get_cartesian_coordinates function and test

Author: cadenmyers13

src/diffpy/structure/structure.py

@@ -174,7 +174,7 @@ def getLastAtom(self):
         last_atom = self[-1]
         return last_atom
 
-    def get_chemical_symbols(self, include_charge_state=False):
+    def get_chemical_symbols(self):
         """Return list of chemical symbols for all `Atoms` in this
         structure.
 
@@ -194,7 +194,8 @@ def get_fractional_coordinates(self):
         Returns
         -------
         numpy.ndarray
-            The array of fractional coordinates of all `Atoms` in this structure.
+            The array of fractional coordinates of all `Atoms` in this structure
+            in the same order as `Structure.get_chemical_symbols()`.
         """
         coords = numpy.array([a.xyz for a in self])
         return coords
@@ -206,9 +207,12 @@ def get_cartesian_coordinates(self):
         Returns
         -------
         numpy.ndarray
-            The array of Cartesian coordinates of all `Atoms` in this structure.
+            The array of Cartesian coordinates of all `Atoms` in this structure
+            in the same order as `Structure.get_chemical_symbols()`.
         """
         cartn_coords = numpy.array([a.xyz_cartn for a in self])
+        # round coordinates to avoid negative numbers close to zero
+        cartn_coords = numpy.round(cartn_coords, 5)
         return cartn_coords
 
     def get_anisotropic_displacement_parameters(self):

tests/test_structure.py

@@ -634,12 +634,22 @@ def test_get_fractional_coordinates(datafile):
             [0.5, 0.5, 0.0],
         ]
     )
-    assert actual_fractional_coords.tolist() == expected_fractional_coords.tolist()
+    assert numpy.allclose(actual_fractional_coords, expected_fractional_coords)
 
 
-# def test_get_cartesian_coordinates(datafile):
-#     """Check Structure.get_cartesian_coordinates()"""
-#     assert False
+def test_get_cartesian_coordinates(datafile):
+    """Check Structure.get_cartesian_coordinates()"""
+    cdse_stru = Structure(filename=datafile("CdSe_bulk.stru"))
+    actual_cartesian_coords = cdse_stru.get_cartesian_coordinates()
+    expected_cartesian_coords = numpy.array(
+        [
+            [1.22284, 2.1176, 0.0],
+            [2.44495, 0.0, 3.45301],
+            [1.22284, 2.1176, 2.60129],
+            [2.44495, 0.0, 6.05431],
+        ]
+    )
+    assert numpy.allclose(actual_cartesian_coords, expected_cartesian_coords)
 
 
 # def test_get_anisotropic_displacement_parameters(datafile):