def test__read():
""" test read
"""
val1 = dict_.values_by_unordered_tuple(DCT4, ('C', 'H'))
val2 = dict_.values_by_unordered_tuple(DCT4, ('H', 'C'))
assert numpy.isclose(val1, val2, 1.54)
def alpha(freqs, cfc_dct, vr4=None):
""" calculate alpha from expansion
"""
# Obtain the imaginary frequency (finds negative
ridxs = (idx for idx, freq in enumerate(freqs) if freq < 0.0)
assert len(ridxs) == 1, ('Freqs should only have one imag')
freqs = (abs(freq) for freq in freqs)
ridx = ridxs[0]
rfreq = freqs[ridx]
# Calculate alpha with cubic contributions
term1 = (5.0 / 3.0) * (cfc_dct[(ridx, ridx, ridx)]**2 / rfreq**3)
term2 = 0.0
for i, ifreq in enumerate(freqs):
vval = dict_.values_by_unordered_tuple(cfc_dct, (i, ridx, ridx))
tm1 = (vval**2 / ifreq**3)
tm2 = 2.0 * ifreq**(-2) + (1.0 / (4.0 * rfreq**2 + ifreq**2))
term2 += ((tm1 * tm2), )
_alpha = (numpy.pi / 8.0) * (term1 - term2)
# Calculate quartic contributions to alpha, if available
if vr4 is not None:
_alpha -= (numpy.pi / 8.0) * (cfc_dct[(ridx, ridx, ridx, ridx)] /
rfreq**6)
return _alpha
def _ts_bnd_len(zma, scan_coord):
""" Obtain the current value of the bond defined by the scam coordinate
"""
symbs = automol.zmat.symbols(zma)
dist_coo, = automol.zmat.coordinates(zma)[scan_coord]
ts_bnd_symbs = tuple(sorted(map(symbs.__getitem__, dist_coo)))
ts_bnd_len = dict_.values_by_unordered_tuple(bnd.LEN_DCT, ts_bnd_symbs)
return ts_bnd_len
def _pairwise_potentials(geo, idx_pair, potential='exp6'):
""" Calculate the sum of the pairwise potential for a
given pair of atoms in a geometry.
:param geo: automol geometry object
:type geo: tuple(tuple(float))
:param idx_pair: indices of atoms for which to calculate interaction
:type idx_pair: tuple(int, int)
:param potential: potential model of the atomic interactions
:type potential: str
:rtype: nd.array
"""
assert potential in ('exp6', 'lj_12_6'), (
f'potential {potential} != exp6 or lj_12_6')
# Get the indexes and symbols
idx1, idx2 = idx_pair
if idx1 != idx2:
# Get the symbols of the atoms
symbs = symbols(geo)
symb1, symb2 = symbs[idx1], symbs[idx2]
# Calculate interatomic distance
rdist = (distance(geo, idx1, idx2) * phycon.BOHR2ANG)
# Calculate the potential
if potential == 'exp6':
params = dict_.values_by_unordered_tuple(EXP6_DCT, (symb1, symb2))
pot_val = exp6_potential(rdist, *params)
elif potential == 'lj_12_6':
params = dict_.values_by_unordered_tuple(LJ_DCT, (symb1, symb2))
pot_val = lj_potential(rdist, *params)
else:
pot_val = 1.0e10
return pot_val
def test__read():
""" test dict_.values_by_unordered_tuple
test dict_.values_in_multilevel
"""
# Unordered unordered tuple reads
val1 = dict_.values_by_unordered_tuple(DCT4, ('C', 'H'))
val2 = dict_.values_by_unordered_tuple(DCT4, ('H', 'C'))
assert numpy.isclose(1.54, val1, val2)
val3 = dict_.values_by_unordered_tuple(DCT4, ('C', 'H'), fill_val=1.15)
val4 = dict_.values_by_unordered_tuple(DCT4, ('C', 'N'), fill_val=1.15)
assert numpy.isclose(1.54, val3)
assert numpy.isclose(1.15, val4)
# Multilevel dct reads
val1 = dict_.values_in_multilevel_dct(GDCT3,
'key1',
'subkey2',
fill_val='fill')
val2 = dict_.values_in_multilevel_dct(GDCT3,
'key2',
'subkey1',
fill_val='fill')
val3 = dict_.values_in_multilevel_dct(GDCT3,
'key1',
'subkey3',
fill_val='fill')
val4 = dict_.values_in_multilevel_dct(GDCT3,
'key3',
'subkey1',
fill_val='fill')
assert val1 == 'subval1-2'
assert val2 == 'subval2-1'
assert val3 == 'fill'
assert val4 == 'fill'
def _ts_compare(ref_zma, zma, zrxn):
""" Perform a series of checks to assess the viability
of a transition state geometry prior to saving
"""
# Initialize viable
viable = True
# Get the bond dists and calculate the distance of bond being formed
ref_geo = automol.zmat.geometry(ref_zma)
cnf_geo = automol.zmat.geometry(zma)
grxn = automol.reac.relabel_for_geometry(zrxn)
frm_bnd_keys = automol.reac.forming_bond_keys(grxn)
brk_bnd_keys = automol.reac.breaking_bond_keys(grxn)
cnf_dist_lst = []
ref_dist_lst = []
bnd_key_lst = []
cnf_ang_lst = []
ref_ang_lst = []
for frm_bnd_key in frm_bnd_keys:
frm_idx1, frm_idx2 = list(frm_bnd_key)
cnf_dist = distance(cnf_geo, frm_idx1, frm_idx2)
ref_dist = distance(ref_geo, frm_idx1, frm_idx2)
cnf_dist_lst.append(cnf_dist)
ref_dist_lst.append(ref_dist)
bnd_key_lst.append(frm_bnd_key)
for brk_bnd_key in brk_bnd_keys:
brk_idx1, brk_idx2 = list(brk_bnd_key)
cnf_dist = distance(cnf_geo, brk_idx1, brk_idx2)
ref_dist = distance(ref_geo, brk_idx1, brk_idx2)
cnf_dist_lst.append(cnf_dist)
ref_dist_lst.append(ref_dist)
bnd_key_lst.append(brk_bnd_key)
for frm_bnd_key in frm_bnd_keys:
for brk_bnd_key in brk_bnd_keys:
for frm_idx in frm_bnd_key:
for brk_idx in brk_bnd_key:
if frm_idx == brk_idx:
idx2 = frm_idx
idx1 = list(frm_bnd_key - frozenset({idx2}))[0]
idx3 = list(brk_bnd_key - frozenset({idx2}))[0]
cnf_ang = central_angle(cnf_geo, idx1, idx2, idx3)
ref_ang = central_angle(ref_geo, idx1, idx2, idx3)
cnf_ang_lst.append(cnf_ang)
ref_ang_lst.append(ref_ang)
# print('bnd_key_list', bnd_key_lst)
# print('conf_dist', cnf_dist_lst)
# print('ref_dist', ref_dist_lst)
# print('conf_angle', cnf_ang_lst)
# print('ref_angle', ref_ang_lst)
# Set the maximum allowed displacement for a TS conformer
max_disp = 0.6
# better to check for bond-form length in bond scission with ring forming
if 'addition' in grxn.class_:
max_disp = 0.8
if 'abstraction' in grxn.class_:
# this was 1.4 - SJK reduced it to work for some OH abstractions
max_disp = 1.0
# Check forming bond angle similar to ini config
if 'elimination' not in grxn.class_:
for ref_angle, cnf_angle in zip(ref_ang_lst, cnf_ang_lst):
if abs(cnf_angle - ref_angle) > .44:
print('angle', ref_angle, cnf_angle)
viable = False
symbs = symbols(cnf_geo)
lst_info = zip(ref_dist_lst, cnf_dist_lst, bnd_key_lst)
for ref_dist, cnf_dist, bnd_key in lst_info:
if 'add' in grxn.class_ or 'abst' in grxn.class_:
bnd_key1, bnd_key2 = min(list(bnd_key)), max(list(bnd_key))
symb1 = symbs[bnd_key1]
symb2 = symbs[bnd_key2]
if bnd_key in frm_bnd_keys:
# Check if radical atom is closer to some atom
# other than the bonding atom
cls = automol.zmat.base.is_atom_closest_to_bond_atom(
zma, bnd_key2, cnf_dist)
if not cls:
print('distance', ref_dist, cnf_dist)
print(' - Radical atom now has a new nearest neighbor')
viable = False
# check forming bond distance
if abs(cnf_dist - ref_dist) > max_disp:
print('distance', ref_dist, cnf_dist)
viable = False
# Check distance relative to equi. bond
equi_bnd = dict_.values_by_unordered_tuple(bnd.LEN_DCT,
(symb1, symb2),
fill_val=0.0)
displace_from_equi = cnf_dist - equi_bnd
dchk1 = abs(cnf_dist - ref_dist) > 0.1
dchk2 = displace_from_equi < 0.2
if dchk1 and dchk2:
print(cnf_dist, equi_bnd)
viable = False
else:
# check forming/breaking bond distance
# if abs(cnf_dist - ref_dist) > 0.4:
# max disp of 0.4 causes problems for bond scission w/ ring forming
# not sure if setting it to 0.3 will cause problems for other cases
if abs(cnf_dist - ref_dist) > 0.3:
print('distance', ref_dist, cnf_dist)
viable = False
return viable