single point calcjob (#84)

add singlepoint calcuations for aiida and model management
---------

Co-authored-by: Alin Marin Elena <alin@elena.re>
Co-authored-by: ElliottKasoar <45317199+ElliottKasoar@users.noreply.github.com>
Co-authored-by: Jacob Wilkins <46597752+oerc0122@users.noreply.github.com>

.github/workflows/ci.yml

@@ -46,11 +46,14 @@ jobs:
       run: |
         poetry env use ${{ matrix.python-version }}
         poetry install --with dev
+        echo "JANUS_PATH=$(poetry run which janus)" >> $GITHUB_ENV
 
     - name: Run test suite
+
       env:
-        # show timings of tests
+        # show timings of test
         PYTEST_ADDOPTS: "--durations=0"
+        JANUS_PATH: ${{ env.JANUS_PATH }}
       run: poetry run pytest --cov aiida_mlip --cov-append .
 
     - name: Report coverage to Coveralls

README.md

@@ -18,67 +18,59 @@ intended to help developers get started with their AiiDA plugins.
 * [`.github/`](.github/): [Github Actions](https://github.com/features/actions) configuration
   * [`ci.yml`](.github/workflows/ci.yml): runs tests, checks test coverage and builds documentation at every new commit
   * [`publish-on-pypi.yml`](.github/workflows/publish-on-pypi.yml): automatically deploy git tags to PyPI - just generate a [PyPI API token](https://pypi.org/help/#apitoken) for your PyPI account and add it to the `pypi_token` secret of your github repository
+  * [`docs.yml`](.github/workflows/docs.yml): builds and deploys the documentation
 * [`aiida_mlip/`](aiida_mlip/): The main source code of the plugin package
-  * [`data/`](aiida_mlip/data/): A new `DiffParameters` data class, used as input to the `DiffCalculation` `CalcJob` class
-  * [`calculations.py`](aiida_mlip/calculations.py): A new `DiffCalculation` `CalcJob` class
-  * [`cli.py`](aiida_mlip/cli.py): Extensions of the `verdi data` command line interface for the `DiffParameters` class
-  * [`helpers.py`](aiida_mlip/helpers.py): Helpers for setting up an AiiDA code for `diff` automatically
-  * [`parsers.py`](aiida_mlip/parsers.py): A new `Parser` for the `DiffCalculation`
-* [`docs/`](docs/): A documentation template ready for publication on [Read the Docs](http://aiida-diff.readthedocs.io/en/latest/)
-* [`examples/`](examples/): An example of how to submit a calculation using this plugin
+  * [`data/`](aiida_mlip/data/): Plugin `Data` classes
+    * [`model.py/`](aiida_mlip/data/model.py) `ModelData` class to save mlip models as AiiDA data types
+  * [`calculations/`](aiida_mlip/calculations/): Plugin `Calcjob` classes
+    * [`singlepoint.py](aiida_mlip/calculations/singlepoint.py ): `Calcjob` class to run single point calculations using mlips
+  * [`parsers.py`](aiida_mlip/parsers.py): `Parser` for the `Singlepoint` calculation
+* [`docs/`](docs/source/): Code documentation
+  * [`apidoc/`](docs/source/apidoc/): API documentation
+  * [`developer_guide/`](docs/source/developer_guide/): Documentation for developers
+  * [`user_guide/`](docs/source/user_guide/): Documentation for users
+  * [`images/`](docs/source/images/): Logos etc used in the documentation
+* [`examples/`](examples/): Examples for submitting calculations using this plugin
+  * [`calculations/submit_singlepoint.py`](examples/calculations/submit_singlepoint.py): Script for submitting a singlepoint calculation
 * [`tests/`](tests/): Basic regression tests using the [pytest](https://docs.pytest.org/en/latest/) framework (submitting a calculation, ...). Install `pip install -e .[testing]` and run `pytest`.
+  * [`conftest.py`](tests/conftest.py): Configuration of fixtures for [pytest](https://docs.pytest.org/en/latest/)
+  * [`calculations/`](tests/calculations): Calculations
+    * [`test_singlepoint.py`](tests/calculations/test_singlepoint.py): Test `SinglePoint` calculation
+  * [`data/`](tests/data): `ModelData`
+    * [`test_model.py`](tests/data/test_model.py): Test `ModelData` type
 * [`.gitignore`](.gitignore): Telling git which files to ignore
 * [`.pre-commit-config.yaml`](.pre-commit-config.yaml): Configuration of [pre-commit hooks](https://pre-commit.com/) that sanitize coding style and check for syntax errors. Enable via `pip install -e .[pre-commit] && pre-commit install`
-* [`.readthedocs.yml`](.readthedocs.yml): Configuration of documentation build for [Read the Docs](https://readthedocs.org/)
-* [`LICENSE`](LICENSE): License for your plugin
+* [`LICENSE`](LICENSE): License for the plugin
 * [`README.md`](README.md): This file
-* [`conftest.py`](conftest.py): Configuration of fixtures for [pytest](https://docs.pytest.org/en/latest/)
-* [`pyproject.toml`](setup.json): Python package metadata for registration on [PyPI](https://pypi.org/) and the [AiiDA plugin registry](https://aiidateam.github.io/aiida-registry/) (including entry points)
-
-See also the following video sequences from the 2019-05 AiiDA tutorial:
-
- * [run aiida-diff example calculation](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=403s)
- * [aiida-diff CalcJob plugin](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=685s)
- * [aiida-diff Parser plugin](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=936s)
- * [aiida-diff computer/code helpers](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1238s)
- * [aiida-diff input data (with validation)](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1353s)
- * [aiida-diff cli](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1621s)
- * [aiida-diff tests](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1931s)
- * [Adding your plugin to the registry](https://www.youtube.com/watch?v=760O2lDB-TM&t=112s)
- * [pre-commit hooks](https://www.youtube.com/watch?v=760O2lDB-TM&t=333s)
-
-For more information, see the [developer guide](https://aiida-diff.readthedocs.io/en/latest/developer_guide) of your plugin.
-
-
-## Features
-
- * Add input files using `SinglefileData`:
-   ```python
-   SinglefileData = DataFactory('core.singlefile')
-   inputs['file1'] = SinglefileData(file='/path/to/file1')
-   inputs['file2'] = SinglefileData(file='/path/to/file2')
-   ```
-
- * Specify command line options via a python dictionary and `DiffParameters`:
-   ```python
-   d = { 'ignore-case': True }
-   DiffParameters = DataFactory('mlip')
-   inputs['parameters'] = DiffParameters(dict=d)
-   ```
-
- * `DiffParameters` dictionaries are validated using [voluptuous](https://github.com/alecthomas/voluptuous).
-   Find out about supported options:
-   ```python
-   DiffParameters = DataFactory('mlip')
-   print(DiffParameters.schema.schema)
-   ```
+* [`tox.ini`](tox.ini): File to set up tox
+* [`pyproject.toml`](pyproject.toml): Python package metadata for registration on [PyPI](https://pypi.org/) and the [AiiDA plugin registry](https://aiidateam.github.io/aiida-registry/) (including entry points)
+
+
+
+## Features (in development)
+
+- [x] Supports multiple MLIPs
+  - MACE
+  - M3GNET
+  - CHGNET
+- [x] Single point calculations
+- [ ] Geometry optimisation
+- [ ] Molecular Dynamics:
+  - NVE
+  - NVT (Langevin(Eijnden/Ciccotti flavour) and Nosé-Hoover (Melchionna flavour))
+  - NPT (Nosé-Hoover (Melchiona flavour))
+- [ ] Training ML potentials (MACE only planned)
+- [ ] Fine tunning MLIPs (MACE only planned)
+
+The code relies heavily on ASE, unless something else is mentioned.
+
 
 ## Installation
 
 ```shell
 pip install aiida-mlip
 verdi quicksetup  # better to set up a new profile
-verdi plugin list aiida.calculations  # should now show your calclulation plugins
+verdi plugin list aiida.calculations  # should now show your calculation plugins
 ```
 
 
@@ -90,16 +82,10 @@ A quick demo of how to submit a calculation:
 ```shell
 verdi daemon start     # make sure the daemon is running
 cd examples
-./example_01.py        # run test calculation
+verdi run submit_singlepoint.py "janus@localhost" --calctype "singlepoint"  --architecture mace --model "~./cache/mlips/mace/46jrkm3v"       # run test calculation
 verdi process list -a  # check record of calculation
 ```
 
-The plugin also includes verdi commands to inspect its data types:
-```shell
-verdi data mlip list
-verdi data mlip export <PK>
-```
-
 ## Development
 
 1. Install [poetry](https://python-poetry.org/docs/#installation)

aiida_mlip/__init__.py

@@ -1,7 +1,5 @@
 """
-aiida_mlip
-
-machine learning interatomic potentials aiida plugin
+Machine learning interatomic potentials aiida plugin.
 """
 
 __version__ = "0.1.0a1"

aiida_mlip/calculations/__init__.py

@@ -0,0 +1,3 @@
+"""
+Calculations using MLIPs.
+"""