MAINT: Convert to using np.atleast_2d

matscipy/dislocation.py

@@ -2618,24 +2618,37 @@ def _build_bulk_cyl(self, radius, core_positions, fix_rad, extension,
             Bulk cyl, cut down based on radius, complete
             with FixAtoms constraints
         '''
-        from matscipy.utils import radial_mask_from_polygon2D
-
-        if self_consistent is None:
-            self_consistent = self.self_consistent
 
-        # Validate core position, extension, and fixed_points args
-        errs = []
-        for argname, arg in [["core_position", core_positions], ["extension", extension], ["fixed_points", fixed_points]]:
+        def enforce_arr_shape(argname, arg, errs):
+            '''
+            Enforce correct array dimensionality for 
+            
+            '''
             if type(arg) == np.ndarray:
                 if arg.shape[-1] != 3:
                     # Needs to be 3d vectors
                     errs.append(f"Argument {argname} misspecified. Should be an array of shape (N, 3)")
                 if len(arg.shape) == 1:
                     # Convert all arrays to 2D
-                    arg.reshape((np.newaxis, arg.shape[-1]))
+                    arg = np.atleast_2d(arg)
             elif arg is not None:
                 # non-array, and not None arg provided, which is not allowed
                 errs.append(f"Argument {argname} misspecified. Should be an array of shape (N, 3)")
+            return arg, errs
+
+
+        from matscipy.utils import radial_mask_from_polygon2D
+
+        if self_consistent is None:
+            self_consistent = self.self_consistent
+
+        # Validate core position, extension, and fixed_points args
+        errs = []
+
+        core_positions, errs = enforce_arr_shape("core_positions", core_positions, errs)
+        extension, errs = enforce_arr_shape("extension", extension, errs)
+        fixed_points, errs = enforce_arr_shape("fixed_points", fixed_points, errs)
+
         if len(errs):
             raise RuntimeError("\n".join(errs))
 
@@ -2953,6 +2966,10 @@ def build_glide_configurations(self, radius, average_positions=False, **kwargs):
 
         fixed_points = np.vstack([initial_core_position, final_core_position])
 
+        if "partial_distance" in kwargs.keys():
+            # Account for dissociated glide
+            fixed_points[1, 0] += kwargs["partial_distance"] * self.glide_distance
+
         bulk_ini, disloc_ini, cyl_mask = self.build_cylinder(radius,
                                                    core_position=initial_core_position,
                                                    fixed_points=fixed_points,