qha: A Powerful Python toolkit for quasi-harmonic approximation
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
qha is written in Python, and can be installed from Python package index (PyPI) or local source files.
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
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.,
$ 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
- Error raised about
mpfr.hfile: To solve this error,
MPFRlibraries are required to use
- On Linux, install
libmpfr-dev, for example, on Ubuntu type
apt-get install libmpfr-dev;
- On Windows,
bigfloatcan 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.
- On Linux, install
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 source code consists of three major parts.
./qhadirectory contains all the source code.
./examplesdirectory contains two examples,
./examples/siliconis the example for single-configuration calculation,
./examples/ice VIIis 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
setup.py: setup file needed for installation of the
qha Python package.
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.
qha/readers/read_input.py: This module is used to read the input file.
This folder contains files used for the command-line interface.
This folder contains files to calculate Helmholtz free energy for the multi-configuration system.
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.
this folder contains unit test files
This folder contains two examples for demonstration purpose.
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
examples/silicon/settings.yaml: This file is the computational settings file.
./examples/ice VII folder
examples/ice VII/input_01 :
input_52 are the input files of 52 distinguish configurations;
examples/ice VII/settings.yaml: This file is the computational settings file, see our online tutorial for more details.
The official documentation is hosted on our GitHub page.