maxmix=
35, #https://www.vasp.at/vasp-workshop/slides/handsonIV.pdf #for badly behaved clusters.
voskown=0,
ismear=1,
sigma=0.1,
isym=2,
iwavpr=11)
mpirun = spawn.find_executable('mpirun')
vasp = '/home/mmm0007/vasp/vasp.5.4.1/bin/vasp_std'
vasp_client = VaspClient(client_id=0,
npj=96,
ppn=1,
exe=vasp,
mpirun=mpirun,
parmode='mpi',
ibrion=13,
nsw=1000000,
npar=4,
**vasp_args)
if not args.no_relax:
traj = io.Trajectory('relaxation.traj', 'a', gam_cell)
qm_pot = SocketCalculator(vasp_client)
gam_cell.set_calculator(qm_pot)
opt = PreconLBFGS(gam_cell)
opt.attach(traj.write, interval=1)
opt.run(fmax=args.fmax)
traj.close()
qm_pot.shutdown()
vasp_client = VaspClient(client_id=0,
kpts=[16, 16, 1],
amix=0.01,
amin=0.001,
bmix=0.001,
amix_mag=0.01,
bmix_mag=0.001,
npj=npj,
ppn=ppn,
block=block,
corner=corner,
shape=shape,
exe=vasp,
ediffg=-0.05,
nelmin=6,
nelmdl=-15,
kpar=32,
parmode='cobalt',
xc='PBE',
lreal=False,
ibrion=13,
nsw=40,
algo='VeryFast',
npar=8,
lplane=False,
lwave=False,
lcharg=False,
nsim=1,
voskown=1,
ismear=1,
sigma=0.01,
iwavpr=11,
isym=2,
nelm=100)
block, corner, shape = list(block_corner_iter(blocks, npj))[0]
print block, corner, shape
vasp_client = VaspClient(client_id=0,
kpts=[14, 14, 14],
npj=npj,
ppn=ppn,
block=block,
corner=corner,
shape=shape,
exe=vasp,
parmode='cobalt',
xc='PBE',
lreal=False,
ibrion=13,
nsw=1000000,
algo='VeryFast',
npar=8,
lplane=False,
lwave=False,
lcharg=False,
nsim=1,
voskown=1,
ismear=0,
sigma=0.01,
iwavpr=11,
isym=0,
nelm=150)
sock_calc = SocketCalculator(vasp_client, ip=ip, bgq=True)
(0.5, 0.5, 0), (0.25, 0.25, 0.25), (0.25, 0.75, 0.75),
(0.75, 0.25, 0.75), (0.75, 0.75, 0.25)],
pbc=True)
bulk.set_cell((a, a, a), scale_atoms=True)
vasp_client = VaspClient(client_id=0,
npj=1,
ppn=8,
exe=vasp,
mpirun=mpirun,
parmode='mpi',
xc='LDA',
lreal=False,
ibrion=13,
nsw=1000000,
algo='VeryFast',
npar=8,
lplane=False,
lwave=False,
lcharg=False,
nsim=1,
voskown=1,
ismear=0,
sigma=0.01,
iwavpr=11,
isym=0,
nelm=150)
sock_calc = SocketCalculator(vasp_client)
bulk.set_calculator(sock_calc)
sock_e = bulk.get_potential_energy()
qsub_args = 'qsub -A %s -n %d -t %d -q %s --mode script --disable_preboot %s' % \
(acct, nodes, runtime, queue, ' '.join(sys.argv))
print qsub_args
os.system(qsub_args)
sys.exit(1)
blocks = get_bootable_blocks(partition, nodes)
print('Available blocks: %s' % blocks)
boot_blocks(blocks)
qm_subblocks = [
(i, bcs) for (i, bcs) in enumerate(block_corner_iter(blocks, qm_npj))
]
print 'qm_subblocks', qm_subblocks
qm_clients = [
VaspClient(client_id, qm_exe, qm_env, qm_npj, qm_ppn, block, corner,
shape, jobname, **vasp_args)
for client_id, (block, corner, shape) in qm_subblocks
]
else:
qm_clients = []
hostname, ip = '<dummy>', 0
print 'FEN hostname: %s' % hostname
print 'FEN server IP: %s' % ip
print 'QM nodes per job: %r' % qm_npj
print 'QM MPI tasks per node: %r' % qm_ppn
print 'Number of QM jobs: %d' % n_qm_jobs
print 'Total number of sub-block jobs: %d' % njobs
print 'Total number of nodes: %d' % nodes
# ******* End of parameters *************
hysteretic_buffer=True,
hysteretic_buffer_inner_radius=hyst_buffer_inner,
hysteretic_buffer_outer_radius=hyst_buffer_outer,
min_images_only=True,
terminate=False,
force_no_fix_termination_clash=True,
randomise_buffer=False)
vasp_args=dict(parmode='cobalt', xc='PBE', amix=0.01, amin=0.001, bmix=0.001, amix_mag=0.01, bmix_mag=0.001,
kpts=[1, 1, 8], kpar=4, lreal='auto', ibrion=13, nsw=1000000, nelmdl=-15, ispin=2,
nelm=100, algo='VeryFast', npar=32, lplane=False, lwave=False, lcharg=False, istart=0,
voskown=1, ismear=1, sigma=0.1, isym=0) # possibly try iwavpr=12, should be faster if it works
para_args = dict(npj=npj, ppn=ppn, block=block, corner=corner, shape=shape)
all_args = dict(vasp_args.items() + para_args.items())
qm_clients = [VaspClient(client_id=0, exe=vasp, **all_args)]
##### Finished VASP INITIALIZATION AND SOCKET CONFIGURATION ######
##### MAIN PROGRAM ############
if continuation:
# restart from last frame of most recent trajectory file
traj_files = sorted(glob.glob('[0-9]*.traj.xyz'))
if len(traj_files) > 0:
last_traj = traj_files[-1]
input_file = last_traj #+ '@-1'
print 'Loading atoms from file %s' % input_file
atoms = Atoms(input_file)
atoms = Atoms(atoms)