def cluster(path):
rec = 'Cluster Cutting begins.\n'
rec += '---' * 25
print(rec)
record(path, rec)
# read parameters from ini file
Ini = ReadIni()
name, slab_or_molecule, group, lattice_parameter, number_of_atoms, geometry, fixed_atoms = Ini.get_basic_info(
)
center_atoms, factors, deleted_atoms, coord, add_h, out_layer_number = Ini.get_cluster(
)
cutting_setting = [coord, add_h]
record_data_json(path, 'central atoms', center_atoms, section='cluster')
record_data_json(path, 'cutting factors', factors, section='cluster')
record_data_json(path, 'deleted atoms', deleted_atoms, section='cluster')
cutting_setting_dict = {
'coord': coord,
'add_h': add_h,
'out_layer_number': out_layer_number
}
record_data_json(path,
'cutting setting',
cutting_setting_dict,
section='cluster')
# get bilayer jobs
rpa_jobs = get_jobs(path)
cluster_jobs = [job for job in rpa_jobs if job.layertype == 'bilayer']
for job in cluster_jobs:
if 'rpa' in job.path:
job.path = job.path.replace('rpa', 'cluster')
elif 'geo_opt' in job.path:
job.path = job.path.replace('geo_opt', 'cluster')
job.method = 'cluster'
# generate clusters
cluster_path = os.path.join(path, 'cluster')
mkdir(cluster_path)
Cluster.creat_json_file(cluster_path)
for job in cluster_jobs:
Clu = Cluster.ClusterCutter(job,
center=center_atoms,
name=name,
fixed_atoms=fixed_atoms,
factors=factors,
cutting_setting=cutting_setting,
deleted_atoms=deleted_atoms)
if not Cluster.if_cluster_already_generated(job):
Clu.get_cluster()
if out_layer_number is True:
Clu.write_xyz_with_layernumber()
else:
Clu.write_xyz()
rec = 'Cluster Cutting finished!\n'
rec += '***' * 25
print(rec)
record(path, rec)
def write_xyz_with_layernumber(self, cluster=[]):
if len(self.choosed_atoms) == 0:
self.get_cluster()
if len(cluster) == 0:
cluster = self.choosed_atoms
file_name = '{}_Cluster.xyz'.format(self.name)
file_path = os.path.join(self.cluster_path, file_name)
if not os.path.exists(self.cluster_path):
mkdir(self.cluster_path)
with open(file_path, 'w') as f:
f.write(str(len(cluster)) + '\n')
f.write('{}_Cluster'.format(self.name) + '\n')
for atom in cluster:
ele = periodic_table_rev[int(atom.nat)]
f.write((str(ele) + str(atom.layer)).center(6) + ' ')
f.write('{:.12E}'.format(float(atom.x)).rjust(19) + ' ')
f.write('{:.12E}'.format(float(atom.y)).rjust(19) + ' ')
f.write('{:.12E}'.format(float(atom.z)).rjust(19))
f.write('\n')
rec = str(self.cluster_job) + '\n'
rec += 'Geometry file generated.\n'
rec += 'Number of atoms in cluster: {}\n'.format(len(cluster))
rec += '---' * 25
print(rec)
record(self.cluster_job.root_path, rec)
def menu():
ini_path = os.path.dirname(os.path.realpath(__file__))
ini_path = os.path.join(ini_path, 'input.ini')
Ini = ReadIni(ini_path)
path = Ini.project_path
start = Ini.start
end = Ini.end
test_begin(end, start)
now = datetime.now()
now = now.strftime("%b %d %Y %H:%M:%S")
mkdir(path)
rec = 'Project begins.'
rec += '\n' + '***'*25
rename_file(path, 'record')
record(path, rec, init=True)
print('***'*25)
print(now)
print(rec)
try:
shutil.copy(ini_path, path + '/input.ini')
except Exception as e:
print(e)
Pipeline.pipeline(path, start, end)
def write_lmp2_part1(self):
mkdir(self.lmp2_path)
with open(self.input_path, 'w') as f:
f.write('READC14' + '\n')
f.write('DUALBAS' + '\n')
f.write('KNET' + '\n')
f.write('8' + '\n')
f.write('MEMORY' + '\n')
f.write('40000' + '\n')
f.write('NOSING\n')
def write_part1(self):
mkdir(self.lmp2_path)
with open(self.input_path, 'w') as f:
f.write('READC14' + '\n')
f.write('DUALBAS' + '\n')
f.write('KNET' + '\n')
f.write('8' + '\n')
f.write('MEMORY' + '\n')
f.write('40000' + '\n')
f.write('NOSYM12' + '\n')
f.write('CLUSCOR' + '\n')
f.write('LPairlst' + '\n')
f.write('100000' + '\n')
f.write('MOG_DIST' + '\n')
f.write('9 9' + '\n')
f.write('NOSING' + '\n')
f.write('NFITCEL' + '\n')
f.write('-100' + '\n')
f.write('STREAMIN' + '\n')
f.write('SMAL3IDX' + '\n')
def copy_molpro_inp(self):
mkdir(self.rpa_path)
inp_from = self.lmp2_job.path
inp_from = os.path.join(inp_from, 'molpro.inp')
inp_to = os.path.join(self.rpa_path, 'rpa.inp')
shutil.copy(inp_from, inp_to)