fix deepcopy bug in autograd

tidy3d/components/base.py

@@ -261,13 +261,15 @@ def updated_copy(self, path: str = None, deep: bool = True, **kwargs) -> Tidy3dB
             sub_component = sub_component_list[index]
             sub_path = "/".join(path_components[2:])
 
-            sub_component_list[index] = sub_component.updated_copy(path=sub_path, **kwargs)
+            sub_component_list[index] = sub_component.updated_copy(
+                path=sub_path, deep=deep, **kwargs
+            )
             new_component = tuple(sub_component_list)
         else:
             sub_path = "/".join(path_components[1:])
-            new_component = sub_component.updated_copy(path=sub_path, **kwargs)
+            new_component = sub_component.updated_copy(path=sub_path, deep=deep, **kwargs)
 
-        return self._updated_copy(**{field_name: new_component})
+        return self._updated_copy(deep=deep, **{field_name: new_component})
 
     def _updated_copy(self, deep: bool = True, **kwargs) -> Tidy3dBaseModel:
         """Make copy of a component instance with ``**kwargs`` indicating updated field values."""

tidy3d/components/data/data_array.py

@@ -79,6 +79,23 @@ def __init__(self, data, *args, **kwargs):
             # NOTE: this is done because if we pass the traced array directly, it will create a
             # numpy array of `ArrayBox`, which is extremely slow
 
+    def __deepcopy__(self, memo):
+        """Define the behavior of ``deepcopy()`` a ``xr.DataArray``."""
+
+        # if we detect that this has tracers, we need to shallow copy
+        # otherwise it confuses autograd..
+        if self.has_tracers:
+            return self.__copy__()
+
+        return super().__deepcopy__(memo)
+
+    @property
+    def has_tracers(self) -> bool:
+        """Whether the ``DataArray`` has ``autograd`` derivative information."""
+        traced_data = self.data.dtype == object and isbox(self.data.flat[0])
+        traced_attrs = AUTOGRAD_KEY in self.attrs
+        return traced_data or traced_attrs
+
     @classmethod
     def __get_validators__(cls):
         """Validators that get run when :class:`.DataArray` objects are added to pydantic models."""

tidy3d/components/geometry/polyslab.py

@@ -1414,8 +1414,7 @@ def compute_derivative_vertices(
 
         # compute center positions between each edge
         edge_centers_plane = (vertices_next + vertices) / 2.0
-        edge_centers_axis = np.mean(self.slab_bounds) * np.ones(num_vertices)
-
+        edge_centers_axis = self.center_axis * np.ones(num_vertices)
         edge_centers_xyz = self.unpop_axis_vect(edge_centers_axis, edge_centers_plane)
 
         assert edge_centers_xyz.shape == (num_vertices, 3), "something bad happened"