Merge pull request #1714 from ReactionMechanismGenerator/arkane_speci…

…es_xyz

Modified the ArkaneSpecies.update_xyz_string() method

arkane/common.py

@@ -42,7 +42,7 @@
 
 import rmgpy.constants as constants
 from rmgpy import __version__
-from rmgpy.molecule.element import elementList
+from rmgpy.molecule.element import elementList, getElement
 from rmgpy.molecule.translator import toInChI, toInChIKey
 from rmgpy.pdep.collision import SingleExponentialDown
 from rmgpy.quantity import ScalarQuantity, ArrayQuantity
@@ -195,26 +195,22 @@ def update_species_attributes(self, species=None):
 
     def update_xyz_string(self):
         """
-        Return an xyz string built from self.conformer
+        Generate an xyz string built from self.conformer, and standardize the result
+
+        Returns:
+            str: 3D coordinates in an XYZ format.
         """
+        xyz_list = list()
         if self.conformer is not None and self.conformer.number is not None:
-            # generate the xyz-format string from the Conformer coordinates
-            xyz_string = '{0}\n{1}'.format(len(self.conformer.number.value_si), self.label)
-            for i, coorlist in enumerate(self.conformer.coordinates.value_si):
-                for element in elementList:
-                    if element.number == int(self.conformer.number.value_si[i]):
-                        element_symbol = element.symbol
-                        break
-                else:
-                    raise ValueError('Could not find element symbol corresponding to atom number {0}'.format(
-                        self.conformer.number.value_si[i]))
-                xyz_string += '\n{0} {1} {2} {3}'.format(element_symbol,
-                                                         coorlist[0],
-                                                         coorlist[1],
-                                                         coorlist[2])
-        else:
-            xyz_string = ''
-        return xyz_string
+            # generate the xyz-format string from self.conformer.coordinates and self.conformer.number
+            xyz_list.append(str(len(self.conformer.number.value_si)))
+            xyz_list.append(self.label)
+            for number, coordinate in zip(self.conformer.number.value_si, self.conformer.coordinates.value_si):
+                element_symbol = getElement(int(number)).symbol
+                row = '{0:4}'.format(element_symbol)
+                row += '{0:14.8f}{1:14.8f}{2:14.8f}'.format(*(coordinate * 1e10).tolist())  # convert m to Angstrom
+                xyz_list.append(row)
+        return '\n'.join(xyz_list)
 
     def save_yaml(self, path):
         """

arkane/commonTest.py

@@ -366,8 +366,18 @@ def test_create_and_load_yaml(self):
         self.assertEqual(arkane_spc.level_of_theory, 'cbs-qb3')
         self.assertIsInstance(arkane_spc.thermo_data, ThermoData)
         self.assertTrue(arkane_spc.use_hindered_rotors)
-        self.assertTrue('C 7.54e-14 1.193e-13 5.52e-14' in arkane_spc.xyz)
         self.assertIsInstance(arkane_spc.chemkin_thermo_string, str)
+        expected_xyz = """8
+C2H6
+C       0.00075400    0.00119300    0.00055200
+H       0.00074000    0.00117100    1.09413800
+H       1.04376600    0.00117100   -0.32820200
+H      -0.44760300    0.94289500   -0.32825300
+C      -0.76014200   -1.20389600   -0.55748300
+H      -0.76012800   -1.20387400   -1.65106900
+H      -0.31178500   -2.14559800   -0.22867800
+H      -1.80315400   -1.20387400   -0.22872900"""
+        self.assertEqual(arkane_spc.xyz, expected_xyz)
 
     def test_load_existing_yaml(self):
         """