Merge pull request #1 from jthorton/de

DE-Force-1

.gitattributes

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+deforcefields/_version.py export-subst

.github/workflows/CI.yaml

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+name: CI
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    - cron: "0 0 * * *"
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  test:
+    name: 🖥️ ${{ matrix.os }}, 🐍=${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - macOS-latest
+          - ubuntu-latest
+        python-version:
+          - "3.9"
+
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Additional info about the build
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+          
+      - name: Install conda environment
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: devtools/conda-envs/test_env.yaml
+          extra-specs: |
+            python=${{ matrix.python-version }}
+
+      - name: Install DE-ForceFields
+        run: |
+          python -m pip install .
+
+      - name: Environment Information
+        run: |
+          conda info
+          conda list --show-channel-urls
+
+      - name: PyTest
+        run: |
+          pytest -v  deforcefields/tests/

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+.pytest_cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# PyCharm
+*.idea/
+
+# OS X extra files
+*.DS_Store

MANIFEST.in

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+recursive-include deforcefields  *

README.md

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-# de-forcefields
-Transferable Doube Exponential non-bonded potential for condensed phase simulations of small molecules
+# DE-Force Fields
+Transferable Double Exponential non-bonded potential for condensed phase simulations of small molecules.
+
+
+[![CI](https://github.com/jthorton/de-forcefields/actions/workflows/CI.yaml/badge.svg)](https://github.com/jthorton/de-forcefields/actions/workflows/CI.yaml)
+
+This repository contains general transferable force fields that use the Double Exponential functional form first proposed by [Brooks](http://aip.scitation.org/doi/10.1063/1.5107505). 
+These force fields use the SMIRKS Native Open Force Field (SMIRNOFF) format. 
+By convention these files use the `.offxml` file extension. 
+The SMIRNOFF format has a [specification](https://openforcefield.github.io/standards/standards/smirnoff/) and is discussed in a [JCTC publication](https://doi.org/10.1021/acs.jctc.8b00640) and associated [pre-print](https://www.biorxiv.org/content/10.1101/286542v3).
+
+The [OpenFF Toolkit](https://github.com/openforcefield/openff-toolkit) (version >0.10.6, <0.11.0) provides a reference implementation of the SMIRNOFF format. 
+In particular, the `ForceField` class is used to load SMIRNOFF-format force fields and the `create_openmm_system` method enables the parametrization of small molecules into OpenMM objects.
+[Smirnoff-plugins](https://github.com/openforcefield/smirnoff-plugins) provides a framework to extend the SMIRNOFF specification with custom force field functional forms such as the Double Exponential form used here, using a plugin system. 
+See `smirnoff-plugins` for a list of the currently supported potentials.
+
+Detailed usage examples can be found in the OpenFF Toolkit repository.
+
+Each force field is currently available in two forms -- both with and without bond constraints to hydrogen. The default version of each force field (i.e. de-1.0.0.offxml) is suitable for typical molecular dynamics simulations with constrained bonds to hydrogen. 
+The "unconstrained" version of each force field (i.e. de_unconstrained-1.0.0.offxml) should be used when single-point energies are a major concern (e.g. geometry optimizations) and when comparing the force field to QM data.
+
+| Filename                              | DOI  | FF line    | Release Date | Major format changes? |
+|---------------------------------------|------|------------|--------------|-----------------------|
+| `de-force-1.0.0.offxml`               | TODO | DE-Force-1 | Feb 17, 2023 | No                    |
+| `de-force_unconstrained-1.0.0.offxml` | TODO | DE-Force-1 | Feb 17, 2023 | No                    |
+
+
+## Installation
+
+```shell
+conda install -c conda-forge de-forcefields
+```
+
+
+## Use
+
+Installing this package exposes an entry point that makes the `deforcefields/offxml/` directory easily accessible by other packages in the same Python installation. 
+If the [OpenFF Toolkit](https://github.com/openforcefield/openff-toolkit) is installed, it will automatically detect and use this entry point:
+
+```python3
+>>> from openff.toolkit.typing.engines.smirnoff import ForceField
+>>> ff = ForceField('de-force-1.0.0.offxml', load_plugins=True)
+```
+
+Otherwise, the entry point can be accessed by querying the `openforcefield.smirnoff_forcefield_directory` entry point group.
+
+```python3
+>>> from pkg_resources import iter_entry_points
+>>> for entry_point in iter_entry_points(group='openforcefield.smirnoff_forcefield_directory'):
+...     print(entry_point.load()())
+```
+
+
+# History
+
+Force fields in the `DE-Force-1` lines are descended from [OpenFF-2.0.0 Sage](https://doi.org/10.5281/zenodo.5214478).
+
+## General versioning guidelines
+
+Force fields moving forward will be called `name-X.Y.Z`
+
+* `X` denotes some major change in functional form or fitting strategy.
+* `Y` is the parameterization epoch / generation, or a minor change that can affect energy.
+* `Z` is a bugfix version -- e.g. something we've caught and corrected.
+
+
+## Versions
+- `DE-Force-1` : Proof of concept general transferable Double Exponential force field fit using [Sage training data](https://doi.org/10.26434/chemrxiv-2022-n2z1c-v2). 

deforcefields/__init__.py

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+from . import _version
+
+versions = _version.get_versions()
+__version__ = versions["version"]
+__git_revision = versions["full-revisionid"]
+del versions