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add misc files (#5)
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‎.gitignore‎

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

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.2.0
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hooks:
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- id: end-of-file-fixer
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- id: fix-encoding-pragma
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- id: mixed-line-ending
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- id: trailing-whitespace
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- id: check-json
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- repo: https://github.com/pycqa/isort
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rev: 5.12.0
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hooks:
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- id: isort
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args: ["--profile", "black"]
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- repo: https://github.com/psf/black
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rev: 23.3.0
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hooks:
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- id: black
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args: ["--line-length", "88"]
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- repo: https://github.com/pycqa/flake8
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rev: 6.0.0
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hooks:
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- id: flake8
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args: ["--max-line-length=88", "--ignore=E203,W503"]

‎environment.yaml‎

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name: mattersim
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channels:
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- pyg
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- pytorch
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- conda-forge
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dependencies:
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- python=3.9
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- pytorch==1.11.0
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- pytorch-sparse=0.6.15
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- pytorch-scatter=2.0.9
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- ca-certificates
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- openssl
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- numpy<2
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- phonopy==2.14.0
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- phono3py==2.3.0
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- cython
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- loguru
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- pip:
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- seekpath
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- torch==1.11.0+cu113
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- torchvision==0.12.0+cu113
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- torchaudio==0.11.0
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- --extra-index-url https://download.pytorch.org/whl/cu113

‎setup.py‎

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# -*- coding: utf-8 -*-
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import numpy as np
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from setuptools import Extension, find_packages, setup
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from setuptools.command.build_ext import build_ext as _build_ext
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class build_ext(_build_ext):
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def finalize_options(self):
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_build_ext.finalize_options(self)
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if self.distribution.ext_modules:
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import pyximport
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pyximport.install()
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setup(
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name="mattersim",
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version="1.0",
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description=(
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"MatterSim: MatterSim: A Deep Learning Atomistic Model Across "
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"Elements, Temperatures and Pressures."
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),
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author=(
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"Han Yang, Chenxi Hu, Yichi Zhou, Xixian Liu, Yu Shi, Jielan Li, "
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"Guanzhi Li, Zekun Chen, Shuizhou Chen, Claudio Zeni, Matthew Horton, "
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"Robert Pinsler, Andrew Fowler, Daniel Zügner, Tian Xie, Jake Smith, "
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"Lixin Sun, Qian Wang, Lingyu Kong, Chang Liu, Hongxia Hao, Ziheng Lu"
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),
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author_email=(
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"hanyang@microsoft.com; jielanli@microsoft.com; "
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"hongxiahao@microsoft.com; zihenglu@microsoft.com;"
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),
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python_requires=">=3.9",
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packages=find_packages(where="src", include=["mattersim", "mattersim.*"]),
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package_dir={"": "src"},
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url="https://github.com/msr-ai4science/mattersim",
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requires=[
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"torch",
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],
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install_requires=[
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"ase>=3.23.0",
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"Cython>=0.29.32",
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"e3nn==0.5.0",
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"numpy<2",
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"pymatgen",
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"torch_geometric==2.0.4",
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"torch_runstats==0.2.0",
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"torchmetrics>=0.10.0",
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"torch-ema==0.3",
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"opt_einsum_fx",
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"pre-commit",
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"Pathlib",
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"pytest",
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"pytest-testmon",
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"azure-storage-blob",
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"azure-identity",
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],
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setup_requires=[
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"Cython>=0.29.32",
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],
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cmdclass={"build_ext": build_ext},
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ext_modules=[
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Extension(
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"mattersim.datasets.utils.threebody_indices",
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["src/mattersim/datasets/utils/threebody_indices.pyx"],
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include_dirs=[np.get_include()],
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)
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],
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)

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