def reagent_energies(save_prefix, rgt_ichs, rgt_chgs, rgt_muls, sp_thy_info,
geo_thy_info):
""" reagent energies """
enes = []
for rgt_ich, rgt_chg, rgt_mul in zip(rgt_ichs, rgt_chgs, rgt_muls):
# Set filesys
spc_save_fs = autofile.fs.species(save_prefix)
rgt_info = [rgt_ich, rgt_chg, rgt_mul]
spc_save_path = spc_save_fs[-1].path(rgt_info)
mod_geo_thy_info = modify_orb_restrict(rgt_info, geo_thy_info)
mod_sp_thy_info = modify_orb_restrict(rgt_info, sp_thy_info)
thy_save_fs = autofile.fs.theory(spc_save_path)
thy_save_path = thy_save_fs[-1].path(mod_geo_thy_info[1:4])
cnf_save_fs = autofile.fs.conformer(thy_save_path)
min_cnf_locs, _ = min_energy_conformer_locators(
cnf_save_fs, mod_geo_thy_info)
# Read energy
ene = None
if min_cnf_locs:
cnf_path = cnf_save_fs[-1].path(min_cnf_locs)
sp_fs = autofile.fs.single_point(cnf_path)
if sp_fs[-1].file.energy.exists(mod_sp_thy_info[1:4]):
ene = sp_fs[-1].file.energy.read(mod_sp_thy_info[1:4])
enes.append(ene)
if any(ene is None for ene in enes):
enes = None
return enes
def set_model_filesys(spc_dct_i, level, run_prefix, save_prefix, saddle):
""" Gets filesystem objects for reading many calculations
"""
# Set the spc_info
spc_info = finf.get_spc_info(spc_dct_i)
# Set some path stuff
if saddle:
save_path = spc_dct_i['rxn_fs'][3]
run_path = spc_dct_i['rxn_fs'][2]
else:
spc_save_fs = autofile.fs.species(save_prefix)
spc_save_fs[-1].create(spc_info)
save_path = spc_save_fs[-1].path(spc_info)
spc_run_fs = autofile.fs.species(run_prefix)
spc_run_fs[-1].create(spc_info)
run_path = spc_run_fs[-1].path(spc_info)
# Set theory filesystem used throughout
thy_save_fs = autofile.fs.theory(save_path)
thy_run_fs = autofile.fs.theory(run_path)
# Set the level for the model
levelp = finf.modify_orb_restrict(spc_info, level)
# Get the save fileystem path
save_path = thy_save_fs[-1].path(levelp[1:4])
run_path = thy_run_fs[-1].path(levelp[1:4])
thy_run_fs[-1].create(levelp[1:4])
if saddle:
save_fs = autofile.fs.transition_state(save_path)
save_fs[0].create()
save_path = save_fs[0].path()
run_fs = autofile.fs.transition_state(run_path)
run_fs[0].create()
run_path = run_fs[0].path()
# Get the fs object and the locs
cnf_run_fs = autofile.fs.conformer(run_path)
cnf_save_fs = autofile.fs.conformer(save_path)
min_cnf_locs, cnf_save_path = mincnf.min_energy_conformer_locators(
cnf_save_fs, levelp)
# Get the save path for the conformers
# if min_cnf_locs:
# cnf_save_path = cnf_save_fs[-1].path(min_cnf_locs)
# else:
# cnf_save_path = ''
return [cnf_save_fs, cnf_save_path, min_cnf_locs, save_path, cnf_run_fs]
def rpath_ref_idx(ts_dct, scn_vals, coord_name, scn_prefix,
ene_info1, ene_info2):
""" Get the reference energy along a reaction path
"""
# Set up the filesystem
zma_fs = autofile.fs.manager(scn_prefix, 'ZMATRIX')
zma_path = zma_fs[-1].path([0])
scn_fs = autofile.fs.scan(zma_path)
ene_info1 = ene_info1[1][0][1]
ene_info2 = ene_info2[0]
print('mod_eneinf1', ene_info1)
print('mod_eneinf2', ene_info2)
mod_ene_info1 = finf.modify_orb_restrict(
finf.get_spc_info(ts_dct), ene_info1)
mod_ene_info2 = finf.modify_orb_restrict(
finf.get_spc_info(ts_dct), ene_info2)
ene1, ene2, ref_val = None, None, None
for val in reversed(scn_vals):
locs = [[coord_name], [val]]
path = scn_fs[-1].path(locs)
hs_fs = autofile.fs.high_spin(path)
if hs_fs[-1].file.energy.exists(mod_ene_info1[1:4]):
ene1 = hs_fs[-1].file.energy.read(mod_ene_info1[1:4])
if hs_fs[-1].file.energy.exists(mod_ene_info2[1:4]):
ene2 = hs_fs[-1].file.energy.read(mod_ene_info2[1:4])
if ene1 is not None and ene2 is not None:
print('found', val)
ref_val = val
break
if ref_val is not None:
scn_idx = scn_vals.index(ref_val)
return scn_idx, ene1, ene2
def get_geos(spcs, spc_dct, ini_thy_info, save_prefix, run_prefix,
kickoff_size, kickoff_backward):
"""get geos for reactants and products using the initial level of theory
"""
spc_geos = []
cnf_save_fs_lst = []
for spc in spcs:
spc_info = [
spc_dct[spc]['inchi'], spc_dct[spc]['charge'], spc_dct[spc]['mult']
]
ini_thy_lvl = modify_orb_restrict(spc_info, ini_thy_info)
spc_save_fs = autofile.fs.species(save_prefix)
spc_save_fs[-1].create(spc_info)
spc_save_path = spc_save_fs[-1].path(spc_info)
ini_thy_save_fs = autofile.fs.theory(spc_save_path)
ini_thy_save_path = ini_thy_save_fs[-1].path(ini_thy_lvl[1:4])
cnf_save_fs = autofile.fs.conformer(ini_thy_save_path)
cnf_save_fs_lst.append(cnf_save_fs)
min_cnf_locs, _ = min_energy_conformer_locators(
cnf_save_fs, ini_thy_lvl)
# print('min_cnf_locs test:', min_cnf_locs)
if min_cnf_locs:
geo = cnf_save_fs[-1].file.geometry.read(min_cnf_locs)
# else:
# spc_run_fs = autofile.fs.species(run_prefix)
# spc_run_fs[-1].create(spc_info)
# spc_run_path = spc_run_fs[-1].path(spc_info)
# ini_thy_run_fs = autofile.fs.theory(spc_run_path)
# ini_thy_run_path = ini_thy_run_fs[-1].path(ini_thy_lvl[1:4])
# cnf_run_fs = autofile.fs.conformer(ini_thy_run_path)
# run_fs = autofile.fs.run(ini_thy_run_path)
# run_fs[0].create()
# geo = geom.reference_geometry(
# spc_dct[spc], spc_info,
# ini_thy_lvl, ini_thy_lvl,
# ini_thy_run_fs, ini_thy_save_fs,
# ini_thy_save_fs,
# cnf_run_fs, cnf_save_fs,
# run_fs,
# opt_script_str, overwrite,
# kickoff_size=kickoff_size,
# kickoff_backward=kickoff_backward)
spc_geos.append(geo)
return spc_geos, cnf_save_fs_lst
def electronic_energy(spc_dct_i, pf_filesystems, pf_levels):
""" get high level energy at low level optimized geometry
"""
print('- Calculating electronic energy')
# spc_dct_i = spc_dct[spc_name]
spc_info = finf.get_spc_info(spc_dct_i)
# Get the harmonic filesys information
[_, cnf_path, _, _, _] = pf_filesystems['harm']
# Get the electronic energy levels
ene_levels = pf_levels['ene'][1]
# Read the energies from the filesystem
e_elec = None
if os.path.exists(cnf_path):
e_elec = 0.0
# print('lvls', ene_levels)
for (coeff, level) in ene_levels:
# Build SP filesys
mod_thy_info = finf.modify_orb_restrict(spc_info, level)
sp_save_fs = autofile.fs.single_point(cnf_path)
sp_save_fs[-1].create(mod_thy_info[1:4])
# Read the energy
sp_path = sp_save_fs[-1].path(mod_thy_info[1:4])
if os.path.exists(sp_path):
print('Energy read from path {}'.format(sp_path))
ene = sp_save_fs[-1].file.energy.read(mod_thy_info[1:4])
e_elec += (coeff * ene)
else:
print('No energy at path')
e_elec = None
break
else:
print('No conformer to calculate the energy')
return e_elec
def set_rpath_filesys(ts_dct, level):
""" Gets filesystem objects for reading many calculations
"""
# Set the spc_info
spc_info = finf.get_spc_info(ts_dct)
# Set some path stuff
save_path = ts_dct['rxn_fs'][3]
run_path = ts_dct['rxn_fs'][2]
# Set theory filesystem used throughout
thy_save_fs = autofile.fs.theory(save_path)
thy_run_fs = autofile.fs.theory(run_path)
levelp = finf.modify_orb_restrict(spc_info, level[1])
# Get the save fileystem path
print('level', levelp)
save_path = thy_save_fs[-1].path(levelp[1:4])
run_path = thy_run_fs[-1].path(levelp[1:4])
thy_save_fs[-1].create(levelp[1:4])
thy_run_fs[-1].create(levelp[1:4])
thy_save_path = thy_save_fs[-1].path(levelp[1:4])
thy_run_path = thy_run_fs[-1].path(levelp[1:4])
ts_save_fs = autofile.fs.transition_state(thy_save_path)
ts_save_fs[0].create()
ts_save_path = ts_save_fs[0].path()
ts_run_fs = autofile.fs.transition_state(thy_run_path)
ts_run_fs[0].create()
ts_run_path = ts_run_fs[0].path()
return ts_run_path, ts_save_path, thy_run_path, thy_save_path