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Merge pull request #1 from deepmodeling/master
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denghuilu authored Jan 26, 2021
2 parents 9528a5a + 4002aa5 commit 27854e4
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -23,3 +23,6 @@ dist
.eggs
_version.py
venv*
.vscode/**
_build
_templates
16 changes: 6 additions & 10 deletions .travis.yml
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Expand Up @@ -66,34 +66,30 @@ jobs:
env:
- CC=gcc-5
- CXX=g++-5
- TENSORFLOW_VERSION=2.1
- TENSORFLOW_VERSION=2.3
- python: 3.7
env:
- CC=gcc-8
- CXX=g++-8
- TENSORFLOW_VERSION=2.1
- TENSORFLOW_VERSION=2.3
- stage: build whls
services: docker
env:
- TWINE_USERNAME=__token__
- CIBW_BUILD="cp36-* cp37-*"
- CIBW_BEFORE_BUILD="pip install tensorflow && sed -i 's/libresolv.so.2\"/libresolv.so.2\", \"libtensorflow_framework.so.2\"/g' \$(find / -name policy.json)"
- CIBW_BEFORE_BUILD="sed -i 's/libresolv.so.2\"/libresolv.so.2\", \"libtensorflow_framework.so.2\"/g' \$(find / -name policy.json)"
- CIBW_SKIP="*-win32 *-manylinux_i686"
- CC=gcc-7
- CXX=g++-7
- TENSORFLOW_VERSION=2.1
- TENSORFLOW_VERSION=2.3
install:
- python -m pip install twine cibuildwheel==1.1.0 scikit-build setuptools_scm
- python -m pip install twine cibuildwheel==1.6.3 scikit-build setuptools_scm
script:
- python -m cibuildwheel --output-dir wheelhouse
- python setup.py sdist
after_success:
- if [[ $TRAVIS_TAG ]]; then python -m twine upload wheelhouse/*; python -m twine upload dist/*.tar.gz; fi
before_install:
#- pip install --upgrade pip
- pip install --upgrade setuptools
- pip install tensorflow==$TENSORFLOW_VERSION
install:
- pip install --verbose .[test]
- pip install .[cpu,test]
script:
- cd source/tests && python -m unittest
549 changes: 15 additions & 534 deletions README.md

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37 changes: 37 additions & 0 deletions data/json/json2yaml.py
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#!/usr/bin/env python3

import argparse
import json
from pathlib import Path
from warnings import warn

import yaml


def _main():
parser = argparse.ArgumentParser(
description="convert json config file to yaml",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)

# get all json files in dir
jsons = [p for p in Path.cwd().glob("*.json")]
# use the newest as autosuggestion
jsons.sort(key=lambda x: x.stat().st_mtime, reverse=True)
jfile = jsons[0]
yfile = jfile.with_suffix(".yaml")

parser.add_argument("INPUT", default=jfile, type=Path, nargs="?",
help="input json file")
parser.add_argument("OUTPUT", default=yfile, type=Path, nargs="?",
help="output yaml file")
args = parser.parse_args()

with args.INPUT.open("r") as infile, args.OUTPUT.open("w") as outfile:
yaml.dump(json.load(infile), outfile, default_flow_style=False,
sort_keys=False)

warn("The order of the keys won't be preserved!", SyntaxWarning)
warn("_comment keys will also be lostt in the conversion")

if __name__ == "__main__":
_main()
20 changes: 20 additions & 0 deletions doc/Makefile
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# Minimal makefile for Sphinx documentation
#

# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
SOURCEDIR = .
BUILDDIR = _build

# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

.PHONY: help Makefile

# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
3 changes: 3 additions & 0 deletions doc/_static/css/custom.css
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pre{
overflow: auto;
}
91 changes: 91 additions & 0 deletions doc/api.rst
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DeePMD-kit API
===============

.. toctree::
:maxdepth: 2
:caption: Contents:

.. automodule:: deepmd.Data
:members:
:undoc-members:

.. automodule:: deepmd.DataModifier
:members:
:undoc-members:

.. automodule:: deepmd.DataSystem
:members:
:undoc-members:

.. automodule:: deepmd.DeepDipole
:members:
:undoc-members:

.. automodule:: deepmd.DeepEval
:members:
:undoc-members:

.. automodule:: deepmd.DeepPolar
:members:
:undoc-members:

.. automodule:: deepmd.DeepPot
:members:
:undoc-members:

.. automodule:: deepmd.DeepWFC
:members:
:undoc-members:

.. automodule:: deepmd.DescrptLocFrame
:members:
:undoc-members:

.. automodule:: deepmd.DescrptSeA
:members:
:undoc-members:

.. automodule:: deepmd.DescrptSeAR
:members:
:undoc-members:

.. automodule:: deepmd.DescrptSeR
:members:
:undoc-members:

.. automodule:: deepmd.EwaldRecp
:members:
:undoc-members:

.. automodule:: deepmd.Fitting
:members:
:undoc-members:

.. automodule:: deepmd.LearningRate
:members:
:undoc-members:

.. automodule:: deepmd.Local
:members:
:undoc-members:

.. automodule:: deepmd.Loss
:members:
:undoc-members:

.. automodule:: deepmd.Model
:members:
:undoc-members:

.. automodule:: deepmd.Network
:members:
:undoc-members:

.. automodule:: deepmd.TabInter
:members:
:undoc-members:

.. automodule:: deepmd.Trainer
:members:
:undoc-members:

60 changes: 60 additions & 0 deletions doc/conf.py
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# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html

# -- Path setup --------------------------------------------------------------

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))


# -- Project information -----------------------------------------------------

project = 'DeePMD-kit'
copyright = '2020, Deep Potential'
author = 'Deep Potential'


# -- General configuration ---------------------------------------------------

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'recommonmark',
"sphinx_rtd_theme",
'sphinx.ext.autosummary'
]

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']


# -- Options for HTML output -------------------------------------------------

# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'sphinx_rtd_theme'

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
html_css_files = ['css/custom.css']

autodoc_default_flags = ['members']
autosummary_generate = True
master_doc = 'index'
26 changes: 26 additions & 0 deletions doc/index.rst
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.. deepmd-kit documentation master file, created by
sphinx-quickstart on Sat Nov 21 18:36:24 2020.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
DeePMD-kit's documentation
======================================

.. toctree::
:maxdepth: 2
:caption: Contents:


install
use-deepmd-kit
train-input
lammps-pair-style-deepmd
api


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
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