def get_geometry(self):
try:
geometry = read_from_record(self.root_path, 'optimized_geometry',
'geo_opt')
if isinstance(self.fixed_atoms, list) and len(
self.fixed_atoms) == 2:
geometry = Geometry(geometry=geometry,
fixed_atoms=self.fixed_atoms)
else:
geometry = Geometry(geometry=geometry)
except KeyError as e:
print(e)
print('Optimized lattice parameter not found!' 'Please check out?')
sys.exit() # here need a better way to deal with
return geometry
def geo_opt(path):
rec = 'Geometry Optimization 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(
)
record_data_json(path, 'project_name', project_name)
record_data_json(path, 'system_type', system_type)
record_data_json(path, 'lattice_parameter', lattice_parameter)
record_data_json(path, 'geometry', geometry)
record_data_json(path, 'fixed_atoms', fixed_atoms)
if isinstance(fixed_atoms, list) and len(fixed_atoms) == 2:
geometry = Geometry(geometry=geometry, fixed_atoms=fixed_atoms)
else:
geometry = Geometry(geometry=geometry)
bs, functional, nodes, crystal_path = Ini.get_geo_opt()
record_data_json(path, 'basis_set', bs, section='geo_opt')
record_data_json(path, 'functional', functional, section='geo_opt')
record_data_json(path, 'nodes', nodes, section='geo_opt')
job = os.path.join(path, 'geo_opt')
job = Job(job)
if not GeoOpt.if_job_finish(job):
# generation of INPUT
Geo_Inp = GeoOpt.Geo_Opt_Input(job, project_name, system_type,
group_type, lattice_parameter, geometry,
bs, functional)
Geo_Inp.gen_input()
# copy file and submit the job
job = GeoOpt.submit(job, nodes, crystal_path, path)
else:
job.status = 'finished'
# read and record the results
GeoOpt.read_record_result(job, path)
rec = 'Geometry optimization finished!\n'
rec += '***' * 25
print(rec)
record(path, rec)
def get_geometry(self):
path = self.hf1_job.root_path
json_file = os.path.join(path, 'opt_geo_and_latt.json')
with open(json_file, 'r') as f:
data = json.load(f)
geo_data = data['geometry']
coor = '({}, {})'.format(self.hf1_job.x, self.hf1_job.z)
try:
geometry = geo_data[coor]
if type(self.fixed_atoms) == list and len(self.fixed_atoms) == 2:
geometry = Geometry(json_form=geometry,
fixed_atoms=self.fixed_atoms)
else:
geometry = Geometry(json_form=geometry)
except KeyError as e:
print(e)
print('Geometry not found!' 'Please check out?')
sys.exit() # here need a better way to deal with
return geometry
def get_diff_geometry(self):
new_geometrys = []
new_geometrys_dict = {}
z_coord = []
for atom in self.upper_layer:
z = float(atom[4])
z_coord.append(z)
for dist in self.delta_distances:
# print(dist)
new_upper_layer = deepcopy(self.upper_layer)
for i in range(len(self.upper_layer)):
new_atom_z = z_coord[i] + dist
new_atom_z = round(new_atom_z, 12)
new_upper_layer[i][4] = new_atom_z
new_geometry = new_upper_layer + self.under_layer
new_geometry = Geometry(geometry=new_geometry)
new_geometrys.append(new_geometry)
new_geometrys_dict[dist] = new_geometry
return new_geometrys_dict
def get_new_geometrys(self):
new_geometrys = []
new_geometrys_dict = {}
x_coord = []
for atom in self.upper_layer:
x = float(atom[2])
x_coord.append(x)
if self.shift_series != 'default':
self.delta_displacement = [s for s in self.shift_series if s != 0
] # setting the relative shift manually
for displace in self.delta_displacement:
new_upper_layer = deepcopy(self.upper_layer)
for i in range(len(self.upper_layer)):
new_x = x_coord[i] + displace
new_upper_layer[i][2] = new_x
new_geometry = new_upper_layer + self.under_layer
new_geometry = Geometry(geometry=new_geometry)
new_geometrys.append(new_geometry)
new_geometrys_dict[displace] = new_geometry
return new_geometrys_dict
def hf1(path, moni):
rec = 'First Hartree Fock Calculation begins.\n'
rec += '---' * 25
print(rec)
record(path, rec)
# read info from input.ini file
init_dist = HF1.read_init_dis(path)
Ini = ReadIni()
name, slab_or_molecule, group, lattice_parameter, number_of_atoms, geometry, fixed_atoms = Ini.get_basic_info(
)
geometry = Geometry(geometry=geometry)
bs_type, nodes, crystal_path = Ini.get_hf1()
cal_parameters = Ini.get_cal_parameters('HF1')
if nodes == '' or nodes == 'default':
nodes = 12
record_data_json(path, 'basis_set', bs_type, section='hf1')
record_data_json(path, 'nodes', nodes, section='hf1')
jobs_GeoOpt = HF1.select_jobs(path)
jobs_HF1 = []
new_jobs = []
hf1_jobs_finished = []
# input for the whole system
# print('number Geo Opt', len(jobs_GeoOpt))
for job in jobs_GeoOpt:
path_GeoOpt = job.path
# Bilayer
path_HF1 = path_GeoOpt.replace('geo_opt', 'hf1')
new_job = Job(path_HF1)
if not HF1.if_cal_finish(new_job):
Inp = HF1.Input(job,
name,
slab_or_molecule,
group,
bs_type,
layertype='bilayer',
fiexed_atoms=fixed_atoms,
cal_parameters=cal_parameters,
geometry=geometry,
lattice_parameters=lattice_parameter)
Inp.gen_input()
HF1.copy_submit_scr(new_job, nodes, crystal_path)
new_jobs.append(new_job)
else:
hf1_jobs_finished.append(new_job)
jobs_HF1.append(new_job)
# upperlayer
path_upper = os.path.join(path_HF1, 'upperlayer')
new_job = Job(path_upper)
if not HF1.if_cal_finish(new_job):
Inp = HF1.Layer_Inp(job,
name,
slab_or_molecule,
group,
bs_type,
layertype='upperlayer',
fiexed_atoms=fixed_atoms,
cal_parameters=cal_parameters)
Inp.gen_input()
HF1.copy_submit_scr(new_job, nodes, crystal_path)
new_jobs.append(new_job)
else:
hf1_jobs_finished.append(new_job)
jobs_HF1.append(new_job)
# underlayer
path_under = os.path.join(path_HF1, 'underlayer')
new_job = Job(path_under)
if not HF1.if_cal_finish(new_job):
Inp = HF1.Layer_Inp(job,
name,
slab_or_molecule,
group,
bs_type,
layertype='underlayer',
fiexed_atoms=fixed_atoms,
cal_parameters=cal_parameters)
Inp.gen_input()
HF1.copy_submit_scr(new_job, nodes, crystal_path)
new_jobs.append(new_job)
else:
hf1_jobs_finished.append(new_job)
jobs_HF1.append(new_job)
# Submit the calculation job
hf1_jobs_finished_new = HF1.submit(new_jobs, nodes, crystal_path, moni)
hf1_jobs_finished += hf1_jobs_finished_new
# read calculation results
HF1.read_all_results_hf1(hf1_jobs_finished, init_dist)
# deal with not-converged jobs
# jobs_not_converged = [job for job in hf1_jobs_finished if job.status == 'not converged']
# hf1_jobs_finished = [job for job in hf1_jobs_finished if job.status != 'not converged']
# # try to not use GUESSP
# for job in jobs_not_converged:
# HF1.delete_guessp(job)
# new_jobs_finished = HF1.submit(jobs_not_converged)
# hf1_jobs_finished += new_jobs_finished
# jobs_not_converged = [job for job in hf1_jobs_finished if job.status == 'not converged']
# hf1_jobs_finished = [job for job in hf1_jobs_finished if job.status != 'not converged']
# # if still not converged, try to change some parameters
# while len(jobs_not_converged) > 0:
# HF1.change_parameters(jobs_not_converged)
# new_jobs_finished = HF1.submit(jobs_not_converged)
# hf1_jobs_finished += hf1_jobs_finished_new
# jobs_not_converged = [job for job in hf1_jobs_finished if job.status == 'not converged']
# hf1_jobs_finished = [job for job in hf1_jobs_finished if job.status != 'not converged']
rec = 'HF1 finished!\n'
rec += '***' * 25
print(rec)
record(path, rec)
def hf1_start(path, moni):
rec = 'First Hartree Fock Calculation begins.\n'
rec += '---' * 25
print(rec)
record(path, rec)
# read infos from input.ini file
Ini = ReadIni()
name, slab_or_molecule, group, lattice_parameter, number_atoms, geometry, fixed_atoms = Ini.get_basic_info(
)
distance_series, shift_series = Ini.get_series()
cal_parameters = Ini.get_cal_parameters('Geo_Opt')
record_data_json(path, 'project_name', name)
record_data_json(path, 'system_type', slab_or_molecule)
record_data_json(path, 'lattice_parameter', lattice_parameter)
record_data_json(path, 'geometry', geometry)
record_data_json(path, 'fixed_atoms', fixed_atoms)
if isinstance(fixed_atoms, list) and len(fixed_atoms) == 2:
geometry = Geometry(geometry=geometry, fixed_atoms=fixed_atoms)
else:
geometry = Geometry(geometry=geometry)
original_geometry = deepcopy(geometry)
bs_type, nodes, crystal_path = Ini.get_hf1()
cal_parameters = Ini.get_cal_parameters('HF1')
if nodes == '' or nodes == 'default':
nodes = 12
record_data_json(path, 'basis_set', bs_type, section='hf1')
record_data_json(path, 'nodes', nodes, section='hf1')
jobs_HF1 = []
new_jobs = []
hf1_jobs_finished = []
# generation of the first INPUT
dirname = 'x_0/z_0'
job = os.path.join(path, 'hf1')
job = os.path.join(job, dirname)
job = Job(job)
jobs_finished = []
GeoOPt.write_init_dist(geometry, path)
job_geo_dict = {job: geometry}
# Generation of the job with different layer distance
diff_distances = GeoOPt.Range_of_Distances(geometry, distance_series)
geo_with_diff_distance = diff_distances.get_geo_series()
init_distance = diff_distances.init_distance
for distance, geometry in geo_with_diff_distance.items():
new_job = deepcopy(job)
new_z_dirname = 'z_{0:.3f}'.format(distance)
new_job.reset('z_dirname', new_z_dirname)
job_geo_dict[new_job] = geometry
# Generation of the job with different displacement, produce ((0.1, 0),
# (0.25, 0), (0.35, 0), (0.5, 0))
range_of_displacement = GeoOPt.Range_of_Displacement(
original_geometry, shift_series)
geo_with_diff_displacement = range_of_displacement.get_geo_series()
job_geo_dict_dis = {}
for displacement, geometry in geo_with_diff_displacement.items():
new_job = deepcopy(job)
new_x_dirname = 'x_{0:.2f}'.format(displacement)
new_job.reset('x_dirname', new_x_dirname)
job_geo_dict_dis[new_job] = geometry
job_geo_dict[new_job] = geometry
# generate jobs with various distance under different relatvie shifts
for shift, geometry in geo_with_diff_displacement.items():
Geo_with_diff_Dis_diff_Distance = GeoOPt.Range_of_Distances(
geometry, distance_series)
geo_with_diff_dis_diff_distance = Geo_with_diff_Dis_diff_Distance.get_geo_series(
)
distances = sorted(geo_with_diff_dis_diff_distance.keys())
loc = 3
for i in range(len(distances)):
if distances[i - 1] <= 0 and distances[i] >= 0:
loc = i
# Select the some of the distance values
for key in list(geo_with_diff_dis_diff_distance.keys()):
if key not in distances[loc - 2:loc + 2]:
del geo_with_diff_dis_diff_distance[key]
# print(list(geo_with_diff_dis_diff_distance.keys()))
for distance, geo in geo_with_diff_dis_diff_distance.items():
dirname = 'x_{0:.2f}/z_{1:.3f}'.format(shift, distance)
new_path = os.path.join(path, os.path.join('geo_opt', dirname))
new_job = Job(new_path)
# print(new_job)
job_geo_dict[new_job] = geo
# generation all INPUT files
for job, geometry in job_geo_dict.items():
if not HF1.if_cal_finish(job):
# print('JOB not finished yet: ', job)
HF1_Inp = HF1.Input(job,
name,
slab_or_molecule,
group,
bs_type,
layertype='bilayer',
fiexed_atoms=fixed_atoms,
cal_parameters=cal_parameters,
geometry=geometry,
lattice_parameters=lattice_parameter)
HF1_Inp.gen_input()
HF1.copy_submit_scr(job, nodes, crystal_path)
new_jobs.append(job)
else:
jobs_finished.append(job)
jobs_HF1.append(job)
# deal with layers
# upperlayer
path_upper = os.path.join(job.path, 'upperlayer')
upper_job = Job(path_upper)
if not HF1.if_cal_finish(upper_job):
Inp = HF1.Layer_Inp(job,
name,
slab_or_molecule,
group,
bs_type,
layertype='upperlayer',
fiexed_atoms=fixed_atoms,
cal_parameters=cal_parameters,
geometry=geometry,
lattice_parameters=lattice_parameter)
Inp.gen_input()
HF1.copy_submit_scr(upper_job, nodes, crystal_path)
new_jobs.append(upper_job)
else:
hf1_jobs_finished.append(upper_job)
jobs_HF1.append(upper_job)
# underlayer
path_under = os.path.join(job.path, 'underlayer')
under_job = Job(path_under)
if not HF1.if_cal_finish(under_job):
Inp = HF1.Layer_Inp(job,
name,
slab_or_molecule,
group,
bs_type,
layertype='underlayer',
fiexed_atoms=fixed_atoms,
cal_parameters=cal_parameters,
geometry=geometry,
lattice_parameters=lattice_parameter)
Inp.gen_input()
HF1.copy_submit_scr(under_job, nodes, crystal_path)
new_jobs.append(under_job)
else:
hf1_jobs_finished.append(under_job)
jobs_HF1.append(upper_job)
# Submit the calculation job
hf1_jobs_finished_new = HF1.submit(new_jobs, nodes, crystal_path, moni)
hf1_jobs_finished += hf1_jobs_finished_new
# read calculation results
init_dist = HF1.read_init_dis(path)
HF1.read_all_results_hf1(hf1_jobs_finished, init_dist)
rec = 'HF1 finished!\n'
rec += '***' * 25
print(rec)
record(path, rec)
def geo_opt(path, moni):
rec = 'Geometry Optimization begins.'
print(rec)
record(path, rec)
GeoOPt.creat_geo_lat_json(path) # might be deleted
# read infos from input.ini file
Ini = ReadIni()
name, slab_or_molecule, group, lattice_parameter, number_atoms, geometry, fixed_atoms = Ini.get_basic_info()
distance_series, shift_series = Ini.get_series()
cal_parameters = Ini.get_cal_parameters('Geo_Opt')
record_data_json(path, 'project_name', name)
record_data_json(path, 'system_type', slab_or_molecule)
record_data_json(path, 'lattice_parameter', lattice_parameter)
record_data_json(path, 'geometry', geometry)
record_data_json(path, 'fixed_atoms', fixed_atoms)
if isinstance(fixed_atoms, list) and len(fixed_atoms) == 2:
geometry = Geometry(geometry=geometry, fixed_atoms=fixed_atoms)
else:
geometry = Geometry(geometry=geometry)
original_geometry = deepcopy(geometry)
bs_type, functional, nodes, crystal_path = Ini.get_geo_opt()
record_data_json(path, 'basis_set', bs_type, section='geo_opt')
record_data_json(path, 'functional', functional, section='geo_opt')
record_data_json(path, 'nodes', nodes, section='geo_opt')
# test_ini_read(group, lattice_parameter, number_atoms, slab_or_molecule)
jobs = []
new_jobs = []
# generation of the first INPUT
dirname = 'x_0/z_0'
job = os.path.join(path, 'geo_opt')
job = os.path.join(job, dirname)
job = Job(job)
jobs_finished = []
if not if_cal_finish(job):
Geo_Inp = GeoOPt.Geo_Opt_Input(
job,
name,
slab_or_molecule,
group,
lattice_parameter,
geometry,
bs_type,
functional,
cal_parameters)
Geo_Inp.gen_input()
new_jobs.append(job)
else:
jobs_finished.append(job)
jobs.append(job)
GeoOPt.write_init_dist(geometry, path)
job_geo_dict = {}
# Generation of the job with different layer distance
diff_distances = GeoOPt.Range_of_Distances(geometry, distance_series)
geo_with_diff_distance = diff_distances.get_geo_series()
init_distance = diff_distances.init_distance
for distance, geometry in geo_with_diff_distance.items():
new_job = deepcopy(job)
new_z_dirname = 'z_{0:.3f}'.format(distance)
new_job.reset('z_dirname', new_z_dirname)
job_geo_dict[new_job] = geometry
# Generation of the job with different displacement, produce ((0.1, 0),
# (0.25, 0), (0.35, 0), (0.5, 0))
range_of_displacement = GeoOPt.Range_of_Displacement(
original_geometry, shift_series)
geo_with_diff_displacement = range_of_displacement.get_geo_series()
job_geo_dict_dis = {}
for displacement, geometry in geo_with_diff_displacement.items():
new_job = deepcopy(job)
new_x_dirname = 'x_{0:.2f}'.format(displacement)
new_job.reset('x_dirname', new_x_dirname)
job_geo_dict_dis[new_job] = geometry
job_geo_dict[new_job] = geometry
# generate jobs with various distance under different relatvie shifts
for shift, geometry in geo_with_diff_displacement.items():
Geo_with_diff_Dis_diff_Distance = GeoOPt.Range_of_Distances(geometry, distance_series)
geo_with_diff_dis_diff_distance = Geo_with_diff_Dis_diff_Distance.get_geo_series()
distances = list(geo_with_diff_dis_diff_distance.keys())
distances.sort()
loc = 3
for i in range(len(distances)):
if distances[i-1] <= 0 and distances[i] >= 0:
loc = i
# Select the some of the distance values
for key in list(geo_with_diff_dis_diff_distance.keys()):
if key not in distances[loc-2:loc+2]:
del geo_with_diff_dis_diff_distance[key]
# print(list(geo_with_diff_dis_diff_distance.keys()))
for distance, geo in geo_with_diff_dis_diff_distance.items():
dirname = 'x_{0:.2f}/z_{1:.3f}'.format(shift, distance)
new_path = os.path.join(path, os.path.join('geo_opt', dirname))
new_job = Job(new_path)
# print(new_job)
job_geo_dict[new_job] = geo
# generation all INPUT files besides the first one above
for job, geometry in job_geo_dict.items():
if not if_cal_finish(job):
# print('JOB not finished yet: ', job)
Geo_Inp = GeoOPt.Geo_Opt_Input(
job,
name,
slab_or_molecule,
group,
lattice_parameter,
geometry,
bs_type,
functional,
cal_parameters)
Geo_Inp.gen_input()
new_jobs.append(job)
else:
jobs_finished.append(job)
jobs.append(job)
# Copy files and Submit the calculation job above
new_jobs_finished = GeoOPt.submit(
new_jobs, nodes, crystal_path, moni)
jobs_finished += new_jobs_finished
# # Select the optimal distance of each x point
# para = [
# name,
# slab_or_molecule,
# group,
# lattice_parameter,
# bs_type,
# functional,
# nodes,
# crystal_path]
# # x_10
# x_10 = {job: geometry for job, geometry in job_geo_dict_dis.items()
# if job.x == '0.10'}
# jobs_10 = [job for job in job_geo_dict_dis.keys() if job.x == '0.10']
# init_job_10 = jobs_10[0]
# jobs_10, x_10, min_job_10, jobs_10_finished = GeoOPt.select_optimal_dist(
# x_10, 0, para)
# jobs += jobs_10
# # x_25
# x_25 = {job: geometry for job, geometry in job_geo_dict_dis.items()
# if job.x == '0.25'}
# jobs_25 = [job for job in job_geo_dict_dis.keys() if job.x == '0.25']
# init_job_25 = jobs_25[0]
# pos_min_10 = look_for_in_list(jobs_10, min_job_10)
# pos_init_10 = look_for_in_list(jobs_10, init_job_10)
# diff = pos_min_10 - pos_init_10
# jobs_25, x_25, min_job_25, jobs_25_finished = GeoOPt.select_optimal_dist(
# x_25, diff, para)
# jobs += jobs_25
# # x_35
# x_35 = {job: geometry for job, geometry in job_geo_dict_dis.items()
# if job.x == '0.35'}
# init_job_35 = list(x_35.keys())[0]
# pos_min_25 = look_for_in_list(jobs_25, min_job_25)
# pos_init_25 = look_for_in_list(jobs_25, init_job_25)
# diff = pos_min_25 - pos_init_25
# jobs_35, x_35, min_job_35, jobs_35_finished = GeoOPt.select_optimal_dist(
# x_35, diff, para)
# jobs += jobs_35
# # x_50
# x_50 = {job: geometry for job, geometry in job_geo_dict_dis.items()
# if job.x == '0.50'}
# init_job_50 = list(x_50.keys())[0]
# pos_min_35 = look_for_in_list(jobs_35, min_job_35)
# pos_init_35 = look_for_in_list(jobs_35, init_job_35)
# diff = pos_min_35 - pos_init_35
# jobs_50, x_50, min_job_50, jobs_50_finished = GeoOPt.select_optimal_dist(
# x_50, diff, para)
# jobs += jobs_50
#
# # read calculation results
# jobs_finished += jobs_10_finished
# jobs_finished += jobs_25_finished
# jobs_finished += jobs_35_finished
# jobs_finished += jobs_50_finished
GeoOPt.read_all_results(jobs_finished, init_distance)
rec = 'Geometry optimization finished!\n'
rec += '***'*25
print(rec)
record(path, rec)