Merge branch 'update.solver_module' into update

extra/function/README.md

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+# Analytical function solver module for Py2DMAT

extra/function/doc/.gitignore

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+build

extra/function/doc/en/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = pyMC
+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)" -W $(SPHINXOPTS) $(O)

extra/function/doc/en/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=python -msphinx
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=pyMC
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The Sphinx module was not found. Make sure you have Sphinx installed,
+	echo.then set the SPHINXBUILD environment variable to point to the full
+	echo.path of the 'sphinx-build' executable. Alternatively you may add the
+	echo.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% -W %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

extra/function/doc/en/source/acknowledgement.rst

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+***************************
+Acknowledgements
+***************************
+
+The development of 2DMAT was supported by JSPS KAKENHI Grant Number 19H04125 "Unification of computational statistics and measurement technology by massively parallel machine"
+and "Project for advancement of software usability in materials science" (fiscal year 2020, 2021, 2024) of The Institute for Solid State Physics, The University of Tokyo.

extra/function/doc/en/source/conf.py

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+# -*- coding: utf-8 -*-
+#
+# MateriApps-Installer documentation build configuration file, created by
+# sphinx-quickstart on Sun May 1 14:29:22 2020.
+#
+# 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('.'))
+
+
+# -- 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.mathjax']
+
+# 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 = u'2DMAT solver module: Functions'
+copyright = u'2020, Institute for Solid State Physics, University of Tokyo'
+author = u'2DMAT Developer team'
+
+# 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 = u'1.0'
+# The full version, including alpha/beta/rc tags.
+release = u'1.0-dev'
+
+# 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 = 'en'
+
+# 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 = 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 = 'haiku'
+
+# 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 = {
+    # 'font_family': 'Helvetica',
+    # 'sidebar_search_button': 'pink_1'
+}
+
+# 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 = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+
+# 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']
+
+numfig = True
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = '2DMATdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+# latex_engine = 'uplatex'
+
+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, 'userguide_functions.tex', u'2DMAT Functions Documentation',
+     author, 'manual', 'True'),
+]
+
+
+# -- 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, '2dmat-functions', u'2DMAT Documentation',
+     [author], 1)
+]
+
+#latex_docclass =  {'manual': 'jsbook'}
+
+# -- 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, '2dmat-functions', u'2DMAT Documentation',
+     author, '2DMAT', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+
+

extra/function/doc/en/source/contact.rst

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+Contact
+=========================================
+
+- Bug Reports
+
+  Please report all problems and bugs on the github `Issues <https://github.com/issp-center-dev/2DMAT/releases>`_ page.
+
+  To resolve bugs early, follow these guidelines when reporting:
+
+  1. Please specify the version of 2DMAT and 2DMAT-Functions you are using.
+
+  2. If there are problems for installation, please inform us about your operating system and the compiler.
+
+  3. If a problem occurs during execution, enter the input file used for execution and its output.
+
+  Thank you for your cooperation.
+
+- Others
+
+  If you have any questions about your research that are difficult to consult at Issues on GitHub, please send an e-mail to the following address:
+
+  E-mail: ``2dmat-dev__at__issp.u-tokyo.ac.jp`` (replace _at_ by @)

extra/function/doc/en/source/index.rst

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+.. 2dmat documentation master file, created by
+   sphinx-quickstart on Tue May 26 18:44:52 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to 2DMAT's documentation!
+==================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   introduction
+   install
+   tutorial/index
+   solver
+   acknowledgement
+   contact
+
+..
+   input
+   output
+   algorithm/index
+   solver/index
+   tool
+   customize/index

extra/function/doc/en/source/install.rst

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+Installation of 2DMAT-Functions
+================================================================
+
+Prerequisites
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+- Python3 (>=3.6.8)
+
+  - The following Python packages are required.
+
+    - tomli >= 1.2
+    - numpy >= 1.14
+
+- py2dmat version 3.0 and later
+
+
+How to download and install
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+1. Install py2dmat
+
+   - From source files:
+
+     Download source files of py2dmat from the repository as follows:
+
+     .. code-block:: bash
+
+	$ git clone -b update https://github.com/issp-center-dev/2DMAT.git
+
+     Install py2dmat using ``pip`` command:
+
+     .. code-block:: bash
+
+	$ cd 2DMAT
+	$ python3 -m pip install .
+
+     You may add ``--user`` option to install py2dmat locally (in ``$HOME/.local``).
+
+     If you run the following command instead, optional packages will also be installed at the same time.
+
+     .. code-block:: bash
+
+	$ python3 -m pip install .[all]
+
+2. Install py2dmat-function
+
+   - From source files:
+
+     At present, the source files of 2dmat-functions are placed in ``extra`` directory of py2dmat source package. After obtaining the source files following the step 1, install 2dmat-functions using ``pip`` command as follows:
+
+     .. code-block:: bash
+
+	$ cd 2DMAT/extra/function
+	$ python3 -m pip install .
+
+     You may add ``--user`` option to install the package locally (in ``$HOME/.local``).
+
+     Then, the library of 2DMAT-Functions wil be installed.
+
+
+How to run
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In 2DMAT, the analysis is done by using a predefined optimization algorithm and a direct problem solver.
+The ways to do analyses of Functions is to write a program for the analysis with 2DMAT-Functions library and 2DMAT framework.
+The type of the inverse problem algorithms can be chosen by importing the appropriate module.
+A flexible use would be possible, for example, to include data generation within the program.
+The types of parameters and the instruction to use the library will be given in the subsequent sections.
+
+
+How to uninstall
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In order to uninstall 2DMAT-Functions and 2DMAT modules, type the following commands:
+
+.. code-block:: bash
+
+   $ python3 -m pip uninstall py2dmat-function py2dmat