def __init__(self, configfile):
if os.path.isfile(configfile):
self.configfile = configfile
else:
print('file:{} is not found.'.format(configfile))
exit()
self.generator = ParseGenerator()
self.main()
def __init__(self,
min_spg_index=8,
max_spg_index=None,
natoms=1,
use_progress_bar=False):
spg = ParseGenerator()
self.min_spg_index = spg.get_ispg(min_spg_index)
if max_spg_index is None:
self.max_spg_index = spg.get_ispg(min_spg_index)
else:
self.max_spg_index = spg.get_ispg(max_spg_index)
self.natoms = natoms
self.use_tqdm = use_progress_bar
self.get_wyckoff_list()
def __init__(self, configfile):
configure = ParseConfig(configfile)
self.wyckoff = ParseWyckoff()
self.generator = ParseGenerator()
self.min_spg_index = configure.min_spg_index
self.max_spg_index = configure.max_spg_index
self.ichoice = configure.ichoice
self.main()
def set_space_group(self, ispg, ichoice=1):
ispg = ParseGenerator().get_ispg(ispg)
spg_obj = self.generator_obj.generator_list[ispg - 1][ichoice - 1]
self.schname = spg_obj.schname
self.hmname = spg_obj.hmname
self.il = spg_obj.il
wyckoff_obj = self.wyckoff_obj.wyckoff_position[ispg - 1][ichoice - 1]
self.npos = wyckoff_obj.npos
self.wyckoff_position_list = wyckoff_obj.position
self.set_position_index_list()
return self
def __init__(self, ispg, ichoice=1):
Gen_obj = ParseGenerator()
self.generator = Gen_obj.get_generator(ispg, ichoice)
self.il = Gen_obj.get_il(ispg, ichoice)
self.schname = Gen_obj.get_schname(ispg, ichoice)
self.hmname = Gen_obj.get_hmname(ispg, ichoice)
self.ispg = Gen_obj.get_ispg(ispg, ichoice)
self.ichoice = ichoice
self.define_rotation_operator()
self.initialize_operator()
self.generate_group_elements()
self.set_point_group_info()
def __init__(self):
self.generator_obj = ParseGenerator()
self.wyckoff_obj = ParseWyckoff()
import GenerateWyckoffPositionsList
from Metis.SpaceGroup.IdentifySubIndex \
import IdentifySubIndex
from Metis.SpaceGroup.ParseGenerator import ParseGenerator
import random
import sys
min_spg = 8
max_spg = 230
max_natoms = 16
max_sub_index = 0
jspg = 0
hmname = ''
schname = ''
generator = ParseGenerator()
for natoms in range(1, max_natoms):
total_pattern = 0
for ispg in range(min_spg, max_spg + 1):
wyckoff_obj = GenerateWyckoffPositionsList(min_spg_index=ispg,
natoms=natoms,
use_progress_bar=False)
wyckoff_dic = wyckoff_obj.wyckoff_list[0]['wyckoff_positions']
for i in range(len(wyckoff_dic)):
total_pattern += 1
target_list = wyckoff_dic[i]
random.shuffle(target_list)
sys.stdout.write('\r')
sys.stdout.write('> natoms = {0:>2d} '.format(natoms))
sys.stdout.write('ispg = {0:>3d} '.format(ispg))
#!/usr/bin/env python3
from Metis.SpaceGroup.ParseGenerator import ParseGenerator
import sys
def get_args():
if len(sys.argv) < 2:
print('usage {0} [ispg] [ichoice]'.format(sys.argv[0]))
exit()
ispg = sys.argv[1]
if len(sys.argv) == 2:
ichoice = 1
else:
ichoice = int(sys.argv[2])
return [ispg, ichoice]
if __name__ == '__main__':
ispg, ichoice = get_args()
obj = ParseGenerator('generator')
for gen in obj.get_generator(ispg, ichoice=ichoice):
print(gen)
def __init__(self,
configfile,
qe_inputfile='espresso_relax.in',
ispg=None,
sub_index=None,
atom_info=None,
submit_job=False,
logfile=None):
if os.path.isfile(configfile):
self.configfile = configfile
else:
print('===== Error(GenerateEspressoIn) ======')
print('file:{} is not found.'.format(configfile))
exit()
#
# temporary dir:
# if you need, you can change it.
#
self.tmpdir = os.path.join('/work', os.environ['USER'])
self.ispg = ispg
self.sub_index = sub_index
self.atom_info = atom_info
self.qe_inputfile = qe_inputfile
self.logfile = logfile
self.main()
if self.eliminate_redundancy:
compound_name = self.crystal_structure.compound_name
redundancy = CheckRedundancy()
consistency, prim_cell = redundancy.check(compound_name, self.ispg,
self.sub_index)
spg_obj = ParseGenerator()
hmname_try = spg_obj.get_hmname(self.ispg)
#
# for bug for trigonal by H.F on 5 Sep. 2019
#
if 143 <= ispg <= 164:
redundancy = False
consistency = True
# end of bug kaihi
if not consistency:
if prim_cell.ispg is None:
hmname_true = hmname_try
else:
hmname_true = spg_obj.get_hmname(prim_cell.ispg)
if hmname_try == hmname_true:
fout = open(self.logfile, 'a')
if compound_name == prim_cell.compound_name:
consistency = True
print(' Acceptation: redundancy check was passed ',
end='')
print('for DIR:{}.'.format(self.wkdir), end='')
print(' This calculation will be performed.')
fout.write(' Acceptation: ')
fout.write('redundancy check was passed ')
fout.write('for DIR:{}.'.format(self.wkdir))
fout.write(' This calculation will be performed.\n')
fout.close()
else:
print(' Redundancy : For {0:6s},'.format(self.wkdir),
end='')
fout.write(' Redundancy : For {0:6s},'.format(
self.wkdir))
print(' cell is over size', end='')
fout.write(' cell is over size')
print(' Alternative calculation ', end='')
print('will be performed in {}.'.format(
prim_cell.dirname))
fout.write(' Alternative calculation ')
fout.write('will be performed in {}.\n'.format(
prim_cell.dirname))
fout.close()
for (i, atom) in enumerate(prim_cell.atom_info):
if atom['element'] != self.atom_info[i]['element']:
print('=== Error(GenerateEspressoIn) ===')
print('logic error for prim_cell.atom_info')
exit()
prim_cell.atom_info[i]['semi_core'] =\
self.atom_info[i]['semi_core']
GenerateEspressoIn(configfile=self.configfile,
ispg=prim_cell.ispg,
qe_inputfile=qe_inputfile,
sub_index=prim_cell.sub_index,
atom_info=prim_cell.atom_info,
submit_job=submit_job,
logfile=self.logfile)
else: # space group is different case
fout = open(self.logfile, 'a')
print(' Redundancy : For {0:6s},'.format(self.wkdir),
end='')
fout.write(' Redundancy : For {0:6s},'.format(self.wkdir))
print(' you assumed the symmetry:{0}, '.format(hmname_try),
end='')
print('but metis found higher symmetry:{0}.'.format(
hmname_true),
end='')
fout.write(
' you assumed the symmetry:{0}, '.format(hmname_try))
fout.write('but metis found higher symmetry:{0}.'.format(
hmname_true))
for (i, atom) in enumerate(prim_cell.atom_info):
if atom['element'] != self.atom_info[i]['element']:
print('=== Error(GenerateEspressoIn) ===')
print('logic error for prim_cell.atom_info')
exit()
prim_cell.atom_info[i]['semi_core'] =\
self.atom_info[i]['semi_core']
if compound_name == prim_cell.compound_name:
print(' This calculation will be skipped.')
fout.write(' This calculation will be skipped.\n')
fout.close()
else:
if os.path.isdir(prim_cell.dirname):
print(' This calculation will be skipped.')
fout.write(' This calculation will be skipped.\n')
fout.close()
else:
print(' Alternative calculation ', end='')
print('will be performed in {}.'.format(
prim_cell.dirname))
fout.write(' Alternative calculation ')
fout.write('will be performed in {}.\n'.format(
prim_cell.dirname))
fout.close()
os.makedirs(prim_cell.dirname)
qe_inputfile = os.path.basename(self.qe_inputfile)
GenerateEspressoIn(configfile=self.configfile,
ispg=prim_cell.ispg,
qe_inputfile=qe_inputfile,
sub_index=prim_cell.sub_index,
atom_info=prim_cell.atom_info,
submit_job=submit_job,
logfile=self.logfile)
if not consistency:
if os.path.isdir(self.wkdir):
shutil.rmtree(self.wkdir)
return
else:
fout = open(self.logfile, 'a')
print(' Acceptation: redundancy check was passed ', end='')
print('for DIR:{}.'.format(self.wkdir), end='')
print(' This calculation will be performed.')
fout.write(' Acceptation: redundancy check was passed ')
fout.write('for DIR:{}.'.format(self.wkdir))
fout.write(' This calculation will be performed.\n')
fout.close()
if submit_job:
self.submit_job()
class ParseConfig(object):
def __init__(self, configfile):
if os.path.isfile(configfile):
self.configfile = configfile
else:
print('file:{} is not found.'.format(configfile))
exit()
self.generator = ParseGenerator()
self.main()
def main(self):
self.set_default_value()
self.parse()
self.check_spg()
def get_linebuf(self, line):
linebuf = line.strip()
if '#' in linebuf:
linebuf = linebuf.split('#')[0].strip()
return linebuf
def get_key_and_value(self, linedata, token='='):
if token not in linedata:
return [None, None]
key, value = [x.strip() for x in linedata.split(token)[:2]]
key = key.lower()
return [key, value]
def spg2ispg(self, spg):
return self.generator.get_ispg(spg)
def set_default_value(self):
self.min_spg_index = None
self.max_spg_index = None
self.ichoice = 1
def check_spg(self):
if [self.min_spg_index, self.max_spg_index] == [None] * 2:
print('space group is not defined')
exit()
if self.min_spg_index is not None:
if self.max_spg_index is None:
self.max_spg_index = self.min_spg_index
if self.max_spg_index is not None:
if self.min_spg_index is None:
self.mim_spg_index = self.max_spg_index
if self.min_spg_index > self.max_spg_index:
self.min_spg_index, self.max_spg_index =\
self.max_spg_index, self.min_spg_index
def parse(self):
for line in open(self.configfile, 'r'):
linebuf = self.get_linebuf(line)
if linebuf == '':
continue
if '=' in linebuf:
key, value = self.get_key_and_value(linebuf)
if key is None:
continue
if value == '':
continue
if key == 'min_spg_index':
self.min_spg_index = self.spg2ispg(value)
elif key == 'max_spg_index':
self.max_spg_index = self.spg2ispg(value)
elif key == 'ichoice':
self.ichoice = int(value)