def get_standard_orientation(self):
stdsect = section_by_pattern(self.contents, pattern="Standard Nuclear Orientation")[1]
coord_lines = section_by_pattern(stdsect, pattern="--------------------------------------")[1][1:]
keys = ["I", "element", "x", "y", "z"]
parsed = lines_to_dct(coord_lines, keys)
self.elements = parsed['element']
arr_cols = [parsed['x'], parsed['y'], parsed['z']]
self.std_coords = np.array(arr_cols, dtype=np.float64).transpose()
self.n_atoms = len(self.elements)
def get_method(self):
rem = section_by_pattern(self.contents, pattern="\$rem")[1]
rembody = section_by_pattern(rem, pattern="\$end")[0]
for line in rembody:
if "method" in line.lower() and "solvent" not in line.lower():
self.method = line.split()[1].strip().upper()
if "basis" in line.lower():
self.basis = line.split()[1].strip().upper()
return self.method
def get_solvation(self):
try:
smx = section_by_pattern(self.contents, pattern="\$smx")[1]
smxbody = section_by_pattern(smx, pattern="\$end")[0]
for line in smxbody:
if "solvent" in line.lower():
self.solvent = line.split()[1].strip().lower()
self.solvate = True
except IndexError:
self.solvate = False
self.solvent = None
def get_coordinates(self):
molecule = section_by_pattern(self.contents, pattern="\$molecule")[1]
molbody = section_by_pattern(molecule, pattern="\$end")[0]
mollines = [x.strip() for x in molbody]
mollines = [x for x in mollines if x]
self.charge, self.multiplicity = map(int, mollines[1].split())
keys = ["element", "x", "y", "z"]
self.parsed_coords = lines_to_dct(mollines[2:], keys)
xyzs = [self.parsed_coords[col] for col in ["x", "y", "z"]]
coordinates = np.array(xyzs, dtype=np.float64)
self.coordinates = np.transpose(coordinates)
def get_standard_orientation(self):
sto = section_by_pattern(self.contents, pattern="Standard orientation")
stdsect = section_by_pattern(self.contents, pattern="Standard orientation")[-1]
coord_lines = section_by_pattern(stdsect, pattern="--------------------------------------")[2][1:]
keys = ["center", "at_z", "at_type", "x", "y", "z"]
parsed = lines_to_dct(coord_lines, keys)
arr_cols = [parsed['x'], parsed['y'], parsed['z']]
try:
self.std_coords = np.array(arr_cols, dtype=np.float64).transpose()
except ValueError:
print(self.filename)
raise ValueError
self.n_atoms = len(parsed['x'])
self.at_z = np.array(parsed['at_z'], dtype=int)
def get_dft_details(self, verbose=0, scale=False, **kwargs):
try:
thermochem = section_by_pattern(self.contents, pattern="Thermochemistry")[1:][-1]
self.thermochemistry = thermochem
if verbose > 2:
print("Thermochemistry found.")
factors = scaling_factors["DEFAULT"]
if scale:
try:
factors = scaling_factors[self.method][self.basis]
except KeyError:
printred(f"{self.method} {self.basis} scaling factors not specified yet.")
self.__dict__.update(factors)
if verbose > 2:
print("\n".join([f"{k:>20}: {v}" for k, v in factors.items()]))
self.temperature = float(self.search("Temperature", lines=thermochem).split()[1])
self.mass_total = float(self.search("Molecular mass", lines=thermochem).split(":")[1].strip().split()[0])
self.mass_total_kg = self.mass_total*AMU_TO_KG
atom_lines = [x for x in thermochem if "Atom " in x]
self.mass_atoms = [float(x.strip().split()[-1]) for x in atom_lines]
if verbose > 2:
print(f"""\
Temperature: {self.temperature} K
Molecular mass: {self.mass_total_kg} kg \
""")
self.check_frequencies(verbose=verbose)
self.get_entropy(verbose=verbose)
self.get_zero_point(verbose=verbose)
self.get_hlc(verbose=verbose)
self.get_thermal_correction(verbose=verbose)
except:
pass
def get_solvation(self):
try:
scrf_lines = section_by_pattern(self.contents, pattern="SCRF")[1][:2]
scrf = "".join(scrf_lines)
smodel, solvent_ = scrf.split("SCRF=(")[-1].strip().split(",")
self.solvate = True
self.solvent_model = smodel
solvent = solvent_.split("=")[1].strip().split(")")[0].strip()
if solvent == "h2o":
self.solvent = "water"
else:
self.solvent = solvent
except (ValueError, IndexError):
self.solvate = False
self.solvent = None
self.solvent_model = None
return dict(solvate=self.solvate, solvent=self.solvent, solvent_model=self.solvent_model)