Package: clims
Table of Contents[[TOC]]climsCommand-line interface for materials simulations.Basically pulls together usefull python packages of the materials simulation community:ASEspglib(cyrstal symmetry properties)phonopy(phonon properties from finite-differences)This package is tailored for the needs of FHI-aims.System requirementsA python 3 installation with a versionpython>=3.7is required. To check your python version type:python --versionIn the following instructions on some systems it may be needed to usepython3andpip3.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 installIt is best to installclimsin a virtual environment. May not always true, e.g. on computing clusters.Install/Activate virtualenv (optional)Make sure thatvirtualenvis installed:pip show virtualenvIf not installed, install it:pip install --user virtualenvGo into the root directory of clims. Initialize the virtual environment:python -m venv envActivate the virtual environment:source env/bin/activateYou should now see(env)in at the beginning of your command line.Install climsInstall 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 bypipcan 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 -vvTroubleshootingInstallation under CentOS: In order for this installation to work, we noticed that the_ctypesmodule is required. This only works if the librarylibffi(including development headers - sometimes calledlibffi-devorlibffi-devel) is also required and the computer's python version must have been built with support forlibffi-dev(orlibffi-devel). If support forlibffiheaders 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 climsThe most important thing to set is the path to the FHI-aims species defaults:clims-configure --species-path <your/path/to/FHIaims/species_defaults>FeaturesAfter successful installation the following commands should be available in the terminal:clims commanddescriptionclims-unit-cell-infoGet brief overview of input structure, if periodic: generate primitive or conventional unit cell.clims-supercellGenerate supercell.clims-real2frac,clims-frac2realConvert atomic coordinates of periodic structure from Cartesian to real and vice versa.clims-phonopy-initialize,clims-phonopy-postprocessGenerate supercell structures with displaced atoms (initialize) and read forces after FHI-aims calculation to plot phonon DOS (postprocess).clims-wigner-seitz-clusterConstructs a Cluster of the shape of the Wigner-Seitz cell.clims-aimsplotFamous aimsplot script for plotting band structure and DOS from FHI-aims.clims-xyplotSimple X-Y plot of data files.clims-prepare-runCreatecontrol.intemplate based on ageometry.infile. If requested a submission file is provided, too.clims-configureConfigure Path to exectutable and species defaults directory, mpi run command, submission header. Needed e.g. forclims-prepare-runclims-testsuiteCreate a testsuite of all defined input parameter combinations.