def get_pwscf_sim(type='scf'):
from nexus_base import nexus_core
from machines import job
from pwscf import Pwscf,generate_pwscf
nexus_core.runs = ''
sim = None
if type=='scf':
sim = generate_pwscf(
identifier = 'scf',
path = 'scf',
job = job(machine='ws1',cores=1),
input_type = 'generic',
calculation = 'scf',
input_dft = 'lda',
ecutwfc = 200,
conv_thr = 1e-8,
nosym = True,
wf_collect = True,
system = get_system(),
pseudos = ['C.BFD.upf'],
nogamma = True,
)
else:
failed()
#end if
assert(sim is not None)
assert(isinstance(sim,Pwscf))
return sim
def test_minimal_init():
from machines import job
from pwscf import Pwscf,generate_pwscf
sim = generate_pwscf(
job = job(machine='ws1',cores=1),
system = get_system(),
)
assert(isinstance(sim,Pwscf))
clear_all_sims()
def twist_averaged_qmc(identifier='',
system=None,
pseudos=None,
functional=None,
jastrows='generateJ12',
meshfactor=1.0,
ecut=200,
conv_thr=1e-8,
kgrid=None,
kshift=None,
kinetic_E=True,
shared_orb=True,
perform_opt=False,
opt=None,
opt_calcs=None,
opt_kpoint=(0, 0, 0),
block_opt=False,
qmc_calcs=None,
force_write=False,
block_qmc=False,
basepath='',
directory='twist_average',
dftdir='dft',
optdir='opt',
qmcdir='qmc',
dftjob=None,
p2cjob=None,
p2qjob=None,
wfcjob=None,
optjob=None,
qmcjob=None):
error(
'do not use this function (twist_averaged_qmc) unless you update it!')
if p2cjob is None:
p2cjob = Job(cores=1)
#end if
if p2qjob is None:
p2qjob = Job(cores=1)
#end if
if wfcjob is None:
wfcjob = Job(cores=1)
#end if
sims = []
if system is None:
error('system is a required input to basic_qmc')
#end if
if pseudos is None:
error('pseudos is a required input to basic_qmc')
#end if
if identifier != '':
directory = directory + '_' + identifier
qmcid = identifier
else:
qmcid = 'qmc'
#end if
dftpseudos, qmcpseudos = sort_pseudos(pseudos)
structure = system.structure
if kgrid != None and kshift != None:
system = system.copy()
structure = system.structure
structure.clear_kpoints()
structure.add_kmesh(kgrid, kshift)
#end if
if shared_orb:
kpoints = ['shared_orb']
else:
kpoints = structure.kpoints
#end if
optpath = os.path.join(basepath, directory, optdir)
qmcpath = os.path.join(basepath, directory, qmcdir)
if perform_opt and opt is None:
optsims = optimization(identifier=identifier,
system=system,
pseudos=pseudos,
functional=functional,
jastrows=jastrows,
meshfactor=meshfactor,
ecut=ecut,
conv_thr=conv_thr,
kinetic_E=kinetic_E,
block_qmc=block_opt,
force_write=force_write,
opt_calcs=opt_calcs,
opt_kpoint=opt_kpoint,
basepath=os.path.join(basepath, directory),
dftjob=dftjob,
p2cjob=p2cjob,
p2qjob=p2qjob,
wfcjob=wfcjob,
optjob=optjob)
opt = optsims[-1]
sims.extend(optsims)
#end if
n = 0
qmcs = []
for kpoint in kpoints:
if shared_orb:
sys = system
idext = ''
else:
sys = system.copy()
sys.structure.kpoints = array([kpoint])
idext = '_' + str(n).zfill(3)
#end if
dftpath = os.path.join(basepath, directory, dftdir + idext)
if sys.folded_system != None:
dftsys = sys.folded_system
else:
dftsys = sys
#end if
scf = generate_pwscf(identifier='scf',
path=dftpath,
job=dftjob,
input_type='scf',
input_dft=functional,
ecut=ecut,
conv_thr=conv_thr,
pseudos=dftpseudos,
system=dftsys)
p2q = generate_pw2qmcpack(identifier='p2q',
path=dftpath,
job=p2qjob,
write_psir=False)
wfc = generate_wfconvert(identifier='wfc',
path=dftpath,
job=wfcjob,
spline=False)
qmc = generate_qmcpack(identifier=qmcid + '_twist' + idext,
path=qmcpath,
job=qmcjob,
block=block_qmc,
force_write=force_write,
input_type='basic',
pseudos=qmcpseudos,
system=sys,
jastrows=jastrows,
meshfactor=meshfactor,
calculations=qmc_calcs)
qmcs.append(qmc)
p2q.depends(scf, 'orbitals')
wfc.depends(p2q, 'orbitals')
qmc.depends(wfc, 'orbitals')
if opt is not None:
qmc.depends(opt, 'jastrow')
#end if
sims += [scf, p2q, wfc]
if kinetic_E:
p2c = generate_pw2casino(identifier='p2c',
path=dftpath,
job=p2cjob)
p2c.depends(scf, 'orbitals')
sims.append(p2c)
#end if
n += 1
#end for
if shared_orb:
sims.extend(qmcs)
else:
taqmc = BundledQmcpack(identifier=identifier,
path=qmcpath,
job=qmcjob,
block=block_qmc,
force_write=force_write,
app_name='qmcapp_complex',
sims=qmcs,
system=system)
sims.append(taqmc)
for qmc in qmcs:
qmc.block = True
#end for
#end if
return sims
def optimization(identifier='',
system=None,
pseudos=None,
functional=None,
jastrows='generateJ12',
meshfactor=1.0,
ecut=200,
conv_thr=1e-8,
kinetic_E=True,
block_qmc=False,
force_write=False,
opt_calcs=None,
opt_kpoint=None,
basepath='',
directory='optimization',
dftdir='dft',
optdir='opt',
dftjob=None,
p2cjob=None,
p2qjob=None,
wfcjob=None,
optjob=None):
error('do not use this function (optimization) unless you update it!')
if p2cjob is None:
p2cjob = Job(cores=1)
#end if
if p2qjob is None:
p2qjob = Job(cores=1)
#end if
if wfcjob is None:
wfcjob = Job(cores=1)
#end if
if system is None:
error('system is a required input to optimization')
#end if
if pseudos is None:
error('pseudos is a required input to optimization')
#end if
if identifier != '':
directory = directory + '_' + identifier
qmcid = identifier
else:
qmcid = 'qmc'
#end if
dftpath = os.path.join(basepath, directory, dftdir)
optpath = os.path.join(basepath, directory, optdir)
dftpseudos, qmcpseudos = sort_pseudos(pseudos)
sys = system.copy()
if opt_kpoint != None:
sys.structure.kpoints = array([array(opt_kpoint)])
#end if
optjob.set_processes()
if sys.folded_system != None:
dftsys = sys.folded_system
else:
dftsys = sys
#end if
scf = generate_pwscf(identifier='scf',
path=dftpath,
job=dftjob,
input_type='scf',
input_dft=functional,
ecut=ecut,
conv_thr=conv_thr,
pseudos=dftpseudos,
system=dftsys)
p2q = generate_pw2qmcpack(identifier='p2q',
path=dftpath,
job=p2qjob,
write_psir=False)
wfc = generate_wfconvert(identifier='wfc',
path=dftpath,
job=wfcjob,
spline=False)
opt = generate_qmcpack(identifier='opt',
path=optpath,
job=optjob,
block=block_qmc,
force_write=force_write,
input_type='opt_jastrow',
pseudos=qmcpseudos,
system=sys,
jastrows=jastrows,
meshfactor=meshfactor,
opt_calcs=opt_calcs,
processes=optjob.processes,
threads=optjob.threads)
p2q.depends(scf, 'orbitals')
wfc.depends(p2q, 'orbitals')
opt.depends(wfc, 'orbitals')
if kinetic_E:
p2c = generate_pw2casino(identifier='p2c', path=dftpath, job=p2cjob)
p2c.depends(scf, 'orbitals')
sims = [scf, p2c, p2q, wfc, opt]
else:
sims = [scf, p2q, wfc, opt]
#end if
return sims
def standard_qmc(identifier='',
scf_kgrid=None,
scf_kshift=(1, 1, 1),
system=None,
pseudos=None,
folded_dft=True,
functional=None,
ecut=200,
ecutrho=None,
conv_thr=1e-8,
mixing_beta=.7,
nosym=False,
nscf_nosym=True,
hubbard_u=None,
start_mag=None,
kinetic_E=False,
wfconvert=False,
bconds=None,
jastrows='generateJ12',
meshfactor=1.0,
det_format='new',
precision='float',
vmc_timestep=None,
nonlocalmoves=None,
perform_opt=False,
opt=None,
opt_calcs=None,
opt_kpoint=None,
sample_factor=1.0,
block_opt=False,
skip_submit_opt=False,
qmc_calcs=None,
estimators=None,
corrections=None,
block_qmc=False,
force_write=False,
skip_submit_qmc=False,
basepath='',
directory='qmc_calc',
scfdir='scf',
nscfdir='nscf',
nscfoptdir='nscfopt',
optdir='opt',
qmcdir='qmc',
scfjob=None,
nscfjob=None,
p2cjob=None,
p2qjob=None,
wfcjob=None,
optjob=None,
qmcjob=None,
dft_dependencies=None,
opt_dependencies=None,
remove_cell=False,
return_list=True):
if p2cjob is None:
p2cjob = Job(cores=1)
#end if
if p2qjob is None:
p2qjob = Job(cores=1)
#end if
if wfcjob is None:
wfcjob = Job(cores=1)
#end if
if system is None:
error('system is a required input to standard_qmc')
#end if
if pseudos is None:
error('pseudos is a required input to standard_qmc')
#end if
if scf_kgrid is None:
error('scf_kgrid is a required input to standard_qmc')
#end if
scfpath = os.path.join(basepath, directory, scfdir)
dftpseudos, qmcpseudos = sort_pseudos(pseudos)
sys = system.copy()
scf = generate_pwscf(identifier='scf',
path=scfpath,
job=scfjob,
input_type='scf',
input_dft=functional,
ecut=ecut,
ecutrho=ecutrho,
conv_thr=conv_thr,
mixing_beta=mixing_beta,
nosym=nosym,
hubbard_u=hubbard_u,
start_mag=start_mag,
pseudos=dftpseudos,
system=sys,
kgrid=scf_kgrid,
kshift=scf_kshift,
wf_collect=False,
use_folded=folded_dft)
if dft_dependencies is None:
dft_dependencies = []
else:
scf.depends(*dft_dependencies)
dft_dependencies = list(dft_dependencies)
#end if
dft_dependencies.append((scf, 'charge_density'))
sims = basic_qmc(nscf=True,
identifier=identifier,
system=system,
pseudos=pseudos,
folded_dft=folded_dft,
functional=functional,
jastrows=jastrows,
meshfactor=meshfactor,
det_format=det_format,
precision=precision,
ecut=ecut,
ecutrho=ecutrho,
conv_thr=conv_thr,
mixing_beta=mixing_beta,
nosym=nscf_nosym,
hubbard_u=hubbard_u,
start_mag=start_mag,
kinetic_E=kinetic_E,
wfconvert=wfconvert,
bconds=bconds,
vmc_timestep=vmc_timestep,
nonlocalmoves=nonlocalmoves,
perform_opt=perform_opt,
opt=opt,
opt_calcs=opt_calcs,
opt_kpoint=opt_kpoint,
sample_factor=sample_factor,
block_opt=block_opt,
skip_submit_opt=skip_submit_opt,
qmc_calcs=qmc_calcs,
estimators=estimators,
corrections=corrections,
block_qmc=block_qmc,
force_write=force_write,
skip_submit_qmc=skip_submit_qmc,
basepath=basepath,
directory=directory,
dftdir=nscfdir,
dftoptdir=nscfoptdir,
optdir=optdir,
qmcdir=qmcdir,
scfjob=nscfjob,
p2cjob=p2cjob,
p2qjob=p2qjob,
wfcjob=wfcjob,
optjob=optjob,
qmcjob=qmcjob,
dft_dependencies=dft_dependencies,
opt_dependencies=opt_dependencies,
remove_cell=remove_cell,
return_list=return_list)
if return_list:
sims = [scf] + sims
else:
if 'scf' in sims:
sims.nscf = sims.scf
del sims.scf
#end if
if 'scfopt' in sims:
sims.nscfopt = sims.scfopt
del sims.scfopt
#end if
sims.scf = scf
#end if
return sims
def basic_qmc(identifier='',
system=None,
pseudos=None,
functional=None,
folded_dft=True,
ecut=200,
ecutrho=None,
conv_thr=1e-8,
mixing_beta=.7,
nosym=True,
nscf=False,
hubbard_u=None,
start_mag=None,
kinetic_E=False,
wfconvert=False,
bconds=None,
jastrows='generateJ12',
meshfactor=1.0,
det_format='new',
precision='float',
vmc_timestep=None,
nonlocalmoves=None,
perform_opt=False,
opt=None,
opt_calcs=None,
opt_kpoint=None,
sample_factor=1.0,
block_opt=False,
skip_submit_opt=False,
qmc_calcs=None,
estimators=None,
corrections=None,
block_qmc=False,
force_write=False,
skip_submit_qmc=False,
basepath='',
directory='qmc_calc',
dftdir='scf',
dftoptdir='scfopt',
optdir='opt',
qmcdir='qmc',
scfjob=None,
p2cjob=None,
p2qjob=None,
wfcjob=None,
optjob=None,
qmcjob=None,
dft_dependencies=None,
opt_dependencies=None,
remove_cell=False,
return_list=True):
if p2cjob is None:
p2cjob = Job(cores=1)
#end if
if p2qjob is None:
p2qjob = Job(cores=1)
#end if
if wfcjob is None:
wfcjob = Job(cores=1)
#end if
if system is None:
error('system is a required input to basic_qmc')
#end if
if pseudos is None:
error('pseudos is a required input to basic_qmc')
#end if
if identifier != '':
directory = directory + '_' + identifier
qmcid = identifier
else:
qmcid = 'qmc'
#end if
dftpath = os.path.join(basepath, directory, dftdir)
dftoptpath = os.path.join(basepath, directory, dftoptdir)
optpath = os.path.join(basepath, directory, optdir)
qmcpath = os.path.join(basepath, directory, qmcdir)
dftpseudos, qmcpseudos = sort_pseudos(pseudos)
sys = system.copy()
structdep = None
if dft_dependencies != None:
for dep in dft_dependencies:
if dep[1] == 'structure':
structdep = dep
#end if
#end for
#end if
#add vmc timestep and nonlocalmoves to qmc_calcs, if requested
if qmc_calcs != None:
for calc in qmc_calcs:
if isinstance(calc, loop):
calc = calc.qmc
#end if
if isinstance(calc, vmc) or isinstance(calc, linear) or isinstance(
calc, cslinear):
if vmc_timestep != None and not 'timestep' in calc:
calc.timestep = vmc_timestep
#end if
if nonlocalmoves != None:
calc.nonlocalpp = nonlocalmoves
#end if
elif isinstance(calc, dmc):
if nonlocalmoves != None:
calc.nonlocalmoves = nonlocalmoves
#end if
#end if
#end for
#end if
if not nscf:
scf_id = 'scf'
scf_it = 'scf'
else:
scf_id = 'nscf'
scf_it = 'nscf'
#end if
scf = generate_pwscf(identifier=scf_id,
path=dftpath,
job=scfjob,
input_type=scf_it,
input_dft=functional,
ecut=ecut,
ecutrho=ecutrho,
conv_thr=conv_thr,
mixing_beta=mixing_beta,
nosym=nosym,
hubbard_u=hubbard_u,
start_mag=start_mag,
pseudos=dftpseudos,
system=sys,
use_folded=folded_dft)
p2q = generate_pw2qmcpack(identifier='p2q',
path=dftpath,
job=p2qjob,
write_psir=False)
if wfconvert:
wfc = generate_wfconvert(identifier='wfc',
path=dftpath,
job=wfcjob,
spline=False)
#end if
qmc = generate_qmcpack(identifier=qmcid,
path=qmcpath,
job=qmcjob,
block=block_qmc,
force_write=force_write,
skip_submit=skip_submit_qmc,
input_type='basic',
pseudos=qmcpseudos,
system=sys,
bconds=bconds,
remove_cell=remove_cell,
jastrows=jastrows,
meshfactor=meshfactor,
det_format=det_format,
precision=precision,
estimators=estimators,
corrections=corrections,
calculations=qmc_calcs)
sims = obj(scf=scf, p2q=p2q, qmc=qmc)
if dft_dependencies != None:
scf.depends(*dft_dependencies)
#end if
p2q.depends(scf, 'orbitals')
if wfconvert:
sims.wfc = wfc
wfc.depends(p2q, 'orbitals')
qmc.depends(wfc, 'orbitals')
else:
qmc.depends(p2q, 'orbitals')
#end if
if structdep != None:
qmc.depends(structdep)
#end if
if not perform_opt and opt is None and opt_dependencies != None:
qmc.depends(*opt_dependencies)
#end if
if perform_opt:
if wfconvert:
orbdep = wfc
else:
orbdep = p2q
#end if
opt_sys = sys
if opt_kpoint != None:
kaxes = opt_sys.structure.kaxes.copy()
k = generate_kpoint(opt_kpoint, kaxes, grids=not nscf)
opt_kgrid = k.kgrid
opt_kshift = k.kshift
dftopt_kshift = k.dft_kgrid
dftopt_kgrid = k.dft_kshift
opt_sys = opt_sys.copy()
opt_sys.structure.clear_kpoints()
opt_sys.structure.add_kpoints([k.kpoint], [1.0])
scfopt = generate_pwscf(identifier=scf_id,
path=dftoptpath,
job=scfjob,
input_type=scf_it,
input_dft=functional,
ecut=ecut,
conv_thr=conv_thr,
nosym=nosym,
hubbard_u=hubbard_u,
start_mag=start_mag,
pseudos=dftpseudos,
system=opt_sys,
kgrid=dftopt_kgrid,
kshift=dftopt_kshift)
p2qopt = generate_pw2qmcpack(identifier='p2q',
path=dftoptpath,
job=p2qjob,
write_psir=False)
if wfconvert:
wfcopt = generate_wfconvert(identifier='wfc',
path=dftoptpath,
job=wfcjob,
spline=False)
#end if
if dft_dependencies != None:
scfopt.depends(*dft_dependencies)
#end if
p2qopt.depends(scfopt, 'orbitals')
sims.set(scfopt=scfopt, p2qopt=p2qopt)
if wfconvert:
sims.wfcopt = wfcopt
wfcopt.depends(p2qopt, 'orbitals')
orbdep = wfcopt
else:
orbdep = p2qopt
#end if
#end if
optjob.set_processes()
opt = generate_qmcpack(identifier='opt',
path=optpath,
job=optjob,
block=block_opt,
skip_submit=skip_submit_opt,
force_write=force_write,
input_type='opt_jastrow',
pseudos=qmcpseudos,
system=opt_sys,
bconds=bconds,
remove_cell=remove_cell,
jastrows=jastrows,
meshfactor=meshfactor,
det_format=det_format,
precision=precision,
timestep=vmc_timestep,
nonlocalpp=nonlocalmoves,
corrections=[],
sample_factor=sample_factor,
opt_calcs=opt_calcs,
processes=optjob.processes,
threads=optjob.threads)
opt.depends(orbdep, 'orbitals')
if structdep != None:
opt.depends(structdep)
#end if
if opt_dependencies != None:
opt.depends(*opt_dependencies)
#end if
if kinetic_E and opt_kpoint != None:
p2copt = generate_pw2casino(identifier='p2c',
path=dftoptpath,
job=p2cjob)
p2copt.depends(scfopt, 'orbitals')
sims.p2copt = p2copt
#end if
#end if
if opt is not None:
sims.opt = opt
qmc.depends(opt, 'jastrow')
#end if
if kinetic_E:
p2c = generate_pw2casino(identifier='p2c', path=dftpath, job=p2cjob)
p2c.depends(scf, 'orbitals')
sims.p2c = p2c
#end if
if return_list:
order = [
'scfopt', 'p2copt', 'p2qopt', 'wfcopt', 'opt', 'scf', 'p2c', 'p2q',
'wfc', 'qmc'
]
simlist = []
for simid in order:
if simid in sims:
simlist.append(sims[simid])
del sims[simid]
#end if
#end for
return simlist
else:
return sims
def twist_averaged_qmc(identifier = '',
system = None,
pseudos = None,
functional = None,
jastrows = 'generateJ12',
meshfactor = 1.0,
ecut = 200,
conv_thr = 1e-8,
kgrid = None,
kshift = None,
kinetic_E = True,
shared_orb = True,
perform_opt= False,
opt = None,
opt_calcs = None,
opt_kpoint = (0,0,0),
block_opt = False,
qmc_calcs = None,
force_write= False,
block_qmc = False,
basepath = '',
directory = 'twist_average',
dftdir = 'dft',
optdir = 'opt',
qmcdir = 'qmc',
dftjob = None,
p2cjob = None,
p2qjob = None,
wfcjob = None,
optjob = None,
qmcjob = None):
error('do not use this function (twist_averaged_qmc) unless you update it!')
if p2cjob is None:
p2cjob = Job(cores=1)
#end if
if p2qjob is None:
p2qjob = Job(cores=1)
#end if
if wfcjob is None:
wfcjob = Job(cores=1)
#end if
sims = []
if system is None:
error('system is a required input to basic_qmc')
#end if
if pseudos is None:
error('pseudos is a required input to basic_qmc')
#end if
if identifier!='':
directory = directory+'_'+identifier
qmcid = identifier
else:
qmcid = 'qmc'
#end if
dftpseudos,qmcpseudos = sort_pseudos(pseudos)
structure = system.structure
if kgrid!=None and kshift!=None:
system = system.copy()
structure = system.structure
structure.clear_kpoints()
structure.add_kmesh(kgrid,kshift)
#end if
if shared_orb:
kpoints = ['shared_orb']
else:
kpoints = structure.kpoints
#end if
optpath = os.path.join(basepath,directory,optdir)
qmcpath = os.path.join(basepath,directory,qmcdir)
if perform_opt and opt is None:
optsims = optimization(
identifier = identifier,
system = system,
pseudos = pseudos,
functional = functional,
jastrows = jastrows,
meshfactor = meshfactor,
ecut = ecut,
conv_thr = conv_thr,
kinetic_E = kinetic_E,
block_qmc = block_opt,
force_write= force_write,
opt_calcs = opt_calcs,
opt_kpoint = opt_kpoint,
basepath = os.path.join(basepath,directory),
dftjob = dftjob,
p2cjob = p2cjob,
p2qjob = p2qjob,
wfcjob = wfcjob,
optjob = optjob
)
opt = optsims[-1]
sims.extend(optsims)
#end if
n=0
qmcs = []
for kpoint in kpoints:
if shared_orb:
sys = system
idext = ''
else:
sys = system.copy()
sys.structure.kpoints = array([kpoint])
idext = '_'+str(n).zfill(3)
#end if
dftpath = os.path.join(basepath,directory,dftdir+idext)
if sys.folded_system!=None:
dftsys = sys.folded_system
else:
dftsys = sys
#end if
scf = generate_pwscf(
identifier = 'scf',
path = dftpath,
job = dftjob,
input_type = 'scf',
input_dft = functional,
ecut = ecut,
conv_thr = conv_thr,
pseudos = dftpseudos,
system = dftsys
)
p2q = generate_pw2qmcpack(
identifier = 'p2q',
path = dftpath,
job = p2qjob,
write_psir = False
)
wfc = generate_wfconvert(
identifier = 'wfc',
path = dftpath,
job = wfcjob,
spline = False
)
qmc = generate_qmcpack(
identifier = qmcid+'_twist'+idext,
path = qmcpath,
job = qmcjob,
block = block_qmc,
force_write= force_write,
input_type = 'basic',
pseudos = qmcpseudos,
system = sys,
jastrows = jastrows,
meshfactor = meshfactor,
calculations = qmc_calcs
)
qmcs.append(qmc)
p2q.depends(scf,'orbitals')
wfc.depends(p2q,'orbitals')
qmc.depends(wfc,'orbitals')
if opt is not None:
qmc.depends(opt,'jastrow')
#end if
sims += [scf,p2q,wfc]
if kinetic_E:
p2c = generate_pw2casino(
identifier = 'p2c',
path = dftpath,
job = p2cjob
)
p2c.depends(scf,'orbitals')
sims.append(p2c)
#end if
n+=1
#end for
if shared_orb:
sims.extend(qmcs)
else:
taqmc = BundledQmcpack(
identifier = identifier,
path = qmcpath,
job = qmcjob,
block = block_qmc,
force_write= force_write,
app_name = 'qmcapp_complex',
sims = qmcs,
system = system
)
sims.append(taqmc)
for qmc in qmcs:
qmc.block = True
#end for
#end if
return sims
def optimization(identifier = '',
system = None,
pseudos = None,
functional = None,
jastrows = 'generateJ12',
meshfactor = 1.0,
ecut = 200,
conv_thr = 1e-8,
kinetic_E = True,
block_qmc = False,
force_write= False,
opt_calcs = None,
opt_kpoint = None,
basepath = '',
directory = 'optimization',
dftdir = 'dft',
optdir = 'opt',
dftjob = None,
p2cjob = None,
p2qjob = None,
wfcjob = None,
optjob = None):
error('do not use this function (optimization) unless you update it!')
if p2cjob is None:
p2cjob = Job(cores=1)
#end if
if p2qjob is None:
p2qjob = Job(cores=1)
#end if
if wfcjob is None:
wfcjob = Job(cores=1)
#end if
if system is None:
error('system is a required input to optimization')
#end if
if pseudos is None:
error('pseudos is a required input to optimization')
#end if
if identifier!='':
directory = directory+'_'+identifier
qmcid = identifier
else:
qmcid = 'qmc'
#end if
dftpath = os.path.join(basepath,directory,dftdir)
optpath = os.path.join(basepath,directory,optdir)
dftpseudos,qmcpseudos = sort_pseudos(pseudos)
sys = system.copy()
if opt_kpoint!=None:
sys.structure.kpoints = array([array(opt_kpoint)])
#end if
optjob.set_processes()
if sys.folded_system!=None:
dftsys = sys.folded_system
else:
dftsys = sys
#end if
scf = generate_pwscf(
identifier = 'scf',
path = dftpath,
job = dftjob,
input_type = 'scf',
input_dft = functional,
ecut = ecut,
conv_thr = conv_thr,
pseudos = dftpseudos,
system = dftsys
)
p2q = generate_pw2qmcpack(
identifier = 'p2q',
path = dftpath,
job = p2qjob,
write_psir = False
)
wfc = generate_wfconvert(
identifier = 'wfc',
path = dftpath,
job = wfcjob,
spline = False
)
opt = generate_qmcpack(
identifier = 'opt',
path = optpath,
job = optjob,
block = block_qmc,
force_write= force_write,
input_type = 'opt_jastrow',
pseudos = qmcpseudos,
system = sys,
jastrows = jastrows,
meshfactor = meshfactor,
opt_calcs = opt_calcs,
processes = optjob.processes,
threads = optjob.threads
)
p2q.depends(scf,'orbitals')
wfc.depends(p2q,'orbitals')
opt.depends(wfc,'orbitals')
if kinetic_E:
p2c = generate_pw2casino(
identifier = 'p2c',
path = dftpath,
job = p2cjob
)
p2c.depends(scf,'orbitals')
sims = [scf,p2c,p2q,wfc,opt]
else:
sims = [scf,p2q,wfc,opt]
#end if
return sims
def standard_qmc(identifier = '',
scf_kgrid = None,
scf_kshift = (1,1,1),
system = None,
pseudos = None,
folded_dft = True,
functional = None,
ecut = 200,
ecutrho = None,
conv_thr = 1e-8,
mixing_beta = .7,
nosym = False,
nscf_nosym = True,
hubbard_u = None,
start_mag = None,
kinetic_E = False,
wfconvert = False,
bconds = None,
jastrows = 'generateJ12',
meshfactor = 1.0,
det_format = 'new',
precision = 'float',
vmc_timestep = None,
nonlocalmoves = None,
perform_opt = False,
opt = None,
opt_calcs = None,
opt_kpoint = None,
sample_factor = 1.0,
block_opt = False,
skip_submit_opt = False,
qmc_calcs = None,
estimators = None,
corrections = None,
block_qmc = False,
force_write = False,
skip_submit_qmc = False,
basepath = '',
directory = 'qmc_calc',
scfdir = 'scf',
nscfdir = 'nscf',
nscfoptdir = 'nscfopt',
optdir = 'opt',
qmcdir = 'qmc',
scfjob = None,
nscfjob = None,
p2cjob = None,
p2qjob = None,
wfcjob = None,
optjob = None,
qmcjob = None,
dft_dependencies= None,
opt_dependencies= None,
remove_cell = False,
return_list = True):
if p2cjob is None:
p2cjob = Job(cores=1)
#end if
if p2qjob is None:
p2qjob = Job(cores=1)
#end if
if wfcjob is None:
wfcjob = Job(cores=1)
#end if
if system is None:
error('system is a required input to standard_qmc')
#end if
if pseudos is None:
error('pseudos is a required input to standard_qmc')
#end if
if scf_kgrid is None:
error('scf_kgrid is a required input to standard_qmc')
#end if
scfpath = os.path.join(basepath,directory,scfdir)
dftpseudos,qmcpseudos = sort_pseudos(pseudos)
sys = system.copy()
scf = generate_pwscf(
identifier = 'scf',
path = scfpath,
job = scfjob,
input_type = 'scf',
input_dft = functional,
ecut = ecut,
ecutrho = ecutrho,
conv_thr = conv_thr,
mixing_beta= mixing_beta,
nosym = nosym,
hubbard_u = hubbard_u,
start_mag = start_mag,
pseudos = dftpseudos,
system = sys,
kgrid = scf_kgrid,
kshift = scf_kshift,
wf_collect = False,
use_folded = folded_dft
)
if dft_dependencies is None:
dft_dependencies = []
else:
scf.depends(*dft_dependencies)
dft_dependencies = list(dft_dependencies)
#end if
dft_dependencies.append((scf,'charge_density'))
sims = basic_qmc(
nscf = True ,
identifier = identifier ,
system = system ,
pseudos = pseudos ,
folded_dft = folded_dft ,
functional = functional ,
jastrows = jastrows ,
meshfactor = meshfactor ,
det_format = det_format ,
precision = precision ,
ecut = ecut ,
ecutrho = ecutrho ,
conv_thr = conv_thr ,
mixing_beta = mixing_beta ,
nosym = nscf_nosym ,
hubbard_u = hubbard_u ,
start_mag = start_mag ,
kinetic_E = kinetic_E ,
wfconvert = wfconvert ,
bconds = bconds ,
vmc_timestep = vmc_timestep ,
nonlocalmoves = nonlocalmoves ,
perform_opt = perform_opt ,
opt = opt ,
opt_calcs = opt_calcs ,
opt_kpoint = opt_kpoint ,
sample_factor = sample_factor ,
block_opt = block_opt ,
skip_submit_opt = skip_submit_opt ,
qmc_calcs = qmc_calcs ,
estimators = estimators ,
corrections = corrections ,
block_qmc = block_qmc ,
force_write = force_write ,
skip_submit_qmc = skip_submit_qmc ,
basepath = basepath ,
directory = directory ,
dftdir = nscfdir ,
dftoptdir = nscfoptdir ,
optdir = optdir ,
qmcdir = qmcdir ,
scfjob = nscfjob ,
p2cjob = p2cjob ,
p2qjob = p2qjob ,
wfcjob = wfcjob ,
optjob = optjob ,
qmcjob = qmcjob ,
dft_dependencies = dft_dependencies,
opt_dependencies = opt_dependencies,
remove_cell = remove_cell,
return_list = return_list
)
if return_list:
sims = [scf]+sims
else:
if 'scf' in sims:
sims.nscf = sims.scf
del sims.scf
#end if
if 'scfopt' in sims:
sims.nscfopt = sims.scfopt
del sims.scfopt
#end if
sims.scf = scf
#end if
return sims
def basic_qmc(identifier = '',
system = None,
pseudos = None,
functional = None,
folded_dft = True,
ecut = 200,
ecutrho = None,
conv_thr = 1e-8,
mixing_beta = .7,
nosym = True,
nscf = False,
hubbard_u = None,
start_mag = None,
kinetic_E = False,
wfconvert = False,
bconds = None,
jastrows = 'generateJ12',
meshfactor = 1.0,
det_format = 'new',
precision = 'float',
vmc_timestep = None,
nonlocalmoves = None,
perform_opt = False,
opt = None,
opt_calcs = None,
opt_kpoint = None,
sample_factor = 1.0,
block_opt = False,
skip_submit_opt = False,
qmc_calcs = None,
estimators = None,
corrections = None,
block_qmc = False,
force_write = False,
skip_submit_qmc = False,
basepath = '',
directory = 'qmc_calc',
dftdir = 'scf',
dftoptdir = 'scfopt',
optdir = 'opt',
qmcdir = 'qmc',
scfjob = None,
p2cjob = None,
p2qjob = None,
wfcjob = None,
optjob = None,
qmcjob = None,
dft_dependencies = None,
opt_dependencies = None,
remove_cell = False,
return_list = True):
if p2cjob is None:
p2cjob = Job(cores=1)
#end if
if p2qjob is None:
p2qjob = Job(cores=1)
#end if
if wfcjob is None:
wfcjob = Job(cores=1)
#end if
if system is None:
error('system is a required input to basic_qmc')
#end if
if pseudos is None:
error('pseudos is a required input to basic_qmc')
#end if
if identifier!='':
directory = directory+'_'+identifier
qmcid = identifier
else:
qmcid = 'qmc'
#end if
dftpath = os.path.join(basepath,directory,dftdir)
dftoptpath = os.path.join(basepath,directory,dftoptdir)
optpath = os.path.join(basepath,directory,optdir)
qmcpath = os.path.join(basepath,directory,qmcdir)
dftpseudos,qmcpseudos = sort_pseudos(pseudos)
sys = system.copy()
structdep = None
if dft_dependencies!=None:
for dep in dft_dependencies:
if dep[1]=='structure':
structdep = dep
#end if
#end for
#end if
#add vmc timestep and nonlocalmoves to qmc_calcs, if requested
if qmc_calcs!=None:
for calc in qmc_calcs:
if isinstance(calc,loop):
calc = calc.qmc
#end if
if isinstance(calc,vmc) or isinstance(calc,linear) or isinstance(calc,cslinear):
if vmc_timestep!=None and not 'timestep' in calc:
calc.timestep = vmc_timestep
#end if
if nonlocalmoves!=None:
calc.nonlocalpp = nonlocalmoves
#end if
elif isinstance(calc,dmc):
if nonlocalmoves!=None:
calc.nonlocalmoves = nonlocalmoves
#end if
#end if
#end for
#end if
if not nscf:
scf_id = 'scf'
scf_it = 'scf'
else:
scf_id = 'nscf'
scf_it = 'nscf'
#end if
scf = generate_pwscf(
identifier = scf_id,
path = dftpath,
job = scfjob,
input_type = scf_it,
input_dft = functional,
ecut = ecut,
ecutrho = ecutrho,
conv_thr = conv_thr,
mixing_beta = mixing_beta,
nosym = nosym,
hubbard_u = hubbard_u,
start_mag = start_mag,
pseudos = dftpseudos,
system = sys,
use_folded = folded_dft
)
p2q = generate_pw2qmcpack(
identifier = 'p2q',
path = dftpath,
job = p2qjob,
write_psir = False
)
if wfconvert:
wfc = generate_wfconvert(
identifier = 'wfc',
path = dftpath,
job = wfcjob,
spline = False
)
#end if
qmc = generate_qmcpack(
identifier = qmcid,
path = qmcpath,
job = qmcjob,
block = block_qmc,
force_write = force_write,
skip_submit = skip_submit_qmc,
input_type = 'basic',
pseudos = qmcpseudos,
system = sys,
bconds = bconds,
remove_cell = remove_cell,
jastrows = jastrows,
meshfactor = meshfactor,
det_format = det_format,
precision = precision,
estimators = estimators,
corrections = corrections,
calculations = qmc_calcs
)
sims = obj(
scf = scf,
p2q = p2q,
qmc = qmc
)
if dft_dependencies!=None:
scf.depends(*dft_dependencies)
#end if
p2q.depends(scf,'orbitals')
if wfconvert:
sims.wfc = wfc
wfc.depends(p2q,'orbitals')
qmc.depends(wfc,'orbitals')
else:
qmc.depends(p2q,'orbitals')
#end if
if structdep!=None:
qmc.depends(structdep)
#end if
if not perform_opt and opt is None and opt_dependencies!=None:
qmc.depends(*opt_dependencies)
#end if
if perform_opt:
if wfconvert:
orbdep = wfc
else:
orbdep = p2q
#end if
opt_sys = sys
if opt_kpoint!=None:
kaxes = opt_sys.structure.kaxes.copy()
k = generate_kpoint(opt_kpoint,kaxes,grids=not nscf)
opt_kgrid = k.kgrid
opt_kshift = k.kshift
dftopt_kshift = k.dft_kgrid
dftopt_kgrid = k.dft_kshift
opt_sys = opt_sys.copy()
opt_sys.structure.clear_kpoints()
opt_sys.structure.add_kpoints([k.kpoint],[1.0])
scfopt = generate_pwscf(
identifier = scf_id,
path = dftoptpath,
job = scfjob,
input_type = scf_it,
input_dft = functional,
ecut = ecut,
conv_thr = conv_thr,
nosym = nosym,
hubbard_u = hubbard_u,
start_mag = start_mag,
pseudos = dftpseudos,
system = opt_sys,
kgrid = dftopt_kgrid,
kshift = dftopt_kshift
)
p2qopt = generate_pw2qmcpack(
identifier = 'p2q',
path = dftoptpath,
job = p2qjob,
write_psir = False
)
if wfconvert:
wfcopt = generate_wfconvert(
identifier = 'wfc',
path = dftoptpath,
job = wfcjob,
spline = False
)
#end if
if dft_dependencies!=None:
scfopt.depends(*dft_dependencies)
#end if
p2qopt.depends(scfopt,'orbitals')
sims.set(
scfopt = scfopt,
p2qopt = p2qopt
)
if wfconvert:
sims.wfcopt = wfcopt
wfcopt.depends(p2qopt,'orbitals')
orbdep = wfcopt
else:
orbdep = p2qopt
#end if
#end if
optjob.set_processes()
opt = generate_qmcpack(
identifier = 'opt',
path = optpath,
job = optjob,
block = block_opt,
skip_submit= skip_submit_opt,
force_write= force_write,
input_type = 'opt_jastrow',
pseudos = qmcpseudos,
system = opt_sys,
bconds = bconds,
remove_cell= remove_cell,
jastrows = jastrows,
meshfactor = meshfactor,
det_format = det_format,
precision = precision,
timestep = vmc_timestep,
nonlocalpp = nonlocalmoves,
corrections= [],
sample_factor = sample_factor,
opt_calcs = opt_calcs,
processes = optjob.processes,
threads = optjob.threads
)
opt.depends(orbdep,'orbitals')
if structdep!=None:
opt.depends(structdep)
#end if
if opt_dependencies!=None:
opt.depends(*opt_dependencies)
#end if
if kinetic_E and opt_kpoint!=None:
p2copt = generate_pw2casino(
identifier = 'p2c',
path = dftoptpath,
job = p2cjob
)
p2copt.depends(scfopt,'orbitals')
sims.p2copt = p2copt
#end if
#end if
if opt is not None:
sims.opt = opt
qmc.depends(opt,'jastrow')
#end if
if kinetic_E:
p2c = generate_pw2casino(
identifier = 'p2c',
path = dftpath,
job = p2cjob
)
p2c.depends(scf,'orbitals')
sims.p2c = p2c
#end if
if return_list:
order = ['scfopt','p2copt','p2qopt','wfcopt','opt','scf','p2c','p2q','wfc','qmc']
simlist = []
for simid in order:
if simid in sims:
simlist.append(sims[simid])
del sims[simid]
#end if
#end for
return simlist
else:
return sims
#! /usr/bin/env python
from casino_python import settings, System
from pwscf import generate_pwscf
from analyze_results import results
settings(
rootdir="./",
pspdir="./Psps",
pspname="OPT",
pspcutoffs="psp.txt",
#pspcutoffs=280
machinename="cruller",
)
generic = System(name="Co",
structdir="./Structs",
source="icsd",
supercells=[1, 2, 3, 4],
folded=True,
real_or_complex='Complex',
mindistance=12)
sims = []
scf = generate_pwscf(system=generic, input_dft='lda')
#print generic.structures["radius.1"].kgrid
vmc_old = None
for scell in [1, 2]:
generic = System(name="Li",
structdir="./Structs",
source="icsd",
supercell_size=scell,
folded=True,
real_or_complex='Complex',
mindistance=16
#real_or_complex='Real'
)
scf = generate_pwscf(
system=generic,
input_dft='lda',
job=Job(nodes=2,
time=12,
name='dft',
app='/home/apps/espresso-5.0.3/bin/pw.x -pw2casino'))
psi = pw2casino(dft=scf)
vmc = generate_casino(dft=scf,
psi=psi,
qmc='vmc_opt',
qmc_prev=None,
job=Job(nodes=8, time=12, name='vmc', app='casino'))
vmc_old = vmc
dmc = generate_casino(dft=scf,
psi=psi,
qmc='vmc_dmc',
qmc_prev=vmc,
job=Job(nodes=80, time=12, name='vmc', app='casino'))