Package: cij
Cij: Semiemperical thermal elasticityCalculate high temperature thermal elasticity in Python.InstallationThe package can be installed withpippackage manager.Install from PyPI (Python package index)$python3-mpipinstallcijManual installAt the command prompt, one should navigate to the directory that contains thesetup.pyscript and executepip install .. Then, the package should be ready for use.UsageCommand-line programsAfter installation, the Cij program can be started by typingcijat 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 withcij runCalculation settings file and exampleThesettings.yamlfile 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.qha:
  input: input01
  settings:
    # similar to settings in qha
    DT: 100
    P_MIN: 0
    DELTA_P: 0.5
    NTV: 81
    order: 3
    static_only: False
    T_MIN: 0
    NT: 31
    DT_SAMPLE: 100
    DELTA_P_SAMPLE: 5
    volume_ratio: 1.2
elast:
  input: elast.dat
  settings:
    mode_gamma:
      interpolator: spline
      order: 3
    system: cubic
output:
  pressure_base:
    - cij
    - vs
    - vp
    - bm_V
    - bm_R
    - bm_VRH
    - G_V
    - G_R
    - G_VRH
    - v
  volume_base:
    - p
    # ...Input dataInput 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 theexamplesfolder for detailed example.Command line argumentsUsage: 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 thecijpackageThe cij package is written in Python 3. The Python source code is located in thecijsub-folder.
Input for three examples in theexamplessub-folder, documentation in thedocssub-folder, and the installation scriptsetup.py.The Python code is organized into several modules:cij.core: Core functionalitiescalculator: The calculator that controls the workflow.mode_gamma: Interpolate phonon frequencies and calculate mode Grüneisen parameters.phonon_contribution: Calculate phononcijph.
full_modulus – Interpolatecijstvs.V, and calculatecijSandcijT.
tasks – Handles the ordering ofcijphcalculation.cij.util: Methods used in the main programvoigt: Convert between Voigt (cij) and regular (cijkl) notations of elastic coefficients.units: Handle unit conversion.cij.io: Input output functions and classes.cij.plot: Plotting functionalities.cij.cli: Command-line programscij 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 specificTorPto a table.cij extract-geotherm(geotherm.py) – Extract calculation results along geothermPT(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 betweencij’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.AuthorThe code in this repo is initially authored byChenxing Luo.DocumentationSeeGitHub pages.Build statusLicenceReleased underGNU GPLv3license.