Skip to content

Commit

Permalink
f! tsts
Browse files Browse the repository at this point in the history
  • Loading branch information
@alongd
alongd committed May 28, 2024
1 parent ae4aca5 commit 69759f8
Showing 1 changed file with 117 additions and 28 deletions.
145 changes: 117 additions & 28 deletions arc/job/adapters/ts/linear_test.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,16 +9,19 @@
import shutil
import unittest

from rmgpy.data.kinetics import KineticsFamily

from arc.common import ARC_PATH, almost_equal_coords
from arc.job.adapters.ts.linear import (LinearAdapter,
average_zmat_params,
get_r_constraints,
get_rxn_weight,
get_weight,
interpolate_isomerization,
)
from arc.reaction import ARCReaction
from arc.rmgdb import make_rmg_database_object, load_families_only
from arc.species.converter import str_to_xyz
from arc.species.converter import str_to_xyz, xyz_to_str
from arc.species.species import ARCSpecies
from arc.species.zmat import _compare_zmats

Expand Down Expand Up @@ -73,6 +76,30 @@ def setUpClass(cls):
H 1.36205133 -3.75009763 -2.57288841""")])
cls.rxn_1.determine_family(rmg_database=cls.rmgdb)

cls.rxn_2 = ARCReaction(r_species=[ARCSpecies(label='CCONO', smiles='CCON=O',
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""")],
p_species=[ARCSpecies(label='CCNO2', smiles='CC[N+](=O)[O-]',
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""")])
cls.rxn_2.determine_family(rmg_database=cls.rmgdb)

def test_average_zmat_params(self):
"""Test the average_zmat_params() function."""
zmat_1 = {'symbols': ('H', 'H'),
Expand Down Expand Up @@ -166,8 +193,8 @@ 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):
"""Test the interpolate_isomerization() function."""
def test_interpolate_isomerization_intra_h_migration(self):
"""Test the interpolate_isomerization() function for intra H migration reactions."""
nc3h7_xyz = """C 0.00375165 -0.48895802 -1.20586379
C 0.00375165 -0.48895802 0.28487510
C 0.00375165 0.91997987 0.85403684
Expand All @@ -191,36 +218,76 @@ def test_interpolate_isomerization(self):
nc3h7 = ARCSpecies(label='nC3H7', smiles='[CH2]CC', xyz=nc3h7_xyz)
ic3h7 = ARCSpecies(label='iC3H7', smiles='C[CH]C', xyz=ic3h7_xyz)
rxn = ARCReaction(r_species=[nc3h7], p_species=[ic3h7])
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_xyz = interpolate_isomerization(rxn, use_weights=False)
self.assertTrue(almost_equal_coords(ts_xyz, expected_ts_xyz))
expected_ts_xyz = str_to_xyz("""C 0.00598652 -0.48762088 -1.18600054
C 0.00598652 -0.48762088 0.30473835
C 0.00598652 0.92131703 0.87390011
H 0.57807817 -1.25594905 -1.69382911
H -0.42698663 0.35443110 -1.71434916
H -1.27461406 -1.27709743 -0.24121083
H 0.89172104 -1.02331658 0.66282944
H 0.88735917 1.48171935 0.54398704
H 0.01673891 0.88717852 1.96803717
H -0.88613815 1.47510670 0.56219446""")
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
ts = ARCSpecies(label='TS', is_ts=True, multiplicity=2, xyz=expected_ts_xyz)
ts.e0 = 105
rxn.ts_species = ts
expected_ts_xyz = str_to_xyz("""C 0.01224420 -0.47400672 -1.18787451
C 0.01224420 -0.47400672 0.30286438
C 0.01224420 0.93493122 0.87202615
H 0.47981756 -1.29923732 -1.70742021
H -0.50470551 0.28201158 -1.73526026
H -1.06475721 -1.18141451 0.26785378
H 0.86736552 -1.12118386 0.54383845
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))
expected_ts_xyz = str_to_xyz("""C 0.00591772 -0.48764618 -1.20069282
C 0.00591772 -0.48764618 0.29004607
C 0.00591772 0.92129176 0.85920784
H 0.47693974 -1.30982443 -1.72763512
H -0.52424330 0.28530048 -1.74580953
H -1.07348606 -1.15308709 0.40763997
H 0.89165221 -1.02334186 0.64813718
H 0.88729039 1.48169408 0.52929476
H 0.01667012 0.88715326 1.95334482
H -0.88620694 1.47508143 0.54750218""")
ts_xyzs = interpolate_isomerization(rxn, use_weights=True)
self.assertEqual(len(ts_xyzs), 2)
self.assertTrue(almost_equal_coords(ts_xyzs[0], expected_ts_xyz))

# r_xyz = """C -1.05582103 -0.03329574 -0.10080257
# C 0.41792695 0.17831205 0.21035514
# O 1.19234020 -0.65389683 -0.61111443
# O 2.44749684 -0.41401220 -0.28381363
# H -1.33614002 -1.09151783 0.08714882
# H -1.25953618 0.21489046 -1.16411897
# H -1.67410396 0.62341419 0.54699514
# H 0.59566350 -0.06437686 1.28256640
# H 0.67254676 1.24676329 0.02676370"""
# p_xyz = """C -1.40886397 0.22567351 -0.37379668
# C 0.06280787 0.04097694 -0.38515682
# O 0.44130326 -0.57668419 0.84260864
# O 1.89519755 -0.66754203 0.80966180
# H -1.87218376 0.90693511 -1.07582340
# H -2.03646287 -0.44342165 0.20255768
# H 0.35571681 -0.60165457 -1.22096147
# H 0.56095122 1.01161503 -0.47393734
# H 2.05354047 -0.10415729 1.58865243"""
# r = ARCSpecies(label='R', smiles='CCO[O]', xyz=r_xyz)
# p = ARCSpecies(label='P', smiles='[CH2]COO', xyz=p_xyz)
# rxn = ARCReaction(r_species=[r], p_species=[p])
# expected_ts_xyz = str_to_xyz("""C 0.00598652 -0.48762088 -1.18600054
# C 0.00598652 -0.48762088 0.30473835
# C 0.00598652 0.92131703 0.87390011
# H 0.57807817 -1.25594905 -1.69382911
# H -0.42698663 0.35443110 -1.71434916
# H -1.27461406 -1.27709743 -0.24121083
# H 0.89172104 -1.02331658 0.66282944
# H 0.88735917 1.48171935 0.54398704
# H 0.01673891 0.88717852 1.96803717
# H -0.88613815 1.47510670 0.56219446""")
# ts_xyzs = interpolate_isomerization(rxn, use_weights=False)
# self.assertEqual(len(ts_xyzs), 3)
# for ts_xyz in ts_xyzs:
# print(f'\nTS xyz:\n\n')
# print(xyz_to_str(ts_xyz))
# self.assertTrue(almost_equal_coords(ts_xyzs[0], expected_ts_xyz))

def test_linear_adapter(self):
"""Test the LinearAdapter class."""
Expand All @@ -229,14 +296,36 @@ def test_linear_adapter(self):
reactions=[self.rxn_1],
testing=True,
project='test',
project_directory=os.path.join(ARC_PATH, 'arc', 'testing', 'test_linear', 'tst1'),
project_directory=os.path.join(ARC_PATH, 'arc', 'testing', 'test_linear', 'rxn_1'),
)
self.assertIsNone(self.rxn_1.ts_species)
linear_1.execute()
self.assertEqual(len(self.rxn_1.ts_species.ts_guesses), 1)
self.assertEqual(self.rxn_1.ts_species.ts_guesses[0].initial_xyz['symbols'],
('C', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H'))

def test_linear_adapter_2(self):
self.rxn_2.family = KineticsFamily(label='intra_NO2_ONO_conversion')
self.rxn_2.atom_map = [0, 1, 3, 2, 4, 5, 7, 6, 9, 8]
self.assertEqual(self.rxn_2.family.label, 'intra_NO2_ONO_conversion')
linear_2 = LinearAdapter(job_type='tsg',
reactions=[self.rxn_2],
testing=True,
project='test',
project_directory=os.path.join(ARC_PATH, 'arc', 'testing', 'test_linear', 'rxn_2'),
)
self.assertIsNone(self.rxn_2.ts_species)
linear_2.execute()
self.assertEqual(len(self.rxn_2.ts_species.ts_guesses), 1)
print(xyz_to_str(self.rxn_2.ts_species.ts_guesses[0].initial_xyz))
self.assertEqual(self.rxn_2.ts_species.ts_guesses[0].initial_xyz['symbols'],
('C', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H'))

def test_get_r_constraints(self):
"""Test the get_r_constraints() function."""
self.assertEqual(get_r_constraints([(1, 5)], [(0, 5)]), {'R_atom': [(5, 1)]})
self.assertEqual(get_r_constraints([(1, 5), (7, 2), (8, 2)], [(0, 5), (7, 4), (8, 1)]), {'R_atom': [(1, 5), (5, 0), (7, 2), (2, 8)]})

@classmethod
def tearDownClass(cls):
"""
Expand Down

0 comments on commit 69759f8

Please sign in to comment.