def fs_confs_dict(cnf_save_fs, cnf_save_locs_lst, ini_cnf_save_fs,
ini_cnf_save_locs_lst):
""" Assess which structures from the cnf_save_fs currently exist
within the ini_cnf_save_fs. Generate a dictionary to connect
the two
"""
match_dct = {}
for ini_locs in ini_cnf_save_locs_lst:
match_dct[ini_locs] = None
# Loop over structs in cnf_save, see if they match the current struct
inigeo = ini_cnf_save_fs[-1].file.geometry.read(ini_locs)
inizma = automol.geom.zmatrix(inigeo)
# inizma = ini_cnf_save_fs[-1].file.zmatrix.read(ini_locs)
ini_cnf_save_path = ini_cnf_save_fs[-1].path(ini_locs)
ioprinter.checking('structures', ini_cnf_save_path)
for locs in cnf_save_locs_lst:
geo = cnf_save_fs[-1].file.geometry.read(locs)
zma = automol.geom.zmatrix(geo)
if automol.zmat.almost_equal(inizma,
zma,
dist_rtol=0.1,
ang_atol=.4):
cnf_save_path = cnf_save_fs[-1].path(locs)
ioprinter.info_message(
'- Similar structure found at {}'.format(cnf_save_path))
match_dct[ini_locs] = locs
break
return match_dct
def saddle_point_checker(imags):
""" run things for checking Hessian
"""
big_imag, kick_imag = 0, 0
ioprinter.checking('the imaginary frequencies of the saddle point...')
if len(imags) < 1:
ioprinter.warning_message('No imaginary modes for geometry')
status = 'fail'
else:
if len(imags) > 1:
ioprinter.warning_message('More than one imaginary mode for geometry')
for idx, imag in enumerate(imags):
if imag <= 50.0:
ioprinter.warning_message('Mode {} {} cm-1 is low,'.format(str(idx+1), imag))
elif 50.0 < imag <= 200.0:
lowstr = 'Mode {} {} cm-1 is low,'.format(str(idx+1), imag)
ioprinter.warning_message(lowstr + 'need a kickoff procedure to remove')
kick_imag += 1
else:
ioprinter.debug_message('Mode {} {} cm-1 likely fine,'.format(str(idx+1), imag))
big_imag += 1
if big_imag > 1:
ioprinter.warning_message('WARNING: More than one imaginary mode for geometry')
if kick_imag >= 1:
ioprinter.debug_message('Will kickoff to get saddle point')
status = 'kickoff'
elif big_imag == 1:
status = 'success'
return status
def saddle_point_checker(imags):
""" run things for checking Hessian
"""
big_imag, kick_imag = 0, 0
ioprinter.checking('the imaginary frequencies of the saddle point...')
if len(imags) < 1:
ioprinter.warning_message('No imaginary modes for geometry')
status = 'fail'
else:
if len(imags) > 1:
ioprinter.warning_message(
'More than one imaginary mode for geometry')
status = 'fail'
for idx, imag in enumerate(imags):
if imag <= 50.0:
ioprinter.warning_message(
f'Mode {str(idx+1)} {imag} cm-1 is low,')
elif 50.0 < imag <= 200.0:
lowstr = f'Mode {str(idx+1)} {imag} cm-1 is low,'
ioprinter.debug_message(
lowstr + ' check mode and see if it should be corrected')
big_imag += 1
# Adding to the kick counter kills code for good TSs
# Some addditions of big species have low mode of this
# ioprinter.warning_message(
# lowstr + 'need a kickoff procedure to remove')
# kick_imag += 1
else:
ioprinter.debug_message(
f'Mode {str(idx+1)} {imag} cm-1 likely fine')
big_imag += 1
if big_imag > 1:
ioprinter.warning_message(
'More than one imaginary mode for geometry')
if kick_imag >= 1:
ioprinter.debug_message('Will kickoff to get saddle point')
status = 'kickoff'
else:
status = 'failure'
elif big_imag == 1:
status = 'success'
elif big_imag == 0:
status = 'failure'
ioprinter.warning_message('Did not find any appropriate modes')
return status
def _check_freqs(imags):
""" Check the magnitude of the imaginary modes.
"""
big_imag, kick_imag = 0, 0
ioprinter.checking('the imaginary frequencies of the saddle point...')
if len(imags) < 1:
ioprinter.warning_message('No imaginary modes for geometry')
status = 'fail'
else:
if len(imags) > 1:
ioprinter.warning_message(
'More than one imaginary mode for geometry')
status = 'fail'
for idx, imag in enumerate(imags):
if imag <= 50.0:
ioprinter.warning_message(f'Mode {idx+1} {imag} cm-1 is low,')
elif 50.0 < imag <= 200.0:
lowstr = f'Mode {idx+1} {imag} cm-1 is low,'
ioprinter.debug_message(
lowstr + ' check mode and see if it should be corrected')
big_imag += 1
# Adding to the kick counter kills code for good TSs
# Some addditions of big species have low mode of this
# ioprinter.warning_message(
# lowstr + 'need a kickoff procedure to remove')
# kick_imag += 1
else:
ioprinter.debug_message(
f'Mode {idx+1} {imag} cm-1 is likely fine,')
big_imag += 1
if big_imag > 1:
ioprinter.warning_message(
'More than one imaginary mode for geometry')
if kick_imag >= 1:
ioprinter.debug_message('Will kickoff to get saddle point')
status = 'kick'
else:
status = False
elif big_imag == 1:
status = True
elif big_imag == 0:
status = False
return status
def unique_fs_confs(cnf_save_fs, cnf_save_locs_lst, ini_cnf_save_fs,
ini_cnf_save_locs_lst):
""" Assess which structures from the cnf_save_fs currently exist
within the ini_cnf_save_fs. Generate a lst of unique structures
in the ini_cnf_save_fs.
"""
uni_ini_cnf_save_locs = []
for ini_locs in ini_cnf_save_locs_lst:
# Initialize variable to see if initial struct is found
found = False
# Loop over structs in cnf_save, see if they match the current struct
inigeo = ini_cnf_save_fs[-1].file.geometry.read(ini_locs)
inizma = automol.geom.zmatrix(inigeo)
# inizma = ini_cnf_save_fs[-1].file.zmatrix.read(ini_locs)
ini_cnf_save_path = ini_cnf_save_fs[-1].path(ini_locs)
ioprinter.checking('structures', ini_cnf_save_path)
for locs in cnf_save_locs_lst:
geo = cnf_save_fs[-1].file.geometry.read(locs)
zma = automol.geom.zmatrix(geo)
# zma = cnf_save_fs[-1].file.zmatrix.read(locs)
if automol.zmat.almost_equal(inizma,
zma,
dist_rtol=0.1,
ang_atol=.4):
cnf_save_path = cnf_save_fs[-1].path(locs)
ioprinter.info_message(
'- Similar structure found at {}'.format(cnf_save_path))
found = True
break
# If no match was found, add to unique locs lst
if not found:
uni_ini_cnf_save_locs.append(ini_locs)
return uni_ini_cnf_save_locs
def unique_fs_ring_confs(cnf_save_fs, cnf_locs_lst, ini_cnf_save_fs,
ini_cnf_locs_lst):
""" Assess which structures from the cnf_save_fs currently exist
within the ini_cnf_save_fs. Generate a lst of unique structures
in the ini_cnf_save_fs.
"""
uni_ini_rng_locs = []
uni_ini_cnf_locs = []
rng_dct = {}
for ini_locs in ini_cnf_locs_lst:
ini_rid, _ = ini_locs
if ini_rid in [locs[0] for locs in uni_ini_rng_locs]:
uni_ini_rng_locs.append(ini_locs)
continue
inigeo = ini_cnf_save_fs[-1].file.geometry.read(ini_locs)
ini_cnf_save_path = ini_cnf_save_fs[-1].path(ini_locs)
inizma = automol.geom.zmatrix(inigeo)
ioprinter.checking('structures', ini_cnf_save_path)
# Check to see if a similar ring pucker is in the runlvl filesystem
found_rid = None
if ini_rid in rng_dct:
found_rid = rng_dct[ini_rid]
else:
frag_ini_geo = automol.geom.fragment_ring_geo(inigeo)
if frag_ini_geo is not None:
frag_ini_zma = automol.geom.zmatrix(frag_ini_geo)
skip_trid = []
for tlocs in cnf_save_fs[-1].existing():
trid, _ = tlocs
if frag_ini_geo is None:
found_rid = trid
rng_dct[ini_rid] = trid
break
if trid in skip_trid:
continue
geo = cnf_save_fs[-1].file.geometry.read(tlocs)
frag_geo = automol.geom.fragment_ring_geo(geo)
frag_zma = automol.geom.zmatrix(frag_geo)
if automol.zmat.almost_equal(frag_ini_zma,
frag_zma,
dist_rtol=0.1,
ang_atol=.4):
rng_dct[ini_rid] = trid
found_rid = trid
break
skip_trid.append(trid)
# If no similar runlvl ring pucker, then add it to unique rings
if found_rid is None:
uni_ini_rng_locs.append(ini_locs)
continue
# If similar ring is found,
# check actual conformers under that ring orientation
found = False
for locs in cnf_locs_lst:
rid, _ = locs
if rid != found_rid:
continue
cnf_save_path = cnf_save_fs[-1].path(locs)
geo = cnf_save_fs[-1].file.geometry.read(locs)
zma = automol.geom.zmatrix(geo)
if automol.zmat.almost_equal(inizma,
zma,
dist_rtol=0.1,
ang_atol=.4):
ioprinter.info_message(
'- Similar structure found at {}'.format(cnf_save_path))
found = True
break
# If no match was found, add to unique locs lst
if not found:
uni_ini_cnf_locs.append((ini_locs, found_rid))
return uni_ini_rng_locs, uni_ini_cnf_locs