def _build_molpro_template_str(ref_zma, ts_info, ts_formula, high_mul,
rct_ichs, rct_info, active_space,
mod_var_sp1_thy_info, inf_sep_ene):
""" Write the electronic structure template file
"""
cas_kwargs = wfn.build_wfn(ref_zma, ts_info, ts_formula, high_mul,
rct_ichs, rct_info, active_space,
mod_var_sp1_thy_info)
tml_inp_str = wfn.wfn_string(ts_info, mod_var_sp1_thy_info, inf_sep_ene,
cas_kwargs)
return tml_inp_str
def calc_vrctst_flux(
ini_zma, ts_info, hs_info, ts_formula, high_mul, active_space,
rct_info, rct_ichs, rct_zmas, rcts_cnf_fs, grid1, grid2, coord_name,
mod_var_scn_thy_info, mod_var_sp1_thy_info, var_sp2_thy_info,
hs_var_sp1_thy_info, hs_var_sp2_thy_info, vscnlvl_thy_save_fs,
vscnlvl_ts_run_fs, vscnlvl_scn_run_fs, vscnlvl_scn_save_fs,
vscnlvl_cscn_run_fs, vscnlvl_cscn_save_fs, overwrite, update_guess):
""" Set up n VRC-TST calculations to get the flux file
"""
# Set vrc tst dct
vrc_dct = _vrc_dct()
# Set up the casscf options
ref_zma = automol.zmatrix.set_values(ini_zma, {coord_name: grid1[0]})
cas_kwargs = wfn.build_wfn(ref_zma, ts_info, ts_formula, high_mul,
rct_ichs, rct_info, active_space,
mod_var_scn_thy_info)
_, script_str, _, _ = qchem_params(mod_var_sp1_thy_info[0],
mod_var_sp1_thy_info[1])
# Get indices for potentials and input
bnd_frm_idxs = automol.zmatrix.coord_idxs(ini_zma, coord_name)
min_idx, max_idx = min(bnd_frm_idxs), max(bnd_frm_idxs)
bnd_frm_idxs = (bnd_frm_idxs[0] + 1, bnd_frm_idxs[1] + 1)
# Build the VRC-TST run directory, including the needed scr dir
vrc_path = _build_vrctst_fs(vscnlvl_ts_run_fs)
# Calculate the correction potential along the MEP
inf_sep_ene, npot, zma_for_inp = _build_correction_potential(
ts_info, hs_info, ref_zma, coord_name, bnd_frm_idxs, grid1, grid2,
rct_info, rcts_cnf_fs, rct_zmas, mod_var_scn_thy_info,
mod_var_sp1_thy_info, hs_var_sp1_thy_info, var_sp2_thy_info,
hs_var_sp2_thy_info, vscnlvl_scn_run_fs, vscnlvl_scn_save_fs,
vscnlvl_cscn_run_fs, vscnlvl_cscn_save_fs, vscnlvl_thy_save_fs,
overwrite, update_guess, vrc_dct, vrc_path, cas_kwargs)
# Write remaining VaReCoF input files
_write_varecof_input(zma_for_inp, ts_info, ts_formula, high_mul, rct_ichs,
rct_info, rct_zmas, active_space,
mod_var_sp1_thy_info, npot, inf_sep_ene, min_idx,
max_idx, vrc_dct, vrc_path, script_str)
# Run VaReCoF to generate flux file
_run_varecof(vrc_path)
def radrad_scan(
ts_zma,
ts_info,
hs_info,
ts_formula,
high_mul,
active_space,
rct_info,
rct_ichs,
rcts_cnf_fs,
rcts_gra,
grid1,
grid2,
coord_name,
frm_bnd_keys,
mod_var_scn_thy_info,
mod_var_sp1_thy_info, # Need an unmodifie
var_sp1_thy_info,
var_sp2_thy_info,
hs_var_sp1_thy_info,
hs_var_sp2_thy_info,
mod_thy_info,
vscnlvl_thy_save_fs,
vscnlvl_ts_save_fs,
scn_run_fs,
scn_save_fs,
pot_thresh,
overwrite,
update_guess,
constraint_dct=None,
zma_locs=(0, )):
""" Run the scan for VTST calculations
"""
# Set up the casscf options
ref_zma = automol.zmatrix.set_values(ts_zma, {coord_name: grid1[0]})
cas_kwargs = wfn.build_wfn(ref_zma, ts_info, ts_formula, high_mul,
rct_ichs, rct_info, active_space,
mod_var_scn_thy_info)
# Run the scan along the reaction coordinate
scan.multiref_rscan(ts_zma=ts_zma,
ts_info=ts_info,
grid1=grid1,
grid2=grid2,
coord_name=coord_name,
mod_var_scn_thy_info=mod_var_scn_thy_info,
vscnlvl_thy_save_fs=vscnlvl_thy_save_fs,
scn_run_fs=scn_run_fs,
scn_save_fs=scn_save_fs,
overwrite=overwrite,
update_guess=update_guess,
constraint_dct=constraint_dct,
**cas_kwargs)
# Assess the potentials to see if there is a saddle point zma
print('above vtst max')
sadpt_zma = rxngrid.vtst_max(list(grid1) + list(grid2),
coord_name,
scn_save_fs,
mod_var_scn_thy_info,
constraint_dct,
ethresh=pot_thresh)
print('sadpt_zma', sadpt_zma)
if sadpt_zma is None:
# Calculate and the energies needed for inf sep ene
far_locs = [[coord_name], [grid1[0]]]
ts_zma = scn_save_fs[-1].file.zmatrix.read(far_locs)
geo = scn_save_fs[-1].file.geometry.read(far_locs)
geo_run_path = scn_run_fs[-1].path(far_locs)
geo_save_path = scn_save_fs[-1].path(far_locs)
_ = scan.radrad_inf_sep_ene(hs_info,
ts_zma,
rct_info,
rcts_cnf_fs,
var_sp1_thy_info,
var_sp2_thy_info,
hs_var_sp1_thy_info,
hs_var_sp2_thy_info,
geo,
geo_run_path,
geo_save_path,
scn_save_fs,
far_locs,
overwrite=overwrite,
**cas_kwargs)
# Save the vmatrix for use in reading
_save_traj(ts_zma,
frm_bnd_keys,
rcts_gra,
vscnlvl_ts_save_fs,
zma_locs=zma_locs)
print('\nRunning Hessians and energies...')
_vtst_hess_ene(ts_info, coord_name, mod_var_scn_thy_info,
mod_var_sp1_thy_info, scn_save_fs, scn_run_fs,
overwrite, **cas_kwargs)