Add field data to ModeMonitor (#1274)

Signed-off-by: Lucas Heitzmann Gabrielli <lucas@flexcompute.com>

CHANGELOG.md

@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Integration of the `tidy3d-notebooks` repository.
 - `tidy3d develop` CLI and development guide on the main documentation.
 - Added a convenience method `Simulation.subsection()` to a create a new simulation based on a subregion of another one.
+- Mode field profiles can be stored directly from a `ModeMonitor` by setting `store_fields_direction`.
 
 ### Changed
 - `poetry` based installation. Removal of `setup.py` and `requirements.txt`.
@@ -31,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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.
 - Added an optional argument `field` in class method `.from_vtu()` of `TriangularGridDataset` and `TetrahedralGridDataset` for specifying the name of data field to load.
+- `ModeSolverMonitor` is deprecated. Mode field profiles can be retrieved directly from `ModeMonitor` with `store_fields_direction` set.
 
 ### Fixed
 - Removed spurious warnings realted to reloading simulation containing `PerturbationMedium` with `CustomChargePerturbation`/`CustomHeatPerturbation`

tests/sims/simulation_2_6_0rc1.json

@@ -1603,53 +1603,6 @@
                 "width": null,
                 "type": "ApodizationSpec"
             },
-            "mode_spec": {
-                "num_modes": 1,
-                "target_neff": null,
-                "num_pml": [
-                    0,
-                    0
-                ],
-                "filter_pol": null,
-                "angle_theta": 0.0,
-                "angle_phi": 0.0,
-                "precision": "single",
-                "bend_radius": null,
-                "bend_axis": null,
-                "track_freq": "central",
-                "group_index_step": false,
-                "type": "ModeSpec"
-            }
-        },
-        {
-            "type": "ModeSolverMonitor",
-            "center": [
-                0.0,
-                0.0,
-                0.0
-            ],
-            "size": [
-                1.0,
-                1.0,
-                0.0
-            ],
-            "name": "mode_solver",
-            "interval_space": [
-                1,
-                1,
-                1
-            ],
-            "colocate": true,
-            "freqs": [
-                200000000000000.0,
-                250000000000000.0
-            ],
-            "apodization": {
-                "start": null,
-                "end": null,
-                "width": null,
-                "type": "ApodizationSpec"
-            },
             "mode_spec": {
                 "num_modes": 1,
                 "target_neff": null,
@@ -1667,7 +1620,7 @@
                 "group_index_step": false,
                 "type": "ModeSpec"
             },
-            "direction": "+"
+            "store_fields_direction": null
         },
         {
             "type": "FieldProjectionAngleMonitor",

tests/test_components/test_simulation.py

@@ -6,12 +6,12 @@
 
 import numpy as np
 import tidy3d as td
-from tidy3d.exceptions import SetupError, ValidationError, Tidy3dKeyError
+from tidy3d.exceptions import SetupError, Tidy3dKeyError
 from tidy3d.components import simulation
 from tidy3d.components.simulation import MAX_NUM_SOURCES
 from tidy3d.components.scene import MAX_NUM_MEDIUMS, MAX_GEOMETRY_COUNT
-from ..utils import assert_log_level, SIM_FULL, log_capture, run_emulated, AssertLogLevel
-from tidy3d.constants import LARGE_NUMBER
+from ..utils import assert_log_level, SIM_FULL, run_emulated, AssertLogLevel
+from ..utils import log_capture  # noqa: F401
 
 SIM = td.Simulation(size=(1, 1, 1), run_time=1e-12, grid_spec=td.GridSpec(wavelength=1.0))
 
@@ -164,7 +164,7 @@ def test_monitors_data_size():
     assert len(datas) == 2
 
 
-def test_deprecation_defaults(log_capture):
+def test_deprecation_defaults(log_capture):  # noqa: F811
     """Make sure deprecation warnings NOT thrown if defaults used."""
     _ = td.Simulation(
         size=(1, 1, 1),
@@ -182,7 +182,7 @@ def test_deprecation_defaults(log_capture):
 
 
 @pytest.mark.parametrize("shift_amount, log_level", ((1, None), (2, "WARNING")))
-def test_sim_bounds(shift_amount, log_level, log_capture):
+def test_sim_bounds(shift_amount, log_level, log_capture):  # noqa: F811
     """make sure bounds are working correctly"""
 
     # make sure all things are shifted to this central location
@@ -276,7 +276,7 @@ def _test_monitor_size():
 
 
 @pytest.mark.parametrize("freq, log_level", [(1.5, "WARNING"), (2.5, "INFO"), (3.5, "WARNING")])
-def test_monitor_medium_frequency_range(log_capture, freq, log_level):
+def test_monitor_medium_frequency_range(log_capture, freq, log_level):  # noqa: F811
     # monitor frequency above or below a given medium's range should throw a warning
 
     medium = td.Medium(frequency_range=(2e12, 3e12))
@@ -299,7 +299,7 @@ def test_monitor_medium_frequency_range(log_capture, freq, log_level):
 
 
 @pytest.mark.parametrize("fwidth, log_level", [(0.1e12, "WARNING"), (2e12, "INFO")])
-def test_monitor_simulation_frequency_range(log_capture, fwidth, log_level):
+def test_monitor_simulation_frequency_range(log_capture, fwidth, log_level):  # noqa: F811
     # monitor frequency outside of the simulation's frequency range should throw a warning
 
     src = td.UniformCurrentSource(
@@ -378,7 +378,7 @@ def test_validate_normalize_index():
         )
 
 
-def test_validate_plane_wave_boundaries(log_capture):
+def test_validate_plane_wave_boundaries(log_capture):  # noqa: F811
     src1 = td.PlaneWave(
         source_time=td.GaussianPulse(freq0=2.5e14, fwidth=1e13),
         center=(0, 0, 0),
@@ -456,7 +456,7 @@ def test_validate_plane_wave_boundaries(log_capture):
         )
 
 
-def test_validate_zero_dim_boundaries(log_capture):
+def test_validate_zero_dim_boundaries(log_capture):  # noqa: F811
     # zero-dim simulation with an absorbing boundary in that direction should error
     src = td.PlaneWave(
         source_time=td.GaussianPulse(freq0=2.5e14, fwidth=1e13),
@@ -500,7 +500,7 @@ def test_validate_components_none():
     assert SIM._source_homogeneous_isotropic(val=None, values=SIM.dict()) is None
 
 
-def test_sources_edge_case_validation(log_capture):
+def test_sources_edge_case_validation(log_capture):  # noqa F811
     values = SIM.dict()
     values.pop("sources")
     SIM._warn_monitor_simulation_frequency_range(val="test", values=values)
@@ -521,7 +521,7 @@ def test_validate_size_spatial_and_time(monkeypatch):
         s._validate_size()
 
 
-def test_validate_mnt_size(monkeypatch, log_capture):
+def test_validate_mnt_size(monkeypatch, log_capture):  # noqa F811
     # warning for monitor size
     monkeypatch.setattr(simulation, "WARN_MONITOR_DATA_SIZE_GB", 1 / 2**30)
     s = SIM.copy(update=dict(monitors=(td.FieldMonitor(name="f", freqs=[1e12], size=(1, 1, 1)),)))
@@ -582,7 +582,7 @@ def test_plot_structure():
 
 
 def test_plot_eps():
-    ax = SIM_FULL.plot_eps(x=0)
+    _ = SIM_FULL.plot_eps(x=0)
     plt.close()
 
 
@@ -721,12 +721,12 @@ class MockSim:
     assert td.Simulation.nyquist_step.fget(m) == 1
 
 
-def test_discretize_non_intersect(log_capture):
+def test_discretize_non_intersect(log_capture):  # noqa F811
     SIM.discretize(box=td.Box(center=(-20, -20, -20), size=(1, 1, 1)))
     assert_log_level(log_capture, "ERROR")
 
 
-def test_warn_sim_background_medium_freq_range(log_capture):
+def test_warn_sim_background_medium_freq_range(log_capture):  # noqa F811
     _ = SIM.copy(
         update=dict(
             sources=(
@@ -742,7 +742,7 @@ def test_warn_sim_background_medium_freq_range(log_capture):
 
 
 @pytest.mark.parametrize("grid_size,log_level", [(0.001, None), (3, "WARNING")])
-def test_large_grid_size(log_capture, grid_size, log_level):
+def test_large_grid_size(log_capture, grid_size, log_level):  # noqa F811
     # small fwidth should be inside range, large one should throw warning
 
     medium = td.Medium(permittivity=2, frequency_range=(2e14, 3e14))
@@ -764,7 +764,7 @@ def test_large_grid_size(log_capture, grid_size, log_level):
 
 
 @pytest.mark.parametrize("box_size,log_level", [(0.1, "INFO"), (9.9, "WARNING"), (20, "INFO")])
-def test_sim_structure_gap(log_capture, box_size, log_level):
+def test_sim_structure_gap(log_capture, box_size, log_level):  # noqa F811
     """Make sure the gap between a structure and PML is not too small compared to lambda0."""
     medium = td.Medium(permittivity=2)
     box = td.Structure(geometry=td.Box(size=(box_size, box_size, box_size)), medium=medium)
@@ -951,7 +951,7 @@ def test_sim_monitor_homogeneous():
     )
 
 
-def test_proj_monitor_distance(log_capture):
+def test_proj_monitor_distance(log_capture):  # noqa F811
     """Make sure a warning is issued if the projection distance for exact projections
     is very large compared to the simulation domain size.
     """
@@ -1029,7 +1029,7 @@ def test_proj_monitor_distance(log_capture):
     )
 
 
-def test_proj_monitor_warnings(log_capture):
+def test_proj_monitor_warnings(log_capture):  # noqa F811
     """Test the validator that warns if projecting backwards."""
 
     src = td.PlaneWave(
@@ -1239,7 +1239,7 @@ def test_diffraction_medium():
         ((0.1, 0.1, 1), "WARNING"),
     ],
 )
-def test_sim_structure_extent(log_capture, box_size, log_level):
+def test_sim_structure_extent(log_capture, box_size, log_level):  # noqa F811
     """Make sure we warn if structure extends exactly to simulation edges."""
 
     src = td.UniformCurrentSource(
@@ -1268,7 +1268,9 @@ def test_sim_structure_extent(log_capture, box_size, log_level):
         (2.0, "PML", None),
     ],
 )
-def test_sim_validate_structure_bounds_pml(log_capture, box_length, absorb_type, log_level):
+def test_sim_validate_structure_bounds_pml(
+    log_capture, box_length, absorb_type, log_level  # noqa: F811
+):
     """Make sure we warn if structure bounds are within the PML exactly to simulation edges."""
 
     boundary = td.PML() if absorb_type == "PML" else td.Absorber()
@@ -1534,7 +1536,7 @@ def test_tfsf_symmetry():
         )
 
 
-def test_tfsf_boundaries(log_capture):
+def test_tfsf_boundaries(log_capture):  # noqa F811
     """Test that a TFSF source is allowed to cross boundaries only in particular cases."""
     src_time = td.GaussianPulse(freq0=td.C_0, fwidth=0.1e12)
 
@@ -1617,7 +1619,7 @@ def test_tfsf_boundaries(log_capture):
         )
 
 
-def test_tfsf_structures_grid(log_capture):
+def test_tfsf_structures_grid(log_capture):  # noqa F811
     """Test that a TFSF source is allowed to intersect structures only in particular cases."""
     src_time = td.GaussianPulse(freq0=td.C_0, fwidth=0.1e12)
 
@@ -1724,7 +1726,7 @@ def test_tfsf_structures_grid(log_capture):
 @pytest.mark.parametrize(
     "size, num_struct, log_level", [(1, 1, None), (50, 1, "WARNING"), (1, 11000, "WARNING")]
 )
-def test_warn_large_epsilon(log_capture, size, num_struct, log_level):
+def test_warn_large_epsilon(log_capture, size, num_struct, log_level):  # noqa F811
     """Make sure we get a warning if the epsilon grid is too large."""
 
     structures = [
@@ -1755,7 +1757,7 @@ def test_warn_large_epsilon(log_capture, size, num_struct, log_level):
 
 
 @pytest.mark.parametrize("dl, log_level", [(0.1, None), (0.005, "WARNING")])
-def test_warn_large_mode_monitor(log_capture, dl, log_level):
+def test_warn_large_mode_monitor(log_capture, dl, log_level):  # noqa F811
     """Make sure we get a warning if the mode monitor grid is too large."""
 
     sim = td.Simulation(
@@ -1780,7 +1782,7 @@ def test_warn_large_mode_monitor(log_capture, dl, log_level):
 
 
 @pytest.mark.parametrize("dl, log_level", [(0.1, None), (0.005, "WARNING")])
-def test_warn_large_mode_source(log_capture, dl, log_level):
+def test_warn_large_mode_source(log_capture, dl, log_level):  # noqa F811
     """Make sure we get a warning if the mode source grid is too large."""
 
     sim = td.Simulation(
@@ -1811,7 +1813,6 @@ def test_error_large_monitors():
     mnt_size = (td.inf, 0, td.inf)
     mnt_test = [
         td.ModeMonitor(size=mnt_size, freqs=[1e12], name="test", mode_spec=td.ModeSpec()),
-        td.ModeSolverMonitor(size=mnt_size, freqs=[1e12], name="test", mode_spec=td.ModeSpec()),
         td.FluxMonitor(size=mnt_size, freqs=[1e12], name="test"),
         td.FluxTimeMonitor(size=mnt_size, name="test"),
         td.DiffractionMonitor(size=mnt_size, freqs=[1e12], name="test"),
@@ -1827,7 +1828,7 @@ def test_error_large_monitors():
 
 
 @pytest.mark.parametrize("start, log_level", [(1e-12, None), (1, "WARNING")])
-def test_warn_time_monitor_outside_run_time(log_capture, start, log_level):
+def test_warn_time_monitor_outside_run_time(log_capture, start, log_level):  # noqa F811
     """Make sure we get a warning if the mode monitor grid is too large."""
 
     sim = td.Simulation(
@@ -1865,7 +1866,7 @@ def test_dt():
     assert sim_new.dt == 0.4 * dt
 
 
-def test_sim_volumetric_structures(log_capture, tmp_path):
+def test_sim_volumetric_structures(log_capture, tmp_path):  # noqa F811
     """Test volumetric equivalent of 2D materials."""
     sigma = 0.45
     thickness = 0.01
@@ -2270,11 +2271,7 @@ def test_sim_subsection():
     sim_red = SIM_FULL.subsection(
         region=region,
         symmetry=(1, 0, -1),
-        monitors=[
-            mnt
-            for mnt in SIM_FULL.monitors
-            if not isinstance(mnt, (td.ModeMonitor, td.ModeSolverMonitor))
-        ],
+        monitors=[mnt for mnt in SIM_FULL.monitors if not isinstance(mnt, td.ModeMonitor)],
     )
     assert sim_red.symmetry == (1, 0, -1)
     sim_red = SIM_FULL.subsection(

tests/test_data/test_data_arrays.py

@@ -50,11 +50,11 @@
 FIELD_TIME_MONITOR_2D = td.FieldTimeMonitor(
     size=SIZE_2D, fields=FIELDS, name="field_time_2d", interval=INTERVAL
 )
-MODE_SOLVE_MONITOR = td.ModeSolverMonitor(
-    size=SIZE_2D, name="mode_solver", mode_spec=MODE_SPEC, freqs=FS
-)
 PERMITTIVITY_MONITOR = td.PermittivityMonitor(size=SIZE_3D, name="permittivity", freqs=FREQS)
 MODE_MONITOR = td.ModeMonitor(size=SIZE_2D, name="mode", mode_spec=MODE_SPEC, freqs=FREQS)
+MODE_MONITOR_WITH_FIELDS = td.ModeMonitor(
+    size=SIZE_2D, name="mode_solver", mode_spec=MODE_SPEC, freqs=FS, store_fields_direction="+"
+)
 FLUX_MONITOR = td.FluxMonitor(size=SIZE_2D, freqs=FREQS, name="flux")
 FLUX_TIME_MONITOR = td.FluxTimeMonitor(size=SIZE_2D, interval=INTERVAL, name="flux_time")
 DIFFRACTION_MONITOR = td.DiffractionMonitor(
@@ -67,7 +67,7 @@
 MONITORS = [
     FIELD_MONITOR,
     FIELD_TIME_MONITOR,
-    MODE_SOLVE_MONITOR,
+    MODE_MONITOR_WITH_FIELDS,
     PERMITTIVITY_MONITOR,
     MODE_MONITOR,
     FLUX_MONITOR,
@@ -131,7 +131,7 @@ def make_scalar_field_time_data_array(grid_key: str, symmetry=True):
 
 
 def make_scalar_mode_field_data_array(grid_key: str, symmetry=True):
-    XS, YS, ZS = get_xyz(MODE_SOLVE_MONITOR, grid_key, symmetry)
+    XS, YS, ZS = get_xyz(MODE_MONITOR_WITH_FIELDS, grid_key, symmetry)
     values = (1 + 0.1j) * np.random.random((len(XS), 1, len(ZS), len(FS), len(MODE_INDICES)))
 
     return td.ScalarModeFieldDataArray(
@@ -140,7 +140,7 @@ def make_scalar_mode_field_data_array(grid_key: str, symmetry=True):
 
 
 def make_scalar_mode_field_data_array_smooth(grid_key: str, symmetry=True, rot: float = 0):
-    XS, YS, ZS = get_xyz(MODE_SOLVE_MONITOR, grid_key, symmetry)
+    XS, YS, ZS = get_xyz(MODE_MONITOR_WITH_FIELDS, grid_key, symmetry)
 
     values = np.array([1 + 0.1j])[None, :, None, None, None] * np.sin(
         0.5