def make_variations(self):
source = self.source
source_info = self.source_info
build_order = self.build_order
variable_order = self.variable_order
build_delimiter = self.build_delimiter
variable_delimiter = self.variable_delimiter
boset = set(build_order)
voset = set(variable_order)
invalid = boset - self.build_vars
if len(invalid) > 0:
self.error(
'variables provided in build_order are invalid\n invalid entries: '
+ str(list(invalid)) + '\b valid options are: ' +
str(list(self.build_vars)))
#end if
#assume template input file source for now
qpinput, wf_h5file, pp_files, system, source_path = self.source_info.tuple(
'input', 'wf_h5file', 'pp_files', 'system', 'path')
#get the current date and time
now = datetime.now()
date_time = datetime.strftime(now, '%y%m%d_%H%M%S')
errors = False
for variation in self.variations:
error = False
vars = set(variation.keys())
build_vars = vars & self.build_vars
job_vars = vars & self.job_vars
inflag_vars = vars & self.inflag_vars
input_vars = vars - build_vars - job_vars - inflag_vars
invars = inflag_vars | input_vars
if build_vars < boset:
self.error(
'not enough build variables in variation\n build variables required: '
+ str(build_order),
exit=False,
trace=False)
error = True
#end if
if invars < voset:
self.error(
'not enough input variables in variation\n input variables required: '
+ str(variable_order),
exit=False,
trace=False)
error = True
#end if
# determine the build directory
build_list = []
build_dir = ''
for var in build_order:
if var in variation:
val = variation[var]
build_list.append(val)
if var == 'revision' and isinstance(val, int):
val = 'r' + str(val)
#end if
build_dir += str(val) + build_delimiter
else:
self.error('variable ' + str(var) +
' in build_order is not in variation',
exit=False,
trace=False)
error = True
#end if
#end for
if len(build_list) > 0:
build_dir = build_dir[:-len(build_delimiter)]
#end if
# determine the input var directory
var_list = []
var_dir = ''
for var in variable_order:
if var in variation:
val = variation[var]
var_list.append(val)
var_dir += '{0}-{1}{2}'.format(var, val,
variable_delimiter)
else:
self.error('variable ' + str(var) +
' in variable_order is not in variation',
exit=False,
trace=False)
error = True
#end if
#end for
if len(var_list) > 0:
var_dir = var_dir[:-len(variable_delimiter)]
#end if
if error:
self.error(' variation provided:\n' + str(variation),
exit=False,
trace=False)
#end if
# make the job object
jin = variation.obj(*job_vars)
if len(inflag_vars) > 0:
inflags = ''
for var in inflag_vars:
val = variation[var]
if val:
inflags += ' --' + var
#end if
#end for
jin.app_flags = inflags
#end if
job = Job(**jin)
# set the simulation path
path = os.path.join(self.name, self.machine, var_dir,
build_dir + build_delimiter + date_time)
# fill out the template input file
# assume simple and unique find and replace variations for now
input = qpinput.copy()
assignments = variation.obj(*input_vars)
input.assign(**assignments)
# add the relative path location of the wavefunction file
runpath = os.path.join(nexus_core.local_directory, nexus_core.runs,
path)
wftmp = os.path.join(source_path, wf_h5file)
wfpath = os.path.relpath(wftmp, runpath)
ds = input.get('determinantset')
if ds != None:
ds.href = wfpath
#end if
# check that the build exists
app_loc = os.path.join(self.build_path, build_dir, self.app_loc)
if not os.path.exists(app_loc) and not nexus_core.generate_only:
print ' Error: no qmcapp at ' + app_loc
error = True
#end if
job.app_name = app_loc
# locate pp files
files = []
if pp_files != None:
files = list(pp_files)
#end if
# make the simulation object
qmc = Qmcpack(identifier='qmc',
path=path,
job=job,
system=system,
input=input,
files=files)
self.sims[tuple(var_list + build_list)] = qmc
# add it to the global simulation list
self.simulations.append(qmc)
errors = errors or error
#end for
if errors:
self.error('errors encountered, see above')
kshift=(0, 0, 0),
net_charge=0,
net_spin=0,
C=4 # one line like this for each atomic species
)
my_bconds = 'ppp' # ppp/nnn for periodic/open BC's in QMC
# if nnn, center atoms about (a1+a2+a3)/2
sims = []
# scf run to generate orbitals
scf = generate_pwscf(
identifier='scf',
path=my_project_name,
job=Job(nodes=32, hours=2, app=pwscf),
input_type='scf',
system=my_system,
pseudos=my_dft_pps,
input_dft='lda',
ecut=200, # PW energy cutoff in Ry
conv_thr=1e-8,
mixing_beta=.7,
nosym=True,
wf_collect=True)
sims.append(scf)
# conversion step to create h5 file with orbitals
p2q = generate_pw2qmcpack(identifier='p2q',
path=my_project_name,
job=Job(cores=1, hours=2, app=pw2qmcpack),
def make_variations(self):
source = self.source
source_info = self.source_info
build_order = self.build_order
variable_order = self.variable_order
build_delimiter = self.build_delimiter
variable_delimiter = self.variable_delimiter
boset = set(build_order)
voset = set(variable_order)
invalid = boset - self.build_vars
if len(invalid)>0:
self.error('variables provided in build_order are invalid\n invalid entries: '+str(list(invalid))+'\b valid options are: '+str(list(self.build_vars)))
#end if
#assume template input file source for now
qpinput,wf_h5file,pp_files,system,source_path = self.source_info.tuple('input','wf_h5file','pp_files','system','path')
#get the current date and time
now = datetime.now()
date_time = datetime.strftime(now,'%y%m%d_%H%M%S')
errors = False
for variation in self.variations:
error = False
vars = set(variation.keys())
build_vars = vars & self.build_vars
job_vars = vars & self.job_vars
inflag_vars = vars & self.inflag_vars
input_vars = vars-build_vars-job_vars-inflag_vars
invars = inflag_vars | input_vars
if build_vars<boset:
self.error('not enough build variables in variation\n build variables required: '+str(build_order),exit=False,trace=False)
error = True
#end if
if invars<voset:
self.error('not enough input variables in variation\n input variables required: '+str(variable_order),exit=False,trace=False)
error = True
#end if
# determine the build directory
build_list = []
build_dir = ''
for var in build_order:
if var in variation:
val = variation[var]
build_list.append(val)
if var=='revision' and isinstance(val,int):
val = 'r'+str(val)
#end if
build_dir += str(val)+build_delimiter
else:
self.error('variable '+str(var)+' in build_order is not in variation',exit=False,trace=False)
error = True
#end if
#end for
if len(build_list)>0:
build_dir = build_dir[:-len(build_delimiter)]
#end if
# determine the input var directory
var_list = []
var_dir = ''
for var in variable_order:
if var in variation:
val = variation[var]
var_list.append(val)
var_dir += '{0}-{1}{2}'.format(var,val,variable_delimiter)
else:
self.error('variable '+str(var)+' in variable_order is not in variation',exit=False,trace=False)
error = True
#end if
#end for
if len(var_list)>0:
var_dir = var_dir[:-len(variable_delimiter)]
#end if
if error:
self.error(' variation provided:\n'+str(variation),exit=False,trace=False)
#end if
# make the job object
jin = variation.obj(*job_vars)
if len(inflag_vars)>0:
inflags = ''
for var in inflag_vars:
val = variation[var]
if val:
inflags+=' --'+var
#end if
#end for
jin.app_flags = inflags
#end if
job = Job(**jin)
# set the simulation path
path = os.path.join(self.name,self.machine,var_dir,build_dir+build_delimiter+date_time)
# fill out the template input file
# assume simple and unique find and replace variations for now
input = qpinput.copy()
assignments = variation.obj(*input_vars)
input.assign(**assignments)
# add the relative path location of the wavefunction file
runpath = os.path.join(Pobj.local_directory,Pobj.runs,path)
wftmp = os.path.join(source_path,wf_h5file)
wfpath = os.path.relpath(wftmp,runpath)
ds = input.get('determinantset')
if ds!=None:
ds.href = wfpath
#end if
# check that the build exists
app_loc = os.path.join(self.build_path,build_dir,self.app_loc)
if not os.path.exists(app_loc) and not self.generate_only:
print ' Error: no qmcapp at '+app_loc
error = True
#end if
job.app_name = app_loc
# locate pp files
files = []
if pp_files!=None:
files = list(pp_files)
#end if
# make the simulation object
qmc = Qmcpack(
identifier = 'qmc',
path = path,
job = job,
system = system,
input = input,
files = files
)
self.sims[tuple(var_list+build_list)] = qmc
# add it to the global simulation list
self.simulations.append(qmc)
errors = errors or error
#end for
if errors:
self.error('errors encountered, see above')
supercell_kgrids = [
(1, 1, 1), # 1 k-point
(2, 2, 2), # 8 k-points
(4, 4, 4), # 64 k-points
(6, 6, 6)
] # 216 k-points
# describe the relaxation calculations
# and link them together into a simulation cascade
relaxations = [] # list of relax simulation objects
for kgrid in supercell_kgrids: # loop over supercell kgrids
relax = generate_pwscf( # make each relax simulation
identifier='relax', # file prefix
# run directory
path='relax/kgrid_{0}{1}{2}'.format(*kgrid),
job=Job(cores=16), # will run with mpirun -np 16
input_type='relax', # this is a relax calculation
input_dft='pbe', # PBE functional
ecut=50, # 50 Ry planewave cutoff
conv_thr=1e-6, # convergence threshold
kgrid=kgrid, # supercell k-point grid
kshift=(1, 1, 1), # grid centered at supercell L point
pseudos=['Ge.pbe-kjpaw.UPF'], # PBE pseudopotential
system=T_system # the interstitial system
)
# link together the simulation cascade
# current relax gets structure from previous
if len(relaxations) > 0: # if it exists
relax.depends(relaxations[-1], 'structure')
#end if
relaxations.append(relax) # add relax simulation to the list
net_spin=0, # net spin in units of e-spin
C=4 # C has 4 valence electrons
)
#generate the simulations for the qmc workflow
qsims = basic_qmc(
# subdirectory of runs
directory='c20_test',
# description of the physical system
system=c20,
pseudos=[
'C.BFD.upf', # pwscf PP file
'C.BFD.xml'
], # qmcpack PP file
# job parameters
scfjob=Job(cores=16), # cores to run scf
optjob=Job(
cores=16, # cores for optimization
app_name='qmcapp'), # use real-valued qmcpack
qmcjob=Job(
cores=16, # cores for qmc
app_name='qmcapp'), # use real-valued qmcpack
# dft parameters (pwscf)
functional='lda', # dft functional
ecut=150, # planewave energy cutoff (Ry)
conv_thr=1e-6, # scf convergence threshold (Ry)
mixing_beta=.7, # charge mixing factor
# qmc wavefunction parameters (qmcpack)
bconds='nnn', # open boundary conditions
meshfactor=1.0, # bspline grid spacing, larger is finer
jastrows=[
kshift=(.5, .5, .5), # and shift
C=4 # C has 4 valence electrons
)
#generate the simulations for the qmc workflow
qsims = standard_qmc(
# subdirectory of runs
directory='graphene_test',
# description of the physical system
system=graphene,
pseudos=[
'C.BFD.upf', # pwscf PP file
'C.BFD.xml'
], # qmcpack PP file
# job parameters
scfjob=Job(cores=16), # cores to run scf
nscfjob=Job(cores=16), # cores to run non-scf
optjob=Job(cores=16), # cores for optimization
qmcjob=Job(cores=16), # cores for qmc
# dft parameters (pwscf)
functional='lda', # dft functional
ecut=150, # planewave energy cutoff (Ry)
conv_thr=1e-6, # scf convergence threshold (Ry)
mixing_beta=.7, # charge mixing factor
scf_kgrid=(8, 8, 8), # MP grid of primitive cell
scf_kshift=(1, 1, 1), # to converge charge density
# qmc wavefunction parameters (qmcpack)
meshfactor=1.0, # bspline grid spacing, larger is finer
jastrows=[
dict(
type='J1', # 1-body