A pure Python package for calculating thermodynamic properties under quasi-harmonic approximation, using data from ab-initio calculations
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README.md

qha: A Powerful Python toolkit for quasi-harmonic approximation

[TOC]

Stable docs

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.

Please do not use Python 3.7.x at this moment, since it contains breaking changes and many Python packages don’t support Python 3.7.x yet. We may support Python 3.7.x in the future.

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 .

Trouble shooting of installation

  1. Error raised about mpfr.h file: To solve this error, GMP and MPFR libraries are required to use bigfloat package.
    • On Linux, install libmpfr-dev , for example, on Ubuntu type apt-get install libmpfr-dev;
    • On Windows, bigfloat can be installed from the binary file, please check “Unofficial Windows Binaries for Python Extension Packages”, download the version suitable for the system, for example, for a 64-bit system, use pip to install it pip(3) install /the/path/to/bigfloat‑0.3.0‑cp36‑cp36m‑win_amd64.whl;
    • On macOS, install these libraries via brew install mpfr. Of course, you need the Homebrew package manager installed to run this command.

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

Structure of the qha package

The qha source code consists of three major parts.

  1. ./qha directory contains all the source code.

  2. ./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.

The ./qha/ folder

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 $(T, V)$ grid to $(T, P)$ grid;

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.

The ./qha/readers folder

qha/readers/__init__.py

qha/readers/read_input.py: This module is used to read the input file.

The ./qha/cli folder

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

The ./qha/multi_configurations folder

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.

The ./qha/tests folder

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

The ./examples/ folder

This folder contains two examples for demonstration purpose.

The ./examples/silicon folder

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.

The ./examples/ice VII folder

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

GNU General Public License v3

Documentation

The official documentation is hosted on our GitHub page.