<commit_before>.. pymatgen documentation master file, created by
   sphinx-quickstart on Tue Nov 15 00:13:52 2011.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Introduction
============

Pymatgen (python materials genomics) is the python library that powers the 
Materials Project (http://www.materialsproject.org). These are some of the main 
features:

1. Highly flexible classes for the representation of Element, Site, Structure objects.
2. Extensive io capabilities to manipulate many VASP input and output files 
   (http://cms.mpi.univie.ac.at/vasp/) and the crystallographic information file 
   format.  This includes generating Structure objects from vasp input and output.
3. Comprehensive tool to generate and view compositional and grand canonical phase 
   diagrams.
4. Electronic structure analyses (DOS and Bandstructure).

The public version of pymatgen is free (as in free beer) to download and to use. 
However, we would also like you to help us improve this library by making your 
own contributions as well.  These contributions can be in the form of additional 
tools or modules you develop, or even simple things such as bug reports.  Please 
contact the maintainer of this library (<EMAIL>) to find out how to include 
your contributions via github or for bug reports.

Note that pymatgen, like all scientific research, will always be a work in
progress. While the development team will always strive to avoid backward 
incompatible changes, they are sometimes unavoidable, and tough decisions have 
to be made for the long term health of the code.

   *The code is mightier than the pen.*

Latest Change Log (v1.7.3)
--------------------------

1. Beta support for additional properties on Specie (Spin) and Site 
   (magmom, charge).
2. Beta Molecule class to support molecules without periodicity.

.. toctree::
   :maxdepth: 2

   changelog

Installation
============

.. toctree::
   :maxdepth: 3

   installation

Usage
=====

.. toctree::
   :maxdepth: 2 
   
   usage


API/Reference Docs
==================

The API documentation for pymatgen is provided at the link below.

.. toctree::
   :maxdepth: 1

   modules

The API docs are generated using Sphinx auto-doc and outlines the purpose of all 
modules and classes, and the expected argument and returned objects for most 
methods. 

Citing pymatgen
===============

Some of pymatgen's functionality is based on scientific advances / principles
developed by the computational materials scientists in our team. If you 
use some of these functionality in your research, you may wish to consider citing
the following works:

pymatgen.io.vaspio_set module
-----------------------------

The parameter sets, which are optimized for high-throughput computing, are 
outlined the following work:
      
   <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, 
   <NAME>, and <NAME>. A high-throughput infrastructure for density 
   functional theory calculations. Computational Materials Science, 2011, 
   50(8), 2295-2310. doi:10.1016/j.commatsci.2011.02.023
      
pymatgen.phasediagram package
-----------------------------

The phase diagram code, in particular the grand canonical phase diagram
analysis, is based on the work of Ong et al. and are used in following works:

   <NAME>, <NAME>, <NAME>, and <NAME>. Li-Fe-P-O2 Phase Diagram from 
   First Principles Calculations. Chemistry of Materials, 2008, 20(5), 1798-1807.
   doi:10.1021/cm702327g
      
   <NAME>, <NAME>, <NAME>, <NAME>, and <NAME>. Thermal stabilities 
   of delithiated olivine MPO4 (M=Fe, Mn) cathodes investigated using first 
   principles calculations. Electrochemistry Communications, 2010, 12(3), 
   427-430. doi:10.1016/j.elecom.2010.01.010

pymatgen.entries.compatibility module
-------------------------------------

The compatibility processing, which allows mixing of GGA and GGA+U runs that 
have been calculated using the MaterialsProjectVaspInputSet or MITVaspInputSet,
is based on the following work:
      
   <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, and 
   <NAME>. Formation enthalpies by mixing GGA and GGA + U calculations. 
   Physical Review B, 2011, 84(4), 045115. doi:10.1103/PhysRevB.84.045115


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

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

<commit_msg>Update docs for changelog.<commit_after>.. pymatgen documentation master file, created by
   sphinx-quickstart on Tue Nov 15 00:13:52 2011.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Introduction
============

Pymatgen (python materials genomics) is the python library that powers the 
Materials Project (http://www.materialsproject.org). These are some of the main 
features:

1. Highly flexible classes for the representation of Element, Site, Structure objects.
2. Extensive io capabilities to manipulate many VASP input and output files 
   (http://cms.mpi.univie.ac.at/vasp/) and the crystallographic information file 
   format.  This includes generating Structure objects from vasp input and output.
3. Comprehensive tool to generate and view compositional and grand canonical phase 
   diagrams.
4. Electronic structure analyses (DOS and Bandstructure).

The public version of pymatgen is free (as in free beer) to download and to use. 
However, we would also like you to help us improve this library by making your 
own contributions as well.  These contributions can be in the form of additional 
tools or modules you develop, or even simple things such as bug reports.  Please 
contact the maintainer of this library (<EMAIL>) to find out how to include 
your contributions via github or for bug reports.

Note that pymatgen, like all scientific research, will always be a work in
progress. While the development team will always strive to avoid backward 
incompatible changes, they are sometimes unavoidable, and tough decisions have 
to be made for the long term health of the code.

   *The code is mightier than the pen.*

Latest Change Log (v1.8.0)
--------------------------

1. Support for additional properties on Specie (Spin) and Site (magmom, charge).
2. Molecule class to support molecules without periodicity.
3. Beta io class for XYZ and GaussianInput.

.. toctree::
   :maxdepth: 2

   changelog

Installation
============

.. toctree::
   :maxdepth: 3

   installation

Usage
=====

.. toctree::
   :maxdepth: 2 
   
   usage


API/Reference Docs
==================

The API documentation for pymatgen is provided at the link below.

.. toctree::
   :maxdepth: 1

   modules

The API docs are generated using Sphinx auto-doc and outlines the purpose of all 
modules and classes, and the expected argument and returned objects for most 
methods. 

Citing pymatgen
===============

Some of pymatgen's functionality is based on scientific advances / principles
developed by the computational materials scientists in our team. If you 
use some of these functionality in your research, you may wish to consider citing
the following works:

pymatgen.io.vaspio_set module
-----------------------------

The parameter sets, which are optimized for high-throughput computing, are 
outlined the following work:
      
   <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, 
   <NAME>, and <NAME>. A high-throughput infrastructure for density 
   functional theory calculations. Computational Materials Science, 2011, 
   50(8), 2295-2310. doi:10.1016/j.commatsci.2011.02.023
      
pymatgen.phasediagram package
-----------------------------

The phase diagram code, in particular the grand canonical phase diagram
analysis, is based on the work of Ong et al. and are used in following works:

   <NAME>, <NAME>, <NAME>, and <NAME>. Li-Fe-P-O2 Phase Diagram from 
   First Principles Calculations. Chemistry of Materials, 2008, 20(5), 1798-1807.
   doi:10.1021/cm702327g
      
   <NAME>, <NAME>, <NAME>, <NAME>, and <NAME>. Thermal stabilities 
   of delithiated olivine MPO4 (M=Fe, Mn) cathodes investigated using first 
   principles calculations. Electrochemistry Communications, 2010, 12(3), 
   427-430. doi:10.1016/j.elecom.2010.01.010

pymatgen.entries.compatibility module
-------------------------------------

The compatibility processing, which allows mixing of GGA and GGA+U runs that 
have been calculated using the MaterialsProjectVaspInputSet or MITVaspInputSet,
is based on the following work:
      
   <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, and 
   <NAME>. Formation enthalpies by mixing GGA and GGA + U calculations. 
   Physical Review B, 2011, 84(4), 045115. doi:10.1103/PhysRevB.84.045115


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

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


{'fraction_non_alphanumeric': 0.110781517398745, 'fraction_numerical': 0.031831146605818594, 'mean_word_length': 3.5069408740359895, 'pattern_counts': {'":': 0, '<': 53, '<?xml version=': 0, '>': 53, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6835983', 'n_tokens_mistral': 2677, 'n_tokens_neox': 2343, 'n_words': 1095}