from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
from nexus import generate_qmcpack, vmc, loop, linear, dmc
# Nexus settings
settings(pseudo_dir='./pseudopotentials',
runs='',
results='',
status_only=0,
generate_only=0,
sleep=10,
machine='vesta',
account='QMCPACK-Training')
# allow max of one job at a time (lab only)
vesta = get_machine('vesta')
vesta.queue_size = 1
# locations of pwscf, pw2qmcpack and qmcpack executables
pwscf = '/soft/applications/qmcpack/Binaries/pw.x'
pw2qmcpack = '/soft/applications/qmcpack/Binaries/pw2qmcpack.x'
qmcpack = '/soft/applications/qmcpack/Binaries/qmcpack'
# run directory and pseudopotentials
directory = 'bcc-beryllium' # directory to perform runs
dft_pps = ['Be.ncpp'] # pwscf pseudopotentials
qmc_pps = ['Be.xml'] # qmcpack pseudopotentials
# job details
dft_job = job(cores=16, hours=2, queue="qmcpack", app=pwscf)
p2q_job = job(cores=1, hours=2, queue="qmcpack", app=pw2qmcpack)
threads=1,
hours=1,
queue='qmcpack',
app=appdir + 'pw.x')
p2qjob = job(cores=1,
threads=1,
hours=1,
queue='qmcpack',
app=appdir + 'pw2qmcpack.x')
qmcjob = job(nodes=32,
threads=16,
hours=1,
queue='qmcpack',
app=appdir + 'qmcpack')
vesta = get_machine('vesta') # allow one job at a time (lab only)
vesta.queue_size = 1
#end if
# details of your physical system (diamond conventional cell below)
my_project_name = 'diamond_vmc' # directory to perform runs
my_dft_pps = ['C.BFD.upf'] # pwscf pseudopotentials
my_qmc_pps = ['C.BFD.xml'] # qmcpack pseudopotentials
# generate your system
# units : 'A'/'B' for Angstrom/Bohr
# axes : simulation cell axes in cartesian coordinates (a1,a2,a3)
# elem : list of atoms in the system
# pos : corresponding atomic positions in cartesian coordinates
# kgrid : Monkhorst-Pack grid
# kshift : Monkhorst-Pack shift (between 0 and 0.5)
from nexus import generate_physical_system
from nexus import generate_pwscf
b = '\n'+40*'='+'\n'
settings(
pseudo_dir = './pseudopotentials',
machine = 'ws16'
#machine = 'titan',
#account = 'XYZ123',
)
if settings.machine=='ws16':
scf_job = job(cores=16,app='pw.x')
elif settings.machine=='titan':
titan = get_machine('titan')
titan.queue_size = 2
scf_job = job(nodes=1,hours=1,app='pw.x')
else:
print 'no jobs for machine!'
#end if
s = read_structure('d16bulk.POSCAR')
s.remove([[0.8925,0.8925,0.8925]])
print b+'structure w/ vacancy\n',s
s.write('d16vac.xsf')
dia16vac = generate_physical_system(
structure = s,
C = 4,
)
