Add all current files of version 1.0.0

with slightly modification

Author: singularitti

.gitignore

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+# qha: A powerful tool for quasi-harmonic approximation
+
+[TOC]
+
+This repo is created by [Tian Qin](mailto:[email protected]) (Sunny), for in-group use for [Renata Wentzcovitch](mailto:[email protected]). It is now maintained by [Qi Zhang](mailto:[email protected]) and Sunny.
+
+## What can be done
+
+This code is designed to calculate the thermodynamics properties of crystalline phases with contribution from Phonons (Vibrational Energy). In short, calculate the volume ($V(T, P)$), bulk modulus ($B(T, P)$), enthalpy ($H(T, P)$), Helmholtz free energy ($F(T, P)$), Gibbs free energy ($G(T, P)$) at certain pressure ($P$) and Temperature ($T$).
+
+## Input files needed
+
+1. Input data file: `input`
+2. Input control file: You can create your own settings according to the template given in `settings.yaml`.
+
+## Output files
+
+volume ($V(T, P)$), bulk modulus ($B(T, P)$), enthalpy ($H(T, P)$), Helmholtz free energy ($F(T, P)$), Gibbs free energy ($G(T, P)$) at certain pressure ($P$) and Temperature ($T$).
+
+## Where to get it
+
+The source code is currently hosted on [Bitbucket](https://bitbucket.org/singularitti/qha).
+
+Binary installers for the latest released version are available at the Python package index and on conda.
+
+```shell
+# conda
+$ conda install qha
+```
+
+```shell
+# or PyPI
+$ pip install qha
+```
+
+## Dependencies
+
+- [bigfloat](https://pypi.python.org/pypi/bigfloat)[^1]
+- [lazy-property](https://github.com/jackmaney/lazy-property)
+- [matplotlib](https://matplotlib.org)
+- [Numba](http://numba.pydata.org)
+- [NumPy](http://www.numpy.org)
+- [pandas](https://pandas.pydata.org)
+- [PyYAML](http://pyyaml.org)
+- [scientific-string](https://github.com/singularitti/scientific-string)
+- [SciPy](https://www.scipy.org)
+- [text-stream](https://github.com/singularitti/text-stream)
+
+[^1]: `GMP` and `MPFR` libraries are required to use `bigfloat` package. On macOS, install these libraries via `brew install mpfr`; on Linux, install `libmpfr-dev` , for example, on Ubuntu use `[sudo] apt-get install libmpfr-dev`; on Windows, `bigfloat` can be installed from the binary file, please check  "[Unofficial Windows Binaries for Python Extension Packages](https://www.lfd.uci.edu/~gohlke/pythonlibs/)"
+
+## Installation from sources
+
+Download the latest release, and go to the top-level directory, run
+
+```shell
+$ python setup.py install
+```
+
+Notice that you have to use Python version above 3.5 to install.
+
+## Simple run
+
+```shell
+$ qha /path/to/settings.yaml
+```
+
+## License
+
+GNU General Public License 3

LICENSE

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = qha
+SOURCEDIR     = source
+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)

README.md

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=qha
+
+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

docs/Makefile

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+.. currentmodule:: qha
+.. _api:
+
+API Reference
+=============
+
+.. contents:: Table of contents:
+   :local:
+
+.. autosummary::
+
+   eos

docs/make.bat

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# qha documentation build configuration file, created by
+# sphinx-quickstart on Fri Feb  2 20:24:08 2018.
+#
+# 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
+
+import sphinx_bootstrap_theme
+
+sys.path.insert(0, os.path.abspath('../../'))
+
+
+# -- 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.autosummary',
+              'sphinx.ext.doctest',
+              'sphinx.ext.intersphinx',
+              'sphinx.ext.todo',
+              'sphinx.ext.coverage',
+              'sphinx.ext.mathjax',
+              'sphinx.ext.ifconfig',
+              'sphinx.ext.viewcode',
+              'sphinx.ext.githubpages',
+              'sphinx_autodoc_typehints']
+
+# 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 = 'qha'
+copyright = '2018, Tian Qin, Qi Zhang'
+author = 'Tian Qin, Qi Zhang'
+
+# 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 = '0.0.1'
+# The full version, including alpha/beta/rc tags.
+release = '0.0.1'
+
+# 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 = []
+
+# 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 = True
+
+
+# -- 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 = 'bootstrap'
+html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
+
+# 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 = {'bootswatch_theme': "paper", }
+
+# 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 = 'qhadoc'
+
+
+# -- 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, 'qha.tex', 'qha Documentation',
+     'Tian Qin, Qi Zhang', '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, 'qha', 'qha 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, 'qha', 'qha Documentation',
+     author, 'qha', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output ----------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+epub_author = author
+epub_publisher = author
+epub_copyright = copyright
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}

docs/source/api.rst

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+.. _contributing:
+
+*********************
+Contributing to qha
+*********************
+
+.. contents:: Table of contents:
+   :local:
+

docs/source/conf.py

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+.. qha documentation master file, created by
+   sphinx-quickstart on Fri Feb  2 20:24:08 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+qha documentation
+=================
+
+.. toctree::
+   :numbered:
+   :maxdepth: 2
+
+   user/index
+   reference/index
+   contributing
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`

docs/source/contributing.rst

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+Reference Manual
+================
+
+.. toctree::
+
+    type