def reagent_geometries(rxn_info, thy_info, save_prefix):
""" Identify the reaction and build the object
:param rxn_info: reaction info object
:type rxn_info: mechanalyzer.inf.rxn object
:rtype: (tuple(automol.Reaction object), tuple(automol.zmat object))
"""
# Check the save filesystem for the reactant and product geometries
rct_info = rinfo.rgt_info(rxn_info, 'reacs')
prd_info = rinfo.rgt_info(rxn_info, 'prods')
_rcts_cnf_fs = filesys.rcts_cnf_fs(rct_info, thy_info, None, save_prefix)
_prds_cnf_fs = filesys.rcts_cnf_fs(prd_info, thy_info, None, save_prefix)
# If min cnfs found for all rcts and prds, read the geometries
rct_geos, prd_geos = (), ()
rct_paths, prd_paths = (), ()
if (
_rcts_cnf_fs.count(None) == 0 and _prds_cnf_fs.count(None) == 0
):
for (_, cnf_save_fs, min_locs, _) in _rcts_cnf_fs:
geo = cnf_save_fs[-1].file.geometry.read(min_locs)
path = cnf_save_fs[-1].file.geometry.path(min_locs)
rct_geos += (geo,)
rct_paths += (path,)
for (_, cnf_save_fs, min_locs, _) in _prds_cnf_fs:
geo = cnf_save_fs[-1].file.geometry.read(min_locs)
path = cnf_save_fs[-1].file.geometry.path(min_locs)
prd_geos += (geo,)
prd_paths += (path,)
return rct_geos, prd_geos, rct_paths, prd_paths
def _set_thy_inf_dcts(tsname,
ts_dct,
thy_dct,
es_keyword_dct,
run_prefix,
save_prefix,
zma_locs=(0, )):
""" set the theory
"""
rxn_info = ts_dct['rxn_info']
ts_info = rinfo.ts_info(rxn_info)
rct_info = rinfo.rgt_info(rxn_info, 'reacs')
rxn_info = rinfo.sort(rxn_info)
ts_locs = (int(tsname.split('_')[-1]), )
high_mult = rinfo.ts_mult(rxn_info, rxn_mul='high')
# Set the hs info
hs_info = (ts_info[0], ts_info[1], high_mult)
# Initialize the theory objects
ini_thy_info, mod_ini_thy_info = None, None
thy_info, mod_thy_info = None, None
vscnlvl_thy_info, mod_vscnlvl_thy_info = None, None
vsp1lvl_thy_info, mod_vsp1lvl_thy_info = None, None
vsp2lvl_thy_info, mod_vsp2lvl_thy_info = None, None
hs_vscnlvl_thy_info = None
hs_vsp1lvl_thy_info = None
hs_vsp2lvl_thy_info = None
hs_thy_info = None
# Initialize the necessary run filesystem
runlvl_ts_run_fs = None
runlvl_scn_run_fs = None
runlvl_cscn_run_fs = None
vscnlvl_ts_run_fs = None
vscnlvl_scn_run_fs = None
vscnlvl_cscn_run_fs = None
vrctst_run_fs = None
# Initialize the necessary save filesystem
ini_zma_save_fs = None
runlvl_ts_save_fs = None
runlvl_scn_save_fs = None # above cnf filesys, for search scans
runlvl_cscn_save_fs = None # above cnf filesys, for search scans
runlvl_cnf_save_fs = None
vscnlvl_thy_save_fs = None
vscnlvl_ts_save_fs = None
vscnlvl_scn_save_fs = None
vscnlvl_cscn_save_fs = None
vrctst_save_fs = None
runlvl_ts_zma_fs = None
if es_keyword_dct.get('inplvl', None) is not None:
ini_method_dct = thy_dct.get(es_keyword_dct['inplvl'])
ini_thy_info = tinfo.from_dct(ini_method_dct)
mod_ini_thy_info = tinfo.modify_orb_label(ini_thy_info, ts_info)
ini_cnf_run_fs, ini_cnf_save_fs = build_fs(
run_prefix,
save_prefix,
'CONFORMER',
rxn_locs=rxn_info,
ts_locs=ts_locs,
thy_locs=mod_ini_thy_info[1:])
ini_loc_info = filesys.mincnf.min_energy_conformer_locators(
ini_cnf_save_fs, mod_ini_thy_info)
ini_min_cnf_locs, ini_path = ini_loc_info
if ini_path:
ini_zma_save_fs = autofile.fs.zmatrix(
ini_cnf_save_fs[-1].path(ini_min_cnf_locs))
if es_keyword_dct.get('runlvl', None) is not None:
method_dct = thy_dct.get(es_keyword_dct['runlvl'])
thy_info = tinfo.from_dct(method_dct)
mod_thy_info = tinfo.modify_orb_label(thy_info, ts_info)
hs_thy_info = tinfo.modify_orb_label(thy_info, hs_info)
runlvl_cnf_run_fs, runlvl_cnf_save_fs = build_fs(
run_prefix,
save_prefix,
'CONFORMER',
rxn_locs=rxn_info,
ts_locs=ts_locs,
thy_locs=mod_thy_info[1:])
_, runlvl_ts_zma_save_fs = build_fs(run_prefix,
save_prefix,
'ZMATRIX',
rxn_locs=rxn_info,
ts_locs=ts_locs,
thy_locs=mod_thy_info[1:])
runlvl_loc_info = filesys.mincnf.min_energy_conformer_locators(
runlvl_cnf_save_fs, mod_thy_info)
runlvl_min_cnf_locs, _ = runlvl_loc_info
runlvl_cnf_save_fs = (runlvl_cnf_save_fs, runlvl_min_cnf_locs)
runlvl_scn_run_fs, runlvl_scn_save_fs = build_fs(
run_prefix,
save_prefix,
'SCAN',
rxn_locs=rxn_info,
ts_locs=ts_locs,
thy_locs=mod_thy_info[1:],
zma_locs=(0, ))
runlvl_cscn_run_fs, runlvl_cscn_save_fs = build_fs(
run_prefix,
save_prefix,
'CSCAN',
rxn_locs=rxn_info,
ts_locs=ts_locs,
thy_locs=mod_thy_info[1:],
zma_locs=(0, ))
if es_keyword_dct.get('var_scnlvl', None) is not None:
method_dct = thy_dct.get(es_keyword_dct['var_scnlvl'])
vscnlvl_thy_info = tinfo.from_dct(method_dct)
mod_vscnlvl_thy_info = tinfo.modify_orb_label(vscnlvl_thy_info,
ts_info)
hs_vscnlvl_thy_info = tinfo.modify_orb_label(vscnlvl_thy_info, hs_info)
vscnlvl_scn_run_fs, vscnlvl_scn_save_fs = build_fs(
run_prefix,
save_prefix,
'SCAN',
rxn_locs=rxn_info,
ts_locs=ts_locs,
thy_locs=mod_thy_info[1:],
zma_locs=(0, ))
vscnlvl_cscn_run_fs, vscnlvl_cscn_save_fs = build_fs(
run_prefix,
save_prefix,
'CSCAN',
rxn_locs=rxn_info,
ts_locs=ts_locs,
thy_locs=mod_thy_info[1:],
zma_locs=(0, ))
vrctst_run_fs, vrctst_save_fs = build_fs(run_prefix,
save_prefix,
'VRCTST',
rxn_locs=rxn_info,
ts_locs=ts_locs,
thy_locs=mod_thy_info[1:])
if es_keyword_dct.get('var_splvl1', None) is not None:
method_dct = thy_dct.get(es_keyword_dct['var_scnlvl1'])
vsplvl1_thy_info = tinfo.from_dct(method_dct)
mod_vsplvl1_thy_info = tinfo.modify_orb_label(
vsplvl1_thy_info, ts_info)
hs_vsplvl1_thy_info = tinfo.modify_orb_label(
vsplvl1_thy_info, hs_info)
if es_keyword_dct.get('var_splvl2', None) is not None:
method_dct = thy_dct.get(es_keyword_dct['var_scnlvl2'])
vsplvl2_thy_info = tinfo.from_dct(method_dct)
mod_vsplvl2_thy_info = tinfo.modify_orb_label(
vsplvl2_thy_info, ts_info)
hs_vsplvl2_thy_info = tinfo.modify_orb_label(
vsplvl2_thy_info, hs_info)
# Get the conformer filesys for the reactants
_rcts_cnf_fs = rcts_cnf_fs(rct_info, thy_dct, es_keyword_dct, run_prefix,
save_prefix)
thy_inf_dct = {
'inplvl': ini_thy_info,
'runlvl': thy_info,
'var_scnlvl': vscnlvl_thy_info,
'var_splvl1': vsp1lvl_thy_info,
'var_splvl2': vsp2lvl_thy_info,
'mod_inplvl': mod_ini_thy_info,
'mod_runlvl': mod_thy_info,
'mod_var_scnlvl': mod_vscnlvl_thy_info,
'mod_var_splvl1': mod_vsp1lvl_thy_info,
'mod_var_splvl2': mod_vsp2lvl_thy_info,
'hs_var_scnlvl': hs_vscnlvl_thy_info,
'hs_var_splvl1': hs_vsp1lvl_thy_info,
'hs_var_splvl2': hs_vsp2lvl_thy_info,
'hs_runlvl': hs_thy_info
}
runfs_dct = {
'runlvl_scn_fs': runlvl_scn_run_fs,
'runlvl_cscn_fs': runlvl_cscn_run_fs,
'runlvl_cnf_fs': runlvl_cnf_run_fs,
'vscnlvl_ts_fs': vscnlvl_ts_run_fs,
'vscnlvl_scn_fs': vscnlvl_scn_run_fs,
'vscnlvl_cscn_fs': vscnlvl_cscn_run_fs,
'vrctst_fs': vrctst_run_fs,
}
savefs_dct = {
'inilvl_zma_fs': ini_zma_save_fs,
'runlvl_scn_fs': runlvl_scn_save_fs,
'runlvl_cscn_fs': runlvl_cscn_save_fs,
'runlvl_cnf_fs': runlvl_cnf_save_fs,
'vscnlvl_scn_fs': vscnlvl_scn_save_fs,
'vscnlvl_cscn_fs': vscnlvl_cscn_save_fs,
'vrctst_fs': vrctst_save_fs,
'rcts_cnf_fs': _rcts_cnf_fs,
'runlvl_ts_zma_fs': runlvl_ts_zma_save_fs
}
return thy_inf_dct, runfs_dct, savefs_dct
def thy_dcts(tsname, ts_dct, thy_dct, es_keyword_dct,
run_prefix, save_prefix):
""" set the theory
"""
# Get transition state info
ts_zma = ts_dct['zma']
aspace = ts_dct['active']
# Set reaction info
rxn_info = ts_dct['rxn_info']
ts_info = rinfo.ts_info(rxn_info)
rct_info = rinfo.rgt_info(rxn_info, 'reacs')
rxn_info_sort = rinfo.sort(rxn_info)
# Set the high-sping ts info
high_mult = rinfo.ts_mult(rxn_info, rxn_mul='high')
hs_info = (ts_info[0], ts_info[1], high_mult)
# Set the filesystem locs
ts_locs = (int(tsname.split('_')[-1]),)
zma_locs = (ts_dct.get('zma_idx', 0),)
# Initialize the theory objects
ini_thy_info, mod_ini_thy_info = None, None
thy_info, mod_thy_info = None, None
vscnlvl_thy_info, mod_vscnlvl_thy_info = None, None
vsp1lvl_thy_info, mod_vsp1lvl_thy_info = None, None
vsp2lvl_thy_info, mod_vsp2lvl_thy_info = None, None
hs_vscnlvl_thy_info = None
hs_vsp1lvl_thy_info = None
hs_vsp2lvl_thy_info = None
hs_thy_info = None
# Method dicts
ini_method_dct = None
run_method_dct = None
vscn_method_dct = None
vsp1_method_dct = None
vsp2_method_dct = None
# Multireference Params
inplvl_mref_params = {}
runlvl_mref_params = {}
vscn_mref_params = {}
vsp1_mref_params = {}
vsp2_mref_params = {}
# Initialize the necessary run filesystem
runlvl_scn_run_fs = None
runlvl_cscn_run_fs = None
vscnlvl_ts_run_fs = None
vscnlvl_scn_run_fs = None
vscnlvl_cscn_run_fs = None
vrctst_run_fs = None
# Initialize the necessary save filesystem
inplvl_cnf_save_fs = None
runlvl_scn_save_fs = None # above cnf filesys, for search scans
runlvl_cscn_save_fs = None # above cnf filesys, for search scans
runlvl_cnf_save_fs = None
vscnlvl_scn_save_fs = None
vscnlvl_cscn_save_fs = None
vrctst_save_fs = None
if es_keyword_dct.get('inplvl', None) is not None:
ini_method_dct = thy_dct.get(es_keyword_dct['inplvl'])
ini_thy_info = tinfo.from_dct(ini_method_dct)
mod_ini_thy_info = tinfo.modify_orb_label(
ini_thy_info, ts_info)
# Conformer Layer for saddle point structures
_, inplvl_cnf_save_fs = build_fs(
run_prefix, save_prefix, 'CONFORMER',
rxn_locs=rxn_info_sort, ts_locs=ts_locs,
thy_locs=mod_ini_thy_info[1:])
inplvl_loc_info = filesys.mincnf.min_energy_conformer_locators(
inplvl_cnf_save_fs, mod_thy_info)
inplvl_min_cnf_locs, _ = inplvl_loc_info
inplvl_cnf_save_tuple = (inplvl_cnf_save_fs, inplvl_min_cnf_locs)
if elstruct.par.Method.is_multiref(ini_thy_info[1]):
inplvl_mref_params = multireference_calculation_parameters(
ts_zma, ts_info, hs_info,
aspace, mod_ini_thy_info, rxn_info=rxn_info)
if es_keyword_dct.get('runlvl', None) is not None:
run_method_dct = thy_dct.get(es_keyword_dct['runlvl'])
thy_info = tinfo.from_dct(run_method_dct)
mod_thy_info = tinfo.modify_orb_label(
thy_info, ts_info)
hs_thy_info = tinfo.modify_orb_label(
thy_info, hs_info)
# Conformer Layer for saddle point structures
runlvl_cnf_run_fs, runlvl_cnf_save_fs = build_fs(
run_prefix, save_prefix, 'CONFORMER',
rxn_locs=rxn_info_sort, ts_locs=ts_locs,
thy_locs=mod_thy_info[1:])
runlvl_loc_info = filesys.mincnf.min_energy_conformer_locators(
runlvl_cnf_save_fs, mod_thy_info)
runlvl_min_cnf_locs, _ = runlvl_loc_info
runlvl_cnf_save_tuple = (runlvl_cnf_save_fs, runlvl_min_cnf_locs)
# TS/IDX/Z Layer used for coordinate scans (perhaps for guesses)
_, runlvl_z_save_fs = build_fs(
run_prefix, save_prefix, 'ZMATRIX',
rxn_locs=rxn_info_sort, ts_locs=ts_locs,
thy_locs=mod_thy_info[1:])
runlvl_scn_run_fs, runlvl_scn_save_fs = build_fs(
run_prefix, save_prefix, 'SCAN',
rxn_locs=rxn_info_sort, ts_locs=ts_locs,
thy_locs=mod_thy_info[1:], zma_locs=zma_locs)
runlvl_cscn_run_fs, runlvl_cscn_save_fs = build_fs(
run_prefix, save_prefix, 'CSCAN',
rxn_locs=rxn_info_sort, ts_locs=ts_locs,
thy_locs=mod_thy_info[1:], zma_locs=zma_locs)
if elstruct.par.Method.is_multiref(thy_info[1]):
runlvl_mref_params = multireference_calculation_parameters(
ts_zma, ts_info, hs_info,
aspace, mod_thy_info, rxn_info=rxn_info)
if es_keyword_dct.get('var_scnlvl', None) is not None:
vscn_method_dct = thy_dct.get(es_keyword_dct['var_scnlvl'])
vscnlvl_thy_info = tinfo.from_dct(vscn_method_dct)
mod_vscnlvl_thy_info = tinfo.modify_orb_label(
vscnlvl_thy_info, ts_info)
hs_vscnlvl_thy_info = tinfo.modify_orb_label(
vscnlvl_thy_info, hs_info)
vscnlvl_scn_run_fs, vscnlvl_scn_save_fs = build_fs(
run_prefix, save_prefix, 'SCAN',
rxn_locs=rxn_info_sort, ts_locs=ts_locs,
thy_locs=mod_vscnlvl_thy_info[1:], zma_locs=zma_locs)
vscnlvl_cscn_run_fs, vscnlvl_cscn_save_fs = build_fs(
run_prefix, save_prefix, 'CSCAN',
rxn_locs=rxn_info_sort, ts_locs=ts_locs,
thy_locs=mod_vscnlvl_thy_info[1:], zma_locs=zma_locs)
vrctst_run_fs, vrctst_save_fs = build_fs(
run_prefix, save_prefix, 'VRCTST',
rxn_locs=rxn_info_sort, ts_locs=ts_locs,
thy_locs=mod_vscnlvl_thy_info[1:])
if elstruct.par.Method.is_multiref(vscnlvl_thy_info[1]):
vscn_mref_params = multireference_calculation_parameters(
ts_zma, ts_info, hs_info,
aspace, mod_vscnlvl_thy_info, rxn_info=rxn_info)
if es_keyword_dct.get('var_splvl1', None) is not None:
vsp1_method_dct = thy_dct.get(es_keyword_dct['var_splvl1'])
vsp1lvl_thy_info = tinfo.from_dct(vsp1_method_dct)
mod_vsp1lvl_thy_info = tinfo.modify_orb_label(
vsp1lvl_thy_info, ts_info)
hs_vsp1lvl_thy_info = tinfo.modify_orb_label(
vsp1lvl_thy_info, hs_info)
if elstruct.par.Method.is_multiref(vsp1lvl_thy_info[1]):
vsp1_mref_params = multireference_calculation_parameters(
ts_zma, ts_info, hs_info,
aspace, mod_vsp1lvl_thy_info, rxn_info=rxn_info)
if es_keyword_dct.get('var_splvl2', None) is not None:
vsp2_method_dct = thy_dct.get(es_keyword_dct['var_splvl2'])
vsp2lvl_thy_info = tinfo.from_dct(vsp2_method_dct)
mod_vsp2lvl_thy_info = tinfo.modify_orb_label(
vsp2lvl_thy_info, ts_info)
hs_vsp2lvl_thy_info = tinfo.modify_orb_label(
vsp2lvl_thy_info, hs_info)
if elstruct.par.Method.is_multiref(vsp2lvl_thy_info[1]):
vsp2_mref_params = multireference_calculation_parameters(
ts_zma, ts_info, hs_info,
aspace, mod_vsp2lvl_thy_info, rxn_info=rxn_info)
# Get the conformer filesys for the reactants
_rcts_cnf_fs = rcts_cnf_fs(rct_info, ini_thy_info, run_prefix, save_prefix)
if _rcts_cnf_fs is None:
_rcts_cnf_fs = rcts_cnf_fs(rct_info, thy_info, run_prefix, save_prefix)
thy_inf_dct = {
'inplvl': ini_thy_info,
'runlvl': thy_info,
'var_scnlvl': vscnlvl_thy_info,
'var_splvl1': vsp1lvl_thy_info,
'var_splvl2': vsp2lvl_thy_info,
'mod_inplvl': mod_ini_thy_info,
'mod_runlvl': mod_thy_info,
'mod_var_scnlvl': mod_vscnlvl_thy_info,
'mod_var_splvl1': mod_vsp1lvl_thy_info,
'mod_var_splvl2': mod_vsp2lvl_thy_info,
'hs_var_scnlvl': hs_vscnlvl_thy_info,
'hs_var_splvl1': hs_vsp1lvl_thy_info,
'hs_var_splvl2': hs_vsp2lvl_thy_info,
'hs_runlvl': hs_thy_info,
'rct_info': rct_info
}
thy_method_dct = {
'inplvl': ini_method_dct,
'runlvl': run_method_dct,
'var_scnlvl': vscn_method_dct,
'var_splvl1': vsp1_method_dct,
'var_splvl2': vsp2_method_dct,
}
mref_params_dct = {
'inplvl': inplvl_mref_params,
'runlvl': runlvl_mref_params,
'var_scnlvl': vscn_mref_params,
'var_splvl1': vsp1_mref_params,
'var_splvl2': vsp2_mref_params,
}
runfs_dct = {
'runlvl_scn': runlvl_scn_run_fs,
'runlvl_cscn': runlvl_cscn_run_fs,
'runlvl_cnf': runlvl_cnf_run_fs,
'vscnlvl_ts': vscnlvl_ts_run_fs,
'vscnlvl_scn': vscnlvl_scn_run_fs,
'vscnlvl_cscn': vscnlvl_cscn_run_fs,
'vrctst': vrctst_run_fs,
'prefix': run_prefix
}
savefs_dct = {
'runlvl_scn': runlvl_scn_save_fs,
'runlvl_cscn': runlvl_cscn_save_fs,
'runlvl_ts_zma': runlvl_z_save_fs,
'inplvl_cnf_tuple': inplvl_cnf_save_tuple,
'runlvl_cnf_tuple': runlvl_cnf_save_tuple,
'vscnlvl_scn': vscnlvl_scn_save_fs,
'vscnlvl_cscn': vscnlvl_cscn_save_fs,
'vrctst': vrctst_save_fs,
'rcts_cnf': _rcts_cnf_fs,
'prefix': save_prefix
}
return (thy_inf_dct, thy_method_dct,
mref_params_dct,
runfs_dct, savefs_dct)