fix(mode): fixed bug where mode solver was not respecting location of PEC

[dmarek-flex]

Greptile Overview

Greptile Summary

This PR fixes a bug where the mode solver grid would extend beyond simulation domain boundaries, causing incorrect PEC boundary condition application. The fix implements grid truncation at simulation boundaries and zero-pads fields outside the domain.

Key changes:

• Added _sim_boundary_positions method to detect PEC boundaries and determine where to truncate the computational grid
• Implemented truncation logic in compute_modes that clips coordinates, permittivity, permeability, and basis fields to simulation bounds
• Added zero-padding to restore fields to original grid size after solving on truncated domain
• Added warnings for unsupported boundary types (PMC, Periodic, Bloch) when mode plane intersects them
• Added comprehensive tests verifying zero fields outside simulation and PEC boundary conditions

The implementation correctly handles the core issue, but there's a minor inconsistency in the boundary intersection detection logic that could cause edge cases.

Confidence Score: 4/5

• This PR is generally safe to merge with one logical inconsistency that should be addressed
• The implementation is well-designed with comprehensive tests, proper documentation, and correct changelog entry. However, there's a logical inconsistency in the boundary intersection detection (using np.isclose vs fp_eps threshold) that could cause edge case failures. The core truncation and zero-padding logic appears sound
• Pay close attention to tidy3d/components/mode/mode_solver.py for the boundary intersection logic inconsistency

Important Files Changed

File Analysis

Filename	Score	Overview
CHANGELOG.md	5/5	Added changelog entry describing the bug fix for mode solver grid extending beyond simulation bounds
tests/test_plugins/test_mode_solver.py	4/5	Added comprehensive tests for PEC boundary truncation and zero-padding, including warning tests for unsupported boundary types. Tests verify field values outside simulation bounds and at PEC boundaries
tidy3d/components/mode/mode_solver.py	4/5	Added _sim_boundary_positions method to detect PEC boundaries and determine truncation positions. Passes boundary positions to solver for grid truncation. Minor inconsistency in boundary checking logic
tidy3d/components/mode/solver.py	4/5	Implements core truncation logic: truncates grid/eps/mu/fields to simulation bounds when needed, then zero-pads results. Adds _truncate_medium_data helper method

Sequence Diagram

sequenceDiagram
    participant MS as ModeSolver
    participant MSC as ModeSolver._solve_single_freq
    participant SBP as ModeSolver._sim_boundary_positions
    participant CM as compute_modes (solver.py)
    participant TMD as _truncate_medium_data
    
    MS->>MS: User calls .data property
    MS->>MSC: _solve_single_freq(freq, coords, symmetry)
    MSC->>SBP: Get PEC boundary positions
    SBP->>SBP: Check boundary types (PEC, PMC, etc.)
    SBP->>SBP: Determine if solver grid intersects boundaries
    SBP-->>MSC: Return (pos_min, pos_max) tuples
    
    MSC->>CM: compute_modes(eps_cross, coords, ..., sim_pec_pos_min, sim_pec_pos_max)
    
    CM->>CM: Calculate truncation indices from PEC positions
    CM->>CM: Check if truncation needed (trim_min != [0,0] or trim_max != [Nx,Ny])
    
    alt Truncation needed
        CM->>CM: Truncate coords arrays
        CM->>TMD: Truncate eps_cross
        TMD-->>CM: Truncated eps
        CM->>TMD: Truncate mu_cross (if present)
        TMD-->>CM: Truncated mu
        CM->>CM: Truncate split_curl_scaling (if present)
        CM->>CM: Truncate solver_basis_fields (if present)
    end
    
    CM->>CM: Solve eigenvalue problem on truncated grid
    CM->>CM: Reshape fields to (2, 3, Nx_trunc, Ny_trunc, 1, num_modes)
    
    alt Truncation was applied
        CM->>CM: Zero-pad fields back to original size
        Note over CM: np.pad with trim_min/trim_max offsets
    end
    
    CM-->>MSC: Return (n_complex, fields, eps_spec)
    MSC-->>MS: Return mode data with correct boundary conditions

Loading

[greptile-apps]

_{3 files reviewed, 1 comment}

_{Edit Code Review Agent Settings | Greptile}

[github-actions]

Diff Coverage

Diff: origin/develop...HEAD, staged and unstaged changes

• tidy3d/components/mode/mode_solver.py (97.4%): Missing lines 1670
• tidy3d/components/mode/solver.py (87.5%): Missing lines 167,171,1170,1172,1174
• tidy3d/components/types/base.py (100%)

Summary

• Total: 79 lines
• Missing: 6 lines
• Coverage: 92%

tidy3d/components/mode/mode_solver.py

  1666     ) -> tuple[list[float], list[dict[str, ArrayComplex4D]], list[EpsSpecType]]:
  1667         """Call the mode solver at all requested frequencies."""
  1668         if tidy3d_extras["use_local_subpixel"]:
  1669             subpixel_ms = tidy3d_extras["mod"].SubpixelModeSolver.from_mode_solver(self)
! 1670             return subpixel_ms._solve_all_freqs(
  1671                 coords=coords,
  1672                 symmetry=symmetry,
  1673             )

---

tidy3d/components/mode/solver.py

  163             eps_cross = cls._truncate_medium_data(eps_cross, cell_min, cell_max)
  164 
  165             # Truncate mu_cross if provided
  166             if mu_cross is not None:
! 167                 mu_cross = cls._truncate_medium_data(mu_cross, cell_min, cell_max)
  168 
  169             # Truncate split_curl_scaling if provided
  170             if split_curl_scaling is not None:
! 171                 split_curl_scaling = tuple(
  172                     s[cell_min[0] : cell_max[0], cell_min[1] : cell_max[1]]
  173                     for s in split_curl_scaling
  174                 )

---

  1166 
  1167         if isinstance(mat_data, Numpy):
  1168             # Tensorial format: shape (9, Nx, Ny)
  1169             return mat_data[:, x_slice, y_slice]
! 1170         if len(mat_data) == 9:
  1171             # Nine separate 2D arrays
! 1172             return tuple(arr[x_slice, y_slice] for arr in mat_data)
  1173 
! 1174         raise ValueError("Wrong input to mode solver permittivity/permeability truncation!")
  1175 
  1176     @staticmethod
  1177     def format_medium_data(mat_data):
  1178         """

---

[dmarek-flex]

@greptileai another round

[greptile-apps]

_{4 files reviewed, 1 comment}

_{Edit Code Review Agent Settings | Greptile}

[weiliangjin2021]

Yes, so far I was trying to match existing behavior, but fix the bug. So if the mode plane is smaller than the Simulation plane bounds, there is no change in behavior when compared to develop. And if we choose the closest grid boundary, or say the closest grid boundary that encompasses the mode plane, then basically we have the same problem (adding additional space), just potentially not quite as bad as the one complete cell in the bug.

I think it's quite common to have mode plane smaller than the simulation domain, and it'll be very useful to fix that too?

Regarding closest grid boundary, i guess it should work in most cases, as it's expected to have the mode plane boundary to lie at the metal surface, and metal surface is snapped to grid.

[dmarek-flex]

I think it's quite common to have mode plane smaller than the simulation domain, and it'll be very useful to fix that too?

It's not really an issue though if the mode plane is smaller than the simulation domain. All that will happen is an extra cell will be added that is outside the monitor bounds. But since in the simulation there is no PEC boundary at the monitor bounds anyways, it is an accurate representation. A structure just outside/touching the monitor bounds will still be captured by the mode solver, and is the current workaround for this bug.

[caseyflex]

I think the warnings make sense if the boundary won’t be used.

the only unclear case is PML, which you don’t earn for just because it would be annoying. I guess that can be a separate discussion about unifying PML treatment