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chazeon committed Jan 2, 2021
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## Installation

### Additional information

Pint need to be updated to the GitHub master branch for the code to work with atomic units, so it is installed from GitHub.
The package can be installed with `pip` package manager.

## Usage

### Configuration file
### Command-line programs

The packge is shipped with the following command-line programs:

- **`qha-cij`** - Perform SAM-Cij calculation.
- **`qha-cij-static`** - Calculate elastic moduli and acoustic velocities.
- **`qha-cij-extract`** - Extract the value and create table for multiple variables at spcific P or T.
- **`qha-cij-fill`** - Fill non-zero Cij terms based on symmetry.
- **`qha-cij-modes`** - Plot interpolated mode frequency vs volume.
- **`qha-cij-plot`** - Plot SAM-Cij calculation results.

And is avaliable as sub-commands of the `cij` program:


```
Usage: cij [OPTIONS] COMMAND [ARGS]...
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
extract Extract the value and create table for multiple variables at...
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 `qha-cij` or `cij run`

#### Configuration file

```yml
qha:
input: input01
settings:
# QHA INPUT FILE HERE ...
# QHA settings here ...
elast:
input: elast.dat
settings:
mode_gamma:
# Refer to cij.core.mode_gamma
interpolator: spline
order: 5
cij_keys: [11, 22, 33, 12, 13, 23, 44, 55, 66]
disable_phonon_contribution: False
settings:
mode_gamma:
interpolator: spline
order: 5
symmetry: cubic
```
### Command line arguments
#### Command line arguments
```txt
usage: qha-cij [-h] [-V] CONF.yml
Usage: cij run [OPTIONS] SETTINGS_FILENAME

positional arguments:
CONF.yml name of the configuration file
Perform SAM-Cij calculation.

optional arguments:
-h, --help show this help message and exit
-V, --version show program's version number and exit
Options:
--version Show the version and exit.
--debug [CRITICAL|ERROR|WARNING|INFO|DEBUG|NOTSET]
Logging level
--help Show this message and exit.
```

## Documentation

See [GitHub pages][1].

[1]: https://mineralscloud.github.io/qha-cij

## Author

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

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