Utility scripts and programs for VASP calculations of (liquid or solid) interface systems

by

Julien Steffen, [email protected]

Andreas Mölkner, [email protected]

This repository contains a list of scripts and programs that can be used to set up, manage and evaluate VASP calcuations. It was initially designed to support calculations within the CRC 1453 CLINT (catalysis at liquid interfaces), but the scripts and programs should be general enough to use them for arbitrary VASP calculations of surface or bulk systems.

A description of all scripts/programs as well as an overview of important VASP calculations and how to do them is given in the VASP4CLINT-Wiki!

In addition to the scripts, a manual is delivered (subfolder manual), where a general overview for the setup of VASP calculations for interface systems is given besides the detailed explanation of all included scripts and programs.

The scripts and programs are grouped by the programming language of their implementation and alphabetically within their sections.

Currently included are:

• built_adsorbates.py : Place adsorbate atoms or molecules on or in surface slabs. Positions and rotations can be controlled by input files.
• build_scalms.py : Build unit cells of liquid metal alloys on a simple cubic grid (bulk, slab and cluster possible)
• check_vac.py : Checks if single atoms have departed from a surface during ML (utility for ml_long.sh!)
• eval_neb.py : Evaluates a nudged elastic band calculation, no matter if already started or finished
• integrate_dens.py : Calculates elemental concentrations in SCALMS from elemental density distributions
• manage_mlff_md.py : Starts and supervises a ML-FF trajectory of a surface slab, restarts if errors occur
• modify_poscar.py : Perform several simple operations on a POSCAR file, such as shifting its atoms, multiply the cel, transform from cartesian to internal coordinates and the other way round
• struc_insert.py : Insert one POSCAR (e.g. a molecule or crystal) into another POSCAR (e.g. a solvent)

• manage_MDs.sh : Management-tool for MD simulations plus example MD.in.
• ml_long.sh : Do VASP machine learning force field on-the-fly learning trajectories for arbitrary long times, even if the calculation cluster has a walltime limit.
• opt_long.sh : Do a VASP geometry optimization run for arbitrary long times, even if the calculation cluster has a wallime limit

• analyze_slab : Analyze trajectories of surface slab simulations
• cut_unitcell : Cut an arbitrary shaped surface slab unit cell from a given larger surface slab
• eval_bader : Evaluates and visualizes Bader charge calculations
• mlff_select : Selects basis functions for a VASP machine learning force field from given ML_AB files
• manage_cls : Prepares and evaluates core level shift calculations for many atoms in a system
• modify_xdatcar : Modify XDATCAR trajectory files: shifts, multiplications, writing of xyz files
• rdf_pca : Calculates the weight of chosen components in a time-dependent radial distribution function given from td_rdf
• split_freq : Splits a large frequency calculation into arbitrary many parts and combine the results after finishing
• td_rdf : Calculates time-dependent radial-distribution functions from a XDATCAR trajectory
• partial_dos : Extract the partial density of states for certain atoms, elements or orbitals from a DOSCAR file