def save_cscan(cscn_run_fs, cscn_save_fs, scn_typ,
constraint_dct, mod_thy_info, in_zma_fs=True):
""" save the scans that have been run so far
"""
if not cscn_run_fs[1].exists([constraint_dct]):
print("No scan to save. Skipping...")
else:
locs_lst = []
for locs1 in cscn_run_fs[2].existing([constraint_dct]):
if cscn_run_fs[2].exists(locs1):
for locs2 in cscn_run_fs[3].existing(locs1):
# Set run filesys
run_path = cscn_run_fs[-1].path(locs2)
run_fs = autofile.fs.run(run_path)
print("Reading from scan run at {}".format(run_path))
# Save the structure
saved = filesys.save_struct(
run_fs, cscn_save_fs, locs2, _set_job(scn_typ),
mod_thy_info, in_zma_fs=in_zma_fs)
# Add to locs lst if the structure is saved
if saved:
locs_lst.append(locs2)
else:
print("No scan to save. Skipping...")
# Build the trajectory file
if locs_lst:
_write_traj(constraint_dct, cscn_save_fs, mod_thy_info, locs_lst)
def save_scan(scn_run_fs, scn_save_fs, scn_typ,
coo_names, mod_thy_info, in_zma_fs=False):
""" save the scans that have been run so far
"""
if not scn_run_fs[1].exists([coo_names]):
print("No scan to save. Skipping...")
else:
locs_lst = []
for locs in scn_run_fs[-1].existing([coo_names]):
# Set run filesys
run_path = scn_run_fs[-1].path(locs)
run_fs = autofile.fs.run(run_path)
print("Reading from scan run at {}".format(run_path))
# Save the structure
saved = filesys.save_struct(
run_fs, scn_save_fs, locs, _set_job(scn_typ),
mod_thy_info, in_zma_fs=in_zma_fs)
# Add to locs lst if the structure is saved
if saved:
locs_lst.append(locs)
# Build the trajectory file
if locs_lst:
_write_traj(coo_names, scn_save_fs, mod_thy_info, locs_lst)
def _optimize_atom(spc_info, zma_init, mod_thy_info, thy_run_fs, cnf_save_fs,
run_fs, overwrite, opt_script_str, **opt_kwargs):
""" Deal with an atom separately
"""
geo, zma = _init_geom_opt(zma_init, spc_info, mod_thy_info, run_fs,
thy_run_fs, opt_script_str, overwrite,
**opt_kwargs)
if geo is not None and zma is not None:
locs = [autofile.schema.generate_new_conformer_id()]
job = elstruct.Job.OPTIMIZATION
filesys.save_struct(run_fs,
cnf_save_fs,
locs,
job,
mod_thy_info,
zma_locs=(0, ),
in_zma_fs=False)
conf_found = True
else:
conf_found = False
return conf_found
def _optimize_molecule(spc_info,
zma_init,
mod_thy_info,
thy_run_fs,
thy_save_fs,
cnf_save_fs,
run_fs,
opt_script_str,
overwrite,
kickoff_size=0.1,
kickoff_backward=False,
**opt_kwargs):
""" Optimize a proper geometry
"""
# Optimize the initial geometry
geo, zma = _init_geom_opt(zma_init, spc_info, mod_thy_info, run_fs,
thy_run_fs, opt_script_str, overwrite,
**opt_kwargs)
# If connected, check for imaginary modes and fix them if possible
if automol.geom.connected(geo):
# Remove the imaginary mode
geo, imag_fix_needed = _remove_imag(spc_info,
geo,
mod_thy_info,
thy_run_fs,
run_fs,
kickoff_size,
kickoff_backward,
overwrite=overwrite)
# Recheck connectivity for imag-checked geometry
if geo is not None:
conf_found = True
if automol.geom.connected(geo):
print('\nSaving structure as the first conformer...')
locs = [autofile.schema.generate_new_conformer_id()]
job = elstruct.Job.OPTIMIZATION
filesys.save_struct(run_fs,
cnf_save_fs,
locs,
job,
mod_thy_info,
zma_locs=(0, ),
in_zma_fs=False,
cart_to_zma=imag_fix_needed)
else:
print('Saving disconnected species...')
_, opt_ret = es_runner.read_job(job=elstruct.Job.OPTIMIZATION,
run_fs=run_fs)
structure.instab.write_instab(zma_init,
zma,
thy_save_fs,
mod_thy_info[1:4],
opt_ret,
zma_locs=(0, ),
save_cnf=True)
else:
print('\n No geom found...')
conf_found = False
else:
print('Saving disconnected species...')
conf_found = False
_, opt_ret = es_runner.read_job(job=elstruct.Job.OPTIMIZATION,
run_fs=run_fs)
structure.instab.write_instab(zma_init,
zma,
thy_save_fs,
mod_thy_info[1:4],
opt_ret,
zma_locs=(0, ),
save_cnf=True)
# Save geom in thy filesys if a good geom is found
if conf_found:
thy_save_fs[-1].create(mod_thy_info[1:4])
thy_save_path = thy_save_fs[-1].path(mod_thy_info[1:4])
thy_save_fs[-1].file.geometry.write(geo, mod_thy_info[1:4])
print('Saving reference geometry')
print(" - Save path: {}".format(thy_save_path))
return conf_found