VASP Tools
Peter’s collection of small, but useful, VASP scripts. Some of these may be found on NSC’s computers by loading the “vasptools” module.
vaspcheck
The “vaspcheck” script scans your input files and looks for common errors such as: forgetting to copy CONTCAR to POSCAR, misspelled INCAR tags, and various inconsistent configurations such as having N atoms but only N-x magnetic moments specified. If you supply it with information about the intended number of cpu cores and nodes that you will run on, it will also check the NPAR and KPAR values and warn if they are unreasonable.
An alpha version is available in the “vasptools” module on Triolith, and once the script has become more robust, I will make a version available for download here. The idea is to integrate it with the queue system in the future, so that your VASP jobs will be automatically checked when running the “sbatch” command.
Install: Click here to download to the Python script. Install it by putting it in a folder in your $PATH (such as~/bin) and then do:
mv vaspcheck-standalone.py vaspcheck
chmod u+x vaspcheck
This should allow you to write “vaspcheck” in any job folder.
grad2
The gradient program is used to quickly get an overview of VASP geometry optimization runs. It also works for molecular dynamics. It parses the OUTCAR file and writes a one-line summary per ionic step, including average forces and run-time per step. The output looks like this:
$ grad2 OUTCAR
Step 1 Energy: -42.794090 Log|dE|: +1.631 Avg|F|: 1.720176 Max|F|: 2.710237 SCF: 15 Time: 0.52m
Step 2 Energy: -43.336931 Log|dE|: -0.265 Avg|F|: 0.513256 Max|F|: 0.696803 SCF: 9 Time: 0.32m
Step 3 Energy: -43.384337 Log|dE|: -1.324 Avg|F|: 0.095940 Max|F|: 0.178813 SCF: 7 Time: 0.24m
Step 4 Energy: -43.387267 Log|dE|: -2.533 Avg|F|: 0.050399 Max|F|: 0.071963 SCF: 6 Time: 0.20m
Step 5 Energy: -43.388250 Log|dE|: -3.007 Avg|F|: 0.043184 Max|F|: 0.061866 SCF: 4 Time: 0.13m
Step 6 Energy: -43.390384 Log|dE|: -2.671 Avg|F|: 0.030630 Max|F|: 0.047413 SCF: 5 Time: 0.18m
Step 7 Energy: -43.392498 Log|dE|: -2.675 Avg|F|: 0.003760 Max|F|: 0.005849 SCF: 6 Time: 0.20m
Step 8 Energy: -43.392509 Log|dE|: -4.959 Avg|F|: 0.001285 Max|F|: 0.001861 SCF: 3 Time: 0.09m
The Log\|dE\| is the base-10 logarithm of the absolute value of the energy difference between steps, essentially the number of “stable” decimals in the total energy, i.e. for a VASP run with EDIFF=1.0E-5, Log\|dE\| should approach -5 for convergence.
If your terminal has colors, each line will be color-coded with red color signalling convergence problems, and green color corresponding to energy convergence having been reached (as judged by the EDIFF tag in the INCAR file.)
Install: Click here to download to the Python script (version 2012-01-07). Install it by putting it in a folder in your $PATH (such as~/bin) and then do:
mv grad2.py grad2
chmod u+x grad2
This should allow you to write “grad2 OUTCAR” in any job folder.
vasp2cif
The vasp2cif program creates a CIF-file from a POSCAR/CONTCAR file, which can be used for visualization in graphical applications, such as VESTA. Note that it will not preserve symmetries from VASP – the output CIF is always in P1 symmetry. If there is no POTCAR file available, the script has a flag (“–elements”) whereby you can specify the atomic species.
Install: Click here to download to the Python script (version 2012-12-15). Install it by putting it in a folder in your $PATH (such as~/bin) and then do:
mv vasp2cif.py vasp2cif
chmod u+x vasp2cif
This should allow you to write e.g. “vasp2cif CONTCAR” in any job folder.
cif2vasp
For CIF to VASP input conversion, a recommend a program by Torbjörn Björkman called cif2cell, which can generate input from CIF files for many ab initio programs, including VASP.
If anyone is interested in doing high-performance CIF to VASP conversion with optimized C code, I can provide source code to a CIF lexer written with the Ragel state machine compiler and CIF parser written with Lemon. Unfortunately, the tool I built to do CIF to VASP with this framework does not compile correctly anymore on recent platforms, so I cannot put up any binaries for download. You can email me at pla@nsc.liu.se if you want to give it a try.
supersize
Yet another script to make supercells out of VASP’s POSCAR/CONTCAR files. It is basically a wrapper around the corresponding feature in ASE.
It works like this:
$ supersize POSCAR 4x4x4
And you get a new POSCAR file called “POSCAR.4x4x4” containing the supercell repeated 4 times in a,b,c directions. You can achieve the same effect with three lines of Python code in ASE:
import ase.io.vasp
cell = ase.io.vasp.read_vasp("POSCAR")
ase.io.vasp.write_vasp("POSCAR.4x4x4",cell*(4,4,4), label='444supercell',direct=True,sort=True)
The script is a little bit more elaborate, however, since it includes error checks.