Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

change status #132

Merged
merged 9 commits into from
May 31, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 5 additions & 5 deletions docs/source/user_guide/calculations.rst
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ Below is a usage example with the minimum required parameters. These parameters

.. code-block:: python

SinglePointCalculation = CalculationFactory("janus.sp")
SinglePointCalculation = CalculationFactory("mlip.sp")
submit(SinglePointCalculation, code=InstalledCode, structure=StructureData, metadata={"options": {"resources": {"num_machines": 1}}})

The inputs can be grouped into a dictionary:
Expand All @@ -43,7 +43,7 @@ The inputs can be grouped into a dictionary:
"precision": Str,
"device": Str,
}
SinglePointCalculation = CalculationFactory("janus.sp")
SinglePointCalculation = CalculationFactory("mlip.sp")
submit(SinglePointCalculation, **inputs)


Expand Down Expand Up @@ -72,7 +72,7 @@ And it is used as shown below. Note that some parameters, which are specific to
config = JanusConfigfile("path/to/config.yaml")

# Define calculation to run
SinglePointCalculation = CalculationFactory("janus.sp")
SinglePointCalculation = CalculationFactory("mlip.sp")

# Run calculation
result, node = run_get_node(
Expand Down Expand Up @@ -140,7 +140,7 @@ Below is a usage example with some additional geometry optimisation parameters.
.. code-block:: python


GeomOptCalculation = CalculationFactory("janus.opt")
GeomOptCalculation = CalculationFactory("mlip.opt")
submit(GeomOptCalculation, code=InstalledCode, structure=StructureData, max_force=Float(0.1), vectors_only=Bool(True))


Expand Down Expand Up @@ -177,7 +177,7 @@ Below is a usage example with some additional geometry optimisation parameters.
.. code-block:: python


MDCalculation = CalculationFactory("janus.md")
MDCalculation = CalculationFactory("mlip.md")
submit(MDCalculation, code=InstalledCode, structure=StructureData, ensemble=Str("nve"), md_dict=Dict({'temp':300,'steps': 4,'traj-every':3,'stats-every':1}))

.. note::
Expand Down
4 changes: 2 additions & 2 deletions docs/source/user_guide/training.rst
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ Below is a usage example with some additional training parameters. These paramet

.. code-block:: python

TrainCalculation = CalculationFactory("janus.train")
TrainCalculation = CalculationFactory("mlip.train")
submit(TrainCalculation, code=InstalledCode, mlip_config=JanusConfigfile, metadata=Dict({'options': {'output_filename': 'aiida-stdout.txt'}}))


Expand Down Expand Up @@ -90,7 +90,7 @@ In that case some additional parameters must be used: foundation_model and fine_
foundation_model=ModelData
}

TrainCalculation = CalculationFactory("janus.train")
TrainCalculation = CalculationFactory("mlip.train")
submit(TrainCalculation,inputs)

A model to fine-tune has to be provided as an input, either as a `ModelData` type (in which case it has to be a model file), or in the config file at the keyword `foundation_model`.
Expand Down
6 changes: 3 additions & 3 deletions docs/source/user_guide/tutorial.rst
Original file line number Diff line number Diff line change
Expand Up @@ -75,9 +75,9 @@ The calculation must be set:
.. code-block:: python

from aiida.plugins import CalculationFactory
geomoptCalculation = CalculationFactory("janus.opt")
geomoptCalculation = CalculationFactory("mlip.opt")

In this case, since we are running a geometry optimisation, the entry point for the calculation is `janus.opt`. For a single point calculation, the entry point would be `janus.sp`.
In this case, since we are running a geometry optimisation, the entry point for the calculation is `mlip.opt`. For a single point calculation, the entry point would be `mlip.sp`.

Finally, run the calculation:

Expand Down Expand Up @@ -129,7 +129,7 @@ while `node` is the node of the calculation
Out : aiida.orm.nodes.process.calculation.calcjob.CalcJobNode

In : print(node)
Out: uuid: 1d46ad08-2ea7-4892-9dd6-0240b9aeda8b (pk: 1130) (aiida.calculations:janus.opt)
Out: uuid: 1d46ad08-2ea7-4892-9dd6-0240b9aeda8b (pk: 1130) (aiida.calculations:mlip.opt)


The calculation can also be interacted with through verdi cli. Use `verdi process list` to show the list of calculations.
Expand Down
8 changes: 4 additions & 4 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,10 @@ name = "aiida-mlip"
version = "0.2.0"
description = "machine learning interatomic potentials aiida plugin"
authors = [
"Federica Zanca",
"Federica Zanca <[email protected]>",
"Elliott Kasoar",
"Jacob Wilkins",
"Alin M. Elena",
"Alin M. Elena"
]
readme = "README.md"
packages = [{include = "aiida_mlip"}]
Expand All @@ -15,7 +15,7 @@ classifiers = [
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",
"Natural Language :: English",
"Development Status :: 3 - Alpha",
"Development Status :: 5 - Production/Stable",
"Framework :: AiiDA"
]
keywords = ["aiida", "plugin"]
Expand All @@ -30,10 +30,10 @@ python = "^3.9"
aiida-core = "^2.5"
ase = "^3.22.1"
voluptuous = "^0.14"
janus-core = "^v0.5.0b0"

[tool.poetry.group.dev.dependencies]
coverage = {extras = ["toml"], version = "^7.4.1"}
janus-core = "^v0.4.0b0"
pgtest = "^1.3.2"
pytest = "^8.0"
pytest-cov = "^4.1.0"
Expand Down