VASP
| Description | ||
 |
VAMP/VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing. [more...] |
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| Site | Version (Latest: v5.2) | Notes |
| ngs.rl.ac.uk | v4.6 | Available only to licensed users |
| ngs.oerc.ox.ac.uk | v4.6 | Available only to licensed users. Not available for use via the WMS |
License
VAMP/VASP is not public domain - if you are interested in using this package please contact the VASP developers to obtain a license. You may then be able to use the code on some sites on the NGS but this is at the site's and the developers discretion. Please contact the helpdesk.
Users of this application should credit the code authors and the NGS accordingly and where applicable the specific site where the code is installed, when publishing work using NGS resources.
Running VASP on the NGS in General
VASP can be run via a number of different routes which are documented below. They all use the example inputs files which can be found here:
gsiftp://ngs.rl.ac.uk:2811/apps/vasp/examples
Please make use of the VASP STOPCAR file to control the run times of your VASP jobs on the NGS to stop your jobs at an ionic or electronic step. NGS Sites with VASP installed have batch queues with a 48 hour elapsed or 'Wall clock', limit. Vasp jobs need to exit cleanly inside this time to return valid output files. Using STOPCAR avoids wasted CPU calculating steps that are aborted when reaching the queue CPU limit and allows VASP to return valid output.
Using the STOPCAR file it is possible to stop VASP during the program execution. If the STOPCAR file contains the line:
LSTOP = .TRUE.
then VASP stops at the next ionic step. On the other hand, if the STOPCAR file contains the line:
LABORT = .TRUE.
VASP stops at the next electronic step, i.e. WAVECAR and CHGCAR might contain non converged results. If possible use the first option.
- Submission Using the UI/WMS
To submit a VASP job via the WMS, login to the UI and create a JDL file as below, replacing your ngs ID on the UI for ngsxxxx, then submit using:
glite-wms-job-submit -o jobIDs -a vasp.jdl
Type = "Job"; JobType = "mpich"; Executable = "/usr/ngs/VASP_4_6"; CpuNumber = 16; StdOutput = "vasp.out"; StdError = "stderr.out"; InputSandbox = {"INCAR","KPOINTS","OSZICAR","PO","POSCAR","POTCAR"}; InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/vasp"; OutputSandbox = {"vasp.out","stderr.out","IBZKPT","XDATCAR","PCDAT","DOSCAR","CONTCAR","CHG","WAVECAR","vasprun.xml", "OUTCAR","EIGENVAL","CHGCAR"}; # Note vasp/outputs directory must exist before the job is submitted. OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/vasp/outputs"; # # Forces to job to run on ngs.rl.ac.uk Requirements = ( member("NGS-UEE-VASP_4_6", other.GlueHostApplicationSoftwareRunTimeEnvironment) ); Rank = other.GlueCEStateFreeCPUs; MyProxyServer = "myproxy.ngs.ac.uk"; ShallowRetryCount = -1; - NGS Web Portal Submission
There is currently no Portal template for running VASP. However you can either create your own or contact the NGS helpdesk for help in doing so.
- Submission Using Globus
Eg To submit a VASP job on ngs.rl.ac.uk use the following command (one line. You should not include the backslashes):
globus-url-copy -cd -rp file:///$PWD/INCAR gsiftp://ngs.rl.ac.uk/home/ngsxxx/vasp/INCAR
globus-url-copy -cd -rp file:///$PWD/KPOINTS gsiftp://ngs.rl.ac.uk/home/ngsxxx/vasp/KPOINTS
(repeat for OSZICAR, PO, POSCAR, POTCAR files) \
globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf '(executable=/usr/ngs/VASP) \
(stdout=vasp.out)(stderr=std.err)(jobtype=mpi)(count=16)('
or
globus-job-run ngs.rl.ac.uk/jobmanager-lsf -np 16 -d vasp /usr/ngs/VASP
globus-url-copy -rp gsiftp://ngs.rl.ac.uk/vasp/output.file file:///$PWD/output.file
- This runs the default version. To run e.g. 4.6 use VASP_4_6 instead of VASP.
Compilation Information
ngs.rl.ac.uk: PGI 10.0 , ScaliMPI
Further Information
Applications Support
The NGS cannot offer scientific support for applications. However if you require further information or believe there is something wrong with the installation, please contact the NGS support centre.
Acknowledgements
Please note: When publishing work based on use of the NGS, users should acknowledge both the authors of any programs used (see the individual program web sites, or contact the authors directly) and the NGS directly using the following line:
"The authors would like to acknowledge the use of the UK National Grid Service in carrying out this work"
This line must also accompany any use of the NGS logos.
