f! converter tests

ReactionMechanismGenerator · Feb 13, 2025 · dc2296b · dc2296b
1 parent d2c7d5d
commit dc2296b
Showing 1 changed file with 25 additions and 5 deletions.
diff --git a/arc/species/converter_test.py b/arc/species/converter_test.py
@@ -5150,7 +5150,7 @@ 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),
-                                     (-1.0399130826377951, -1.4521481683234707, 1.2864453881141027))}
+                                     (-1.039912604216098, -1.452147996238371, 1.2864453361731114))}
         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)
@@ -5164,9 +5164,8 @@ def test_add_atom_to_xyz_using_internal_coords(self):
                                                                     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.assertEqual(new_xyz_2['coords'][-1], (-1.0397636319111052, -1.4416335009202348, 1.2856955291862382))
         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)
@@ -5194,7 +5193,7 @@ 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),
-                                   (1.4828269120297688, -2.3770289575185632, 0.3030781302151979))}
+                                   (1.4828289681716378, -2.3770210854217706, 0.303080727235734))}
         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)
@@ -5223,11 +5222,32 @@ def test_add_atom_to_xyz_using_internal_coords(self):
                                                                     a_value=77.4,
                                                                     d_value=140,
                                                                     )
-        self.assertEqual(new_xyz_4['coords'][-1], (1.89932405279869, 0.9989208520839763, 0.8144268165647406))
+        self.assertEqual(new_xyz_4['coords'][-1], (1.8993241065114546, 0.9989208721112074, 0.8144267234280602))
         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)
 
+        xyz_5 = """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_5 = converter.add_atom_to_xyz_using_internal_coords(xyz=xyz_5,
+                                                                    element='O',
+                                                                    r_index=2,
+                                                                    a_indices=(1, 2),
+                                                                    d_indices=(3, 7, 2),
+                                                                    r_value=1.8,
+                                                                    a_value=77,
+                                                                    d_value=140,
+                                                                    )
+        self.assertAlmostEqual(calculate_param(coords=new_xyz_5['coords'], atoms=[2, 8]), 1.8, places=2)
+        self.assertAlmostEqual(calculate_param(coords=new_xyz_5['coords'], atoms=[1, 2, 8]), 77, places=1)
+        self.assertAlmostEqual(calculate_param(coords=new_xyz_5['coords'], atoms=[3, 7, 2, 8]), 140, places=1)
+
 
     @classmethod
     def tearDownClass(cls):