def unimolecular_elimination_grid(bnd_atoms, ts_zma, brk_name):
""" Build forward 2D grid for elimination reaction
"""
syms = automol.zmatrix.symbols(ts_zma)
print('syms', syms)
brk_coo, = automol.zmatrix.coordinates(ts_zma)[brk_name]
print('brk_coo', brk_coo)
print(automol.zmatrix.string(ts_zma))
brk_len_key = tuple(sorted(map(syms.__getitem__, brk_coo)))
# interval = 0.2 * phycon.ANG2BOHR
# rmin = 1.4 * phycon.ANG2BOHR
# rmax = 2.8 * phycon.ANG2BOHR
print('Check bad grid')
npoints1 = 8
npoints2 = 4
bnd_len = bnd.read_len(bnd_atoms)
if bnd_len is not None:
brk_len = bnd.LEN_DCT[brk_len_key]
r1min = bnd_len + 0.2 * phycon.ANG2BOHR
r1max = bnd_len + 1.4 * phycon.ANG2BOHR
r2min = brk_len + 0.2 * phycon.ANG2BOHR
r2max = brk_len + 0.8 * phycon.ANG2BOHR
grid1 = numpy.linspace(r1min, r1max, npoints1)
grid2 = numpy.linspace(r2min, r2max, npoints2)
grid = [grid1, grid2]
update_guess = False
print('grid', grid)
# sys.exit()
return grid, update_guess
def hydrogen_migration_grid(npoints, bnd_atoms, ts_zma, dist_name):
""" Build forward 1D grid for addition reaction
"""
interval = 0.3 * phycon.ANG2BOHR
# get rmax from ts_zma
rmax = automol.zmatrix.values(ts_zma)[dist_name]
rmin1 = 2.0 * phycon.ANG2BOHR
rmin2 = 1.3 * phycon.ANG2BOHR
# print('ts_zma:', automol.zmatrix.string(ts_zma))
# print('rmin1, rmin2, rmax:', rmin1, rmin2, rmax)
bnd_len = bnd.read_len(bnd_atoms)
if bnd_len is not None:
rmin2 = bnd_len + 0.05 * phycon.ANG2BOHR
if rmax > rmin1:
npoints = math.ceil((rmax - rmin1) / interval)
if npoints < 1:
grid1 = []
else:
grid1 = numpy.linspace(rmax, rmin1, npoints)
else:
grid1 = []
grid2 = numpy.linspace(rmin1, rmin2, 18)
grid = numpy.concatenate((grid1, grid2), axis=None)
update_guess = True
# print('grids:', grid, grid1, grid2)
return grid, update_guess
def ring_forming_scission_grid(npoints, bnd_atoms):
""" Build forward WD grid for a ring forming scission reaction
"""
# the following allows for a 2-d grid search in the initial ts_search
# for now try 1-d grid and see if it is effective
npoints1 = 7 if npoints is None else npoints
# npoints2 = 8
# syms = automol.zmatrix.symbols(ts_zma)
# brk_coo, = automol.zmatrix.coordinates(ts_zma)[brk_name]
# brk_len_key = tuple(sorted(map(syms.__getitem__, brk_coo)))
# brk_len = bnd.LEN_DCT[brk_len_key]
bnd_len = bnd.read_len(bnd_atoms)
if bnd_len is not None:
r1min = bnd_len + 0.1 * phycon.ANG2BOHR
r1max = bnd_len + 0.7 * phycon.ANG2BOHR
# r2min = brk_len + 0.1 * phycon.ANG2BOHR
# r2max = brk_len + 0.8 * phycon.ANG2BOHR
grid1 = numpy.linspace(r1min, r1max, npoints1)
# grid2 = numpy.linspace(r2min, r2max, npoints2)
grid = grid1
# grid = [grid1, grid2]
update_guess = False
return grid, update_guess
def addition_bkp_grid(npoints, bnd_atoms):
""" Build backward 1D grid for a beta scission reaction
"""
rmin = 1.6 * phycon.ANG2BOHR
rmax = 2.8 * phycon.ANG2BOHR
bnd_len = bnd.read_len(bnd_atoms)
if bnd_len is not None:
npoints = 14
rmin = bnd_len + 0.1 * phycon.ANG2BOHR
rmax = bnd_len + 1.4 * phycon.ANG2BOHR
bkp_grid = numpy.linspace(rmin, rmax, npoints)
bkp_update_guess = False
return bkp_grid, bkp_update_guess
def insertion(npoints, bnd_atoms):
""" Build forward 1D grid for insertion reaction
"""
npoints = 16
rmin = 1.4 * phycon.ANG2BOHR
rmax = 2.4 * phycon.ANG2BOHR
bnd_len = bnd.read_len(bnd_atoms)
if bnd_len is not None:
rmin = bnd_len
rmax = bnd_len + 1.4 * phycon.ANG2BOHR
grid = numpy.linspace(rmin, rmax, npoints)
update_guess = False
return grid, update_guess
def hydrogen_abstraction(npoints, bnd_atoms):
""" Build forward 1D grid for hydrogen abstraction reaction
"""
npoints = 8
rmin = 0.7 * phycon.ANG2BOHR
rmax = 2.2 * phycon.ANG2BOHR
bnd_len = bnd.read_len(bnd_atoms)
if bnd_len is not None:
rmin = bnd_len + 0.2
rmax = bnd_len + 1.0 * phycon.ANG2BOHR
grid = numpy.linspace(rmin, rmax, npoints)
update_guess = False
return grid, update_guess
def addition_grid(npoints, bnd_atoms):
""" Build forward 1D grid for addition reaction
"""
npoints = 14
rmin = 1.6 * phycon.ANG2BOHR
rmax = 2.8 * phycon.ANG2BOHR
bnd_len = bnd.read_len(bnd_atoms)
if bnd_len is not None:
rmin = bnd_len + 0.1 * phycon.ANG2BOHR
rmax = bnd_len + 1.2 * phycon.ANG2BOHR
grid = _geometric_progression(rmin, rmax, npoints, gfact=1.1, rstp=0.05)
update_guess = False
return grid, update_guess
def beta_scission_grid(npoints, bnd_atoms):
""" Build forward 1D grid for a beta scission reaction
"""
# This logic seems backward - sjk
npoints = 8 if npoints is not None else npoints
rmin = 1.4 * phycon.ANG2BOHR
rmax = 2.0 * phycon.ANG2BOHR
bnd_len = bnd.read_len(bnd_atoms)
if bnd_len is not None:
npoints = 14
rmin = bnd_len + 0.1 * phycon.ANG2BOHR
rmax = bnd_len + 0.8 * phycon.ANG2BOHR
grid = numpy.linspace(rmin, rmax, npoints)
update_guess = False
return grid, update_guess