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 STRU_to_POSCAR(cls, srcfile: str_PathLike, tofile: str_PathLike,
ntype: int) -> None:
"""Convert STRU of ABACUS to POSCAR of VASP
:params srcfile: str_PathLike, source file
:params tofile: str_PathLike, converted file
"""
def convert_pos(elements: list, positions: dict):
newpos = []
for elem in elements:
for pos in positions[elem]:
newpos.append(' ' + ''.ljust(20).join(list_elem2str(pos)))
return newpos
stru = read_stru(ntype, srcfile)
line = [f"From {srcfile}"]
line.append(str(stru.lat0 * BOHR_TO_A))
for i in stru.cell:
line.append('\t' + '\t'.join(list_elem2str(i)))
line.append(' ' + ''.ljust(10).join(stru.elements))
line.append(' ' +
''.ljust(10).join(list_elem2str(stru.numbers.values())))
line.append(stru._ctype)
if stru._ctype == "Direct":
line.append('\n'.join(
convert_pos(stru.elements, stru.scaled_positions)))
if stru._ctype == "Cartesian":
line.append('\n'.join(convert_pos(stru.elements, stru.positions)))
else:
ValueError(f"Type {stru._ctype} is not supported for VASP.")
with open(tofile, 'w') as file:
file.write('\n'.join(line))
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 _parse(self, **kwargs) -> dict:
"""parse output of scf calculation"""
res = super()._parse(**kwargs)
with open(self.logfile, 'r') as file:
for line in file:
if re.search(r"TOTAL ATOM NUMBER = [0-9]+", line):
natom = int(re.search("[0-9]+", line).group())
force = np.zeros((natom, 3))
if re.search("TOTAL-FORCE \(eV/Angstrom\)", line):
for i in range(3):
file.readline()
for i in range(natom):
element, fx, fy, fz = file.readline().split()
force[i] = (float(fx), float(fy), float(fz))
res["force_mean"] = force.mean()
obj = read_stru(self.input_dict["ntype"], "OUT.test/STRU_ION_D")
plist = []
for elem in obj.elements:
plist = np.mean(obj.positions[elem])
res["positions_mean"] = np.mean(plist)
res["lattice_mean"] = np.mean(obj.cell)
return res
def cal_emission(self, num_mode):
stru = read_stru(self.input_dict["ntype"], 'phonon_ground/STRU')
mass = []
for elem in stru.elements:
mass += [atom_data[symbol_map[elem]][3]] * stru.numbers[elem]
mass = np.array(mass) * 1.660539040e-27 # in unit AMU
os.mkdir('photon')
shutil.copyfile(extract_largest_number_file(dst='./ground/OUT*'),
'photon/STRU_GS')
shutil.copyfile(extract_largest_number_file(dst='./excite/OUT*'),
'photon/STRU_ES')
shutil.copy2('phonon_ground/band.yaml', 'photon/')
os.chdir('photon')
Convert.STRU_to_POSCAR('STRU_GS', 'CONTCAR_GS',
self.input_dict["ntype"])
Convert.STRU_to_POSCAR('STRU_ES', 'CONTCAR_ES',
self.input_dict["ntype"])
from pyphotonics.photoluminescence import Photoluminescence
p = Photoluminescence('./',
'CONTCAR_GS',
'CONTCAR_ES',
num_mode,
"phonopy",
mass,
1000,
shift_vector=[0.0, 0.0, 0.0])
import matplotlib.pyplot as plt
print("Delta_R=", p.Delta_R)
print("Delta_Q=", p.Delta_Q)
print("HuangRhyes=", p.HuangRhyes)
plt.figure(figsize=(10, 10))
plt.plot(p.S_omega)
plt.ylabel('$S(\hbar\omega)$')
plt.xlabel('Phonon energy (meV)')
plt.xlim(0, 200)
# plt.ylim(0, 0.01)
plt.savefig('S_omega', bbox_inches='tight')
p.write_S('S')
A, I = p.PL(2, 2, 1.95)
plt.figure(figsize=(10, 10))
plt.plot(I.__abs__())
plt.ylabel('$I(\hbar\omega)$')
plt.xlabel('Photon energy (eV)')
plt.xlim(1200, 2000)
x_values, labels = plt.xticks()
labels = [float(x) / p.resolution for x in x_values]
plt.xticks(x_values, labels)
plt.ylim(0, 600)
plt.savefig('I', bbox_inches='tight')
os.chdir('../')
def STRU_to_CIF(cls,
srcfile: str_PathLike,
tofile: str_PathLike,
ntype: int,
find_symmetry: bool = False) -> None:
"""Convert STRU of ABACUS to CIF(Crystallographic Information Framework)
:params srcfile: str_PathLike, source file
:params tofile: str_PathLike, converted file
"""
stru = read_stru(ntype, srcfile)
stru.write_cif(tofile, find_symmetry)
def cal_phono_band(self, path, labels, points=51):
os.chdir('phonon_ground')
stru = read_stru(self.input_dict["ntype"], 'STRU')
with open("band.conf", 'w') as f:
f.write(
dedent(f"""\
ATOM_NAME = {' '.join(stru.elements)}
BAND = {convert_path_to_string(path)}
BAND_POINTS = {points}
BAND_LABELS = {' '.join(labels)}
BAND_CONNECTION = .TRUE.
FORCE_CONSTANTS= WRITE
"""))
os.system("phonopy band.conf -p -s")
os.chdir('../')
from abacuskit.utils.constants import BOHR_TO_A
from pathlib import Path
tpath = "./" # target directory
ntype = 4
E = []
a = []
V = []
lat = 10.4805927277
for i in range(0, 5):
spath = Path(tpath, f"{i}")
obj = read_stru(ntype, Path(spath, "STRU"))
obj.set_energy(Path(spath, "OUT.test/running_scf.log"))
V.append(obj.volume)
E.append(obj.energy)
a.append(obj.lat0 * lat * BOHR_TO_A)
with open("V_E_res", 'w') as f1, open("a_E_res", 'w') as f2:
for i in range(0, 5):
f1.write(f"{V[i]}\t{E[i]}\n")
f2.write(f"{a[i]}\t{E[i]}\n")
import os
factor = 1
fit_script = "fit-bulk.py"
os.system(f"python {fit_script} V_E_res > hse_V_fit")
from abacuskit.schedulers.data import Code
from abacuskit.calculations.plugins.exx import SetDimers, OptABFs, EXX
from abacuskit.utils.IO import write_input, read_kpt, read_stru
ntype = 4
ecut = 100
stru = read_stru(ntype, "STRU")
Nu = [6, 5, 4, 3, 2, 1]
kpt = read_kpt("KPT")
input_dict = {
"ntype" : ntype,
"ecutwfc" : ecut,
"nbands" : 200,
"dr2" : 1e-6,
"niter" : 400,
"basis_type" : "lcao",
"ks_solver" : "genelpa",
"smearing" : "gaussian",
"sigma" : 0.0005,
"mixing_type" : "pulay",
"mixing_beta" : 0.4,
"pseudo_dir" : "/home/jiyy/SG15_upf",
"newdm" : 1,
"exx_hybrid_type": "hse",
"exx_opt_orb_ecut": ecut,
"exx_opt_orb_tolerence": 1e-12,
"exx_ccp_rmesh_times": 1.5,
"exx_dm_threshold": 1e-5,
"exx_cauchy_threshold": 1e-9,
"exx_schwarz_threshold": 1e-5,
"exx_c_threshold": 1e-5,
''' Date: 2021-05-25 23:01:57 LastEditors: jiyuyang LastEditTime: 2021-05-25 23:01:58 Mail: [email protected], [email protected] ''' from abacuskit.postprocess.symmetry import Spacegroup from abacuskit.utils.IO import read_stru from pathlib import Path ntype = 4 filename = r"C:\Users\jiyuyang\Desktop\STRU" pardir = Path(filename).parent stru = read_stru(4, r"C:\Users\jiyuyang\Desktop\STRU") obj = Spacegroup(stru) pri_stru, kpt = obj.get_kpath() pri_stru.write_stru(pardir / "STRU-pri") kpt.write_kpt(pardir / "KPT-band")
def configure(config_file: str_PathLike, version: list) -> Return_2:
"""Configure commands and workflow for Autotest
:params config_file: configure file for Autotest
:params version: list of absolute path of executable file
"""
workflow = []
allcommands = []
with open(config_file, 'r') as file:
text = json.load(file)
src = Path(config_file).parent
workflowinput = text["workflow"]
for index, cal in enumerate(workflowinput.keys()):
if re.match(f"cal_{index}", cal):
cal_elem = workflowinput[cal]
name = cal_elem.pop("name", None)
if not name:
raise KeyError(f"Key `name` in {cal} isn't set")
code = cal_elem.pop("code", None)
cmdline_params = code.pop("cmdline_params", [])
stdin_name = code.pop("stdin_name", None)
join_files = code.pop("join_files", False)
withmpi = code.pop("withmpi", "mpirun")
commands = []
for j, ver in enumerate(version):
commands.append(
Code(code_name=ver,
cmdline_params=cmdline_params,
stdin_name=stdin_name,
stdout_name=f"{cal}.log",
stderr_name=f"{cal}.err",
join_files=join_files,
withmpi=withmpi))
allcommands.append(commands)
input_dict = cal_elem.pop("input_params", None)
# STRU
stru_file = src / cal_elem.pop("stru_file", "STRU")
if stru_file.exists():
stru = read_stru(input_dict["ntype"], stru_file)
for elem in stru.elements:
if input_dict and "pseudo_dir" not in input_dict.keys():
stru.pps[elem] = Path(src, stru.pps[elem])
stru.orbitals[elem] = Path(src, stru.orbitals[elem])
else:
stru = None
# KPT
kpt_file = src / cal_elem.pop("kpt_file", "KPT")
if kpt_file.exists():
kpt = read_kpt(kpt_file)
else:
kpt = None
obj = set_cal(name=name,
input_dict=input_dict,
stru=stru,
kpt=kpt,
**cal_elem)
workflow.append(obj)
else:
raise KeyError(
"Wrong keyword `cal` settings, it should be set in numerical order."
)
return allcommands, workflow
from abacuskit.utils.IO import read_stru
from pathlib import Path
import shutil
import os
ppath = "/home/jiyy/ABACUS/AutoTest/new/testlib/MgO" # source file directory
stru_path = Path(ppath, "STRU")
filelist = os.listdir(ppath)
filelist.remove("STRU")
tpath = "./" # target directory
ntype = 2
obj = read_stru(ntype, stru_path)
latc = obj.lat0
delta = 0.01
for i in range(-1, 4):
obj.lat0 = latc + i * delta
spath = Path(tpath, str(i + 1))
spath.mkdir()
obj.write_stru(Path(spath, "STRU"))
for j in filelist:
file = Path(ppath, j)
shutil.copy(file, spath)
