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Tests: converter add_atom_to_xyz_using_internal_coords()
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added test for add_atom_to_xyz_using_internal_coords
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@alongd
alongd committed Jan 2, 2025
1 parent e19e95c commit c3ea0ba
Showing 1 changed file with 108 additions and 1 deletion.
109 changes: 108 additions & 1 deletion arc/species/converter_test.py
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Original file line number Diff line number Diff line change
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from arc.common import ARC_PATH, almost_equal_coords, almost_equal_coords_lists, almost_equal_lists
from arc.exceptions import ConverterError
from arc.species.species import ARCSpecies
from arc.species.vectors import calculate_dihedral_angle
from arc.species.vectors import calculate_dihedral_angle, calculate_param
from arc.species.zmat import _compare_zmats, xyz_to_zmat


Expand Down Expand Up @@ -5058,6 +5058,113 @@ def test_cluster_confs_by_rmsd(self):
xyzs3 = [nco_1, nco_2, nco_6, nco_7, nco_8, nco_9]
self.assertEqual(len(converter.cluster_confs_by_rmsd(xyzs3)), 4)

def test_add_atom_to_xyz_using_internal_coords(self):
"""Test the add_atom_to_xyz_using_internal_coords() function."""
xyz_1 = """ C -3.63243985 -0.48299420 -0.05541310
H -3.27244945 -1.49054926 -0.06723326
H -3.24128971 0.04543562 -0.89960709
H -4.70149255 -0.48565830 -0.10034895
C -3.17488405 0.21042224 1.24128129
H -3.53487445 1.21797729 1.25310144
H -3.56603419 -0.31800758 2.08547528
C -1.63624745 0.21425655 1.30595531
H -1.24509731 0.74268637 0.46176133
H -1.31833530 0.69604590 2.20690531"""
new_xyz_1 = converter.add_atom_to_xyz_using_internal_coords(xyz=xyz_1,
element='Cl',
r_index=7,
a_indices=(4, 7),
d_indices=(0, 4, 7),
r_value=1.77,
a_value=109.5,
d_value=-60.0,
)
expected_xyz_1 = {'symbols': ('C', 'H', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'Cl'),
'isotopes': (12, 1, 1, 1, 12, 1, 1, 12, 1, 1, 35),
'coords': ((-3.63243985, -0.4829942, -0.0554131), (-3.27244945, -1.49054926, -0.06723326),
(-3.24128971, 0.04543562, -0.89960709), (-4.70149255, -0.4856583, -0.10034895),
(-3.17488405, 0.21042224, 1.24128129), (-3.53487445, 1.21797729, 1.25310144),
(-3.56603419, -0.31800758, 2.08547528), (-1.63624745, 0.21425655, 1.30595531),
(-1.24509731, 0.74268637, 0.46176133), (-1.3183353, 0.6960459, 2.20690531),
(-1.0399130826377951, -1.4521481683234707, 1.2864453881141027))}
self.assertEqual(new_xyz_1, expected_xyz_1)
self.assertAlmostEqual(calculate_param(coords=new_xyz_1['coords'], atoms=[7, 10]), 1.77, places=2)
self.assertAlmostEqual(calculate_param(coords=new_xyz_1['coords'], atoms=[4, 7, 10]), 109.5, places=1)
self.assertAlmostEqual(calculate_param(coords=new_xyz_1['coords'], atoms=[0, 4, 7, 10]), 300, places=1)

new_xyz_2 = converter.add_atom_to_xyz_using_internal_coords(xyz=xyz_1,
element='Cl',
r_index=4,
a_indices=(4, 0),
d_indices=(0, 4, 7),
r_value=2.70,
a_value=61.46,
d_value=-60.0,
opt_method='BFGS',
)
self.assertEqual(new_xyz_2['coords'][-1], (-1.0966631688164716, -1.5123640474266677, 1.296181153302943))
self.assertAlmostEqual(calculate_param(coords=new_xyz_1['coords'], atoms=[4, 10]), 2.70, places=1)
self.assertAlmostEqual(calculate_param(coords=new_xyz_1['coords'], atoms=[4, 0, 10]), 61.46, places=0)
self.assertAlmostEqual(calculate_param(coords=new_xyz_1['coords'], atoms=[0, 4, 7, 10]), 300, places=1)

xyz_3 = """C -1.01765390 -0.08355112 0.05206009
O 0.22303684 -0.79051481 0.05294172
C 0.35773087 -1.66017412 -0.97863090
O -0.45608483 -1.87500387 -1.86208833
H -1.82486467 -0.81522856 0.14629516
H -1.06962462 0.60119223 0.90442455
H -1.14968688 0.45844916 -0.88969505
H 1.33643417 -2.15859899 -0.90083808"""
new_xyz_3 = converter.add_atom_to_xyz_using_internal_coords(xyz=xyz_3,
element='O',
r_index=2,
a_indices=(1, 2),
d_indices=(3, 7, 2),
r_value=1.85,
a_value=77.4,
d_value=140,
)
expected_xyz = {'symbols': ('C', 'O', 'C', 'O', 'H', 'H', 'H', 'H', 'O'),
'isotopes': (12, 16, 12, 16, 1, 1, 1, 1, 16),
'coords': ((-1.0176539, -0.08355112, 0.05206009), (0.22303684, -0.79051481, 0.05294172),
(0.35773087, -1.66017412, -0.9786309), (-0.45608483, -1.87500387, -1.86208833),
(-1.82486467, -0.81522856, 0.14629516), (-1.06962462, 0.60119223, 0.90442455),
(-1.14968688, 0.45844916, -0.88969505), (1.33643417, -2.15859899, -0.90083808),
(1.4828269120297688, -2.3770289575185632, 0.3030781302151979))}
self.assertEqual(new_xyz_3, expected_xyz)
self.assertAlmostEqual(calculate_param(coords=new_xyz_3['coords'], atoms=[2, 8]), 1.85, places=2)
self.assertAlmostEqual(calculate_param(coords=new_xyz_3['coords'], atoms=[1, 2, 8]), 77.4, places=1)
self.assertAlmostEqual(calculate_param(coords=new_xyz_3['coords'], atoms=[3, 7, 2, 8]), 140, places=1)

xyz_4 = """C 2.44505336 0.33426556 -0.05839486
C 1.22268719 -0.52813666 0.01896600
O 1.23293886 -1.74943142 -0.03929182
O 0.11391589 0.24824549 0.16222715
C -1.11109125 -0.48993657 0.24566449
C -2.25017001 0.49859954 0.40179846
H 2.37692031 0.99705687 -0.92466676
H 3.32902965 -0.29956749 -0.17330464
H 2.54916374 0.91324784 0.86263828
H -1.08105124 -1.15952384 1.11255293
H -1.25277743 -1.07595826 -0.66934869
H -2.28059310 1.18899674 -0.44763085
H -3.21043340 -0.02017141 0.47000585
H -2.11200849 1.10694712 1.30175876"""
new_xyz_4 = converter.add_atom_to_xyz_using_internal_coords(xyz=xyz_4,
element='O',
r_index=1,
a_indices=(3, 1),
d_indices=(2, 0, 1),
r_value=1.85,
a_value=77.4,
d_value=140,
)
self.assertEqual(new_xyz_4['coords'][-1], (1.89932405279869, 0.9989208520839763, 0.8144268165647406))
self.assertAlmostEqual(calculate_param(coords=new_xyz_4['coords'], atoms=[1, 14]), 1.85, places=2)
self.assertAlmostEqual(calculate_param(coords=new_xyz_4['coords'], atoms=[3, 1, 14]), 77.4, places=1)
self.assertAlmostEqual(calculate_param(coords=new_xyz_4['coords'], atoms=[2, 0, 1, 14]), 140, places=1)


@classmethod
def tearDownClass(cls):
"""
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