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BugFix: NUMBER_BY_SYMBOL is a dict #798

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Merged
kfir4444 merged 3 commits into from
Jan 3, 2026
Merged

BugFix: NUMBER_BY_SYMBOL is a dict #798

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d97acae
BugFix: NUMBER_BY_SYMBOL is a dict
alongd Sep 7, 2025
af60235
Tests: plotter save_irc_traj_animation()
alongd Dec 29, 2025
ecca8c5
Tests: Lower the accuracy of get_zmat_param_value almost equal checks
alongd Dec 31, 2025
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2 changes: 1 addition & 1 deletion arc/plotter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -751,7 +751,7 @@ def save_irc_traj_animation(irc_f_path, irc_r_path, out_path):
f.write(' Number Number Type X Y Z\n')
f.write(' ---------------------------------------------------------------------\n')
for i, symbol in enumerate(xyz['symbols']):
el_num, x, y, z = NUMBER_BY_SYMBOL(symbol), xs[i], ys[i], zs[i]
el_num, x, y, z = NUMBER_BY_SYMBOL[symbol], xs[i], ys[i], zs[i]
f.write(f' {i + 1:>5} {el_num} 0 {x} {y} {z}\n')
f.write(' ---------------------------------------------------------------------\n')
f.write(' GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad\n')
Expand Down
14 changes: 13 additions & 1 deletion arc/plotter_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -209,6 +209,16 @@ def test_delete_multi_species_output_file(self):
self.assertFalse(os.path.isfile(os.path.join(ARC_PATH, 'arc', 'testing', 'acetylene.log')))
self.assertFalse(os.path.isfile(os.path.join(ARC_PATH, 'arc', 'testing', 'N-Valeric_Acid.log')))

def test_save_irc_traj_animation(self):
"""Test the save_irc_traj_animation function"""
irc_f_path = os.path.join(ARC_PATH, 'arc', 'testing', 'irc', 'rxn_1_irc_1.out')
irc_r_path = os.path.join(ARC_PATH, 'arc', 'testing', 'irc', 'rxn_1_irc_2.out')
out_path = os.path.join(ARC_PATH, 'arc', 'testing', 'irc', 'rxn_1_irc_animation.out')
self.assertFalse(os.path.isfile(out_path))
plotter.save_irc_traj_animation(irc_f_path, irc_r_path, out_path)
self.assertTrue(os.path.isfile(out_path))


@classmethod
def tearDownClass(cls):
"""A function that is run ONCE after all unit tests in this class."""
Expand All @@ -218,7 +228,9 @@ def tearDownClass(cls):
files_to_remove = [os.path.join(ARC_PATH, 'arc', 'testing', 'bde_report_test.txt'),
os.path.join(ARC_PATH, 'arc', 'testing', 'water.log'),
os.path.join(ARC_PATH, 'arc', 'testing', 'acetylene.log'),
os.path.join(ARC_PATH, 'arc', 'testing', 'N-Valeric_Acid.log'),]
os.path.join(ARC_PATH, 'arc', 'testing', 'N-Valeric_Acid.log'),
os.path.join(ARC_PATH, 'arc', 'testing', 'irc', 'rxn_1_irc_animation.out'),
]
for file_path in files_to_remove:
if os.path.isfile(file_path):
os.remove(file_path)
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14 changes: 7 additions & 7 deletions arc/species/converter_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4003,7 +4003,7 @@ def test_modify_coords(self):
new_xyz = converter.modify_coords(coords=xyz1, indices=indices, new_value=new_val,
modification_type=modification_type, mol=mol1)
self.assertTrue(almost_equal_coords_lists(new_xyz, expected_xyz))
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 5)
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 3)

indices, new_val = [1, 0], -1.5
expected_xyz = {'symbols': ('O', 'C', 'C', 'O', 'H', 'H', 'H', 'H'), 'isotopes': (16, 12, 12, 16, 1, 1, 1, 1),
Expand Down Expand Up @@ -4034,7 +4034,7 @@ def test_modify_coords(self):
new_xyz = converter.modify_coords(coords=xyz1, indices=indices, new_value=new_val,
modification_type=modification_type, mol=mol1)
self.assertTrue(almost_equal_coords_lists(new_xyz, expected_xyz))
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 5)
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 3)

# test changing an angle to 180 degrees
indices, new_val = [0, 1, 2], 180
Expand Down Expand Up @@ -4080,7 +4080,7 @@ def test_modify_coords(self):
new_xyz = converter.modify_coords(coords=xyz1, indices=indices, new_value=new_val,
modification_type=modification_type, mol=mol1)
self.assertTrue(almost_equal_coords_lists(new_xyz, expected_xyz))
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 5)
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 3)

indices, new_val = [3, 2, 1, 0], -30
expected_xyz = {'symbols': ('O', 'C', 'C', 'O', 'H', 'H', 'H', 'H'), 'isotopes': (16, 12, 12, 16, 1, 1, 1, 1),
Expand Down Expand Up @@ -4131,7 +4131,7 @@ def test_modify_coords(self):
new_xyz = converter.modify_coords(coords=xyz1, indices=indices, new_value=new_val,
modification_type=modification_type, mol=mol1)
self.assertTrue(almost_equal_coords_lists(new_xyz, expected_xyz))
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 5)
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 3)

# test A_group modification
indices, new_val = [0, 1, 2], 160
Expand All @@ -4147,7 +4147,7 @@ def test_modify_coords(self):
new_xyz = converter.modify_coords(coords=xyz1, indices=indices, new_value=new_val,
modification_type=modification_type, mol=mol1)
self.assertTrue(almost_equal_coords_lists(new_xyz, expected_xyz))
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 5)
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 3)

indices, new_val = [1, 2, 5], 160
expected_xyz = {'symbols': ('O', 'C', 'C', 'S', 'O', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'),
Expand Down Expand Up @@ -4211,7 +4211,7 @@ def test_modify_coords(self):
new_xyz = converter.modify_coords(coords=xyz1, indices=indices, new_value=new_val,
modification_type=modification_type, mol=mol1)
self.assertTrue(almost_equal_coords_lists(new_xyz, expected_xyz))
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 5)
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 3)

indices, new_val = [5, 2, 1, 0], 180
expected_xyz = {'symbols': ('O', 'C', 'C', 'S', 'O', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'),
Expand Down Expand Up @@ -4278,7 +4278,7 @@ def test_modify_coords(self):
new_xyz = converter.modify_coords(coords=xyz1, indices=indices, new_value=new_val,
modification_type=modification_type, mol=mol1)
self.assertTrue(almost_equal_coords_lists(new_xyz, expected_xyz))
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 4)
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=indices, mol=mol1), new_val, 3)
self.assertAlmostEqual(converter.get_zmat_param_value(coords=xyz1, indices=[4, 1, 2, 3], mol=mol1),
176.7937925, 4)
self.assertAlmostEqual(converter.get_zmat_param_value(coords=new_xyz, indices=[4, 1, 2, 3], mol=mol1),
Expand Down
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