Damian's comments

Author: dbochkov-flexcompute

tests/test_components/test_absorbers.py

@@ -62,7 +62,7 @@ def test_port_absorbers_simulations():
         ],
     )
 
-    _ = td.Simulation(
+    sim = td.Simulation(
         center=[0, 0, 0],
         size=[1, 1, 1],
         grid_spec=td.GridSpec.auto(
@@ -79,6 +79,7 @@ def test_port_absorbers_simulations():
             )
         ],
     )
+    sim.plot(x=0)
 
     # validate no fully anisotropic mediums
     with pytest.raises(SetupError):
@@ -290,7 +291,7 @@ def test_abc_boundaries_simulations():
     )
 
     # in Simulation
-    _ = td.Simulation(
+    sim = td.Simulation(
         center=[0, 0, 0],
         size=[1, 1, 1],
         grid_spec=td.GridSpec.auto(
@@ -301,6 +302,7 @@ def test_abc_boundaries_simulations():
         run_time=1e-20,
         boundary_spec=td.BoundarySpec.all_sides(td.ABCBoundary()),
     )
+    sim.plot(x=0)
 
     # validate ABC medium is not anisotorpic
     with pytest.raises(pydantic.ValidationError):
@@ -402,7 +404,7 @@ def test_abc_boundaries_simulations():
         )
 
     # disallow ABC boundaries in zero dimensions
-    with pytest.raises(pydantic.ValidationError):
+    with AssertLogLevel("WARNING", contains_str="The simulation has zero size along the z axis"):
         _ = td.Simulation(
             center=[0, 0, 0],
             size=[1, 1, 0],

tidy3d/components/boundary.py

@@ -15,7 +15,7 @@
     PlotParams,
     plot_params_absorber,
 )
-from tidy3d.constants import EPSILON_0, MU_0, PML_SIGMA
+from tidy3d.constants import CONDUCTIVITY, EPSILON_0, MU_0, PML_SIGMA
 from tidy3d.exceptions import DataError, SetupError, ValidationError
 from tidy3d.log import log
 
@@ -86,7 +86,6 @@ class PMCBoundary(BoundaryEdge):
     """Perfect magnetic conductor boundary condition class."""
 
 
-# ABC keyword
 class AbstractABCBoundary(BoundaryEdge, ABC):
     """One-way wave equation absorbing boundary conditions abstract base class."""
 
@@ -96,12 +95,13 @@ class ABCBoundary(AbstractABCBoundary):
     See, for example, John B. Schneider, Understanding the Finite-Difference Time-Domain Method, Chapter 6.
     """
 
-    permittivity: Optional[pd.PositiveFloat] = pd.Field(
+    permittivity: Optional[float] = pd.Field(
         None,
         title="Effective Permittivity",
         description="Effective permittivity for determining propagation constant. "
         "If ``None``, this value will be automatically inferred from the medium at "
         "the domain boundary and the central frequency of the source.",
+        ge=1.0,
     )
 
     conductivity: Optional[pd.NonNegativeFloat] = pd.Field(
@@ -110,6 +110,7 @@ class ABCBoundary(AbstractABCBoundary):
         description="Effective conductivity for determining propagation constant. "
         "If ``None``, this value will be automatically inferred from the medium at "
         "the domain boundary and the central frequency of the source.",
+        units=CONDUCTIVITY,
     )
 
     @pd.validator("conductivity", always=True)
@@ -237,7 +238,7 @@ class InternalAbsorber(Box):
     direction: Direction = pd.Field(
         ...,
         title="Absorption Direction",
-        description="Direction in which field is absorbed.",
+        description="Indicates which direction of traveling waves are absorbed.",
     )
 
     grid_shift: int = pd.Field(

tidy3d/components/geometry/utils.py

@@ -15,7 +15,9 @@
 from tidy3d.components.types import (
     ArrayFloat2D,
     Axis,
+    Bound,
     Coordinate,
+    Direction,
     MatrixReal4x4,
     PlanePosition,
     Shapely,
@@ -486,3 +488,77 @@ def snap_point_to_grid(
         snapped_point[axis] = get_closest_value(point[axis], snap_coords, min_upper_bound_idx)
 
     return tuple(snapped_point)
+
+
+def _shift_value_signed(
+    obj: Box,
+    grid: Grid,
+    bounds: Bound,
+    direction: Direction,
+    shift: int,
+    name: Optional[str] = None,
+) -> float:
+    """Calculate the signed distance corresponding to moving the object by ``shift`` number
+    of cells in the positive or negative ``direction`` along the dimension given by
+    ``obj._normal_axis``.
+    """
+    if name is None:
+        name = f"A '{obj.type}'"
+
+    # get the grid boundaries and sizes along obj normal from the simulation
+    normal_axis = obj._normal_axis
+    grid_boundaries = grid.boundaries.to_list[normal_axis]
+    grid_centers = grid.centers.to_list[normal_axis]
+
+    # get the index of the grid cell where the obj lies
+    obj_position = obj.center[normal_axis]
+    obj_pos_gt_grid_bounds = np.argwhere(obj_position > grid_boundaries)
+
+    # no obj index can be determined
+    if len(obj_pos_gt_grid_bounds) == 0 or obj_position > grid_boundaries[-1]:
+        raise SetupError(
+            f"{name} position '{obj_position}' is outside of simulation bounds '({grid_boundaries[0]}, {grid_boundaries[-1]})' along dimension '{'xyz'[normal_axis]}'."
+        )
+    obj_index = obj_pos_gt_grid_bounds[-1]
+
+    # shift the obj to the left
+    signed_shift = shift if direction == "+" else -shift
+    if signed_shift < 0:
+        shifted_index = obj_index + signed_shift
+        if shifted_index < 0 or grid_centers[shifted_index] <= bounds[0][normal_axis]:
+            raise SetupError(
+                f"{name} normal is less than 2 cells to the boundary "
+                f"on -{'xyz'[normal_axis]} side. "
+                "Please either increase the mesh resolution near the obj or "
+                "move the obj away from the boundary."
+            )
+
+    # shift the obj to the right
+    else:
+        shifted_index = obj_index + signed_shift
+        if (
+            shifted_index >= len(grid_centers)
+            or grid_centers[shifted_index] >= bounds[1][normal_axis]
+        ):
+            raise SetupError(
+                f"{name} normal is less than 2 cells to the boundary "
+                f"on +{'xyz'[normal_axis]} side."
+                "Please either increase the mesh resolution near the obj or "
+                "move the obj away from the boundary."
+            )
+
+    new_pos = grid_centers[shifted_index]
+    return new_pos - obj_position
+
+
+def _shift_object(obj: Box, grid: Grid, bounds: Bound, direction: Direction, shift: int) -> Box:
+    """Move a plane-like object by ``shift`` number
+    of cells in the positive or negative ``direction`` along the dimension given by
+    ``obj._normal_axis``.
+    """
+    shift = _shift_value_signed(obj=obj, grid=grid, bounds=bounds, direction=direction, shift=shift)
+    new_center = np.array(obj.center)
+    new_center[obj._normal_axis] += shift
+    # note: if this needs to be generalized beyond absorber, one would probably
+    # slightly adjust the code below regarding grid_shift
+    return obj.updated_copy(center=tuple(new_center), grid_shift=0)

tidy3d/components/simulation.py

@@ -52,7 +52,7 @@
 from .data.utils import CustomSpatialDataType
 from .geometry.base import Box, Geometry, GeometryGroup
 from .geometry.mesh import TriangleMesh
-from .geometry.utils import flatten_groups, traverse_geometries
+from .geometry.utils import _shift_object, flatten_groups, traverse_geometries
 from .geometry.utils_2d import get_bounds, get_thickened_geom, snap_coordinate_to_grid, subdivide
 from .grid.grid import Coords, Coords1D, Grid
 from .grid.grid_spec import AutoGrid, GridSpec, UniformGrid
@@ -113,7 +113,6 @@
     Ax,
     Axis,
     CoordinateOptional,
-    Direction,
     FreqBound,
     InterpMethod,
     PermittivityComponent,
@@ -470,8 +469,10 @@ def _shifted_internal_absorbers(self) -> list[InternalAbsorber]:
         """List of absorber shifted to their actual locations based on their grid_shift's."""
 
         return [
-            self._shift_object(
+            _shift_object(
                 obj=absorber,
+                grid=self.grid,
+                bounds=self.bounds,
                 direction=absorber.direction,
                 shift=absorber.grid_shift,
             )
@@ -1876,7 +1877,7 @@ def subsection(
             Used internally.
         deep_copy: bool = True
             Recursively copy all nested objects in the generated simulation object.
-        internal_absorbers : Tuple[SourceType, ...] = None
+        internal_absorbers : Tuple[InternalAbsorber, ...] = None
             New list of internal absorbers. If ``None``, then the absorbers intersecting the new simulation
             domain are inherited from the original simulation.
         **kwargs
@@ -2108,73 +2109,6 @@ def _invalidate_solver_cache(self) -> None:
         """Clear cached attributes that become stale when subpixel changes."""
         self._cached_properties.pop("_mode_solver", None)
 
-    def _shift_value_signed(
-        self, obj: Box, direction: Direction, shift: int, name: Optional[str] = None
-    ) -> float:
-        """Calculate the signed distance corresponding to moving the object by ``shift`` number
-        of cells in the positive or negative ``direction`` along the dimension given by
-        ``obj._normal_axis``.
-        """
-        if name is None:
-            name = f"A '{obj.type}'"
-
-        # get the grid boundaries and sizes along obj normal from the simulation
-        normal_axis = obj._normal_axis
-        grid_boundaries = self.grid.boundaries.to_list[normal_axis]
-        grid_centers = self.grid.centers.to_list[normal_axis]
-
-        # get the index of the grid cell where the obj lies
-        obj_position = obj.center[normal_axis]
-        obj_pos_gt_grid_bounds = np.argwhere(obj_position > grid_boundaries)
-
-        # no obj index can be determined
-        if len(obj_pos_gt_grid_bounds) == 0 or obj_position > grid_boundaries[-1]:
-            raise SetupError(
-                f"{name} position '{obj_position}' is outside of simulation bounds '({grid_boundaries[0]}, {grid_boundaries[-1]})' along dimension '{'xyz'[normal_axis]}'."
-            )
-        obj_index = obj_pos_gt_grid_bounds[-1]
-
-        # shift the obj to the left
-        signed_shift = shift if direction == "+" else -shift
-        if signed_shift < 0:
-            shifted_index = obj_index + signed_shift
-            if shifted_index < 0 or grid_centers[shifted_index] <= self.bounds[0][normal_axis]:
-                raise SetupError(
-                    f"{name} normal is less than 2 cells to the boundary "
-                    f"on -{'xyz'[normal_axis]} side. "
-                    "Please either increase the mesh resolution near the obj or "
-                    "move the obj away from the boundary."
-                )
-
-        # shift the obj to the right
-        else:
-            shifted_index = obj_index + signed_shift
-            if (
-                shifted_index >= len(grid_centers)
-                or grid_centers[shifted_index] >= self.bounds[1][normal_axis]
-            ):
-                raise SetupError(
-                    f"{name} normal is less than 2 cells to the boundary "
-                    f"on +{'xyz'[normal_axis]} side."
-                    "Please either increase the mesh resolution near the obj or "
-                    "move the obj away from the boundary."
-                )
-
-        new_pos = grid_centers[shifted_index]
-        return new_pos - obj_position
-
-    def _shift_object(self, obj: InternalAbsorber, direction: Direction, shift: int) -> float:
-        """Move a plane-like object by ``shift`` number
-        of cells in the positive or negative ``direction`` along the dimension given by
-        ``obj._normal_axis``.
-        """
-        shift = self._shift_value_signed(obj, direction, shift)
-        new_center = np.array(obj.center)
-        new_center[obj._normal_axis] += shift
-        # note: if this needs to be generalized beyond absorber, one would probably
-        # slightly adjust the code below regarding grid_shift
-        return obj.updated_copy(center=tuple(new_center), grid_shift=0)
-
 
 class Simulation(AbstractYeeGridSimulation):
     """
@@ -3496,7 +3430,10 @@ def _projection_monitors_homogeneous(cls, val, values):
 
     @classmethod
     def _get_mediums_on_abc(
-        cls, boundary_spec, medium, center, size, structures
+        cls,
+        boundary_spec: BoundarySpec,
+        sim_structure: Structure,
+        structures: tuple[Structure, ...],
     ) -> tuple[
         list[MediumType3D],
         list[MediumType3D],
@@ -3510,19 +3447,14 @@ def _get_mediums_on_abc(
         """
 
         # list of structures including background as a Box()
-        structure_bg = Structure(
-            geometry=Box(
-                size=size,
-                center=center,
-            ),
-            medium=medium,
-        )
-
-        surfaces = Box.surfaces(
-            center=structure_bg.geometry.center, size=structure_bg.geometry.size
+        surface_box = sim_structure.geometry
+        # expand zero dimensions to make sure surface are extracted correctly and treatment is uniform
+        surface_box = surface_box.updated_copy(
+            size=[1e-6 if s == 0 else s for s in surface_box.size]
         )
+        surfaces = Box.surfaces(center=surface_box.center, size=surface_box.size)
 
-        total_structures = [structure_bg, *list(structures)]
+        total_structures = [sim_structure, *list(structures)]
 
         mediums = []
         for boundary, surface in zip(np.ravel(boundary_spec.to_list), surfaces):
@@ -3541,14 +3473,14 @@ def _abc_boundaries_homogeneous(cls, val, values):
         if val is None:
             return val
 
-        # expand zero dimensions to make the treatment uniform
-        size = [fp_eps if s == 0 else s for s in values.get("size")]
+        sim_structure = Structure(
+            geometry=Box(size=values.get("size"), center=values.get("center")),
+            medium=values.get("medium"),
+        )
 
         mediums_all_sides = cls._get_mediums_on_abc(
             boundary_spec=val,
-            medium=values.get("medium"),
-            size=size,
-            center=values.get("center"),
+            sim_structure=sim_structure,
             structures=values.get("structures") or [],
         )
 

tidy3d/components/source/field.py

@@ -406,7 +406,7 @@ class ModeSource(DirectionalSource, PlanarSource, BroadbandSource):
 
     frame: Optional[PECFrame] = pydantic.Field(
         None,
-        title="Source Frame.",
+        title="Source Frame",
         description="Add a thin frame around the source during the FDTD run to improve "
         "the injection quality. The frame is positioned along the primal grid lines "
         "so that it aligns with the boundaries of the mode solver used to obtain the source profile.",

tidy3d/plugins/smatrix/component_modelers/base.py

@@ -12,6 +12,7 @@
 from tidy3d.components.base import Tidy3dBaseModel, cached_property
 from tidy3d.components.data.data_array import DataArray
 from tidy3d.components.data.sim_data import SimulationData
+from tidy3d.components.geometry.utils import _shift_value_signed
 from tidy3d.components.simulation import Simulation
 from tidy3d.components.types import FreqArray
 from tidy3d.config import config
@@ -255,8 +256,13 @@ def inv(matrix: DataArray):
     def _shift_value_signed(self, port: Union[Port, WavePort]) -> float:
         """How far (signed) to shift the source from the monitor."""
 
-        return self.simulation._shift_value_signed(
-            obj=port, direction=port.direction, shift=-2, name=f"Port {port.name}"
+        return _shift_value_signed(
+            obj=port,
+            grid=self.simulation.grid,
+            bounds=self.simulation.bounds,
+            direction=port.direction,
+            shift=-2,
+            name=f"Port {port.name}",
         )
 
     def sim_data_by_task_name(self, task_name: str) -> SimulationData: