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vasp-ver-bsub <version> myscript.py vasp-ver-bsub-native <version> -q suncat-test -n 2 -o junk.log |
See the bottom of this page for available versions.
The first is the ASE style. The second is native VASP style, and assumes all input files (POTCAR, INCAR, etc.) are created by the user are in the current directory. POTCARs can be assembled from the directory /nfs/slac/g/suncatfs/sw/vasp/pseudo52.
Thanks to Joel Varley for providing this BEEF example.
#!/usr/bin/env python #LSF -q suncat-test #LSF -n 2 #LSF -o std.out #LSF -e std.err from ase import * from ase import io from ase.lattice.spacegroup import crystal from ase.io.trajectory import PickleTrajectory from ase.optimize import BFGS, QuasiNewton from ase.units import kJ, Hartree from ase.utils.eos import EquationOfState from ase.calculators.vasp import Vasp from ase.data.molecules import molecule as molecule from ase.vibrations import Vibrations import os, sys ############################################################################# ############################################################################# name = 'H' a = 5.0 atoms = Atoms([Atom('H',(a/2, a/2, a/2))], cell=(a, a, a)) # note that BEEF is only available in suncat vasp version 2 (v2) or later. xcf = 'BEEF' encut = 400 nkp = 1 sigma = 0.05 ibrion= -1 # no atomic displacement done by VASP (only ASE) ispin = 1 # NOT spin-polarized (ispin=2 for SP) # some types of GGA vaspgga = {'RPBE' : 'RP', 'PBE' : 'PE', 'AM05' : 'AM', 'PBEsol' : 'PS', 'PW86' : 'PW', 'PW91' : '91', 'BEEF' : 'BF', 'GGA' : '--', } if xcf=='BEEF': luse_vdw=True if not (os.path.exists('vdw_kernel.bindat')): os.symlink('/nfs/slac/g/suncatfs/sw/vasp/vdw_kernel.bindat','vdw_kernel.bindat') else: luse_vdw=False # VASP uses LDA or PBE PAW pseudopotentials as a start (gga flag modifies the GGA paramaterization if xcf in vaspgga.keys(): xc = 'PBE' else: xc = 'LDA' vaspgga['LDA'] = '--' ############################################################################# ############################################################################# calc = Vasp(encut=encut, xc=xc, gga=vaspgga[xcf], kpts = (nkp,nkp,nkp), gamma = False, # Gamma-centered (defaults to Monkhorst-Pack) ismear=0, sigma=sigma, ibrion=ibrion, nsw=0, # don't use the VASP internal relaxation, only use ASE #potim=potim, # use to take smaller ionic steps (or for vibration/normal mode calculations) lvtot=False, npar=1, # use this if you run on one node (most calculations). see suncat confluence page for optimal setting lwave=False, luse_vdw=luse_vdw, ispin=ispin, zab_vdw=-1.8867, # this selects vdw-DF2 #lreal=True, # can speed up if supercells are large ) atoms.set_calculator(calc) dyn = QuasiNewton(atoms, logfile=name+'.log', trajectory=name+'.traj') dyn.run(fmax=0.05) electronicenergy = atoms.get_potential_energy() f = open('out.energy','w') f.write(str(electronicenergy)) f.close() # clean up big leftover files (WAVECAR or CHGCAR could be of use for some calculations) os.system('rm CHG vasprun.xml PCDAT WAVECAR CHGCAR') ############################################################################# |
Version | Date | Comment |
1 | 12/5/2012 | initial version |
2,2a | 1/31/2013 | add BEEF support courtesy of Johannes Voss ("a" for suncat3 farm) |
3 | 1/31/2013 | like v2, but change pseudo potentials to the "52" versions. no suncat3 version yet |
4 | 2/28/2013 | like v3, but add VTST support |
5 | 3/15/2013 | includes BEEF, VTST, and 30% performance improvement from using fftmpiw.F |
6 | 7/9/2013 | copy of v5 but without -DNGZhalf flag. requested by junyan for a non-collinear calculation. not recommended for general use |
This information comes from Yian Zhu, who ran several 3x3x4 spin-polarized Nickel calculations with the PBE functional.