flexcompute · tylerflex · Jun 19, 2024 · Jun 20, 2024 · Jun 10, 2024 · Jun 27, 2024
diff --git a/.github/workflows/sync-to-readthedocs-repo.yaml b/.github/workflows/sync-to-readthedocs-repo.yaml
@@ -63,10 +63,11 @@ jobs:
           ref: ${{ needs.extract_branch_or_tag.outputs.ref_name }}
           fetch-tags: true
 
+
       - name: Push corresponding reference to mirror repo if a tag
         if: contains(github.ref, 'refs/tags/')
         run: |
           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.GITHUB_TOKEN }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,14 +3,50 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [2.8.0rc1]
 
 ### Added
-- Added value_and_grad function to the autograd plugin, importable via `from tidy3d.plugins.autograd import value_and_grad`. Supports differentiating functions with auxiliary data (`value_and_grad(f, has_aux=True)`).
+- Support for differentiation with respect to `ComplexPolySlab.vertices`.
+- Introduce RF material library. Users can now import `rf_material_library` from `tidy3d.plugins.microwave`.
+- Users can specify the background medium for a structure in automatic differentiation by supplying `Structure.background_permittivity`.
+- `DirectivityMonitor` to compute antenna directivity.
+- Added `plot_length_units` to `Simulation` and `Scene` to allow for specifying units, which improves axis labels and scaling when plotting.
+- Added the helper function `compute_power_delivered_by_port`  to `TerminalComponentModeler` which computes power delivered to a microwave network from a port.
+- Added the account function `account` to check credit balance and daily free simulation balance.
+- Added `WavePort` to the `TerminalComponentModeler` which is the suggested port type for exciting transmission lines.
+- Added plotting functionality to voltage and current path integrals in the `microwave` plugin.
+- Added convenience functions `from_terminal_positions` and `from_circular_path` to simplify setup of `VoltageIntegralAxisAligned` and `CustomCurrentIntegral2D`, respectively.
+- Added `axial_ratio` to `DirectivityData.axial_ratio` for the `DirectivityMonitor`, defined as the ratio of the major axis to the minor axis of the polarization ellipse. 
+`ComponentModeler.batch_data` convenience property to access the `BatchData` corresponding to the component modeler run.
+- Added optimization methods to the Design plugin. The plugin has been expanded to include Bayesian optimization, genetic algorithms and particle swarm optimization. Explanations of these methods are available in new and updated notebooks.
+- Added new support functions for the Design plugin: automated batching of `Simulation` objects, and summary functions with `DesignSpace.estimate_cost` and `DesignSpace.summarize`.
+- Added validation and repair methods for `TriangleMesh` with inward-facing normals.
+- Added `from_admittance_coeffs` to `PoleResidue`, which allows for directly constructing a `PoleResidue` medium from an admittance function in the Laplace domain.
+- Added material type `LossyMetalMedium` that has high DC-conductivity. Its boundaries can be modeled by a surface impedance boundary condition (SIBC). This is treated as a subpixel method, which can be switched by setting `SubpixelSpec(lossy_metal=method)` where `method` can be `Staircasing()`, `VolumetricAveraging()`, or `SurfaceImpedance()`.
+- Added mode solver option `precision='auto'` to automatically select single or double precision for optimizing performance and accuracy.
+- Added `LinearLumpedElement` as a new supported `LumpedElement` type. This enhancement allows for the modeling of two-terminal passive networks, which can include any configuration of resistors, inductors, and capacitors, within the `Simulation`. Simple RLC networks are described using `RLCNetwork`, while more complex networks can be represented by their admittance transfer function through `AdmittanceNetwork`.
+
+### Changed
+- Priority is given to `snapping_points` in `GridSpec` when close to structure boundaries, which reduces the chance of them being skipped.
+- Gradients for autograd are computed server-side by default. They can be computed locally (requiring more data download) by passing `local_gradient=True` to the `web.run()` and related functions.
+- Passing `path_dir` to `ComponentModeler` methods is deprecated in favor of setting `ComponentModeler.path_dir` and will result in an error if the two don't match.
+- `BatchData` is now a mapping and can be accessed and iterated over like a Python dictionary (`.keys()`, `.values()`, `.items()`).
+- `MethodRandom` and `MethodRandomCustom` have been removed from the Design plugin, and `DesignSpace.run_batch` has been superseded by `.run`.
+- Design plugin has been significantly reworked to improve ease of use and allow for new optimization methods.
+- Behavior of `FieldProjector` now matches the server-side computation, which does not truncate the integration surface when it extends into PML regions.
+- Enabled the user to set the `ModeMonitor.colocate` field and changed to `True` by default (fields were actually already returned colocated even though this field was `False` previously).
+- More robust mode solver at radio frequencies.
+- Disallow very small polygons when subdividing 2D structures.
 
 ### Fixed
-- `DataArray` interpolation failure due to incorrect ordering of coordinates when interpolating with autograd tracers.
-- Error in `CustomSourceTime` when evaluating at a list of times entirely outside of the range of the envelope definition times.
+- Significant speedup for field projection computations.
+- Fix numerical precision issue in `FieldProjectionCartesianMonitor`.
+- Bug where lumped elements in the `Simulation` were being overwritten by the `TerminalComponentModeler`.
+- Bug in `Simulation.subsection` where lumped elements were not being correctly removed.
+- Bug when adding 2D structures to the `Simulation` that are composed of multiple overlapping polygons.
+- Fields stored in `ModeMonitor` objects were computed colocated to the grid boundaries, but the built-in `ModeMonitor.colocate=False` was resulting in wrong results in some cases, most notably if symmetries are also involved.
+- Small inaccuracy when applying a mode solver `bend_radius` when the simulation grid is not symmetric w.r.t. the mode plane center. Previously, the radius was defined w.r.t. the middle grid coordinate, while now it is correctly applied w.r.t. the plane center.
+- Silence warning in graphene from checking fit quality at large frequencies.
 
 ## [2.7.2] - 2024-08-07
 
@@ -57,6 +93,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [2.7.0] - 2024-06-17
 
 ### Added
+- `HeatSimulation` is now under the more generic class `HeatChargeSimulation`. This new class sallows for imulations of both HEAT and electric CONDUCTION types. One-way coupling between these is possible in which the CONDUCTION simulation is used to compute Joule heating which is subsequently used as a source in the HEAT simulation.
 - EME solver through `EMESimulation` class.
 - 2D heat simulations are now fully supported. 
 - `tidy3d.plugins.adjoint.web.run_local` used in place of `run` will skip validators that restrict the size or number of `input_structures`.
@@ -1273,8 +1310,8 @@ 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/v2.7.2...develop
-[2.7.2]: https://github.com/flexcompute/tidy3d/compare/v2.7.1...v2.7.2
+[Unreleased]: https://github.com/flexcompute/tidy3d/compare/v2.8.0rc1...pre/2.8
+[2.8.0rc1]: https://github.com/flexcompute/tidy3d/compare/v2.7.1...v2.8.0rc1
 [2.7.1]: https://github.com/flexcompute/tidy3d/compare/v2.7.0...v2.7.1
 [2.7.0]: https://github.com/flexcompute/tidy3d/compare/v2.6.4...v2.7.0
 [2.6.4]: https://github.com/flexcompute/tidy3d/compare/v2.6.3...v2.6.4

diff --git a/docs/_static/img/design.png b/docs/_static/img/design.png
diff --git a/docs/api/abstract_models.rst b/docs/api/abstract_models.rst
@@ -42,6 +42,7 @@ These are some classes that are used to organize the tidy3d components, but aren
    tidy3d.components.monitor.PlanarMonitor
    tidy3d.components.monitor.AbstractFieldProjectionMonitor
    tidy3d.components.lumped_element.LumpedElement
+   tidy3d.components.lumped_element.RectangularLumpedElement
    tidy3d.components.grid.grid_spec.GridSpec1d
    tidy3d.components.base_sim.data.sim_data.SimulationData
    tidy3d.components.data.sim_data.AbstractYeeGridSimulationData

diff --git a/docs/api/heat/index.rst b/docs/api/heat/index.rst
diff --git a/docs/api/heat/boundary_conditions.rst → docs/api/heat_charge/boundary_conditions.rst b/docs/api/heat/boundary_conditions.rst → docs/api/heat_charge/boundary_conditions.rst
@@ -1,6 +1,6 @@
 .. currentmodule:: tidy3d
 
-Thermal Boundary Conditions
+Thermal/Charge Boundary Conditions
 -----------------------------
 
 Specifications
@@ -11,6 +11,7 @@ Specifications
    :template: module.rst
 
    tidy3d.HeatBoundarySpec
+   tidy3d.HeatChargeBoundarySpec
 
 
 Types
@@ -23,6 +24,9 @@ Types
    tidy3d.TemperatureBC
    tidy3d.ConvectionBC
    tidy3d.HeatFluxBC
+   tidy3d.VoltageBC
+   tidy3d.CurrentBC,
+   tidy3d.InsulatingBC
 
 
 Placement

diff --git a/docs/api/heat/discretization.rst → docs/api/heat_charge/discretization.rst b/docs/api/heat/discretization.rst → docs/api/heat_charge/discretization.rst
diff --git a/docs/api/heat_charge/index.rst b/docs/api/heat_charge/index.rst
@@ -0,0 +1,22 @@
+HEAT |:fire:|
+=============
+
+.. toctree::
+    :hidden:
+
+    simulation
+    mediums
+    boundary_conditions
+    source
+    discretization
+    monitor
+    output_data
+
+
+.. include:: /api/heat_charge/simulation.rst
+.. include:: /api/heat_charge/mediums.rst
+.. include:: /api/heat_charge/boundary_conditions.rst
+.. include:: /api/heat_charge/source.rst
+.. include:: /api/heat_charge/discretization.rst
+.. include:: /api/heat_charge/monitor.rst
+.. include:: /api/heat_charge/output_data.rst
diff --git a/docs/api/heat/mediums.rst → docs/api/heat_charge/mediums.rst b/docs/api/heat/mediums.rst → docs/api/heat_charge/mediums.rst
@@ -1,6 +1,6 @@
 .. currentmodule:: tidy3d
 
-Material Thermal Specification
+Material Thermal/Charge Specification
 -------------------------------
 
 .. autosummary::
@@ -9,6 +9,8 @@ Material Thermal Specification
 
    tidy3d.FluidSpec
    tidy3d.SolidSpec
+   tidy3d.ConductorSpec
+   tidy3d.InsulatorSpec
 
 
 Thermal Perturbation Specification

diff --git a/docs/api/heat/monitor.rst → docs/api/heat_charge/monitor.rst b/docs/api/heat/monitor.rst → docs/api/heat_charge/monitor.rst
@@ -7,4 +7,5 @@ Monitors
    :toctree: ../_autosummary/
    :template: module.rst
 
-   tidy3d.TemperatureMonitor
+   tidy3d.TemperatureMonitor
+   tidy3d.VoltageMonitor
diff --git a/docs/api/heat/output_data.rst → docs/api/heat_charge/output_data.rst b/docs/api/heat/output_data.rst → docs/api/heat_charge/output_data.rst
@@ -4,14 +4,15 @@ Output Data
 -------------
 
 
-Heat Simulation Data
+Heat/Charge Simulation Data
 ^^^^^^^^^^^^^^^^^^^^
 
 .. autosummary::
    :toctree: ../_autosummary/
    :template: module.rst
 
    tidy3d.HeatSimulationData
+   tidy3d.HeatChargeSimulationData
 
 
 Monitor Data
@@ -22,6 +23,7 @@ Monitor Data
    :template: module.rst
 
    tidy3d.TemperatureData
+   tidy3d.VoltageData
 
 
 Unstructured Data Classes

diff --git a/docs/api/heat/simulation.rst → docs/api/heat_charge/simulation.rst b/docs/api/heat/simulation.rst → docs/api/heat_charge/simulation.rst
@@ -8,3 +8,4 @@ Simulation
    :template: module.rst
 
    tidy3d.HeatSimulation
+   tidy3d.HeatChargeSimulation
diff --git a/docs/api/heat/source.rst → docs/api/heat_charge/source.rst b/docs/api/heat/source.rst → docs/api/heat_charge/source.rst
@@ -7,4 +7,6 @@ Thermal Sources
    :toctree: ../_autosummary/
    :template: module.rst
 
-   tidy3d.UniformHeatSource
+   tidy3d.UniformHeatSource
+   tidy3d.HeatSource
+   tidy3d.HeatFromElectricSource
diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -10,6 +10,7 @@ API |:computer:|
     geometry
     mediums
     material_library
+    rf_material_library
     structures
     sources
     monitors

diff --git a/docs/api/lumped_elements.rst b/docs/api/lumped_elements.rst
@@ -10,4 +10,7 @@ Passive elements
    :template: module.rst
 
    tidy3d.LumpedResistor
-   tidy3d.CoaxialLumpedResistor
+   tidy3d.CoaxialLumpedResistor
+   tidy3d.RLCNetwork
+   tidy3d.AdmittanceNetwork
+   tidy3d.LinearLumpedElement
diff --git a/docs/api/mediums.rst b/docs/api/mediums.rst
@@ -14,6 +14,7 @@ Spatially uniform
    :template: module.rst
 
    tidy3d.Medium
+   tidy3d.LossyMetalMedium
    tidy3d.PECMedium
    tidy3d.FullyAnisotropicMedium
 
@@ -25,6 +26,15 @@ Spatially varying
 
    tidy3d.CustomMedium
 
+Fitting parameters
+^^^^^^^^^^^^^^^^^^
+
+.. autosummary::
+   :toctree: _autosummary/
+   :template: module.rst
+
+   tidy3d.SkinDepthFitterParam
+
 Dispersive Mediums
 ------------------
 
@@ -116,3 +126,4 @@ Material Library
 
 .. toctree::
    material_library
+   rf_material_library
diff --git a/docs/api/monitors.rst b/docs/api/monitors.rst
@@ -22,6 +22,7 @@ Monitor Types
    tidy3d.FieldProjectionAngleMonitor
    tidy3d.FieldProjectionKSpaceMonitor
    tidy3d.DiffractionMonitor
+   tidy3d.DirectivityMonitor
 
 Apodization Specification
 -------------------------

diff --git a/docs/api/output_data.rst b/docs/api/output_data.rst
@@ -30,6 +30,7 @@ Collections of Data from single monitor
    tidy3d.FieldProjectionCartesianData
    tidy3d.FieldProjectionKSpaceData
    tidy3d.DiffractionData
+   tidy3d.DirectivityData
 
 Individual Datasets
 -------------------
@@ -51,3 +52,5 @@ Individual Datasets
    tidy3d.FieldProjectionCartesianDataArray
    tidy3d.FieldProjectionKSpaceDataArray
    tidy3d.DiffractionDataArray
+   tidy3d.DirectivityDataArray
+   tidy3d.AxialRatioDataArray
diff --git a/docs/api/plugins/design.rst b/docs/api/plugins/design.rst
@@ -11,14 +11,13 @@ Design Space Exploration
    :toctree: ../_autosummary/
    :template: module.rst
 
-   tidy3d.plugins.design.Parameter
    tidy3d.plugins.design.ParameterFloat
    tidy3d.plugins.design.ParameterInt
    tidy3d.plugins.design.ParameterAny
-   tidy3d.plugins.design.Method
    tidy3d.plugins.design.MethodGrid
    tidy3d.plugins.design.MethodMonteCarlo
-   tidy3d.plugins.design.MethodRandomCustom
-   tidy3d.plugins.design.MethodRandom
+   tidy3d.plugins.design.MethodBayOpt
+   tidy3d.plugins.design.MethodGenAlg
+   tidy3d.plugins.design.MethodParticleSwarm
    tidy3d.plugins.design.DesignSpace
-   tidy3d.plugins.design.Results
+   tidy3d.plugins.design.Result
diff --git a/docs/api/plugins/smatrix.rst b/docs/api/plugins/smatrix.rst
@@ -11,6 +11,7 @@ Scattering Matrix Calculator
    tidy3d.plugins.smatrix.Port
    tidy3d.plugins.smatrix.ModalPortDataArray
    tidy3d.plugins.smatrix.TerminalComponentModeler
+   tidy3d.plugins.smatrix.TerminalPortDataArray
    tidy3d.plugins.smatrix.LumpedPort
-   tidy3d.plugins.smatrix.LumpedPortDataArray
-   tidy3d.plugins.smatrix.CoaxialLumpedPort
+   tidy3d.plugins.smatrix.CoaxialLumpedPort
+   tidy3d.plugins.smatrix.WavePort