def cal_excite_relax(self,
knum,
ocp_set,
mpi=28,
openmp=1,
num_machines=1,
num_mpiprocs_per_machine=28,
max_wallclock_seconds=86400,
queue_name='gold5120'):
strufile = extract_largest_number_file()
stru = read_stru(self.input_dict["ntype"], glob(strufile))
for elem in stru.orbitals.keys():
stru.orbitals[elem] = os.path.basename(stru.orbitals[elem])
kpt = Kpt('Gamma', knum)
os.mkdir('excite')
os.chdir('excite')
command = Code(
code_name=self.code_name,
cmdline_params=[f"-n {mpi}", f"-env OMP_NUM_THREADS={openmp}"],
stdout_name="job.log",
stderr_name="job.err",
withmpi="mpirun")
submit_command = set_scheduler(
'torque', [command],
num_machines=num_machines,
num_mpiprocs_per_machine=num_mpiprocs_per_machine,
run_mode='p',
max_wallclock_seconds=max_wallclock_seconds,
queue_name=queue_name)
self.excite_relax(ocp_set, stru, kpt)
os.system(submit_command)
os.chdir('../')
def cal_ground_cell_relax(self,
knum,
mpi=28,
openmp=1,
num_machines=1,
num_mpiprocs_per_machine=28,
max_wallclock_seconds=86400,
queue_name='gold5120'):
stru = read_stru(self.input_dict["ntype"], "STRU")
kpt = Kpt('Gamma', knum)
os.mkdir('ground')
os.chdir('ground')
command = Code(
code_name=self.code_name,
cmdline_params=[f"-n {mpi}", f"-env OMP_NUM_THREADS={openmp}"],
stdout_name="job.log",
stderr_name="job.err",
withmpi="mpirun")
submit_command = set_scheduler(
'torque', [command],
num_machines=num_machines,
num_mpiprocs_per_machine=num_mpiprocs_per_machine,
run_mode='p',
max_wallclock_seconds=max_wallclock_seconds,
queue_name=queue_name)
self.ground_cell_relax(stru, kpt)
os.system(submit_command)
os.chdir('../')
def cal_phono(self,
dim=[1, 1, 1],
mpi=28,
openmp=1,
num_machines=1,
num_mpiprocs_per_machine=28,
max_wallclock_seconds=86400,
queue_name='gold5120'):
strufile = extract_largest_number_file()
stru = read_stru(self.input_dict["ntype"], strufile)
for elem in stru.orbitals.keys():
stru.orbitals[elem] = os.path.basename(stru.orbitals[elem])
self.input_dict['gamma_only'] = 1
kpt = Kpt('Gamma', [1, 1, 1])
command = Code(
code_name=self.code_name,
cmdline_params=[f"-n {mpi}", f"-env OMP_NUM_THREADS={openmp}"],
stdout_name="job.log",
stderr_name="job.err",
withmpi="mpirun")
os.mkdir('phonon_ground')
os.chdir('phonon_ground')
stru.write_stru()
with open("setting.conf", 'w') as f:
f.write(
dedent(f"""\
DIM = {' '.join(list_elem2str(dim))}
ATOM_NAME = {' '.join(stru.elements)}
"""))
os.system('phonopy setting.conf --abacus -d')
disp_list = glob('STRU-*')
for i in disp_list:
dst = 'disp-' + i.split('-')[-1]
os.mkdir(dst)
shutil.move(i, dst)
os.chdir(dst)
disp_stru = read_stru(self.input_dict["ntype"], i)
submit_command = set_scheduler(
'torque', [command],
num_machines=num_machines,
num_mpiprocs_per_machine=num_mpiprocs_per_machine,
run_mode='p',
max_wallclock_seconds=max_wallclock_seconds,
queue_name=queue_name)
self.ground_scf(disp_stru, kpt)
os.system(submit_command)
os.chdir('../')
os.chdir('../')
def double_run(self, command: Command, scheduler: str, **kwargs):
"""Check if job is finished and execute again
:params command: abacuskit.schedulers.data.Code` object to execute calculation
:params scheduler: string of scheduler name
:params kwargs: other parameters of scheduler
"""
current_path = Path.cwd()
codes_info = [command]
for folder in read_json("folders"):
if not glob.glob(f"{folder}/matrix_*"):
import warnings
warnings.warn(
f"'matrix_*' file not found in {folder}, it will execute again."
)
os.chdir(folder)
submit_command = set_scheduler(scheduler, codes_info, **kwargs)
os.system(submit_command)
os.chdir(current_path)
def batch_run(self, command: Code, scheduler: str, **kwargs):
"""Batch execute dimer calculation
:params command: abacuskit.schedulers.data.Code` object to execute calculation
:params scheduler: string of scheduler name
:params kwargs: other parameters of scheduler
"""
self._prepare()
filename = "folders"
# TODO: for new dpsi scripts, it should be a dict with key "origin"
subfolder_weight = {
os.path.basename(key): value
for key, value in self.folder_weight.items()
}
with open(filename, 'w') as file:
json.dump(subfolder_weight, file, indent=4)
current_path = Path.cwd()
codes_info = [command]
for folder in self.folder_weight:
os.chdir(folder)
submit_command = set_scheduler(scheduler, codes_info, **kwargs)
os.system(submit_command)
os.chdir(current_path)