Unstructured mesh refinement regions

CHANGELOG.md

@@ -7,13 +7,29 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [2.8.1] - 2025-03-20
+## [2.8.2] - 2025-04-09
+
 ### Added
 - `fill` and `fill_structures` argument in `td.Simulation.plot_structures()` and `td.Simulation.plot()` respectively to disable fill and plot outlines of structures only.
 - New subpixel averaging option `ContourPathAveraging` applied to dielectric material boundaries.
 - A property `interior_angle` in `PolySlab` that stores angles formed inside polygon by two adjacent edges.
+- `eps_component` argument in `td.Simulation.plot_eps()` to optionally select a specific permittivity component to plot (eg. `"xx"`).
+- Monitor `AuxFieldTimeMonitor` for aux fields like the free carrier density in `TwoPhotonAbsorption`.
+- Broadband handling (`num_freqs` argument) to the TFSF source.
+- Ability to define a `WavePort` using only a voltage or current path integral, with the missing quantity inferred via power conservation.
 
 ### Fixed
 - Compatibility with `xarray>=2025.03`.
+- Inaccurate gradient when auto-grabbing permittivities for structures using `td.PolySlab` when using dispersive material models.
+- Fixed scaling for adjoint sources when differentiating with respect to `FieldData` to account for the mesh size of the monitor and thus the created source. This aligns adjoint gradient magnitudes with numerical finite difference gradients for field data.
+- Warn when mode solver pml covers a significant portion of the mode plane.
+- TFSF server errors related to the auxiliary plane wave source that would previously happen on the server are now caught upon simulation creation.
+
+### Changed
+- `num_freqs` in Gaussian beam type sources limited to 20, which should besufficient for all cases.
+- The `angle_phi` parameter of `ModeSpec` is only limited to multiples of `np.pi / 2` if `angle_rotation` is set to `True`, as other values would currently not work correctly.
+- The `ramp_up_iters` parameter of the `ChargeSolver` was changed back to 1 for efficiency. It can be increased in cases with e.g. high doping when convergence is more difficult.
 
 ## [2.8.1] - 2025-03-20
 
@@ -22,6 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Validation step that raises a `ValueError` when no frequency-domain monitors are present, preventing invalid adjoint runs.
 - Metal surface roughness models: modified Hammerstad, Huray Snowball, and Cannonball-Huray.
 - Support for Fermi-Dirac statistics in Charge solver. This option can be activated when defining the analysis type `IsothermalSteadyChargeDCAnalysis` with `fermi_dirac=True`. This option will provide more accurate results in simulations where very high doping may lead the pseudo-Fermi energy levels to approach either the conduction or the valence energy levels.
+- Unstructured grid now supports 2D/3D box-shaped refinement regions and 1D refinement lines of arbitrary direction.
 
 ### Changed
 
@@ -1555,8 +1572,11 @@ which fields are to be projected is now determined automatically based on the me
 - Job and Batch classes for better simulation handling (eventually to fully replace webapi functions).
 - A large number of small improvements and bug fixes.
 
-[Unreleased]: https://github.com/flexcompute/tidy3d/compare/v2.8.1...develop
+[Unreleased]: https://github.com/flexcompute/tidy3d/compare/v2.8.2...develop
+[2.8.2]: https://github.com/flexcompute/tidy3d/compare/v2.8.1...v2.8.2
 [2.8.1]: https://github.com/flexcompute/tidy3d/compare/v2.8.0...v2.8.1
+[Unreleased]: https://github.com/flexcompute/tidy3d/compare/v2.8.1...develop
+[2.8.0]: https://github.com/flexcompute/tidy3d/compare/v2.8.0...v2.8.1
 [2.8.0]: https://github.com/flexcompute/tidy3d/compare/v2.7.9...v2.8.0
 [2.7.9]: https://github.com/flexcompute/tidy3d/compare/v2.7.8...v2.7.9
 [2.7.8]: https://github.com/flexcompute/tidy3d/compare/v2.7.7...v2.7.8

docs/install.rst

@@ -206,7 +206,7 @@ Tidy3D also offers plugins that require additional dependencies:
 
 - ``design``: Design space exploration and optimization.
 - ``pytorch``: A PyTorch wrapper for objective functions defined using autograd.
-- ``adjoint``: Adjoint optimization using JAX (deprecated in favor of native autograd support in Tidy3D)
+- ``adjoint``: Adjoint optimization using JAX (deprecated in favor of native autorad support in Tidy3D)
 
 For example, to install the design plugin dependencies:
 

pyproject.toml

@@ -24,7 +24,7 @@ documentation = "https://docs.flexcompute.com/projects/tidy3d/en/latest/"
 [tool.poetry.dependencies]
 python = ">=3.9,<3.14"
 pyroots = ">=0.5.0"
-xarray = ">=2023.08"
+xarray = ">=2023.08.0,<2025.03.0"
 importlib-metadata = ">=6.0.0"
 h5netcdf = "1.0.2"
 h5py = "^3.0.0"
@@ -275,7 +275,10 @@ ignore = [
 
 [tool.pytest.ini_options]
 # TODO: remove --assert=plain when https://github.com/scipy/scipy/issues/22236 is resolved
-addopts = "--cov=tidy3d --doctest-modules -n auto --dist worksteal --assert=plain"
+addopts = "--cov=tidy3d --doctest-modules -n auto --dist worksteal --assert=plain -m 'not numerical' "
+markers = [
+    "numerical: marks numerical tests for adjoint gradients that require running simulations (deselect with '-m \"not numerical\"')",
+]
 env = ["MPLBACKEND=Agg", "OMP_NUM_THREADS=1"]
 doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS"
 norecursedirs = [

tests/conftest.py

@@ -1,6 +1,8 @@
 import os
+from pathlib import Path
 
 import autograd
+import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
 import psutil
@@ -68,3 +70,33 @@ def pytest_xdist_auto_num_workers(config):
     if os.getenv("GITHUB_ACTIONS"):
         return cores
     return max(1, cores - 1)
+
+
+@pytest.fixture
+def mpl_config_noninteractive():
+    """Configure matplotlib non-interactive backend for all tests in this module."""
+    original_backend = mpl.get_backend()
+    mpl.use("Agg")
+    yield
+    plt.close("all")
+    mpl.use(original_backend)
+
+
+@pytest.fixture
+def mpl_config_interactive():
+    """Configure matplotlib interactive backend for all tests in this module."""
+    original_backend = mpl.get_backend()
+    mpl.use("TkAgg")
+    yield
+    mpl.use(original_backend)
+
+
+@pytest.fixture
+def dir_name(request):
+    return request.param
+
+
+@pytest.fixture
+def create_directory(dir_name):
+    if dir_name is not None:
+        directory = Path(dir_name).mkdir(parents=True, exist_ok=True)

tests/sims/simulation_sample.json

@@ -603,6 +603,72 @@
                 }
             }
         },
+        {
+            "attrs": {},
+            "geometry": {
+                "attrs": {},
+                "type": "Box",
+                "center": [
+                    -1.0,
+                    0.0,
+                    0.0
+                ],
+                "size": [
+                    1.0,
+                    1.0,
+                    1.0
+                ]
+            },
+            "name": "fully_anisotropic_box",
+            "background_permittivity": null,
+            "background_medium": null,
+            "type": "Structure",
+            "medium": {
+                "attrs": {},
+                "name": null,
+                "frequency_range": null,
+                "allow_gain": false,
+                "nonlinear_spec": null,
+                "modulation_spec": null,
+                "viz_spec": null,
+                "heat_spec": null,
+                "type": "FullyAnisotropicMedium",
+                "permittivity": [
+                    [
+                        6.0,
+                        2.0,
+                        3.0
+                    ],
+                    [
+                        2.0,
+                        7.0,
+                        4.0
+                    ],
+                    [
+                        3.0,
+                        4.0,
+                        9.0
+                    ]
+                ],
+                "conductivity": [
+                    [
+                        0.0,
+                        0.0,
+                        0.0
+                    ],
+                    [
+                        0.0,
+                        0.0,
+                        0.0
+                    ],
+                    [
+                        0.0,
+                        0.0,
+                        0.0
+                    ]
+                ]
+            }
+        },
         {
             "attrs": {},
             "geometry": {
@@ -2015,6 +2081,7 @@
                 "offset": 5.0,
                 "remove_dc_component": true
             },
+            "num_freqs": 3,
             "direction": "+",
             "angle_theta": 0.5235987755982988,
             "angle_phi": 0.6283185307179586,
@@ -2192,6 +2259,33 @@
                 "Hz"
             ]
         },
+        {
+            "attrs": {},
+            "type": "AuxFieldTimeMonitor",
+            "center": [
+                0.0,
+                0.0,
+                0.0
+            ],
+            "size": [
+                0.0,
+                0.0,
+                0.0
+            ],
+            "name": "aux_field_time",
+            "interval_space": [
+                1,
+                1,
+                1
+            ],
+            "colocate": true,
+            "start": 0.0,
+            "stop": null,
+            "interval": 100,
+            "fields": [
+                "Nfx"
+            ]
+        },
         {
             "attrs": {},
             "type": "FluxMonitor",
@@ -3107,7 +3201,7 @@
         "layer_refinement_specs": [],
         "type": "GridSpec"
     },
-    "version": "2.8.0",
+    "version": "2.8.1",
     "plot_length_units": "\u03bcm",
     "lumped_elements": [
         {

tests/test_components/test_autograd.py

@@ -380,6 +380,17 @@ def make_structures(params: anp.ndarray) -> dict[str, td.Structure]:
         medium=med,
     )
 
+    polyslab_dispersive = td.Structure(
+        geometry=td.PolySlab(
+            vertices=vertices,
+            slab_bounds=slab_bounds,
+            axis=POLYSLAB_AXIS,
+            sidewall_angle=0.00,
+            dilation=0.00,
+        ),
+        medium=td.material_library["Si3N4"]["Philipp1973Sellmeier"],
+    )
+
     # geometry group
     geo_group = td.Structure(
         geometry=td.GeometryGroup(
@@ -469,6 +480,7 @@ def make_structures(params: anp.ndarray) -> dict[str, td.Structure]:
         custom_med=custom_med,
         custom_med_vec=custom_med_vec,
         polyslab=polyslab,
+        polyslab_dispersive=polyslab_dispersive,
         geo_group=geo_group,
         complex_polyslab=complex_polyslab_geo_group,
         pole_res=pole_res,
@@ -2117,3 +2129,24 @@ def objective(params):
 
     grad_no_flux_monitors = ag.grad(objective_with_monitors(monitors_just_field))(params0)
     grad_with_flux_monitors = ag.grad(objective_with_monitors(monitors_with_flux))(params0)
+
+
+def test_dispersive_no_inf(use_emulated_run):
+    """Test that automatic permittivity grabbing uses the correct freq_adj to
+    retrieve permittivity in dispersive material models.
+    """
+
+    fn_dict = get_functions(args[0][0], args[0][1])
+    make_sim = fn_dict["sim"]
+    postprocess = fn_dict["postprocess"]
+
+    def objective(args):
+        structure_traced = make_structures(args)["polyslab_dispersive"]
+        sim = make_sim(args).updated_copy(structures=[structure_traced])
+        sim_data = run(sim, task_name="adjoint_test", verbose=False)
+        return postprocess(sim_data)
+
+    # the following will raise a warning (and fail) if the dispersive material
+    # model is called without a frequency
+    with AssertLogLevel("INFO"):
+        grad = ag.grad(objective)(params0)