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 cluster(path):
rec = 'Cluster Cutting begins.\n'
rec += '---' * 25
print(rec)
record(path, rec)
# read infos from input.ini file
Ini = IniReader()
project_name, system_type, group_type, lattice_parameter, number_atoms, geometry, fixed_atoms = Ini.get_basic_info(
)
central_atoms, factors, deleted_atoms, coord, add_h, out_layer_number = Ini.get_cluster(
)
cutting_setting = [coord, add_h]
record_data_json(path, 'central atoms', central_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')
geo_file = os.path.join(os.path.join(path, 'geo_opt'), 'geo_opt.out')
job = os.path.join(path, 'cluster')
job = Job(job)
Clu = Cluster.ClusterCutter(job,
geo_file,
factors=factors,
name=project_name,
central_atoms=central_atoms,
fixed_atoms=fixed_atoms,
cutting_setting=cutting_setting,
deleted_atoms=deleted_atoms)
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 test_MgO():
path = r'C:\Users\ccccc\Documents\Theoritische Chemie\Masterarbeit\test\cluster'
Cluster.creat_json_file(path)
job = r'C:\Users\ccccc\Documents\Theoritische Chemie\Masterarbeit\test\geo_opt\x_1\z_2'
dimen, lattice, geo = read_infomation(job)
job = Job(job)
center_upp = [25, 25]
center_und = [9, 9]
center = [center_upp, center_und]
fixed_atoms = [13, 24]
fac_upp = [0.3, 0.5, 0.5]
fac_und = [0.4, 0.6, 0.6]
factors = [fac_upp, fac_und]
Clu = Cluster.ClusterCutter(job, name='MgO', centre=center, basic_infos=[dimen, lattice, geo], factors=factors, fixed_atoms=fixed_atoms)
Clu.final_cluster = Clu.choose_atoms_from_distance()
Clu.write_xyz(Clu.choosed_atoms)
def test_cut_cluster(job):
fac_upp = [1.2, 1.8, 1.3]
fac_und = [1.2, 1.8, 1.3]
factors = [[1, 1, 0.7], [1, 1.5, 0.7]]
Clu = Cluster.ClusterCutter(job, centre=[[3, 4], [7, 8]], name='BlackP', factors=factors, size='S')
nat = Clu.nat[0]
x = Clu.x[0]
y = Clu.y[0]
z = Clu.z[0]
atom = Cluster.Atom(nat, x, y, z)
cent = Clu.centre
test_cal_dis(atom, cent, Clu)
#test_cal_vec_dis(atom, cent, Clu)
# test_choose_atom(Clu)
# test_get_layer(Clu)
# test_cal_atom_dis(Clu)
# test_cal_coordniate_number(Clu)
# test_cal_coor_all_atoms(Clu)
# test_select_atoms_according_coor(Clu)
Clu.write_xyz_with_layernumber()
def test_SiO2():
path = r'C:\Users\ccccc\Documents\Theoritische Chemie\Masterarbeit\test\cluster'
#path = r'/users/shch/project/Masterarbeit/Test/cluster'
Cluster.creat_json_file(path)
job = r'C:\Users\ccccc\Documents\Theoritische Chemie\Masterarbeit\test\geo_opt\x_1\z_1'
#job = r'/users/shch/project/Masterarbeit/Test/geo_opt/x_1/z_1'
dimen, lattice, geo = read_infomation(job)
job = Job(job)
#centre=[16, 16]
centre = [2, 4]
fac_upp = [0.85, 1.1, 1.1]
fac_und = fac_upp
factors = [fac_upp, fac_und]
deleted_atoms = [54, 49]
#deleted_atoms = []
#centre = [[2, 2], [13, 13]]
Clu = Cluster.ClusterCutter(job, name='SiO2-H2O', centre=centre, basic_infos=[dimen, lattice, geo], factors=factors, size='M', fixed_atoms=[10, 17], deleted_atoms=deleted_atoms)
original_atoms = Clu.original_atoms
cnt = 1
Clu.write_xyz()
