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@alongd
alongd committed Jan 28, 2024
1 parent bc9cad4 commit af103f3
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Showing 11 changed files with 336 additions and 201 deletions.
85 changes: 44 additions & 41 deletions arc/job/adapters/ts/linear.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -221,40 +221,41 @@ def execute_incore(self):
)

t0_0 = datetime.datetime.now()
xyz_0 = interpolate(rxn=rxn, use_weights=False)
xyzs_0 = interpolate(rxn=rxn, use_weights=False)
t_ex_0 = datetime.datetime.now() - t0_0

t0_1 = datetime.datetime.now()
xyz_1 = interpolate(rxn=rxn, use_weights=True)
xyzs_1 = interpolate(rxn=rxn, use_weights=True)
t_ex_1 = datetime.datetime.now() - t0_1

for method_index, (xyz, t0, t_ex) in enumerate(zip([xyz_0, xyz_1], [t0_0, t0_1], [t_ex_0, t_ex_1])):
if colliding_atoms(xyz):
continue
unique = True
for other_tsg in rxn.ts_species.ts_guesses:
if almost_equal_coords(xyz, other_tsg.initial_xyz):
if 'linear' not in other_tsg.method.lower():
other_tsg.method += f' and Linear {method_index}'
unique = False
break
if unique:
ts_guess = TSGuess(method=f'linear {method_index}',
index=len(rxn.ts_species.ts_guesses),
method_index=method_index,
t0=t0,
execution_time=t_ex,
success=True,
family=family_label,
xyz=xyz,
)
rxn.ts_species.ts_guesses.append(ts_guess)
save_geo(xyz=xyz,
path=self.local_path,
filename=f'Linear {method_index}',
format_='xyz',
comment=f'Linear {method_index}, family: {family_label}',
)
for method_index, (xyzs, t0, t_ex) in enumerate(zip([xyzs_0, xyzs_1], [t0_0, t0_1], [t_ex_0, t_ex_1])):
for xyz in xyzs:
if colliding_atoms(xyz):
continue
unique = True
for other_tsg in rxn.ts_species.ts_guesses:
if almost_equal_coords(xyz, other_tsg.initial_xyz):
if 'linear' not in other_tsg.method.lower():
other_tsg.method += f' and Linear {method_index}'
unique = False
break
if unique:
ts_guess = TSGuess(method=f'linear {method_index}',
index=len(rxn.ts_species.ts_guesses),
method_index=method_index,
t0=t0,
execution_time=t_ex,
success=True,
family=family_label,
xyz=xyz,
)
rxn.ts_species.ts_guesses.append(ts_guess)
save_geo(xyz=xyz,
path=self.local_path,
filename=f'Linear {method_index}',
format_='xyz',
comment=f'Linear {method_index}, family: {family_label}',
)

if len(self.reactions) < 5:
successes = len([tsg for tsg in rxn.ts_species.ts_guesses if tsg.success and 'linear' in tsg.method])
Expand All @@ -275,7 +276,7 @@ def execute_queue(self):

def interpolate(rxn: 'ARCReaction',
use_weights: bool = False,
) -> Optional[dict]:
) -> Optional[List[dict]]:
"""
Search for a TS by interpolating internal coords.
Expand All @@ -284,7 +285,7 @@ def interpolate(rxn: 'ARCReaction',
use_weights (bool, optional): Whether to use the well energies to determine relative interpolation weights.
Returns:
Optional[dict]: The XYZ coordinates guess.
Optional[List[dict]]: Entries are the XYZ coordinate guesses.
"""
if rxn.is_isomerization():
return interpolate_isomerization(rxn=rxn, use_weights=use_weights)
Expand All @@ -295,7 +296,7 @@ def interpolate(rxn: 'ARCReaction',

def interpolate_isomerization(rxn: 'ARCReaction',
use_weights: bool = False,
) -> Optional[dict]:
) -> Optional[List[dict]]:
"""
Search for a TS of an isomerization reaction by interpolating internal coords.
Expand All @@ -304,23 +305,25 @@ def interpolate_isomerization(rxn: 'ARCReaction',
use_weights (bool, optional): Whether to use the well energies to determine relative interpolation weights.
Returns:
Optional[dict]: The XYZ coordinates guess.
Optional[List[dict]]: Entries are the XYZ coordinate guesses.
"""
rxn.r_species[0].get_xyz()
rxn.p_species[0].get_xyz()
r_zmat = xyz_to_zmat(xyz=rxn.r_species[0].get_xyz(),
consolidate=False,
atom_order=list(range(sum(r.number_of_atoms for r in rxn.r_species))))
p_zmat = xyz_to_zmat(xyz=rxn.p_species[0].get_xyz(),
consolidate=False,
atom_order=rxn.atom_map)
weight = get_rxn_weight(rxn) if use_weights else 0.5
if weight is None:
return None
ts_zmat = average_zmat_params(zmat_1=r_zmat, zmat_2=p_zmat, weight=weight)
if ts_zmat is None:
if weight is None or rxn.atom_maps is None:
return None
return zmat_to_xyz(ts_zmat)
ts_xyzs = list()
for atom_map in rxn.atom_maps:
p_zmat = xyz_to_zmat(xyz=rxn.p_species[0].get_xyz(),
consolidate=False,
atom_order=atom_map)
ts_zmat = average_zmat_params(zmat_1=r_zmat, zmat_2=p_zmat, weight=weight)
if ts_zmat is not None:
ts_xyzs.append(zmat_to_xyz(ts_zmat))
return ts_xyzs


def average_zmat_params(zmat_1: dict,
Expand Down
58 changes: 51 additions & 7 deletions arc/job/adapters/ts/linear_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,9 @@
from arc.species.zmat import _compare_zmats


class TestHeuristicsAdapter(unittest.TestCase):
class TestLinearAdapter(unittest.TestCase):
"""
Contains unit tests for the HeuristicsAdapter class.
Contains unit tests for the LinearAdapter class.
"""

@classmethod
Expand Down Expand Up @@ -129,7 +129,7 @@ def test_get_rxn_weight(self):
rxn_1.ts_species.e0 = 391.6
self.assertAlmostEquals(get_rxn_weight(rxn_1), 0.3417832)

def test_interpolate_isomerization(self):
def test_interpolate_intra_h_migration(self):
"""Test the interpolate_isomerization() function."""
nc3h7_xyz = """C 0.00375165 -0.48895802 -1.20586379
C 0.00375165 -0.48895802 0.28487510
Expand Down Expand Up @@ -164,8 +164,9 @@ def test_interpolate_isomerization(self):
H 0.76979130 1.33747945 0.33815513
H -0.04544494 0.70455273 1.77835334
H -1.00071642 1.24557408 0.38839197""")
ts_xyz = interpolate_isomerization(rxn, use_weights=False)
self.assertTrue(almost_equal_coords(ts_xyz, expected_ts_xyz))
ts_xyzs = interpolate_isomerization(rxn, use_weights=False)
self.assertEqual(len(ts_xyzs), 2)
self.assertTrue(almost_equal_coords(ts_xyzs[0], expected_ts_xyz))

nc3h7.e0 = 101.55
ic3h7.e0 = 88.91
Expand All @@ -182,8 +183,51 @@ def test_interpolate_isomerization(self):
H 0.79813573 1.38347069 0.43772483
H -0.03897336 0.76031233 1.86961141
H -0.97425159 1.33180895 0.47825005""")
ts_xyz = interpolate_isomerization(rxn, use_weights=True)
self.assertTrue(almost_equal_coords(ts_xyz, expected_ts_xyz))
ts_xyzs = interpolate_isomerization(rxn, use_weights=True)
self.assertTrue(almost_equal_coords(ts_xyzs[0], expected_ts_xyz))

def test_interpolate_no2_ono_isomerization(self):
"""Test the interpolate_isomerization() function."""
c2h5no2_xyz = """C -1.12362739 -0.04664655 -0.08575959
C 0.24488022 -0.51587553 0.36119196
N 0.57726975 -1.77875156 -0.37104243
O 1.16476543 -1.66382529 -1.45384186
O 0.24561669 -2.84385320 0.16410116
H -1.87655344 -0.80826847 0.13962125
H -1.14729169 0.14493421 -1.16405294
H -1.41423043 0.87863077 0.42354512
H 1.02430791 0.21530309 0.12674144
H 0.27058353 -0.73979548 1.43184405"""
c2h5ono_xyz = """C -1.36894499 0.07118059 -0.24801399
C -0.01369535 0.17184136 0.42591278
O -0.03967083 -0.62462610 1.60609048
N 1.23538512 -0.53558048 2.24863846
O 1.25629155 -1.21389295 3.27993827
H -2.16063255 0.41812452 0.42429392
H -1.39509985 0.66980796 -1.16284741
H -1.59800183 -0.96960842 -0.49986392
H 0.19191326 1.21800574 0.68271847
H 0.76371340 -0.19234475 -0.25650067"""
c2h5no2 = ARCSpecies(label='C2H5NO2', smiles='CC[N+](=O)[O-]', xyz=c2h5no2_xyz)
c2h5ono = ARCSpecies(label='C2H5ONO', smiles='CCON=O', xyz=c2h5ono_xyz)

rxn = ARCReaction(r_species=[c2h5no2], p_species=[c2h5ono])
expected_ts_xyz = str_to_xyz("""C 0.01099731 -0.46789926 -1.15958911
C 0.01099731 -0.46789926 0.33114978
C 0.01099731 0.94103865 0.90031155
H 0.57795661 -1.24174248 -1.65467180
H -0.39690222 0.34527841 -1.69240298
H -1.19440431 -1.28933062 -0.47327539
H 0.89689057 -1.16420498 0.45967951
H 0.76979130 1.33747945 0.33815513
H -0.04544494 0.70455273 1.77835334
H -1.00071642 1.24557408 0.38839197""")
ts_xyzs = interpolate_isomerization(rxn, use_weights=False)
for xyz in ts_xyzs:
print('\n\n\n')
print(xyz_to_str(xyz))
self.assertEqual(len(ts_xyzs), 1)
self.assertTrue(almost_equal_coords(ts_xyzs[0], expected_ts_xyz))

@classmethod
def tearDownClass(cls):
Expand Down
8 changes: 5 additions & 3 deletions arc/mapping/driver.py
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Original file line number Diff line number Diff line change
Expand Up @@ -257,11 +257,13 @@ def map_rxn(rxn: 'ARCReaction',
logger.error(f"Could not find isomorphism for scissored species: {[cut.mol.smiles for cut in p_cuts]}")
return None

atom_map = map_pairs(pairs_of_reactant_and_products)
if atom_map is not None:
atom_map = glue_maps(atom_map, pairs_of_reactant_and_products)
atom_map_list = map_pairs(pairs_of_reactant_and_products)
if isinstance(atom_map_list, list) and all(e is not None for e in atom_map_list):
atom_map = glue_maps(atom_map_list, pairs_of_reactant_and_products)
atom_maps.append(atom_map)

print(f'atom_maps: {atom_maps}')

return atom_maps


Expand Down
26 changes: 26 additions & 0 deletions arc/mapping/driver_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1047,6 +1047,32 @@ def test_map_intra_h_migration(self):
self.assertIn(atom_map[7], [3, 4, 5, 8])
self.assertIn(atom_map[8], [3, 4, 5, 8])

ic3h7_xyz = """C -0.40735690 -0.74240205 -0.34312948
C 0.38155377 -0.25604705 0.82450968
C 0.54634593 1.25448345 0.81064511
H 0.00637731 -1.58836501 -0.88041673
H -0.98617584 -0.01198912 -0.89732723
H -1.29710684 -1.29092340 0.08598983
H 1.36955428 -0.72869684 0.81102246
H 1.06044877 1.58846788 -0.09702437
H 1.13774084 1.57830484 1.67308862
H -0.42424546 1.75989927 0.85794283"""
nc3h7_xyz = """C 0.00375165 -0.48895802 -1.20586379
C 0.00375165 -0.48895802 0.28487510
C 0.00375165 0.91997987 0.85403684
H 0.41748586 -1.33492098 -1.74315104
H -0.57506729 0.24145491 -1.76006154
H -0.87717095 -1.03203740 0.64280162
H 0.88948616 -1.02465371 0.64296621
H 0.88512433 1.48038223 0.52412379
H 0.01450405 0.88584135 1.94817394
H -0.88837301 1.47376959 0.54233121"""
rxn_1 = ARCReaction(r_species=[ARCSpecies(label='iC3H7', smiles='C[CH]C', xyz=ic3h7_xyz)],
p_species=[ARCSpecies(label='nC3H7', smiles='[CH2]CC', xyz=nc3h7_xyz)])
print('---------')
print(rxn_1.atom_maps[0])
self.assertEqual(rxn_1.atom_maps[0], [0, 1, 2, 6, 3, 4, 5, 7, 8, 9])

def test_map_isomerization_reaction(self):
"""Test the map_isomerization_reaction() function."""
reactant_xyz = """C -1.3087 0.0068 0.0318
Expand Down
35 changes: 16 additions & 19 deletions arc/mapping/engine.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1088,23 +1088,18 @@ def make_bond_changes(rxn: 'ARCReaction',
def assign_labels_to_products(rxn: 'ARCReaction',
p_label_dict: dict):
"""
Add the indices to the reactants and products.
Add labels to the atoms of the reactants and products.
Args:
rxn: ARCReaction object to be mapped
p_label_dict: the labels of the products
Consider changing in rmgpy.
Returns:
Adding labels to the atoms of the reactants and products, to be identified later.
"""

atom_index = 0
for product in rxn.p_species:
for atom in product.mol.atoms:
for product_ in rxn.p_species:
for atom in product_.mol.atoms:
if atom_index in p_label_dict.values() and (atom.label is str or atom.label is None):
atom.label = key_by_val(p_label_dict,atom_index)
atom_index+=1
atom_index += 1


def update_xyz(spcs: List[ARCSpecies]) -> List[ARCSpecies]:
Expand Down Expand Up @@ -1169,7 +1164,7 @@ def pairing_reactants_and_products_for_mapping(r_cuts: List[ARCSpecies],

def map_pairs(pairs):
"""
A function that maps the mached species together
A function that maps the matched species together.
Args:
pairs: A list of the pairs of reactants and species
Expand All @@ -1181,7 +1176,6 @@ def map_pairs(pairs):
maps = list()
for pair in pairs:
maps.append(map_two_species(pair[0], pair[1]))

return maps


Expand All @@ -1196,20 +1190,23 @@ def label_species_atoms(spcs):
for spc in spcs:
for atom in spc.mol.atoms:
atom.label = str(index)
index+=1
index += 1


def glue_maps(maps, pairs_of_reactant_and_products):
def glue_maps(maps: List[List[int]],
pairs_of_reactant_and_products: List[Tuple[ARCSpecies, ARCSpecies]]
) -> List[int]:
"""
a function that joins together the maps from the parts of the reaction.
Args:
rxn: ARCReaction that requires atom mapping
maps: The list of all maps of the isomorphic cuts.
maps (List[List[int]]): The list of all maps of the isomorphic cuts.
pairs_of_reactant_and_products (List[Tuple[ARCSpecies, ARCSpecies]]): The list of all pairs of reactants and products.
Returns:
an Atom Map of the compleate reaction.
List[int]: An Atom Map of the complete reaction.
"""
# print(f'maps: {maps}, pairs_of_reactant_and_products: {pairs_of_reactant_and_products}')
am_dict = dict()
for _map, pair in zip(maps, pairs_of_reactant_and_products):
r_atoms = pair[0].mol.atoms
Expand All @@ -1221,16 +1218,16 @@ def glue_maps(maps, pairs_of_reactant_and_products):

def determine_bdes_on_spc_based_on_atom_labels(spc: "ARCSpecies", bde: Tuple[int, int]) -> bool:
"""
A function for determining whether or not the species in question containt the bond specified by the bond dissociation indices.
A function for determining whether the species in question contains the bond specified by the bond dissociation indices.
Also, assigns the correct BDE to the species.
Args:
spc (ARCSpecies): The species in question, with labels atom indices.
bde (Tuple[int, int]): The bde in question.
add_bdes (bool): Whether or not to add the bde to the species.
add_bdes (bool): Whether to add the bde to the species.
Returns:
bool: Whether or not the bde is based on the atom labels.
bool: Whether the bde is based on the atom labels.
"""
bde = convert_list_index_0_to_1(bde, direction=-1)
index1, index2 = bde[0], bde[1]
Expand Down
4 changes: 2 additions & 2 deletions arc/mapping/engine_test.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -698,7 +698,7 @@ def test_glue_maps(self):
rxn_1_test.determine_family(self.db)
rmg_reactions = get_rmg_reactions_from_arc_reaction(arc_reaction=rxn_1_test, backend="ARC")
r_label_dict, p_label_dict = get_atom_indices_of_labeled_atoms_in_an_rmg_reaction(arc_reaction=rxn_1_test,
rmg_reaction=rmg_reactions[0])
rmg_reaction=rmg_reactions[0])
assign_labels_to_products(rxn_1_test, p_label_dict)
reactants, products = copy_species_list_for_mapping(rxn_1_test.r_species), copy_species_list_for_mapping(rxn_1_test.p_species)
label_species_atoms(reactants), label_species_atoms(products)
Expand All @@ -709,7 +709,7 @@ def test_glue_maps(self):
p_cuts = cut_species_based_on_atom_indices(products, p_bdes)
pairs_of_reactant_and_products = pairing_reactants_and_products_for_mapping(r_cuts, p_cuts)
maps = map_pairs(pairs_of_reactant_and_products)
atom_map = glue_maps(maps,pairs_of_reactant_and_products)
atom_map = glue_maps(maps, pairs_of_reactant_and_products)
self.assertEqual(len(atom_map), self.r_1.mol.get_num_atoms() + self.r_2.mol.get_num_atoms())
atoms_r = [atom for atom in self.r_1.mol.copy(deep=True).atoms] + [atom for atom in self.r_2.mol.copy(deep=True).atoms]
atoms_p = [atom for atom in self.p_1.mol.copy(deep=True).atoms] + [atom for atom in self.p_2.mol.copy(deep=True).atoms]
Expand Down
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