def isif2_highacc(self):
"""
Run high accuracy ISIF2
Returns:
mof (ASE Atoms object): updated ASE Atoms object
"""
acc_levels = self.acc_levels
outcar_paths = self.outcar_paths
error_outcar_paths = self.error_outcar_paths
spin_label = self.spin_label
kpts_hi = self.kpts_dict['kpts_hi']
acc_level = acc_levels[self.run_i]
calcs = self.calcs
prior_results_path = os.path.join(
self.results_partial_paths[self.run_i - 1], spin_label)
if os.path.isfile(outcar_paths[self.run_i - 1]) and not os.path.isfile(
outcar_paths[self.run_i]) and not os.path.isfile(
error_outcar_paths[self.run_i]):
mof = prep_new_run(self)
manage_restart_files(prior_results_path)
pprint('Running ' + spin_label + ', ' + acc_level)
mof, self.calc_swaps = mof_run(self, mof, calcs('isif2_highacc'),
kpts_hi)
if mof is not None and mof.calc.scf_converged and mof.calc.converged:
if 'large_supercell' in self.calc_swaps:
self.calc_swaps.remove('large_supercell')
mof = read('OUTCAR')
mof = continue_magmoms(mof, 'INCAR')
mof, self.calc_swaps = mof_run(self, mof,
calcs('isif2_highacc'),
kpts_hi)
if mof is not None and mof.calc.scf_converged and mof.calc.converged:
write_success(self)
else:
write_errors(self, mof)
else:
write_success(self)
else:
write_errors(self, mof)
elif os.path.isfile(outcar_paths[self.run_i]):
pprint('COMPLETED: ' + spin_label + ', ' + acc_level)
mof = prep_next_run(self)
if mof is None:
pprint('Skipping rest because of errors')
return None
return mof
def scf_test(self, atoms_overwrite=None, quick_test=False):
"""
Run SCF test job to check for errors
Returns:
scf_pass (bool): True if passed SCF test
"""
outcar_paths = self.outcar_paths
error_outcar_paths = self.error_outcar_paths
spin_level = self.spin_level
spin_label = self.spin_label
cif_file = self.cif_file
mofpath = self.mofpath
spin1_final_mof_path = self.spin1_final_mof_path
kpts_lo = self.kpts_dict['kpts_lo']
acc_level = self.acc_levels[self.run_i]
niggli = self.niggli
calcs = self.calcs
if not os.path.isfile(outcar_paths[self.run_i]) and not os.path.isfile(
error_outcar_paths[self.run_i]):
if atoms_overwrite:
mof = deepcopy(atoms_overwrite)
else:
if spin1_final_mof_path is None:
mof = cif_to_mof(os.path.join(mofpath, cif_file), niggli)
else:
mof = read(spin1_final_mof_path)
mof = set_initial_magmoms(mof, spin_level)
if quick_test:
self.calc_swaps.append('nelm=5')
self.calc_swaps.append('lwave=False')
pprint('Running ' + spin_label + ', ' + acc_level)
mof, self.calc_swaps = mof_run(self, mof, calcs('scf_test'),
kpts_lo)
if quick_test:
self.calc_swaps.remove('nelm=5')
self.calc_swaps.remove('lwave=False')
if mof is not None:
write_success(self)
else:
write_errors(self, mof)
elif os.path.isfile(outcar_paths[self.run_i]):
pprint('COMPLETED: ' + spin_label + ', ' + acc_level)
mof = prep_next_run(self)
if mof is None:
pprint('Skipping rest because of errors')
return False
warnings = get_warning_msgs(outcar_paths[self.run_i - 1])
self.calc_swaps.extend(warnings)
return True
def isif3_lowacc(self):
"""
Run low accuracy ISIF3
Returns:
mof (ASE Atoms object): updated ASE Atoms object
"""
acc_levels = self.acc_levels
outcar_paths = self.outcar_paths
error_outcar_paths = self.error_outcar_paths
spin_label = self.spin_label
kpts_lo = self.kpts_dict['kpts_lo']
acc_level = acc_levels[self.run_i]
calcs = self.calcs
prior_results_path = os.path.join(
self.results_partial_paths[self.run_i - 1], spin_label)
if os.path.isfile(outcar_paths[self.run_i - 1]) and not os.path.isfile(
outcar_paths[self.run_i]) and not os.path.isfile(
error_outcar_paths[self.run_i]):
mof = prep_new_run(self)
converged = False
loop_i = 0
n_runs = 15
manage_restart_files(prior_results_path)
while not converged and loop_i < n_runs:
if loop_i == 10 and 'fire' not in self.calc_swaps and 'zbrent' not in self.calc_swaps:
self.calc_swaps.append('fire')
pprint('Running ' + spin_label + ', ' + acc_level +
': iteration ' + str(loop_i) + '/' + str(n_runs - 1))
mof, self.calc_swaps = mof_run(self, mof,
calcs('isif3_lowacc'), kpts_lo)
if mof is None:
break
converged = mof.calc.converged
mof = read('OUTCAR')
mof = continue_magmoms(mof, 'INCAR')
loop_i += 1
if 'fire' in self.calc_swaps:
self.calc_swaps.remove('fire')
if mof is not None and converged:
write_success(self)
else:
write_errors(self, mof)
elif os.path.isfile(outcar_paths[self.run_i]):
pprint('COMPLETED: ' + spin_label + ', ' + acc_level)
mof = prep_next_run(self)
if mof is None:
pprint('Skipping rest because of errors')
return None
return mof
def cineb_lowacc(self, initial_atoms, final_atoms, n_images):
"""
Run CI-NEB low accuracy calculation
Returns:
mof (ASE Atoms object): updated ASE Atoms object
"""
spin_level = self.spin_level
kpts_lo = self.kpts_dict['kpts_lo']
calcs = self.calcs
nprocs = self.nprocs
pwd = os.getcwd()
partial_path = self.results_partial_paths[self.run_i]
data_path = os.path.join(partial_path, 'neb.tar.gz')
partial_error_path = self.error_partial_paths[self.run_i]
error_data_path = os.path.join(partial_error_path, 'neb.tar.gz')
neb_conv = False
if nprocs % n_images != 0:
raise ValueError(
str(nprocs) + ' procs not divisible by ' + str(n_images))
if not os.path.isfile(data_path) and not os.path.isfile(
error_data_path):
if initial_atoms.get_chemical_formula(
) != final_atoms.get_chemical_formula():
raise ValueError('POSCAR1 and POSCAR2 must have same atoms')
nebmake(initial_atoms, final_atoms, n_images)
initial_atoms = set_initial_magmoms(initial_atoms, spin_level)
pprint('Running CI-NEB (pre-dimer)')
initial_atoms, self.calc_swaps = mof_run(self,
initial_atoms,
calcs('cineb_lowacc'),
kpts_lo,
images=n_images)
ediffg = calcs('cineb_lowacc').exp_params['ediffg']
neb_conv = nebef(ediffg)
os.chdir(pwd)
if neb_conv:
write_success(self, neb=True)
else:
write_errors(self, initial_atoms, neb=True)
vtst_cleanup()
elif os.path.isfile(data_path):
pprint('COMPLETED: CI-NEB (pre-dimer)')
neb_conv = True
self.run_i += 1
if not neb_conv:
pprint('Skipping rest because of errors')
return False
return neb_conv
def isif2_medacc(self):
"""
Run medium accuracy ISIF2
Returns:
mof (ASE Atoms object): updated ASE Atoms object
"""
acc_levels = self.acc_levels
outcar_paths = self.outcar_paths
error_outcar_paths = self.error_outcar_paths
spin_label = self.spin_label
kpts_lo = self.kpts_dict['kpts_lo']
kpts_hi = self.kpts_dict['kpts_hi']
acc_level = acc_levels[self.run_i]
calcs = self.calcs
prior_results_path = os.path.join(
self.results_partial_paths[self.run_i - 1], spin_label)
if os.path.isfile(outcar_paths[self.run_i - 1]) and not os.path.isfile(
outcar_paths[self.run_i]) and not os.path.isfile(
error_outcar_paths[self.run_i]):
mof = prep_new_run(self)
if sum(kpts_lo) == 3 and sum(kpts_hi) > 3:
clean_files(['CHGCAR', 'WAVECAR'])
else:
manage_restart_files(prior_results_path)
pprint('Running ' + spin_label + ', ' + acc_level)
mof, self.calc_swaps = mof_run(self, mof, calcs('isif2_medacc'),
kpts_hi)
if mof is not None and mof.calc.scf_converged and mof.calc.converged:
write_success(self)
else:
write_errors(self, mof)
elif os.path.isfile(outcar_paths[self.run_i]):
pprint('COMPLETED: ' + spin_label + ', ' + acc_level)
mof = prep_next_run(self)
if mof is None:
pprint('Skipping rest because of errors')
return None
return mof
def final_spe(self):
"""
Run final single point
Returns:
mof (ASE Atoms object): updated ASE Atoms object
"""
acc_levels = self.acc_levels
outcar_paths = self.outcar_paths
error_outcar_paths = self.error_outcar_paths
spin_label = self.spin_label
kpts_hi = self.kpts_dict['kpts_hi']
acc_level = acc_levels[self.run_i]
calcs = self.calcs
self.calc_swaps = []
prior_results_path = os.path.join(
self.results_partial_paths[self.run_i - 1], spin_label)
if os.path.isfile(outcar_paths[self.run_i - 1]) and not os.path.isfile(
outcar_paths[self.run_i]) and not os.path.isfile(
error_outcar_paths[self.run_i]):
mof = prep_new_run(self)
manage_restart_files(prior_results_path)
pprint('Running ' + spin_label + ', ' + acc_level)
mof, self.calc_swaps = mof_run(self, mof, calcs('final_spe'),
kpts_hi)
if mof is not None and mof.calc.scf_converged:
write_success(self)
else:
write_errors(self, mof)
elif os.path.isfile(outcar_paths[self.run_i]):
pprint('COMPLETED: ' + spin_label + ', ' + acc_level)
mof = prep_next_run(self)
if mof is None:
pprint('Skipping rest because of errors')
return None
return mof
def dimer(self):
"""
Run dimer
Returns:
mof (ASE Atoms object): updated ASE Atoms object
"""
acc_levels = self.acc_levels
outcar_paths = self.outcar_paths
error_outcar_paths = self.error_outcar_paths
spin_level = self.spin_level
spin_label = self.spin_label
prior_spin = self.prior_spin
acc_level = acc_levels[self.run_i]
prior_acc_level = acc_levels[self.run_i - 1]
results_partial_paths = self.results_partial_paths
pwd = os.getcwd()
if 'lowacc' in acc_level:
kpts = self.kpts_dict['kpts_lo']
else:
kpts_lo = self.kpts_dict['kpts_lo']
kpts = self.kpts_dict['kpts_hi']
calcs = self.calcs
if 'neb' in prior_acc_level and prior_spin is None:
prior_results_path = os.path.join(
results_partial_paths[self.run_i - 1])
prior_results_file = os.path.join(prior_results_path, 'neb.tar.gz')
elif 'lowacc' in acc_level and prior_spin is not None:
prior_results_path = os.path.join(results_partial_paths[-1],
prior_spin)
prior_results_file = os.path.join(prior_results_path, 'OUTCAR')
else:
prior_results_file = outcar_paths[self.run_i - 1]
prior_results_path = os.path.join(
results_partial_paths[self.run_i - 1], spin_label)
if os.path.isfile(prior_results_file) and not os.path.isfile(
outcar_paths[self.run_i]) and not os.path.isfile(
error_outcar_paths[self.run_i]):
if 'scf_test' in prior_acc_level:
mof = prep_new_run(self)
manage_restart_files(prior_results_path, dimer=False)
elif 'neb' in prior_acc_level and prior_spin is None:
manage_restart_files(prior_results_path, neb=True)
mof = neb2dim()
mof = set_initial_magmoms(mof, spin_level)
elif 'lowacc' in acc_level and prior_spin is not None:
mof = read(prior_results_file)
mof = set_initial_magmoms(mof, spin_level)
manage_restart_files(prior_results_path,
dimer=True,
wavechg=False)
else:
mof = prep_new_run(self)
manage_restart_files(prior_results_path, dimer=True)
if 'medacc' in acc_level and sum(
kpts_lo) == 3 and sum(kpts) > 3:
clean_files(['CHGCAR', 'WAVECAR'])
if 'highacc' in acc_level and 'large_supercell' in self.calc_swaps:
self.calc_swaps.remove('large_supercell')
pprint('Running ' + spin_label + ', ' + acc_level)
mof, self.calc_swaps = mof_run(self, mof, calcs(acc_level), kpts)
if mof is not None and mof.calc.scf_converged and mof.calc.converged:
write_success(self)
else:
write_errors(self, mof)
vtst_cleanup()
elif os.path.isfile(outcar_paths[self.run_i]):
pprint('COMPLETED: ' + spin_label + ', ' + acc_level)
mof = prep_next_run(self)
os.chdir(pwd)
if mof is None:
pprint('Skipping rest because of errors')
return None
return mof
def isif3_highacc(self):
"""
Run high accuracy ISIF3
Returns:
mof (ASE Atoms object): updated ASE Atoms object
"""
acc_levels = self.acc_levels
outcar_paths = self.outcar_paths
error_outcar_paths = self.error_outcar_paths
spin_label = self.spin_label
kpts_lo = self.kpts_dict['kpts_lo']
kpts_hi = self.kpts_dict['kpts_hi']
acc_level = acc_levels[self.run_i]
calcs = self.calcs
prior_results_path = os.path.join(
self.results_partial_paths[self.run_i - 1], spin_label)
if os.path.isfile(outcar_paths[self.run_i - 1]) and not os.path.isfile(
outcar_paths[self.run_i]) and not os.path.isfile(
error_outcar_paths[self.run_i]):
mof = prep_new_run(self)
converged = False
loop_i = 0
n_runs = 15
V_diff = np.inf
V_cut = 0.01
V0 = mof.get_volume()
if sum(kpts_lo) == 3 and sum(kpts_hi) > 3:
clean_files(['CHGCAR', 'WAVECAR'])
else:
manage_restart_files(prior_results_path)
while (not converged or V_diff > V_cut) and loop_i < n_runs:
if loop_i == 10 and 'fire' not in self.calc_swaps and 'zbrent' not in self.calc_swaps:
self.calc_swaps.append('fire')
pprint('Running ' + spin_label + ', ' + acc_level +
': iteration ' + str(loop_i) + '/' + str(n_runs - 1))
mof, self.calc_swaps = mof_run(self, mof,
calcs('isif3_highacc'), kpts_hi)
if mof is None:
break
if loop_i > 0:
converged = mof.calc.converged
mof = read('OUTCAR')
V = mof.get_volume()
mof = continue_magmoms(mof, 'INCAR')
if loop_i > 0:
V_diff = np.abs((V - V0)) / V0
V0 = V
loop_i += 1
if mof is not None and converged and V_diff <= V_cut and 'large_supercell' in self.calc_swaps:
self.calc_swaps.append('nsw=100')
self.calc_swaps.remove('large_supercell')
pprint('Running ' + spin_label + ', ' + acc_level +
' (LREAL=False)')
mof, self.calc_swaps = mof_run(self, mof,
calcs('isif3_highacc'), kpts_hi)
self.calc_swaps.remove('nsw=100')
if mof is not None and mof.calc.converged:
write_success(self)
else:
write_errors(self, mof)
else:
write_errors(self, mof)
if mof is not None and V_diff > V_cut:
pprint('^ Change in V of ' + str(V_diff) + ' percent')
if 'fire' in self.calc_swaps:
self.calc_swaps.remove('fire')
elif os.path.isfile(outcar_paths[self.run_i]):
pprint('COMPLETED: ' + spin_label + ', ' + acc_level)
mof = prep_next_run(self)
if mof is None:
pprint('Skipping rest because of errors')
return None
return mof
def isif2_lowacc(self):
"""
Run low accuracy ISIF2
Returns:
mof (ASE Atoms object): updated ASE Atoms object
"""
acc_levels = self.acc_levels
outcar_paths = self.outcar_paths
error_outcar_paths = self.error_outcar_paths
spin_level = self.spin_level
spin_label = self.spin_label
cif_file = self.cif_file
mofpath = self.mofpath
prior_spin = self.prior_spin
spin1_final_mof_path = self.spin1_final_mof_path
kpts_lo = self.kpts_dict['kpts_lo']
acc_level = acc_levels[self.run_i]
niggli = self.niggli
calcs = self.calcs
prior_results_path = os.path.join(
self.results_partial_paths[self.run_i - 1], spin_label)
if os.path.isfile(outcar_paths[self.run_i - 1]) and not os.path.isfile(
outcar_paths[self.run_i]) and not os.path.isfile(
error_outcar_paths[self.run_i]):
if prior_spin is None:
mof = cif_to_mof(os.path.join(mofpath, cif_file), niggli)
else:
mof = read(spin1_final_mof_path)
manage_restart_files(prior_results_path)
mof = set_initial_magmoms(mof, spin_level)
fmax = 5.0
pprint('Running ' + spin_label + ', ' + acc_level)
mof, dyn, self.calc_swaps = mof_bfgs_run(self,
mof,
calcs('ase_bfgs'),
kpts_lo,
fmax=fmax)
if mof is not None and dyn:
loop_i = 0
converged = False
clean_files(['opt.traj'])
while mof is not None and loop_i < 4 and not converged and mof.calc.scf_converged:
if loop_i == 2 and 'fire' not in self.calc_swaps and 'zbrent' not in self.calc_swaps:
self.calc_swaps.append('fire')
mof = read('OUTCAR')
mof = continue_magmoms(mof, 'INCAR')
mof, self.calc_swaps = mof_run(self, mof,
calcs('isif2_lowacc'),
kpts_lo)
if mof is None:
break
converged = mof.calc.converged
loop_i += 1
if 'fire' in self.calc_swaps:
self.calc_swaps.remove('fire')
if mof is not None and mof.calc.scf_converged and mof.calc.converged:
write_success(self)
else:
write_errors(self, mof)
elif os.path.isfile(outcar_paths[self.run_i]):
pprint('COMPLETED: ' + spin_label + ', ' + acc_level)
mof = prep_next_run(self)
if mof is None:
pprint('Skipping rest because of errors')
return None
return mof