def run_sadpt(spc_dct, tsname, method_dct, es_keyword_dct, thy_inf_dct,
runfs_dct, savefs_dct):
""" find a transition state
"""
# Get objects for the calculations
ts_dct = spc_dct[tsname]
# Find the TS
cnf_info = savefs_dct['runlvl_cnf_fs']
cnf_save_fs, cnf_save_locs = cnf_info
overwrite = es_keyword_dct['overwrite']
if not cnf_save_locs[0]:
print('No transition state found in filesys',
'at {} level...'.format(es_keyword_dct['runlvl']),
'Proceeding to find it...')
_run = True
elif overwrite:
print('User specified to overwrite energy with new run...')
_run = True
else:
print('TS found and saved previously in ',
cnf_save_fs[-1].path(cnf_save_locs))
_run = False
if _run:
# split below in guess, scan
guess_zmas = sadpt.generate_guess_structure(ts_dct, method_dct,
es_keyword_dct, runfs_dct,
savefs_dct)
sadpt.obtain_saddle_point(guess_zmas, ts_dct, method_dct, runfs_dct,
savefs_dct, es_keyword_dct)
def run_sadpt(spc_dct,
tsname,
method_dct,
es_keyword_dct,
thy_inf_dct,
runfs_dct,
savefs_dct,
zma_locs=(0, )):
""" find a transition state
"""
# if not _scan_finished(coord_names, coord_grids,
# scn_save_fs, constraint_dct=None):
# Get objects for the calculations
ts_dct = spc_dct[tsname]
# Assess if saddle pt exists in the filesystem at runlvl
_run = _check_filesys_for_sadpt(savefs_dct, es_keyword_dct)
if _run:
# Assess if saddle pt exists in the filesystem at inplvl for guess
guess_zmas = _check_filesys_for_guess(savefs_dct,
es_keyword_dct,
zma_locs=zma_locs)
if guess_zmas:
# Run a scan along coordinate and attempt to find max for opt
guess_zmas = sadpt.generate_guess_structure(
ts_dct, method_dct, es_keyword_dct, runfs_dct, savefs_dct)
if guess_zmas:
# Optimize the saddle point, run a hessian and save
sadpt.obtain_saddle_point(guess_zmas, ts_dct, method_dct,
runfs_dct, savefs_dct,
es_keyword_dct)
else:
# Calculate add'l data along rxn path and save
_inf_ene()
_save_traj(ts_zma, ts_dct, savefs_dct, zma_locs=zma_locs)
def _opt_by_sadpt():
"""s
"""
sadpt.obtain_saddle_point([sadpt_zma], ts_dct, method_dct, runfs_dct,
savefs_dct, es_keyword_dct)