Update latest docs

.github/workflows/release.yml

@@ -81,7 +81,7 @@ jobs:
       if: contains(github.ref, 'rc') == false
       uses: everlytic/branch-merge@1.1.2
       with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
+        github_token: ${{ secrets.GH_PAT }}
         source_ref: ${{ github.ref }}
         target_branch: "latest"
         commit_message_template: ':tada: RELEASE: Merged {source_ref} into target {target_branch}'
@@ -90,7 +90,7 @@ jobs:
       with:
         generate_release_notes: true      
       env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        GITHUB_TOKEN: ${{ secrets.GH_PAT }}
   pypi-release:
     runs-on: ubuntu-latest
     steps:
@@ -119,7 +119,7 @@ jobs:
       if: contains(github.ref, 'rc') == false
       uses: everlytic/branch-merge@1.1.2
       with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
+        github_token: ${{ secrets.GH_PAT }}
         source_ref: "latest"
         target_branch: "develop"
         commit_message_template: ':tada: RELEASE: Synced latest into develop'

.github/workflows/sync-to-readthedocs-repo.yaml

@@ -50,7 +50,7 @@ jobs:
           git remote add mirror https://github.com/flexcompute-readthedocs/tidy3d-docs.git
           git push mirror ${{ needs.extract_branch_or_tag.outputs.ref_name }} --force # overwrites always
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GH_PAT }}
 
       # Conditional Checkout for Tag
       - name: Checkout Tag if tag-triggered-sync
@@ -69,4 +69,4 @@ jobs:
           git remote add mirror https://github.com/flexcompute-readthedocs/tidy3d-docs.git
           git push mirror ${{ needs.extract_branch_or_tag.outputs.ref_name }} --force # overwrites always
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GH_PAT }}

CHANGELOG.md

@@ -5,6 +5,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+- `TopologyDesignRegion` is now invariant in `z` by default and supports assigning dimensions along which a design should be uniform via `TopologyDesignRegion(uniform=(bool, bool, bool))`.
+
+### Fixed
+- Some validation fixes for design region.
+- Bug in adjoint source creation that included empty sources for extraneous `FieldMonitor` objects, triggering unnecessary errors.
+
 ## [2.7.4] - 2024-09-25
 
 ### Added

tests/test_components/test_autograd.py

@@ -16,7 +16,6 @@
 import tidy3d.web as web
 import xarray as xr
 from tidy3d.components.autograd.derivative_utils import DerivativeInfo
-from tidy3d.components.data.sim_data import AdjointSourceInfo
 from tidy3d.web import run, run_async
 from tidy3d.web.api.autograd.utils import FieldMap
 
@@ -197,15 +196,12 @@ def emulated_run_bwd(simulation, task_name, **run_kwargs) -> td.SimulationData:
             # get the original traced fields
             sim_fields_keys = cache[task_id_fwd][AUX_KEY_SIM_FIELDS_KEYS]
 
-            adjoint_source_info = AdjointSourceInfo(sources=[], post_norm=1.0, normalize_sim=True)
-
             # postprocess (compute adjoint gradients)
             traced_fields_vjp = postprocess_adj(
                 sim_data_adj=sim_data_adj,
                 sim_data_orig=sim_data_orig,
                 sim_data_fwd=sim_data_fwd,
                 sim_fields_keys=sim_fields_keys,
-                adjoint_source_info=adjoint_source_info,
             )
 
             return traced_fields_vjp
@@ -1475,3 +1471,28 @@ def objective(params):
         NotImplementedError, match="Could not formulate adjoint source for 'FluxMonitor' output"
     ):
         g = ag.grad(objective)(params0)
+
+
+def test_extraneous_field(use_emulated_run, log_capture):
+    """Make sure this doesnt fail."""
+
+    def objective(params):
+        structure_traced = make_structures(params)["medium"]
+        sim = SIM_BASE.updated_copy(
+            structures=[structure_traced],
+            monitors=[
+                SIM_BASE.monitors[0],
+                td.ModeMonitor(
+                    size=(1, 1, 0),
+                    center=(0, 0, 0),
+                    mode_spec=td.ModeSpec(),
+                    freqs=[FREQ0 * 0.9, FREQ0 * 1.1],
+                    name="mode",
+                ),
+            ],
+        )
+        data = run(sim, task_name="extra_field")
+        amp = data["mode"].amps.sel(direction="+", f=FREQ0 * 0.9, mode_index=0).values
+        return abs(anp.squeeze(amp.tolist())) ** 2
+
+    g = ag.grad(objective)(params0)

tests/test_plugins/test_invdes.py

@@ -95,6 +95,18 @@ def test_region_params():
     _ = design_region.params_zeros
 
 
+def test_region_uniform():
+    """Test parameter shape for uniform dimensions"""
+    region = make_design_region()
+    shape = region.params_shape
+
+    test_region = region.updated_copy(uniform=(1, 1, 1))
+    assert test_region.params_shape == (1, 1, 1)
+
+    test_region = region.updated_copy(uniform=(1, 0, 1))
+    assert test_region.params_shape == (1, *shape[1:])
+
+
 def test_region_penalties():
     """Test evaluation of penalties of a ``TopologyDesignRegion``."""
 

tidy3d/components/base.py

@@ -91,22 +91,28 @@ def _get_valid_extension(fname: str) -> str:
     )
 
 
-def skip_if_fields_missing(fields: List[str]):
+def skip_if_fields_missing(fields: List[str], root=False):
     """Decorate ``validator`` to check that other fields have passed validation."""
 
     def actual_decorator(validator):
         @wraps(validator)
-        def _validator(cls, val, values):
+        def _validator(cls, *args, **kwargs):
             """New validator function."""
+            values = kwargs.get("values")
+            if values is None:
+                values = args[0] if root else args[1]
             for field in fields:
                 if field not in values:
                     log.warning(
                         f"Could not execute validator '{validator.__name__}' because field "
                         f"'{field}' failed validation."
                     )
-                    return val
+                    if root:
+                        return values
+                    else:
+                        return kwargs.get("val") if "val" in kwargs.keys() else args[0]
 
-            return validator(cls, val, values)
+            return validator(cls, *args, **kwargs)
 
         return _validator
 

tidy3d/components/data/monitor_data.py

@@ -1093,6 +1093,10 @@ def to_adjoint_field_sources(self, fwidth: float) -> List[CustomCurrentSource]:
                 if not np.all(values == 0):
                     src_field_components[name] = ScalarFieldDataArray(values, coords=coords)
 
+            # dont include this source if no data
+            if all(fld_cmp is None for fld_cmp in src_field_components.values()):
+                continue
+
             # construct custom Current source
             dataset = FieldDataset(**src_field_components)
             custom_source = CustomCurrentSource(

tidy3d/components/data/sim_data.py

@@ -1022,7 +1022,7 @@ def split_original_fwd(self, num_mnts_original: int) -> Tuple[SimulationData, Si
 
     def make_adjoint_sim(
         self, data_vjp_paths: set[tuple], adjoint_monitors: list[Monitor]
-    ) -> tuple[Simulation, AdjointSourceInfo]:
+    ) -> Simulation:
         """Make the adjoint simulation from the original simulation and the VJP-containing data."""
 
         sim_original = self.simulation
@@ -1043,6 +1043,7 @@ def make_adjoint_sim(
             sources=adjoint_source_info.sources,
             boundary_spec=bc_adj,
             monitors=adjoint_monitors,
+            post_norm=adjoint_source_info.post_norm,
         )
 
         if not adjoint_source_info.normalize_sim:
@@ -1055,7 +1056,7 @@ def make_adjoint_sim(
             grid_spec_adj = grid_spec_original.updated_copy(wavelength=wavelength_original)
             sim_adj_update_dict["grid_spec"] = grid_spec_adj
 
-        return sim_original.updated_copy(**sim_adj_update_dict), adjoint_source_info
+        return sim_original.updated_copy(**sim_adj_update_dict)
 
     def make_adjoint_sources(self, data_vjp_paths: set[tuple]) -> dict[str, SourceType]:
         """Generate all of the non-zero sources for the adjoint simulation given the VJP data."""

tidy3d/components/simulation.py

@@ -30,6 +30,7 @@
     PMCBoundary,
     StablePML,
 )
+from .data.data_array import FreqDataArray
 from .data.dataset import CustomSpatialDataType, Dataset
 from .geometry.base import Box, Geometry
 from .geometry.mesh import TriangleMesh
@@ -210,6 +211,13 @@ class AbstractYeeGridSimulation(AbstractSimulation, ABC):
         "``autograd`` gradient processing.",
     )
 
+    post_norm: Union[float, FreqDataArray] = pydantic.Field(
+        1.0,
+        title="Post Normalization Values",
+        description="Factor to multiply the fields by after running, "
+        "given the adjoint source pipeline used. Note: this is used internally only.",
+    )
+
     """
     Supply :class:`SubpixelSpec` to select subpixel averaging methods separately for dielectric, metal, and
     PEC material interfaces. Alternatively, supply ``True`` to use default subpixel averaging methods,

tidy3d/components/validators.py

@@ -136,8 +136,7 @@ def check_symmetry(cls, val, values):
                         and geometric_object.center[dim] != sim_center[dim]
                     ):
                         raise SetupError(
-                            f"Mode object '{geometric_object}' "
-                            f"(at 'simulation.{field_name}[{position_index}]') "
+                            f"{obj_type} at 'simulation.{field_name}[{position_index}]' "
                             "in presence of symmetries must be in the main quadrant, "
                             "or centered on the symmetry axis."
                         )

tidy3d/plugins/invdes/optimizer.py

@@ -10,6 +10,7 @@
 import pydantic.v1 as pd
 
 import tidy3d as td
+from tidy3d.components.types import TYPE_TAG_STR
 
 from .base import InvdesBaseModel
 from .design import InverseDesignType
@@ -23,6 +24,7 @@ class AbstractOptimizer(InvdesBaseModel, abc.ABC):
         ...,
         title="Inverse Design Specification",
         description="Specification describing the inverse design problem we wish to optimize.",
+        discriminator=TYPE_TAG_STR,
     )
 
     learning_rate: pd.NonNegativeFloat = pd.Field(
@@ -69,6 +71,10 @@ class AbstractOptimizer(InvdesBaseModel, abc.ABC):
     def initial_state(self, parameters: np.ndarray) -> dict:
         """The initial state of the optimizer."""
 
+    def validate_pre_upload(self) -> None:
+        """Validate the fully initialized optimizer is ok for upload to our servers."""
+        pass
+
     def display_fn(self, result: InverseDesignResult, step_index: int) -> None:
         """Default display function while optimizing."""
         print(f"step ({step_index + 1}/{self.num_steps})")

tidy3d/plugins/invdes/region.py

@@ -124,6 +124,13 @@ class TopologyDesignRegion(DesignRegion):
         "a value on the same order as the grid size.",
     )
 
+    uniform: tuple[bool, bool, bool] = pd.Field(
+        (False, False, True),
+        title="Uniform",
+        description="Axes along which the design should be uniform. By default, the structure "
+        "is assumed to be uniform, i.e. invariant, in the z direction.",
+    )
+
     transformations: typing.Tuple[TransformationType, ...] = pd.Field(
         (),
         title="Transformations",
@@ -166,12 +173,10 @@ def _check_params(params: anp.ndarray = None):
     @property
     def params_shape(self) -> typing.Tuple[int, int, int]:
         """Shape of the parameters array in (x, y, z), given the ``pixel_size`` and bounds."""
-        # rmin, rmax = np.array(self.geometry.bounds)
-        # lengths = rmax - rmin
         side_lengths = np.array(self.size)
         num_pixels = np.ceil(side_lengths / self.pixel_size)
         # TODO: if the structure is infinite but the simulation is finite, need reduced bounds
-        num_pixels[np.isinf(num_pixels)] = 1
+        num_pixels[np.logical_or(np.isinf(num_pixels), self.uniform)] = 1
         return tuple(int(n) for n in num_pixels)
 
     def _warn_deprecate_params(self):

tidy3d/plugins/invdes/validators.py

@@ -5,6 +5,7 @@
 import pydantic.v1 as pd
 
 import tidy3d as td
+from tidy3d.components.base import skip_if_fields_missing
 
 # warn if pixel size is > PIXEL_SIZE_WARNING_THRESHOLD * (minimum wavelength in material)
 PIXEL_SIZE_WARNING_THRESHOLD = 0.1
@@ -45,9 +46,9 @@ def check_pixel_size_sim(sim: td.Simulation, pixel_size: float, index: int = Non
             )
 
     @pd.root_validator(allow_reuse=True)
+    @skip_if_fields_missing(["design_region"], root=True)
     def _check_pixel_size(cls, values):
         """Make sure region pixel_size isn't too large compared to sim's wavelength in material."""
-
         sim = values.get(sim_field_name)
         region = values.get("design_region")
         pixel_size = region.pixel_size