qha: A Powerful Python toolkit for quasi-harmonic approximation
[TOC]
Contributors
This repository is now maintained by Tian Qin and Qi Zhang. Thanks to the contribution from Chenxing Luo.
How to cite
The associated paper is published on Computer Physics Communications.
Please cite this article as: T. Qin, Q. Zhang, R.M. Wentzcovitch et al., qha: A Python package for quasiharmonic free energy calculation for multi-configuration systems, Computer Physics Communications (2018), https://doi.org/10.1016/j.cpc.2018.11.003.
Quick start: installation
Python environment
qha
is written in Python, and can be installed from Python package index (PyPI) or local source files.
Python 3 can be downloaded from its official website for systems including Windows, macOS, and Linux, please check more details on Python 3 documentation.
To install qha
, currently, Python 3.6.x distributions are recommended.
Where to get it
Binary installers for the latest released version are available at the PyPI.
# use PyPI
$ pip install qha
Dependencies
Installation from sources
The source code is currently hosted on GitHub. Please go to the “releases” page to download the tagged releases. Unzip the downloaded sources, go to the top-level directory (e.g., /path/to/repo/qha
), run
$ pip install .
Notice that you have to use Python version > 3.6.x to install. If you want to install qha
in development mode, instead run
$ pip install -e .
Checking the examples
To run the examples, go to examples/ice VII/
or examples/silicon/
directories and type in terminal:
$ qha run /path/to/settings.yaml
If you want to plot your results, in the same folder, run
$ qha plot /path/to/settings.yaml
qha
package
Structure of the The qha
source code consists of three major parts.
-
./qha
directory contains all the source code. -
./examples
directory contains two examples,./examples/silicon
is the example for single-configuration calculation,./examples/ice VII
is the example for multi-configuration calculation.
The brief of the organization of these directories follows as below:
./
The main folder This main folder contains three folders, license file, readme file, and setup file.
LICENSE.txt
: The license file attached with the qha
code;
README.md
: Readme file of the code, it would be better to view it in a Markdown editor, e.g., Typora;
setup.py
: setup file needed for installation of the qha
Python package.
./qha/
folder
The qha/__init__.py
: Tells Python interpreter that this is a Python package;
qha/calculator.py
: Perform single-, multi-configuration calculations, one of the most crucial modules in this code;
qha/fitting.py
: Perform the Birch—Murnaghan (BM) equation-of-state (EOS) fitting;
qha/grid_interpolation.py
: Find the most suitable volume grid to perform the BM EOS fitting;
qha/plotting.py
: A simple module to plot the calculated physical properties;
qha/settings.py
: Define some computational settings for the calculation;
qha/single_configuration.py
: Calculate the Helmholtz free energy for a single-configuration system;
qha/statmech.py
: Define some useful statistical mechanics functions;
qha/thermodynamics.py
: Derive the internal energy($U$), enthalpy($H$), and Gibbs free energy ($G$) from the calculated Helmholtz free energy ($F$) via basic thermodynamics relationship;
qha/tools.py
: Define some miscellaneous functions used in the code, e.g., function used to perform Lagrange interpolation;
qha/type_aliases.py
: Define some types for annotation in the code;
qha/unit_conversion.py
: A module to convert units used in the calculation;
qha/v2p.py
: Contain the function v2p
used to convert calculated properties on
qha/input_maker.py
: Generate the input file for qha
from results obtained from ab initio calculation;
qha/out.py
: Functions used to write calculated properties into files.
./qha/readers
folder
The qha/readers/__init__.py
qha/readers/read_input.py
: This module is used to read the input file.
./qha/cli
folder
The This folder contains files used for the command-line interface.
qha/cli/__init__.py
qha/cli/converter.py
qha/cli/handler.py
qha/cli/parser.py
qha/cli/plotter.py
qha/cli/runner.py
./qha/multi_configurations
folder
The This folder contains files to calculate Helmholtz free energy for the multi-configuration system.
qha/multi_configurations/__init__.py
qha/multi_configurations/different_phonon_dos.py
: Work with qha/calculator.py
to calculate Helmholtz free energy for the multi-configuration system with different phonon density of states (VDOS) for each configuration;
qha/multi_configurations/same_phonon_dos.py
: Work with qha/calculator.py
to calculate Helmholtz free energy for multi-configuration system with the same VDOS for all configurations.
./qha/tests
folder
The this folder contains unit test files
qha/tests/__init__.py
qha/tests/test_overall_run.py
qha/tests/test_read_input.py
qha/tests/test_samevdos_overall.py
qha/tests/test_single_configuration.py
qha/tests/test_unit_conversion.py
./examples/
folder
The This folder contains two examples for demonstration purpose.
./examples/silicon
folder
The This folder conations an example to perform the single-configuration calculation. Also, an example to generate the input file for the qha
code is included, check examples/silicon/make_input/README
for details;
examples/silicon/input
: The input file for qha
;
examples/silicon/settings.yaml
: This file is the computational settings file.
./examples/ice VII
folder
The examples/ice VII/input_01
: input_01
through input_52
are the input files of 52 distinguish configurations;
examples/ice VII/input_02
examples/ice VII/input_03
…
examples/ice VII/input_52
examples/ice VII/settings.yaml
: This file is the computational settings file, see our online tutorial for more details.
License
Documentation
The official documentation is hosted on our GitHub page.