Rearranging make_coords_initial and fixing symmetry bug in auto mesh

tests/test_meshgenerate.py

@@ -326,4 +326,62 @@ def test_grid_refinement():
         )
 
 
-#     # print(max_shrink)
+def test_parse_structures():
+    """Test some aspects of the structure parsing."""
+
+    source = td.PointDipole(
+        source_time=td.GaussianPulse(freq0=1e14, fwidth=1e13),
+        size=(0, 0, 0),
+        polarization="Ex",
+    )
+
+    box1 = td.Structure(
+        geometry=td.Box(center=(0, 0, 0), size=(2, 2, 2)), medium=td.Medium(permittivity=9)
+    )
+    # covers box1 along x and y but not z, smaller permittivity
+    box2 = td.Structure(
+        geometry=td.Box(center=(0, 0, 0), size=(200, 200, 1)), medium=td.Medium(permittivity=4)
+    )
+    # covers box1 along x only, smaller permittivity
+    box3 = td.Structure(
+        geometry=td.Box(center=(0, 1.5, 0), size=(200, 4, 1)), medium=td.Medium(permittivity=4)
+    )
+    # fully covers one edge of box1
+    box4 = td.Structure(
+        geometry=td.Box(center=(0, 1.01, 0), size=(200, 0.2, 2)), medium=td.Medium(permittivity=2)
+    )
+
+    # Test that the box2 permittivity is used along z in the region where it fully covers box1
+    sim = td.Simulation(
+        size=(3, 3, 3),
+        grid_spec=td.GridSpec.auto(),
+        run_time=1e-13,
+        structures=[box1, box2],
+        sources=[source],
+    )
+    sizes = sim.grid.sizes.to_list[2]
+    assert sizes[sizes.size // 2] > 0.1
+
+    # Test that the box3 permittivity is not used along z as it doesn't fully cover box1
+    sim = td.Simulation(
+        size=(3, 3, 3),
+        grid_spec=td.GridSpec.auto(),
+        run_time=1e-13,
+        structures=[box1, box3],
+        sources=[source],
+    )
+    sizes = sim.grid.sizes.to_list[2]
+    assert sizes[sizes.size // 2] < 0.1
+
+    # Test that there is no grid boundary along y at the box1 right side covered by box4
+    boundaries = sim.grid.boundaries.to_list[1]
+    assert 1.0 in boundaries
+    sim = td.Simulation(
+        size=(3, 3, 3),
+        grid_spec=td.GridSpec.auto(),
+        run_time=1e-13,
+        structures=[box1, box4],
+        sources=[source],
+    )
+    boundaries = sim.grid.boundaries.to_list[1]
+    assert 1.0 not in boundaries

tidy3d/components/grid/grid_spec.py

@@ -12,6 +12,7 @@
 from ..types import Axis, Symmetry
 from ..source import SourceType
 from ..structure import Structure
+from ..geometry import Box
 from ...log import SetupError, log
 from ...constants import C_0, MICROMETER
 
@@ -22,11 +23,9 @@ class GridSpec1d(Tidy3dBaseModel, ABC):
 
     def make_coords(  # pylint:disable = too-many-arguments
         self,
-        center: float,
-        size: float,
         axis: Axis,
         structures: List[Structure],
-        symmetry: Symmetry,
+        symmetry: Tuple[Symmetry, Symmetry, Symmetry],
         wavelength: pd.PositiveFloat,
         num_pml_layers: Tuple[pd.NonNegativeInt, pd.NonNegativeInt],
     ) -> Coords1D:
@@ -35,17 +34,13 @@ def make_coords(  # pylint:disable = too-many-arguments
 
         Parameters
         ----------
-        center : float
-            Center of simulation domain along a given axis.
-        size : float
-            Size of simulation domain along a given axis.
         axis : Axis
             Axis of this direction.
         structures : List[Structure]
-            List of structures present in simulation.
-        symmetry : Symmetry
-            Reflection symmetry across a plane bisecting the simulation domain normal
-            to a given axis.
+            List of structures present in simulation, the first one being the simulation domain.
+        symmetry : Tuple[Symmetry, Symmetry, Symmetry]
+            Reflection symmetry across a plane bisecting the simulation domain
+            normal to each of the three axes.
         wavelength : float
             Free-space wavelength.
         num_pml_layers : Tuple[int, int]
@@ -59,16 +54,21 @@ def make_coords(  # pylint:disable = too-many-arguments
 
         # Determine if one should apply periodic boundary condition.
         # This should only affect auto nonuniform mesh generation for now.
-        is_periodic = sum(num_pml_layers) == 0
+        is_periodic = sum(num_pml_layers) == 0 and symmetry[axis] == 0
 
         # generate boundaries
         bound_coords = self._make_coords_initial(
-            center, size, axis, structures, wavelength, is_periodic
+            axis=axis,
+            structures=structures,
+            wavelength=wavelength,
+            symmetry=symmetry,
+            is_periodic=is_periodic,
         )
 
         # incooperate symmetries
-        if symmetry != 0:
+        if symmetry[axis] != 0:
             # Offset to center if symmetry present
+            center = structures[0].geometry.center[axis]
             center_ind = np.argmin(np.abs(center - bound_coords))
             bound_coords += center - bound_coords[center_ind]
             bound_coords = bound_coords[bound_coords >= center]
@@ -81,9 +81,9 @@ def make_coords(  # pylint:disable = too-many-arguments
     @abstractmethod
     def _make_coords_initial(
         self,
-        center: float,
-        size: pd.NonNegativeFloat,
-        *args,
+        axis: Axis,
+        structures: List[Structure],
+        **kwargs,
     ) -> Coords1D:
         """Generate 1D coords to be used as grid boundaries, based on simulation parameters.
         Symmetry, PML etc. are not considered in this method.
@@ -92,11 +92,9 @@ def _make_coords_initial(
 
         Parameters
         ----------
-        center : float
-            Center of simulation domain along a given axis.
-        size : float
-            Sie of simulation domain along a given axis.
-        *args
+        structures : List[Structure]
+            List of structures present in simulation, the first one being the simulation domain.
+        **kwargs
             Other arguments
 
         Returns
@@ -152,19 +150,19 @@ class UniformGrid(GridSpec1d):
 
     def _make_coords_initial(
         self,
-        center: float,
-        size: float,
-        *args,
+        axis: Axis,
+        structures: List[Structure],
+        **kwargs,
     ) -> Coords1D:
         """Uniform 1D coords to be used as grid boundaries.
 
         Parameters
         ----------
-        center : float
-            Center of simulation domain along a given axis.
-        size : float
-            Size of simulation domain along a given axis.
-        *args:
+        axis : Axis
+            Axis of this direction.
+        structures : List[Structure]
+            List of structures present in simulation, the first one being the simulation domain.
+        **kwargs:
             Other arguments all go here.
 
         Returns
@@ -173,6 +171,8 @@ def _make_coords_initial(
             1D coords to be used as grid boundaries.
         """
 
+        center, size = structures[0].geometry.center[axis], structures[0].geometry.size[axis]
+
         # Take a number of steps commensurate with the size; make dl a bit smaller if needed
         num_cells = int(np.ceil(size / self.dl))
 
@@ -210,19 +210,19 @@ class CustomGrid(GridSpec1d):
 
     def _make_coords_initial(
         self,
-        center: float,
-        size: float,
-        *args,
+        axis: Axis,
+        structures: List[Structure],
+        **kwargs,
     ) -> Coords1D:
         """Customized 1D coords to be used as grid boundaries.
 
         Parameters
         ----------
-        center : float
-            Center of simulation domain along a given axis.
-        size : float
-            Size of simulation domain along a given axis.
-        *args
+        axis : Axis
+            Axis of this direction.
+        structures : List[Structure]
+            List of structures present in simulation, the first one being the simulation domain.
+        *kwargs
             Other arguments all go here.
 
         Returns
@@ -231,6 +231,8 @@ def _make_coords_initial(
             1D coords to be used as grid boundaries.
         """
 
+        center, size = structures[0].geometry.center[axis], structures[0].geometry.size[axis]
+
         # get bounding coordinates
         dl = np.array(self.dl)
         bound_coords = np.append(0.0, np.cumsum(dl))
@@ -284,29 +286,27 @@ class AutoGrid(GridSpec1d):
         description="The type of mesher to use to generate the grid automatically.",
     )
 
-    def _make_coords_initial(  # pylint:disable = arguments-differ, too-many-arguments
+    def _make_coords_initial(  # pylint:disable=too-many-arguments,arguments-differ,too-many-locals
         self,
-        center: float,
-        size: float,
         axis: Axis,
         structures: List[Structure],
         wavelength: float,
+        symmetry: Symmetry,
         is_periodic: bool,
     ) -> Coords1D:
         """Customized 1D coords to be used as grid boundaries.
 
         Parameters
         ----------
-        center : float
-            Center of simulation domain along a given axis.
-        size : float
-            Size of simulation domain along a given axis.
         axis : Axis
             Axis of this direction.
         structures : List[Structure]
             List of structures present in simulation.
         wavelength : float
             Free-space wavelength.
+        symmetry : Tuple[Symmetry, Symmetry, Symmetry]
+            Reflection symmetry across a plane bisecting the simulation domain
+            normal to each of the three axes.
         is_periodic : bool
             Apply periodic boundary condition or not.
 
@@ -316,14 +316,29 @@ def _make_coords_initial(  # pylint:disable = arguments-differ, too-many-argumen
             1D coords to be used as grid boundaries.
         """
 
+        sim_cent = list(structures[0].geometry.center)
+        sim_size = list(structures[0].geometry.size)
+        for dim, sym in enumerate(symmetry):
+            if sym != 0:
+                sim_cent[dim] += sim_size[dim] / 4
+                sim_size[dim] /= 2
+
+        struct_list = [
+            Structure(geometry=Box(center=sim_cent, size=sim_size), medium=structures[0].medium)
+        ]
+        # Remove structures that are outside the simulation domain (with symmetry applied)
+        for structure in structures[1:]:
+            if struct_list[0].geometry.intersects(structure.geometry):
+                struct_list.append(structure)
+
         # parse structures
         interval_coords, max_dl_list = self.mesher.parse_structures(
-            axis, structures, wavelength, self.min_steps_per_wvl
+            axis, struct_list, wavelength, self.min_steps_per_wvl
         )
         # Put just a single pixel if 2D-like simulation
         if interval_coords.size == 1:
             dl = wavelength / self.min_steps_per_wvl
-            return np.array([center - dl / 2, center + dl / 2])
+            return np.array([sim_cent[axis] - dl / 2, sim_cent[axis] + dl / 2])
 
         # generate mesh steps
         interval_coords = np.array(interval_coords).flatten()
@@ -444,38 +459,30 @@ def make_grid(
             Entire simulation grid.
         """
 
-        center, size = structures[0].geometry.center, structures[0].geometry.size
-
         # Set up wavelength for automatic mesh generation if needed.
         wavelength = self.wavelength
         if self.wavelength is None and self.auto_grid_used:
             wavelength = self.wavelength_from_sources(sources)
             log.info(f"Auto meshing using wavelength {wavelength:1.4f} defined from sources.")
 
         coords_x = self.grid_x.make_coords(
-            center=center[0],
-            size=size[0],
             axis=0,
             structures=structures + self.override_structures,
-            symmetry=symmetry[0],
+            symmetry=symmetry,
             wavelength=wavelength,
             num_pml_layers=num_pml_layers[0],
         )
         coords_y = self.grid_y.make_coords(
-            center=center[1],
-            size=size[1],
             axis=1,
             structures=structures + self.override_structures,
-            symmetry=symmetry[1],
+            symmetry=symmetry,
             wavelength=wavelength,
             num_pml_layers=num_pml_layers[1],
         )
         coords_z = self.grid_z.make_coords(
-            center=center[2],
-            size=size[2],
             axis=2,
             structures=structures + self.override_structures,
-            symmetry=symmetry[2],
+            symmetry=symmetry,
             wavelength=wavelength,
             num_pml_layers=num_pml_layers[2],
         )