VASPTools
VASPTools
vasptools [1] is a python module which define the class VaspRun and provide a set of functions in order to do simple post treatments on VASP calculations. The main features are the following :
extract or plot density of state
extract or plot bands
get structural data
control convergence
simple operations on CHGCAR file (split, sum)
Installed Versions
All the available versions of VaspTools for use can be viewed by issuing the following command. This applies for other applications as well.
module avail vasptools
output:
---------------------- /usr/local/share/modulefiles -------------------------
vasptools/2014(D)
The default version is identified by "(D)" behind the module name and can be loaded as:
module load vasptools
The other versions of Gaussian can be loaded as:
module load vasptools/<version>
Running VaspTools in HPC
Copy the VASP input files from the workshop VASP fcc Ni [2] included at
cp -r /usr/local/doc/MolecularModeling/vasptools .
cd vasptools
Generate the VASP output files running vasp (details in HPC Guide to VASP) through batch submission
sbatch job.slurm
Besides other output files such as KPOINTS, OUTCAR, POSCAR etc you will also see the xml file "vasprun.xml" that vasptools uses for analysis and visualization.
Analysis and Visualization
Request a compute node
srun --x11 --pty bash
Load the vasptools module
module load vasptools
Run Python, import vasptools, and run vasprun [3]
>>> import vasptools
>>> run = vasptools.VaspRun("vasprun.xml")
output:
...
# Read final structure
* a = 2.49609 * alpha = 60.000
* b = 2.49609 * beta = 60.000
* c = 2.49609 * gamma = 60.000
...
MAGMOM = 1.00000000 ISTART = 0 SYSTEM = fcc ENCUT = 270.0
ICHARG = 2 PREC = medium ISPIN = 2
ISMEAR = -5 LORBIT = F
...
* atom number : 1
* type number : 1
* atom list : Ni
...
Atom Ni :
weight : 58.69
Valence electrons : 10
type : 1
Pseudopotential : PAW_PBE Ni 06Sep2000
Plot Density of States and Energy Bands
getDOS &
getBandes &
output:
Create a VMD file "vis.vmd" and open it with VMD Software. See VMD details at HPC Guide to VMD and Molecular Modeling and Visualization @HPC
visVMD -u -n 5x5x5
References:
[1] VASPTools Home
[2] VASP Workshop