def read_kpt(kpt_file: str_PathLike) -> Kpt:
"""Read k-points file
:params kpt_file: absolute path of k-points file
"""
number = 0
with open(kpt_file, "r") as file:
if search_sentence(file, ["K_POINTS", "KPOINTS", "K"]):
number = int(file.readline())
mode = search_sentence(file, ["Gamma", "MP", "Line"])
if mode in ["Gamma", "MP"]:
line = skip_notes(file.readline()).split()
numbers = list_elem_2int(line[:3])
offset = list_elem_2float(line[3:])
return Kpt(mode, numbers, special_k=[], offset=offset)
elif mode == "Line":
special_k = []
numbers = []
klabel = []
for k in range(number):
line = file.readline()
if re.match("#", line):
continue
else:
linesplit = line.split(maxsplit=4)
special_k.append(list_elem_2float(linesplit[:3]))
numbers.append(int(linesplit[3]))
if len(linesplit) == 5:
klabel.append(linesplit[4].strip('#\n '))
return Kpt(mode, numbers, special_k, offset=[], klabel=klabel)
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_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_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 get_kpath(self,
numbers: list = [],
with_time_reversal: bool = True,
recipe: str = 'hpkot',
threshold: float = 1e-7,
symprec: float = 1e-5,
angle_tolerance: float = -1) -> Tuple[Stru, Kpt]:
"""Obtain primitive cell and its band paths in the Brillouin zone of crystal structures.
:params numbers: list of number of k points between two adjacent special k points.
:params with_time_reversal: if time-reversal symmetry is present or not. Default: True
:params recipe: currently only the string 'hpkot' is supported. Default: 'hpkot'
:params threshold: numerical threshold. Default: 1e-7
:params symprec: distance tolerance in Cartesian coordinates to find crystal symmetry. Default: 1e-5
:params angle_tolerance: tolerance of angle between basis vectors in degrees to be tolerated in the symmetry finding. Default: -1
"""
import seekpath
if numbers:
set_already = True
else:
set_already = False
res = seekpath.get_path(self.spgcell, with_time_reversal, recipe,
threshold, symprec, angle_tolerance)
newcell = (res['primitive_lattice'], res['primitive_positions'],
res['primitive_types'])
stru = self.modified_stru(newcell)
klabel = []
special_k = []
for k_tuple in res['path']:
klabel.append(k_tuple[0])
if not set_already:
numbers.append(20)
klabel.append(k_tuple[1])
if not set_already:
numbers.append(1)
for label in klabel:
special_k.append(res['point_coords'][label])
kpt = Kpt(mode='Line',
numbers=numbers,
special_k=special_k,
klabel=klabel)
return stru, kpt