Merge branch 'develop' into momchil/merge_develop_in_26

Author: momchil-flex

CHANGELOG.md

@@ -18,16 +18,27 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `poetry` based installation. Removal of `setup.py` and `requirements.txt`.
 - Upgrade to sphinx 6 for the documentation build, and change of theme.
 - Remote mode solver web api automatically reduces the associated `Simulation` object to the mode solver plane before uploading it to server.
+- All solver output is now compressed. However, it is automatically unpacked to the same `simulation_data.hdf5` by default when loading simulation data from the server.
+- Internal refactor of `adjoint` plugin to separate `jax`-traced fields from regular `tidy3d` fields.
 
 ### Fixed
 
+## [2.5.1] - 2024-01-08
+
+### Added
+- `ModeData.dispersion` and `ModeSolverData.dispersion` are calculated together with the group index.
+- String matching feature `contains_str` to `assert_log_level` testing utility.
+- Warning in automatic grid generation if a structure has a non-zero size along a given direction that is too small compared to a single mesh step.
+- `assert_log_level` adds string matching with `contains_str` and ensures no higher log level recorded than expected.
+- `AssertLogLevel` context manager for testing log level and automatically clearing capture.
+- More robust validation for boundary conditions and symmetry in 1D and 2D simulations.
 
 ### Changed
-- All solver output is now compressed. However, it is automatically unpacked to the same `simulation_data.hdf5` by default when loading simulation data from the server.
-- Internal refactor of `adjoint` plugin to separate `jax`-traced fields from regular `tidy3d` fields.
+- `jax` and `jaxlib` versions bumped to `0.4.*`.
+- Improved and unified warning message for validation failure of dependency fields in validators.
 
 ### Fixed
-
+- Error in automatic grid generation in specific cases with multiple thin structures.
 
 ## [2.5.0] - 2023-12-13
 
@@ -1063,7 +1074,8 @@ 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/v2.5.0...develop
+[Unreleased]: https://github.com/flexcompute/tidy3d/compare/v2.5.1...develop
+[2.5.1]: https://github.com/flexcompute/tidy3d/compare/v2.5.0...v2.5.1
 [2.5.0]: https://github.com/flexcompute/tidy3d/compare/v2.4.3...v2.5.0
 [2.4.3]: https://github.com/flexcompute/tidy3d/compare/v2.4.2...v2.4.3
 [2.4.2]: https://github.com/flexcompute/tidy3d/compare/v2.4.1...v2.4.2

tests/test_components/test_meshgenerate.py

@@ -5,9 +5,10 @@
 
 import tidy3d as td
 from tidy3d.constants import fp_eps
-
 from tidy3d.components.grid.mesher import GradedMesher
 
+from ..utils import assert_log_level, log_capture
+
 np.random.seed(4)
 
 MESHER = GradedMesher()
@@ -648,6 +649,52 @@ def test_mesher_timeout():
     _ = sim.grid
 
 
+def test_small_structure_size(log_capture):
+    """Test that a warning is raised if a structure size is small during the auto meshing"""
+    box_size = 0.03
+    medium = td.Medium(permittivity=4)
+    box = td.Structure(geometry=td.Box(size=(box_size, td.inf, td.inf)), medium=medium)
+    src = td.UniformCurrentSource(
+        source_time=td.GaussianPulse(freq0=2e14, fwidth=1e13),
+        size=(0, 0, 0),
+        polarization="Ex",
+    )
+    sim = td.Simulation(
+        size=(10, 10, 10),
+        sources=[src],
+        structures=[box],
+        run_time=1e-12,
+        grid_spec=td.GridSpec.auto(wavelength=1),
+    )
+
+    # Warning raised as structure is too thin
+    assert_log_level(log_capture, "WARNING")
+
+    # Warning not raised if structure is higher index
+    log_capture.clear()
+    box2 = box.updated_copy(medium=td.Medium(permittivity=300))
+    sim2 = sim.updated_copy(structures=[box2])
+    assert len(log_capture) == 0
+
+    # Warning not raised if structure is covered by an override structure
+    log_capture.clear()
+    override = td.MeshOverrideStructure(geometry=box.geometry, dl=(box_size, td.inf, td.inf))
+    sim3 = sim.updated_copy(grid_spec=sim.grid_spec.updated_copy(override_structures=[override]))
+    assert len(log_capture) == 0
+    # Also check that the structure boundaries are in the grid
+    ind_mid_cell = int(sim3.grid.num_cells[0] // 2)
+    bounds = [-box_size / 2, box_size / 2]
+    assert np.allclose(bounds, sim3.grid.boundaries.x[ind_mid_cell : ind_mid_cell + 2])
+
+    # Test that the error coming from two thin slabs on top of each other is resolved
+    log_capture.clear()
+    box3 = td.Structure(
+        geometry=td.Box(center=(box_size, 0, 0), size=(box_size, td.inf, td.inf)), medium=medium
+    )
+    sim4 = sim.updated_copy(structures=[box3, box])
+    assert_log_level(log_capture, "WARNING")
+
+
 def test_shapely_strtree_warnings():
     with warnings.catch_warnings():
         warnings.simplefilter("error")

tests/test_components/test_simulation.py

@@ -500,11 +500,11 @@ def test_validate_components_none():
     assert SIM._source_homogeneous_isotropic(val=None, values=SIM.dict()) is None
 
 
-def test_sources_edge_case_validation():
+def test_sources_edge_case_validation(log_capture):
     values = SIM.dict()
     values.pop("sources")
-    with pytest.raises(ValidationError):
-        SIM._warn_monitor_simulation_frequency_range(val="test", values=values)
+    SIM._warn_monitor_simulation_frequency_range(val="test", values=values)
+    assert_log_level(log_capture, "WARNING")
 
 
 def test_validate_size_run_time(monkeypatch):
@@ -1826,6 +1826,27 @@ def test_error_large_monitors():
             s.validate_pre_upload()
 
 
+@pytest.mark.parametrize("start, log_level", [(1e-12, None), (1, "WARNING")])
+def test_warn_time_monitor_outside_run_time(log_capture, start, log_level):
+    """Make sure we get a warning if the mode monitor grid is too large."""
+
+    sim = td.Simulation(
+        size=(2.0, 2.0, 2.0),
+        grid_spec=td.GridSpec.uniform(dl=0.1),
+        run_time=1e-12,
+        sources=[
+            td.ModeSource(
+                size=(0.1, 0.1, 0),
+                direction="+",
+                source_time=td.GaussianPulse(freq0=1e12, fwidth=0.1e12),
+            )
+        ],
+        monitors=[td.FieldTimeMonitor(size=(td.inf, 0, td.inf), start=start, name="test")],
+    )
+    with AssertLogLevel(log_capture, log_level_expected=log_level, contains_str="start time"):
+        sim.validate_pre_upload()
+
+
 def test_dt():
     """make sure dt is reduced when there is a medium with eps_inf < 1."""
     sim = td.Simulation(

tests/test_components/test_source.py

@@ -6,7 +6,7 @@
 import tidy3d as td
 from tidy3d.exceptions import SetupError
 from tidy3d.components.source import DirectionalSource, CHEB_GRID_WIDTH
-from ..utils import assert_log_level, log_capture
+from ..utils import assert_log_level, log_capture, AssertLogLevel
 
 ST = td.GaussianPulse(freq0=2e14, fwidth=1e14)
 S = td.PointDipole(source_time=ST, polarization="Ex")
@@ -309,12 +309,12 @@ def test_custom_source_time(log_capture):
     assert_log_level(log_capture, None)
 
     # test normalization warning
-    sim = sim.updated_copy(normalize_index=0)
-    assert_log_level(log_capture, "WARNING")
-    log_capture.clear()
-    source = source.updated_copy(source_time=td.ContinuousWave(freq0=freq0, fwidth=0.1e12))
-    sim = sim.updated_copy(sources=[source])
-    assert_log_level(log_capture, "WARNING")
+    with AssertLogLevel(log_capture, "WARNING"):
+        sim = sim.updated_copy(normalize_index=0)
+
+    with AssertLogLevel(log_capture, "WARNING"):
+        source = source.updated_copy(source_time=td.ContinuousWave(freq0=freq0, fwidth=0.1e12))
+        sim = sim.updated_copy(sources=[source])
 
     # test single value validation error
     with pytest.raises(pydantic.ValidationError):

tests/test_package/test_log.py

@@ -9,6 +9,8 @@
 from tidy3d.exceptions import Tidy3dError
 from tidy3d.log import DEFAULT_LEVEL, _get_level_int, set_logging_level
 
+from ..utils import assert_log_level, log_capture, AssertLogLevel
+
 
 def test_log():
     td.log.debug("debug test")
@@ -268,3 +270,29 @@ def test_log_suppression():
         assert td.log._counts is None
 
     td.config.log_suppression = True
+
+
+def test_assert_log_level(log_capture):
+    """Test features of the assert_log_level"""
+
+    # log was captured
+    with AssertLogLevel(log_capture, "WARNING", contains_str="ABC"):
+        td.log.warning("ABC")
+
+    # string was not matched (manually clear because not sure any other way using context manager)
+    td.log.warning("ABC")
+    with pytest.raises(Exception):
+        assert_log_level(log_capture, "WARNING", contains_str="DEF")
+    log_capture.clear()
+
+    # string was matched at the wrong level
+    td.log.info("ABC")
+    with pytest.raises(Exception):
+        assert_log_level(log_capture, "WARNING", contains_str="ABC")
+    log_capture.clear()
+
+    # log exceeds expected level
+    td.log.warning("ABC")
+    with pytest.raises(Exception):
+        assert_log_level(log_capture, "INFO")
+    log_capture.clear()

tests/test_plugins/test_adjoint.py

@@ -325,7 +325,7 @@ def make_sim(
         output_monitors=(output_mnt1, output_mnt2, output_mnt3, output_mnt4),
         sources=[src],
         boundary_spec=td.BoundarySpec.pml(x=False, y=False, z=False),
-        symmetry=(0, 1, -1),
+        symmetry=(1, 0, -1),
     )
 
     return sim

tidy3d/components/apodization.py

@@ -3,7 +3,7 @@
 import pydantic.v1 as pd
 import numpy as np
 
-from .base import Tidy3dBaseModel
+from .base import Tidy3dBaseModel, skip_if_fields_missing
 from ..constants import SECOND
 from ..exceptions import SetupError
 from .types import ArrayFloat1D, Ax
@@ -40,6 +40,7 @@ class ApodizationSpec(Tidy3dBaseModel):
     )
 
     @pd.validator("end", always=True, allow_reuse=True)
+    @skip_if_fields_missing(["start"])
     def end_greater_than_start(cls, val, values):
         """Ensure end is greater than or equal to start."""
         start = values.get("start")
@@ -48,6 +49,7 @@ def end_greater_than_start(cls, val, values):
         return val
 
     @pd.validator("width", always=True, allow_reuse=True)
+    @skip_if_fields_missing(["start", "end"])
     def width_provided(cls, val, values):
         """Check that width is provided if either start or end apodization is requested."""
         start = values.get("start")

tidy3d/components/base.py

@@ -86,6 +86,28 @@ def _get_valid_extension(fname: str) -> str:
     )
 
 
+def skip_if_fields_missing(fields: List[str]):
+    """Decorate ``validator`` to check that other fields have passed validation."""
+
+    def actual_decorator(validator):
+        @wraps(validator)
+        def _validator(cls, val, values):
+            """New validator function."""
+            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
+
+            return validator(cls, val, values)
+
+        return _validator
+
+    return actual_decorator
+
+
 class Tidy3dBaseModel(pydantic.BaseModel):
     """Base pydantic model that all Tidy3d components inherit from.
     Defines configuration for handling data structures

tidy3d/components/base_sim/data/sim_data.py

@@ -12,6 +12,7 @@
 from ..simulation import AbstractSimulation
 from ...data.dataset import UnstructuredGridDatasetType
 from ...base import Tidy3dBaseModel
+from ...base import skip_if_fields_missing
 from ...types import FieldVal
 from ....exceptions import DataError, Tidy3dKeyError, ValidationError
 
@@ -51,13 +52,13 @@ def monitor_data(self) -> Dict[str, AbstractMonitorData]:
         return {monitor_data.monitor.name: monitor_data for monitor_data in self.data}
 
     @pd.validator("data", always=True)
+    @skip_if_fields_missing(["simulation"])
     def data_monitors_match_sim(cls, val, values):
         """Ensure each :class:`AbstractMonitorData` in ``.data`` corresponds to a monitor in
         ``.simulation``.
         """
         sim = values.get("simulation")
-        if sim is None:
-            raise ValidationError("'.simulation' failed validation, can't validate data.")
+
         for mnt_data in val:
             try:
                 monitor_name = mnt_data.monitor.name
@@ -70,14 +71,11 @@ def data_monitors_match_sim(cls, val, values):
         return val
 
     @pd.validator("data", always=True)
+    @skip_if_fields_missing(["simulation"])
     def validate_no_ambiguity(cls, val, values):
         """Ensure all :class:`AbstractMonitorData` entries in ``.data`` correspond to different
         monitors in ``.simulation``.
         """
-        sim = values.get("simulation")
-        if sim is None:
-            raise ValidationError("'.simulation' failed validation, can't validate data.")
-
         names = [mnt_data.monitor.name for mnt_data in val]
 
         if len(set(names)) != len(names):

tidy3d/components/base_sim/simulation.py

@@ -9,7 +9,7 @@
 
 from .monitor import AbstractMonitor
 
-from ..base import cached_property
+from ..base import cached_property, skip_if_fields_missing
 from ..validators import assert_unique_names, assert_objects_in_sim_bounds
 from ..geometry.base import Box
 from ..types import Ax, Bound, Axis, Symmetry, TYPE_TAG_STR
@@ -196,6 +196,7 @@ class AbstractSimulation(Box, ABC):
     _structures_in_bounds = assert_objects_in_sim_bounds("structures", error=False)
 
     @pd.validator("structures", always=True)
+    @skip_if_fields_missing(["size", "center"])
     def _structures_not_at_edges(cls, val, values):
         """Warn if any structures lie at the simulation boundaries."""