Tests: zmat update_zmat_by_xyz()

Author: alongd

arc/species/zmat_test.py

@@ -9,6 +9,7 @@
 
 import arc.species.zmat as zmat
 from arc.exceptions import ZMatError
+from arc.species.converter import str_to_xyz
 from arc.species.species import ARCSpecies
 
 
@@ -2121,6 +2122,47 @@ def test_check_ordered_zmats(self):
         self.assertFalse(zmat.check_ordered_zmats(zmat_2, zmat_3))
         self.assertTrue(zmat.check_ordered_zmats(zmat_1, zmat_3))
 
+    def test_update_zmat_by_xyz(self):
+        """Test the update_zmat_by_xyz() function."""
+        xyz_1 = str_to_xyz("""C                 -2.02459021    0.31147541    0.00000000
+                              H                 -1.66791737    0.81587360    0.87365150
+                              H                 -3.09459021    0.31148859    0.00000000
+                              N                 -1.53460703   -1.07445983    0.00000000
+                              H                 -1.86794423   -1.54585934    0.81649790
+                              H                 -1.86794803   -1.54586068   -0.81649557
+                              O                 -1.54791529    0.98557766   -1.16759033
+                              H                 -1.82476883    1.90445028   -1.14258591""")
+        zmat_1 = zmat.xyz_to_zmat(xyz=xyz_1, mol=ARCSpecies(label='NCO', xyz=xyz_1).mol, consolidate=False)
+        xyz_2 = str_to_xyz("""C                 -2.12697003    0.60106045    0.00000000
+                              H                 -1.77029719    1.10545864    0.87365150
+                              H                 -3.19697003    0.60107363    0.00000000
+                              N                 -1.43222721   -1.36404487    0.00000000
+                              H                 -1.76556441   -1.83544438    0.81649790
+                              H                 -1.76556821   -1.83544572   -0.81649557
+                              O                 -1.65029511    1.27516270   -1.16759033
+                              H                 -1.11689351    0.67210652   -1.69047270""")
+        zmat_2 = zmat.update_zmat_by_xyz(zmat_1, xyz_2)
+        expected_zmat_2 = {'symbols': ('N', 'C', 'O', 'H', 'H', 'H', 'H', 'H'),
+                           'coords': ((None, None, None),
+                                      ('R_1_0', None, None),
+                                      ('R_2_1', 'A_2_1_0', None),
+                                      ('R_3_1', 'A_3_1_0', 'D_3_1_0_2'),
+                                      ('R_4_1', 'A_4_1_0', 'D_4_1_0_3'),
+                                      ('R_5_0', 'A_5_0_1', 'D_5_0_1_4'),
+                                      ('R_6_0', 'A_6_0_1', 'D_6_0_1_5'),
+                                      ('R_7_2', 'A_7_2_1', 'D_7_2_1_0')),
+                           'vars': {'A_2_1_0': 109.47120138885585, 'A_3_1_0': 109.47119974631076,
+                                    'A_4_1_0': 109.47123024500976, 'A_5_0_1': 109.47119888440865,
+                                    'A_6_0_1': 109.47120176378891, 'A_7_2_1': 109.49999787419641,
+                                    'D_3_1_0_2': 239.9999860097654, 'D_4_1_0_3': 240.00000689317258,
+                                    'D_5_0_1_4': 299.9998481421676, 'D_6_0_1_5': 120.00001661106755,
+                                    'D_7_2_1_0': 359.9999980909041, 'R_1_0': 2.084299994953611,
+                                    'R_2_1': 1.4300000625556986, 'R_3_1': 1.0700000390382562,
+                                    'R_4_1': 1.0699999276277037, 'R_5_0': 0.9999999701976772,
+                                    'R_6_0': 1.000000059604643, 'R_7_2': 0.9599999917546908},
+                           'map': {0: 3, 1: 0, 2: 6, 3: 1, 4: 2, 5: 4, 6: 5, 7: 7}}
+        self.assertEqual(zmat_2, expected_zmat_2)
+
 
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))