Dfttk

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Revised dfttk/script/run_dfttk.py
made workflow "get_wf_gibbs" run on "robust" with get_wf_gibbs_robust
changed test module from get_wf_gibbs into get_wf_gibbs_robust

================

(Contributor: `YiWang`_, `mxf469`_)

- Change List:
- added codes in the dfttk/scripts directory:
- run_dfttk_ext.py
- handle the argumetns for the thelec and thfind modules

- added python code in the dfttk directory:
- pyfind.py
- database search engine

- pythelec.py
- for compatibiliy with Yphon
- generating the majority of thermodynamic properties, such as thermal expansion coefficient, Seebech coefficients, Lorenz number etc

- pyphon.py for
- calculate the phonon contributions to the various thermodynamic properties

- added python code in the dfttk/analysis directory:
- database
- for plot phonon dispersions for all crystalline systems

- ywutils.py
- general utils code

- ywplot.py
- for plots of ~20 different phonon and thermodynamic properties in the png format

* made Yphon compatibile with phonopy
- added codes in the CRO-soc directory:
- phonopy2yphon, phonopy2yphon.py
- convert the phonopy force constant matrix in hdf5 format into superfij.out format used by Yphon

- changed codes:
- in the dfttk/scripts directory:
- run_dfttk.py
- added the following lines aimed to handle the argumetns for the thelec and thfind modules

extension by Yi Wang, finalized on August 4, 2020
-----------------------------------
from dfttk.scripts.run_dfttk_ext import run_ext_thelec
run_ext_thelec(subparsers)

- in the dfttk/analysis directory:
- debye.py is renamed as debye_ext.py
- to include the vibrational entropy (S_vib) and heat capacity (C_vib) into the "qha" MongoDB collection

- quasiharmonic.py:
- copy the S_vib and C_vib from the "phonon" collection into the "qha_phonon" MongoDB collection

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New features

(Contributor: `bocklund`_ , Peng_Gao, `hitliaomq`_ )

* The relax scheme is optimized. (from ``ISIF=3`` to ``ISIF=2`` followed by ``ISIF=4``) (Peng_Gao)
* Change the static workflow to dynamic workflow. (``EVcheck_QHA.py`` increase the data points atomately if the fitting of initial points is incorrect) (Peng_Gao)
* Support run dfttk by command. (Add ``dfttk run [options]``) (`hitliaomq`_)
* Support configrate dfttk automately. (Add ``dfttk config [options]``) (`hitliaomq`_)
* Documents' enhance. (`hitliaomq`_)
* Bug fix. (Including `8`_ ) (`bocklund`_, Peng_Gao, `hitliaomq`_)

.. _`8`: https://github.com/PhasesResearchLab/dfttk/issues/8

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Initial release. Includes

(Contributor: `bocklund`_, `mxf469`_)

* Gibbs workflow for stable structures
* Analysis code and libraries for calculation quasiharmonic Gibbs energies with 0K, vibrational and thermal electronic contributions
* Useful utilities for interfacing with structure, calculations and the Materials Project

.. _`bocklund`: https://github.com/bocklund
.. _`mxf469`: https://github.com/mxf469
.. _`hitliaomq`: https://github.com/hitliaomq
.. _`YiWang`: https://github.com/yiwang62