Symfunc paramgen

src/libnnp/version.h

@@ -18,8 +18,8 @@
 #define VERSION_H
 
 #define NNP_VERSION "2.0.0"
-#define NNP_GIT_REV "98f117d8273b1747972a3ff1a66198defe1ad714"
-#define NNP_GIT_REV_SHORT "98f117d"
-#define NNP_GIT_BRANCH "master"
+#define NNP_GIT_REV "62f67caed5fb85b19edf1be8ec565ea3568648d4"
+#define NNP_GIT_REV_SHORT "62f67ca"
+#define NNP_GIT_BRANCH "symfunc_paramgen"
 
 #endif

tools/python/symfunc_paramgen/doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = symfunc_paramgen
+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)

tools/python/symfunc_paramgen/doc/README.md

@@ -0,0 +1,14 @@
+#### Building the documentation
+
+run
+
+	make html
+
+to generate the documentation using sphinx.
+This tool uses numpydoc-style docstrings.
+
+*Requires*: 
+
+* Sphinx
+* Sphinx alabaster theme (while the rtd theme might look nicer in principle, there seemed to be rendering issues when using it)
+* numpydoc

tools/python/symfunc_paramgen/doc/_static/readme.txt

@@ -0,0 +1 @@
+Any static files might go here.

tools/python/symfunc_paramgen/doc/code_structure.rst

@@ -0,0 +1,10 @@
+module sfparamgen
+---------------------------
+
+.. currentmodule:: sfparamgen
+
+class SymFuncParamGenerator
+===========================
+.. autoclass:: SymFuncParamGenerator
+   :members:
+   :undoc-members:

tools/python/symfunc_paramgen/doc/conf.py

@@ -0,0 +1,193 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# symfunc_paramgen documentation build configuration file, created by
+# sphinx-quickstart on Wed May  8 15:37:02 2019.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# 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('../src/'))
+sys.setrecursionlimit(1500)
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc',
+              'sphinx.ext.doctest',
+              'sphinx.ext.coverage',
+              'sphinx.ext.mathjax',
+              'sphinx.ext.viewcode',
+              'sphinx.ext.autosummary',
+              'numpydoc']
+              # 'sphinx.ext.napoleon']
+
+# TODO: remove if no longer needed with napoleon
+# numpydoc_show_class_members = False
+
+# # Napoleon settings
+# napoleon_google_docstring = False
+# napoleon_numpy_docstring = True
+# napoleon_include_private_with_doc = False
+# napoleon_include_special_with_doc = True
+# napoleon_use_admonition_for_examples = False
+# napoleon_use_admonition_for_notes = False
+# napoleon_use_admonition_for_references = False
+# napoleon_use_ivar = False
+# napoleon_use_param = True
+# napoleon_use_rtype = False
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'symfunc_paramgen'
+copyright = '2019, Florian Buchner'
+author = 'Florian Buchner'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '1.0'
+# The full version, including alpha/beta/rc tags.
+release = '1.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- 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 = 'alabaster'
+# html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+html_theme_options = {'show_related': True}
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'symfunc_paramgendoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'symfunc_paramgen.tex', 'symfunc\\_paramgen Documentation',
+     'Florian Buchner', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'symfunc_paramgen', 'symfunc_paramgen Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'symfunc_paramgen', 'symfunc_paramgen Documentation',
+     author, 'symfunc_paramgen', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+

tools/python/symfunc_paramgen/doc/index.rst

@@ -0,0 +1,39 @@
+.. symfunc_paramgen documentation master file, created by
+   sphinx-quickstart on Wed May  8 15:37:02 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to symfunc_paramgen's documentation!
+============================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+This tool generates sets of symmetry function parameters, according to rules proposed in the literature ([1]_, [2]_), and outputs
+them in the format required by n2p2.
+
+
+
+Code documentation
+==================
+
+.. toctree::
+   :maxdepth: 2
+
+   code_structure
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+.. rubric:: References
+
+.. [1] https://doi.org/10.1063/1.5019667
+.. [2] https://doi.org/10.1063/1.5024611
+

tools/python/symfunc_paramgen/doc/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=symfunc_paramgen
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd