def read_locs_harmonic_freqs(cnf_fs, cnf_locs, run_prefix, zrxn=None):
""" Read the harmonic frequencies for a specific conformer
Do the freqs obtain for two species for fake and pst?
"""
if cnf_locs is not None:
geo_exists = cnf_fs[-1].file.geometry.exists(cnf_locs)
hess_exists = cnf_fs[-1].file.hessian.exists(cnf_locs)
if not geo_exists:
ioprinter.error_message(
'No Reference geometry for harmonic frequencies at path',
cnf_fs[-1].file.hessian.path(cnf_locs))
if not hess_exists:
ioprinter.error_message(
'No Hessian available for harmonic frequencies at path',
cnf_fs[-1].file.hessian.path(cnf_locs))
else:
geo_exists, hess_exists = False, False
if geo_exists and hess_exists:
# Obtain geom and freqs from filesys
geo = cnf_fs[-1].file.geometry.read(cnf_locs)
hess = cnf_fs[-1].file.hessian.read(cnf_locs)
ioprinter.reading('Hessian', cnf_fs[-1].path(cnf_locs))
# Build the run filesystem using locs
fml_str = automol.geom.formula_string(geo)
vib_path = job_path(run_prefix, 'PROJROT', 'FREQ', fml_str)
# Obtain the frequencies
ioprinter.info_message(
'Calling ProjRot to diagonalize Hessian and get freqs...')
script_str = autorun.SCRIPT_DCT['projrot']
freqs, _, imag_freqs, _ = autorun.projrot.frequencies(
script_str, vib_path, [geo], [[]], [hess])
# Obtain the displacements
norm_coord_str, _ = autorun.projrot.displacements(
script_str, vib_path, [geo], [[]], [hess])
# Calculate the zpve
ioprinter.frequencies(freqs)
zpe = (sum(freqs) / 2.0) * phycon.WAVEN2EH
# Check imaginary frequencies and set freqs
if zrxn is not None:
if len(imag_freqs) > 1:
ioprinter.warning_message('Saddle Point has more than',
'one imaginary frequency')
imag = imag_freqs[0]
else:
imag = None
ret = (freqs, imag, zpe, norm_coord_str)
else:
ret = None
return ret
def _hess_freqs(geo, geo_save_fs, save_path, locs, run_prefix, overwrite):
""" Calculate harmonic frequencies using Hessian
"""
if _json_database(save_path):
exists = geo_save_fs[-1].json.harmonic_frequencies.exists(locs)
else:
exists = geo_save_fs[-1].file.harmonic_frequencies.exists(locs)
if not exists:
ioprinter.info_message(
'No harmonic frequencies found in save filesys...')
_run = True
elif overwrite:
ioprinter.info_message(
'User specified to overwrite frequencies with new run...')
_run = True
else:
_run = False
if _run:
# Read the Hessian from the filesystem
if _json_database(save_path):
hess = geo_save_fs[-1].json.hessian.read(locs)
else:
hess = geo_save_fs[-1].file.hessian.read(locs)
# Calculate and save the harmonic frequencies
ioprinter.info_message(
" - Calculating harmonic frequencies from Hessian...")
script_str = autorun.SCRIPT_DCT['projrot']
fml_str = automol.geom.formula_string(geo)
vib_path = job_path(run_prefix, 'PROJROT', 'FREQ', fml_str)
rt_freqs, _, rt_imags, _ = autorun.projrot.frequencies(
script_str, vib_path, [geo], [[]], [hess])
rt_imags = tuple(-1 * imag_freq for imag_freq in rt_imags)
freqs = sorted(rt_imags + rt_freqs)
ioprinter.frequencies(freqs)
ioprinter.geometry(geo)
if _json_database(save_path):
geo_save_fs[-1].json.harmonic_frequencies.write(freqs, locs)
else:
geo_save_fs[-1].file.harmonic_frequencies.write(freqs, locs)
ioprinter.save_frequencies(save_path)
else:
ioprinter.existing_path('Harmonic frequencies', save_path)
freqs = geo_save_fs[-1].file.harmonic_frequencies.read(locs)
ioprinter.frequencies(freqs)
def read_locs_harmonic_freqs(cnf_fs,
harm_path,
cnf_locs,
run_prefix,
zrxn=None):
""" Read the harmonic frequencies for a specific conformer
"""
# probably should read freqs
# Do the freqs obtain for two species for fake and pst
if cnf_locs is not None:
# Obtain geom and freqs from filesys
geo = cnf_fs[-1].file.geometry.read(cnf_locs)
hess = cnf_fs[-1].file.hessian.read(cnf_locs)
ioprinter.reading('Hessian', cnf_fs[-1].path(cnf_locs))
# Build the run filesystem using locs
fml_str = automol.geom.formula_string(geo)
vib_path = job_path(run_prefix, 'PROJROT', 'FREQ', fml_str)
# Obtain the frequencies
ioprinter.info_message(
'Calling ProjRot to diagonalize Hessian and get freqs...')
script_str = autorun.SCRIPT_DCT['projrot']
freqs, _, imag_freqs, _ = autorun.projrot.frequencies(
script_str, vib_path, [geo], [[]], [hess])
# Calculate the zpve
ioprinter.frequencies(freqs)
zpe = (sum(freqs) / 2.0) * phycon.WAVEN2EH
# Check imaginary frequencies and set freqs
if zrxn is not None:
if len(imag_freqs) > 1:
ioprinter.warning_message('Saddle Point has more than',
'one imaginary frequency')
imag = imag_freqs[0]
else:
imag = None
else:
ioprinter.error_message(
'Reference geometry is missing for harmonic frequencies')
return freqs, imag, zpe
def _assess_imags(freqs, ref_freqs, cnf_run_fs, cnf_save_fs, locs):
""" Check if the frequencies signal a bad transition state
"""
# Initialize success variable to be changed if needed
success = True
# Assume first (lowest) frequency is the imaginary mode
imags = tuple(x for x in freqs if x < 0.0)
imag_freq, ref_imag_freq = abs(imags[0]), abs(ref_freqs[0])
print('\nChecking imaginary mode of potential saddle-point conformer '
'(frequencies below)\n'
f'versus reference imaginary mode {ref_imag_freq:.1f} cm-1.')
ioprinter.frequencies(freqs)
print('Checking if deviation from reference mode less than 100.0 cm-1')
imag_diff = abs(imag_freq - ref_imag_freq)
if imag_diff <= 100.0:
print(f' - Deviation = {imag_diff:.1f} cm-1. Small, likely fine.')
else:
print(f' - Deviation = {imag_diff:1f} cm-1. Large, could be bad')
print(' - Checking if value of mode greater than 150.0 cm-1')
if imag_freq >= 150.0:
print(f' - Mode = {imag_freq:.1f} cm-1. Large, likely fine\n')
else:
print(f' - Mode = {imag_freq:.1f} cm-1. Small, likely bad\n')
success = False
if success:
print('Frequencies appear fine. Proceeding to save Hessian info.')
else:
cnf_run_path = cnf_run_fs[-1].path(locs)
cnf_save_path = cnf_save_fs[-1].path(locs)
shutil.rmtree(cnf_run_path)
shutil.rmtree(cnf_save_path)
print('Based on checks, saddle-point conformer likely bad. '
'Removing conformer from both RUN and SAVE filesystem at\n'
f'{cnf_run_path}\n'
f'{cnf_save_path}\n')
return success
def conformer_tsk(job,
spc_dct,
spc_name,
thy_dct,
es_keyword_dct,
run_prefix,
save_prefix,
print_debug=False):
""" Prepares and executes all electronic structure tasks that
generate information for species and transition state conformers.
This includes sampling and optimization procedures to generate
conformer structures, as well as __ calculations using some
saved conformer as input.
:param job(subtask): calculatiion(s) to perform for conformer
:type job: str
:param spc_dct:
:type spc_dct:
:param spc_name: name of species
:type spc_name: str
:param thy_dct:
:type thy_dct:
:param es_keyword_dct: keyword-values for electronic structure task
:type es_keyword_dct: dict[str:str]
: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
"""
saddle = bool('ts_' in spc_name)
spc_dct_i = spc_dct[spc_name]
# Set the spc_info
if not saddle:
spc_info = sinfo.from_dct(spc_dct_i)
else:
spc_info = rinfo.ts_info(spc_dct_i['rxn_info'])
zrxn = spc_dct_i.get('zrxn', None)
overwrite = es_keyword_dct['overwrite']
retryfail = es_keyword_dct['retryfail']
nprocs = 1
# Modify the theory
method_dct = thy_dct.get(es_keyword_dct['runlvl'])
ini_method_dct = thy_dct.get(es_keyword_dct['inplvl'])
thy_info = tinfo.from_dct(method_dct)
ini_thy_info = tinfo.from_dct(ini_method_dct)
mod_thy_info = tinfo.modify_orb_label(thy_info, spc_info)
mod_ini_thy_info = tinfo.modify_orb_label(ini_thy_info, spc_info)
# New filesystem objects
_root = root_locs(spc_dct_i, saddle=saddle, name=spc_name)
ini_cnf_run_fs, ini_cnf_save_fs = build_fs(run_prefix,
save_prefix,
'CONFORMER',
thy_locs=mod_ini_thy_info[1:],
**_root)
cnf_run_fs, cnf_save_fs = build_fs(run_prefix,
save_prefix,
'CONFORMER',
thy_locs=mod_thy_info[1:],
**_root)
if job == 'samp':
# Build the ini zma filesys
user_conf_ids = spc_dct_i.get('conf_id')
if user_conf_ids is None:
ini_loc_info = filesys.mincnf.min_energy_conformer_locators(
ini_cnf_save_fs, mod_ini_thy_info)
ini_locs, ini_min_cnf_path = ini_loc_info
else:
print(f'Using user specified conformer IDs: {user_conf_ids}')
ini_locs = user_conf_ids
if any(ini_locs):
ini_zma_save_fs = autofile.fs.zmatrix(ini_min_cnf_path)
# Set up the run scripts
script_str, kwargs = qchem_params(method_dct,
elstruct.Job.OPTIMIZATION)
# Set variables if it is a saddle
two_stage = saddle
mc_nsamp = spc_dct_i['mc_nsamp']
resave = es_keyword_dct['resave']
# Read the geometry and zma from the ini file system
geo = ini_cnf_save_fs[-1].file.geometry.read(ini_locs)
zma = ini_zma_save_fs[-1].file.zmatrix.read([0])
# Read the torsions from the ini file sys
if ini_zma_save_fs[-1].file.torsions.exists([0]):
tors_dct = ini_zma_save_fs[-1].file.torsions.read([0])
rotors = automol.rotor.from_data(zma, tors_dct)
tors_names = automol.rotor.names(rotors, flat=True)
else:
tors_names = ()
geo_path = ini_cnf_save_fs[-1].path(ini_locs)
ioprinter.initial_geom_path('Sampling started', geo_path)
# Check runsystem for equal ring CONF make conf_fs
# Else make new ring conf directory
rid = conformer.rng_loc_for_geo(geo, cnf_save_fs)
if rid is None:
conformer.single_conformer(zma,
spc_info,
mod_thy_info,
cnf_run_fs,
cnf_save_fs,
script_str,
overwrite,
retryfail=retryfail,
zrxn=zrxn,
**kwargs)
rid = conformer.rng_loc_for_geo(geo, cnf_save_fs)
# Run the sampling
conformer.conformer_sampling(zma,
spc_info,
mod_thy_info,
cnf_run_fs,
cnf_save_fs,
rid,
script_str,
overwrite,
nsamp_par=mc_nsamp,
tors_names=tors_names,
zrxn=zrxn,
two_stage=two_stage,
retryfail=retryfail,
resave=resave,
repulsion_thresh=40.0,
print_debug=print_debug,
**kwargs)
else:
ioprinter.info_message('Missing conformers. Skipping task...')
elif job == 'pucker':
# Build the ini zma filesys
ini_loc_info = filesys.mincnf.min_energy_conformer_locators(
ini_cnf_save_fs, mod_ini_thy_info)
ini_min_locs, ini_min_cnf_path = ini_loc_info
ini_zma_save_fs = autofile.fs.zmatrix(ini_min_cnf_path)
# Set up the run scripts
script_str, kwargs = qchem_params(method_dct,
elstruct.Job.OPTIMIZATION)
# Set variables if it is a saddle
two_stage = saddle
mc_nsamp = spc_dct_i['mc_nsamp']
# Read the geometry and zma from the ini file system
geo = ini_cnf_save_fs[-1].file.geometry.read(ini_min_locs)
zma = ini_zma_save_fs[-1].file.zmatrix.read([0])
# Read the torsions from the ini file sys
if ini_zma_save_fs[-1].file.ring_torsions.exists([0]):
ring_tors_dct = ini_zma_save_fs[-1].file.ring_torsions.read([0])
else:
ring_tors_dct = {}
geo_path = ini_cnf_save_fs[-1].path(ini_min_locs)
ioprinter.initial_geom_path('Sampling started', geo_path)
# Run the sampling
conformer.ring_conformer_sampling(zma,
spc_info,
mod_thy_info,
cnf_run_fs,
cnf_save_fs,
script_str,
overwrite,
nsamp_par=mc_nsamp,
ring_tors_dct=ring_tors_dct,
zrxn=zrxn,
two_stage=two_stage,
retryfail=retryfail,
**kwargs)
elif job == 'opt':
cnf_range = es_keyword_dct['cnf_range']
hbond_cutoffs = spc_dct_i['hbond_cutoffs']
cnf_sort_info_lst = _sort_info_lst(es_keyword_dct['sort'], thy_dct,
spc_info)
# Set up the run scripts
script_str, kwargs = qchem_params(method_dct,
elstruct.Job.OPTIMIZATION)
rng_cnf_locs_lst, _ = filesys.mincnf.conformer_locators(
cnf_save_fs, mod_thy_info, cnf_range='all', nprocs=nprocs)
ini_rng_cnf_locs_lst, _ = filesys.mincnf.conformer_locators(
ini_cnf_save_fs,
mod_ini_thy_info,
cnf_range=cnf_range,
sort_info_lst=cnf_sort_info_lst,
hbond_cutoffs=hbond_cutoffs,
print_enes=True,
nprocs=nprocs)
# Truncate the list of the ini confs
uni_rng_locs_lst, uni_cnf_locs_lst = conformer.unique_fs_ring_confs(
cnf_save_fs, rng_cnf_locs_lst, ini_cnf_save_fs,
ini_rng_cnf_locs_lst)
# ioprinter.debug_message(
# 'uni lst that has no similar ring', uni_rng_locs_lst)
# ioprinter.debug_message(
# 'uni lst that has similar ring', uni_cnf_locs_lst)
for locs in uni_rng_locs_lst:
rid, cid = locs
# Obtain the zma from ini loc
ini_cnf_save_path = ini_cnf_save_fs[-1].path(locs)
ini_zma_save_fs = autofile.fs.zmatrix(ini_cnf_save_path)
zma = ini_zma_save_fs[-1].file.zmatrix.read((0, ))
# Make the ring filesystem
conformer.single_conformer(zma,
spc_info,
mod_thy_info,
cnf_run_fs,
cnf_save_fs,
script_str,
overwrite,
retryfail=retryfail,
zrxn=zrxn,
use_locs=locs,
**kwargs)
for locs in uni_cnf_locs_lst:
ini_locs, rid = locs
# Obtain the zma from ini loc
ini_cnf_save_path = ini_cnf_save_fs[-1].path(ini_locs)
ini_zma_save_fs = autofile.fs.zmatrix(ini_cnf_save_path)
zma = ini_zma_save_fs[-1].file.zmatrix.read((0, ))
# obtain conformer filesys associated with ring at the runlevel
cid = autofile.schema.generate_new_conformer_id()
conformer.single_conformer(zma,
spc_info,
mod_thy_info,
cnf_run_fs,
cnf_save_fs,
script_str,
overwrite,
retryfail=retryfail,
zrxn=zrxn,
use_locs=(rid, cid),
**kwargs)
# print all geometres within cnfrange
rng_cnf_locs_lst, _ = filesys.mincnf.conformer_locators(
cnf_save_fs,
mod_thy_info,
cnf_range=cnf_range,
sort_info_lst=cnf_sort_info_lst,
hbond_cutoffs=hbond_cutoffs,
nprocs=nprocs)
for locs in rng_cnf_locs_lst:
geo = cnf_save_fs[-1].file.geometry.read(locs)
ioprinter.geometry(geo)
elif job in ('energy', 'grad', 'hess', 'vpt2', 'prop'):
cnf_range = es_keyword_dct['cnf_range']
hbond_cutoffs = spc_dct_i['hbond_cutoffs']
cnf_sort_info_lst = _sort_info_lst(es_keyword_dct['sort'], thy_dct,
spc_info)
user_conf_ids = spc_dct_i.get('conf_id')
if user_conf_ids is None:
ini_rng_cnf_locs_lst, _ = filesys.mincnf.conformer_locators(
ini_cnf_save_fs,
mod_ini_thy_info,
cnf_range=cnf_range,
sort_info_lst=cnf_sort_info_lst,
hbond_cutoffs=hbond_cutoffs,
print_enes=True,
nprocs=nprocs)
else:
print(f'Using user specified conformer IDs: {user_conf_ids}')
ini_rng_cnf_locs_lst = (user_conf_ids, )
# Check if locs exist, kill if it doesn't
if not ini_rng_cnf_locs_lst:
ioprinter.error_message('No min-energy conformer found for level:')
else:
# Set up the run scripts
script_str, kwargs = qchem_params(method_dct)
# Grab frequencies for the reference, print ref freqs
if job == 'hess':
if ini_cnf_save_fs[-1].file.harmonic_frequencies.exists(
ini_rng_cnf_locs_lst[0]):
frq = ini_cnf_save_fs[-1].file.harmonic_frequencies.read(
ini_rng_cnf_locs_lst[0])
ref_val = frq
else:
ref_val = None
if ref_val is not None and zrxn is not None:
ref_path = cnf_save_fs[-1].path(ini_rng_cnf_locs_lst[0])
print('Found reference frequencies for saddle-point '
f'checks for conformer at\n {ref_path}')
ioprinter.frequencies(ref_val)
else:
ref_val = None
# Run the job over all the conformers requested by the user
print('Going over all requested conformers for task...\n')
for ini_locs in ini_rng_cnf_locs_lst:
ini_cnf_run_fs[-1].create(ini_locs)
geo_save_path = ini_cnf_save_fs[-1].path(ini_locs)
ini_zma_save_fs = autofile.fs.zmatrix(geo_save_path)
print('Running task for geometry at ', geo_save_path)
geo = ini_cnf_save_fs[-1].file.geometry.read(ini_locs)
zma = ini_zma_save_fs[-1].file.zmatrix.read((0, ))
ES_TSKS[job](zma,
geo,
spc_info,
mod_thy_info,
ini_cnf_run_fs,
ini_cnf_save_fs,
ini_locs,
run_prefix,
script_str,
overwrite,
zrxn=zrxn,
retryfail=retryfail,
method_dct=method_dct,
ref_val=ref_val,
**kwargs)
print('\n === FINISHED CONF ===\n')