def run_gradient(zma,
geo,
spc_info,
thy_info,
geo_run_fs,
geo_save_fs,
locs,
run_prefix,
script_str,
overwrite,
zrxn=None,
retryfail=True,
method_dct=None,
ref_val=None,
**kwargs):
""" Determine the gradient for the geometry in the given location
"""
# Set unneeded vals
_, _, _, _ = zrxn, method_dct, ref_val, run_prefix
geo_run_path = geo_run_fs[-1].path(locs)
geo_save_path = geo_save_fs[-1].path(locs)
# Set input geom
if geo is not None:
job_geo = geo
else:
job_geo = automol.zmat.geometry(zma)
is_atom = automol.geom.is_atom(job_geo)
if not is_atom:
if _json_database(geo_save_path):
exists = geo_save_fs[-1].json.gradient.exists(locs)
else:
exists = geo_save_fs[-1].file.gradient.exists(locs)
if not exists:
ioprinter.info_message(
'No gradient found in save filesys. Running gradient...')
_run = True
elif overwrite:
ioprinter.info_message(
'User specified to overwrite gradient with new run...')
_run = True
else:
_run = False
if _run:
run_fs = autofile.fs.run(geo_run_path)
success, ret = es_runner.execute_job(
job=elstruct.Job.GRADIENT,
script_str=script_str,
run_fs=run_fs,
geo=job_geo,
spc_info=spc_info,
thy_info=thy_info,
zrxn=zrxn,
overwrite=overwrite,
retryfail=retryfail,
**kwargs,
)
if success:
inf_obj, inp_str, out_str = ret
if is_atom:
grad = ()
else:
ioprinter.info_message(
" - Reading gradient from output...")
grad = elstruct.reader.gradient(inf_obj.prog, out_str)
ioprinter.info_message(" - Saving gradient...")
if _json_database(geo_save_path):
geo_save_fs[-1].json.gradient_info.write(inf_obj, locs)
geo_save_fs[-1].json.gradient_input.write(
inp_str, locs)
geo_save_fs[-1].json.gradient.write(grad, locs)
else:
geo_save_fs[-1].file.gradient_info.write(inf_obj, locs)
geo_save_fs[-1].file.gradient_input.write(
inp_str, locs)
geo_save_fs[-1].file.gradient.write(grad, locs)
ioprinter.save_geo(geo_save_path)
else:
ioprinter.existing_path('Gradient', geo_save_path)
else:
ioprinter.info_message('Species is an atom. Skipping gradient task.')
def run_prop(zma,
geo,
spc_info,
thy_info,
geo_run_fs,
geo_save_fs,
locs,
run_prefix,
script_str,
overwrite,
zrxn=None,
retryfail=True,
method_dct=None,
ref_val=None,
**kwargs):
""" Determine the properties in the given location
"""
# Set unneeded vals
_, _, _, _ = zrxn, method_dct, ref_val, run_prefix
# Set input geom
geo_run_path = geo_run_fs[-1].path(locs)
geo_save_path = geo_save_fs[-1].path(locs)
if geo is not None:
job_geo = geo
else:
job_geo = automol.zmat.geometry(zma)
if _json_database(geo_save_path):
dmom_exists = geo_save_fs[-1].json.dipole_moment.exists(locs)
polar_exists = geo_save_fs[-1].json.polarizability.exists(locs)
else:
dmom_exists = geo_save_fs[-1].file.dipole_moment.exists(locs)
polar_exists = geo_save_fs[-1].file.polarizability.exists(locs)
if not dmom_exists or not polar_exists:
ioprinter.info_message(
'Either no dipole moment or polarizability found in'
'in save filesys. Running properties...')
_run = True
elif overwrite:
ioprinter.info_message(
'User specified to overwrite property with new run...')
_run = True
else:
_run = False
if _run:
run_fs = autofile.fs.run(geo_run_path)
success, ret = es_runner.execute_job(
job=elstruct.Job.MOLPROP,
script_str=script_str,
run_fs=run_fs,
geo=job_geo,
spc_info=spc_info,
thy_info=thy_info,
zrxn=zrxn,
overwrite=overwrite,
retryfail=retryfail,
**kwargs,
)
if success:
inf_obj, _, out_str = ret
ioprinter.info_message(" - Reading dipole moment from output...")
dmom = elstruct.reader.dipole_moment(inf_obj.prog, out_str)
ioprinter.info_message(" - Reading polarizability from output...")
polar = elstruct.reader.polarizability(inf_obj.prog, out_str)
ioprinter.debug_message('dip mom', dmom)
ioprinter.debug_message('polar', polar)
ioprinter.info_message(
" - Saving dipole moment and polarizability...")
if _json_database(geo_save_path):
# geo_save_fs[-1].json.property_info.write(inf_obj, locs)
# geo_save_fs[-1].json.property_input.write(
# inp_str, locs)
geo_save_fs[-1].json.dipole_moment.write(dmom, locs)
geo_save_fs[-1].json.polarizability.write(polar, locs)
else:
# geo_save_fs[-1].file.property_info.write(inf_obj, locs)
# geo_save_fs[-1].file.property_input.write(
# inp_str, locs)
geo_save_fs[-1].file.dipole_moment.write(dmom, locs)
geo_save_fs[-1].file.polarizability.write(polar, locs)
ioprinter.save_geo(geo_save_path)
else:
ioprinter.existing_path('Dipole moment and polarizability',
geo_save_path)
def save_tau(tau_run_fs, tau_save_fs, mod_thy_info):
""" save the tau dependent geometries that have been found so far
"""
# db_style = 'jsondb'
db_style = 'directory'
if db_style == 'jsondb':
saved_locs = tau_save_fs[-1].json_existing()
saved_geos = tau_save_fs[-1].json.geometry.read_all(saved_locs)
elif db_style == 'directory':
saved_geos = [tau_save_fs[-1].file.geometry.read(locs)
for locs in tau_save_fs[-1].existing()]
if not tau_run_fs[0].exists():
ioprinter.info_message("No tau geometries to save. Skipping...")
else:
if db_style == 'jsondb':
save_info = [[], [], [], [], []]
sp_save_info = [[], [], [], [], []]
for locs in tau_run_fs[-1].existing():
run_path = tau_run_fs[-1].path(locs)
run_fs = autofile.fs.run(run_path)
save_path = tau_save_fs[-1].root.path()
ioprinter.reading("tau run", run_path)
success, ret = es_runner.read_job(
job=elstruct.Job.OPTIMIZATION, run_fs=run_fs)
if success:
inf_obj, inp_str, out_str = ret
prog = inf_obj.prog
method = inf_obj.method
ene = elstruct.reader.energy(prog, method, out_str)
geo = elstruct.reader.opt_geometry(prog, out_str)
if db_style == 'directory':
ioprinter.save_geo(save_path)
tau_save_fs[-1].create(locs)
tau_save_fs[-1].file.geometry_info.write(inf_obj, locs)
tau_save_fs[-1].file.geometry_input.write(inp_str, locs)
tau_save_fs[-1].file.energy.write(ene, locs)
tau_save_fs[-1].file.geometry.write(geo, locs)
# Saving the energy to a SP filesystem
save_path = tau_save_fs[-1].path(locs)
ioprinter.save_energy(save_path)
sp_save_fs = autofile.fs.single_point(save_path)
sp_save_fs[-1].create(mod_thy_info[1:4])
sp_save_fs[-1].file.input.write(inp_str, mod_thy_info[1:4])
sp_save_fs[-1].file.info.write(inf_obj, mod_thy_info[1:4])
sp_save_fs[-1].file.energy.write(ene, mod_thy_info[1:4])
elif db_style == 'jsondb':
# tau_save_fs[-1].json.geometry_info.write(inf_obj, locs)
# tau_save_fs[-1].json.geometry_input.write(inp_str, locs)
# tau_save_fs[-1].json.energy.write(ene, locs)
# tau_save_fs[-1].json.geometry.write(geo, locs)
ioprinter.info_message(
" - Saving energy and geo of unique geometry...")
save_info[0].append(locs)
save_info[1].append(inf_obj)
save_info[2].append(inp_str)
save_info[3].append(ene)
save_info[4].append(geo)
sp_save_fs = autofile.fs.single_point(
save_path, json_layer=locs)
sp_save_info[0].append(sp_save_fs)
sp_save_info[1].append(mod_thy_info[1:4])
sp_save_info[2].append(inp_str)
sp_save_info[3].append(inf_obj)
sp_save_info[4].append(ene)
sp_save_fs[-1].json.input.write(inp_str, mod_thy_info[1:4])
sp_save_fs[-1].json.info.write(inf_obj, mod_thy_info[1:4])
sp_save_fs[-1].json.energy.write(ene, mod_thy_info[1:4])
saved_geos.append(geo)
if db_style == 'jsondb':
tau_save_fs[-1].json_create()
tau_save_fs[-1].json.geometry_info.write_all(
save_info[1], save_info[0])
tau_save_fs[-1].json.geometry_input.write_all(
save_info[2], save_info[0])
tau_save_fs[-1].json.energy.write_all(
save_info[3], save_info[0])
tau_save_fs[-1].json.geometry.write_all(
save_info[4], save_info[0])
for i, sp_save_fs_i in enumerate(sp_save_info[0]):
sp_save_fs_i[-1].json.input.write(
sp_save_info[2][i], sp_save_info[1][i])
sp_save_fs_i[-1].json.info.write(
sp_save_info[3][i], sp_save_info[1][i])
sp_save_fs_i[-1].json.energy.write(
sp_save_info[4][i], sp_save_info[1][i])
# update the tau trajectory file
filesys.mincnf.traj_sort(tau_save_fs, mod_thy_info)