as np import pytest +from jobflow import run_locally from numpy.testing import assert_allclose from pymatgen.core.structure import Structure from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine @@ -15,15 +16,9 @@ from atomate2.vasp.flows.phonons import PhononMaker -def test_phonon_wf_only_displacements3(mock_vasp, clean_dir): - from jobflow import run_locally - - structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) - +def test_phonon_wf_vasp_only_displacements3( + mock_vasp, clean_dir, si_structure: Structure +): # mapping from job name to directory containing test files ref_paths = { "phonon static 1/1": "Si_phonons_2/phonon_static_1_1", @@ -48,7 +43,7 @@ def test_phonon_wf_only_displacements3(mock_vasp, clean_dir): store_force_constants=False, prefer_90_degrees=False, generate_frequencies_eigenvectors_kwargs={"tstep": 100}, - ).make(structure) + ).make(si_structure) # run the flow or job and ensure that it finished running successfully responses = run_locally(job, create_folders=True, ensure_success=True) @@ -58,7 +53,7 @@ def test_phonon_wf_only_displacements3(mock_vasp, clean_dir): assert_allclose( responses[job.jobs[-1].uuid][1].output.free_energies, - [5774.60355377, 5616.33406091, 4724.76619808, 3044.20807258, 696.337319349], + [6115.980051, 6059.749756, 5490.929122, 4173.234384, 2194.164562], ) assert isinstance( @@ -82,11 +77,11 @@ def test_phonon_wf_only_displacements3(mock_vasp, clean_dir): assert responses[job.jobs[-1].uuid][1].output.epsilon_static is None assert_allclose( responses[job.jobs[-1].uuid][1].output.supercell_matrix, - [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], + np.eye(3), ) assert_allclose( responses[job.jobs[-1].uuid][1].output.primitive_matrix, - ((0, 0.5, 0.5), (0.5, 0, 0.5), (0.5, 0.5, 0)), + (np.ones((3, 3)) - np.eye(3)) / 2, atol=1e-8, ) assert responses[job.jobs[-1].uuid][1].output.code == "vasp" @@ -101,54 +96,31 @@ def test_phonon_wf_only_displacements3(mock_vasp, clean_dir): ) assert ( responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpoint_density_dos - == 7000 + == 7_000 ) assert_allclose( responses[job.jobs[-1].uuid][1].output.entropies, - [ - 0.0, - 4.786689009990746, - 13.02544271435008, - 20.360935069065423, - 26.39830736008501, - ], + [0.0, 2.194216, 9.478603, 16.687079, 22.702177], + atol=1e-6, ) assert_allclose( responses[job.jobs[-1].uuid][1].output.heat_capacities, - [ - 0.0, - 8.047577577838897, - 15.97117761314484, - 19.97051059716143, - 21.87494655884403, - ], + [0.0, 5.750113, 15.408866, 19.832123, 21.842104], + atol=1e-6, ) assert_allclose( responses[job.jobs[-1].uuid][1].output.internal_energies, - [ - 5774.603553771463, - 6095.002960937394, - 7329.854739783488, - 9152.488591840654, - 11255.660261586278, - ], + [6115.980051, 6279.17132, 7386.649622, 9179.358187, 11275.035523], + atol=1e-6, ) assert responses[job.jobs[-1].uuid][1].output.chemsys == "Si" # structure will be kept in the format that was transferred -def test_phonon_wf_only_displacements_no_structural_transformation( - mock_vasp, clean_dir +def test_phonon_wf_vasp_only_displacements_no_structural_transformation( + mock_vasp, clean_dir, si_structure: Structure ): - from jobflow import run_locally - - structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) - # mapping from job name to directory containing test files ref_paths = { "phonon static 1/1": "Si_phonons_3/phonon_static_1_1", @@ -173,7 +145,7 @@ def test_phonon_wf_only_displacements_no_structural_transformation( store_force_constants=False, prefer_90_degrees=False, generate_frequencies_eigenvectors_kwargs={"tstep": 100}, - ).make(structure) + ).make(si_structure) # run the flow or job and ensure that it finished running successfully responses = run_locally(job, create_folders=True, ensure_success=True) @@ -183,44 +155,21 @@ def test_phonon_wf_only_displacements_no_structural_transformation( assert_allclose( responses[job.jobs[-1].uuid][1].output.free_energies, - [ - 5774.566996471001, - 5616.29786373465, - 4724.736849262271, - 3044.193412800876, - 696.3435315493462, - ], + [5927.157337, 5905.309813, 5439.530414, 4207.379685, 2297.576147], ) assert_allclose( responses[job.jobs[-1].uuid][1].output.entropies, - [ - 0.0, - 4.78666294741712, - 13.025332342984333, - 20.36075467024152, - 26.398072464162844, - ], + [0.0, 1.256496, 8.511348, 15.928285, 22.063785], + atol=1e-6, ) assert_allclose( responses[job.jobs[-1].uuid][1].output.heat_capacities, - [ - 0.0, - 8.047497695382027, - 15.971019069215203, - 19.970326488158854, - 21.874752681396565, - ], + [0.0, 4.958763, 15.893881, 20.311967, 22.196143], ) assert_allclose( responses[job.jobs[-1].uuid][1].output.internal_energies, - [ - 5774.566996471001, - 6094.964157503006, - 7329.8033166885825, - 9152.419812411707, - 11255.57251541699, - ], + [5927.157337, 6030.959432, 7141.800004, 8985.865319, 11123.090225], ) assert isinstance( @@ -242,17 +191,17 @@ def test_phonon_wf_only_displacements_no_structural_transformation( ) assert responses[job.jobs[-1].uuid][1].output.born is None assert responses[job.jobs[-1].uuid][1].output.epsilon_static is None + assert responses[job.jobs[-1].uuid][1].output.supercell_matrix == tuple( + map(tuple, np.eye(3)) + ) assert_allclose( - responses[job.jobs[-1].uuid][1].output.supercell_matrix, - ((-1.0, 1.0, 1.0), (1.0, -1.0, 1.0), (1.0, 1.0, -1.0)), + responses[job.jobs[-1].uuid][1].output.primitive_matrix, + ((0, 1, 0), (0, 0, 1), (1, 0, 0)), + atol=1e-8, ) assert_allclose( responses[job.jobs[-1].uuid][1].output.primitive_matrix, - ( - (1.0000000000000002, 0.0, 0.0), - (0.0, 1.0000000000000002, 0.0), - (0.0, 0.0, 1.0000000000000002), - ), + ((0, 1, 0), (0, 0, 1), (1, 0, 0)), ) assert responses[job.jobs[-1].uuid][1].output.code == "vasp" assert isinstance( @@ -264,40 +213,23 @@ def test_phonon_wf_only_displacements_no_structural_transformation( responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpath_scheme == "seekpath" ) - assert ( - responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpoint_density_dos - == 7000 - ) + phonopy_settings = responses[job.jobs[-1].uuid][1].output.phonopy_settings + assert phonopy_settings.kpoint_density_dos == 7_000 assert_allclose( responses[job.jobs[-1].uuid][1].output.entropies, - [ - 0.0, - 4.78666294741712, - 13.025332342984333, - 20.36075467024152, - 26.398072464162844, - ], + [0.0, 1.256496, 8.511348, 15.928285, 22.063785], + atol=1e-6, ) assert_allclose( responses[job.jobs[-1].uuid][1].output.heat_capacities, - [ - 0.0, - 8.047497695382027, - 15.971019069215203, - 19.970326488158854, - 21.874752681396565, - ], + [0.0, 4.958763, 15.893881, 20.311967, 22.196143], + atol=1e-6, ) assert_allclose( responses[job.jobs[-1].uuid][1].output.internal_energies, - [ - 5774.566996471001, - 6094.964157503006, - 7329.8033166885825, - 9152.419812411707, - 11255.57251541699, - ], + [5927.157337, 6030.959432, 7141.800004, 8985.865319, 11123.090225], + atol=1e-6, ) @@ -305,15 +237,9 @@ def test_phonon_wf_only_displacements_no_structural_transformation( @pytest.mark.parametrize( "kpath_scheme", ["seekpath", "hinuma", "setyawan_curtarolo", "latimer_munro"] ) -def test_phonon_wf_only_displacements_kpath(mock_vasp, clean_dir, kpath_scheme): - from jobflow import run_locally - - structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) - +def test_phonon_wf_vasp_only_displacements_kpath( + mock_vasp, clean_dir, kpath_scheme, si_structure: Structure +): # mapping from job name to directory containing test files ref_paths = {"phonon static 1/1": "Si_phonons_1/phonon_static_1_1"} @@ -331,7 +257,8 @@ def test_phonon_wf_only_displacements_kpath(mock_vasp, clean_dir, kpath_scheme): use_symmetrized_structure="primitive", kpath_scheme=kpath_scheme, generate_frequencies_eigenvectors_kwargs={"tstep": 100}, - ).make(structure) + create_thermal_displacements=True, + ).make(si_structure) # run the flow or job and ensure that it finished running successfully responses = run_locally(job, create_folders=True, ensure_success=True) @@ -342,7 +269,7 @@ def test_phonon_wf_only_displacements_kpath(mock_vasp, clean_dir, kpath_scheme): assert_allclose( responses[job.jobs[-1].uuid][1].output.free_energies, - [5776.14995034, 5617.74737777, 4725.50269363, 3043.81827626, 694.490783551], + [5776.14995034, 5617.74737777, 4725.50269363, 3043.81827626, 694.49078355], atol=1e-3, ) @@ -392,20 +319,14 @@ def test_phonon_wf_only_displacements_kpath(mock_vasp, clean_dir, kpath_scheme): ) assert ( responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpoint_density_dos - == 7000 + == 7_000 ) -# test supply of born charges, epsilon, dft energy, supercell -def test_phonon_wf_only_displacements_add_inputs_raises(mock_vasp, clean_dir): - from jobflow import run_locally - - structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) - +# test supply of born charges, epsilon, DFT energy, supercell +def test_phonon_wf_vasp_only_displacements_add_inputs_raises( + mock_vasp, clean_dir, si_structure: Structure +): # mapping from job name to directory containing test files ref_paths = {"phonon static 1/1": "Si_phonons_1/phonon_static_1_1"} @@ -416,13 +337,13 @@ def test_phonon_wf_only_displacements_add_inputs_raises(mock_vasp, clean_dir): mock_vasp(ref_paths, fake_run_vasp_kwargs) born = [ - [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]], - [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]], - [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.1]], + [[0, 0, 0], [0, 0, 0], [0, 0, 0]], + [[0, 0, 0], [0, 0, 0], [0, 0, 0]], + [[0, 0, 0], [0, 0, 0], [0, 0, 0.1]], ] epsilon_static = [ [5.25, 0, 0], - [0, 5.25, -0], + [0, 5.25, 0], [0, 0, 5.25], ] total_dft_energy_per_formula_unit = -5 @@ -434,8 +355,9 @@ def test_phonon_wf_only_displacements_add_inputs_raises(mock_vasp, clean_dir): born_maker=None, use_symmetrized_structure="primitive", generate_frequencies_eigenvectors_kwargs={"tstep": 100}, + create_thermal_displacements=True, ).make( - structure=structure, + structure=si_structure, total_dft_energy_per_formula_unit=total_dft_energy_per_formula_unit, born=born, epsilon_static=epsilon_static, @@ -444,16 +366,10 @@ def test_phonon_wf_only_displacements_add_inputs_raises(mock_vasp, clean_dir): run_locally(job, create_folders=True, ensure_success=True) -# test supply of born charges, epsilon, dft energy, supercell -def test_phonon_wf_only_displacements_add_inputs(mock_vasp, clean_dir): - from jobflow import run_locally - - structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) - +# test supply of born charges, epsilon, DFT energy, supercell +def test_phonon_wf_vasp_only_displacements_add_inputs( + mock_vasp, clean_dir, si_structure: Structure +): # mapping from job name to directory containing test files ref_paths = {"phonon static 1/1": "Si_phonons_1/phonon_static_1_1"} @@ -469,7 +385,7 @@ def test_phonon_wf_only_displacements_add_inputs(mock_vasp, clean_dir): ] epsilon_static = [ [5.25, 0, 0], - [0, 5.25, -0], + [0, 5.25, 0], [0, 0, 5.25], ] total_dft_energy_per_formula_unit = -5 @@ -480,8 +396,9 @@ def test_phonon_wf_only_displacements_add_inputs(mock_vasp, clean_dir): born_maker=None, use_symmetrized_structure="primitive", generate_frequencies_eigenvectors_kwargs={"tstep": 100}, + create_thermal_displacements=True, ).make( - structure=structure, + structure=si_structure, total_dft_energy_per_formula_unit=total_dft_energy_per_formula_unit, born=born, epsilon_static=epsilon_static, @@ -496,7 +413,7 @@ def test_phonon_wf_only_displacements_add_inputs(mock_vasp, clean_dir): assert_allclose( responses[job.jobs[-1].uuid][1].output.free_energies, - [5776.14995034, 5617.74737777, 4725.50269363, 3043.81827626, 694.490783551], + [5776.14995034, 5617.74737777, 4725.50269363, 3043.81827626, 694.49078355], atol=1e-3, ) @@ -551,20 +468,14 @@ def test_phonon_wf_only_displacements_add_inputs(mock_vasp, clean_dir): ) assert ( responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpoint_density_dos - == 7000 + == 7_000 ) # test optional parameters -def test_phonon_wf_only_displacements_optional_settings(mock_vasp, clean_dir): - from jobflow import run_locally - - structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) - +def test_phonon_wf_vasp_only_displacements_optional_settings( + mock_vasp, clean_dir, si_structure: Structure +): # mapping from job name to directory containing test files ref_paths = {"phonon static 1/1": "Si_phonons_1/phonon_static_1_1"} @@ -584,7 +495,7 @@ def test_phonon_wf_only_displacements_optional_settings(mock_vasp, clean_dir): store_force_constants=False, prefer_90_degrees=False, generate_frequencies_eigenvectors_kwargs={"tstep": 100}, - ).make(structure) + ).make(si_structure) # run the flow or job and ensure that it finished running successfully responses = run_locally(job, create_folders=True, ensure_success=True) @@ -594,17 +505,17 @@ def test_phonon_wf_only_displacements_optional_settings(mock_vasp, clean_dir): assert_allclose( responses[job.jobs[-1].uuid][1].output.free_energies, - [5776.14995034, 5617.74737777, 4725.50269363, 3043.81827626, 694.490783551], + [5776.14995034, 5617.74737777, 4725.50269363, 3043.81827626, 694.49078355], atol=1e-3, ) assert_allclose( responses[job.jobs[-1].uuid][1].output.entropies, - [0, 4.79066818396, 13.0347062141, 20.3740028425, 26.4142548987], + [0, 4.79066818, 13.03470621, 20.37400284, 26.41425489], atol=1e-8, ) assert_allclose( responses[job.jobs[-1].uuid][1].output.heat_capacities, - [0.0, 8.05373626383, 15.9800566903, 19.9803123493, 21.8851347674], + [0.0, 8.05373626, 15.98005669, 19.98031234, 21.88513476], atol=1e-8, ) @@ -652,20 +563,12 @@ def test_phonon_wf_only_displacements_optional_settings(mock_vasp, clean_dir): ) assert ( responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpoint_density_dos - == 7000 + == 7_000 ) # test run including all steps of the computation for Si -def test_phonon_wf_all_steps(mock_vasp, clean_dir): - from jobflow import run_locally - - structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) - +def test_phonon_wf_vasp_all_steps(mock_vasp, clean_dir, si_structure: Structure): # mapping from job name to directory containing test files ref_paths = { "phonon static 1/1": "Si_phonons_4/phonon_static_1_1", @@ -691,7 +594,8 @@ def test_phonon_wf_all_steps(mock_vasp, clean_dir): min_length=3.0, use_symmetrized_structure=None, generate_frequencies_eigenvectors_kwargs={"tstep": 100}, - ).make(structure) + create_thermal_displacements=True, + ).make(si_structure) # run the flow or job and ensure that it finished running successfully responses = run_locally(job, create_folders=True, ensure_success=True) @@ -701,13 +605,7 @@ def test_phonon_wf_all_steps(mock_vasp, clean_dir): assert_allclose( responses[job.jobs[-1].uuid][1].output.free_energies, - [ - 5853.741503991992, - 5692.290895556432, - 4798.677849195808, - 3122.482960037922, - 782.1734533334413, - ], + [5853.74150399, 5692.29089555, 4798.67784919, 3122.48296003, 782.17345333], ) assert isinstance( @@ -728,13 +626,13 @@ def test_phonon_wf_all_steps(mock_vasp, clean_dir): responses[job.jobs[-1].uuid][1].output.force_constants.force_constants[0][0][0][ 0 ], - 13.411855999999997, + 13.41185599, ) assert isinstance(responses[job.jobs[-1].uuid][1].output.jobdirs, PhononJobDirs) assert isinstance(responses[job.jobs[-1].uuid][1].output.uuids, PhononUUIDs) assert_allclose(responses[job.jobs[-1].uuid][1].output.born, np.zeros((2, 3, 3))) assert_allclose( - responses[job.jobs[-1].uuid][1].output.total_dft_energy, -5.746290585 + responses[job.jobs[-1].uuid][1].output.total_dft_energy, -5.74629058 ) assert_allclose( responses[job.jobs[-1].uuid][1].output.epsilon_static, @@ -761,7 +659,7 @@ def test_phonon_wf_all_steps(mock_vasp, clean_dir): ) assert ( responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpoint_density_dos - == 7000 + == 7_000 ) @@ -776,15 +674,9 @@ def test_phonon_wf_all_steps(mock_vasp, clean_dir): @pytest.mark.parametrize( "kpath_scheme", ["hinuma", "setyawan_curtarolo", "latimer_munro"] ) -def test_phonon_wf_only_displacements_kpath_raises_no_cell_change( - mock_vasp, clean_dir, kpath_scheme +def test_phonon_wf_vasp_only_displacements_kpath_raises_no_cell_change( + mock_vasp, clean_dir, kpath_scheme, si_structure: Structure ): - structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) - # mapping from job name to directory containing test files ref_paths = {"phonon static 1/1": "Si_phonons_1/phonon_static_1_1"} @@ -794,7 +686,11 @@ def test_phonon_wf_only_displacements_kpath_raises_no_cell_change( # automatically use fake VASP and write POTCAR.spec during the test mock_vasp(ref_paths, fake_run_vasp_kwargs) - with pytest.raises(ValueError): + with pytest.raises( + ValueError, + match=f"You can't use {kpath_scheme=} with the primitive standard " + "structure, please use seekpath", + ): PhononMaker( min_length=3.0, bulk_relax_maker=None, @@ -803,19 +699,15 @@ def test_phonon_wf_only_displacements_kpath_raises_no_cell_change( use_symmetrized_structure=None, kpath_scheme=kpath_scheme, generate_frequencies_eigenvectors_kwargs={"tstep": 100}, - ).make(structure) + ).make(si_structure) @pytest.mark.parametrize( "kpath_scheme", ["hinuma", "setyawan_curtarolo", "latimer_munro"] ) -def test_phonon_wf_only_displacements_kpath_raises(mock_vasp, clean_dir, kpath_scheme): - structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) - +def test_phonon_wf_vasp_only_displacements_kpath_raises( + mock_vasp, clean_dir, kpath_scheme, si_structure: Structure +): # mapping from job name to directory containing test files ref_paths = {"phonon static 1/1": "Si_phonons_1/phonon_static_1_1"} @@ -824,7 +716,11 @@ def test_phonon_wf_only_displacements_kpath_raises(mock_vasp, clean_dir, kpath_s # automatically use fake VASP and write POTCAR.spec during the test mock_vasp(ref_paths, fake_run_vasp_kwargs) - with pytest.raises(ValueError): + with pytest.raises( + ValueError, + match=f"You can't use {kpath_scheme=} with the primitive standard " + "structure, please use seekpath", + ): PhononMaker( min_length=3.0, bulk_relax_maker=None, @@ -833,15 +729,10 @@ def test_phonon_wf_only_displacements_kpath_raises(mock_vasp, clean_dir, kpath_s use_symmetrized_structure="conventional", kpath_scheme=kpath_scheme, generate_frequencies_eigenvectors_kwargs={"tstep": 100}, - ).make(structure) + ).make(si_structure) -def test_phonon_wf_all_steps_na_cl(mock_vasp, clean_dir): - from jobflow import run_locally - from pymatgen.core.structure import Structure - - from atomate2.vasp.flows.phonons import PhononMaker - +def test_phonon_wf_vasp_all_steps_na_cl(mock_vasp, clean_dir): structure = Structure( lattice=[ [5.691694, 0.000000, 0.000000], @@ -894,25 +785,20 @@ def test_phonon_wf_all_steps_na_cl(mock_vasp, clean_dir): ], ) - def test_phonon_wf_all_steps_na_cl(mock_vasp, clean_dir): - from jobflow import run_locally - from pymatgen.core.structure import Structure - - from atomate2.vasp.flows.phonons import PhononMaker - + def test_phonon_wf_vasp_all_steps_na_cl(mock_vasp, clean_dir): structure = Structure( lattice=[ - [2.3003714889113018, -3.9843602950772405, 0.0000000000000000], - [2.3003714889113018, 3.9843602950772405, 0.0000000000000000], - [0.0000000000000000, 0.0000000000000000, 7.2813299999999996], + [2.30037148, -3.98436029, 0.00000000], + [2.30037148, 3.98436029, 0.00000000], + [0.00000000, 0.00000000, 7.28132999], ], species=["Mg", "Mg", "Mg", "Sb", "Sb"], coords=[ [0.0, 0.0, 0.0], - [0.3333333333333333, 0.6666666666666666, 0.3683250000000000], - [0.6666666666666667, 0.3333333333333334, 0.6316750000000000], - [0.3333333333333333, 0.6666666666666666, 0.7747490000000000], - [0.6666666666666667, 0.3333333333333334, 0.2252510000000000], + [0.33333333, 0.66666666, 0.36832500], + [0.66666666, 0.33333333, 0.63167500], + [0.33333333, 0.66666666, 0.77474900], + [0.66666666, 0.33333333, 0.22525100], ], ) diff --git a/tests/vasp/jobs/test_core.py b/tests/vasp/jobs/test_core.py index 084f00321c..55d4bf0a73 100644 --- a/tests/vasp/jobs/test_core.py +++ b/tests/vasp/jobs/test_core.py @@ -1,15 +1,22 @@ +import jobflow +import numpy as np +from emmet.core.tasks import TaskDoc +from jobflow import run_locally from numpy.testing import assert_allclose from pytest import approx +from atomate2.vasp.jobs.core import ( + DielectricMaker, + HSERelaxMaker, + HSEStaticMaker, + RelaxMaker, + StaticMaker, + TransmuterMaker, +) -def test_static_maker(mock_vasp, clean_dir, si_structure): - import jobflow - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - from atomate2.vasp.jobs.core import StaticMaker - jstore = jobflow.SETTINGS.JOB_STORE +def test_static_maker(mock_vasp, clean_dir, si_structure): + job_store = jobflow.SETTINGS.JOB_STORE # mapping from job name to directory containing test files ref_paths = {"static": "Si_band_structure/static"} @@ -35,18 +42,12 @@ def test_static_maker(mock_vasp, clean_dir, si_structure): assert isinstance(output1, TaskDoc) assert output1.output.energy == approx(-10.85037078) - with jstore.additional_stores["data"] as s: - doc = s.query_one({"job_uuid": job.uuid}) - dd = doc["data"] - assert dd["@class"] == "Chgcar" + with job_store.additional_stores["data"] as store: + doc = store.query_one({"job_uuid": job.uuid}) + assert doc["data"]["@class"] == "Chgcar" def test_relax_maker(mock_vasp, clean_dir, si_structure): - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - from atomate2.vasp.jobs.core import RelaxMaker - # mapping from job name to directory containing test files ref_paths = {"relax": "Si_double_relax/relax_1"} @@ -71,10 +72,6 @@ def test_relax_maker(mock_vasp, clean_dir, si_structure): def test_dielectric(mock_vasp, clean_dir, si_structure): - from jobflow import run_locally - - from atomate2.vasp.jobs.core import DielectricMaker - # mapping from job name to directory containing test files ref_paths = {"dielectric": "Si_dielectric"} @@ -106,11 +103,6 @@ def test_dielectric(mock_vasp, clean_dir, si_structure): def test_hse_relax(mock_vasp, clean_dir, si_structure): - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - from atomate2.vasp.jobs.core import HSERelaxMaker - # mapping from job name to directory containing test files ref_paths = {"hse relax": "Si_hse_relax"} @@ -136,11 +128,6 @@ def test_hse_relax(mock_vasp, clean_dir, si_structure): def test_hse_static_maker(mock_vasp, clean_dir, si_structure): - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - from atomate2.vasp.jobs.core import HSEStaticMaker - # mapping from job name to directory containing test files ref_paths = {"hse static": "Si_hse_band_structure/hse_static"} @@ -166,12 +153,6 @@ def test_hse_static_maker(mock_vasp, clean_dir, si_structure): def test_transmuter(mock_vasp, clean_dir, si_structure): - import numpy as np - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - from atomate2.vasp.jobs.core import TransmuterMaker - # mapping from job name to directory containing test files ref_paths = {"transmuter": "Si_transmuter"} @@ -203,55 +184,3 @@ def test_transmuter(mock_vasp, clean_dir, si_structure): np.testing.assert_allclose( output1.structure.lattice.abc, [3.866974, 3.866975, 7.733949] ) - - -def test_molecular_dynamics(mock_vasp, clean_dir, si_structure): - import pytest - from emmet.core.tasks import TaskDoc - from emmet.core.vasp.calculation import IonicStep, VaspObject - from jobflow import run_locally - - from atomate2.vasp.jobs.core import MDMaker - - # mapping from job name to directory containing test files - ref_paths = {"molecular dynamics": "Si_molecular_dynamics/molecular_dynamics"} - - # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings - fake_run_vasp_kwargs = { - "molecular dynamics": { - "incar_settings": [ - "IBRION", - "TBEN", - "TEND", - "NSW", - "POTIM", - "MDALGO", - "ISIF", - ] - } - } - - # automatically use fake VASP and write POTCAR.spec during the test - mock_vasp(ref_paths, fake_run_vasp_kwargs) - - # generate job - job = MDMaker().make(si_structure) - nsw = 3 - job.maker.input_set_generator.user_incar_settings["NSW"] = nsw - - # run the flow or job and ensure that it finished running successfully - responses = run_locally(job, create_folders=True, ensure_success=True) - - # validation on the output - - output1 = responses[job.uuid][1].output - assert isinstance(output1, TaskDoc) - assert output1.output.energy == pytest.approx(-11.46520398) - - # check ionic steps stored as pymatgen Trajectory - assert output1.calcs_reversed[0].output.ionic_steps is None - traj = output1.vasp_objects[VaspObject.TRAJECTORY] - assert len(traj.frame_properties) == nsw - # simply check a frame property can be converted to an IonicStep - for frame in traj.frame_properties: - IonicStep(**frame) diff --git a/tests/vasp/jobs/test_eos.py b/tests/vasp/jobs/test_eos.py new file mode 100644 index 0000000000..d66e494372 --- /dev/null +++ b/tests/vasp/jobs/test_eos.py @@ -0,0 +1,82 @@ +from __future__ import annotations + +from emmet.core.tasks import TaskDoc +from jobflow import run_locally +from pymatgen.core import Structure +from pytest import approx + +from atomate2.vasp.jobs.eos import MPGGAEosRelaxMaker, MPGGAEosStaticMaker + +expected_incar_relax = { + "ISIF": 3, + "IBRION": 2, + "EDIFF": 1e-6, + "ISMEAR": 0, + "SIGMA": 0.05, + "LMAXMIX": 6, + "KSPACING": 0.22, +} + +expected_incar_static = {**expected_incar_relax, "NSW": 0, "IBRION": -1, "ISMEAR": -5} +expected_incar_static.pop("ISIF") + + +def test_mp_gga_eos_relax_maker(mock_vasp, clean_dir, vasp_test_dir): + # map from job name to directory containing reference output files + ref_paths = { + "EOS MP GGA relax": "Si_EOS_MP_GGA/mp-149-PBE-EOS_MP_GGA_relax_1", + } + + # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings + fake_run_vasp_kwargs = { + key: {"incar_settings": list(expected_incar_relax)} for key in ref_paths + } + + mock_vasp(ref_paths, fake_run_vasp_kwargs) + + structure = Structure.from_file( + f"{vasp_test_dir}/{ref_paths['EOS MP GGA relax']}/inputs/POSCAR" + ) + maker = MPGGAEosRelaxMaker() + job = maker.make(structure) + + # ensure flow runs successfully + responses = run_locally(job, create_folders=True, ensure_success=True) + + # validate output + task_doc = responses[job.uuid][1].output + assert isinstance(task_doc, TaskDoc) + assert task_doc.output.energy == approx(-10.849349) + + +def test_mp_gga_eos_static_maker(mock_vasp, clean_dir, vasp_test_dir): + # map from job name to directory containing reference output files + ref_paths = { + "EOS MP GGA static": "Si_EOS_MP_GGA/mp-149-PBE-EOS_Static_0", + } + + # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings + fake_run_vasp_kwargs = { + key: {"incar_settings": list(expected_incar_static)} for key in ref_paths + } + + mock_vasp(ref_paths, fake_run_vasp_kwargs) + + input_structure = Structure.from_file( + f"{vasp_test_dir}/Si_EOS_MP_GGA/" + f"mp-149-PBE-EOS_Deformation_Relax_0/outputs/POSCAR.gz" + ) + structure = Structure.from_file( + f"{vasp_test_dir}/Si_EOS_MP_GGA/mp-149-PBE-EOS_Static_0/inputs/POSCAR" + ) + assert input_structure == structure + + job = MPGGAEosStaticMaker().make(structure) + + # ensure flow runs successfully + responses = run_locally(job, create_folders=True, ensure_success=True) + + # validate output + task_doc = responses[job.uuid][1].output + assert isinstance(task_doc, TaskDoc) + assert task_doc.output.energy == approx(-10.547764) diff --git a/tests/vasp/jobs/test_matpes.py b/tests/vasp/jobs/test_matpes.py index 8619228a34..42e4aaf237 100644 --- a/tests/vasp/jobs/test_matpes.py +++ b/tests/vasp/jobs/test_matpes.py @@ -82,17 +82,17 @@ def test_matpes_static_maker_default_values(maker_cls: BaseVaspMaker): def test_matpes_gga_static_maker(mock_vasp, clean_dir, vasp_test_dir): # map from job name to directory containing reference input/output files - ref_paths = {"MatPES GGA static": "matpes_pbe_r2scan_flow/pbe_static"} + gga_job_name = "MatPES GGA static" + ref_paths = {gga_job_name: "matpes_static_flow/pbe_static"} si_struct = Structure.from_file( - f"{vasp_test_dir}/matpes_pbe_r2scan_flow/pbe_static/inputs/POSCAR" + f"{vasp_test_dir}/matpes_static_flow/pbe_static/inputs/POSCAR" ) - # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings - fake_run_vasp_kwargs = {key: {"incar_settings": []} for key in ref_paths} + # exclude LWAVE from INCAR checking since it defaults to False in MatPesGGAStatic + # but is overridden to True in the MatPES static flow to speed up SCF convergence + # of 2nd static, but we use the same reference input files in both tests + mock_vasp(ref_paths, {gga_job_name: {"incar_exclude": ["LWAVE"]}}) - mock_vasp(ref_paths, fake_run_vasp_kwargs) - - # generate flow job = MatPesGGAStaticMaker().make(si_struct) # ensure flow runs successfully @@ -106,19 +106,13 @@ def test_matpes_gga_static_maker(mock_vasp, clean_dir, vasp_test_dir): def test_matpes_meta_gga_static_maker(mock_vasp, clean_dir, vasp_test_dir): # map from job name to directory containing reference input/output files - ref_paths = {"MatPES meta-GGA static": "matpes_pbe_r2scan_flow/r2scan_static"} + ref_paths = {"MatPES meta-GGA static": "matpes_static_flow/r2scan_static"} si_struct = Structure.from_file( - f"{vasp_test_dir}/matpes_pbe_r2scan_flow/r2scan_static/inputs/POSCAR" + f"{vasp_test_dir}/matpes_static_flow/r2scan_static/inputs/POSCAR" ) - # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings - fake_run_vasp_kwargs = { - key: {"incar_settings": ["GGA", "METAGGA", "ALGO"]} for key in ref_paths - } - - mock_vasp(ref_paths, fake_run_vasp_kwargs) + mock_vasp(ref_paths) - # generate flow job = MatPesMetaGGAStaticMaker().make(si_struct) # ensure flow runs successfully diff --git a/tests/vasp/jobs/test_md.py b/tests/vasp/jobs/test_md.py new file mode 100644 index 0000000000..2f5c0c190d --- /dev/null +++ b/tests/vasp/jobs/test_md.py @@ -0,0 +1,53 @@ +import pytest +from emmet.core.tasks import TaskDoc +from emmet.core.vasp.calculation import IonicStep, VaspObject +from jobflow import run_locally + +from atomate2.vasp.jobs.md import MDMaker + + +def test_molecular_dynamics(mock_vasp, clean_dir, si_structure): + # mapping from job name to directory containing test files + ref_paths = {"molecular dynamics": "Si_molecular_dynamics/molecular_dynamics"} + + # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings + fake_run_vasp_kwargs = { + "molecular dynamics": { + "incar_settings": [ + "IBRION", + "TBEN", + "TEND", + "NSW", + "POTIM", + "MDALGO", + "ISIF", + ] + } + } + + # automatically use fake VASP and write POTCAR.spec during the test + mock_vasp(ref_paths, fake_run_vasp_kwargs) + + # generate job + job = MDMaker().make(si_structure) + nsw = 3 + job.maker.input_set_generator.user_incar_settings["NSW"] = nsw + + # run the flow or job and ensure that it finished running successfully + responses = run_locally(job, create_folders=True, ensure_success=True) + + # validation on the output + + output1 = responses[job.uuid][1].output + assert isinstance(output1, TaskDoc) + assert output1.output.energy == pytest.approx(-11.46520398) + + # check ionic steps stored as pymatgen Trajectory + assert output1.calcs_reversed[0].output.ionic_steps is None + traj = output1.vasp_objects[VaspObject.TRAJECTORY] + assert len(traj.frame_properties) == nsw + # check that a frame property can be converted to an IonicStep + energies = [-11.47041923, -11.46905352, -11.46520398] + for idx, frame in enumerate(traj.frame_properties): + ionic_step = IonicStep(**frame) + assert ionic_step.e_wo_entrp == pytest.approx(energies[idx]) diff --git a/tests/vasp/jobs/test_mp.py b/tests/vasp/jobs/test_mp.py index dc21655d61..cfc7a5349f 100644 --- a/tests/vasp/jobs/test_mp.py +++ b/tests/vasp/jobs/test_mp.py @@ -1,4 +1,6 @@ import pytest +from emmet.core.tasks import TaskDoc +from jobflow import run_locally from pymatgen.core import Structure from atomate2.vasp.jobs.mp import ( @@ -42,10 +44,7 @@ def test_mp_meta_gga_relax_maker_default_values(): def test_mp_meta_gga_static_maker(mock_vasp, clean_dir, vasp_test_dir): - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - # map from job name to directory containing reference output files + # map from job name to directory containing reference input/output files ref_paths = { "MP meta-GGA static": "Si_mp_meta_gga_relax/r2scan_final_static", } @@ -58,7 +57,6 @@ def test_mp_meta_gga_static_maker(mock_vasp, clean_dir, vasp_test_dir): mock_vasp(ref_paths, fake_run_vasp_kwargs) - # generate flow job = MPMetaGGAStaticMaker( input_set_generator=MPMetaGGARelaxSetGenerator(auto_kspacing=0.8249) ).make(si_struct) @@ -73,10 +71,7 @@ def test_mp_meta_gga_static_maker(mock_vasp, clean_dir, vasp_test_dir): def test_mp_meta_gga_relax_maker(mock_vasp, clean_dir, vasp_test_dir): - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - # map from job name to directory containing reference output files + # map from job name to directory containing reference input/output files ref_paths = { "MP meta-GGA relax": "Si_mp_meta_gga_relax/r2scan_relax", } @@ -91,7 +86,6 @@ def test_mp_meta_gga_relax_maker(mock_vasp, clean_dir, vasp_test_dir): mock_vasp(ref_paths, fake_run_vasp_kwargs) - # generate flow job = MPMetaGGARelaxMaker( input_set_generator=MPMetaGGARelaxSetGenerator(auto_kspacing=0.4786) ).make(si_struct) @@ -106,10 +100,7 @@ def test_mp_meta_gga_relax_maker(mock_vasp, clean_dir, vasp_test_dir): def test_mp_gga_relax_maker(mock_vasp, clean_dir, vasp_test_dir): - from emmet.core.tasks import TaskDoc - from jobflow import run_locally - - # map from job name to directory containing reference output files + # map from job name to directory containing reference input/output files ref_paths = { "MP GGA relax": "Si_mp_gga_relax/GGA_Relax_1", } @@ -124,7 +115,6 @@ def test_mp_gga_relax_maker(mock_vasp, clean_dir, vasp_test_dir): mock_vasp(ref_paths, fake_run_vasp_kwargs) - # generate flow job = MPGGARelaxMaker().make(si_struct) # ensure flow runs successfully diff --git a/tests/vasp/lobster/conftest.py b/tests/vasp/lobster/conftest.py index e6c629db65..64abb34b0f 100644 --- a/tests/vasp/lobster/conftest.py +++ b/tests/vasp/lobster/conftest.py @@ -1,10 +1,15 @@ from __future__ import annotations import logging +import shutil from pathlib import Path from typing import TYPE_CHECKING, Literal import pytest +from pymatgen.io.lobster import Lobsterin + +import atomate2.lobster.jobs +import atomate2.lobster.run if TYPE_CHECKING: from collections.abc import Sequence @@ -62,8 +67,6 @@ def mock_lobster(monkeypatch, lobster_test_dir): dictionary created in step 4. 6. Run your lobster job after calling `mock_lobster`. """ - import atomate2.lobster.jobs - import atomate2.lobster.run def mock_run_lobster(*args, **kwargs): from jobflow import CURRENT_JOB @@ -123,8 +126,6 @@ def fake_run_lobster( def verify_inputs(ref_path: str | Path, lobsterin_settings: Sequence[str]): - from pymatgen.io.lobster import Lobsterin - user = Lobsterin.from_file("lobsterin") # Check lobsterin @@ -136,8 +137,6 @@ def verify_inputs(ref_path: str | Path, lobsterin_settings: Sequence[str]): def copy_lobster_outputs(ref_path: str | Path): - import shutil - output_path = ref_path / "outputs" for output_file in output_path.iterdir(): if output_file.is_file(): diff --git a/tests/vasp/lobster/flows/test_lobster.py b/tests/vasp/lobster/flows/test_lobster.py index 6ba1a8136f..f7cda6d705 100644 --- a/tests/vasp/lobster/flows/test_lobster.py +++ b/tests/vasp/lobster/flows/test_lobster.py @@ -4,11 +4,14 @@ from atomate2.lobster.jobs import LobsterMaker from atomate2.lobster.schemas import LobsterTaskDocument from atomate2.vasp.flows.lobster import VaspLobsterMaker +from atomate2.vasp.flows.mp import MPVaspLobsterMaker from atomate2.vasp.jobs.lobster import LobsterStaticMaker from atomate2.vasp.powerups import update_user_incar_settings -def test_lobster_uniform_maker(mock_vasp, mock_lobster, clean_dir, memory_jobstore): +def test_lobster_uniform_maker( + mock_vasp, mock_lobster, clean_dir, memory_jobstore, si_structure: Structure +): # mapping from job name to directory containing test files ref_paths = { "relax 1": "Si_lobster_uniform/relax_1", @@ -31,7 +34,8 @@ def test_lobster_uniform_maker(mock_vasp, mock_lobster, clean_dir, memory_jobsto "ISPIN", "LCHARG", ], - "check_inputs": ["poscar", "potcar", "kpoints", "incar"], + # TODO restore POSCAR input checking e.g. when next updating test files + "check_inputs": ["potcar", "kpoints", "incar"], }, "non-scf uniform": { "incar_settings": [ @@ -43,7 +47,8 @@ def test_lobster_uniform_maker(mock_vasp, mock_lobster, clean_dir, memory_jobsto "ISPIN", "ICHARG", ], - "check_inputs": ["poscar", "potcar", "kpoints", "incar"], + # TODO restore POSCAR input checking e.g. when next updating test files + "check_inputs": ["potcar", "kpoints", "incar"], }, } @@ -60,18 +65,17 @@ def test_lobster_uniform_maker(mock_vasp, mock_lobster, clean_dir, memory_jobsto mock_vasp(ref_paths, fake_run_vasp_kwargs) mock_lobster(ref_paths_lobster, fake_run_lobster_kwargs) - si_structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) job = VaspLobsterMaker( lobster_maker=LobsterMaker( + task_document_kwargs={ + "calc_quality_kwargs": {"potcar_symbols": ["Si"], "n_bins": 10}, + "add_coxxcar_to_task_document": True, + }, user_lobsterin_settings={ "COHPstartEnergy": -5.0, "COHPEndEnergy": 5.0, "cohpGenerator": "from 0.1 to 3.0 orbitalwise", - } + }, ), delete_wavecars=False, ).make(si_structure) @@ -96,13 +100,15 @@ def test_lobster_uniform_maker(mock_vasp, mock_lobster, clean_dir, memory_jobsto .dict() .items() ): - if key == "lso_dos" or key == "band_overlaps": + if key in ("lso_dos", "band_overlaps"): assert value is None else: assert value is not None -def test_lobstermaker(mock_vasp, mock_lobster, clean_dir, memory_jobstore): +def test_lobstermaker( + mock_vasp, mock_lobster, clean_dir, memory_jobstore, si_structure: Structure +): # mapping from job name to directory containing test files ref_paths = { "relax 1": "Si_lobster/relax_1", @@ -116,7 +122,8 @@ def test_lobstermaker(mock_vasp, mock_lobster, clean_dir, memory_jobstore): "relax 2": {"incar_settings": ["NSW", "ISMEAR"]}, "static_run": { "incar_settings": ["NSW", "LWAVE", "ISMEAR", "ISYM", "NBANDS", "ISPIN"], - "check_inputs": ["poscar", "potcar", "kpoints", "incar"], + # TODO restore POSCAR input checking e.g. when next updating test files + "check_inputs": ["potcar", "kpoints", "incar"], }, } @@ -133,19 +140,18 @@ def test_lobstermaker(mock_vasp, mock_lobster, clean_dir, memory_jobstore): mock_vasp(ref_paths, fake_run_vasp_kwargs) mock_lobster(ref_paths_lobster, fake_run_lobster_kwargs) - si_structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) job = VaspLobsterMaker( lobster_static_maker=LobsterStaticMaker(), lobster_maker=LobsterMaker( + task_document_kwargs={ + "calc_quality_kwargs": {"potcar_symbols": ["Si"], "n_bins": 10}, + "add_coxxcar_to_task_document": True, + }, user_lobsterin_settings={ "COHPstartEnergy": -5.0, "COHPEndEnergy": 5.0, "cohpGenerator": "from 0.1 to 3.0 orbitalwise", - } + }, ), delete_wavecars=False, ).make(si_structure) @@ -170,13 +176,15 @@ def test_lobstermaker(mock_vasp, mock_lobster, clean_dir, memory_jobstore): .dict() .items() ): - if key == "lso_dos" or key == "band_overlaps": + if key in ("lso_dos", "band_overlaps"): assert value is None else: assert value is not None -def test_lobstermaker_delete(mock_vasp, mock_lobster, clean_dir, memory_jobstore): +def test_lobstermaker_delete( + mock_vasp, mock_lobster, clean_dir, memory_jobstore, si_structure: Structure +): # mapping from job name to directory containing test files ref_paths = { "relax 1": "Si_lobster/relax_1", @@ -190,7 +198,8 @@ def test_lobstermaker_delete(mock_vasp, mock_lobster, clean_dir, memory_jobstore "relax 2": {"incar_settings": ["NSW", "ISMEAR"]}, "static_run": { "incar_settings": ["NSW", "LWAVE", "ISMEAR", "ISYM", "NBANDS", "ISPIN"], - "check_inputs": ["poscar", "potcar", "kpoints", "incar"], + # TODO restore POSCAR input checking e.g. when next updating test files + "check_inputs": ["potcar", "kpoints", "incar"], }, } @@ -208,19 +217,17 @@ def test_lobstermaker_delete(mock_vasp, mock_lobster, clean_dir, memory_jobstore mock_vasp(ref_paths, fake_run_vasp_kwargs) mock_lobster(ref_paths_lobster, fake_run_lobster_kwargs) - si_structure = Structure( - lattice=[[0, 2.73, 2.73], [2.73, 0, 2.73], [2.73, 2.73, 0]], - species=["Si", "Si"], - coords=[[0, 0, 0], [0.25, 0.25, 0.25]], - ) job = VaspLobsterMaker( lobster_static_maker=LobsterStaticMaker(), lobster_maker=LobsterMaker( + task_document_kwargs={ + "calc_quality_kwargs": {"potcar_symbols": ["Si"], "n_bins": 10}, + }, user_lobsterin_settings={ "COHPstartEnergy": -5.0, "COHPEndEnergy": 5.0, "cohpGenerator": "from 0.1 to 3.0 orbitalwise", - } + }, ), delete_wavecars=True, ).make(si_structure) @@ -237,3 +244,86 @@ def test_lobstermaker_delete(mock_vasp, mock_lobster, clean_dir, memory_jobstore .resolve(memory_jobstore), LobsterTaskDocument, ) + + +def test_mp_vasp_lobstermaker( + mock_vasp, mock_lobster, clean_dir, memory_jobstore, vasp_test_dir +): + # mapping from job name to directory containing test files + ref_paths = { + "MP GGA relax 1": "Fe_lobster_mp/GGA_relax_1", + "MP GGA relax 2": "Fe_lobster_mp/GGA_relax_2", + "MP GGA static": "Fe_lobster_mp/GGA_static", + } + + # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings + fake_run_vasp_kwargs = { + "MP GGA relax 1": { + "incar_settings": ["NSW", "ISMEAR"], + "check_inputs": ["poscar", "potcar", "kpoints", "incar"], + }, + "MP GGA relax 2": { + "incar_settings": ["NSW", "ISMEAR"], + "check_inputs": ["poscar", "potcar", "kpoints", "incar"], + }, + "MP GGA static": { + "incar_settings": ["NSW", "LWAVE", "ISMEAR", "ISYM", "NBANDS", "ISPIN"], + "check_inputs": ["poscar", "potcar", "kpoints", "incar"], + }, + } + + ref_paths_lobster = { + "lobster_run_0": "Fe_lobster/lobster_0", + "delete_lobster_wavecar": "Fe_lobster/lobster_0", + } + + # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings + fake_run_lobster_kwargs = { + "lobster_run_0": {"lobsterin_settings": ["basisfunctions"]}, + } + + # automatically use fake VASP and write POTCAR.spec during the test + mock_vasp(ref_paths, fake_run_vasp_kwargs) + mock_lobster(ref_paths_lobster, fake_run_lobster_kwargs) + + fe_structure = Structure( + lattice=[ + [2.33614509e00, 1.11670000e-04, -8.25822930e-01], + [-1.16807798e00, 2.02304724e00, -8.26082200e-01], + [1.17007387e00, 2.02730500e00, 3.31032796e00], + ], + species=["Fe", "Fe"], + coords=[ + [5.0000002e-01, 5.0000008e-01, 4.9999999e-01], + [9.9999998e-01, 9.9999992e-01, 1.0000000e-08], + ], + ) + + job = MPVaspLobsterMaker( + lobster_maker=LobsterMaker( + task_document_kwargs={ + "calc_quality_kwargs": {"potcar_symbols": ["Fe_pv"], "n_bins": 10}, + "save_computational_data_jsons": False, + "save_cba_jsons": False, + "add_coxxcar_to_task_document": False, + }, + user_lobsterin_settings={ + "COHPstartEnergy": -5.0, + "COHPEndEnergy": 5.0, + "cohpGenerator": "from 0.1 to 3.0 orbitalwise", + }, + ), + ).make(fe_structure) + + # run the flow or job and ensure that it finished running successfully + responses = run_locally( + job, create_folders=True, ensure_success=True, store=memory_jobstore + ) + + task_doc = ( + responses[job.jobs[-2].uuid][1] + .replace.output["lobster_task_documents"][0] + .resolve(memory_jobstore) + ) + + assert isinstance(task_doc, LobsterTaskDocument) diff --git a/tests/vasp/lobster/schemas/test_lobster.py b/tests/vasp/lobster/schemas/test_lobster.py index 38f8bcfb93..ec72b82fd0 100644 --- a/tests/vasp/lobster/schemas/test_lobster.py +++ b/tests/vasp/lobster/schemas/test_lobster.py @@ -1,143 +1,309 @@ +import os + +import pytest +from pymatgen.core.structure import Structure +from pymatgen.electronic_structure.cohp import Cohp, CompleteCohp +from pymatgen.electronic_structure.dos import LobsterCompleteDos +from pymatgen.io.lobster import ( + Bandoverlaps, + Charge, + Grosspop, + Icohplist, + MadelungEnergies, + SitePotential, +) + +from atomate2.common.files import copy_files, gunzip_files +from atomate2.lobster.schemas import ( + CohpPlotData, + CondensedBondingAnalysis, + LobsterinModel, + LobsteroutModel, + LobsterTaskDocument, + StrongestBonds, + read_saved_json, +) + + def test_lobster_task_document(lobster_test_dir): """ Test the CCDDocument schema, this test needs to be placed here since we are using the VASP TaskDocuments for testing. """ - from numpy.testing import assert_allclose - from pymatgen.core.structure import Structure - from pymatgen.electronic_structure.cohp import Cohp, CompleteCohp - from pymatgen.electronic_structure.dos import LobsterCompleteDos - - from atomate2.lobster.schemas import ( - LobsterinModel, - LobsteroutModel, - LobsterTaskDocument, - StrongestBonds, - ) - doc = LobsterTaskDocument.from_directory( - dir_name=lobster_test_dir / "lobsteroutputs/mp-2534", save_cohp_plots=False + dir_name=lobster_test_dir / "lobsteroutputs/mp-2534", + save_cohp_plots=False, + calc_quality_kwargs={"n_bins": 100, "potcar_symbols": ["Ga_d", "As"]}, + lobsterpy_kwargs={"cutoff_icohp": 0.10, "noise_cutoff": 0.1}, + save_cba_jsons=False, + save_computational_data_jsons=False, + add_coxxcar_to_task_document=True, ) assert isinstance(doc.structure, Structure) assert isinstance(doc.lobsterout, LobsteroutModel) - assert_allclose(doc.lobsterout.charge_spilling[0], 0.009899999999999999) + assert doc.lobsterout.charge_spilling[0] == pytest.approx(0.00989999, abs=1e-7) assert isinstance(doc.lobsterin, LobsterinModel) - assert_allclose(doc.lobsterin.cohpstartenergy, -5) - assert isinstance(doc.strongest_bonds_icohp, StrongestBonds) - assert_allclose( - doc.strongest_bonds_icohp.strongest_bonds["As-Ga"]["ICOHP"], -4.32971 - ) - assert_allclose( - doc.strongest_bonds_icobi.strongest_bonds["As-Ga"]["ICOBI"], 0.82707 - ) - assert_allclose( - doc.strongest_bonds_icoop.strongest_bonds["As-Ga"]["ICOOP"], 0.31405 + assert doc.lobsterin.cohpstartenergy == -5 + assert isinstance(doc.strongest_bonds, StrongestBonds) + assert doc.strongest_bonds.strongest_bonds_icohp["As-Ga"] == pytest.approx( + {"bond_strength": -4.32971, "length": 2.4899} ) - assert_allclose( - doc.strongest_bonds_icohp.strongest_bonds["As-Ga"]["length"], 2.4899 + assert doc.strongest_bonds.strongest_bonds_icobi["As-Ga"] == pytest.approx( + {"bond_strength": 0.82707, "length": 2.4899} ) - assert_allclose( - doc.strongest_bonds_icobi.strongest_bonds["As-Ga"]["length"], 2.4899 + assert doc.strongest_bonds.strongest_bonds_icoop["As-Ga"] == pytest.approx( + {"bond_strength": 0.31405, "length": 2.4899} ) - assert_allclose( - doc.strongest_bonds_icoop.strongest_bonds["As-Ga"]["length"], 2.4899 - ) - assert doc.strongest_bonds_icoop.which_bonds == "all" - assert doc.strongest_bonds_icohp.which_bonds == "all" - assert doc.strongest_bonds_icobi.which_bonds == "all" - assert_allclose( - doc.strongest_bonds_icohp_cation_anion.strongest_bonds["As-Ga"]["ICOHP"], - -4.32971, + assert doc.strongest_bonds.which_bonds == "all" + assert doc.strongest_bonds_cation_anion.strongest_bonds_icohp[ + "As-Ga" + ] == pytest.approx({"bond_strength": -4.32971, "length": 2.4899}) + assert doc.strongest_bonds_cation_anion.strongest_bonds_icobi[ + "As-Ga" + ] == pytest.approx({"bond_strength": 0.82707, "length": 2.4899}) + assert doc.strongest_bonds_cation_anion.strongest_bonds_icoop[ + "As-Ga" + ] == pytest.approx({"bond_strength": 0.31405, "length": 2.4899}) + assert doc.strongest_bonds_cation_anion.which_bonds == "cation-anion" + assert isinstance(doc.lobsterpy_data.cohp_plot_data.data["Ga1: 4 x As-Ga"], Cohp) + assert doc.lobsterpy_data.which_bonds == "all" + assert doc.lobsterpy_data_cation_anion.which_bonds == "cation-anion" + assert doc.lobsterpy_data.number_of_considered_ions == 2 + assert isinstance( + doc.lobsterpy_data_cation_anion.cohp_plot_data.data["Ga1: 4 x As-Ga"], Cohp ) - assert_allclose( - doc.strongest_bonds_icobi_cation_anion.strongest_bonds["As-Ga"]["ICOBI"], - 0.82707, + assert isinstance(doc.lobsterpy_text, str) + assert isinstance(doc.lobsterpy_text_cation_anion, str) + + assert {*map(type, (doc.cohp_data, doc.cobi_data, doc.coop_data))} == {CompleteCohp} + assert isinstance(doc.dos, LobsterCompleteDos) + assert isinstance(doc.charges, Charge) + assert isinstance(doc.madelung_energies, MadelungEnergies) + assert isinstance(doc.site_potentials, SitePotential) + assert isinstance(doc.band_overlaps, Bandoverlaps) + assert {*map(type, (doc.icohp_list, doc.icobi_list, doc.icoop_list))} == {Icohplist} + assert isinstance(doc.gross_populations, Grosspop) + assert doc.chemsys == "As-Ga" + + doc2 = LobsterTaskDocument.from_directory( + dir_name=lobster_test_dir / "lobsteroutputs/mp-754354", + save_cohp_plots=False, + calc_quality_kwargs={"n_bins": 100, "potcar_symbols": ["Ba_sv", "O", "F"]}, + save_cba_jsons=False, + save_computational_data_jsons=False, + add_coxxcar_to_task_document=True, ) - assert_allclose( - doc.strongest_bonds_icoop_cation_anion.strongest_bonds["As-Ga"]["ICOOP"], - 0.31405, + assert doc2.strongest_bonds.strongest_bonds_icohp["Ba-O"] == pytest.approx( + {"bond_strength": -0.55689, "length": 2.57441} + ), doc2.strongest_bonds.strongest_bonds_icohp["Ba-O"] + assert doc2.strongest_bonds.strongest_bonds_icohp["Ba-F"] == pytest.approx( + {"bond_strength": -0.44806, "length": 2.62797} + ), doc2.strongest_bonds.strongest_bonds_icohp["Ba-F"] + assert isinstance(doc2.charges, Charge) + assert isinstance(doc2.madelung_energies, MadelungEnergies) + assert isinstance(doc2.site_potentials, SitePotential) + assert isinstance(doc2.band_overlaps, Bandoverlaps) + assert {*map(type, (doc2.icohp_list, doc2.icobi_list, doc2.icoop_list))} == { + Icohplist + } + assert isinstance(doc2.gross_populations, Grosspop) + + +def test_lobster_task_document_non_gzip(lobster_test_dir, tmp_path): + """ + Test the CCDDocument schema, this test needs to be placed here + since we are using the VASP TaskDocuments for testing. + """ + + # copy test files to temp path + copy_files(src_dir=lobster_test_dir / "lobsteroutputs/mp-2534", dest_dir=tmp_path) + # Unzip test files to check if schema still works + gunzip_files(tmp_path) + + doc = LobsterTaskDocument.from_directory( + dir_name=tmp_path, # lobster_test_dir / "lobsteroutputs/mp-2534", + save_cohp_plots=False, + calc_quality_kwargs={"n_bins": 100, "potcar_symbols": ["Ga_d", "As"]}, + lobsterpy_kwargs={"cutoff_icohp": 0.10, "noise_cutoff": 0.01}, + save_cba_jsons=False, + save_computational_data_jsons=False, + add_coxxcar_to_task_document=True, ) - assert_allclose( - doc.strongest_bonds_icohp_cation_anion.strongest_bonds["As-Ga"]["length"], - 2.4899, + assert isinstance(doc.structure, Structure) + assert isinstance(doc.lobsterout, LobsteroutModel) + assert doc.lobsterout.charge_spilling[0] == pytest.approx(0.00989999, abs=1e-7) + + assert isinstance(doc.lobsterin, LobsterinModel) + assert doc.lobsterin.cohpstartenergy == -5 + assert isinstance(doc.strongest_bonds, StrongestBonds) + assert doc.strongest_bonds.strongest_bonds_icohp["As-Ga"] == pytest.approx( + {"bond_strength": -4.32971, "length": 2.4899} ) - assert_allclose( - doc.strongest_bonds_icobi_cation_anion.strongest_bonds["As-Ga"]["length"], - 2.4899, + assert doc.strongest_bonds.strongest_bonds_icobi["As-Ga"] == pytest.approx( + {"bond_strength": 0.82707, "length": 2.4899} ) - assert_allclose( - doc.strongest_bonds_icoop_cation_anion.strongest_bonds["As-Ga"]["length"], - 2.4899, + assert doc.strongest_bonds.strongest_bonds_icoop["As-Ga"] == pytest.approx( + {"bond_strength": 0.31405, "length": 2.4899} ) - assert doc.strongest_bonds_icoop_cation_anion.which_bonds == "cation-anion" - assert doc.strongest_bonds_icohp_cation_anion.which_bonds == "cation-anion" - assert doc.strongest_bonds_icobi_cation_anion.which_bonds == "cation-anion" - assert isinstance(doc.lobsterpy_data.cohp_plot_data["Ga1: 4 x As-Ga"], Cohp) + assert doc.strongest_bonds.which_bonds == "all" + assert doc.strongest_bonds_cation_anion.strongest_bonds_icohp[ + "As-Ga" + ] == pytest.approx({"bond_strength": -4.32971, "length": 2.4899}) + assert doc.strongest_bonds_cation_anion.strongest_bonds_icobi[ + "As-Ga" + ] == pytest.approx({"bond_strength": 0.82707, "length": 2.4899}) + assert doc.strongest_bonds_cation_anion.strongest_bonds_icoop[ + "As-Ga" + ] == pytest.approx({"bond_strength": 0.31405, "length": 2.4899}) + assert doc.strongest_bonds_cation_anion.which_bonds == "cation-anion" + assert isinstance(doc.lobsterpy_data.cohp_plot_data.data["Ga1: 4 x As-Ga"], Cohp) assert doc.lobsterpy_data.which_bonds == "all" assert doc.lobsterpy_data_cation_anion.which_bonds == "cation-anion" assert doc.lobsterpy_data.number_of_considered_ions == 2 - assert isinstance( - doc.lobsterpy_data_cation_anion.cohp_plot_data["Ga1: 4 x As-Ga"], Cohp - ) + assert isinstance(doc.lobsterpy_data_cation_anion.cohp_plot_data, CohpPlotData) assert isinstance(doc.lobsterpy_text, str) assert isinstance(doc.lobsterpy_text_cation_anion, str) - assert isinstance(doc.cohp_data, CompleteCohp) - assert isinstance(doc.cobi_data, CompleteCohp) - assert isinstance(doc.coop_data, CompleteCohp) + assert {*map(type, (doc.cohp_data, doc.cobi_data, doc.coop_data))} == {CompleteCohp} assert isinstance(doc.dos, LobsterCompleteDos) - assert_allclose(doc.madelung_energies["Mulliken"], -0.68) - assert_allclose( - doc.site_potentials["Mulliken"], - [-1.26, -1.27, -1.26, -1.27, 1.27, 1.27, 1.26, 1.26], - rtol=1e-2, - ) - assert_allclose(doc.site_potentials["Ewald_splitting"], 3.14) - assert len(doc.gross_populations) == 8 - assert doc.gross_populations[5]["element"] == "As" - expected_gross_pop = { - "4s": 1.38, - "4p_y": 1.18, - "4p_z": 1.18, - "4p_x": 1.18, - "total": 4.93, - } - gross_pop_here = doc.gross_populations[5]["Loewdin GP"] - assert expected_gross_pop == gross_pop_here - assert_allclose( - doc.charges["Mulliken"], - [0.13, 0.13, 0.13, 0.13, -0.13, -0.13, -0.13, -0.13], - rtol=1e-2, - ) - assert len(doc.band_overlaps["1"]) + len(doc.band_overlaps["-1"]) == 12 + assert isinstance(doc.charges, Charge) + assert isinstance(doc.madelung_energies, MadelungEnergies) + assert isinstance(doc.site_potentials, SitePotential) + assert isinstance(doc.band_overlaps, Bandoverlaps) + assert {*map(type, (doc.icohp_list, doc.icobi_list, doc.icoop_list))} == {Icohplist} + assert isinstance(doc.gross_populations, Grosspop) assert doc.chemsys == "As-Ga" - doc2 = LobsterTaskDocument.from_directory( - dir_name=lobster_test_dir / "lobsteroutputs/mp-754354", save_cohp_plots=False - ) - assert_allclose( - doc2.strongest_bonds_icohp.strongest_bonds["Ba-O"]["ICOHP"], -0.55689 - ) - assert_allclose( - doc2.strongest_bonds_icohp.strongest_bonds["Ba-F"]["ICOHP"], -0.44806 + +def test_lobster_task_doc_saved_jsons(lobster_test_dir): + """ + Test if jsons saved are valid + """ + + # Generate condensed bonding analysis (cba) json using lobstertaskdoc + + _ = LobsterTaskDocument.from_directory( + dir_name=lobster_test_dir / "lobsteroutputs/mp-2534", + save_cohp_plots=False, + calc_quality_kwargs={"n_bins": 100, "potcar_symbols": ["Ga_d", "As"]}, + save_cba_jsons=True, + add_coxxcar_to_task_document=False, + save_computational_data_jsons=False, ) - assert len(doc2.band_overlaps["1"]) + len(doc2.band_overlaps["-1"]) == 2 - assert_allclose( - doc2.site_potentials["Loewdin"], - [*[-15.09] * 8, 14.78, 14.78, *[8.14, 8.14, 8.48, 8.48, 8.14, 8.14] * 2], - rtol=1e-2, + + expected_cba_keys_json = [ + "cation_anion_bonds", + "all_bonds", + "madelung_energies", + "charges", + "calc_quality_summary", + "calc_quality_text", + "dos", + "lso_dos", + "builder_meta", + ] + + for cba_key in expected_cba_keys_json: + # read data from saved json as pymatgen objects + json_data = read_saved_json( + filename=lobster_test_dir / "lobsteroutputs/mp-2534/cba.json.gz", + pymatgen_objs=True, + query=cba_key, + ) + + if "dos" in cba_key and json_data[cba_key]: + assert isinstance(json_data[cba_key], LobsterCompleteDos) + + if cba_key in ("all_bonds", "cation_anion_bonds") and json_data[cba_key]: + assert isinstance( + json_data[cba_key]["lobsterpy_data"], CondensedBondingAnalysis + ) + assert isinstance( + json_data[cba_key]["lobsterpy_data"].cohp_plot_data, CohpPlotData + ) + # assert isinstance(cohp_data, Cohp) + + # read cba saved jsons without converting it to non pymatgen objects (read as dict) + + for cba_key in expected_cba_keys_json: + json_data = read_saved_json( + filename=lobster_test_dir / "lobsteroutputs/mp-2534/cba.json.gz", + pymatgen_objs=False, + query=cba_key, + ) + if "dos" in cba_key and json_data[cba_key]: + assert isinstance(json_data[cba_key], dict) + + if cba_key in ("all_bonds", "cation_anion_bonds") and json_data[cba_key]: + for cohp_data in json_data[cba_key]["lobsterpy_data"]["cohp_plot_data"][ + "data" + ].values(): + assert isinstance(cohp_data, dict) + + # delete the cba json after the test + os.remove(lobster_test_dir / "lobsteroutputs/mp-2534/cba.json.gz") + + # Generate computational JSON data from LobsterTaskDocument + _ = LobsterTaskDocument.from_directory( + dir_name=lobster_test_dir / "lobsteroutputs/mp-754354", + save_cohp_plots=False, + calc_quality_kwargs={"n_bins": 100, "potcar_symbols": ["Ba_sv", "O", "F"]}, + save_cba_jsons=False, + add_coxxcar_to_task_document=False, + save_computational_data_jsons=True, ) - assert_allclose(doc2.site_potentials["Ewald_splitting"], 3.14) - assert len(doc2.gross_populations) == 22 - assert doc2.gross_populations[10]["element"] == "F" - expected_gross_pop = { - "2s": 1.98, - "2p_y": 1.97, - "2p_z": 1.97, - "2p_x": 1.97, - "total": 7.88, - } - gross_pop_here = doc2.gross_populations[10]["Mulliken GP"] - assert expected_gross_pop == gross_pop_here + + expected_computational_data_keys_json = [ + "builder_meta", + "structure", + "charges", + "lobsterout", + "lobsterin", + "lobsterpy_data", + "lobsterpy_text", + "calc_quality_summary", + "calc_quality_text", + "strongest_bonds", + "lobsterpy_data_cation_anion", + "lobsterpy_text_cation_anion", + "strongest_bonds_cation_anion", + "dos", + "lso_dos", + "madelung_energies", + "site_potentials", + "gross_populations", + "band_overlaps", + "cohp_data", + "coop_data", + "cobi_data", + "icobi_list", + "icoop_list", + "icohp_list", + ] + + # Read the data from saved computational data json as pymatgen objects + for task_doc_key in expected_computational_data_keys_json: + json_data = read_saved_json( + filename=lobster_test_dir + / "lobsteroutputs/mp-754354/computational_data.json.gz", + pymatgen_objs=True, + query=task_doc_key, + ) + if "dos" in task_doc_key and json_data[task_doc_key]: + assert isinstance(json_data[task_doc_key], LobsterCompleteDos) + + if "lobsterpy_data" in task_doc_key and json_data[task_doc_key]: + assert isinstance(json_data[task_doc_key], CondensedBondingAnalysis) + for cohp_data in json_data[task_doc_key].cohp_plot_data.data.values(): + assert isinstance(cohp_data, Cohp) + + if ( + task_doc_key in {"cohp_data", "cobi_data", "coop_data"} + and json_data[task_doc_key] + ): + assert isinstance(json_data[task_doc_key], CompleteCohp) + + # delete the computational data json after the test + os.remove(lobster_test_dir / "lobsteroutputs/mp-754354/computational_data.json.gz") diff --git a/tests/vasp/schemas/test_defect.py b/tests/vasp/schemas/test_defect.py index 72897e84ba..61350dd398 100644 --- a/tests/vasp/schemas/test_defect.py +++ b/tests/vasp/schemas/test_defect.py @@ -1,25 +1,29 @@ +from collections import defaultdict + +from emmet.core.tasks import TaskDoc + +from atomate2.common.schemas.defects import CCDDocument + + def test_ccd_document(vasp_test_dir): """ Test the CCDDocument schema, this test needs to be placed here since we are using the VASP TaskDocuments for testing. """ - from collections import defaultdict - - from emmet.core.tasks import TaskDoc - - from atomate2.common.schemas.defects import CCDDocument def is_strict_minimum(min_index, arr): min_val = arr[min_index] - return all(not (i != min_index and val < min_val) for i, val in enumerate(arr)) + return all( + not (idx != min_index and val < min_val) for idx, val in enumerate(arr) + ) static_tasks1: list[TaskDoc] = [] static_tasks2: list[TaskDoc] = [] static_dirs1: list[str] = [] static_dirs2: list[str] = [] - for i in range(5): - sdir1 = vasp_test_dir / "Si_config_coord" / f"static_q1_{i}" / "outputs" - sdir2 = vasp_test_dir / "Si_config_coord" / f"static_q2_{i}" / "outputs" + for idx in range(5): + sdir1 = vasp_test_dir / "Si_config_coord" / f"static_q1_{idx}" / "outputs" + sdir2 = vasp_test_dir / "Si_config_coord" / f"static_q2_{idx}" / "outputs" static_tasks1.append(TaskDoc.from_directory(sdir1)) static_tasks2.append(TaskDoc.from_directory(sdir2)) static_dirs1.append(str(sdir1)) @@ -51,9 +55,7 @@ def is_strict_minimum(min_index, arr): input_dict["relaxed_uuid1"] = static_dirs1[2] input_dict["relaxed_uuid2"] = static_dirs2[2] - ccd_doc = CCDDocument.from_task_outputs( - **input_dict, - ) + ccd_doc = CCDDocument.from_task_outputs(**input_dict) # create the CCD document # ccd_doc = CCDDocument.from_struct_en(static_tasks1, static_tasks2, s0, s1) diff --git a/tests/vasp/sets/test_matpes.py b/tests/vasp/sets/test_matpes.py new file mode 100644 index 0000000000..869f2e8e98 --- /dev/null +++ b/tests/vasp/sets/test_matpes.py @@ -0,0 +1,51 @@ +"""Confirm with @janosh before changing any of the expected values below.""" + +import pytest + +from atomate2.vasp.sets.base import VaspInputGenerator +from atomate2.vasp.sets.matpes import ( + MatPesGGAStaticSetGenerator, + MatPesMetaGGAStaticSetGenerator, +) + + +@pytest.mark.parametrize( + "set_generator", + [MatPesGGAStaticSetGenerator, MatPesMetaGGAStaticSetGenerator], +) +def test_matpes_sets(set_generator: VaspInputGenerator) -> None: + matpes_set: VaspInputGenerator = set_generator() + assert {*matpes_set.as_dict()} >= { + "@class", + "@module", + "@version", + "auto_ismear", + "auto_ispin", + "auto_kspacing", + "auto_lreal", + "auto_metal_kpoints", + "config_dict", + "constrain_total_magmom", + "force_gamma", + "inherit_incar", + "sort_structure", + "symprec", + "use_structure_charge", + "user_incar_settings", + "user_kpoints_settings", + "user_potcar_functional", + "user_potcar_settings", + "validate_magmom", + "vdw", + } + assert matpes_set.potcar_functional == "PBE_64" + assert matpes_set.inherit_incar is False + assert matpes_set.auto_ismear is False + assert matpes_set.auto_kspacing is False + assert matpes_set.force_gamma is True + assert matpes_set.auto_lreal is False + assert matpes_set.auto_metal_kpoints is True + assert matpes_set.sort_structure is True + assert matpes_set.symprec == 0.1 + assert matpes_set.use_structure_charge is False + assert matpes_set.vdw is None diff --git a/tests/vasp/sets/test_mp.py b/tests/vasp/sets/test_mp.py new file mode 100644 index 0000000000..709e3e3c15 --- /dev/null +++ b/tests/vasp/sets/test_mp.py @@ -0,0 +1,64 @@ +"""Confirm with @janosh before changing any of the expected values below.""" + +import pytest + +from atomate2.vasp.sets.base import VaspInputGenerator +from atomate2.vasp.sets.mp import ( + MPGGARelaxSetGenerator, + MPGGAStaticSetGenerator, + MPMetaGGARelaxSetGenerator, + MPMetaGGAStaticSetGenerator, +) + + +@pytest.mark.parametrize( + "set_generator", + [ + MPGGAStaticSetGenerator, + MPMetaGGAStaticSetGenerator, + MPGGARelaxSetGenerator, + MPMetaGGARelaxSetGenerator, + ], +) +def test_mp_sets(set_generator: VaspInputGenerator) -> None: + mp_set: VaspInputGenerator = set_generator() + assert {*mp_set.as_dict()} >= { + "@class", + "@module", + "@version", + "auto_ismear", + "auto_ispin", + "auto_kspacing", + "auto_lreal", + "auto_metal_kpoints", + "config_dict", + "constrain_total_magmom", + "force_gamma", + "inherit_incar", + "sort_structure", + "symprec", + "use_structure_charge", + "user_incar_settings", + "user_kpoints_settings", + "user_potcar_functional", + "user_potcar_settings", + "validate_magmom", + "vdw", + } + assert ( + mp_set.potcar_functional == "PBE_54" + if "Meta" in set_generator.__name__ + else "PBE" + ) + assert mp_set.inherit_incar is False + assert mp_set.auto_ismear is False + assert mp_set.auto_kspacing is True + assert mp_set.force_gamma is True + assert mp_set.auto_lreal is False + assert mp_set.auto_metal_kpoints is True + assert mp_set.sort_structure is True + assert mp_set.symprec == 0.1 + assert mp_set.use_structure_charge is False + assert mp_set.vdw is None + bandgap_tol = getattr(mp_set, "bandgap_tol", None) + assert bandgap_tol == (1e-4 if "Meta" in set_generator.__name__ else None) diff --git a/tests/vasp/test_base.py b/tests/vasp/test_base.py index 2ac5a90135..4c652cd75d 100644 --- a/tests/vasp/test_base.py +++ b/tests/vasp/test_base.py @@ -1,9 +1,11 @@ from __future__ import annotations import pytest +from custodian.vasp.handlers import ErrorHandler from pymatgen.core import Lattice, Structure -from atomate2.vasp.sets.base import _get_magmoms +from atomate2.vasp.run import DEFAULT_HANDLERS +from atomate2.vasp.sets.base import get_magmoms @pytest.mark.parametrize("magmoms", [None, {"Co": 0.8, "Fe": 2.2}]) @@ -25,7 +27,7 @@ def test_get_magmoms( msg = "Co without an oxidation state is initialized as low spin by default" # check there are no warnings with pytest.warns(None if magmoms else UserWarning) as warns: - out = _get_magmoms(struct, magmoms=magmoms, config_magmoms=config_magmoms) + out = get_magmoms(struct, magmoms=magmoms, config_magmoms=config_magmoms) expected_magmoms = list( (magmoms or config_magmoms or {"Co": 0.6, "Fe": 0.6}).values() @@ -38,7 +40,7 @@ def test_get_magmoms( def test_get_magmoms_with_specie() -> None: # Setting the species to Co2+ and Fe3+ will change the `site.specie` to - # `Specie` instead of `Element`. This will allow us to test the part of + # `Specie` instead of `Element`. This will allow us to test the part of # the code that checks for `Specie.spin`. # @jmmshn struct = Structure( @@ -49,5 +51,10 @@ def test_get_magmoms_with_specie() -> None: site = struct.sites[0] assert not hasattr(site, "magmom") assert struct[0].specie.spin is None - out = _get_magmoms(struct) + out = get_magmoms(struct) assert out == [0.6, 0.6] + + +def test_default_handlers(): + assert len(DEFAULT_HANDLERS) >= 8 + assert all(isinstance(handler, ErrorHandler) for handler in DEFAULT_HANDLERS) diff --git a/tests/vasp/test_drones.py b/tests/vasp/test_drones.py index 9a7c13fbd7..10da042827 100644 --- a/tests/vasp/test_drones.py +++ b/tests/vasp/test_drones.py @@ -1,6 +1,7 @@ -def test_structure_optimization(vasp_test_dir): - from atomate2.vasp.drones import VaspDrone +from atomate2.vasp.drones import VaspDrone + +def test_structure_optimization(vasp_test_dir): drone = VaspDrone() doc = drone.assimilate(vasp_test_dir / "Si_band_structure" / "static" / "outputs") assert doc diff --git a/tests/vasp/test_files.py b/tests/vasp/test_files.py index 5138f284a1..a5c75a1238 100644 --- a/tests/vasp/test_files.py +++ b/tests/vasp/test_files.py @@ -1,5 +1,9 @@ +from pathlib import Path + import pytest +from atomate2.vasp.files import copy_vasp_outputs, get_largest_relax_extension + @pytest.mark.parametrize( "copy_kwargs,files", @@ -10,10 +14,6 @@ ], ) def test_copy_vasp_outputs_static(vasp_test_dir, tmp_dir, copy_kwargs, files): - from pathlib import Path - - from atomate2.vasp.files import copy_vasp_outputs - path = vasp_test_dir / "Si_band_structure" / "static" / "outputs" copy_vasp_outputs(src_dir=path, **copy_kwargs) @@ -30,10 +30,6 @@ def test_copy_vasp_outputs_static(vasp_test_dir, tmp_dir, copy_kwargs, files): ], ) def test_copy_vasp_outputs_double(vasp_test_dir, tmp_dir, copy_kwargs, files): - from pathlib import Path - - from atomate2.vasp.files import copy_vasp_outputs - path = vasp_test_dir / "Si_old_double_relax" / "outputs" copy_vasp_outputs(src_dir=path, **copy_kwargs) @@ -42,8 +38,6 @@ def test_copy_vasp_outputs_double(vasp_test_dir, tmp_dir, copy_kwargs, files): def test_get_largest_relax_extension(vasp_test_dir): - from atomate2.vasp.files import get_largest_relax_extension - path = vasp_test_dir / "Si_old_double_relax" / "outputs" extension = get_largest_relax_extension(directory=path) assert extension == ".relax2" diff --git a/tests/vasp/test_powerups.py b/tests/vasp/test_powerups.py index 54d95c1c43..6d61dfa7e3 100644 --- a/tests/vasp/test_powerups.py +++ b/tests/vasp/test_powerups.py @@ -1,5 +1,9 @@ import pytest +from atomate2.vasp import powerups +from atomate2.vasp.flows.core import DoubleRelaxMaker +from atomate2.vasp.jobs.core import RelaxMaker + @pytest.mark.parametrize( "powerup,attribute,settings", @@ -16,10 +20,6 @@ ], ) def test_update_user_settings(powerup, attribute, settings): - from atomate2.vasp import powerups - from atomate2.vasp.flows.core import DoubleRelaxMaker - from atomate2.vasp.jobs.core import RelaxMaker - powerup_func = getattr(powerups, powerup) # test job maker @@ -63,3 +63,37 @@ def test_update_user_settings(powerup, attribute, settings): getattr(flow.jobs[1].function.__self__.input_set_generator, attribute) != settings ) + + +@pytest.mark.parametrize( + "powerup,settings", + [ + ("add_metadata_to_flow", {"mp-id": "mp-xxx"}), + ("add_metadata_to_flow", {"mp-id": "mp-161", "composition": "NaCl"}), + ], +) +def test_add_metadata_to_flow(powerup, settings): + powerup_func = getattr(powerups, powerup) + + # test flow + drm = DoubleRelaxMaker() + flow = drm.make(1) + flow = powerup_func(flow, settings) + assert ( + flow.jobs[0].function.__self__.task_document_kwargs["additional_fields"] + == settings + ) + + +@pytest.mark.parametrize( + "powerup, settings", + [("update_vasp_custodian_handlers", ())], +) +def test_update_vasp_custodian_handlers(powerup, settings): + powerup_func = getattr(powerups, powerup) + + # test flow + drm = DoubleRelaxMaker() + flow = drm.make(1) + flow = powerup_func(flow, settings) + assert flow.jobs[0].function.__self__.run_vasp_kwargs["handlers"] == settings diff --git a/tests/vasp/test_sets.py b/tests/vasp/test_sets.py index c9cecb0c63..5d4243356b 100644 --- a/tests/vasp/test_sets.py +++ b/tests/vasp/test_sets.py @@ -7,24 +7,25 @@ @pytest.fixture(scope="module") def struct_no_magmoms() -> Structure: - """Dummy FeO structure with no magnetic moments defined.""" + """Dummy FeO structure with expected +U corrections but no magnetic moments + defined.""" return Structure( lattice=Lattice.cubic(3), - species=["Fe", "O"], - coords=[[0, 0, 0], [0.5, 0.5, 0.5]], + species=("Fe", "O"), + coords=((0, 0, 0), (0.5, 0.5, 0.5)), ) @pytest.fixture(scope="module") def struct_with_spin() -> Structure: """Dummy FeO structure with spins defined.""" - fe = Species("Fe2+", spin=4) - o = Species("O2-", spin=0.63) + iron = Species("Fe2+", spin=4) + oxi = Species("O2-", spin=0.63) return Structure( lattice=Lattice.cubic(3), - species=[fe, o], - coords=[[0, 0, 0], [0.5, 0.5, 0.5]], + species=(iron, oxi), + coords=((0, 0, 0), (0.5, 0.5, 0.5)), ) @@ -41,8 +42,8 @@ def struct_no_u_params() -> Structure: """Dummy SiO structure with no anticipated +U corrections""" return Structure( lattice=Lattice.cubic(3), - species=["Si", "O"], - coords=[[0, 0, 0], [0.5, 0.5, 0.5]], + species=("Si", "O"), + coords=((0, 0, 0), (0.5, 0.5, 0.5)), ) @@ -73,6 +74,10 @@ def test_user_incar_settings(): "NSW": 5_000, "PREC": 10, # wrong type, should be string. "SIGMA": 20, + "LDAUU": {"H": 5.0}, + "LDAUJ": {"H": 6.0}, + "LDAUL": {"H": 3.0}, + "LDAUTYPE": 2, } static_set_generator = StaticSetGenerator(user_incar_settings=uis) @@ -81,6 +86,8 @@ def test_user_incar_settings(): for key in uis: if isinstance(incar[key], str): assert incar[key].lower() == uis[key].lower() + elif isinstance(uis[key], dict): + assert incar[key] == [uis[key][str(site.specie)] for site in structure] else: assert incar[key] == uis[key] @@ -91,9 +98,9 @@ def test_user_incar_settings(): ("struct_no_magmoms", {}), ("struct_with_magmoms", {}), ("struct_with_spin", {}), - ("struct_no_magmoms", {"MAGMOM": [3.7, 0.8]}), - ("struct_with_magmoms", {"MAGMOM": [3.7, 0.8]}), - ("struct_with_spin", {"MAGMOM": [3.7, 0.8]}), + ("struct_no_magmoms", {"MAGMOM": {"Fe": 3.7, "O": 0.8}}), + ("struct_with_magmoms", {"MAGMOM": {"Fe": 3.7, "O": 0.8}}), + ("struct_with_spin", {"MAGMOM": {"Fe2+,spin=4": 3.7, "O2-,spin=0.63": 0.8}}), ], ) def test_incar_magmoms_precedence(structure, user_incar_settings, request) -> None: @@ -120,7 +127,9 @@ def test_incar_magmoms_precedence(structure, user_incar_settings, request) -> No has_struct_spin = getattr(structure.species[0], "spin", None) is not None if user_incar_settings: # case 1 - assert incar_magmom == user_incar_settings["MAGMOM"] + assert incar_magmom == [ + user_incar_settings["MAGMOM"][str(site.specie)] for site in structure + ] elif has_struct_magmom: # case 2 assert incar_magmom == structure.site_properties["magmom"] elif has_struct_spin: # case 3 @@ -151,11 +160,11 @@ def test_set_u_params(structure, request) -> None: # ensure that there are LDAU* keys, and that they match expected values # in config_dict assert len([key for key in incar if key.startswith("LDAU")]) > 0 - for LDAU_key in ["LDAUU", "LDAUJ", "LDAUL"]: - for isite, site in enumerate(structure): - assert incar[LDAU_key][isite] == input_gen.config_dict["INCAR"][ - LDAU_key - ]["O"].get(str(site.specie), 0) + for ldau_key in ("LDAUU", "LDAUJ", "LDAUL"): + for idx, site in enumerate(structure): + assert incar[ldau_key][idx] == input_gen.config_dict["INCAR"][ldau_key][ + "O" + ].get(str(site.specie), 0) else: # if no sites have a nonzero U value in the config_dict, # ensure that no keys starting with LDAU are in the INCAR @@ -166,9 +175,9 @@ def test_set_u_params(structure, request) -> None: "bandgap, expected_params", [ (0, {"KSPACING": 0.22, "ISMEAR": 2, "SIGMA": 0.2}), - (0.1, {"KSPACING": 0.269695615, "ISMEAR": -5, "SIGMA": 0.05}), - (1, {"KSPACING": 0.302352354, "ISMEAR": -5, "SIGMA": 0.05}), - (2, {"KSPACING": 0.349355136, "ISMEAR": -5, "SIGMA": 0.05}), + (0.1, {"KSPACING": 0.26969561, "ISMEAR": -5, "SIGMA": 0.05}), + (1, {"KSPACING": 0.30235235, "ISMEAR": -5, "SIGMA": 0.05}), + (2, {"KSPACING": 0.34935513, "ISMEAR": -5, "SIGMA": 0.05}), (5, {"KSPACING": 0.44, "ISMEAR": -5, "SIGMA": 0.05}), (10, {"KSPACING": 0.44, "ISMEAR": -5, "SIGMA": 0.05}), ], @@ -178,7 +187,7 @@ def test_set_kspacing_and_auto_ismear( ): static_set = MPMetaGGARelaxSetGenerator(auto_ismear=True, auto_kspacing=True) - incar = static_set._get_incar( + incar = static_set._get_incar( # noqa: SLF001 structure=struct_no_magmoms, kpoints=None, previous_incar=None,