def test_if_cal_finish():
path = r'C:\Users\ccccc\PycharmProjects\Layer_Structure_Caculation\test_may\cluster\x_0\z_-0.106'
job = Job(path)
# job.method = 'avdz_iext1_lmp2'
job.method = 'avdz_lmp2_cc'
finished = Correction.if_cal_finish(job)
print(finished)
def test_read_results():
path = r'C:\Users\ccccc\PycharmProjects\Layer_Structure_Caculation\Test\cluster\x_0\z_0'
job = Job(path)
job.method = 'avtz_iext1_rpa'
Res = Correction.Result(job)
Res.get_energy()
print(Res.energy, Res.unit)
Res.unit_transform()
print(Res.energy, Res.unit)
def test_read_results():
path = r'C:\Users\ccccc\PycharmProjects\Layer_Structure_Caculation\test_may\cluster\x_0\z_-0.106'
job = Job(path)
job.method = 'avdz_iext1_lmp2'
Res = Correction.Result(job, ll='lmp2')
Res.get_energy()
print(Res.energy, Res.unit)
Res.unit_transform()
print(Res.energy, Res.unit)
def test_if_finished():
path = os.getcwd()
path = path + '/Test/rpa/x_-0.150/z_-0.106'
job = Job(path)
finished = submit_job_rpa.if_cal_finish(job)
expected = True
assert (finished == expected)
def test_data_saving():
path = 'C:\\Users\\ccccc\\Documents\\Theoritische Chemie\\Masterarbeit\\test\\geo_opt\\x_-0.150\\z_-0.106'
energy = get_optimized_energy(path)
job = Job(path)
path = job.root_path
creatxls_dis(path)
read_and_record_result(2, job, 3.1)
def get_new_job(self):
path_GeoOpt = self.job_GeoOpt.path
path_hf1 = path_GeoOpt.replace('geo_opt', 'hf1')
if self.layertype != 'bilayer':
path_hf1 = os.path.join(path_hf1, self.layertype)
job_hf1 = Job(path_hf1)
return job_hf1
def get_jobs(path):
path = os.path.join(path, 'rpa')
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if 'rpa.out' in files:
new_job = Job(root)
if if_cal_finish(new_job):
jobs.append(new_job)
# directly select job from geo_opt directory
if len(jobs) == 0:
path = path.replace('rpa', 'geo_opt')
for root, dirs, files in os.walk(path):
if 'geo_opt.out' in files or 'hf.out' in files:
new_job = Job(root)
jobs.append(new_job)
return jobs
def test_Molpro_Bs():
path = r'C:\Users\ccccc\PycharmProjects\Layer_Structure_Caculation\Test\cluster\x_0\z_0'
job = Job(path)
xyz = r'C:\Users\ccccc\PycharmProjects\Layer_Structure_Caculation\Test\cluster\x_0\z_0\BlackP_Cluster_M.xyz'
inp_name = 'per_bas_rpa_iext1.inp'
MB = Correction.Molpro_Bs(job, inp_name)
MB.get_molpro_bs()
MB.write_bs()
def get_running_jobs(self):
running_jobs = []
with open(self.status_file, 'r') as f:
data = json.load(f)
for job in data.keys():
if data[job]['status'] == 'running':
curr_job = Job(data[job]['path'])
running_jobs.append(curr_job)
return running_jobs
def test_read_all_results():
path = r'C:\Users\ccccc\PycharmProjects\Layer_Structure_Caculation\Test'
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if 'geo_opt.out' in files:
job = Job(root)
jobs.append(job)
read_all_results(jobs, 3.1)
def test_too_many_cycles():
job = r'C:\Users\ccccc\PycharmProjects\Layer_Structure_Caculation\Test\hf1\x_0.35\z_0'
job2 = r'C:\Users\ccccc\PycharmProjects\Layer_Structure_Caculation\Test\hf1\x_0.35\z_0\underlayer'
job = Job(job)
e = HF1.read_results_hf1.get_energy(job.path)
print(e)
print('---'*20)
e1 = HF1.read_results_hf1.get_energy(job2)
print(e1)
def get_jobs(path):
path = os.path.join(path, 'lmp2')
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if 'lmp2.out' in files and 'molpro.inp' in files:
new_job = Job(root)
if if_cal_finish(new_job):
jobs.append(new_job)
return jobs
def test_read_lowest_e():
#path = 'C:\\Users\\ccccc\\Documents\\Theoritische Chemie\\Masterarbeit\\test'
path = r'/users/shch/project/Masterarbeit/Test/'
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if 'geo_opt.out' in files:
job = Job(root)
jobs.append(job)
read_and_select_lowest_e(jobs)
def test_read_all_results():
path = 'C:\\Users\\ccccc\\Documents\\Theoritische Chemie\\Masterarbeit\\test\\hf_1'
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if 'hf.out' in files:
job = Job(root)
if if_cal_finish(job):
jobs.append(job)
read_all_results_hf1(jobs, init_dist=3.1)
def test_read_all_results():
path = os.getcwd()
path = os.path.join(path, 'Test')
path = os.path.join(path, 'rpa')
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if 'rpa.out' in files:
job = Job(root)
jobs.append(job)
read_results_rpa.read_and_record_all_results(jobs)
def get_finished_jobs(job):
path = os.path.join(job.root_path, job.method)
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if ('geo_opt.out' in files) and ('fort.9' in files):
new_path = root
new_job = Job(new_path)
if if_cal_finish(new_job):
jobs.append(new_job)
return jobs
def get_jobs(path):
path = os.path.join(path, 'hf1')
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if ('hf.out' in files) and ('fort.9' in files):
new_path = root
new_job = Job(new_path)
if if_cal_finish(new_job):
jobs.append(new_job)
return jobs
def get_jobs(path):
path = os.path.join(path, 'cluster')
walks = os.walk(path)
jobs = set()
root_jobs = set()
for root, dirs, files in walks:
if len(files) > 0:
for file in files:
if os.path.splitext(file)[-1] == '.out':
new_job = Job(root)
new_job.method = os.path.splitext(file)[0]
if if_cal_finish(
new_job
) and new_job not in jobs and '20' not in new_job.method:
jobs.add(new_job)
root_jobs.add(Job(root))
# print(new_job)
# print(root)
jobs = list(jobs)
root_jobs = list(root_jobs)
return jobs, root_jobs
def factor_calculation():
# parameters input
path = r'C:\Users\ccccc\Documents\Theoritische Chemie\Masterarbeit\test\geo_opt\x_1\z_2'
name = 'MgO'
center_upp = [25, 25]
center_und = [9, 9]
center = [center_upp, center_und]
atom = (-2.99725, 0, 16.835625996)
atom2 = (-1.498625, 5.352278396, 16.891833116)
atom3 = (-2.99725, -2.99725, 19.963182233)
atoms = [atom, atom2, atom3]
#if needed
dimen = 2
lattice_parameter = []
geometry = []
vector = []
dimen, lattice_parameter, geometry = read_infomation(path)
#calculation part
job = Job(path)
json_path = os.path.join(job.root_path, 'cluster')
if not os.path.exists(os.path.join(json_path, 'geometry.json')):
ClusterCutter.creat_json_file(json_path)
if lattice_parameter != [] and geometry != []:
basic_info = [dimen, lattice_parameter, geometry]
Clu = ClusterCutter(job,
name=name,
centre=center,
basic_infos=basic_info)
else:
Clu = ClusterCutter(job, name=name, centre=center)
Fac = FactorCalculator(Clu)
for atom in atoms:
dis_fac = Fac.get_distance_to_center(atom, factor=True)
print('---' * 20)
print(atom)
print('cluster factor of distance: ', dis_fac)
if vector == []:
print(Clu.centre)
a_fac = Fac.get_distance_to_vector(atom, vec=1, factor=True)
print('cluster factor of lattice vector 1: ', a_fac)
b_fac = Fac.get_distance_to_vector(atom, vec=2, factor=True)
print('cluster factor of lattice vector 2: ', b_fac)
if Clu.dimensionality != 2:
c_fac = Fac.get_distance_to_vector(atom, vec=3, factor=True)
print('cluster factor of lattice vector 3: ', c_fac)
else:
fac = Fac.get_distance_to_vector(atom, vector, True)
def test_calculation(j, init_jobs, submitted_jobs, finished_jobs):
# ----------------------------------------- test ---------------------------------------------------
if j >= 2:
# categorization of out jobs
path = r'C:\Users\ccccc\Documents\Theoritische Chemie\Masterarbeit\BlackP\hf2'
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if 'hf2.out' in files:
jobs.append(Job(root))
out_jobs = {}
for job in jobs:
if job.layertype not in out_jobs:
out_jobs[job.layertype] = {}
if job.x not in out_jobs[job.layertype]:
out_jobs[job.layertype][job.x] = [job]
else:
out_jobs[job.layertype][job.x].append(job)
for layertype, jobs_dict in out_jobs.items():
for key, value in jobs_dict.items():
sorted(value, key=lambda job: float(job.z))
# categorization of running jobs
all_jobs = init_jobs + finished_jobs + submitted_jobs
runing_jobs_dict = {}
for job in all_jobs:
if job.layertype not in runing_jobs_dict:
runing_jobs_dict[job.layertype] = {}
if job.x not in runing_jobs_dict[job.layertype]:
runing_jobs_dict[job.layertype][job.x] = [job]
else:
runing_jobs_dict[job.layertype][job.x].append(job)
# find corresponding jobs
for layertype, jobs_dict in runing_jobs_dict.items():
for x, job_list in jobs_dict.items():
corr_list = out_jobs[layertype]['%.1f' % (float(x) * 10 + 2.5)]
job_list = sorted(job_list, key=lambda job: float(job.z))
for i in range(len(job_list)):
out_from = corr_list[i].path
fort_from = os.path.join(out_from, 'fort.9')
fort_78_from = os.path.join(out_from, 'fort.78')
out_from = os.path.join(out_from, 'hf2.out')
out_to = job_list[i].path
fort_to = os.path.join(out_to, 'fort.9')
fort_78_to = os.path.join(out_to, 'fort.78')
out_to = os.path.join(out_to, 'hf2.out')
shutil.copy(out_from, out_to)
shutil.copy(fort_from, fort_to)
shutil.copy(fort_78_from, fort_78_to)
def get_jobs(path):
path = os.path.join(path, 'cluster')
walks = os.walk(path)
jobs = []
path_set = set()
for root, dirs, files in walks:
if len(files) > 0:
for file in files:
if os.path.splitext(
file)[-1] == '.xyz' and root not in path_set:
path_set.add(root)
new_job = Job(root)
jobs.append(new_job)
return jobs
def test_write_geo_json():
path = r'C:\Users\ccccc\PycharmProjects\Layer_Structure_Caculation\Test'
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if 'geo_opt.out' in files:
job = Job(root)
jobs.append(job)
for job in jobs:
# if job.x == '0.10':
# print(job)
path = job.path
lattice_para, geometry = get_optimized_geometry(path)
write_geometry_json(job, geometry)
write_latt_json(job, lattice_para)
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_calculation(j, init_jobs, finished_jobs):
# ----------------------------------------- test ---------------------------------------------------
if j >= 2:
from Common import Job
# categorization of out jobs
path = r'F:\BlackP\RPA'
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if 'rpa.out' in files:
jobs.append(Job(root))
out_jobs = {}
for job in jobs:
if job.layertype not in out_jobs:
out_jobs[job.layertype] = {}
if job.x not in out_jobs[job.layertype]:
out_jobs[job.layertype][job.x] = [job]
else:
out_jobs[job.layertype][job.x].append(job)
for layertype, jobs_dict in out_jobs.items():
for key, value in jobs_dict.items():
sorted(value, key=lambda job: float(job.z))
# categorization of running jobs
all_jobs = init_jobs + finished_jobs
runing_jobs_dict = {}
for job in all_jobs:
if job.layertype not in runing_jobs_dict:
runing_jobs_dict[job.layertype] = {}
if job.x not in runing_jobs_dict[job.layertype]:
runing_jobs_dict[job.layertype][job.x] = [job]
else:
runing_jobs_dict[job.layertype][job.x].append(job)
# find corresponding jobs
for layertype, jobs_dict in runing_jobs_dict.items():
for x, job_list in jobs_dict.items():
corr_list = out_jobs[layertype]['%.1f' % (float(x) * 10 + 2.5)]
job_list = sorted(job_list, key=lambda job: float(job.z))
for i in range(len(job_list)):
out_from = corr_list[i].path
out_from = os.path.join(out_from, 'rpa.out')
out_to = job_list[i].path
out_to = os.path.join(out_to, 'rpa.out')
shutil.copy(out_from, out_to)
def test_blackP():
path = r'C:\Users\ccccc\PycharmProjects\Layer_Structure_Caculation\Test\geo_opt'
path = r'C:\Users\ccccc\Documents\Theoritische Chemie\Masterarbeit\job\geo_opt'
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if 'hf.out' in files:
job = Job(root)
jobs.append(job)
path = r'C:\Users\ccccc\Documents\Theoritische Chemie\Masterarbeit\job\cluster'
#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_1'
# job = jobs[0]
# # print(job)
# # # job = Job_path(job)
# test_cut_cluster(job)
for job in jobs:
test_cut_cluster(job)
def select_jobs(path):
# find all possible jobs
walks = os.walk(path)
jobs = []
for root, dirs, files in walks:
if 'geo_opt.out' in files:
jobs.append(root)
jobs = [Job(job) for job in jobs]
# categorization jobs according to x
jobs_dict = {}
for job in jobs:
x = job.x
if x in jobs_dict:
jobs_dict[x].append(job)
else:
jobs_dict[x] = [job]
# select jobs at each x
selected_jobs = []
for key, value in jobs_dict.items():
if key == '0':
new_list = value
else:
jobs_list = value[:]
min_dist, min_job = read_and_select_lowest_e(value)
# print(min_dist, min_job)
jobs_list = sorted(jobs_list, key=lambda job: float(job.z))
# print(jobs_list)
position = look_for_in_list(jobs_list, min_job)
if len(jobs_list) > 3:
new_list = [min_job]
new_list.append(jobs_list[position - 1])
new_list.append(jobs_list[position + 1])
new_list.append(jobs_list[position + 2])
else:
new_list = [job for job in jobs_list]
# print(new_list)
selected_jobs += new_list
return selected_jobs
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()
def lmp2(path, moni):
rec = 'LMP2 Calculation begins.\n'
rec += '---' * 25
print(rec)
record(path, rec)
init_dist = read_init_dis(path)
# read basic computation information
hf2_jobs = LMP2.get_jobs(path)
Ini = ReadIni()
nodes, cryscor_path = Ini.get_lmp2()
cal_parameters = Ini.get_cal_parameters('LMP2')
ll = Ini.ll
if nodes == '' or nodes == 'default':
nodes = 1
record_data_json(path, 'nodes', nodes, section='lmp2')
# categorization
bilayer = []
singlelayer = []
for job in hf2_jobs:
if job.layertype == 'bilayer':
bilayer.append(job)
elif job.layertype == 'underlayer' or job.layertype == 'upperlayer':
singlelayer.append(job)
# generation of all input files and copy needed files
lmp2_jobs = []
lmp2_jobs_finished = []
for job in bilayer:
new_path = job.path
new_path = new_path.replace('hf2', 'lmp2')
new_job = Job(new_path)
if not LMP2.if_cal_finish(new_job):
Inp = LMP2.Lmp2Input(job, ll, cal_parameters)
Inp.write_input()
LMP2.copy_files(new_job, nodes, cryscor_path)
lmp2_jobs.append(new_job)
else:
lmp2_jobs_finished.append(new_job)
for job in singlelayer:
new_path = job.path
new_path = new_path.replace('hf2', 'lmp2')
new_job = Job(new_path)
if not LMP2.if_cal_finish(new_job):
Inp = LMP2.Lmp2InputLayer(job, cal_parameters)
Inp.write_input()
LMP2.copy_files(new_job, nodes, cryscor_path)
lmp2_jobs.append(new_job)
else:
lmp2_jobs_finished.append(new_job)
# submit the jobs
if len(lmp2_jobs) > 0:
new_finished_jobs = LMP2.submit(lmp2_jobs, moni)
lmp2_jobs_finished += new_finished_jobs
# read calculation results
# if len(lmp2_jobs_finished) > 0:
# LMP2.read_all_results_lmp2(lmp2_jobs_finished, init_distance=init_dist)
rec = 'LMP2 finished!\n'
rec += '***' * 25
print(rec)
record(path, rec)
def test_delete_guessp():
job = r'C:\Users\ccccc\PycharmProjects\Layer_Structure_Caculation\Test\hf1\x_0.35\z_0'
job2 = r'C:\Users\ccccc\PycharmProjects\Layer_Structure_Caculation\Test\hf1\x_0.35\z_0\underlayer'
job = Job(job)
HF1.delete_guessp(job)
def test_if_finished():
path = r'C:\Users\ccccc\Documents\Theoritische Chemie\Masterarbeit\test\hf_1\x_-0.150\z_-0.106'
job = Job(path)
res = if_cal_finish(job)
print(res)
