examples

examples/doi-10.48550-arXiv.2311.01545/_frameworks.py

@@ -9,7 +9,7 @@
 
 # Model used in https://arxiv.org/abs/2311.01545
 
-INPUT_GDOWN_LINK = 'https://drive.google.com/drive/folders/1VxK5mPu8bveaqFSSYnxrsKfZrTW_qXOX?usp=sharing' # Folder with model weights, sample graphs etc. Permission needs to be anyone with the link.
+INPUT_GDOWN_LINK = 'https://drive.google.com/drive/folders/1VxK5mPu8bveaqFSSYnxrsKfZrTW_qXOX?usp=drive_link' # Folder with model weights, sample graphs etc. Permission needs to be anyone with the link.
 
 class SyntheticChemicalMotifIdentifier(BaseSyntheticChemicalMotifIdentifier):
     """Just a class that re use the framework above but that matches the parameters of the first paper.

examples/doi-TBD/_additional_packages/NshellFinder/.github/workflows/black.yml

@@ -0,0 +1,12 @@
+name: black-action
+on: [push, pull_request]
+jobs:
+  linter_name:
+    name: runner / black formatter
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: rickstaa/action-black@v1
+        with:
+          black_args: ". --check"
+          fail_on_error: "False"

examples/doi-TBD/_additional_packages/NshellFinder/.github/workflows/python-tests.yml

@@ -0,0 +1,47 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python Tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  repository_dispatch:
+    types: [ovito_update]
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 15
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.7", "3.10", "3.11"]
+        exclude:
+          - os: macos-latest
+            python-version: "3.7"
+          - os: windows-latest
+            python-version: "3.7"
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install apt dependencies
+      if:  matrix.os == 'ubuntu-latest'
+      run: |
+        sudo apt install -y libegl1 libegl1-mesa libegl-mesa0 libgl1-mesa-glx libopengl0
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+        check-latest: true
+    - name: Install python dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pytest
+        python -m pip install --pre ovito
+        python -m pip install .
+    - name: Test with pytest
+      run: |
+        pytest

examples/doi-TBD/_additional_packages/NshellFinder/.gitignore

@@ -0,0 +1,161 @@
+# Byte-compiled / optimized / DLL files
+.vscode
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

examples/doi-TBD/_additional_packages/NshellFinder/README.md

@@ -0,0 +1,53 @@
+# NShellFinder
+
+![tests](https://github.com/killiansheriff/NShellFinder/actions/workflows/python-tests.yml/badge.svg)
+
+Ovito Python modifier to find the n-th coordination shell neighbors. 
+
+## Utilisation 
+Here is an example on how to find the indices of nearest neighbors -- cluster by shells up to certain cutoff -- for the fcc crystal structure. The scrip can be found in the ``examples/`` folder.  
+
+```python
+from ovito.io import import_file
+from NshellFinder import NshellFinder
+
+pipeline = import_file("fcc.dump")
+mod = NshellFinder(crystal_structure="fcc", cutoff=18.2)
+pipeline.modifiers.append(mod)
+data = pipeline.compute()
+
+neighbor_indices_per_shell = data.attributes["Neighbor indices per shell"]
+# (number of nearest neighbor shells up to cutoff, number of atoms, number of nearest neighbors in the shell)
+
+first_nn = neighbor_indices_per_shell[0] # (number of atoms, 12 first nearest neigbors)
+second_nn = neighbor_indices_per_shell[1] # (number of atoms, 6 second nearest neighbors)
+```
+
+
+## Installation
+For a standalone Python package or Conda environment, please use:
+```bash
+pip install --user NshellFinder
+```
+
+For *OVITO PRO* built-in Python interpreter, please use:
+```bash
+ovitos -m pip install --user NshellFinder
+```
+
+If you want to install the lastest git commit, please replace ``NshellFinder`` by ``git+https://github.com/killiansheriff/NshellFinder.git``.
+
+## Contact
+If any questions, feel free to contact me (ksheriff at mit dot edu).
+
+## References & Citing 
+If you use this repository in your work, please cite:
+
+```
+@article{TBD,
+  title={TBD},
+  author={Sheriff, Killian and Cao, Yifan and Freitas, Rodrigo},
+  journal={arXiv preprint TBD},
+  year={2024}
+}
+```