Merge recent development on devel to master

.gitignore

@@ -23,3 +23,6 @@ dist
 .eggs
 _version.py
 venv*
+.vscode/**
+_build
+_templates

.travis.yml

@@ -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

data/json/json2yaml.py

@@ -0,0 +1,37 @@
+#!/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()

doc/Makefile

@@ -0,0 +1,20 @@
+# 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)

doc/_static/css/custom.css

@@ -0,0 +1,3 @@
+pre{
+	overflow: auto;
+}

doc/api.rst

@@ -0,0 +1,91 @@
+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:
+

doc/conf.py

@@ -0,0 +1,60 @@
+# 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'

doc/index.rst

@@ -0,0 +1,26 @@
+.. 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`