C_ij: Semiemperical thermal elasticity

Calculate high temperature thermal elasticity in Python.

Installation

The package can be installed with pip package manager.

Install from PyPI (Python package index)

shell $ python3 -m pip install cij

Manual install

At the command prompt, one should navigate to the directory that contains the setup.py script and execute pip install .. Then, the package should be ready for use.

Usage

Command-line programs

After installation, the Cij program can be started by typing cij at your command prompt:

``` Usage: cij [OPTIONS] COMMAND [ARGS]...

Options: --version Show the version and exit. --help Show this message and exit.

Commands: extract Create data table at specific P or T. extract-geotherm Create data table at geotherm PT. fill Fill non-zero Cij terms based on symmetry. modes Plot interpolated mode frequency vs volume. plot Plot SAM-Cij calculation results. run Perform SAM-Cij calculation. run-static Calculate elastic moduli and acoustic velocities. ```

SAM-Cij calculations with cij run

Calculation settings file and example

The settings.yaml file is home to all calculation settings. One needs to specify calculation parameters, such as thermal EoS fitting parameters, phonon interpolation settings, input data location, and output variables to store in YAML format. The following is an example settings file.

```yml qha: input: input01 settings: # similar to settings in qha DT: 100 PMIN: 0 DELTAP: 0.5 NTV: 81 order: 3 staticonly: False TMIN: 0 NT: 31 DTSAMPLE: 100 DELTAPSAMPLE: 5 volumeratio: 1.2 elast: input: elast.dat settings: modegamma: interpolator: spline order: 3 symmetry: system: cubic output: pressurebase: - cij - vs - vp - bmV - bmR - bmVRH - GV - GR - GVRH - v volume_base: - p # ...

```

Input data

Input data include a QHA input data file (input01) and a static elasticity input data (elast.dat). See the paper or detailed documentation for description and the examples folder for detailed example.

Command line arguments

```txt Usage: cij run [OPTIONS] SETTINGS_FILENAME

Perform SAM-Cij calculation.

Options: --version Show the version and exit. --debug [CRITICAL|ERROR|WARNING|INFO|DEBUG|NOTSET] Logging level --help Show this message and exit. ```

Structure of the cij package

The cij package is written in Python 3. The Python source code is located in the cij sub-folder. Input for three examples in the examples sub-folder, documentation in the docs sub-folder, and the installation script setup.py.

The Python code is organized into several modules:

• cij.core: Core functionalities
  • calculator: The calculator that controls the workflow.
  • mode_gamma: Interpolate phonon frequencies and calculate mode Grüneisen parameters.
  • phonon_contribution: Calculate phonon c<sub>ij</sub><sup>ph</sup>. full_modulus – Interpolate c<sub>ij</sub><sup>st</sup> vs. V, and calculate c<sub>ij</sub><sup>S</sup> and c<sub>ij</sub><sup>T</sup>. tasks – Handles the ordering of c<sub>ij</sub><sup>ph</sup> calculation.
• cij.util: Methods used in the main program
  • voigt: Convert between Voigt (c<sub>ij</sub>) and regular (c<sub>ijkl</sub>) notations of elastic coefficients.
  • units: Handle unit conversion.
• cij.io: Input output functions and classes.
• cij.plot: Plotting functionalities.
• cij.cli: Command-line programs
  • cij run (main.py) – Perform a SAM-Cij calculation.
  • cij run-static (static.py) – Calculate static elastic properties.
  • cij extract (extract.py) – Extract calculation results for a specific T or P to a table.
  • cij extract-geotherm (geotherm.py) – Extract calculation results along geotherm PT (given as input) to a table.
  • cij plot (plot.py) – Convert output data table to PNG plot.
  • cij modes (modes.py) – Plot phonon frequency interpolation results.
  • cij fill (fill.py) – Fill all the non-zero terms for elastic coefficients given the constraint of a crystal system.
• cij.data: Data distributed with the program, e.g., the relationship between c<sub>ij</sub>’s for different crystal systems, the naming scheme for output files, etc.
• cij.misc: Miscellaneous functionalities that are not used in the main program, e.g., methods that facilitate the preparation of input files.

Author

The code in this repo is initially authored by Chenxing Luo.

Documentation

See GitHub pages.

Build status

How to cite

If you use this software in any publication, please cite:

Luo, C., Deng, X., Wang, W., Shukla, G., Wu, Z., & Wentzcovitch, R. M. (2021). cij: A Python code for quasiharmonic thermoelasticity. Computer Physics Communications, 108067. https://doi.org/10.1016/j.cpc.2021.108067

The paper is also available from arXiv: https://arxiv.org/abs/2101.12596

Licence

Released under GNU GPLv3 license.