Adress #234

Author: viljarjf

diffsims/crystallography/_diffracting_vector.py

@@ -202,11 +202,11 @@ def intensity(self, value):
             raise ValueError("Length of intensity array must match number of vectors")
         self._intensity = np.array(value)
 
-    def calculate_structure_factor(self):
-        raise NotImplementedError(
-            "Structure factor calculation not implemented for DiffractionVector. "
-            "Use ReciprocalLatticeVector instead."
-        )
+    # def calculate_structure_factor(self):
+    #     raise NotImplementedError(
+    #         "Structure factor calculation not implemented for DiffractionVector. "
+    #         "Use ReciprocalLatticeVector instead."
+    #     )
 
     def to_flat_polar(self):
         """Return the vectors in polar coordinates as projected onto the x,y plane"""

diffsims/crystallography/reciprocal_lattice_vector.py

@@ -644,7 +644,9 @@ def allowed(self):
 
     # ------------------------- Custom methods ----------------------- #
 
-    def calculate_structure_factor(self, scattering_params="xtables"):
+    def calculate_structure_factor(
+        self, scattering_params="xtables", debye_waller_factors=None
+    ):
         r"""Populate :attr:`structure_factor` with the complex
         kinematical structure factor :math:`F_{hkl}` for each vector.
 
@@ -653,6 +655,8 @@ def calculate_structure_factor(self, scattering_params="xtables"):
         scattering_params : str
             Which atomic scattering factors to use, either ``"xtables"``
             (default) or ``"lobato"``.
+        debye_waller_factors: dict
+            Debye-Waller factors for atoms in the structure.
 
         Examples
         --------
@@ -712,6 +716,7 @@ def calculate_structure_factor(self, scattering_params="xtables"):
             structure=self.phase.structure,
             g_indices=hkl_unique,
             g_hkls_array=self.phase.structure.lattice.rnorm(hkl_unique),
+            debye_waller_factors=debye_waller_factors,
             scattering_params=scattering_params,
         )
 
@@ -933,6 +938,12 @@ def sanitise_phase(self):
         space_group = self.phase.space_group
         structure = self.phase.structure
 
+        # Lattice basis transform for hexagonal crystals can sometimes move atoms below 0
+        for atom in structure:
+            for i in range(3):
+                if -1e-6 < atom.xyz[i] < 0:
+                    atom.xyz[i] = 0
+
         new_structure = _expand_unit_cell(space_group, structure)
         for atom in new_structure:
             if np.issubdtype(type(atom.element), np.integer):