Merge branch 'develop' into rc

.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
     - name: Install symfc develop branch
       run: |
         conda activate test
@@ -45,8 +45,5 @@ jobs:
         PHPHCALC_USE_MTBLAS=ON pip install -e . -vvv
     - name: Run pytest
       run: |
-        pytest -v --cov=./ --cov-report=xml test
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        verbose: true
+        conda activate test
+        pytest -v test

.github/workflows/phono3py-pytest-conda-mkl-v2.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
     - name: Install symfc develop branch
       run: |
         conda activate test
@@ -45,8 +45,5 @@ jobs:
         pip install -e . -vvv
     - name: Run pytest
       run: |
-        pytest --v2 -v --cov=./ --cov-report=xml test
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        verbose: true
+        conda activate test
+        pytest --v2 -v test

.github/workflows/phono3py-pytest-conda-mkl.yml

@@ -45,6 +45,7 @@ jobs:
         pip install -e . -vvv
     - name: Run pytest
       run: |
+        conda activate test
         pytest -v --cov=./ --cov-report=xml test
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3

.github/workflows/phono3py-pytest-conda-numpy2.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py "numpy=2" scipy pytest codecov pytest-cov cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py "numpy=2" scipy pytest cmake c-compiler cxx-compiler
     - name: Install spglib develop branch
       run: |
         conda activate test
@@ -52,8 +52,5 @@ jobs:
         pip install -e . -vvv
     - name: Run pytest
       run: |
+        conda activate test
         pytest -v test
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        verbose: true

.github/workflows/phono3py-pytest-conda-phphmtblas.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
     - name: Install symfc develop branch
       run: |
         conda activate test
@@ -45,8 +45,5 @@ jobs:
         PHPHCALC_USE_MTBLAS=ON pip install -e . -vvv
     - name: Run pytest
       run: |
-        pytest -v --cov=./ --cov-report=xml test
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        verbose: true
+        conda activate test
+        pytest -v test

.github/workflows/phono3py-pytest-conda.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
     - name: Install phonopy develop branch
       run: |
         conda activate test
@@ -38,8 +38,5 @@ jobs:
         pip install -e . -vvv
     - name: Run pytest
       run: |
-        pytest -v --cov=./ --cov-report=xml test
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        verbose: true
+        conda activate test
+        pytest -v test

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
   - id: check-added-large-files
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.2
+  rev: v0.5.6
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

doc/changelog.md

@@ -2,6 +2,14 @@
 
 # Change Log
 
+## Jul-22-2024: Version 3.3.3
+
+- Provide functionality by `--cf3` and `--cf2` command options to create force
+  constants from displacement-force dataset of random displacements when
+  an external force constants calculator is specified.
+- New command line options `--rd`, `--rd-fc2`, `--fc-calc`, `--fc-calc-opt` and
+  `--sp` to support random displacements.
+
 ## Jul-22-2024: Version 3.3.2
 
 - Minor fix of `phono3py.load` function for reading displacements from

doc/command-options.md

@@ -27,13 +27,13 @@ CELL_FILENAME = POSCAR-unitcell
 where the setting tag names are case insensitive. This is run by
 
 ```bash
-% phono3py setting.conf [comannd options]
+% phono3py setting.conf [command options]
 ```
 
 or
 
 ```bash
-% phono3py [comannd options] -- setting.conf
+% phono3py [command options] -- setting.conf
 ```
 
 ```{contents}
@@ -48,7 +48,7 @@ or
 This specifies input unit cell filename.
 
 ```bash
-% phono3py -c POSCAR-unitcell ... (many options)
+% phono3py -c POSCAR-unitcell ... (options)
 ```
 
 ## Calculator interface
@@ -174,6 +174,27 @@ created from `FORCES_FC2` and `phono3py_disp.yaml` instead of `FORCES_FC3` and
 % phono3py --cfs --dim-fc2="x x x"
 ```
 
+(sp_option)=
+
+### `--sp` or `--save-params`
+
+Instead of `FORCES_FC3`, `phono3py_params.yaml` is generated. This option must
+be used with `--cf3`, and optionally with `--cf2`. If the force calculator
+supports reading energy of supercell, those are written into
+`phono3y_params.yaml`. These energies are necessary for using `--pypolymlp`
+option.
+
+```bash
+% phono3py --cf3 disp-{00001..00755}/vasprun.xml --sp
+```
+
+When using with `--cf2`, `--cf3` has to be specified simultaneously as below,
+
+```bash
+% phono3py --cf3 disp-{00001..00755}/vasprun.xml --cf2 disp_fc2-{00001..00002}/vasprun.xml --sp
+```
+
+
 ## Supercell, primitive cell, masses, magnetic moments
 
 (dim_option)=
@@ -250,7 +271,6 @@ web page](https://phonopy.github.io/phonopy/setting-tags.html#magmom).
 ## Displacement creation
 
 (create_displacements_option)=
-
 ### `-d` (`CREATE_DISPLACEMENTS = .TRUE.`)
 
 Supercell with displacements are created. Using with `--amplitude` option,
@@ -259,15 +279,16 @@ supercells with displacements and `phono3py_disp.yaml` file are created. `--pa`
 should be specified if the input unit cell structure is not a primitive cell,
 e.g., `--pa="F"` if the input unit cell has F-centring.
 
-(amplitude_option)=
 
+(random_displacements_option)=
 ### `--rd` (`RANDOM_DISPLACEMENTS`), `--rd-fc2` (`RANDOM_DISPLACEMENTS_FC2`) and `--random-seed` (`RANDOM_SEED`)
 
 Random directional displacements are generated for fc3 and fc2 supercells by
 `--rd` and `--rd-fc2`, respectively. `--amplitude` and `--random-seed` options
 may be used together. These are used in the equivalent way to [`--rd` of
 phonopy](https://phonopy.github.io/phonopy/setting-tags.html#random-displacements).
 
+(amplitude_option)=
 ### `--amplitude` (`DISPLACEMENT_DISTANCE`)
 
 Atomic displacement distance is specified. This value may be increased for the
@@ -277,6 +298,44 @@ very accurate.
 The default value depends on calculator. See
 {ref}`default_displacement_distance_for_calculator`.
 
+(fc_calculator_option)=
+### `--fc-calc`, `--fc-calculator` (`FC_CALCULATOR`)
+
+Choice of force constants calculator.
+
+```
+% phono3py --fc-calc symfc ...
+```
+
+To use different force constants calculators for fc2 and fc3
+```
+% phono3py --fc-calc "symfc|" ...
+```
+Those for fc2 and fc3 are seprated by `|` such as `symfc|` . Blank means to
+employ the finite difference method for systematic displacements generated by
+the option `-d`.
+
+(fc_calculator_options_option)=
+### `--fc-calc-opt`, `--fc-calculator-options` (`FC_CALCULATOR_OPTIONS`)
+
+Special options for force constants calculators.
+
+```
+% phono3py --fc-calc-opt "cutoff=8" ...
+```
+
+Similarly to `--fc-calc`, `|` can be used to separated those for fc2 and fc3.
+
+#### Options for symfc
+
+* cutoff : cutoff pair distance beyond that third-order force constants are zero
+  (fc3 only).
+* use_mkl : sparse_dot_mkl is employed when it is available.
+
+### `--symfc` and `--alm`
+
+These are shortcuts of `--fc-calc symfc` and `--fc-calc alm`, respectively.
+
 ## Force constants
 
 (compact_fc_option)=
@@ -331,14 +390,16 @@ supercell size and the second choice is using `--cutoff-pair` option.
 
 ### `--cutoff-pair` or `--cutoff-pair-distance` (`CUTOFF_PAIR_DISTANCE`)
 
-This option is only used together with `-d` option.
+This option works differently for the `-d` and `--rd` options.
 
-A cutoff pair-distance in a supercell is used to reduce the number of necessary
-supercells with displacements to obtain third order force constants. As the
-drawback, a certain number of third-order-force-constants elements are abandoned
-or computed with less numerical accuracy. More details are found at
+For `-d`, A cutoff pair-distance in a supercell is used to reduce the number of
+necessary supercells with displacements to obtain third order force constants.
+As the drawback, a certain number of third-order-force-constants elements are
+abandoned or computed with less numerical accuracy. More details are found at
 {ref}`command_cutoff_pair`.
 
+For `--rd`, `--cutoff-pair VAL` is equivalent to `--fc-calc-opt "cutoff=VAL"`.
+
 ### `--alm`
 
 This invokes ALM as the force constants calculator for fc2 and fc3. See the

doc/conf.py

@@ -60,7 +60,7 @@
 # The short X.Y version.
 version = "3.3"
 # The full version, including alpha/beta/rc tags.
-release = "3.3.2"
+release = "3.3.3"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/cutoff-pair.md

@@ -2,7 +2,11 @@
 
 # Force constants calculation with cutoff pair-distance
 
-Here the detail of the command option {ref}`--cutoff_pair <cutoff_pair_option>`
+Since this calculation is a little bit tricky. It may be recommended to try
+{ref}`random-displacements` with `--fc-calc-opt "cutoff = VAL"` before trying
+this option.
+
+Here the detail of the command option {ref}`--cutoff-pair <cutoff_pair_option>`
 is explained.
 
 <!-- See also reference {cite}`Mizokami-PRB-2018`. -->

doc/index.md

@@ -58,6 +58,7 @@ auxiliary-tools
 direct-solution
 wigner-solution
 workload-distribution
+random-displacements
 cutoff-pair
 external-tools
 phono3py-api

doc/install.md

@@ -136,12 +136,13 @@ wrong python libraries can be imported.
    % cd phonopy
    % pip install -e . -vvv
    % cd ../phono3py
-   % pip install -e . -vvv
+   % pip install . -vvv
    ```
 
-   The conda packages dependency can often change and this recipe may not work
-   properly. So if you find this instruction doesn't work, it is very
-   appreciated if letting us know it in the phonopy mailing list.
+   The editable install (`pip install -e`) may not work depending on the
+   computer environment. The conda packages dependency can often change and this
+   recipe may not work properly. So if you find this instruction doesn't work,
+   it is very appreciated if letting us know it in the phonopy mailing list.
 
 (install_lapacke)=
 ## Installation of LAPACKE