def run_energy(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,
highspin=False,
ref_val=None,
**kwargs):
""" Assesses if an electronic energy exists in the CONFS/SP/THY layer
of the save filesys for a species at the specified level of theory.
If an energy does not exist, or if a user requests overwrite,
the appropriate electronic struture calculation is set-up, launched,
and then parsed within the run filesys, then that the energy and
job input is written into the save filesys.
:param zma: Z-Matrix for molecular structure to perform calculation
:type zma: automol.zmat object
:param geo: goemetry for molecular structure to perform calculation
:type geo: automol.geom object
:param spc_info:
:type spc_info:
:param thy_info:
:type thy_info:
:geo_run_fs: filesystem object for layer where structure is in RUN
:geo_run_fs: autofile.fs object
:geo_save_fs: filesystem object for layer where structure is in SAVE
:geo_save_fs: autofile.fs object
:param script_str: shell script for executing electronic structure job
:type script_str: str
:param overwrite:
"""
# Set unneeded vals to
_, _, _, _ = 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)
# Prepare unique filesystem since many energies may be under same directory
if not highspin:
sp_run_fs = autofile.fs.single_point(geo_run_path)
sp_save_fs = autofile.fs.single_point(geo_save_path)
else:
sp_run_fs = autofile.fs.high_spin(geo_run_path)
sp_save_fs = autofile.fs.high_spin(geo_save_path)
sp_run_path = sp_run_fs[-1].path(thy_info[1:4])
sp_save_path = sp_save_fs[-1].path(thy_info[1:4])
# Set input geom
if geo is not None:
job_geo = geo
else:
job_geo = zma
exists = sp_save_fs[-1].file.energy.exists(thy_info[1:4])
if not exists:
ioprinter.info_message(
'No energy found in save filesys. Running energy...')
_run = True
elif overwrite:
ioprinter.info_message(
'User specified to overwrite energy with new run...')
_run = True
else:
_run = False
if _run:
# Add options matrix for energy runs for molpro
_kwargs = copy.deepcopy(kwargs)
if thy_info[0] == 'molpro2015':
errs, optmat = es_runner.molpro_opts_mat(spc_info, geo)
_kwargs.update({'errors': errs, 'options_mat': optmat})
sp_run_fs[-1].create(thy_info[1:4])
run_fs = autofile.fs.run(sp_run_path)
success, ret = es_runner.execute_job(
job=elstruct.Job.ENERGY,
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
ioprinter.info_message(" - Reading energy from output...")
ene = elstruct.reader.energy(inf_obj.prog, inf_obj.method, out_str)
ioprinter.energy(ene)
sp_save_fs[-1].create(thy_info[1:4])
sp_save_fs[-1].file.input.write(inp_str, thy_info[1:4])
sp_save_fs[-1].file.info.write(inf_obj, thy_info[1:4])
sp_save_fs[-1].file.energy.write(ene, thy_info[1:4])
ioprinter.save_energy(sp_save_path)
else:
ioprinter.existing_path('Energy', sp_save_path)
ene = sp_save_fs[-1].file.energy.read(thy_info[1:4])
ioprinter.energy(ene)
ioprinter.info_message('')
def run_energy(zma,
geo,
spc_info,
thy_info,
geo_save_fs,
geo_run_path,
geo_save_path,
locs,
script_str,
overwrite,
retryfail=True,
highspin=False,
**kwargs):
""" Assesses if an electronic energy exists in the CONFS/SP/THY layer
of the save filesys for a species at the specified level of theory.
If an energy does not exist, or if a user requests overwrite,
the appropriate electronic struture calculation is set-up, launched,
and then parsed within the run filesys, then that the energy and
job input is written into the save filesys.
:param zma: Z-Matrix for species/TS conformer
:type zma: automol Z-Matrix data structure
"""
# geo_save_fs and locs unneeded for this
_, _ = geo_save_fs, locs
# Prepare unique filesystem since many energies may be under same directory
if not highspin:
sp_run_fs = autofile.fs.single_point(geo_run_path)
sp_save_fs = autofile.fs.single_point(geo_save_path)
else:
sp_run_fs = autofile.fs.high_spin(geo_run_path)
sp_save_fs = autofile.fs.high_spin(geo_save_path)
sp_run_fs[-1].create(thy_info[1:4])
sp_run_path = sp_run_fs[-1].path(thy_info[1:4])
sp_save_fs[-1].create(thy_info[1:4])
sp_save_path = sp_save_fs[-1].path(thy_info[1:4])
run_fs = autofile.fs.run(sp_run_path)
# Set input geom
if geo is not None:
job_geo = geo
else:
job_geo = zma
exists = sp_save_fs[-1].file.energy.exists(thy_info[1:4])
# _run = need_job((exists, 'energy'), overwrite)
if not exists:
ioprinter.info_message(
'No energy found in save filesys. Running energy...')
_run = True
elif overwrite:
ioprinter.info_message(
'User specified to overwrite energy with new run...')
_run = True
else:
_run = False
if _run:
# Add options matrix for energy runs for molpro
if thy_info[0] == 'molpro2015':
errs, optmat = es_runner.molpro_opts_mat(spc_info, geo)
else:
errs = ()
optmat = ()
success, ret = es_runner.execute_job(
job=elstruct.Job.ENERGY,
script_str=script_str,
run_fs=run_fs,
geo=job_geo,
spc_info=spc_info,
thy_info=thy_info,
errors=errs,
options_mat=optmat,
overwrite=overwrite,
retryfail=retryfail,
**kwargs,
)
if success:
inf_obj, inp_str, out_str = ret
ioprinter.info_message(" - Reading energy from output...")
ene = elstruct.reader.energy(inf_obj.prog, inf_obj.method, out_str)
ioprinter.energy(ene)
sp_save_fs[-1].file.input.write(inp_str, thy_info[1:4])
sp_save_fs[-1].file.info.write(inf_obj, thy_info[1:4])
sp_save_fs[-1].file.energy.write(ene, thy_info[1:4])
ioprinter.save_energy(sp_save_path)
else:
ioprinter.existing_path('Energy', sp_save_path)
ene = sp_save_fs[-1].file.energy.read(thy_info[1:4])
ioprinter.energy(ene)
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)
def run_energy(zma,
geo,
spc_info,
thy_info,
geo_save_fs,
geo_run_path,
geo_save_path,
locs,
script_str,
overwrite,
retryfail=True,
highspin=False,
**kwargs):
""" Find the energy for the given structure
"""
# geo_save_fs and locs unneeded for this
_, _ = geo_save_fs, locs
# Prepare unique filesystem since many energies may be under same directory
if not highspin:
sp_run_fs = autofile.fs.single_point(geo_run_path)
sp_save_fs = autofile.fs.single_point(geo_save_path)
else:
sp_run_fs = autofile.fs.high_spin(geo_run_path)
sp_save_fs = autofile.fs.high_spin(geo_save_path)
sp_run_fs[-1].create(thy_info[1:4])
sp_run_path = sp_run_fs[-1].path(thy_info[1:4])
sp_save_fs[-1].create(thy_info[1:4])
sp_save_path = sp_save_fs[-1].path(thy_info[1:4])
run_fs = autofile.fs.run(sp_run_path)
# Set input geom
if geo is not None:
job_geo = geo
else:
job_geo = zma
exists = sp_save_fs[-1].file.energy.exists(thy_info[1:4])
# _run = need_job((exists, 'energy'), overwrite)
if not exists:
ioprinter.info_message(
'No energy found in save filesys. Running energy...')
_run = True
elif overwrite:
ioprinter.info_message(
'User specified to overwrite energy with new run...')
_run = True
else:
_run = False
if _run:
# Add options matrix for energy runs for molpro
if thy_info[0] == 'molpro2015':
errs, optmat = es_runner.molpro_opts_mat(spc_info, geo)
else:
errs = ()
optmat = ()
success, ret = es_runner.execute_job(
job='energy',
script_str=script_str,
run_fs=run_fs,
geo=job_geo,
spc_info=spc_info,
thy_info=thy_info,
errors=errs,
options_mat=optmat,
overwrite=overwrite,
retryfail=retryfail,
**kwargs,
)
if success:
inf_obj, inp_str, out_str = ret
ioprinter.info_message(" - Reading energy from output...")
ene = elstruct.reader.energy(inf_obj.prog, inf_obj.method, out_str)
ioprinter.energy(ene)
sp_save_fs[-1].file.input.write(inp_str, thy_info[1:4])
sp_save_fs[-1].file.info.write(inf_obj, thy_info[1:4])
sp_save_fs[-1].file.energy.write(ene, thy_info[1:4])
ioprinter.save_energy(sp_save_path)
else:
ioprinter.existing_path('Energy', sp_save_path)
ene = sp_save_fs[-1].file.energy.read(thy_info[1:4])
ioprinter.energy(ene)