ScriptsForVASP

Making life easier using scripting languages (Bash and Python) to facilitate multiple VASP simulation jobs preparation, submission and analysis.

NOTE

Due to the specific workflow related nature of this project, it did not and perhaps will not be of too much use to most VASP users. Since it has come to a level handy enough to suit my own research need, I will not actively maintain this project anymore, and the documentation will not be added either. However, I selected some of the generally useful features, like plotting, fitting, POSCAR manipulation and reorganized them, made a Python package out of it, named pydass_vasp. It should be interesting to you. Just take a look.

Introduction

There are multiple ways to carry out VASP calculations. Contrary to the Pythonic scheme the famous ASE uses, this project does things in an old-fashioned way, providing a collection of scripts, written in Bash, and accompanying them with scripts written in Python, in the same directory, with careful use of file names and input arguments, and letting users add this single directory into their PATH environmental variable to have direct access. The scripts will be used as executables. This approach is less comprehensive than the one ASE uses, but it is more file- and directory-wise convenient thanks to the fact that Bash is a shell scripting language. Standalone Python scripts (with capitalized first letter) can be imported in an Python interpreter.

Scripts structure

Python scripts

• StrainApplier.py - to add strain to the cell lattice vectors in POSCAR for a series of runs, determining the value of a combination of elastic constants
• IonsRotator.py - to rotate ions in selected lines in POSCAR at a certain point, around a certain axis, to a certain angle

Bash convenient scripts

• CellInfo.sh [rwigs] - to show the important info from OUTCAR. With the optional rwigs, displays the RWIGS values for different species to 100 % fill the cell
• DelFiles.sh [DIRECTORY] - to delete the output files, default to current directory
• SwapFileNames.sh A B - to exchange the names of two files A and B
• M [DIRECTORY] - to submit the job in a specified directory or default to the current directory

Bash job submission scripts

• Prepare.sh DIRECTORY - a fast way to create a directory with necessary input files
• SequenceTest.sh TEST_TYPE [OPTIONS] - to create a series of runs, performing a routine test
• SequenceDisp.sh TEST_TYPE - to do the post-analysis of a series of runs described above and determine physical quantities
• Elastic.sh TEST_TYPE CRYST_SYS [OPTIONS] - to do a full set of independent elastic constant determination runs
• Electronic.sh TEST_TYPE [OPTIONS] - to carry out electronic-related runs
• BatchElements.sh [OPTIONS] 'COMMANDS' - a wrapper script to execute the above routines and almost random Bash code for multiple species

Supportive scripts

These are used by Bash scripts and better left unvisited.

• _qsub_replacer.sh - to do some replacement to the job submission file so that it corresponds to the right working directory. Machine dependent
• _sequence_fit_plot.py - to perform different fitting techniques, including Birch-Murnaghan equation of state and polynomial
• _elastic_solver.py - to solve the independent elastic constants from the same number of combination runs with linear algebra
• _cell_info_solver.py - to obtain the RWIGS values for different species to 100 % fill the cell