def atm_data(spc_dct, spc_name, pes_mod_dct_i, spc_mod_dct_i, run_prefix,
save_prefix):
""" Pull all neccessary info for the atom
"""
spc_dct_i = spc_dct[spc_name]
# Set up all the filesystem objects using models and levels
pf_filesystems = filesys.models.pf_filesys(spc_dct_i, spc_mod_dct_i,
run_prefix, save_prefix, False)
ioprinter.info_message('Obtaining the geometry...', newline=1)
geom = rot.read_geom(pf_filesystems)
ioprinter.info_message('Obtaining the electronic energy...', newline=1)
ene_chnlvl = ene.read_energy(spc_dct_i,
pf_filesystems,
spc_mod_dct_i,
run_prefix,
read_ene=True,
read_zpe=False)
ene_reflvl = None
zpe_chnlvl = None
hf0k, hf0k_trs, _, _ = basis.enthalpy_calculation(spc_dct,
spc_name,
ene_chnlvl, {},
pes_mod_dct_i,
spc_mod_dct_i,
run_prefix,
save_prefix,
pforktp='ktp',
zrxn=None)
ene_chnlvl = hf0k * phycon.KCAL2EH
hf0k_trs *= phycon.KCAL2EH
# Create info dictionary
inf_dct = {
'geom': geom,
'sym_factor': 1.0,
'freqs': tuple(),
'mess_hr_str': '',
'mass': util.atom_mass(spc_dct_i),
'elec_levels': spc_dct_i['elec_levels'],
'ene_chnlvl': ene_chnlvl,
'ene_reflvl': ene_reflvl,
'ene_tsref': hf0k_trs,
'zpe_chnlvl': zpe_chnlvl
}
return inf_dct
def mol_data(spc_name,
spc_dct,
pes_mod_dct_i,
spc_mod_dct_i,
chn_basis_ene_dct,
run_prefix,
save_prefix,
calc_chn_ene=True,
zrxn=None):
""" Pull all of the neccessary information from the filesystem for a species
"""
spc_dct_i = spc_dct[spc_name]
ene_chnlvl = None
ene_reflvl = None
zpe = None
hf0k_trs = None
# Initialize all of the elements of the inf dct
geom, sym_factor, freqs, imag, elec_levels = None, None, None, None, None
allr_str, mdhr_dat = '', ''
xmat, rovib_coups, rot_dists = None, None, None
# Set up all the filesystem objects using models and levels
pf_filesystems = filesys.models.pf_filesys(spc_dct_i,
spc_mod_dct_i,
run_prefix,
save_prefix,
zrxn is not None,
name=spc_name)
# Obtain rotation partition function information
ioprinter.info_message('Obtaining info for rotation partition function...',
newline=1)
geom = rot.read_geom(pf_filesystems)
if typ.nonrigid_rotations(spc_mod_dct_i):
rovib_coups, rot_dists = rot.read_rotational_values(pf_filesystems)
# Obtain vibration partition function information
ioprinter.info_message(
'Preparing internal rotor info building partition functions...',
newline=1)
rotors = tors.build_rotors(spc_dct_i, pf_filesystems, spc_mod_dct_i)
ioprinter.info_message(
'Obtaining the vibrational frequencies and zpves...', newline=1)
freqs, imag, zpe, tors_strs = vib.vib_analysis(spc_dct_i,
pf_filesystems,
spc_mod_dct_i,
run_prefix,
zrxn=zrxn)
allr_str = tors_strs[0]
# ioprinter.info_message('zpe in mol_data test:', zpe)
if typ.anharm_vib(spc_mod_dct_i):
xmat = vib.read_anharmon_matrix(pf_filesystems)
# Obtain symmetry factor
ioprinter.info_message('Determining the symmetry factor...', newline=1)
zma = None
if zrxn:
[cnf_fs, cnf_save_path, min_cnf_locs, _, _] = pf_filesystems['harm']
# Build the rotors
if cnf_save_path:
zma_fs = autofile.fs.zmatrix(cnf_save_path)
zma = zma_fs[-1].file.zmatrix.read([0])
sym_factor = symm.symmetry_factor(pf_filesystems,
spc_mod_dct_i,
spc_dct_i,
rotors,
grxn=zrxn,
zma=zma)
# Obtain electronic energy levels
elec_levels = spc_dct_i['elec_levels']
# Obtain energy levels
ioprinter.info_message('Obtaining the electronic energy + zpve...',
newline=1)
if calc_chn_ene:
chn_ene = ene.read_energy(spc_dct_i,
pf_filesystems,
spc_mod_dct_i,
run_prefix,
read_ene=True,
read_zpe=False,
saddle=zrxn is not None)
ene_chnlvl = chn_ene + zpe
zma = None
# Determine info about the basis species used in thermochem calcs
hf0k, hf0k_trs, chn_basis_ene_dct, _ = basis.enthalpy_calculation(
spc_dct,
spc_name,
ene_chnlvl,
chn_basis_ene_dct,
pes_mod_dct_i,
spc_mod_dct_i,
run_prefix,
save_prefix,
zrxn=zrxn)
ene_chnlvl = hf0k * phycon.KCAL2EH
hf0k_trs *= phycon.KCAL2EH
ene_reflvl = None
# Build the energy transfer section strings
if zrxn is None:
ioprinter.info_message('Determining energy transfer parameters...',
newline=1)
well_info = sinfo.from_dct(spc_dct_i)
# ioprinter.debug_message('well_inf', well_info)
# bath_info = ['InChI=1S/N2/c1-2', 0, 1] # how to do...
bath_info = ['InChI=1S/Ar', 0, 1] # how to do...
etrans_dct = etrans.build_etrans_dct(spc_dct_i)
edown_str, collid_freq_str = etrans.make_energy_transfer_strs(
well_info, bath_info, etrans_dct)
else:
edown_str, collid_freq_str = None, None
# Create info dictionary
keys = [
'geom', 'sym_factor', 'freqs', 'imag', 'elec_levels', 'mess_hr_str',
'mdhr_dat', 'xmat', 'rovib_coups', 'rot_dists', 'ene_chnlvl',
'ene_reflvl', 'zpe_chnlvl', 'ene_tsref', 'edown_str', 'collid_freq_str'
]
vals = [
geom, sym_factor, freqs, imag, elec_levels, allr_str, mdhr_dat, xmat,
rovib_coups, rot_dists, ene_chnlvl, ene_reflvl, zpe, hf0k_trs,
edown_str, collid_freq_str
]
inf_dct = dict(zip(keys, vals))
return inf_dct, chn_basis_ene_dct
def run_tsk(tsk, spc_dct, rxn_lst, thy_dct, print_keyword_dct, model_dct,
run_prefix, save_prefix):
""" run an electronic structure task
for generating a list of conformer or tau sampling geometries
"""
# Print the head of the task
ioprinter.output_task_header(tsk)
ioprinter.obj('line_dash')
ioprinter.output_keyword_list(print_keyword_dct, thy_dct)
# Setup csv data dictionary for specific task
csv_data = util.set_csv_data(tsk)
chn_basis_ene_dct = {}
spc_array = []
# Loop over species to collect task info
spc_queue = parser.species.build_spc_queue(rxn_lst)
for spc_name, (pf_model, spc_model) in spc_queue:
# print species
ioprinter.obj('line_dash')
ioprinter.info_message("Species: ", spc_name)
# If species is unstable, set task to 'none'
# stable = instab.check_unstable_species(
# tsk, spc_dct, spc_name, thy_info, save_prefix)
# if not stable:
# ioprinter.info_message(
# 'Properties for species {}'.format(spc_name),
# 'will not be included in output',
# 'because species is unstable')
# continue
# Heat of formation basis molecules and coefficients
# is not conformer specific
if 'coeffs' in tsk:
pf_levels, pf_models, _, _ = set_pf_info(model_dct, thy_dct,
pf_model, pf_model)
thy_info = pf_levels['geo'][1]
filelabel = 'coeffs'
filelabel += '_{}'.format(pf_models['ref_scheme'])
filelabel += '.csv'
label = spc_name
basis_dct, uniref_dct = basis.prepare_refs(pf_models['ref_scheme'],
spc_dct,
[[spc_name, None]],
run_prefix, save_prefix)
# Get the basis info for the spc of interest
spc_basis, coeff_basis = basis_dct[spc_name]
coeff_array = []
for spc_i in spc_basis:
if spc_i not in spc_array:
spc_array.append(spc_i)
for spc_i in spc_array:
if spc_i in spc_basis:
coeff_array.append(coeff_basis[spc_basis.index(spc_i)])
else:
coeff_array.append(0)
csv_data[label] = [*coeff_array]
else:
# unpack spc and level info
spc_dct_i = spc_dct[spc_name]
if print_keyword_dct['geolvl']:
thy_info = tinfo.from_dct(
thy_dct.get(print_keyword_dct['geolvl']))
else:
pf_levels, pf_models, _, _ = set_pf_info(
model_dct, thy_dct, pf_model, pf_model)
thy_info = pf_levels['geo'][1]
# Loop over conformers
if print_keyword_dct['geolvl']:
_, rng_cnf_locs_lst, rng_cnf_locs_path = util.conformer_list(
print_keyword_dct, save_prefix, run_prefix, spc_dct_i,
thy_dct)
pf_levels, pf_models = None, None
else:
pf_levels, pf_models, _, _ = set_pf_info(
model_dct, thy_dct, spc_model, spc_model)
ret = util.conformer_list_from_models(print_keyword_dct,
save_prefix, run_prefix,
spc_dct_i, thy_dct,
pf_levels, pf_models)
_, rng_cnf_locs_lst, rng_cnf_locs_path = ret
for locs, locs_path in zip(rng_cnf_locs_lst, rng_cnf_locs_path):
label = spc_name + '_' + '_'.join(locs)
_, cnf_fs = filesys.build_fs(run_prefix, save_prefix,
'CONFORMER')
if 'freq' in tsk:
filelabel = 'freq'
if pf_levels:
filelabel += '_m{}'.format(pf_levels['harm'][0])
else:
filelabel += '_{}'.format(print_keyword_dct['geolvl'])
filelabel += '.csv'
if pf_models:
pf_filesystems = filesys.models.pf_filesys(
spc_dct_i,
pf_levels,
run_prefix,
save_prefix,
saddle=False)
ret = vib.full_vib_analysis(spc_dct_i,
pf_filesystems,
pf_models,
pf_levels,
run_prefix,
saddle=False)
freqs, imag, tors_zpe, scale_fact, tors_freqs, all_freqs = ret
csv_data['tfreq'][label] = tors_freqs
csv_data['allfreq'][label] = all_freqs
csv_data['scalefactor'][label] = [scale_fact]
else:
es_model = util.freq_es_levels(print_keyword_dct)
pf_levels = parser.model.pf_level_info(
es_model, thy_dct)
try:
freqs, _, zpe = vib.read_locs_harmonic_freqs(
cnf_fs, locs_path, locs, saddle=False)
except:
freqs = []
zpe = 0
tors_zpe = 0.0
spc_data = []
zpe = tors_zpe + (sum(freqs) / 2.0) * phycon.WAVEN2EH
if freqs and print_keyword_dct['scale'] is not None:
freqs, zpe = vib.scale_frequencies(freqs,
tors_zpe,
pf_levels,
scale_method='3c')
spc_data = [locs_path, zpe, *freqs]
csv_data['freq'][label] = spc_data
elif 'geo' in tsk:
filelabel = 'geo'
if pf_levels:
filelabel += '_{}'.format(pf_levels['harm'])
else:
filelabel += '_{}'.format(print_keyword_dct['geolvl'])
filelabel += '.txt'
if cnf_fs[-1].file.geometry.exists(locs):
geo = cnf_fs[-1].file.geometry.read(locs)
energy = cnf_fs[-1].file.energy.read(locs)
comment = 'energy: {0:>15.10f}'.format(energy)
xyz_str = automol.geom.xyz_string(geo, comment=comment)
else:
xyz_str = '\t -- Missing --'
spc_data = '\n\nSPC: {}\tConf: {}\tPath: {}\n'.format(
spc_name, locs, locs_path) + xyz_str
csv_data[label] = spc_data
elif 'zma' in tsk:
filelabel = 'zmat'
if pf_levels:
filelabel += '_{}'.format(pf_levels['harm'])
else:
filelabel += '_{}'.format(print_keyword_dct['geolvl'])
filelabel += '.txt'
geo = cnf_fs[-1].file.geometry.read(locs)
zma = automol.geom.zmatrix(geo)
energy = cnf_fs[-1].file.energy.read(locs)
comment = 'energy: {0:>15.10f}\n'.format(energy)
zma_str = automol.zmat.string(zma)
spc_data = '\n\nSPC: {}\tConf: {}\tPath: {}\n'.format(
spc_name, locs, locs_path) + comment + zma_str
csv_data[label] = spc_data
elif 'ene' in tsk:
filelabel = 'ene'
if pf_levels:
filelabel += '_{}'.format(pf_levels['harm'])
filelabel += '_{}'.format(pf_levels['ene'])
else:
filelabel += '_{}'.format(print_keyword_dct['geolvl'])
filelabel += '_{}'.format(print_keyword_dct['proplvl'])
filelabel += '.csv'
energy = None
if pf_levels:
pf_filesystems = filesys.models.pf_filesys(
spc_dct_i,
pf_levels,
run_prefix,
save_prefix,
saddle=False)
energy = ene.electronic_energy(spc_dct_i,
pf_filesystems,
pf_levels,
conf=(locs, locs_path,
cnf_fs))
else:
spc_info = sinfo.from_dct(spc_dct_i)
thy_info = tinfo.from_dct(
thy_dct.get(print_keyword_dct['proplvl']))
mod_thy_info = tinfo.modify_orb_label(
thy_info, spc_info)
sp_save_fs = autofile.fs.single_point(locs_path)
sp_save_fs[-1].create(mod_thy_info[1:4])
# Read the energy
sp_path = sp_save_fs[-1].path(mod_thy_info[1:4])
if os.path.exists(sp_path):
if sp_save_fs[-1].file.energy.exists(
mod_thy_info[1:4]):
ioprinter.reading('Energy', sp_path)
energy = sp_save_fs[-1].file.energy.read(
mod_thy_info[1:4])
csv_data[label] = [locs_path, energy]
elif 'enthalpy' in tsk:
filelabel = 'enthalpy'
if pf_levels:
filelabel += '_{}'.format(pf_levels['harm'])
filelabel += '_{}'.format(pf_levels['ene'])
else:
filelabel += '_{}'.format(print_keyword_dct['geolvl'])
filelabel += '_{}'.format(print_keyword_dct['proplvl'])
filelabel = '.csv'
energy = None
pf_filesystems = filesys.models.pf_filesys(spc_dct_i,
pf_levels,
run_prefix,
save_prefix,
saddle=False)
ene_abs = ene.read_energy(spc_dct_i,
pf_filesystems,
pf_models,
pf_levels,
run_prefix,
conf=(locs, locs_path, cnf_fs),
read_ene=True,
read_zpe=True,
saddle=False)
ts_geom = None
hf0k, _, chn_basis_ene_dct, hbasis = basis.enthalpy_calculation(
spc_dct,
spc_name,
ts_geom,
ene_abs,
chn_basis_ene_dct,
pf_levels,
pf_models,
run_prefix,
save_prefix,
pforktp='pf',
saddle=False)
spc_basis, coeff_basis = hbasis[spc_name]
coeff_array = []
for spc_i in spc_basis:
if spc_i not in spc_array:
spc_array.append(spc_i)
for spc_i in spc_array:
if spc_i in spc_basis:
coeff_array.append(
coeff_basis[spc_basis.index(spc_i)])
else:
coeff_array.append(0)
csv_data[label] = [locs_path, ene_abs, hf0k, *coeff_array]
util.write_csv_data(tsk, csv_data, filelabel, spc_array)