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VASP

VASP

VASP [1] is a complex ab-initio quantum-mechanical molecular dynamics (MD) simulations package.

Important Notes

  • VASP is licensed to a vasp group. Al Anderson (aba@case.edu) and Dan Lacks (djl15@case.edu) must authorize “vasp” group privileges for any users on the cluster. 
  • If you are interested in using VASP, please get permission from vasp group and contact CCing vasp group.
  • Create different sub-directories for different jobs so as not to copy huge data back and froth.

Installed Versions

All the available versions of VASPfor use can be viewed by issuing the following command. This applies for other applications as well.
module avail vasp
output:
----------------------------------------------- /usr/local/share/modulefiles ------------------------------------------------
vasp/4.6(default)

The default version is identified by "(default)" behind the module name and can be loaded as:
module load vasp

Running VASP

Copy the directory “silica_work” from /usr/local/doc/VASP/silica_work to your home directory and go to silica_work directory.
cp -r /usr/local/doc/VASP/silica_work .
cd silica_work
You will also find pbs script file “job” in that directory along with other input files.

Serial Job

Make sure that NPAR = 1 in INCAR input file or you can delete that entry.
Submit your job:
qsub job
Excerpt from "OUTCAR" outputfile:
...
 maximum distance moved by ions :      0.76E-03
 mean value of Nose-termostat <S>:     1.000 mean value of <T> :   589.812
 mean temperature <T/S>/<1/S>  :   589.812

    WAVPRE:  VPU time    2.19: CPU time    2.19
    FEWALD:  VPU time    0.01: CPU time    0.01
    ORTHCH:  VPU time    1.63: CPU time    1.64
 Prediction of Wavefunctions ALPHA= 1.993 BETA=-0.994
    POTLOK:  VPU time    0.12: CPU time    0.12
    EDDIAG:  VPU time    2.41: CPU time    2.42
 writing wavefunctions
     LOOP+:  VPU time   34.92: CPU time   38.20
    
 General timing and accounting informations for this job:
 ========================================================
  
                  Total CPU time used (sec):      550.589
                            User time (sec):      549.169
                          System time (sec):        1.421
                         Elapsed time (sec):      685.154
  
                   Maximum memory used (kb):      122256.
                   Average memory used (kb):           0.
  
                          Minor page faults:       435336
                          Major page faults:            5
                 Voluntary context switches:          526

Parallel Job

Make sure that NPAR = #processors (nodes*ppn) in INCAR file. For example, if you you using NPAR=4, one option is to modify the #PBS line in a job file as:
#PBS -l nodes=2:ppn=2

Excerpt from "OUTCAR" outputfile. Note the speedup using 4 processors.
...
Total CPU time used (sec):    514.967
..
 

Parallel job may require more than 1gb memory and may go through many iterations. So, request the walltime appropriately. Also, follow references for parallel implementations.

Analyze and Visualize

To analyze and visualize the output, visit HPC Guide to VaspTools.

References:

[1] VASP Home: http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html
[2] For more examples, copy the VASP-examples.tar at /usr/local/src/vasp/ obtained from workshop http://www.nsc.liu.se/lcsc2005/tutor.html .
[3] http://www.cuhk.edu.hk/itsc/compenv/research-computing/organon/vasp.html