clims 0.4.2

Command-Line Interface for Materials Simulations

Table of Contents

[[TOC]]

clims

Command-line interface for materials simulations.

Basically pulls together usefull python packages of the materials simulation community:

• ASE
• spglib (cyrstal symmetry properties)
• phonopy (phonon properties from finite-differences)

This package is tailored for the needs of FHI-aims.

System requirements

A python 3 installation with a version python>=3.7 is required. To check your python version type:

python --version

In the following instructions on some systems it may be needed to use python3 and pip3.

On a computer with such an installation, the below commands will install a number of other useful community packages for atomistic simulations as prerequisites, most importantly, ASE, spglib, phonopy, as well as several others.

Please also see the troubleshooting notes below in case you encounter a particular, missing prerequisite during the installation process.

How to install

It is best to install clims in a virtual environment. May not always true, e.g. on computing clusters.

Install/Activate virtualenv (optional)

Make sure that virtualenv is installed:

pip show virtualenv 

If not installed, install it:

pip install --user virtualenv

Go into the root directory of clims. Initialize the virtual environment:

python -m venv env

Activate the virtual environment:

source env/bin/activate

You should now see (env) in at the beginning of your command line.

Install clims

Install clims (make sure that you are in the root director of clims (where this README is)) with:

pip install --user .

If all goes well, you will have a working clims installation after this step. If something does not work (for instance, if a particular installation prerequisite that should be part of python is missing), unfortunately the error messages written by pip can be somewhat cryptic. As an approximate rule, the final line of a python error message often identifies the piece that was missing.

To test your installation you can run:

pytest -vv

Troubleshooting

Installation under CentOS: In order for this installation to work, we noticed that the _ctypes module is required. This only works if the library libffi (including development headers - sometimes called libffi-dev or libffi-devel) is also required and the computer's python version must have been built with support for libffi-dev (or libffi-devel). If support for libffi headers is not present, then someone will unfortunately have to rebuild and reinstall the python >= 3.7 installation on the computer you are using from scratch.

How to configure clims

The most important thing to set is the path to the FHI-aims species defaults:

clims-configure --species-path <your/path/to/FHIaims/species_defaults>

Features

After successful installation the following commands should be available in the terminal:

clims command	description
clims-unit-cell-info	Get brief overview of input structure, if periodic: generate primitive or conventional unit cell.
clims-supercell	Generate supercell.
clims-real2frac,clims-frac2real	Convert atomic coordinates of periodic structure from Cartesian to real and vice versa.
clims-phonopy-initialize, clims-phonopy-postprocess	Generate supercell structures with displaced atoms (initialize) and read forces after FHI-aims calculation to plot phonon DOS (postprocess).
clims-wigner-seitz-cluster	Constructs a Cluster of the shape of the Wigner-Seitz cell.
clims-aimsplot	Famous aimsplot script for plotting band structure and DOS from FHI-aims.
clims-xyplot	Simple X-Y plot of data files.
clims-prepare-run	Create control.in template based on a geometry.in file. If requested a submission file is provided, too.
clims-configure	Configure Path to exectutable and species defaults directory, mpi run command, submission header. Needed e.g. for clims-prepare-run
clims-testsuite	Create a testsuite of all defined input parameter combinations.