def diverged_ts(param, ref_param, cnf_param):
""" a
"""
info_message(
"- Transition State conformer has",
"diverged from original structure of",
f"{param} {ref_param:.3f} with angle {cnf_param:.3f}")
def molecular_properties(dmom, polar):
""" a
"""
if dmom is not None and polar is not None:
dmom_str = automol.util.vec.string(dmom)
polar_str = automol.util.mat.string(polar)
info_message(f'Dipole Moment [Debye]:\n{dmom_str}', newline=1)
info_message(f'Polarizability []: {polar_str}')
def bad_equil_ts(cnf_dist, equi_bnd):
""" a
"""
info_message(
" - Transition State conformer has",
"converged to an",
"equilibrium structure with dist",
f" {cnf_dist:.3f} comp with equil {equi_bnd:.3f}")
def frequencies(freqs):
""" Print out the Harmonic frequencies and ZPVE
"""
if freqs is not None:
freq_str = automol.util.vec.string(
freqs, num_per_row=6, val_format='{0:>12.3f}')
harm_zpe = (sum(freqs) / 2.0) * phycon.WAVEN2KCAL
info_message(f'\nHarmonic frequencies [cm-1]:\n{freq_str}')
info_message(f'\nHarmonic ZPVE [kcal mol-1]: {harm_zpe}\n')
def lennard_jones_params(sigmas, epsilons):
""" Print Lennard-Jones parameters on individual lines.
Need to convert?
:param sigmas: list of sigma values
:type sigmas: tuple(float)
:param epsilons: list of epsilon values
:type epsilons: tuple(float)
"""
if sigmas and epsilons:
info_message(f'{"Sigma (Ang)":<14s}{"Epsilon (cm-1)":<16s}')
for sig, eps in zip(sigmas, epsilons):
info_message(f'{sig:<14.4f}{eps:<16.4f}')
def lennard_jones_params(sigmas, epsilons):
""" Print Lennard-Jones parameters on individual lines.
Need to convert?
:param sigmas: list of sigma values
:type sigmas: tuple(float)
:param epsilons: list of epsilon values
:type epsilons: tuple(float)
"""
if sigmas and epsilons:
info_message(
'{0:<14s}{1:<16s}'.format('\nSigma (Ang)', 'Epsilon (cm-1)'))
for sig, eps in zip(sigmas, epsilons):
info_message(
'{0:<14.4f}{1:<16.4f}'.format(sig, eps))
def therm_paths_messpf_write_locations(spc_name, spc_locs_lst, spc_mods,
thm_paths_dct):
""" prints out a table with the path that the messpf thermo input is
written for each conformer and model
"""
info_message('MESSPF location table:')
info_message(f'{"species name":<16}'
f'{"rid":<16}{"cid":<16}{"model":<16}{"path":<16}')
info_message(f'{"============":<16}'
f'{"=======":<16}{"=======":<16}{"=======":<16}'
f'{"============":<16}')
for spc_locs in spc_locs_lst:
for spc_mod in spc_mods:
path = thm_paths_dct[spc_name][tuple(spc_locs)][spc_mod][0]
info_message(f'{spc_name:<16}'
f'{spc_locs[0]:<16}'
f'{spc_locs[1]:<16}'
f'{spc_mod:<16}'
f'{path:<16}')
def run_rotors(run_tors_names, const_names):
""" a
"""
info_message('Running hindered rotor scans for the following rotors...',
newline=1)
for names in run_tors_names:
info_message(names)
if const_names is not None:
if set(list(chain(*run_tors_names))) == set(const_names):
info_message(
'User requested all torsions of system will be fixed.',
newline=1)
def save_conformer_energy(sp_save_path):
""" a
"""
info_message(f" - Saving energy of unique geometry at {sp_save_path}...")
def initial_geom_path(label, path):
""" a
"""
info_message(label, 'using geom from', path)
def bad_conformer(reason):
""" a
"""
info_message(
f'- Geometry is {reason}. Conformer will not be saved.')
def constraint_dictionary(dct):
""" a
"""
if dct is not None:
info_message('Contraint dictionary:', dct)
def existing_path(label, path):
""" a
"""
# info_message(label, 'found and saved previously in', path)
info_message(' -', label, 'found and saved previously in', path)
def bad_conformer(reason):
""" a
"""
info_message(
'- Geometry is {}. Conformer will not be saved.'.format(reason))
def save_irc(save_path):
""" a
"""
info_message(" - Saving IRC...")
info_message(f" - Save path: {save_path}")
def existing_path(label, path):
""" a
"""
info_message(label + ' found and saved previously in ', path)
def gradient(grad):
""" a
"""
grad_str = automol.util.mat.string(grad)
info_message(f'Gradient [au]:\n{grad_str}', newline=1)
def geometry(geom):
""" a
"""
geom_str = automol.geom.string(geom)
info_message(f'Geometry [Angstrom]:\n{geom_str}', newline=1)
def therm_paths_messpf_run_locations(spc_name, spc_locs_lst, spc_mods,
thm_paths_dct):
""" prints out a table with the path that the messpf thermo is calculated
for each conformer and model
"""
info_message('MESSPF location table:')
info_message(f'{"species name":<16}'
f'{"rid":<16}{"cid":<16}{"model":<16}{"path":<16}')
info_message(f'{"============":<16}'
f'{"=======":<16}{"=======":<16}{"=======":<16}'
f'{"============":<16}')
for spc_locs in spc_locs_lst:
for spc_mod in spc_mods:
path1 = thm_paths_dct[spc_name][tuple(spc_locs)][spc_mod][0]
path2 = thm_paths_dct[spc_name][tuple(spc_locs)]['mod_total'][0]
info_message(f'{spc_name:<16}'
f'{spc_locs[0]:<16}'
f'{spc_locs[1]:<16}'
f'{spc_mod:<16}'
f'{path1:<16}')
info_message(f'{spc_name:<16}'
f'{spc_locs[0]:<16}'
f'{spc_locs[1]:<16}'
f'{"mod combo":<16}'
f'{path2:<16}')
info_message(f'{spc_name:<16}'
f'{"":<16}'
f'{"spc combo":<16}'
f'{"mod combo":<16}'
f'{thm_paths_dct[spc_name]["spc_total"][0]:<16}')
def save_anharmonicity(geo_save_path):
""" a
"""
info_message(" - Saving anharmonicities...")
info_message(f" - Save path: {geo_save_path}")
def save_energy(sp_save_path):
""" a
"""
info_message(" - Saving energy...")
info_message(f" - Save path: {sp_save_path}")
def save_geo(save_path):
""" a
"""
info_message(" - Saving geoemetry...")
info_message(f" - Save path: {save_path}")
def energy(ene):
""" Print an energy value
"""
if ene is not None:
info_message(f"Energy [au]: {ene:<16.8f}", newline=1)
def already_running(task, path):
""" a
"""
info_message(f'{task} already running in {path}')
def save_conformer(cnf_save_path):
""" a
"""
info_message(" - Geometry is unique. Saving...")
info_message(f" - Save path: {cnf_save_path}")
def save_symmetry(sym_save_path):
""" a
"""
info_message(" - Saving structure in a sym directory at path "
f"{sym_save_path}")
def save_frequencies(save_path):
""" a
"""
info_message(" - Saving frequencies...")
info_message(f" - Save path: {save_path}")
def save_reference(save_path):
""" a
"""
info_message(" - Saving reference geometry...")
info_message(f" - Save path: {save_path}")
def print_thermo(spc_dct, ckin_nasa_str, spc_locs_dct, spc_locs_idx, spc_mod):
""" Generate and print thermo properties with the nasa polynomial string
"""
nasa7_params_all = chemkin_io.parser.thermo.create_spc_nasa7_dct(
ckin_nasa_str)
templist = (298.15, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200,
1300, 1400, 1500)
# templist = (
# 298.15, 300, 400, 500, 600, 800,
# 1000, 1500, 2000, 2500, 3000)
info_message('SPECIES H0f(0 K) H0f(298 K) in kcal/mol:')
info_message(' T (K) H - H(T) S(T) Cp(T) ')
info_message('Kelvin kcal/mol cal/(mol K) cal/(mol K)')
whitespace2 = 45
whitespace2 = whitespace2 * ' '
for spc_name in nasa7_params_all:
nasa7_params = nasa7_params_all[spc_name]
whitespace = 18 - len(spc_name)
whitespace = whitespace * ' '
if spc_locs_idx == 0:
hf0 = (spc_dct[spc_name]['Hfs']['final'][0] * phycon.EH2KCAL)
info_message(f'{spc_name}---{"boltzmann_weighted_combo"}')
else:
hf0 = (spc_dct[spc_name]['Hfs'][spc_locs_idx - 1][spc_mod][0] *
phycon.EH2KCAL)
idx_str = '_'.join(spc_locs_dct[spc_name][spc_locs_idx - 1])
info_message(f'{spc_name}---{idx_str}')
hf298 = mechanalyzer.calculator.thermo.enthalpy(nasa7_params,
298.15) / 1000.
info_message(f'{whitespace2}{hf0:>9.2f}{hf298:>9.2f}')
hincref = hf298
for temp in templist:
hinct = mechanalyzer.calculator.thermo.enthalpy(
nasa7_params, temp) / 1000. - hincref
entt = mechanalyzer.calculator.thermo.entropy(nasa7_params, temp)
cpt = mechanalyzer.calculator.thermo.heat_capacity(
nasa7_params, temp)
info_message(f'{temp:>8.2f}{hinct:>9.2f}{entt:>9.2f}{cpt:>9.2f}')
def save_gradient(save_path):
""" a
"""
info_message(' - Gradient found in Hessian job output.')
info_message(" - Saving gradient...")
info_message(f" - Save path: {save_path}")
