def freq_fw(self,
charge,
spin_multiplicity,
fw_id_cal,
fw_id_db,
priority=None,
method=None):
if not method:
if self.large:
method = "PBE-D3/6-31+G*"
else:
method = "B3lYP/6-31+G*"
task_type = "vibrational frequency"
state_name = self.get_state_name(charge, spin_multiplicity)
title = self.molname + " " + state_name + " " + method + " " + task_type
exchange, correlation, basis_set, aux_basis, rem_params, method_token, ecp = self. \
get_exchange_correlation_basis_auxbasis_remparams(method, self.mol)
if exchange.lower() in ["xygjos"]:
rem_params["IDERIV"] = 1
qctask = QcTask(self.mol,
charge=charge,
spin_multiplicity=spin_multiplicity,
jobtype="freq",
title=title,
exchange=exchange,
correlation=correlation,
basis_set=basis_set,
aux_basis_set=aux_basis,
ecp=ecp,
rem_params=rem_params)
if self.large:
qctask.set_scf_algorithm_and_iterations(iterations=100)
qcinp = QcInput([qctask])
spec = self.base_spec()
spec["qcinp"] = qcinp.as_dict()
spec['task_type'] = task_type
spec['charge'] = charge
spec['spin_multiplicity'] = spin_multiplicity
spec['run_tags']['methods'] = method_token
spec["qm_method"] = method
if priority:
spec['_priority'] = priority
task_name = self.molname + ' ' + state_name + ' ' + task_type
from rubicon.firetasks.qchem.multistep_qchem_task \
import QChemFrequencyDBInsertionTask
fw_freq_cal = Firework([QChemTask()],
spec=spec,
name=task_name,
fw_id=fw_id_cal)
spec_db = copy.deepcopy(spec)
del spec_db['_dupefinder']
spec_db['_allow_fizzled_parents'] = True
spec_db['task_type'] = task_type + ' DB Insertion'
del spec_db["_trackers"][:2]
task_name_db = task_name + " DB Insertion"
fw_freq_db = Firework([QChemFrequencyDBInsertionTask()],
spec=spec_db,
name=task_name_db,
fw_id=fw_id_db)
return fw_freq_cal, fw_freq_db
def from_dict(cls, d):
h = QChemErrorHandler(input_file=d["input_file"],
output_file=d["output_file"],
ex_backup_list=d["ex_backup_list"],
rca_gdm_thresh=d["rca_gdm_thresh"],
scf_max_cycles=d["scf_max_cycles"],
geom_max_cycles=d["geom_max_cycles"])
h.outdata = d["outdata"]
h.qcinp = QcInput.from_dict(d["qcinp"]) if d["qcinp"] else None
h.error_step_id = d["error_step_id"]
h.errors = d["errors"]
h.fix_step = QcTask.from_dict(d["fix_step"]) if d["fix_step"] else None
return h
def from_dict(cls, d):
h = QChemErrorHandler(input_file=d["input_file"],
output_file=d["output_file"],
ex_backup_list=d["ex_backup_list"],
rca_gdm_thresh=d["rca_gdm_thresh"],
scf_max_cycles=d["scf_max_cycles"],
geom_max_cycles=d["geom_max_cycles"])
h.outdata = d["outdata"]
h.qcinp = QcInput.from_dict(d["qcinp"]) if d["qcinp"] else None
h.error_step_id = d["error_step_id"]
h.errors = d["errors"]
h.fix_step = QcTask.from_dict(d["fix_step"]) if d["fix_step"] else None
return h
def aimd_fw(self,
charge,
spin_multiplicity,
fw_id_cal,
fw_id_db,
num_steps,
time_step,
temperature,
priority=None,
qm_method=None):
if not qm_method:
qm_method = "B3LYP/6-31+G*"
spec = self.base_spec()
if priority:
spec['_priority'] = priority
task_type = "ab initio molecule dynamics"
state_name = self.get_state_name(charge, spin_multiplicity)
title = self.molname + " " + state_name + " " + qm_method + " " + task_type
exchange, correlation, basis_set, aux_basis, rem_params, method_token, ecp = self. \
get_exchange_correlation_basis_auxbasis_remparams(qm_method,
self.mol)
if rem_params is None:
rem_params = dict()
rem_params["aimd_method"] = "bomd"
rem_params["time_step"] = time_step
rem_params["aimd_steps"] = num_steps
rem_params["aimd_init_veloc"] = "thermal"
rem_params["aimd_temp"] = temperature
rem_params["fock_extrap_order"] = 6
rem_params["fock_extrap_points"] = 12
qctask_vac = QcTask(self.mol,
charge=charge,
spin_multiplicity=spin_multiplicity,
jobtype="aimd",
title=title,
exchange=exchange,
correlation=correlation,
basis_set=basis_set,
aux_basis_set=aux_basis,
ecp=ecp,
rem_params=rem_params)
qctask_vac.set_scf_algorithm_and_iterations(iterations=100)
qcinp = QcInput([qctask_vac])
spec["qcinp"] = qcinp.as_dict()
spec['task_type'] = task_type
spec['charge'] = charge
spec['spin_multiplicity'] = spin_multiplicity
spec['run_tags']['methods'] = method_token
spec['run_tags']['rem_params'] = rem_params
spec["qm_method"] = qm_method
task_name = self.molname + ' ' + state_name + ' ' + task_type
from rubicon.firetasks.qchem.multistep_qchem_task \
import QChemAIMDDBInsertionTask
fw_sp_cal = Firework([QChemTask()],
spec=spec,
name=task_name,
fw_id=fw_id_cal)
spec_db = copy.deepcopy(spec)
del spec_db['_dupefinder']
spec_db['_allow_fizzled_parents'] = True
spec_db['task_type'] = task_type + ' DB Insertion'
del spec_db["_trackers"][:2]
task_name_db = task_name + " DB Insertion"
fw_sp_db = Firework([QChemAIMDDBInsertionTask()],
spec=spec_db,
name=task_name_db,
fw_id=fw_id_db)
return fw_sp_cal, fw_sp_db
def vacuum_only_sp_fw(self,
charge,
spin_multiplicity,
fw_id_cal,
fw_id_db,
priority=None,
qm_method=None,
population_method=None,
mixed_basis_generator=None,
mixed_aux_basis_generator=None,
super_mol_snlgroup_id=None,
super_mol_egsnl=None,
super_mol_inchi_root=None,
ghost_atoms=None,
bs_overlap=False):
if not qm_method:
qm_method = "B3LYP/6-31+G*"
spec = self.base_spec()
if priority:
spec['_priority'] = priority
if super_mol_snlgroup_id:
from rubicon.workflows.qchem.bsse_wf import BSSEFragment
task_type = "bsse {} fragment".format(
BSSEFragment.OVERLAPPED if bs_overlap else BSSEFragment.
ISOLATED)
else:
task_type = "vacuum only single point energy"
if mixed_basis_generator or mixed_aux_basis_generator:
population_method = population_method if population_method else "nbo"
task_type = "atomic charge"
state_name = self.get_state_name(charge, spin_multiplicity)
title = self.molname + " " + state_name + " " + qm_method + " " + task_type
title += "\n Gas Phase"
exchange, correlation, basis_set, aux_basis, rem_params, method_token, ecp = self. \
get_exchange_correlation_basis_auxbasis_remparams(qm_method,
self.mol)
if population_method:
if not rem_params:
rem_params = dict()
if population_method.lower() == "nbo":
rem_params["nbo"] = 1
elif population_method.lower() == "chelpg":
rem_params["chelpg"] = True
elif population_method.lower() == "hirshfeld":
rem_params["hirshfeld"] = True
ga = ghost_atoms if bs_overlap else None
qctask_vac = QcTask(self.mol,
charge=charge,
spin_multiplicity=spin_multiplicity,
jobtype="sp",
title=title,
exchange=exchange,
correlation=correlation,
basis_set=basis_set,
aux_basis_set=aux_basis,
ecp=ecp,
rem_params=rem_params,
ghost_atoms=ga)
if (not self.large) and (mixed_basis_generator is None
and mixed_aux_basis_generator is None):
qctask_vac.set_dft_grid(128, 302)
qctask_vac.set_integral_threshold(12)
qctask_vac.set_scf_convergence_threshold(8)
else:
qctask_vac.set_scf_algorithm_and_iterations(iterations=100)
qcinp = QcInput([qctask_vac])
spec["qcinp"] = qcinp.as_dict()
spec['task_type'] = task_type
spec['charge'] = charge
spec['spin_multiplicity'] = spin_multiplicity
spec['run_tags']['methods'] = method_token
spec["qm_method"] = qm_method
if super_mol_snlgroup_id:
spec["run_tags"]["super_mol_snlgroup_id"] = super_mol_snlgroup_id
spec["snlgroup_id"] = super_mol_snlgroup_id
spec["egsnl"] = super_mol_egsnl
spec["inchi_root"] = super_mol_inchi_root
if ghost_atoms:
spec["run_tags"]["ghost_atoms"] = sorted(set(ghost_atoms))
from rubicon.workflows.qchem.bsse_wf import BSSEFragment
spec["run_tags"][
"bsse_fragment_type"] = BSSEFragment.OVERLAPPED if bs_overlap else BSSEFragment.ISOLATED
if mixed_basis_generator:
spec["_mixed_basis_set_generator"] = mixed_basis_generator
if mixed_aux_basis_generator:
spec["_mixed_aux_basis_set_generator"] = mixed_aux_basis_generator
task_name = self.molname + ' ' + state_name + ' ' + task_type
from rubicon.firetasks.qchem.multistep_qchem_task \
import QChemSinglePointEnergyDBInsertionTask
fw_sp_cal = Firework([QChemTask()],
spec=spec,
name=task_name,
fw_id=fw_id_cal)
spec_db = copy.deepcopy(spec)
del spec_db['_dupefinder']
spec_db['_allow_fizzled_parents'] = True
spec_db['task_type'] = task_type + ' DB Insertion'
del spec_db["_trackers"][:2]
task_name_db = task_name + " DB Insertion"
fw_sp_db = Firework([QChemSinglePointEnergyDBInsertionTask()],
spec=spec_db,
name=task_name_db,
fw_id=fw_id_db)
return fw_sp_cal, fw_sp_db
def sp_fw(self,
charge,
spin_multiplicity,
fw_id_cal,
fw_id_db,
solvent_method="ief-pcm",
use_vdw_surface=False,
solvent="water",
priority=None,
qm_method=None,
population_method=None,
task_type_name=None):
if not qm_method:
qm_method = "B3LYP/6-31+G*"
spec = self.base_spec()
if priority:
spec['_priority'] = priority
task_type = task_type_name if task_type_name else "single point energy"
state_name = self.get_state_name(charge, spin_multiplicity)
title = self.molname + " " + state_name + " " + qm_method + " " + task_type
title += "\n Gas Phase"
exchange, correlation, basis_set, aux_basis, rem_params, method_token, ecp = self. \
get_exchange_correlation_basis_auxbasis_remparams(qm_method,
self.mol)
if population_method:
if not rem_params:
rem_params = dict()
if population_method.lower() == "nbo":
rem_params["nbo"] = 1
elif population_method.lower() == "chelpg":
rem_params["chelpg"] = True
qctask_vac = QcTask(self.mol,
charge=charge,
spin_multiplicity=spin_multiplicity,
jobtype="sp",
title=title,
exchange=exchange,
correlation=correlation,
basis_set=basis_set,
aux_basis_set=aux_basis,
ecp=ecp,
rem_params=rem_params)
if not self.large:
qctask_vac.set_dft_grid(128, 302)
qctask_vac.set_integral_threshold(12)
qctask_vac.set_scf_convergence_threshold(8)
else:
qctask_vac.set_scf_algorithm_and_iterations(iterations=100)
title = " Solution Phase, {}".format(solvent)
qctask_sol = QcTask(self.mol,
charge=charge,
spin_multiplicity=spin_multiplicity,
jobtype="sp",
title=title,
exchange=exchange,
correlation=correlation,
basis_set=basis_set,
aux_basis_set=aux_basis,
ecp=ecp,
rem_params=rem_params)
qctask_sol.set_scf_initial_guess(guess="read")
implicit_solvent = self.set_solvent_method(qctask_sol, solvent,
solvent_method,
use_vdw_surface)
qcinp = QcInput([qctask_vac, qctask_sol])
spec["qcinp"] = qcinp.as_dict()
spec['task_type'] = task_type
spec['charge'] = charge
spec['spin_multiplicity'] = spin_multiplicity
spec['run_tags']['methods'] = method_token
spec["qm_method"] = qm_method
spec['implicit_solvent'] = implicit_solvent
task_name = self.molname + ' ' + state_name + ' ' + task_type
from rubicon.firetasks.qchem.multistep_qchem_task \
import QChemSinglePointEnergyDBInsertionTask
fw_sp_cal = Firework([QChemTask()],
spec=spec,
name=task_name,
fw_id=fw_id_cal)
spec_db = copy.deepcopy(spec)
del spec_db['_dupefinder']
spec_db['_allow_fizzled_parents'] = True
spec_db['task_type'] = task_type + ' DB Insertion'
del spec_db["_trackers"][:2]
task_name_db = task_name + " DB Insertion"
fw_sp_db = Firework([QChemSinglePointEnergyDBInsertionTask()],
spec=spec_db,
name=task_name_db,
fw_id=fw_id_db)
return fw_sp_cal, fw_sp_db
def geom_fw(self,
charge,
spin_multiplicity,
fw_id_cal,
fw_id_db,
priority=None,
method=None,
task_type_prefix=None):
task_type = "geometry optimization"
if task_type_prefix:
task_type = task_type_prefix + " " + task_type
state_name = self.get_state_name(charge, spin_multiplicity)
if not method:
if self.large:
method = "PBE-D3/6-31+G*"
else:
method = "B3lYP/6-31+G*"
title = self.molname + " " + state_name + " " + method + " " + task_type
exchange, correlation, basis_set, aux_basis, rem_params, method_token, ecp = self. \
get_exchange_correlation_basis_auxbasis_remparams(method, self.mol)
qctask = QcTask(self.mol,
charge=charge,
spin_multiplicity=spin_multiplicity,
jobtype="opt",
title=title,
exchange=exchange,
correlation=correlation,
basis_set=basis_set,
aux_basis_set=aux_basis,
ecp=ecp,
rem_params=rem_params)
if self.large:
qctask.set_geom_max_iterations(200)
qctask.set_scf_algorithm_and_iterations(iterations=100)
qctask.scale_geom_opt_threshold(gradient=1.0,
displacement=10.0,
energy=10.0)
qcinp = QcInput([qctask])
spec = self.base_spec()
spec["qcinp"] = qcinp.as_dict()
spec['task_type'] = task_type
spec['charge'] = charge
spec['spin_multiplicity'] = spin_multiplicity
spec['run_tags']['methods'] = method_token
spec["qm_method"] = method
if priority:
spec['_priority'] = priority
task_name = self.molname + ' ' + state_name + ' ' + task_type
from rubicon.firetasks.qchem.multistep_qchem_task \
import QChemGeomOptDBInsertionTask
fw_geom_cal = Firework([QChemTask()],
spec=spec,
name=task_name,
fw_id=fw_id_cal)
spec_db = copy.deepcopy(spec)
del spec_db['_dupefinder']
spec_db['_allow_fizzled_parents'] = True
spec_db['task_type'] = task_type + ' DB Insertion'
del spec_db["_trackers"][:2]
task_name_db = task_name + " DB Insertion"
fw_geom_db = Firework([QChemGeomOptDBInsertionTask()],
spec=spec_db,
name=task_name_db,
fw_id=fw_id_db)
return fw_geom_cal, fw_geom_db