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 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 prep_new_run(workflow):
acc_levels = workflow.acc_levels
acc_level = acc_levels[workflow.run_i - 1]
refcode = workflow.refcode
spin_label = workflow.spin_label
basepath = workflow.basepath
success_path = os.path.join(basepath, 'results', refcode, acc_level,
spin_label)
outcarpath = os.path.join(success_path, 'OUTCAR')
incarpath = os.path.join(success_path, 'INCAR')
mof = read(outcarpath)
mof_initialized = deepcopy(mof)
mof_initialized = continue_magmoms(mof_initialized, incarpath)
return mof_initialized
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