def prepare_folder(self, entry_id, workdir='.', source_dir='.'):
"""
Prepare directories for abinit execution
:param entry_id: bson.ObjectID of the entry that will be used for preparing the folder
:param source_dir: (str) is the directory where 'abinit.files' and 'batch.pbs' should be present
those directories will be symbolically linked inside the individual work directories
:param workdir: (str) Base work directory for abinit executions. Inside this directory, a set of subdirectories
will be created using the mongo ID as name.
"""
# Individual workdir
iworkdir = workdir + os.sep + str(entry_id)
if not os.path.isdir(iworkdir):
os.mkdir(iworkdir)
if os.path.lexists(iworkdir + os.sep + 'abinit.files'):
os.remove(iworkdir + os.sep + 'abinit.files')
if not os.path.isfile(source_dir + os.sep + 'abinit.files'):
print(
'WARNIG: The file %s should be present on %s, symbolic links will be created pointing '
'to that location' % ('abinit.files', source_dir))
os.symlink(os.path.abspath(source_dir + os.sep + 'abinit.files'),
iworkdir + os.sep + 'abinit.files')
abiinput = AbinitInput(self.input_path)
params = self.get_correlation_params(entry_id, final=False)
dmatpawu = params2dmatpawu(params)
abiinput['dmatpawu'] = list(dmatpawu.flatten())
abiinput.write(iworkdir + os.sep + 'abinit.in')
d_abiinput = AbinitInput(iworkdir + os.sep + 'abinit.in')
d_dmatpawu = d_abiinput['dmatpawu']
assert (d_dmatpawu is not None)
d_params = dmatpawu2params(d_dmatpawu, self.ndim)
if not np.all(
np.sum(d_params['occupations'], axis=1) == np.array(
self.num_electrons_dftu)):
print(
'ERROR: Inconsistent number of DFT+U electrons for correlated orbitals: %s'
% entry_id)
print('From the population: %s ' % self.num_electrons_dftu)
print('From "abinit.in": %s ' % d_params['occupations'])
def prepare_folder(self, entry_id, workdir='.', source_dir='.'):
"""
Prepare directories for abinit execution
:param entry_id: bson.ObjectID of the entry that will be used for preparing the folder
:param source_dir: (str) is the directory where 'abinit.files' and 'batch.pbs' should be present
those directories will be symbolically linked inside the individual work directories
:param workdir: (str) Base work directory for abinit executions. Inside this directory, a set of subdirectories
will be created using the mongo ID as name.
"""
# Individual workdir
iworkdir = workdir+os.sep+str(entry_id)
if not os.path.isdir(iworkdir):
os.mkdir(iworkdir)
if os.path.lexists(iworkdir + os.sep + 'abinit.files'):
os.remove(iworkdir + os.sep + 'abinit.files')
if not os.path.isfile(source_dir + os.sep + 'abinit.files'):
print('WARNIG: The file %s should be present on %s, symbolic links will be created pointing '
'to that location' % ('abinit.files', source_dir))
os.symlink(os.path.abspath(source_dir + os.sep + 'abinit.files'), iworkdir + os.sep + 'abinit.files')
abiinput = AbinitInput(self.input_path)
params = self.get_correlation_params(entry_id, final=False)
dmatpawu = params2dmatpawu(params)
abiinput['dmatpawu'] = list(dmatpawu.flatten())
abiinput.write(iworkdir + os.sep + 'abinit.in')
d_abiinput = AbinitInput(iworkdir + os.sep + 'abinit.in')
d_dmatpawu = d_abiinput['dmatpawu']
assert(d_dmatpawu is not None)
d_params = dmatpawu2params(d_dmatpawu, self.ndim)
if not np.all(np.sum(d_params['occupations'], axis=1) == np.array(self.num_electrons_dftu)):
print('ERROR: Inconsistent number of DFT+U electrons for correlated orbitals: %s' % entry_id)
print('From the population: %s ' % self.num_electrons_dftu)
print('From "abinit.in": %s ' % d_params['occupations'])
print('Yes')
print("Checking that abinit.in contains value for lpawu...", end='')
if 'lpawu' not in abi.variables:
print('No')
raise ValueError("ERROR: Could not open abinit.in")
else:
print('Yes, max lpawu=%d' % max(abi['lpawu']))
print('Setting ABINIT variables usedmatpu=%d, nstep=%d and tolvrs=%e' %
(usedmatpu, nstep, tolvrs))
abi['usedmatpu'] = usedmatpu
abi['nstep'] = nstep
abi['tolvrs'] = tolvrs
print('Writting modified abinit.in')
abi.write('abinit.in')
# Getting the index from the last execution and adding one for the next run
index = 0
while True:
if os.path.isfile('abinit_%02d.in' % index):
index += 1
else:
break
if index >= max_nruns:
print(
"Total number of runs has been achieve already, increse 'max_nruns' if you want to continue"
)
parser.print_help()
exit(1)
if not os.path.isdir(args.basepath + os.sep + name):
os.mkdir(args.basepath + os.sep + name)
abi = AbinitInput(args.basepath + os.sep + 'abinit.in')
abi['upawu'] = ""
for i in dbi['u']:
abi['upawu'] += str(i) + " "
abi['upawu'] += 'eV'
abi['jpawu'] = ""
for i in dbi['j']:
abi['jpawu'] += str(i) + " "
abi['jpawu'] += 'eV'
abipath = args.basepath + os.sep + name + os.sep + 'abinit.in'
abi.write(abipath)
abifiles = args.basepath + os.sep + name + os.sep + 'abinit.files'
if os.path.lexists(abifiles):
os.remove(abifiles)
os.symlink(
os.path.abspath(args.basepath + os.sep + 'abinit.files'),
abifiles)
for i in [x for x in os.listdir(args.basepath) if x[-3:] == 'xml']:
psp = args.basepath + os.sep + name + os.sep + i
if os.path.lexists(psp):
os.remove(psp)
os.symlink(os.path.abspath(args.basepath + os.sep + i), psp)
popu[name] = OrbitalDFTU(pcdb, abipath)
if not os.path.isdir(args.basepath + os.sep + name):
os.mkdir(args.basepath + os.sep + name)
abi = AbinitInput(args.basepath + os.sep + 'abinit.in')
abi['upawu'] = ""
for i in dbi['u']:
abi['upawu'] += str(i) + " "
abi['upawu'] += 'eV'
abi['jpawu'] = ""
for i in dbi['j']:
abi['jpawu'] += str(i) + " "
abi['jpawu'] += 'eV'
abipath = args.basepath + os.sep + name + os.sep + 'abinit.in'
abi.write(abipath)
abifiles = args.basepath + os.sep + name + os.sep + 'abinit.files'
if os.path.lexists(abifiles):
os.remove(abifiles)
os.symlink(os.path.abspath(args.basepath + os.sep + 'abinit.files'), abifiles)
for i in [x for x in os.listdir(args.basepath) if x[-3:] == 'xml']:
psp = args.basepath + os.sep + name + os.sep + i
if os.path.lexists(psp):
os.remove(psp)
os.symlink(os.path.abspath(args.basepath + os.sep + i), psp)
popu[name] = OrbitalDFTU(pcdb, abipath)
# Specific actions for 'populate', 'run', 'search' and 'plot'
if args.subparser_name == 'populate':