Merge pull request #60 from pc494/fix-simulate-rotate-structure

Fix simulations of rotated structure

diffsims/generators/diffraction_generator.py

@@ -22,6 +22,7 @@
 
 import numpy as np
 from math import pi
+from transforms3d.euler import euler2mat
 
 from diffsims.sims.diffraction_simulation import DiffractionSimulation
 from diffsims.sims.diffraction_simulation import ProfileSimulation
@@ -83,6 +84,7 @@ def __init__(self,
     def calculate_ed_data(self,
                           structure,
                           reciprocal_radius,
+                          rotation=(0,0,0),
                           with_direct_beam=True):
         """Calculates the Electron Diffraction data for a structure.
 
@@ -95,6 +97,9 @@ def calculate_ed_data(self,
         reciprocal_radius : float
             The maximum radius of the sphere of reciprocal space to sample, in
             reciprocal angstroms.
+        rotation : tuple
+            Euler angles, in degrees, in the rzxz convention. Default is (0,0,0)
+            which aligns 'z' with the electron beam
         with_direct_beam : bool
             If True, the direct beam is included in the simulated diffraction
             pattern. If False, it is not.
@@ -118,6 +123,10 @@ def calculate_ed_data(self,
         spot_indicies, cartesian_coordinates, spot_distances = get_points_in_sphere(
             recip_latt, reciprocal_radius)
 
+        ai,aj,ak = np.deg2rad(rotation[0]),np.deg2rad(rotation[1]),np.deg2rad(rotation[2])
+        R = euler2mat(ai,aj,ak,axes='rzxz')
+        cartesian_coordinates = np.matmul(R,cartesian_coordinates.T).T
+
         # Identify points intersecting the Ewald sphere within maximum
         # excitation error and store the magnitude of their excitation error.
         r_sphere = 1 / wavelength

diffsims/generators/library_generator.py

@@ -30,7 +30,6 @@
 from diffsims.libraries.vector_library import DiffractionVectorLibrary
 
 from diffsims.utils.sim_utils import get_points_in_sphere
-from diffsims.utils.sim_utils import simulate_rotated_structure
 from diffsims.utils.vector_utils import get_angle_cartesian_vec
 
 
@@ -101,8 +100,7 @@ def get_diffraction_library(self,
             intensities = np.empty(num_orientations, dtype='object')
             # Iterate through orientations of each phase.
             for i, orientation in enumerate(tqdm(orientations, leave=False)):
-                matrix = euler2mat(*np.deg2rad(orientation), 'rzxz')
-                simulation = simulate_rotated_structure(diffractor, structure, matrix, reciprocal_radius, with_direct_beam)
+                simulation = diffractor.calculate_ed_data(structure,reciprocal_radius,rotation=orientation,with_direct_beam=with_direct_beam)
 
                 # Calibrate simulation
                 simulation.calibration = calibration

diffsims/utils/sim_utils.py

@@ -346,46 +346,6 @@ def simulate_kinematic_scattering(atomic_coordinates,
 
     return intensity
 
-
-def simulate_rotated_structure(diffraction_generator, structure, rotation_matrix, reciprocal_radius, with_direct_beam):
-    """Calculate electron diffraction data for a structure after rotating it.
-
-    Parameters
-    ----------
-    diffraction_generator : DiffractionGenerator
-        Diffraction generator used to simulate diffraction patterns
-    structure : diffpy.structure.Structure
-        Structure object to simulate
-    rotation_matrix : ndarray
-        3x3 matrix describing the base rotation to apply to the structure, applied on the left of the vector
-    reciprocal_radius : float
-        The maximum g-vector magnitude to be included in the simulations.
-    with_direct_beam : bool
-        Include the direct beam peak
-
-    Returns
-    -------
-    simulation : DiffractionSimulation
-        The simulation data generated from the given structure and rotation.
-    """
-    # Convert left multiply (input) to right multiply (diffpy)
-    stdbase = structure.lattice.stdbase
-    stdbase_inverse = np.linalg.inv(stdbase)
-    rotation_matrix_diffpy = stdbase_inverse @ rotation_matrix @ stdbase
-
-    lattice_rotated = diffpy.structure.lattice.Lattice(
-        *structure.lattice.abcABG(),
-        baserot=rotation_matrix_diffpy)
-    # Don't change the original
-    structure_rotated = diffpy.structure.Structure(structure)
-    structure_rotated.placeInLattice(lattice_rotated)
-
-    return diffraction_generator.calculate_ed_data(
-        structure_rotated,
-        reciprocal_radius,
-        with_direct_beam)
-
-
 def get_points_in_sphere(reciprocal_lattice, reciprocal_radius):
     """Finds all reciprocal lattice points inside a given reciprocal sphere.
     Utilised within the DiffractionGenerator.