def mc_species(geom, elec_levels,
flux_mode_str, data_file_name,
ground_energy, reference_energy,
freqs=(), no_qc_corr=False, use_cm_shift=False):
""" Writes a monte carlo species section
:param core: `MonteCarlo` section string in MESS format
:type core: str
:param freqs: vibrational frequencies without fluxional mode (cm-1)
:type freqs: list(float)
:param elec_levels: energy and degeneracy of atom's electronic states
:type elec_levels: list(float)
:param hind_rot: string of MESS-format `Rotor` sections for all rotors
:type hind_rot: str
:param ground_energy: energy relative to reference (kcal.mol-1)
:type ground_energy: float
:param reference_energy: reference energy (kcal.mol-1)
:type reference_energy: float
:param freqs: vibrational frequencies (cm-1)
:type freqs: list(float)
:param no_qc_corr: signal to preclude quantum correction
:type no_qc_corr: bool
:param use_cm_chift: signal to include a CM shift
:type use_cm_shift: bool
:rtype: str
"""
# Format the molecule specification section
atom_list = util.molec_spec_format(geom)
# Build a formatted frequencies and elec levels string
nlevels, levels = util.elec_levels_format(elec_levels)
if freqs:
nfreqs, freqs = util.freqs_format(freqs)
no_qc_corr = True
else:
nfreqs = 0
# Indent various strings string if needed
flux_mode_str = util.indent(flux_mode_str, 4)
# Create dictionary to fill template
monte_carlo_keys = {
'atom_list': atom_list,
'flux_mode_str': flux_mode_str,
'data_file_name': data_file_name,
'ground_energy': ground_energy,
'nlevels': nlevels,
'levels': levels,
'nfreqs': nfreqs,
'freqs': freqs,
'reference_energy': reference_energy,
'no_qc_corr': no_qc_corr,
'use_cm_shift': use_cm_shift
}
return build_mako_str(
template_file_name='monte_carlo.mako',
template_src_path=MONTE_CARLO_PATH,
template_keys=monte_carlo_keys)
def molecule(core, freqs, elec_levels,
hind_rot='',
xmat=None, rovib_coups='', rot_dists=''):
""" Writes the molecule section of a MESS input file
:param str core: string for the "Core" section written
by another mess_io function
:param list freqs: vibrational frequencies for the molecule
:param list float elec_levels: energy and degeneracy of
the molecule's electronic states
:return atom_str: String for the atom section
:rtype: string
"""
# Build a formatted frequencies and elec levels string
nfreqs, freqs = util.freqs_format(freqs)
nlevels, levels = util.elec_levels_format(elec_levels)
# Format the rovib couplings and rotational distortions if needed
if rovib_coups != '':
rovib_coups = util.format_rovib_coups(rovib_coups)
if rot_dists != '':
rot_dists = util.format_rot_dist_consts(rot_dists)
if xmat is not None:
anharm = util.format_xmat(xmat)
else:
anharm = ''
# Indent various strings string if needed
if hind_rot != '':
hind_rot = util.indent(hind_rot, 2)
# Create dictionary to fill template
molec_keys = {
'core': core,
'nfreqs': nfreqs,
'freqs': freqs,
'nlevels': nlevels,
'levels': levels,
'hind_rot': hind_rot,
'anharm': anharm,
'rovib_coups': rovib_coups,
'rot_dists': rot_dists
}
# Set template name and path for a molecule
template_file_name = 'molecule.mako'
template_file_path = os.path.join(SPECIES_PATH, template_file_name)
# Build molecule string
molecule_str = Template(filename=template_file_path).render(**molec_keys)
return molecule_str
def molecule(core,
freqs,
elec_levels,
hind_rot='',
xmat=(),
rovib_coups=(),
rot_dists=()):
""" Writes the string that defines the `Species` section
for a molecule for a MESS input file by
formatting input information into strings and filling Mako template.
:param core: `Core` section string in MESS format
:type core: str
:param freqs: vibrational frequencies
:type freqs: list(float)
:param elec_levels: energy and degeneracy of atom's electronic states
:type elec_levels: list(float)
:param hind_rot: string of MESS-format `Rotor` sections for all rotors
:type hind_rot: str
:param xmat: anharmonicity matrix (cm-1)
:type xmat: list(list(float))
:param rovib_coups: rovibrational coupling matrix
:type rovib_coups: numpy.ndarray
:param rot_dists: rotational distortion constants: [['aaa'], [val]]
:type rot_dists: list(list(str), list(float))
:rtype: str
"""
# Add in infrared intensities at some point
# Build a formatted frequencies and elec levels string
nfreqs, freqs = util.freqs_format(freqs)
nlevels, levels = util.elec_levels_format(elec_levels)
# Format the rovib couplings and rotational distortions if needed
if rovib_coups:
rovib_coups = util.format_rovib_coups(rovib_coups)
else:
rovib_coups = ''
if rot_dists:
rot_dists = util.format_rot_dist_consts(rot_dists)
else:
rot_dists = ''
if xmat:
anharm = util.format_xmat(xmat)
else:
anharm = ''
# Indent various strings string if needed
if hind_rot != '':
hind_rot = util.indent(hind_rot, 2)
# Create dictionary to fill template
molec_keys = {
'core': core,
'nfreqs': nfreqs,
'freqs': freqs,
'nlevels': nlevels,
'levels': levels,
'hind_rot': hind_rot,
'anharm': anharm,
'rovib_coups': rovib_coups,
'rot_dists': rot_dists,
}
return build_mako_str(template_file_name='molecule.mako',
template_src_path=SPECIES_PATH,
template_keys=molec_keys)
def mc_species(geom,
sym_factor,
elec_levels,
flux_mode_str,
data_file_name,
ref_config_file_name='',
ground_ene=None,
reference_ene=None,
freqs=(),
use_cm_shift=False):
""" Writes a monte carlo species section
:param core: `MonteCarlo` section string in MESS format
:type core: str
:param sym_factor: symmetry factor of species
:type sym_factor: float
:param elec_levels: energy and degeneracy of atom's electronic states
:type elec_levels: list(float)
:param flux_mode_str: MESS-format `FluxionalMode` sections for rotors
:type flux_mode_str: str
:param data_file_name: Name of data file with molecular info
:type data_file_name: str
:param ground_ene: energy relative to reference n PES (kcal.mol-1)
:type ground_ene: float
:param reference_ene: harmonic ZPVE used for MC PF (kcal.mol-1)
:type reference_ene: float
:param freqs: vibrational frequencies (cm-1)
:type freqs: list(float)
:param use_cm_chift: signal to include a CM shift
:type use_cm_shift: bool
:rtype: str
"""
# Format the molecule specification section
atom_list = util.molec_spec_format(geom)
# Build a formatted frequencies and elec levels string
nlevels, levels = util.elec_levels_format(elec_levels)
levels = indent(levels, 2)
if freqs:
nfreqs, freqs = util.freqs_format(freqs)
else:
nfreqs = 0
# Check if reference config name is present
if nfreqs > 0:
assert ref_config_file_name, (
'Must provide a reference configuration file if no Hessians given')
# Indent various strings string if needed
flux_mode_str = util.indent(flux_mode_str, 4)
# Create dictionary to fill template
monte_carlo_keys = {
'atom_list': atom_list,
'sym_factor': sym_factor,
'flux_mode_str': flux_mode_str,
'data_file_name': data_file_name,
'ref_config_file_name': ref_config_file_name,
'reference_ene': reference_ene,
'ground_ene': ground_ene,
'nlevels': nlevels,
'levels': levels,
'nfreqs': nfreqs,
'freqs': freqs,
'use_cm_shift': use_cm_shift
}
return build_mako_str(template_file_name='monte_carlo.mako',
template_src_path=MONTE_CARLO_PATH,
template_keys=monte_carlo_keys)