Install

ElPh Requirements

Installation on local machine

Install ElPh:

pip install elph

Install gaussian:

Gaussian installation will vary group to group.
Installing Catnip

Download and install Docker

docker pull madettmann/catnip

Set environment variables

Add these lines to your configuration file (.bashrc). The following code uses example paths and must be edited according to your system.

export ELPH_CATNIP_CMD='docker run -i --rm -v $(pwd):/projects -u $(id -u):$(id -g) madettmann/catnip'
export ASE_GAUSSIAN_COMMAND='Your Gaussian Command Here < PREFIX.com > PREFIX.log'

Installation on NERSC

There is no need to install the ElPh package and its dependencies. Just these lines to your configuration file (.bashrc) in your NERSC home folder.

module use /global/common/software/m2734/ElPh/modulefiles
module load elph

Usage

Local machine

Add cif file to current working directory
Run javerage
elph --javerage
Compute the phonon modes

Refer to DCS-Flow for more information.
Run sigma

Copy FORCE_SETS, phonopy_params.yaml to your working directory
```
elph --sigma
```
Compute mobility

Write input files and define correct parameters for the specific system
```
elph --write_files
```
Run mobility
```
elph --mobility
```
Visualize sigma contribution per atom/mode

To generate the visualization per atom:
```
elph --view atoms
```
To generate the visualization per mode (n highest modes):
```
elph --view modes 3
```

NERSC

The step-by-step is basically the same as in a local machine, however add these commands to the following steps

Once all the jobs submited by the Javerage command are done, run
```
elph --read_javg
```

After all the jobs submited by the Sigma command are finished, use
```
elph --read_sigma
```