def run_task(self, fw_spec):
input_file = self.get("input_file", "mol.qin")
# this adds the full path to the input_file
if "write_to_dir" in self:
input_file = os.path.join(self["write_to_dir"], input_file)
# these if statements might need to be reordered at some point
if "molecule" in self:
molecule = self["molecule"]
elif fw_spec.get("prev_calc_molecule"):
molecule = fw_spec.get("prev_calc_molecule")
else:
raise KeyError(
"No molecule present, add as an optional param or check fw_spec"
)
# in the current structure there needs to be a statement for every optional QChem section
# the code below defaults the section to None if the variable is not passed
opt = self.get("opt", None)
pcm = self.get("pcm", None)
solvent = self.get("solvent", None)
smx = self.get("smx", None)
qcin = QCInput(molecule=molecule,
rem=self["rem"],
opt=opt,
pcm=pcm,
solvent=solvent,
smx=smx)
qcin.write_file(input_file)
def run_task(self, fw_spec):
input_file = os.path.join(self.get("write_to_dir", ""),
self.get("input_file", "mol.qin"))
# if a molecule is being passed through fw_spec
if fw_spec.get("prev_calc_molecule"):
prev_calc_mol = fw_spec.get("prev_calc_molecule")
# if a molecule is also passed as an optional parameter
if self.get("molecule"):
mol = self.get("molecule")
# check if mol and prev_calc_mol are isomorphic
mol_graph = MoleculeGraph.with_local_env_strategy(
mol, OpenBabelNN(), reorder=False, extend_structure=False)
prev_mol_graph = MoleculeGraph.with_local_env_strategy(
prev_calc_molecule,
OpenBabelNN(),
reorder=False,
extend_structure=False,
)
if mol_graph.isomorphic_to(prev_mol_graph):
mol = prev_calc_mol
else:
print(
"WARNING: Molecule from spec is not isomorphic to passed molecule!"
)
else:
mol = prev_calc_mol
elif self.get("molecule"):
mol = self.get("molecule")
else:
raise KeyError(
"No molecule present, add as an optional param or check fw_spec"
)
# in the current structure there needs to be a statement for every optional QChem section
# the code below defaults the section to None if the variable is not passed
opt = self.get("opt", None)
pcm = self.get("pcm", None)
solvent = self.get("solvent", None)
qcin = QCInput(molecule=mol,
rem=self["rem"],
opt=opt,
pcm=pcm,
solvent=solvent)
qcin.write_file(input_file)
def opt_with_frequency_flattener(
cls,
qchem_command,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
qclog_file="mol.qclog",
max_iterations=10,
max_molecule_perturb_scale=0.3,
check_connectivity=True,
linked=True,
transition_state=False,
freq_before_opt=False,
save_final_scratch=False,
**QCJob_kwargs,
):
"""
Optimize a structure and calculate vibrational frequencies to check if the
structure is in a true minima.
If there are an inappropriate number of imaginary frequencies (>0 for a
minimum-energy structure, >1 for a transition-state), attempt to re-calculate
using one of two methods:
- Perturb the geometry based on the imaginary frequencies and re-optimize
- Use the exact Hessian to inform a subsequent optimization
After each geometry optimization, the frequencies are re-calculated to
determine if a true minimum (or transition-state) has been found.
Note: Very small imaginary frequencies (-15cm^-1 < nu < 0) are allowed
if there is only one more than there should be. In other words, if there
is one very small imaginary frequency, it is still treated as a minimum,
and if there is one significant imaginary frequency and one very small
imaginary frequency, it is still treated as a transition-state.
Args:
qchem_command (str): Command to run QChem.
multimode (str): Parallelization scheme, either openmp or mpi.
input_file (str): Name of the QChem input file.
output_file (str): Name of the QChem output file.
max_iterations (int): Number of perturbation -> optimization -> frequency
iterations to perform. Defaults to 10.
max_molecule_perturb_scale (float): The maximum scaled perturbation that
can be applied to the molecule. Defaults to 0.3.
check_connectivity (bool): Whether to check differences in connectivity
introduced by structural perturbation. Defaults to True.
linked (bool): Whether or not to use the linked flattener. If set to True (default),
then the explicit Hessians from a vibrational frequency analysis will be used
as the initial Hessian of subsequent optimizations. In many cases, this can
significantly improve optimization efficiency.
transition_state (bool): If True (default False), use a ts
optimization (search for a saddle point instead of a minimum)
freq_before_opt (bool): If True (default False), run a frequency
calculation before any opt/ts searches to improve understanding
of the local potential energy surface.
save_final_scratch (bool): Whether to save full scratch directory contents
at the end of the flattening. Defaults to False.
**QCJob_kwargs: Passthrough kwargs to QCJob. See
:class:`custodian.qchem.jobs.QCJob`.
"""
if not os.path.exists(input_file):
raise AssertionError("Input file must be present!")
if transition_state:
opt_method = "ts"
perturb_index = 1
else:
opt_method = "opt"
perturb_index = 0
energy_diff_cutoff = 0.0000001
orig_input = QCInput.from_file(input_file)
freq_rem = copy.deepcopy(orig_input.rem)
freq_rem["job_type"] = "freq"
opt_rem = copy.deepcopy(orig_input.rem)
opt_rem["job_type"] = opt_method
first = True
energy_history = list()
if freq_before_opt:
if not linked:
warnings.warn(
"WARNING: This first frequency calculation will not inform subsequent optimization!"
)
yield (QCJob(
qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".freq_pre",
save_scratch=True,
backup=first,
**QCJob_kwargs,
))
if linked:
opt_rem["geom_opt_hessian"] = "read"
opt_rem["scf_guess_always"] = True
opt_QCInput = QCInput(
molecule=orig_input.molecule,
rem=opt_rem,
opt=orig_input.opt,
pcm=orig_input.pcm,
solvent=orig_input.solvent,
smx=orig_input.smx,
)
opt_QCInput.write_file(input_file)
first = False
if linked:
opt_rem["geom_opt_hessian"] = "read"
opt_rem["scf_guess_always"] = True
for ii in range(max_iterations):
yield (QCJob(
qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".{}_".format(opt_method) + str(ii),
save_scratch=True,
backup=first,
**QCJob_kwargs,
))
opt_outdata = QCOutput(output_file +
".{}_".format(opt_method) +
str(ii)).data
opt_indata = QCInput.from_file(input_file +
".{}_".format(opt_method) +
str(ii))
if opt_indata.rem["scf_algorithm"] != freq_rem["scf_algorithm"]:
freq_rem["scf_algorithm"] = opt_indata.rem["scf_algorithm"]
opt_rem["scf_algorithm"] = opt_indata.rem["scf_algorithm"]
first = False
if opt_outdata[
"structure_change"] == "unconnected_fragments" and not opt_outdata[
"completion"]:
if not transition_state:
warnings.warn(
"Unstable molecule broke into unconnected fragments which failed to optimize! Exiting..."
)
break
energy_history.append(opt_outdata.get("final_energy"))
freq_QCInput = QCInput(
molecule=opt_outdata.get(
"molecule_from_optimized_geometry"),
rem=freq_rem,
opt=orig_input.opt,
pcm=orig_input.pcm,
solvent=orig_input.solvent,
smx=orig_input.smx,
)
freq_QCInput.write_file(input_file)
yield (QCJob(
qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".freq_" + str(ii),
save_scratch=True,
backup=first,
**QCJob_kwargs,
))
outdata = QCOutput(output_file + ".freq_" + str(ii)).data
indata = QCInput.from_file(input_file + ".freq_" + str(ii))
if indata.rem["scf_algorithm"] != freq_rem["scf_algorithm"]:
freq_rem["scf_algorithm"] = indata.rem["scf_algorithm"]
opt_rem["scf_algorithm"] = indata.rem["scf_algorithm"]
errors = outdata.get("errors")
if len(errors) != 0:
raise AssertionError(
"No errors should be encountered while flattening frequencies!"
)
if not transition_state:
freq_0 = outdata.get("frequencies")[0]
freq_1 = outdata.get("frequencies")[1]
if freq_0 > 0.0:
warnings.warn("All frequencies positive!")
break
if abs(freq_0) < 15.0 and freq_1 > 0.0:
warnings.warn(
"One negative frequency smaller than 15.0 - not worth further flattening!"
)
break
if len(energy_history) > 1:
if abs(energy_history[-1] -
energy_history[-2]) < energy_diff_cutoff:
warnings.warn("Energy change below cutoff!")
break
opt_QCInput = QCInput(
molecule=opt_outdata.get(
"molecule_from_optimized_geometry"),
rem=opt_rem,
opt=orig_input.opt,
pcm=orig_input.pcm,
solvent=orig_input.solvent,
smx=orig_input.smx,
)
opt_QCInput.write_file(input_file)
else:
freq_0 = outdata.get("frequencies")[0]
freq_1 = outdata.get("frequencies")[1]
freq_2 = outdata.get("frequencies")[2]
if freq_0 < 0.0 < freq_1:
warnings.warn("Saddle point found!")
break
if abs(freq_1) < 15.0 and freq_2 > 0.0:
warnings.warn(
"Second small imaginary frequency (smaller than 15.0) - not worth further flattening!"
)
break
opt_QCInput = QCInput(
molecule=opt_outdata.get(
"molecule_from_optimized_geometry"),
rem=opt_rem,
opt=orig_input.opt,
pcm=orig_input.pcm,
solvent=orig_input.solvent,
smx=orig_input.smx,
)
opt_QCInput.write_file(input_file)
if not save_final_scratch:
shutil.rmtree(os.path.join(os.getcwd(), "scratch"))
else:
orig_opt_input = QCInput.from_file(input_file)
history = list()
for ii in range(max_iterations):
yield (QCJob(
qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".{}_".format(opt_method) + str(ii),
backup=first,
**QCJob_kwargs,
))
opt_outdata = QCOutput(output_file +
".{}_".format(opt_method) +
str(ii)).data
if first:
orig_species = copy.deepcopy(opt_outdata.get("species"))
orig_charge = copy.deepcopy(opt_outdata.get("charge"))
orig_multiplicity = copy.deepcopy(
opt_outdata.get("multiplicity"))
orig_energy = copy.deepcopy(
opt_outdata.get("final_energy"))
first = False
if opt_outdata[
"structure_change"] == "unconnected_fragments" and not opt_outdata[
"completion"]:
if not transition_state:
warnings.warn(
"Unstable molecule broke into unconnected fragments which failed to optimize! Exiting..."
)
break
freq_QCInput = QCInput(
molecule=opt_outdata.get(
"molecule_from_optimized_geometry"),
rem=freq_rem,
opt=orig_opt_input.opt,
pcm=orig_opt_input.pcm,
solvent=orig_opt_input.solvent,
smx=orig_opt_input.smx,
)
freq_QCInput.write_file(input_file)
yield (QCJob(
qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".freq_" + str(ii),
backup=first,
**QCJob_kwargs,
))
outdata = QCOutput(output_file + ".freq_" + str(ii)).data
errors = outdata.get("errors")
if len(errors) != 0:
raise AssertionError(
"No errors should be encountered while flattening frequencies!"
)
if not transition_state:
freq_0 = outdata.get("frequencies")[0]
freq_1 = outdata.get("frequencies")[1]
if freq_0 > 0.0:
warnings.warn("All frequencies positive!")
if opt_outdata.get("final_energy") > orig_energy:
warnings.warn(
"WARNING: Energy increased during frequency flattening!"
)
break
if abs(freq_0) < 15.0 and freq_1 > 0.0:
warnings.warn(
"One negative frequency smaller than 15.0 - not worth further flattening!"
)
break
if len(energy_history) > 1:
if abs(energy_history[-1] -
energy_history[-2]) < energy_diff_cutoff:
warnings.warn("Energy change below cutoff!")
break
else:
freq_0 = outdata.get("frequencies")[0]
freq_1 = outdata.get("frequencies")[1]
freq_2 = outdata.get("frequencies")[2]
if freq_0 < 0.0 < freq_1:
warnings.warn("Saddle point found!")
break
if abs(freq_1) < 15.0 and freq_2 > 0.0:
warnings.warn(
"Second small imaginary frequency (smaller than 15.0) - not worth further flattening!"
)
break
hist = {}
hist["molecule"] = copy.deepcopy(
outdata.get("initial_molecule"))
hist["geometry"] = copy.deepcopy(
outdata.get("initial_geometry"))
hist["frequencies"] = copy.deepcopy(outdata.get("frequencies"))
hist["frequency_mode_vectors"] = copy.deepcopy(
outdata.get("frequency_mode_vectors"))
hist["num_neg_freqs"] = sum(
1 for freq in outdata.get("frequencies") if freq < 0)
hist["energy"] = copy.deepcopy(opt_outdata.get("final_energy"))
hist["index"] = len(history)
hist["children"] = list()
history.append(hist)
ref_mol = history[-1]["molecule"]
geom_to_perturb = history[-1]["geometry"]
negative_freq_vecs = history[-1]["frequency_mode_vectors"][
perturb_index]
reversed_direction = False
standard = True
# If we've found one or more negative frequencies in two consecutive iterations, let's dig in
# deeper:
if len(history) > 1:
# Start by finding the latest iteration's parent:
if history[-1]["index"] in history[-2]["children"]:
parent_hist = history[-2]
history[-1]["parent"] = parent_hist["index"]
elif history[-1]["index"] in history[-3]["children"]:
parent_hist = history[-3]
history[-1]["parent"] = parent_hist["index"]
else:
raise AssertionError(
"ERROR: your parent should always be one or two iterations behind you! Exiting..."
)
# if the number of negative frequencies has remained constant or increased from parent to
# child,
if history[-1]["num_neg_freqs"] >= parent_hist[
"num_neg_freqs"]:
# check to see if the parent only has one child, aka only the positive perturbation has
# been tried,
# in which case just try the negative perturbation from the same parent
if len(parent_hist["children"]) == 1:
ref_mol = parent_hist["molecule"]
geom_to_perturb = parent_hist["geometry"]
negative_freq_vecs = parent_hist[
"frequency_mode_vectors"][perturb_index]
reversed_direction = True
standard = False
parent_hist["children"].append(len(history))
# If the parent has two children, aka both directions have been tried, then we have to
# get creative:
elif len(parent_hist["children"]) == 2:
# If we're dealing with just one negative frequency,
if parent_hist["num_neg_freqs"] == 1:
if history[parent_hist["children"][0]][
"energy"] < history[-1]["energy"]:
good_child = copy.deepcopy(
history[parent_hist["children"][0]])
else:
good_child = copy.deepcopy(history[-1])
if good_child["num_neg_freqs"] > 1:
raise Exception(
"ERROR: Child with lower energy has more negative frequencies! "
"Exiting...")
if good_child["energy"] < parent_hist["energy"]:
make_good_child_next_parent = True
elif (vector_list_diff(
good_child["frequency_mode_vectors"]
[perturb_index],
parent_hist["frequency_mode_vectors"]
[perturb_index],
) > 0.2):
make_good_child_next_parent = True
else:
raise Exception(
"ERROR: Good child not good enough! Exiting..."
)
if make_good_child_next_parent:
good_child["index"] = len(history)
history.append(good_child)
ref_mol = history[-1]["molecule"]
geom_to_perturb = history[-1]["geometry"]
negative_freq_vecs = history[-1][
"frequency_mode_vectors"][
perturb_index]
else:
raise Exception(
"ERROR: Can't deal with multiple neg frequencies yet! Exiting..."
)
else:
raise AssertionError(
"ERROR: Parent cannot have more than two childen! Exiting..."
)
# Implicitly, if the number of negative frequencies decreased from parent to child,
# continue normally.
if standard:
history[-1]["children"].append(len(history))
min_molecule_perturb_scale = 0.1
scale_grid = 10
perturb_scale_grid = (max_molecule_perturb_scale -
min_molecule_perturb_scale) / scale_grid
structure_successfully_perturbed = False
for molecule_perturb_scale in np.arange(
max_molecule_perturb_scale,
min_molecule_perturb_scale,
-perturb_scale_grid,
):
new_coords = perturb_coordinates(
old_coords=geom_to_perturb,
negative_freq_vecs=negative_freq_vecs,
molecule_perturb_scale=molecule_perturb_scale,
reversed_direction=reversed_direction,
)
new_molecule = Molecule(
species=orig_species,
coords=new_coords,
charge=orig_charge,
spin_multiplicity=orig_multiplicity,
)
if check_connectivity and not transition_state:
structure_successfully_perturbed = (
check_for_structure_changes(
ref_mol, new_molecule) == "no_change")
if structure_successfully_perturbed:
break
if not structure_successfully_perturbed:
raise Exception(
"ERROR: Unable to perturb coordinates to remove negative frequency without changing "
"the connectivity! Exiting...")
new_opt_QCInput = QCInput(
molecule=new_molecule,
rem=opt_rem,
opt=orig_opt_input.opt,
pcm=orig_opt_input.pcm,
solvent=orig_opt_input.solvent,
smx=orig_opt_input.smx,
)
new_opt_QCInput.write_file(input_file)
def opt_with_frequency_flattener(cls,
qchem_command,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
qclog_file="mol.qclog",
max_iterations=10,
max_molecule_perturb_scale=0.3,
check_connectivity=True,
linked=True,
**QCJob_kwargs):
"""
Optimize a structure and calculate vibrational frequencies to check if the
structure is in a true minima. If a frequency is negative, iteratively
perturbe the geometry, optimize, and recalculate frequencies until all are
positive, aka a true minima has been found.
Args:
qchem_command (str): Command to run QChem.
multimode (str): Parallelization scheme, either openmp or mpi.
input_file (str): Name of the QChem input file.
output_file (str): Name of the QChem output file.
max_iterations (int): Number of perturbation -> optimization -> frequency
iterations to perform. Defaults to 10.
max_molecule_perturb_scale (float): The maximum scaled perturbation that
can be applied to the molecule. Defaults to 0.3.
check_connectivity (bool): Whether to check differences in connectivity
introduced by structural perturbation. Defaults to True.
**QCJob_kwargs: Passthrough kwargs to QCJob. See
:class:`custodian.qchem.jobs.QCJob`.
"""
if not os.path.exists(input_file):
raise AssertionError("Input file must be present!")
if linked:
energy_diff_cutoff = 0.0000001
orig_input = QCInput.from_file(input_file)
freq_rem = copy.deepcopy(orig_input.rem)
freq_rem["job_type"] = "freq"
opt_rem = copy.deepcopy(orig_input.rem)
opt_rem["geom_opt_hessian"] = "read"
opt_rem["scf_guess_always"] = True
first = True
energy_history = []
for ii in range(max_iterations):
yield (QCJob(qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".opt_" + str(ii),
scratch_dir=os.getcwd(),
save_scratch=True,
save_name="chain_scratch",
backup=first,
**QCJob_kwargs))
opt_outdata = QCOutput(output_file + ".opt_" + str(ii)).data
first = False
if (opt_outdata["structure_change"] == "unconnected_fragments"
and not opt_outdata["completion"]):
print(
"Unstable molecule broke into unconnected fragments which failed to optimize! Exiting..."
)
break
else:
energy_history.append(opt_outdata.get("final_energy"))
freq_QCInput = QCInput(
molecule=opt_outdata.get(
"molecule_from_optimized_geometry"),
rem=freq_rem,
opt=orig_input.opt,
pcm=orig_input.pcm,
solvent=orig_input.solvent,
smx=orig_input.smx,
)
freq_QCInput.write_file(input_file)
yield (QCJob(qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".freq_" + str(ii),
scratch_dir=os.getcwd(),
save_scratch=True,
save_name="chain_scratch",
backup=first,
**QCJob_kwargs))
outdata = QCOutput(output_file + ".freq_" + str(ii)).data
errors = outdata.get("errors")
if len(errors) != 0:
raise AssertionError(
"No errors should be encountered while flattening frequencies!"
)
if outdata.get("frequencies")[0] > 0.0:
print("All frequencies positive!")
break
elif (abs(outdata.get("frequencies")[0]) < 15.0
and outdata.get("frequencies")[1] > 0.0):
print(
"One negative frequency smaller than 15.0 - not worth further flattening!"
)
break
else:
if len(energy_history) > 1:
if (abs(energy_history[-1] - energy_history[-2]) <
energy_diff_cutoff):
print("Energy change below cutoff!")
break
opt_QCInput = QCInput(
molecule=opt_outdata.get(
"molecule_from_optimized_geometry"),
rem=opt_rem,
opt=orig_input.opt,
pcm=orig_input.pcm,
solvent=orig_input.solvent,
smx=orig_input.smx,
)
opt_QCInput.write_file(input_file)
if os.path.exists(os.path.join(os.getcwd(), "chain_scratch")):
shutil.rmtree(os.path.join(os.getcwd(), "chain_scratch"))
else:
if not os.path.exists(input_file):
raise AssertionError("Input file must be present!")
orig_opt_input = QCInput.from_file(input_file)
orig_opt_rem = copy.deepcopy(orig_opt_input.rem)
orig_freq_rem = copy.deepcopy(orig_opt_input.rem)
orig_freq_rem["job_type"] = "freq"
first = True
history = []
for ii in range(max_iterations):
yield (QCJob(qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".opt_" + str(ii),
backup=first,
**QCJob_kwargs))
opt_outdata = QCOutput(output_file + ".opt_" + str(ii)).data
if first:
orig_species = copy.deepcopy(opt_outdata.get("species"))
orig_charge = copy.deepcopy(opt_outdata.get("charge"))
orig_multiplicity = copy.deepcopy(
opt_outdata.get("multiplicity"))
orig_energy = copy.deepcopy(
opt_outdata.get("final_energy"))
first = False
if (opt_outdata["structure_change"] == "unconnected_fragments"
and not opt_outdata["completion"]):
print(
"Unstable molecule broke into unconnected fragments which failed to optimize! Exiting..."
)
break
else:
freq_QCInput = QCInput(
molecule=opt_outdata.get(
"molecule_from_optimized_geometry"),
rem=orig_freq_rem,
opt=orig_opt_input.opt,
pcm=orig_opt_input.pcm,
solvent=orig_opt_input.solvent,
smx=orig_opt_input.smx,
)
freq_QCInput.write_file(input_file)
yield (QCJob(qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".freq_" + str(ii),
backup=first,
**QCJob_kwargs))
outdata = QCOutput(output_file + ".freq_" + str(ii)).data
errors = outdata.get("errors")
if len(errors) != 0:
raise AssertionError(
"No errors should be encountered while flattening frequencies!"
)
if outdata.get("frequencies")[0] > 0.0:
print("All frequencies positive!")
if opt_outdata.get("final_energy") > orig_energy:
print(
"WARNING: Energy increased during frequency flattening!"
)
break
else:
hist = {}
hist["molecule"] = copy.deepcopy(
outdata.get("initial_molecule"))
hist["geometry"] = copy.deepcopy(
outdata.get("initial_geometry"))
hist["frequencies"] = copy.deepcopy(
outdata.get("frequencies"))
hist["frequency_mode_vectors"] = copy.deepcopy(
outdata.get("frequency_mode_vectors"))
hist["num_neg_freqs"] = sum(
1 for freq in outdata.get("frequencies")
if freq < 0)
hist["energy"] = copy.deepcopy(
opt_outdata.get("final_energy"))
hist["index"] = len(history)
hist["children"] = []
history.append(hist)
ref_mol = history[-1]["molecule"]
geom_to_perturb = history[-1]["geometry"]
negative_freq_vecs = history[-1][
"frequency_mode_vectors"][0]
reversed_direction = False
standard = True
# If we've found one or more negative frequencies in two consecutive iterations, let's dig in
# deeper:
if len(history) > 1:
# Start by finding the latest iteration's parent:
if history[-1]["index"] in history[-2]["children"]:
parent_hist = history[-2]
history[-1]["parent"] = parent_hist["index"]
elif history[-1]["index"] in history[-3][
"children"]:
parent_hist = history[-3]
history[-1]["parent"] = parent_hist["index"]
else:
raise AssertionError(
"ERROR: your parent should always be one or two iterations behind you! Exiting..."
)
# if the number of negative frequencies has remained constant or increased from parent to
# child,
if (history[-1]["num_neg_freqs"] >=
parent_hist["num_neg_freqs"]):
# check to see if the parent only has one child, aka only the positive perturbation has
# been tried,
# in which case just try the negative perturbation from the same parent
if len(parent_hist["children"]) == 1:
ref_mol = parent_hist["molecule"]
geom_to_perturb = parent_hist["geometry"]
negative_freq_vecs = parent_hist[
"frequency_mode_vectors"][0]
reversed_direction = True
standard = False
parent_hist["children"].append(
len(history))
# If the parent has two children, aka both directions have been tried, then we have to
# get creative:
elif len(parent_hist["children"]) == 2:
# If we're dealing with just one negative frequency,
if parent_hist["num_neg_freqs"] == 1:
make_good_child_next_parent = False
if (history[parent_hist["children"]
[0]]["energy"] <
history[-1]["energy"]):
good_child = copy.deepcopy(history[
parent_hist["children"][0]])
else:
good_child = copy.deepcopy(
history[-1])
if good_child["num_neg_freqs"] > 1:
raise Exception(
"ERROR: Child with lower energy has more negative frequencies! "
"Exiting...")
elif (good_child["energy"] <
parent_hist["energy"]):
make_good_child_next_parent = True
elif (vector_list_diff(
good_child[
"frequency_mode_vectors"]
[0],
parent_hist[
"frequency_mode_vectors"]
[0],
) > 0.2):
make_good_child_next_parent = True
else:
raise Exception(
"ERROR: Good child not good enough! Exiting..."
)
if make_good_child_next_parent:
good_child["index"] = len(history)
history.append(good_child)
ref_mol = history[-1]["molecule"]
geom_to_perturb = history[-1][
"geometry"]
negative_freq_vecs = history[-1][
"frequency_mode_vectors"][0]
else:
raise Exception(
"ERROR: Can't deal with multiple neg frequencies yet! Exiting..."
)
else:
raise AssertionError(
"ERROR: Parent cannot have more than two childen! Exiting..."
)
# Implicitly, if the number of negative frequencies decreased from parent to child,
# continue normally.
if standard:
history[-1]["children"].append(len(history))
min_molecule_perturb_scale = 0.1
scale_grid = 10
perturb_scale_grid = (
max_molecule_perturb_scale -
min_molecule_perturb_scale) / scale_grid
structure_successfully_perturbed = False
for molecule_perturb_scale in np.arange(
max_molecule_perturb_scale,
min_molecule_perturb_scale,
-perturb_scale_grid,
):
new_coords = perturb_coordinates(
old_coords=geom_to_perturb,
negative_freq_vecs=negative_freq_vecs,
molecule_perturb_scale=molecule_perturb_scale,
reversed_direction=reversed_direction,
)
new_molecule = Molecule(
species=orig_species,
coords=new_coords,
charge=orig_charge,
spin_multiplicity=orig_multiplicity,
)
if check_connectivity:
structure_successfully_perturbed = (
check_for_structure_changes(
ref_mol, new_molecule) == "no_change")
if structure_successfully_perturbed:
break
if not structure_successfully_perturbed:
raise Exception(
"ERROR: Unable to perturb coordinates to remove negative frequency without changing "
"the connectivity! Exiting...")
new_opt_QCInput = QCInput(
molecule=new_molecule,
rem=orig_opt_rem,
opt=orig_opt_input.opt,
pcm=orig_opt_input.pcm,
solvent=orig_opt_input.solvent,
smx=orig_opt_input.smx,
)
new_opt_QCInput.write_file(input_file)
def opt_with_frequency_flattener(cls,
qchem_command,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
qclog_file="mol.qclog",
max_iterations=10,
max_molecule_perturb_scale=0.3,
check_connectivity=True,
**QCJob_kwargs):
"""
Optimize a structure and calculate vibrational frequencies to check if the
structure is in a true minima. If a frequency is negative, iteratively
perturbe the geometry, optimize, and recalculate frequencies until all are
positive, aka a true minima has been found.
Args:
qchem_command (str): Command to run QChem.
multimode (str): Parallelization scheme, either openmp or mpi.
input_file (str): Name of the QChem input file.
output_file (str): Name of the QChem output file.
max_iterations (int): Number of perturbation -> optimization -> frequency
iterations to perform. Defaults to 10.
max_molecule_perturb_scale (float): The maximum scaled perturbation that
can be applied to the molecule. Defaults to 0.3.
check_connectivity (bool): Whether to check differences in connectivity
introduced by structural perturbation. Defaults to True.
**QCJob_kwargs: Passthrough kwargs to QCJob. See
:class:`custodian.qchem.jobs.QCJob`.
"""
min_molecule_perturb_scale = 0.1
scale_grid = 10
perturb_scale_grid = (max_molecule_perturb_scale -
min_molecule_perturb_scale) / scale_grid
if not os.path.exists(input_file):
raise AssertionError('Input file must be present!')
orig_opt_input = QCInput.from_file(input_file)
orig_opt_rem = copy.deepcopy(orig_opt_input.rem)
orig_freq_rem = copy.deepcopy(orig_opt_input.rem)
orig_freq_rem["job_type"] = "freq"
first = True
reversed_direction = False
num_neg_freqs = []
for ii in range(max_iterations):
yield (QCJob(qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".opt_" + str(ii),
backup=first,
**QCJob_kwargs))
first = False
opt_outdata = QCOutput(output_file + ".opt_" + str(ii)).data
if opt_outdata[
"structure_change"] == "unconnected_fragments" and not opt_outdata[
"completion"]:
print(
"Unstable molecule broke into unconnected fragments which failed to optimize! Exiting..."
)
break
else:
freq_QCInput = QCInput(molecule=opt_outdata.get(
"molecule_from_optimized_geometry"),
rem=orig_freq_rem,
opt=orig_opt_input.opt,
pcm=orig_opt_input.pcm,
solvent=orig_opt_input.solvent)
freq_QCInput.write_file(input_file)
yield (QCJob(qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".freq_" + str(ii),
backup=first,
**QCJob_kwargs))
outdata = QCOutput(output_file + ".freq_" + str(ii)).data
errors = outdata.get("errors")
if len(errors) != 0:
raise AssertionError(
'No errors should be encountered while flattening frequencies!'
)
if outdata.get('frequencies')[0] > 0.0:
print("All frequencies positive!")
break
else:
num_neg_freqs += [
sum(1 for freq in outdata.get('frequencies')
if freq < 0)
]
if len(num_neg_freqs) > 1:
if num_neg_freqs[-1] == num_neg_freqs[
-2] and not reversed_direction:
reversed_direction = True
elif num_neg_freqs[-1] == num_neg_freqs[
-2] and reversed_direction:
if len(num_neg_freqs) < 3:
raise AssertionError(
"ERROR: This should only be possible after at least three frequency flattening iterations! Exiting..."
)
else:
raise Exception(
"ERROR: Reversing the perturbation direction still could not flatten any frequencies. Exiting..."
)
elif num_neg_freqs[-1] != num_neg_freqs[
-2] and reversed_direction:
reversed_direction = False
negative_freq_vecs = outdata.get(
"frequency_mode_vectors")[0]
structure_successfully_perturbed = False
for molecule_perturb_scale in np.arange(
max_molecule_perturb_scale,
min_molecule_perturb_scale, -perturb_scale_grid):
new_coords = perturb_coordinates(
old_coords=outdata.get("initial_geometry"),
negative_freq_vecs=negative_freq_vecs,
molecule_perturb_scale=molecule_perturb_scale,
reversed_direction=reversed_direction)
new_molecule = Molecule(
species=outdata.get('species'),
coords=new_coords,
charge=outdata.get('charge'),
spin_multiplicity=outdata.get('multiplicity'))
if check_connectivity:
old_molgraph = MoleculeGraph.with_local_env_strategy(
outdata.get("initial_molecule"),
OpenBabelNN(),
reorder=False,
extend_structure=False)
new_molgraph = MoleculeGraph.with_local_env_strategy(
new_molecule,
OpenBabelNN(),
reorder=False,
extend_structure=False)
if old_molgraph.isomorphic_to(new_molgraph):
structure_successfully_perturbed = True
break
if not structure_successfully_perturbed:
raise Exception(
"ERROR: Unable to perturb coordinates to remove negative frequency without changing the connectivity! Exiting..."
)
new_opt_QCInput = QCInput(molecule=new_molecule,
rem=orig_opt_rem,
opt=orig_opt_input.opt,
pcm=orig_opt_input.pcm,
solvent=orig_opt_input.solvent)
new_opt_QCInput.write_file(input_file)
def opt_with_frequency_flattener(cls,
qchem_command,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
qclog_file="mol.qclog",
max_iterations=10,
max_molecule_perturb_scale=0.3,
reversed_direction=False,
ignore_connectivity=False,
**QCJob_kwargs):
"""
Optimize a structure and calculate vibrational frequencies to check if the
structure is in a true minima. If a frequency is negative, iteratively
perturbe the geometry, optimize, and recalculate frequencies until all are
positive, aka a true minima has been found.
Args:
qchem_command (str): Command to run QChem.
multimode (str): Parallelization scheme, either openmp or mpi.
input_file (str): Name of the QChem input file.
output_file (str): Name of the QChem output file.
max_iterations (int): Number of perturbation -> optimization -> frequency
iterations to perform. Defaults to 10.
max_molecule_perturb_scale (float): The maximum scaled perturbation that
can be applied to the molecule. Defaults to 0.3.
reversed_direction (bool): Whether to reverse the direction of the
vibrational frequency vectors. Defaults to False.
ignore_connectivity (bool): Whether to ignore differences in connectivity
introduced by structural perturbation. Defaults to False.
**QCJob_kwargs: Passthrough kwargs to QCJob. See
:class:`custodian.qchem.jobs.QCJob`.
"""
min_molecule_perturb_scale = 0.1
scale_grid = 10
perturb_scale_grid = (max_molecule_perturb_scale -
min_molecule_perturb_scale) / scale_grid
msc = MoleculeStructureComparator()
if not os.path.exists(input_file):
raise AssertionError('Input file must be present!')
orig_opt_input = QCInput.from_file(input_file)
orig_opt_rem = copy.deepcopy(orig_opt_input.rem)
orig_freq_rem = copy.deepcopy(orig_opt_input.rem)
orig_freq_rem["job_type"] = "freq"
first = True
for ii in range(max_iterations):
yield (QCJob(qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".opt_" + str(ii),
backup=first,
**QCJob_kwargs))
first = False
opt_outdata = QCOutput(output_file + ".opt_" + str(ii)).data
if opt_outdata["structure_change"] == "unconnected_fragments":
print(
"Unstable molecule broke into unconnected fragments! Exiting..."
)
break
else:
freq_QCInput = QCInput(molecule=opt_outdata.get(
"molecule_from_optimized_geometry"),
rem=orig_freq_rem,
opt=orig_opt_input.opt,
pcm=orig_opt_input.pcm,
solvent=orig_opt_input.solvent)
freq_QCInput.write_file(input_file)
yield (QCJob(qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".freq_" + str(ii),
backup=first,
**QCJob_kwargs))
outdata = QCOutput(output_file + ".freq_" + str(ii)).data
errors = outdata.get("errors")
if len(errors) != 0:
raise AssertionError(
'No errors should be encountered while flattening frequencies!'
)
if outdata.get('frequencies')[0] > 0.0:
print("All frequencies positive!")
break
else:
negative_freq_vecs = outdata.get(
"frequency_mode_vectors")[0]
old_coords = outdata.get("initial_geometry")
old_molecule = outdata.get("initial_molecule")
structure_successfully_perturbed = False
for molecule_perturb_scale in np.arange(
max_molecule_perturb_scale,
min_molecule_perturb_scale, -perturb_scale_grid):
new_coords = perturb_coordinates(
old_coords=old_coords,
negative_freq_vecs=negative_freq_vecs,
molecule_perturb_scale=molecule_perturb_scale,
reversed_direction=reversed_direction)
new_molecule = Molecule(
species=outdata.get('species'),
coords=new_coords,
charge=outdata.get('charge'),
spin_multiplicity=outdata.get('multiplicity'))
if msc.are_equal(old_molecule,
new_molecule) or ignore_connectivity:
structure_successfully_perturbed = True
break
if not structure_successfully_perturbed:
raise Exception(
"Unable to perturb coordinates to remove negative frequency without changing the bonding structure"
)
new_opt_QCInput = QCInput(molecule=new_molecule,
rem=orig_opt_rem,
opt=orig_opt_input.opt,
pcm=orig_opt_input.pcm,
solvent=orig_opt_input.solvent)
new_opt_QCInput.write_file(input_file)
def opt_with_frequency_flattener(cls,
qchem_command,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
qclog_file="mol.qclog",
max_iterations=10,
max_molecule_perturb_scale=0.3,
check_connectivity=True,
**QCJob_kwargs):
"""
Optimize a structure and calculate vibrational frequencies to check if the
structure is in a true minima. If a frequency is negative, iteratively
perturbe the geometry, optimize, and recalculate frequencies until all are
positive, aka a true minima has been found.
Args:
qchem_command (str): Command to run QChem.
multimode (str): Parallelization scheme, either openmp or mpi.
input_file (str): Name of the QChem input file.
output_file (str): Name of the QChem output file.
max_iterations (int): Number of perturbation -> optimization -> frequency
iterations to perform. Defaults to 10.
max_molecule_perturb_scale (float): The maximum scaled perturbation that
can be applied to the molecule. Defaults to 0.3.
check_connectivity (bool): Whether to check differences in connectivity
introduced by structural perturbation. Defaults to True.
**QCJob_kwargs: Passthrough kwargs to QCJob. See
:class:`custodian.qchem.jobs.QCJob`.
"""
min_molecule_perturb_scale = 0.1
scale_grid = 10
perturb_scale_grid = (
max_molecule_perturb_scale - min_molecule_perturb_scale
) / scale_grid
if not os.path.exists(input_file):
raise AssertionError('Input file must be present!')
orig_opt_input = QCInput.from_file(input_file)
orig_opt_rem = copy.deepcopy(orig_opt_input.rem)
orig_freq_rem = copy.deepcopy(orig_opt_input.rem)
orig_freq_rem["job_type"] = "freq"
first = True
reversed_direction = False
num_neg_freqs = []
for ii in range(max_iterations):
yield (QCJob(
qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".opt_" + str(ii),
backup=first,
**QCJob_kwargs))
first = False
opt_outdata = QCOutput(output_file + ".opt_" + str(ii)).data
if opt_outdata["structure_change"] == "unconnected_fragments" and not opt_outdata["completion"]:
print("Unstable molecule broke into unconnected fragments which failed to optimize! Exiting...")
break
else:
freq_QCInput = QCInput(
molecule=opt_outdata.get("molecule_from_optimized_geometry"),
rem=orig_freq_rem,
opt=orig_opt_input.opt,
pcm=orig_opt_input.pcm,
solvent=orig_opt_input.solvent)
freq_QCInput.write_file(input_file)
yield (QCJob(
qchem_command=qchem_command,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=".freq_" + str(ii),
backup=first,
**QCJob_kwargs))
outdata = QCOutput(output_file + ".freq_" + str(ii)).data
errors = outdata.get("errors")
if len(errors) != 0:
raise AssertionError('No errors should be encountered while flattening frequencies!')
if outdata.get('frequencies')[0] > 0.0:
print("All frequencies positive!")
break
else:
num_neg_freqs += [sum(1 for freq in outdata.get('frequencies') if freq < 0)]
if len(num_neg_freqs) > 1:
if num_neg_freqs[-1] == num_neg_freqs[-2] and not reversed_direction:
reversed_direction = True
elif num_neg_freqs[-1] == num_neg_freqs[-2] and reversed_direction:
if len(num_neg_freqs) < 3:
raise AssertionError("ERROR: This should only be possible after at least three frequency flattening iterations! Exiting...")
else:
raise Exception("ERROR: Reversing the perturbation direction still could not flatten any frequencies. Exiting...")
elif num_neg_freqs[-1] != num_neg_freqs[-2] and reversed_direction:
reversed_direction = False
negative_freq_vecs = outdata.get("frequency_mode_vectors")[0]
structure_successfully_perturbed = False
for molecule_perturb_scale in np.arange(
max_molecule_perturb_scale, min_molecule_perturb_scale,
-perturb_scale_grid):
new_coords = perturb_coordinates(
old_coords=outdata.get("initial_geometry"),
negative_freq_vecs=negative_freq_vecs,
molecule_perturb_scale=molecule_perturb_scale,
reversed_direction=reversed_direction)
new_molecule = Molecule(
species=outdata.get('species'),
coords=new_coords,
charge=outdata.get('charge'),
spin_multiplicity=outdata.get('multiplicity'))
if check_connectivity:
old_molgraph = MoleculeGraph.with_local_env_strategy(outdata.get("initial_molecule"),
OpenBabelNN(),
reorder=False,
extend_structure=False)
new_molgraph = MoleculeGraph.with_local_env_strategy(new_molecule,
OpenBabelNN(),
reorder=False,
extend_structure=False)
if old_molgraph.isomorphic_to(new_molgraph):
structure_successfully_perturbed = True
break
if not structure_successfully_perturbed:
raise Exception(
"ERROR: Unable to perturb coordinates to remove negative frequency without changing the connectivity! Exiting..."
)
new_opt_QCInput = QCInput(
molecule=new_molecule,
rem=orig_opt_rem,
opt=orig_opt_input.opt,
pcm=orig_opt_input.pcm,
solvent=orig_opt_input.solvent)
new_opt_QCInput.write_file(input_file)
