def enthalpy(spc_name, spc_dct, spc_dct_i, spc_mod_dct_i, model_dct,
chn_basis_ene_dct, spc_array, locs, locs_path, cnf_fs, run_prefix,
save_prefix):
""" collect enthalpies
"""
zrxn = spc_dct_i.get('zrxn')
saddle = bool(zrxn)
# print('spc_mod_dct_i', spc_mod_dct_i)
pf_filesystems = filesys.models.pf_filesys(spc_dct_i,
spc_mod_dct_i,
run_prefix,
save_prefix,
name=spc_name,
saddle=saddle,
spc_locs=locs)
# print(pf_filesystems)
ene_abs = ene.read_energy(spc_dct_i,
pf_filesystems,
spc_mod_dct_i,
run_prefix,
conf=(locs, locs_path, cnf_fs),
read_ene=True,
read_zpe=True,
saddle=saddle)
hf0k, _, chn_basis_ene_dct, hbasis = basis.enthalpy_calculation(
spc_dct,
spc_name,
ene_abs,
chn_basis_ene_dct,
model_dct,
spc_mod_dct_i,
run_prefix,
save_prefix,
pforktp='pf',
zrxn=zrxn)
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)
return ([locs_path, ene_abs, hf0k,
*coeff_array], chn_basis_ene_dct, spc_array)
def run_tsk(tsk, spc_dct, spc_name, thy_dct, proc_keyword_dct, pes_mod_dct_i,
spc_mod_dct_i, run_prefix, save_prefix):
""" run a proc tess 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(proc_keyword_dct, thy_dct)
# Setup csv data dictionary for specific task
csv_data = util.set_csv_data(tsk)
chn_basis_ene_dct = {}
spc_array = []
# print species
ioprinter.obj('line_dash')
ioprinter.info_message("Species: ", spc_name)
# Heat of formation basis molecules and coefficients
# is not conformer specific
if 'coeffs' in tsk:
thy_info = spc_mod_dct_i['geo'][1]
filelabel = 'coeffs'
filelabel += '_{}'.format(pes_mod_dct_i['thermfit']['ref_scheme'])
filelabel += '.csv'
label = spc_name
basis_dct, _ = basis.prepare_refs(
pes_mod_dct_i['thermfit']['ref_scheme'], spc_dct, (spc_name, ))
# 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 proc_keyword_dct['geolvl']:
thy_info = tinfo.from_dct(thy_dct.get(proc_keyword_dct['geolvl']))
else:
thy_info = spc_mod_dct_i['geo'][1]
# Loop over conformers
if proc_keyword_dct['geolvl']:
_, rng_cnf_locs_lst, rng_cnf_locs_path = util.conformer_list(
proc_keyword_dct, save_prefix, run_prefix, spc_dct_i, thy_dct)
spc_mod_dct_i, pf_models = None, None
else:
ret = util.conformer_list_from_models(proc_keyword_dct,
save_prefix, run_prefix,
spc_dct_i, thy_dct,
spc_mod_dct_i, 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 spc_mod_dct_i:
filelabel += '_m{}'.format(spc_mod_dct_i['harm'][0])
else:
filelabel += '_{}'.format(proc_keyword_dct['geolvl'])
filelabel += '.csv'
if pf_models:
pf_filesystems = filesys.models.pf_filesys(spc_dct_i,
spc_mod_dct_i,
run_prefix,
save_prefix,
saddle=False)
ret = vib.full_vib_analysis(spc_dct_i,
pf_filesystems,
spc_mod_dct_i,
run_prefix,
zrxn=None)
freqs, _, tors_zpe, sfactor, torsfreqs, all_freqs = ret
csv_data['tfreq'][label] = torsfreqs
csv_data['allfreq'][label] = all_freqs
csv_data['scalefactor'][label] = [sfactor]
else:
es_model = util.freq_es_levels(proc_keyword_dct)
spc_mod_dct_i = parser.model.pf_level_info(
es_model, thy_dct)
try:
freqs, _, zpe = vib.read_locs_harmonic_freqs(
cnf_fs, locs, run_prefix, zrxn=None)
except:
freqs = []
zpe = 0
tors_zpe = 0.0
spc_data = []
zpe = tors_zpe + (sum(freqs) / 2.0) * phycon.WAVEN2EH
if freqs and proc_keyword_dct['scale'] is not None:
freqs, zpe = vib.scale_frequencies(freqs,
tors_zpe,
spc_mod_dct_i,
scale_method='3c')
spc_data = [locs_path, zpe, *freqs]
csv_data['freq'][label] = spc_data
elif 'geo' in tsk:
filelabel = 'geo'
if spc_mod_dct_i:
filelabel += '_{}'.format(spc_mod_dct_i['harm'])
else:
filelabel += '_{}'.format(proc_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 spc_mod_dct_i:
filelabel += '_{}'.format(spc_mod_dct_i['harm'])
else:
filelabel += '_{}'.format(proc_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 spc_mod_dct_i:
filelabel += '_{}'.format(spc_mod_dct_i['harm'])
filelabel += '_{}'.format(spc_mod_dct_i['ene'])
else:
filelabel += '_{}'.format(proc_keyword_dct['geolvl'])
filelabel += '_{}'.format(proc_keyword_dct['proplvl'])
filelabel += '.csv'
energy = None
if spc_mod_dct_i:
pf_filesystems = filesys.models.pf_filesys(spc_dct_i,
spc_mod_dct_i,
run_prefix,
save_prefix,
saddle=False)
energy = ene.electronic_energy(spc_dct_i,
pf_filesystems,
spc_mod_dct_i,
conf=(locs, locs_path,
cnf_fs))
else:
spc_info = sinfo.from_dct(spc_dct_i)
thy_info = tinfo.from_dct(
thy_dct.get(proc_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 spc_mod_dct_i:
filelabel += '_{}'.format(spc_mod_dct_i['harm'])
filelabel += '_{}'.format(spc_mod_dct_i['ene'])
else:
filelabel += '_{}'.format(proc_keyword_dct['geolvl'])
filelabel += '_{}'.format(proc_keyword_dct['proplvl'])
filelabel = '.csv'
energy = None
pf_filesystems = filesys.models.pf_filesys(spc_dct_i,
spc_mod_dct_i,
run_prefix,
save_prefix,
saddle=False)
ene_abs = ene.read_energy(spc_dct_i,
pf_filesystems,
spc_mod_dct_i,
run_prefix,
conf=(locs, locs_path, cnf_fs),
read_ene=True,
read_zpe=True,
saddle=False)
hf0k, _, chn_basis_ene_dct, hbasis = basis.enthalpy_calculation(
spc_dct,
spc_name,
ene_abs,
chn_basis_ene_dct,
pes_mod_dct_i,
spc_mod_dct_i,
run_prefix,
save_prefix,
pforktp='pf',
zrxn=None)
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)
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,
spc_locs=None):
""" Reads all required data from the SAVE filesystem for a molecule.
Stores data into an info dictionary.
All of the data that is read is determined by the models that
are described in the pes and spc model dictionaries.
:param spc_dct:
:type spc_dct:
:param pes_mod_dct_i: keyword dict of specific PES model
:type pes_mod_dct_i: dict[]
:param spc_mod_dct_i: keyword dict of specific species model
:type spc_mod_dct_i: dict[]
:param run_prefix: root-path to the run-filesystem
:type run_prefix: str
:param save_prefix: root-path to the save-filesystem
:type save_prefix: str
:rtype: dict[]
"""
spc_dct_i = spc_dct[spc_name]
ene_chnlvl = None
ene_reflvl = None
zpe = None
hf0k = None
hf0k_trs = None
hf0k = 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,
spc_locs=spc_locs)
# 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.full_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_save_path, _, _, _] = 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_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, hf0k, ene_reflvl, zpe, hf0k_trs, edown_str,
collid_freq_str
]
inf_dct = dict(zip(keys, vals))
return inf_dct, chn_basis_ene_dct
def atm_data(spc_dct, spc_name, pes_mod_dct_i, spc_mod_dct_i, run_prefix,
save_prefix):
""" Reads all required data from the SAVE filesystem for an atom.
Stores data into an info dictionary.
All of the data that is read is determined by the models that
are described in the pes and spc model dictionaries.
:param spc_dct:
:type spc_dct:
:param pes_mod_dct_i: keyword dict of specific PES model
:type pes_mod_dct_i: dict[]
:param spc_mod_dct_i: keyword dict of specific species model
:type spc_mod_dct_i: dict[]
:param run_prefix: root-path to the run-filesystem
:type run_prefix: str
:param save_prefix: root-path to the save-filesystem
:type save_prefix: str
:rtype: dict[]
"""
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)
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)
# 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': hf0k,
'ene_reflvl': None,
'ene_tsref': hf0k_trs,
'zpe_chnlvl': None
}
return inf_dct