class OrcaFile(File):
"""
Generic class for all Orca `.inp` and `.out` files.
Attributes:
ensemble (ConformationalEnsemble): `ConformationalEnsemble` instance
job_types (list): list of ``OrcaJobType`` instances
header (str): keyword line or lines
variables (dict): list of variables to specify (e.g. ``{"maxcore": 2000}``).
blocks (dict): list of blocks to change specific settings
In general, the key should be the block name and the value should be a list of desired lines.
For instance, configuring a time-dependent DFT job might look like ``{"tddft": ["maxdim 5", "nroots 50"]}``
successful_terminations (int): number of successful terminations
elapsed_time (float): total time for job in seconds
"""
def __init__(self,
job_types,
ensemble=None,
header=None,
variables=None,
blocks=None):
if job_types is not None:
if not all(isinstance(job, OrcaJobType) for job in job_types):
raise TypeError(f"invalid job type {job}")
self.job_types = job_types
else:
raise ValueError("need job types for new Orca file")
if ensemble and isinstance(ensemble, ConformationalEnsemble):
self.ensemble = ensemble
else:
self.ensemble = ConformationalEnsemble()
if header and isinstance(header, str):
self.header = header
else:
self.header = None
if blocks and isinstance(blocks, dict):
for lines in list(blocks.values()):
assert isinstance(lines, list)
self.blocks = blocks
else:
self.blocks = {}
if variables and isinstance(variables, dict):
self.variables = variables
else:
self.variables = {}
@classmethod
def read_file(cls, filename):
if re.search("inp$", filename):
return cls._read_inp_file(filename)
multiple_lines = parse.split_multiple_inputs(filename)
files = []
for lines in multiple_lines:
input_lines = parse.extract_input_file(lines)
header = parse.read_header(input_lines)
job_types = cls._assign_job_types(header)
variables, blocks = parse.read_blocks_and_variables(input_lines)
success = 0
elapsed_time = 0
for line in lines:
if line.strip().startswith("****ORCA TERMINATED NORMALLY****"):
success += 1
elif line.startswith("TOTAL RUN TIME"):
fields = line.split()
assert len(
fields
) == 13, f"unexpected number of fields on elapsed time line:\n{line}"
days = float(fields[3])
hours = float(fields[5])
minutes = float(fields[7])
seconds = float(fields[9])
elapsed_time = days * 86400 + hours * 3600 + minutes * 60 + seconds
energies, iters = parse.read_energies(lines)
if len(energies) == 0:
return None
atomic_numbers, geometries = parse.read_geometries(
lines, num_to_find=len(energies))
assert len(geometries) >= len(
energies
), "can't have an energy without a geometry (cf. pigeonhole principle)"
charge = lines.find_parameter("xyz", 6, 4)[0]
multip = lines.find_parameter("xyz", 6, 5)[0]
#### TODO
# detect Mayer bond orders
f = OrcaFile(job_types,
header=header,
variables=variables,
blocks=blocks)
f.elapsed_time = elapsed_time
f.successful_terminations = success
molecules = [None] * len(geometries)
properties = [{} for _ in range(len(geometries))]
for idx, geom in enumerate(geometries):
molecules[idx] = Molecule(atomic_numbers,
geom,
charge=charge,
multiplicity=multip,
bonds=None)
if idx < len(energies):
properties[idx]["energy"] = energies[idx]
properties[idx]["filename"] = filename
properties[idx]["iteration"] = idx
properties[idx]["scf_iterations"] = iters[idx]
if multip > 1:
s2 = lines.find_parameter("Expectation value of", 6, 5)
for idx, spin_contam in enumerate(s2):
properties[idx]["S**2"] = spin_contam
if OrcaJobType.OPT in job_types:
rms_grad, max_grad, rms_step, max_step = parse.read_gradients(
lines, len(properties))
for idx in range(len(rms_grad)):
if idx < len(rms_grad):
properties[idx]["rms_gradient"] = rms_grad[idx]
if idx < len(max_grad):
properties[idx]["max_gradient"] = max_grad[idx]
if idx < len(rms_step):
properties[idx]["rms_step"] = rms_step[idx]
if idx < len(max_step):
properties[idx]["max_step"] = max_step[idx]
if OrcaJobType.FREQ in job_types:
properties[-1]["frequencies"] = sorted(parse.read_freqs(lines))
enthalpies = lines.find_parameter("Total Enthalpy",
expected_length=5,
which_field=3)
if len(enthalpies) == 1:
properties[-1]["enthalpy"] = enthalpies[0]
elif len(enthalpies) > 1:
raise ValueError(
f"unexpected # of enthalpies found!\nenthalpies = {enthalpies}"
)
gibbs = lines.find_parameter("Final Gibbs free enthalpy",
expected_length=7,
which_field=5)
if len(gibbs) == 1:
properties[-1]["gibbs_free_energy"] = gibbs[0]
elif len(gibbs) > 1:
raise ValueError(
f"unexpected # of gibbs free energies found!\ngibbs free energies = {enthalpies}"
)
temperature = lines.find_parameter("Temperature",
expected_length=4,
which_field=2)
if len(temperature) == 1 and len(gibbs) > 0:
properties[-1]["temperature"] = temperature[0]
corrected_free_energy = get_corrected_free_energy(
gibbs[0],
properties[-1]["frequencies"],
frequency_cutoff=100.0,
temperature=temperature[0])
properties[-1]["quasiharmonic_gibbs_free_energy"] = float(
corrected_free_energy)
if OrcaJobType.NMR in job_types:
nmr_shifts = parse.read_nmr_shifts(lines,
molecules[0].num_atoms())
if nmr_shifts is not None:
properties[-1]["isotropic_shielding"] = nmr_shifts
try:
charges = parse.read_mulliken_charges(lines)
assert len(charges) == len(atomic_numbers)
properties[-1]["mulliken_charges"] = charges
except Exception as e:
pass
try:
charges = parse.read_loewdin_charges(lines)
assert len(charges) == len(atomic_numbers)
properties[-1]["lowdin_charges"] = charges
except Exception as e:
pass
try:
dipole = lines.find_parameter("Magnitude \(Debye\)", 4, 3)
properties[-1]["dipole_moment"] = dipole[0]
except Exception as e:
pass
for mol, prop in zip(molecules, properties):
f.ensemble.add_molecule(mol, properties=prop)
f.check_has_properties()
files.append(f)
if len(files) == 1:
return files[0]
else:
return files
@classmethod
def _read_inp_file(cls, filename):
print("reading ``.inp`` files is not currently supported :(")
return None
def write_file(self,
filename,
molecule=None,
header=None,
variables=None,
blocks=None):
"""
Write a ``.inp`` file, using object attributes. If no header is specified, the object's header will be used.
Args:
filename (str): path to the new file
molecule (int): which molecule to use -- passed to ``self.get_molecule()``.
Default is -1 (e.g. the last molecule), but positive integers will select from self.ensemble.molecules (0-indexed).
A ``Molecule`` object can also be passed, in which case that molecule will be written to the file.
header (str): header for new file
"""
if molecule is None:
molecule = -1
if not isinstance(molecule, Molecule):
molecule = self.ensemble.molecules[molecule]
if header is None:
header = self.header
if variables is None:
variables = self.variables
if blocks is None:
blocks = self.blocks
self.write_molecule_to_file(filename, molecule, header, variables,
blocks)
@classmethod
def write_molecule_to_file(cls,
filename,
molecule,
header,
variables=None,
blocks=None,
print_symbol=False):
"""
Write an ``.inp`` file using the given molecule.
Args:
filename (str): path to the new file
molecule (Molecule): which molecule to use -- a ``Molecule`` object.
header (str): header for new file
print_symbol (Bool): if atomic symbols should be printed instead of atomic numbers
"""
assert isinstance(molecule,
Molecule), "need a valid molecule to write a file!"
assert isinstance(header, str), "can't write a file without a header"
text = f"{header.strip()}\n"
if variables is not None:
assert isinstance(variables, dict), "blocks must be a dictionary"
for k, v in variables.items():
text += f"%{k} {v}\n"
if blocks is not None:
assert isinstance(blocks, dict), "blocks must be a dictionary"
for k, v in blocks.items():
text += f"%{k}\n"
for line in v:
text += f"\t{line}\n"
text += "end\n"
text += "\n"
text += f"* xyz {int(molecule.charge)} {int(molecule.multiplicity)}\n"
for index, Z in enumerate(molecule.atomic_numbers, start=1):
line = molecule.get_vector(index)
if print_symbol:
Z = get_symbol(Z)
text += f"{Z:>2} {line[0]:>13.8f} {line[1]:>13.8f} {line[2]:>13.8f}\n"
else:
text += f"{Z:2d} {line[0]:>13.8f} {line[1]:>13.8f} {line[2]:>13.8f}\n"
text += "*\n"
text += "\n"
#### write the file
super().write_file(filename, text)
def get_molecule(self, num=None):
"""
Returns the last molecule (from an optimization job or other multi-molecule jobs) or the only molecule (from other jobs).
If ``num`` is specified, returns that job (1-indexed for positive numbers). So ``job.get_molecule(3)`` will return the 3rd element of ``job.molecules``, not the 4th.
"""
# some methods pass num=None, which overrides setting the default above
if num is None:
num = -1
if not isinstance(num, int):
raise TypeError("num must be int")
return self.ensemble.molecule_list()[num]
def num_imaginaries(self):
"""
Returns the number of imaginary frequencies.
"""
return len(self.imaginaries())
def imaginaries(self):
"""
Returns the imaginary frequencies, rounded to the nearest integer.
"""
if (OrcaJobType.FREQ
in self.job_types) and (self.ensemble[-1:, "frequencies"]
is not None):
freqs = self.ensemble[-1:, "frequencies"]
if not isinstance(freqs, list) or len(freqs) == 0:
return list()
else:
return list(map(int, np.array(freqs)[np.array(freqs) < 0]))
else:
return list()
@classmethod
def _assign_job_types(cls, header):
"""
Assigns ``OrcaJobType`` objects from route card. ``OrcaJobType.SP`` is assigned by default.
Args:
header (str): Orca header
Returns:
list of ``OrcaJobType`` objects
"""
job_types = []
for name, member in OrcaJobType.__members__.items():
if re.search(f" {member.value}", str(header), re.IGNORECASE):
job_types.append(member)
if OrcaJobType.SP not in job_types:
job_types.append(OrcaJobType.SP)
return job_types
def check_has_properties(self):
"""
Checks that the file has all the appropriate properties for its job types, and raises ``ValueError`` if not.
This only checks the last molecule in ``self.ensemble``, for now.
"""
if self.successful_terminations > 0:
for job_type in self.job_types:
for prop in EXPECTED_PROPERTIES[job_type.value]:
if not self.ensemble.has_property(-1, prop):
raise ValueError(
f"expected property {prop} for job type {job_type}, but it's not there!"
)
else:
return
class GaussianFile(File):
"""
Class representing Gaussian input/output files.
Attributes:
ensemble (ConformationalEnsemble): ``ConformationalEnsemble`` instance
job_types (list): list of `job_type`` instances
route_card (str): optional, route card of .gjf file
link0 (dict): optional, dictionary of Link 0 commands (e.g. {"mem": "32GB", "nprocshared": 16})
footer (str): optional, footer of .gjf file
successful_terminations (int): number of successful terminations (should be 1 for an opt, 2 for opt and then freq, 1 for a single point energy, etc)
elapsed_time (float): total time for job in seconds
title (str): optional, title of .gjf file
"""
def __init__(
self, job_types, route_card=None, link0=None, footer=None, title="title", success=0, elapsed_time=0.0
):
"""
Create new GaussianFile object.
Args:
job_types (list): list of ``job_type`` instances
route_card (str): optional, route card of ``.gjf`` file
link0 (dict): optional, Link 0 commands of ``.gjf`` file
footer (str): optional, footer of ``.gjf`` file
title (str): optional, title of ``.gjf`` file
success (int): num successful terminations
elapsed_time (float): total time for job in seconds
"""
if route_card and not isinstance(route_card, str):
raise TypeError("route card needs to be a string")
if link0 and not isinstance(link0, dict):
raise TypeError("link0 needs to be a dict")
if footer and not isinstance(footer, str):
raise TypeError("footer needs to be a string")
if title and not isinstance(title, str):
raise TypeError("title needs to be a string")
if success and not isinstance(success, int):
raise TypeError("success needs to be an integer")
if not isinstance(elapsed_time, (float, int)) or elapsed_time < 0.0:
raise TypeError(f"elapsed_time invalid: {elapsed_time}")
if job_types is not None:
if isinstance(job_types, str):
raise ValueError(f"invalid job_types {job_types} - did you mean to call GaussianFile.read_file({job_types})?")
if not all(isinstance(job, GaussianJobType) for job in job_types):
raise TypeError(f"invalid job_types {job_types}")
self.ensemble = ConformationalEnsemble()
self.route_card = route_card
self.link0 = link0
self.footer = footer
self.title = title
self.job_types = job_types
self.successful_terminations = success
self.elapsed_time = elapsed_time
def __str__(self):
return f"GaussianFile (title=\"{str(self.title)}\", {len(self.ensemble)} entries in Ensemble)"
@classmethod
def write_molecule_to_file(cls, filename, molecule, route_card, link0={"mem": "32GB", "nprocshared": 16}, footer=None, title="title", append=False, print_symbol=False):
"""
Write a ``.gjf`` file using the given molecule.
Args:
filename (str): path to the new file
molecule (Molecule): which molecule to use -- a ``Molecule`` object.
route_card (str): route card for new file
link0 (dict): dictionary of Link 0 commands
footer (str): footer for new file
title (str): title of the file, defaults to "title"
append (Bool): whether or not to append to file using Link1 specifications
print_symbol (Bool): whether to print atomic symbols (instead of atomic numbers)
"""
if not isinstance(molecule, Molecule):
raise TypeError("need a valid molecule to write a file!")
if (route_card is None) or (not isinstance(route_card, str)):
raise ValueError("can't write a file without a route card")
if not re.match(r"^#p", route_card):
print(f"ALERT - route card doesn't start with #p: {route_card}")
#### generate the text
text = ""
if append:
text += "--Link1--\n"
if isinstance(link0, dict):
for key, val in link0.items():
text += f"%{key}={val}\n"
text += f"{route_card.strip()}\n\n{title}\n\n"
text += f"{int(molecule.charge)} {int(molecule.multiplicity)}\n"
for index, Z in enumerate(molecule.atomic_numbers, start=1):
line = molecule.get_vector(index)
if print_symbol:
Z = get_symbol(Z)
text += f"{Z:>2} {line[0]:>13.8f} {line[1]:>13.8f} {line[2]:>13.8f}\n"
else:
text += f"{Z:2d} {line[0]:>13.8f} {line[1]:>13.8f} {line[2]:>13.8f}\n"
text += "\n"
if footer is not None:
text += f"{footer.strip()}\n\n"
#### write the file
if append:
super().append_to_file(filename, text)
else:
super().write_file(filename, text)
def write_file(self, filename, molecule=None, route_card=None, link0=None, footer=None, **kwargs):
"""
Write a ``.gjf`` file, using object attributes. If no header/footer is specified, the object's header/footer will be used.
Args:
filename (str): path to the new file
molecule (int): which molecule to use -- passed to ``self.get_molecule()``.
Default is -1 (e.g. the last molecule), but positive integers will select from self.ensemble(1-indexed).
A ``Molecule`` object can also be passed, in which case that molecule will be written to the file.
route_card (str): route card for new file
link0 (dict): dictionary of Link 0 commands (e.g. {"mem": "32GB", "nprocshared": 16}
footer (str): footer for new file
"""
if not isinstance(molecule, Molecule):
molecule = self.get_molecule(molecule)
if route_card is None:
route_card = self.route_card
if link0 is None:
link0 = self.link0
if footer is None:
footer = self.footer
self.write_molecule_to_file(filename, molecule, route_card, link0, footer, **kwargs)
def num_imaginaries(self):
"""
Returns the number of imaginary frequencies.
"""
return len(self.imaginaries())
def imaginaries(self):
"""
Returns the imaginary frequencies, rounded to the nearest integer.
"""
if (GaussianJobType.FREQ in self.job_types) and (self.ensemble[-1:,"frequencies"] is not None):
freqs = self.ensemble[-1:,"frequencies"]
if not isinstance(freqs, list) or len(freqs) == 0:
return list()
else:
return list(map(int, np.array(freqs)[np.array(freqs) < 0]))
else:
return list()
@classmethod
# @profile
def read_file(cls, filename, return_lines=False, extended_opt_info=False):
"""
Reads a Gaussian``.out`` or ``.gjf`` file and populates the attributes accordingly.
Only footers from ``opt=modredundant`` can be read automatically -- ``genecep`` custom basis sets, &c must be specified manually.
Note:
Will throw ``ValueError`` if there have been no successful iterations.
Args:
filename (str): path to the out file
return_lines (Bool): whether the lines of the file should be returned
extended_opt_info (Bool): if full parameters about each opt step should be collected
(by default, only ``rms_displacement`` and ``rms_force`` are collected)
Returns:
``GaussianFile`` object (or list of ``GaussianFile`` objects for Link1 files)
(optional) the lines of the file (or list of lines of file for Link1 files)
"""
if re.search("gjf$", filename) or re.search("com$", filename):
return cls._read_gjf_file(filename, return_lines)
link1_lines = parse.split_link1(filename)
files = []
for link1idx, lines in enumerate(link1_lines):
#### automatically assign job types based on header
header = lines.search_for_block("#p", "----", format_line=lambda x: x.lstrip(), join="")
if header is None:
raise ValueError("can't find route card! (perhaps '#p' wasn't employed?)")
job_types = cls._assign_job_types(header)
link0 = parse.extract_link0(lines)
title = ""
title_block = lines.search_for_block("l101.exe", "Symbolic Z-matrix", join="\n")
if title_block is not None:
for line in title_block.split("\n")[1:]:
if not re.search("-----", line):
title += line
(geometries, atom_list, energies, scf_iterations, success, elapsed_time) = parse.read_geometries_and_energies(lines)
success, elapsed_time = parse.extract_success_and_time(lines)
atomic_numbers = []
#### convert to right datatype
try:
atomic_numbers = np.array(atom_list, dtype=np.int8)
except Exception as e:
atomic_numbers = np.array(list(map(get_number, atom_list)), dtype=np.int8)
footer = None
if re.search("modredundant", str(header)):
footer = lines.search_for_block("^ The following ModRedundant input section", "^ $", count=1, join="\n")
if footer is not None:
footer = "\n".join(list(footer.split("\n"))[1:]) # get rid of the first line
footer = "\n".join([" ".join(list(filter(None, line.split(" ")))) for line in footer.split("\n")])
bonds = parse.read_bonds(lines)
charge, multip = lines.find_parameter("Multiplicity", expected_length=4, which_field=[1,3], split_on="=")[0]
f = GaussianFile(job_types=job_types, route_card=header, link0=link0, footer=footer, success=success, elapsed_time=elapsed_time, title=title)
molecules = [None] * len(geometries)
properties = [{} for _ in range(len(geometries))]
for idx, geom in enumerate(geometries):
molecules[idx] = Molecule(atomic_numbers, geom, charge=charge, multiplicity=multip, bonds=bonds)
if idx < len(energies):
properties[idx]["energy"] = energies[idx]
if idx < len(scf_iterations):
properties[idx]["scf_iterations"] = scf_iterations[idx]
properties[idx]["link1_idx"] = link1idx
properties[idx]["filename"] = filename
properties[idx]["iteration"] = idx
#### now for some job-type specific attributes
if GaussianJobType.OPT in job_types:
rms_forces = lines.find_parameter("RMS\s+Force", expected_length=5, which_field=2)
rms_displacements = lines.find_parameter("RMS\s+Displacement", expected_length=5, which_field=2)
if extended_opt_info:
max_forces = lines.find_parameter("Maximum Force", expected_length=5, which_field=2)
max_displacements = lines.find_parameter("Maximum Displacement", expected_length=5, which_field=2)
max_gradients = lines.find_parameter("Cartesian Forces:", expected_length=6, which_field=3)
rms_gradients = lines.find_parameter("Cartesian Forces:", expected_length=6, which_field=5)
max_int_forces = lines.find_parameter("Internal Forces:", expected_length=6, which_field=3)
rms_int_forces = lines.find_parameter("Internal Forces:", expected_length=6, which_field=5)
delta_energy = lines.find_parameter("Predicted change in Energy", expected_length=4, which_field=3, cast_to_float=False)
for idx, force in enumerate(rms_forces):
properties[idx]["rms_force"] = force
properties[idx]["rms_displacement"] = rms_displacements[idx]
if extended_opt_info:
if idx < len(max_forces):
properties[idx]["max_force"] = max_forces[idx]
if idx < len(max_displacements):
properties[idx]["max_displacement"] = max_displacements[idx]
if idx < len(max_gradients):
properties[idx]["max_gradient"] = max_gradients[idx]
if idx < len(rms_gradients):
properties[idx]["rms_gradient"] = rms_gradients[idx]
if idx < len(max_int_forces):
properties[idx]["max_internal_force"] = max_int_forces[idx]
if idx < len(rms_int_forces):
properties[idx]["rms_internal_force"] = rms_int_forces[idx]
if idx < len(delta_energy):
change_in_energy = re.sub(r"Energy=", "", delta_energy[idx])
properties[idx]["predicted_change_in_energy"] = float(change_in_energy.replace('D', 'E'))
if GaussianJobType.FREQ in job_types:
enthalpies = lines.find_parameter("thermal Enthalpies", expected_length=7, which_field=6)
if len(enthalpies) == 1:
properties[-1]["enthalpy"] = enthalpies[0]
elif len(enthalpies) > 1:
raise ValueError(f"unexpected # of enthalpies found!\nenthalpies = {enthalpies}")
gibbs_vals = lines.find_parameter("thermal Free Energies", expected_length=8, which_field=7)
if len(gibbs_vals) == 1:
properties[-1]["gibbs_free_energy"] = gibbs_vals[0]
elif len(gibbs_vals) > 1:
raise ValueError(f"unexpected # gibbs free energies found!\ngibbs free energies = {gibbs_vals}")
if GaussianJobType.FREQ in job_types:
enthalpies = lines.find_parameter("thermal Enthalpies", expected_length=7, which_field=6)
if len(enthalpies) == 1:
properties[-1]["enthalpy"] = enthalpies[0]
elif len(enthalpies) > 1:
raise ValueError(f"unexpected # of enthalpies found!\nenthalpies = {enthalpies}")
gibbs_vals = lines.find_parameter("thermal Free Energies", expected_length=8, which_field=7)
if len(gibbs_vals) == 1:
properties[-1]["gibbs_free_energy"] = gibbs_vals[0]
elif len(gibbs_vals) > 1:
raise ValueError(f"unexpected # gibbs free energies found!\ngibbs free energies = {gibbs_vals}")
frequencies = []
try:
frequencies = sum(lines.find_parameter("Frequencies", expected_length=5, which_field=[2,3,4]), [])
properties[-1]["frequencies"] = sorted(frequencies)
except Exception as e:
raise ValueError("error finding frequencies")
# Temperature 298.150 Kelvin. Pressure 1.00000 Atm.
temperature = lines.find_parameter("Temperature", expected_length=6, which_field=1)
if len(temperature) == 1:
properties[-1]["temperature"] = temperature[0]
try:
corrected_free_energy = get_corrected_free_energy(gibbs_vals[0], frequencies,
frequency_cutoff=100.0, temperature=temperature[0])
properties[-1]["quasiharmonic_gibbs_free_energy"] = float(f"{float(corrected_free_energy):.6f}") # yes this is dumb
except:
pass
if GaussianJobType.NMR in job_types:
nmr_shifts = parse.read_nmr_shifts(lines, molecules[0].num_atoms())
if nmr_shifts is not None:
properties[-1]["isotropic_shielding"] = nmr_shifts.view(OneIndexedArray)
if re.search("nmr=mixed", f.route_card, flags=re.IGNORECASE) or re.search("nmr=spinspin", f.route_card,flags=re.IGNORECASE):
couplings = parse.read_j_couplings(lines, molecules[0].num_atoms())
if couplings is not None:
properties[-1]["j_couplings"] = couplings
if GaussianJobType.FORCE in job_types:
assert len(molecules) == 1, "force jobs should not be combined with optimizations!"
forces = parse.read_forces(lines)
properties[0]["forces"] = forces
if GaussianJobType.POP in job_types:
if re.search("hirshfeld", f.route_card) or re.search("cm5", f.route_card):
charges, spins = parse.read_hirshfeld_charges(lines)
properties[-1]["hirshfeld_charges"] = charges
properties[-1]["hirshfeld_spins"] = spins
try:
charges = parse.read_mulliken_charges(lines)
properties[-1]["mulliken_charges"] = charges
except Exception as e:
pass
try:
dipole = parse.read_dipole_moment(lines)
properties[-1]["dipole_moment"] = dipole
except Exception as e:
pass
for mol, prop in zip(molecules, properties):
f.ensemble.add_molecule(mol, properties=prop)
f.check_has_properties()
files.append(f)
if return_lines:
if len(link1_lines) == 1:
return files[0], link1_lines[0]
else:
return files, link1_lines
else:
if len(link1_lines) == 1:
return files[0]
else:
return files
@classmethod
def _read_gjf_file(cls, filename, return_lines=False):
"""
Reads a Gaussian ``.gjf`` or ``.com`` file and populates the attributes accordingly.
Args:
filename (str): path to the out file
return_lines (Bool): whether the lines of the file should be returned
Returns:
GaussianFile object
(optional) the lines of the file
"""
lines = super().read_file(filename)
header = None
link0 = {}
footer = None
header_done = False
title = None
charge = None
multip = None
in_geom = False
atomic_numbers = []
geometry = []
for idx, line in enumerate(lines):
if header is None:
if re.match("\%", line):
pieces = line[1:].split("=")
link0[pieces[0]] = pieces[1]
continue
if re.match("#", line):
header = line
continue
if (title is None) and (header is not None):
if header_done:
if len(line.strip()) > 0:
title = line
else:
if len(line.strip()) > 0:
header = header + line
else:
header_done = True
continue
if (title is not None) and (charge is None):
if len(line.strip()) > 0:
pieces = list(filter(None, line.split(" ")))
assert len(pieces) == 2, f"can't parse line {line}"
charge = int(pieces[0])
multip = int(pieces[1])
in_geom = True
continue
if in_geom == True:
if len(line.strip()) == 0:
in_geom = False
else:
pieces = list(filter(None, line.split(" ")))
assert len(pieces) == 4, f"can't parse line {line}"
atomic_numbers.append(pieces[0])
geometry.append([pieces[1], pieces[2], pieces[3]])
if (in_geom == False) and (len(geometry) > 0):
if footer:
footer = footer + "\n" + line
else:
if len(line.strip()) > 0:
footer = line
try:
atomic_numbers = np.array(atomic_numbers, dtype=np.int8)
except Exception as e:
atomic_numbers = np.array(list(map(get_number, atomic_numbers)), dtype=np.int8)
job_types = cls._assign_job_types(header)
f = GaussianFile(job_types=job_types, route_card=header, link0=link0, footer=footer, title=title)
f.ensemble.add_molecule(Molecule(atomic_numbers, geometry, charge=charge, multiplicity=multip))
if return_lines:
return f, lines
else:
return f
def get_molecule(self, num=None, properties=False):
"""
Returns the last molecule (from an optimization job) or the only molecule (from other jobs).
If ``num`` is specified, returns ``self.ensemble.molecule_list()[num]``
If ``properties`` is True, returns ``(molecule, properties)``.
"""
# some methods pass num=None, which overrides setting the default above
if num is None:
num = -1
if not isinstance(num, int):
raise TypeError("num must be int")
if properties:
return self.ensemble.molecule_list()[num], self.ensemble.properties_list()[num]
else:
return self.ensemble.molecule_list()[num]
@classmethod
def _assign_job_types(cls, header):
"""
Assigns ``GaussianJobType`` objects from route card. ``GaussianJobType.SP`` is assigned by default.
For instance, "#p opt freq=noraman" would give an output of ``[GaussianJobType.SP, GaussianJobType.OPT, GaussianJobType.FREQ]``.
Args:
header (str): Gaussian route card
Returns:
list of ``GaussianJobType`` objects
"""
job_types = []
for name, member in GaussianJobType.__members__.items():
if re.search(f" {member.value}", str(header), re.IGNORECASE):
job_types.append(member)
if GaussianJobType.SP not in job_types:
job_types.append(GaussianJobType.SP)
return job_types
def check_has_properties(self):
"""
Checks that the file has all the appropriate properties for its job types, and raises ValueError if not.
This only checks the last molecule in ``self.ensemble``, for now.
"""
if self.successful_terminations > 0:
if self.successful_terminations == 1 and ((GaussianJobType.OPT in self.job_types) and (GaussianJobType.FREQ in self.job_types)):
return # opt freq jobs should have two terminations
for job_type in self.job_types:
for prop in EXPECTED_PROPERTIES[job_type.value]:
if not self.ensemble.has_property(-1, prop):
raise ValueError(f"expected property {prop} for job type {job_type}, but it's not there!")
else:
return
@classmethod
def write_ensemble_to_file(cls, filename, ensemble, route_card, link0={"mem": "32GB", "nprocshared": 16}, footer=None, title="title", print_symbol=False):
"""
Write each structure in the specified ensemble to a single Gaussian input file
by using the Link1 specification.
Args:
filename (str): where to write the file
ensemble (Ensemble): ``Ensemble`` object to write
route_card (str or list): to use the same route card for every link, use a single string;
otherwise, provide a list whose entries parallel the ensemble members
link0 (dict or list of dicts): to use the same memory/processors for every link, use a single string;
otherwise, provide a list
footer (None/str or list): use None for no text after geometry, provide a str to specify a footer,
or provide some combination of the above as a list
title (str or list): use a single string to provide a generic title for every link or a list as above
print_symbol (bool or list): whether to print atomic symbols or atomic numbers in the geometry specification;
use a single bool or a list as above
"""
n_geometries = len(ensemble)
assert len(ensemble) > 0, "cannot write a blank ensemble"
if isinstance(route_card, str):
route_card = [route_card for _ in ensemble._items]
elif isinstance(route_card, list):
assert len(route_card) == n_geometries, f"expected {n_geometries} route cards but got {len(route_card)}"
for card in route_card:
assert isinstance(card, str), "expected route card to be a str"
else:
raise ValueError(f"unexpected type for route_card: {str(type(route_card))}")
if isinstance(link0, dict):
link0 = [link0 for _ in ensemble._items]
elif isinstance(link0, list):
assert len(link0) == n_geometries, f"expected {n_geometries} link0 entries, but got {len(link0)}"
for d in link0:
assert isinstance(d, dict), f"expected dict for link0 but got {str(type(d))}"
else:
raise ValueError(f"unexpected type for link0: {str(type(link0))}")
if footer is None or isinstance(footer, str):
footer = [footer for _ in ensemble._items]
elif isinstance(footer, list):
assert len(footer) == n_geometries, f"expected {n_geometries} footers, but got {len(footer)}"
for f in footer:
assert f is None or isinstance(f, str), f"expected str or None for footer but got {str(type(f))}"
else:
raise ValueError(f"unexpected type for footer: {str(type(footer))}")
if isinstance(title, str):
assert len(title.strip()) > 0, "zero-length titles not allowed"
title = [title for _ in ensemble._items]
elif isinstance(title, list):
assert len(title) == n_geometries, f"expected {n_geometries} route cards but got {len(title)}"
for card in title:
assert isinstance(card, str), "expected title to be a str"
assert len(title.strip()) > 0, "zero-length titles are not allowed"
else:
raise ValueError(f"unexpected type for title: {str(type(title))}")
if isinstance(print_symbol, bool):
print_symbol = [print_symbol for _ in ensemble._items]
elif isinstance(print_symbol, list):
assert len(print_symbol) == n_geometries, f"expected {n_geometries} print_symbol entries but got {len(print_symbol)}"
for s in print_symbol:
assert isinstance(s, bool), f"expected bool for print_symbol but got {str(type(s))}"
else:
raise ValueError(f"unexpected type for print_symbol: {str(type(print_symbol))}")
for idx, molecule in enumerate(ensemble._items):
if idx == 0:
cls.write_molecule_to_file(filename, molecule, route_card[idx], link0[idx], footer=footer[idx], title=title[idx], print_symbol=print_symbol[idx], append=False)
else:
cls.write_molecule_to_file(filename, molecule, route_card[idx], link0[idx], footer=footer[idx], title=title[idx], print_symbol=print_symbol[idx], append=True)
def add_custom_basis_set(self, name, add_all_elements=False, return_string=False):
"""
Appends custom basis sets (from Basis Set Exchange) to ``self.footer``. Should be used in combination with the ``gen`` keyword.
Args:
name (str): name of basis set (look it up on Basis Set Exchange)
add_all_elements (bool): whether the complete basis set should be added or just the elements of interest
return_string (bool): if the basis set should be appended to the footer or returned as a string (no change to ``self``)
Returns:
nothing (if return_string is ``False``)
string of basis set definition (if return string is ``True``)
"""
import basis_set_exchange as bse
assert isinstance(name, str), "need basis set name to be a string, for starters"
try:
basis_definition = ""
if add_all_elements:
basis_definition = bse.get_basis(name, fmt="gaussian94", header=False)
else:
elements = list(np.unique(self.get_molecule().atomic_numbers.view(np.ndarray)))
basis_definition = bse.get_basis(name, fmt="gaussian94", header=False, elements=elements)
if self.footer is None:
self.footer = basis_definition
else:
self.footer += basis_definition
self.footer += "\n"
except Exception as e:
raise ValueError(f"adding basis set {name} from basis set exchange failed!\n{e}")
@classmethod
def read_file(cls, filename, return_lines=False, extended_opt_info=False):
# def read_fast(cls, filename, return_lines=False, extended_opt_info=False):
"""
Reads a Gaussian``.out`` or ``.gjf`` file and populates the attributes accordingly.
Only footers from ``opt=modredundant`` can be read automatically -- ``genecep`` custom basis sets, &c must be specified manually.
Note:
Will throw ``ValueError`` if there have been no successful iterations.
Args:
filename (str): path to the out file
return_lines (Bool): whether the lines of the file should be returned
extended_opt_info (Bool): if full parameters about each opt step should be collected
(by default, only ``rms_displacement`` and ``rms_force`` are collected)
Returns:
``GaussianFile`` object (or list of ``GaussianFile`` objects for Link1 files)
(optional) the lines of the file (or list of lines of file for Link1 files) as Lines object
"""
if re.search("gjf$", filename) or re.search("com$", filename):
return cls._read_gjf_file(filename, return_lines)
link1_lines = parse.split_link1_to_text(filename)
files = []
for link1idx, lines in enumerate(link1_lines):
files.append(parse.read_file_fast(lines, filename, link1idx, extended_opt_info=extended_opt_info))
if return_lines:
link1_lines = parse.split_link1(filename)
if len(link1_lines) == 1:
return files[0], link1_lines[0]
else:
return files, link1_lines
else:
if len(link1_lines) == 1:
return files[0]
else:
return files