class QChemSCFErrorHandler(ErrorHandler): """ QChem ErrorHandler class that addresses SCF non-convergence. """ is_monitor = False def __init__( self, input_file="mol.qin", output_file="mol.qout", rca_gdm_thresh=1.0e-3, scf_max_cycles=200, ): """ Initializes the error handler from a set of input and output files. Args: input_file (str): Name of the QChem input file. output_file (str): Name of the QChem output file. rca_gdm_thresh (float): The threshold for the prior scf algorithm. If last deltaE is larger than the threshold try RCA_DIIS first, else, try DIIS_GDM first. scf_max_cycles (int): The max iterations to set to fix SCF failure. """ self.input_file = input_file self.output_file = output_file self.scf_max_cycles = scf_max_cycles self.qcinp = QCInput.from_file(self.input_file) self.outdata = None self.errors = None def check(self): """ Checks output file for errors """ self.outdata = QCOutput(self.output_file).data self.errors = self.outdata.get("errors") return len(self.errors) > 0 def correct(self): """ Corrects errors, but it hasn't been implemented yet """ print("This hasn't been implemented yet!") return {"errors": self.errors, "actions": None}
class QChemSCFErrorHandler(ErrorHandler): """ QChem ErrorHandler class that addresses SCF non-convergence. """ is_monitor = False def __init__(self, input_file="mol.qin", output_file="mol.qout", rca_gdm_thresh=1.0E-3, scf_max_cycles=200): """ Initializes the error handler from a set of input and output files. Args: input_file (str): Name of the QChem input file. output_file (str): Name of the QChem output file. rca_gdm_thresh (float): The threshold for the prior scf algorithm. If last deltaE is larger than the threshold try RCA_DIIS first, else, try DIIS_GDM first. scf_max_cycles (int): The max iterations to set to fix SCF failure. """ self.input_file = input_file self.output_file = output_file self.scf_max_cycles = scf_max_cycles self.geom_max_cycles = geom_max_cycles self.qcinp = QCInput.from_file(self.input_file) self.outdata = None self.errors = None self.qchem_job = qchem_job def check(self): # Checks output file for errors. self.outdata = QCOutput(self.output_file).data self.errors = self.outdata.get("errors") return len(self.errors) > 0 def correct(self): print("This hasn't been implemented yet!") return {"errors": self.errors, "actions": None}
class QChemErrorHandler(ErrorHandler): """ Master QChemErrorHandler class that handles a number of common errors that occur during QChem runs. """ is_monitor = False def __init__( self, input_file="mol.qin", output_file="mol.qout", scf_max_cycles=200, geom_max_cycles=200, ): """ Initializes the error handler from a set of input and output files. Args: input_file (str): Name of the QChem input file. output_file (str): Name of the QChem output file. scf_max_cycles (int): The max iterations to set to fix SCF failure. geom_max_cycles (int): The max iterations to set to fix geometry optimization failure. """ self.input_file = input_file self.output_file = output_file self.scf_max_cycles = scf_max_cycles self.geom_max_cycles = geom_max_cycles self.outdata = None self.errors = [] self.opt_error_history = [] def check(self): """ Checks output file for errors """ self.outdata = QCOutput(self.output_file).data self.errors = self.outdata.get("errors") self.warnings = self.outdata.get("warnings") # If we aren't out of optimization cycles, but we were in the past, reset the history if "out_of_opt_cycles" not in self.errors and len( self.opt_error_history) > 0: self.opt_error_history = [] # If we're out of optimization cycles and we have unconnected fragments, no need to handle any errors if "out_of_opt_cycles" in self.errors and self.outdata[ "structure_change"] == "unconnected_fragments": return False return len(self.errors) > 0 def correct(self): """ Perform corrections """ backup({self.input_file, self.output_file}) actions = [] self.qcinp = QCInput.from_file(self.input_file) if "SCF_failed_to_converge" in self.errors: # Check number of SCF cycles. If not set or less than scf_max_cycles, # increase to that value and rerun. If already set, check if # scf_algorithm is unset or set to DIIS, in which case set to GDM. # Otherwise, tell user to call SCF error handler and do nothing. if str(self.qcinp.rem.get("max_scf_cycles")) != str( self.scf_max_cycles): self.qcinp.rem["max_scf_cycles"] = self.scf_max_cycles actions.append({"max_scf_cycles": self.scf_max_cycles}) elif self.qcinp.rem.get("thresh", "10") != "14": self.qcinp.rem["thresh"] = "14" actions.append({"thresh": "14"}) elif self.qcinp.rem.get("scf_algorithm", "diis").lower() == "diis": self.qcinp.rem["scf_algorithm"] = "diis_gdm" actions.append({"scf_algorithm": "diis_gdm"}) elif self.qcinp.rem.get("scf_algorithm", "diis").lower() == "diis_gdm": self.qcinp.rem["scf_algorithm"] = "gdm" actions.append({"scf_algorithm": "gdm"}) elif self.qcinp.rem.get("scf_guess_always", "none").lower() != "true": self.qcinp.rem["scf_guess_always"] = True actions.append({"scf_guess_always": True}) else: print( "More advanced changes may impact the SCF result. Use the SCF error handler" ) elif "out_of_opt_cycles" in self.errors: # Check number of opt cycles. If less than geom_max_cycles, increase # to that value, set last geom as new starting geom and rerun. if str(self.qcinp.rem.get("geom_opt_max_cycles")) != str( self.geom_max_cycles): self.qcinp.rem["geom_opt_max_cycles"] = self.geom_max_cycles actions.append({"geom_max_cycles:": self.scf_max_cycles}) if len(self.outdata.get("energy_trajectory")) > 1: self.qcinp.molecule = self.outdata.get( "molecule_from_last_geometry") actions.append({"molecule": "molecule_from_last_geometry"}) elif self.qcinp.rem.get("thresh", "10") != "14": self.qcinp.rem["thresh"] = "14" actions.append({"thresh": "14"}) # Will need to try and implement this dmax handler below when I have more time # to fix the tests and the general handling procedure. # elif self.qcinp.rem.get("geom_opt_dmax",300) != 150: # self.qcinp.rem["geom_opt_dmax"] = 150 # actions.append({"geom_opt_dmax": "150"}) # If already at geom_max_cycles, thresh 14, and dmax 150, often can just get convergence # by restarting from the geometry of the last cycle. But we'll also save any structural # changes that happened along the way. else: self.opt_error_history += [self.outdata["structure_change"]] if len(self.opt_error_history) > 1: if self.opt_error_history[-1] == "no_change": # If no structural changes occurred in two consecutive optimizations, # and we still haven't converged, then just exit. return { "errors": self.errors, "actions": None, "opt_error_history": self.opt_error_history, } self.qcinp.molecule = self.outdata.get( "molecule_from_last_geometry") actions.append({"molecule": "molecule_from_last_geometry"}) elif "unable_to_determine_lamda" in self.errors: # Set last geom as new starting geom and rerun. If no opt cycles, # use diff SCF start? Diff initial guess? Change basis? Unclear. if len(self.outdata.get("energy_trajectory")) > 1: self.qcinp.molecule = self.outdata.get( "molecule_from_last_geometry") actions.append({"molecule": "molecule_from_last_geometry"}) elif self.qcinp.rem.get("thresh", "10") != "14": self.qcinp.rem["thresh"] = "14" actions.append({"thresh": "14"}) else: print( "Use a different initial guess? Perhaps a different basis?" ) elif "premature_end_FileMan_error" in self.errors: if self.qcinp.rem.get("thresh", "10") != "14": self.qcinp.rem["thresh"] = "14" actions.append({"thresh": "14"}) elif self.qcinp.rem.get("scf_guess_always", "none").lower() != "true": self.qcinp.rem["scf_guess_always"] = True actions.append({"scf_guess_always": True}) else: print( "We're in a bad spot if we get a FileMan error while always generating a new SCF guess..." ) elif "hessian_eigenvalue_error" in self.errors: if self.qcinp.rem.get("thresh", "10") != "14": self.qcinp.rem["thresh"] = "14" actions.append({"thresh": "14"}) else: print( "Not sure how to fix hessian_eigenvalue_error if thresh is already 14!" ) elif "NLebdevPts" in self.errors: # this error should only be possible if resp_charges or esp_charges is set if self.qcinp.rem.get("resp_charges") or self.qcinp.rem.get( "esp_charges"): # This error is caused by insufficient no. of Lebedev points on # the grid used to compute RESP charges # Increase the density of points on the Lebedev grid using the # esp_surface_density argument (see manual >= v5.4) # the default value is 500 (=0.001 Angstrom) # or disable RESP charges as a last resort if int(self.qcinp.rem.get("esp_surface_density", 500)) >= 500: self.qcinp.rem["esp_surface_density"] = "250" actions.append({"esp_surface_density": "250"}) elif int(self.qcinp.rem.get("esp_surface_density", 250)) >= 250: self.qcinp.rem["esp_surface_density"] = "125" actions.append({"esp_surface_density": "125"}) elif int(self.qcinp.rem.get("esp_surface_density", 125)) >= 125: # switch from Lebedev mode to spherical harmonics mode if self.qcinp.rem.get("resp_charges"): self.qcinp.rem["resp_charges"] = "2" actions.append({"resp_charges": "2"}) if self.qcinp.rem.get("esp_charges"): self.qcinp.rem["esp_charges"] = "2" actions.append({"esp_charges": "2"}) else: if self.qcinp.rem.get("resp_charges"): self.qcinp.rem["resp_charges"] = "false" actions.append({"resp_charges": "false"}) if self.qcinp.rem.get("esp_charges"): self.qcinp.rem["esp_charges"] = "false" actions.append({"esp_charges": "false"}) else: print( "Not sure how to fix NLebdevPts error if resp_charges is disabled!" ) elif "failed_to_transform_coords" in self.errors: # Check for symmetry flag in rem. If not False, set to False and rerun. # If already False, increase threshold? if not self.qcinp.rem.get("sym_ignore") or self.qcinp.rem.get( "symmetry"): self.qcinp.rem["sym_ignore"] = True self.qcinp.rem["symmetry"] = False actions.append({"sym_ignore": True}) actions.append({"symmetry": False}) else: print("Perhaps increase the threshold?") elif "basis_not_supported" in self.errors: print( "Specify a different basis set. At least one of the atoms is not supported." ) return {"errors": self.errors, "actions": None} elif "input_file_error" in self.errors: print( "Something is wrong with the input file. Examine error message by hand." ) return {"errors": self.errors, "actions": None} elif "failed_to_read_input" in self.errors: # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is. actions.append({"rerun_job_no_changes": True}) elif "read_molecule_error" in self.errors: # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is. actions.append({"rerun_job_no_changes": True}) elif "never_called_qchem" in self.errors: # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is. actions.append({"rerun_job_no_changes": True}) elif "licensing_error" in self.errors: # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is. actions.append({"rerun_job_no_changes": True}) elif "unknown_error" in self.errors: if self.qcinp.rem.get("scf_guess", "none").lower() == "read": del self.qcinp.rem["scf_guess"] actions.append({"scf_guess": "deleted"}) elif self.qcinp.rem.get("thresh", "10") != "14": self.qcinp.rem["thresh"] = "14" actions.append({"thresh": "14"}) else: print("Unknown error. Examine output and log files by hand.") return {"errors": self.errors, "actions": None} else: # You should never get here. If correct is being called then errors should have at least one entry, # in which case it should have been caught by the if/elifs above. print("Errors:", self.errors) print( "Must have gotten an error which is correctly parsed but not included in the handler. FIX!!!" ) return {"errors": self.errors, "actions": None} if { "molecule": "molecule_from_last_geometry" } in actions and str( self.qcinp.rem.get("geom_opt_hessian")).lower() == "read": del self.qcinp.rem["geom_opt_hessian"] actions.append({"geom_opt_hessian": "deleted"}) os.rename(self.input_file, self.input_file + ".last") self.qcinp.write_file(self.input_file) return { "errors": self.errors, "warnings": self.warnings, "actions": actions }
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)
class QChemErrorHandler(ErrorHandler): """ Master QChemErrorHandler class that handles a number of common errors that occur during QChem runs. """ is_monitor = False def __init__(self, input_file="mol.qin", output_file="mol.qout", scf_max_cycles=200, geom_max_cycles=200): """ Initializes the error handler from a set of input and output files. Args: input_file (str): Name of the QChem input file. output_file (str): Name of the QChem output file. scf_max_cycles (int): The max iterations to set to fix SCF failure. geom_max_cycles (int): The max iterations to set to fix geometry optimization failure. """ self.input_file = input_file self.output_file = output_file self.scf_max_cycles = scf_max_cycles self.geom_max_cycles = geom_max_cycles self.outdata = None self.errors = [] self.opt_error_history = [] def check(self): # Checks output file for errors. self.outdata = QCOutput(self.output_file).data self.errors = self.outdata.get("errors") # If we aren't out of optimization cycles, but we were in the past, reset the history if "out_of_opt_cycles" not in self.errors and len( self.opt_error_history) > 0: self.opt_error_history = [] # If we're out of optimization cycles and we have unconnected fragments, no need to handle any errors if "out_of_opt_cycles" in self.errors and self.outdata[ "structure_change"] == "unconnected_fragments": return False return len(self.errors) > 0 def correct(self): backup({self.input_file, self.output_file}) actions = [] self.qcinp = QCInput.from_file(self.input_file) if "SCF_failed_to_converge" in self.errors: # Check number of SCF cycles. If not set or less than scf_max_cycles, # increase to that value and rerun. If already set, check if # scf_algorithm is unset or set to DIIS, in which case set to GDM. # Otherwise, tell user to call SCF error handler and do nothing. if str(self.qcinp.rem.get("max_scf_cycles")) != str( self.scf_max_cycles): self.qcinp.rem["max_scf_cycles"] = self.scf_max_cycles actions.append({"max_scf_cycles": self.scf_max_cycles}) elif self.qcinp.rem.get("scf_algorithm", "diis").lower() == "diis": self.qcinp.rem["scf_algorithm"] = "gdm" actions.append({"scf_algorithm": "gdm"}) elif self.qcinp.rem.get("scf_algorithm", "gdm").lower() == "gdm": self.qcinp.rem["scf_algorithm"] = "diis_gdm" actions.append({"scf_algorithm": "diis_gdm"}) else: print( "More advanced changes may impact the SCF result. Use the SCF error handler" ) elif "out_of_opt_cycles" in self.errors: # Check number of opt cycles. If less than geom_max_cycles, increase # to that value, set last geom as new starting geom and rerun. if str(self.qcinp.rem.get("geom_opt_max_cycles")) != str( self.geom_max_cycles): self.qcinp.rem["geom_opt_max_cycles"] = self.geom_max_cycles actions.append({"geom_max_cycles:": self.scf_max_cycles}) if len(self.outdata.get("energy_trajectory")) > 1: self.qcinp.molecule = self.outdata.get( "molecule_from_last_geometry") actions.append({"molecule": "molecule_from_last_geometry"}) # If already at geom_max_cycles, often can just get convergence by restarting # from the geometry of the last cycle. But we'll also save any structural # changes that happened along the way. else: self.opt_error_history += [self.outdata["structure_change"]] if len(self.opt_error_history) > 1: if self.opt_error_history[-1] == "no_change": # If no structural changes occured in two consecutive optimizations, # and we still haven't converged, then just exit. return { "errors": self.errors, "actions": None, "opt_error_history": self.opt_error_history } self.qcinp.molecule = self.outdata.get( "molecule_from_last_geometry") actions.append({"molecule": "molecule_from_last_geometry"}) elif "unable_to_determine_lamda" in self.errors: # Set last geom as new starting geom and rerun. If no opt cycles, # use diff SCF strat? Diff initial guess? Change basis? if len(self.outdata.get("energy_trajectory")) > 1: self.qcinp.molecule = self.outdata.get( "molecule_from_last_geometry") actions.append({"molecule": "molecule_from_last_geometry"}) elif self.qcinp.rem.get("scf_algorithm", "diis").lower() == "diis": self.qcinp.rem["scf_algorithm"] = "rca_diis" actions.append({"scf_algorithm": "rca_diis"}) if self.qcinp.rem.get("gen_scfman"): self.qcinp.rem["gen_scfman"] = False actions.append({"gen_scfman": False}) else: print( "Use a different initial guess? Perhaps a different basis?" ) elif "linear_dependent_basis" in self.errors: # DIIS -> RCA_DIIS. If already RCA_DIIS, change basis? if self.qcinp.rem.get("scf_algorithm", "diis").lower() == "diis": self.qcinp.rem["scf_algorithm"] = "rca_diis" actions.append({"scf_algorithm": "rca_diis"}) if self.qcinp.rem.get("gen_scfman"): self.qcinp.rem["gen_scfman"] = False actions.append({"gen_scfman": False}) else: print("Perhaps use a better basis?") elif "failed_to_transform_coords" in self.errors: # Check for symmetry flag in rem. If not False, set to False and rerun. # If already False, increase threshold? if not self.qcinp.rem.get("sym_ignore") or self.qcinp.rem.get( "symmetry"): self.qcinp.rem["sym_ignore"] = True self.qcinp.rem["symmetry"] = False actions.append({"sym_ignore": True}) actions.append({"symmetry": False}) else: print("Perhaps increase the threshold?") elif "input_file_error" in self.errors: print( "Something is wrong with the input file. Examine error message by hand." ) return {"errors": self.errors, "actions": None} elif "failed_to_read_input" in self.errors: # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is. actions.append({"rerun job as-is"}) elif "IO_error" in self.errors: # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is. actions.append({"rerun job as-is"}) elif "read_molecule_error" in self.errors: # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is. actions.append({"rerun job as-is"}) elif "never_called_qchem" in self.errors: # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is. actions.append({"rerun job as-is"}) elif "unknown_error" in self.errors: print("Examine error message by hand.") return {"errors": self.errors, "actions": None} else: # You should never get here. If correct is being called then errors should have at least one entry, # in which case it should have been caught by the if/elifs above. print( "If you get this message, something has gone terribly wrong!") return {"errors": self.errors, "actions": None} os.rename(self.input_file, self.input_file + ".last") self.qcinp.write_file(self.input_file) return {"errors": self.errors, "actions": actions}
class QChemErrorHandler(ErrorHandler): """ Master QChemErrorHandler class that handles a number of common errors that occur during QChem runs. """ is_monitor = False def __init__(self, input_file="mol.qin", output_file="mol.qout", scf_max_cycles=200, geom_max_cycles=200): """ Initializes the error handler from a set of input and output files. Args: input_file (str): Name of the QChem input file. output_file (str): Name of the QChem output file. scf_max_cycles (int): The max iterations to set to fix SCF failure. geom_max_cycles (int): The max iterations to set to fix geometry optimization failure. """ self.input_file = input_file self.output_file = output_file self.scf_max_cycles = scf_max_cycles self.geom_max_cycles = geom_max_cycles self.outdata = None self.errors = [] self.opt_error_history = [] def check(self): # Checks output file for errors. self.outdata = QCOutput(self.output_file).data self.errors = self.outdata.get("errors") # If we aren't out of optimization cycles, but we were in the past, reset the history if "out_of_opt_cycles" not in self.errors and len(self.opt_error_history) > 0: self.opt_error_history = [] # If we're out of optimization cycles and we have unconnected fragments, no need to handle any errors if "out_of_opt_cycles" in self.errors and self.outdata["structure_change"] == "unconnected_fragments": return False return len(self.errors) > 0 def correct(self): backup({self.input_file, self.output_file}) actions = [] self.qcinp = QCInput.from_file(self.input_file) if "SCF_failed_to_converge" in self.errors: # Check number of SCF cycles. If not set or less than scf_max_cycles, # increase to that value and rerun. If already set, check if # scf_algorithm is unset or set to DIIS, in which case set to GDM. # Otherwise, tell user to call SCF error handler and do nothing. if str(self.qcinp.rem.get("max_scf_cycles")) != str( self.scf_max_cycles): self.qcinp.rem["max_scf_cycles"] = self.scf_max_cycles actions.append({"max_scf_cycles": self.scf_max_cycles}) elif self.qcinp.rem.get("scf_algorithm", "diis").lower() == "diis": self.qcinp.rem["scf_algorithm"] = "gdm" actions.append({"scf_algorithm": "gdm"}) elif self.qcinp.rem.get("scf_algorithm", "gdm").lower() == "gdm": self.qcinp.rem["scf_algorithm"] = "diis_gdm" actions.append({"scf_algorithm": "diis_gdm"}) else: print( "More advanced changes may impact the SCF result. Use the SCF error handler" ) elif "out_of_opt_cycles" in self.errors: # Check number of opt cycles. If less than geom_max_cycles, increase # to that value, set last geom as new starting geom and rerun. if str(self.qcinp.rem.get( "geom_opt_max_cycles")) != str(self.geom_max_cycles): self.qcinp.rem["geom_opt_max_cycles"] = self.geom_max_cycles actions.append({"geom_max_cycles:": self.scf_max_cycles}) if len(self.outdata.get("energy_trajectory")) > 1: self.qcinp.molecule = self.outdata.get( "molecule_from_last_geometry") actions.append({"molecule": "molecule_from_last_geometry"}) # If already at geom_max_cycles, often can just get convergence by restarting # from the geometry of the last cycle. But we'll also save any structural # changes that happened along the way. else: self.opt_error_history += [self.outdata["structure_change"]] if len(self.opt_error_history) > 1: if self.opt_error_history[-1] == "no_change": # If no structural changes occured in two consecutive optimizations, # and we still haven't converged, then just exit. return {"errors": self.errors, "actions": None, "opt_error_history": self.opt_error_history} self.qcinp.molecule = self.outdata.get("molecule_from_last_geometry") actions.append({"molecule": "molecule_from_last_geometry"}) elif "unable_to_determine_lamda" in self.errors: # Set last geom as new starting geom and rerun. If no opt cycles, # use diff SCF strat? Diff initial guess? Change basis? if len(self.outdata.get("energy_trajectory")) > 1: self.qcinp.molecule = self.outdata.get( "molecule_from_last_geometry") actions.append({"molecule": "molecule_from_last_geometry"}) elif self.qcinp.rem.get("scf_algorithm", "diis").lower() == "diis": self.qcinp.rem["scf_algorithm"] = "rca_diis" actions.append({"scf_algorithm": "rca_diis"}) if self.qcinp.rem.get("gen_scfman"): self.qcinp.rem["gen_scfman"] = False actions.append({"gen_scfman": False}) else: print( "Use a different initial guess? Perhaps a different basis?" ) elif "linear_dependent_basis" in self.errors: # DIIS -> RCA_DIIS. If already RCA_DIIS, change basis? if self.qcinp.rem.get("scf_algorithm", "diis").lower() == "diis": self.qcinp.rem["scf_algorithm"] = "rca_diis" actions.append({"scf_algorithm": "rca_diis"}) if self.qcinp.rem.get("gen_scfman"): self.qcinp.rem["gen_scfman"] = False actions.append({"gen_scfman": False}) else: print("Perhaps use a better basis?") elif "failed_to_transform_coords" in self.errors: # Check for symmetry flag in rem. If not False, set to False and rerun. # If already False, increase threshold? if not self.qcinp.rem.get("sym_ignore") or self.qcinp.rem.get( "symmetry"): self.qcinp.rem["sym_ignore"] = True self.qcinp.rem["symmetry"] = False actions.append({"sym_ignore": True}) actions.append({"symmetry": False}) else: print("Perhaps increase the threshold?") elif "input_file_error" in self.errors: print( "Something is wrong with the input file. Examine error message by hand." ) return {"errors": self.errors, "actions": None} elif "failed_to_read_input" in self.errors: # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is. actions.append({"rerun job as-is"}) elif "IO_error" in self.errors: # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is. actions.append({"rerun job as-is"}) elif "read_molecule_error" in self.errors: # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is. actions.append({"rerun job as-is"}) elif "never_called_qchem" in self.errors: # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is. actions.append({"rerun job as-is"}) elif "unknown_error" in self.errors: print("Examine error message by hand.") return {"errors": self.errors, "actions": None} else: # You should never get here. If correct is being called then errors should have at least one entry, # in which case it should have been caught by the if/elifs above. print( "If you get this message, something has gone terribly wrong!") return {"errors": self.errors, "actions": None} os.rename(self.input_file, self.input_file + ".last") self.qcinp.write_file(self.input_file) return {"errors": self.errors, "actions": actions}
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)