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https://github.com/mineralscloud/cij
Semiemperical quasiharmonic thermal elasticity
https://github.com/mineralscloud/cij
ab-initio elasticity high-pressure phonon python scientific scientific-computing solid-state-physics
Last synced: about 1 month ago
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Semiemperical quasiharmonic thermal elasticity
- Host: GitHub
- URL: https://github.com/mineralscloud/cij
- Owner: MineralsCloud
- License: gpl-3.0
- Created: 2019-03-21T20:26:02.000Z (almost 6 years ago)
- Default Branch: dev
- Last Pushed: 2024-04-19T14:17:43.000Z (9 months ago)
- Last Synced: 2024-11-16T23:48:08.951Z (about 2 months ago)
- Topics: ab-initio, elasticity, high-pressure, phonon, python, scientific, scientific-computing, solid-state-physics
- Language: Python
- Homepage: https://mineralscloud.github.io/cij
- Size: 10.2 MB
- Stars: 15
- Watchers: 4
- Forks: 5
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Citation: CITATION.cff
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README
# Cij: 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
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
symmetry:
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 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`](./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 *cij*ph.
full_modulus – Interpolate *cij*st vs. *V*, and calculate *cijS* and *cijT*.
tasks – Handles the ordering of *cij*ph calculation.
- **`cij.util`**: Methods used in the main program
- `voigt`: 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 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 *cij*’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][1].
[1]: https://github.com/chazeon
## Documentation
See [GitHub pages][2].
[2]: https://mineralscloud.github.io/cij
## Build status
[](https://codecov.io/gh/MineralsCloud/cij)
[](https://pypi.org/project/cij/)
[](https://pypi.org/project/cij/)
## 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](./LICENCE) license.