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Correct over-squaring in internal coordinate objective function for adding an atom to XYZ #802

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Merged
alongd merged 2 commits into from
Dec 24, 2025
Merged

Correct over-squaring in internal coordinate objective function for adding an atom to XYZ #802

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e16c585
Correct over-squaring in internal coordinate objective function
alongd Sep 30, 2025
ea972cf
Tests: Updated converter tests for adding a new atom
alongd Dec 3, 2025
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11 changes: 8 additions & 3 deletions arc/species/converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,9 @@
ob.obErrorLog.SetOutputLevel(0)
logger = get_logger()

DIST_PRECISION = 0.01 # Angstrom
ANGL_PRECISION = 0.1 # rad (for both bond angle and dihedral)
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def str_to_xyz(xyz_str: str,
project_directory: Optional[str] = None,
Expand Down Expand Up @@ -2074,7 +2077,7 @@ def calculate_errors(result_coords):

def meets_precision(result_coords):
r_error, a_error, d_error = calculate_errors(result_coords)
return r_error < 0.01 and a_error < 0.1 and d_error < 0.1
return r_error < DIST_PRECISION and a_error < ANGL_PRECISION and d_error < ANGL_PRECISION

guess_functions = [
generate_initial_guess_r_a,
Expand Down Expand Up @@ -2262,7 +2265,9 @@ def angle_eq(x, y, z):
cross_product_length = np.linalg.norm(np.cross(BA, BX))
dot_product = np.dot(BA, BX)
calc_angle = math.atan2(cross_product_length, dot_product)
return (calc_angle - target_angle) ** 2
angle_diff = calc_angle - target_angle
wrapped_diff = np.arctan2(np.sin(angle_diff), np.cos(angle_diff)) # wrapped to the range (-pi, pi]
return wrapped_diff

return angle_eq

Expand Down Expand Up @@ -2310,7 +2315,7 @@ def dihedral_eq(x, y, z):
BC_norm = np.linalg.norm(BC)
cos_calc = np.dot(N1, N2) / (N1_norm * N2_norm)
sin_calc = np.dot(BC, np.cross(N1, N2)) / (BC_norm * N1_norm * N2_norm)
return (cos_calc - cos_d) ** 2 + (sin_calc - sin_d) ** 2
return np.sqrt((cos_calc - cos_d) ** 2 + (sin_calc - sin_d) ** 2)

return dihedral_eq

Expand Down
17 changes: 8 additions & 9 deletions arc/species/converter_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1082,7 +1082,6 @@ def test_zmat_from_xyz(self):
'A_9_0_1': 107.32624053955078, 'D_9_0_1_8': 243.79214484231346,
'R_6|7_4|4': 1.089653491973877},
'map': {0: 1, 1: 0, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9}}
self.assertEqual(zmat_1, expected_zmat_1)
self.assertTrue(_compare_zmats(zmat_1, expected_zmat_1))

zmat_2 = converter.zmat_from_xyz(xyz=self.xyz6['str'],
Expand Down Expand Up @@ -4669,7 +4668,7 @@ def test_add_atom_to_xyz_using_internal_coords(self):
(-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),
(-1.0413732051724125, -1.4526805980775839, 1.2873769860752802))}
(-1.0398666203453495, -1.4521333553792743, 1.2864271004043641))}
self.assertTrue(almost_equal_coords_lists(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)
Expand All @@ -4685,9 +4684,9 @@ def test_add_atom_to_xyz_using_internal_coords(self):
d_value=-60.0,
opt_method='BFGS',
)
self.assertAlmostEqual(new_xyz_2['coords'][-1][0], -1.065095539786487, places=3)
self.assertAlmostEqual(new_xyz_2['coords'][-1][1], -1.4737067126385224, places=3)
self.assertAlmostEqual(new_xyz_2['coords'][-1][2], 1.2912758496528232, places=3)
self.assertAlmostEqual(new_xyz_2['coords'][-1][0], -1.0407054376010356, places=2)
self.assertAlmostEqual(new_xyz_2['coords'][-1][1], -1.4428236405325816, places=2)
self.assertAlmostEqual(new_xyz_2['coords'][-1][2], 1.2912758496528232, places=2)
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)
Expand Down Expand Up @@ -4715,7 +4714,7 @@ def test_add_atom_to_xyz_using_internal_coords(self):
(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),
(1.4820209463152687, -2.3772302636106577, 0.30367261748030894))}
(1.4828150949768655, -2.377060198658591, 0.30306573909787815))}
self.assertTrue(almost_equal_coords(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)
Expand Down Expand Up @@ -4744,9 +4743,9 @@ def test_add_atom_to_xyz_using_internal_coords(self):
a_value=77.4,
d_value=140,
)
self.assertAlmostEqual(new_xyz_4['coords'][-1][0], 1.8986166253764283)
self.assertAlmostEqual(new_xyz_4['coords'][-1][1], 0.9987236974936107)
self.assertAlmostEqual(new_xyz_4['coords'][-1][2], 0.8154061174277444)
self.assertAlmostEqual(new_xyz_4['coords'][-1][0], 1.8986166253764283, places=2)
self.assertAlmostEqual(new_xyz_4['coords'][-1][1], 0.9987236974936107, places=2)
self.assertAlmostEqual(new_xyz_4['coords'][-1][2], 0.8154061174277444, places=2)
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)
Expand Down
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