FEAT: Updating FDTD simulation docs 📝

Author: daquinteroflex

README.md

@@ -29,7 +29,7 @@ This repository contains the python API to allow you to:
 
 Note that while this front end package is open source, to run simulations on Flexcompute servers requires an account with credits.
 You can sign up for an account [here](https://tidy3d.simulation.cloud/signup).
-After that, you can install the front end with the instructions below, or visit [this page](https://docs.flexcompute.com/projects/tidy3d/en/stable/install.html) in our documentation for more details.
+After that, you can install the front end with the instructions below, or visit [this page](https://docs.flexcompute.com/projects/tidy3d/en/latest/install.html) in our documentation for more details.
 
 ### Quickstart Installation
 

docs/_static/css/custom.css

@@ -17,7 +17,7 @@
 .wy-nav-content { max-width: 900px !important; }
 .wy-table-responsive table td { white-space: normal !important; }
 .wy-table-responsive { overflow: visible !important; }
-body { line-height: 1.42857143; }s
+body { line-height: 1.42857143; }
 .heading-style, h1, h2, h3, h4, h5, h6 {margin: 1.6rem 0 1rem;}
 h1 {font-family: 'flexcompute_title', sans-serif;}
 h2, h3, h4, h5, h6 {font-family: 'flexcompute_subtitle', sans-serif;}

docs/api/abstract_base.rst

@@ -1,4 +1,4 @@
-.. currentmodule:: tidy3d.components.base_sim
+.. currentmodule:: tidy3d
 
 Abstract Base Models
 =====================
@@ -10,6 +10,8 @@ Base classes that represent abstractions of the core elements of a Simulation.
    :toctree: _autosummary/
    :template: module.rst
 
-   simulation.AbstractSimulation
-   monitor.AbstractMonitor
-   source.AbstractSource
+   tidy3d.components.base_sim.simulation.AbstractSimulation
+   tidy3d.components.base_sim.monitor.AbstractMonitor
+   tidy3d.components.base_sim.source.AbstractSource
+   tidy3d.components.source.Source
+   tidy3d.components.monitor.Monitor

docs/api/constants.rst

@@ -56,30 +56,30 @@ Units
    :toctree: _autosummary/
    :template: module.rst
 
-   tidy3d.HERTZ
-   tidy3d.TERAHERTZ
-   tidy3d.SECOND
-   tidy3d.PICOSECOND
-   tidy3d.METER
-   tidy3d.MICROMETER
-   tidy3d.NANOMETER
-   tidy3d.RADIAN
-   tidy3d.CONDUCTIVITY
-   tidy3d.PERMITTIVITY
-   tidy3d.PML_SIGMA
-   tidy3d.RADPERSEC
-   tidy3d.ELECTRON_VOLT
-   tidy3d.KELVIN
-   tidy3d.PML_SIGMA
-   tidy3d.CMCUBE
-   tidy3d.PERCMCUBE
-   tidy3d.WATT
-   tidy3d.VOLT
-   tidy3d.THERMAL_CONDUCTIVITY
-   tidy3d.SPECIFIC_HEAT_CAPACITY
-   tidy3d.HEAT_FLUX
-   tidy3d.VOLUMETRIC_HEAT_RATE
-   tidy3d.HEAT_TRANSFER_COEFF
+   tidy3d.constants.HERTZ
+   tidy3d.constants.TERAHERTZ
+   tidy3d.constants.SECOND
+   tidy3d.constants.PICOSECOND
+   tidy3d.constants.METER
+   tidy3d.constants.MICROMETER
+   tidy3d.constants.NANOMETER
+   tidy3d.constants.RADIAN
+   tidy3d.constants.CONDUCTIVITY
+   tidy3d.constants.PERMITTIVITY
+   tidy3d.constants.PML_SIGMA
+   tidy3d.constants.RADPERSEC
+   tidy3d.constants.ELECTRON_VOLT
+   tidy3d.constants.KELVIN
+   tidy3d.constants.PML_SIGMA
+   tidy3d.constants.CMCUBE
+   tidy3d.constants.PERCMCUBE
+   tidy3d.constants.WATT
+   tidy3d.constants.VOLT
+   tidy3d.constants.THERMAL_CONDUCTIVITY
+   tidy3d.constants.SPECIFIC_HEAT_CAPACITY
+   tidy3d.constants.HEAT_FLUX
+   tidy3d.constants.VOLUMETRIC_HEAT_RATE
+   tidy3d.constants.HEAT_TRANSFER_COEFF
 
 
 Precision & Comparator Values
@@ -89,8 +89,8 @@ Precision & Comparator Values
    :toctree: _autosummary/
    :template: module.rst
 
-   tidy3d.dp_eps
-   tidy3d.fp_eps
-   tidy3d.pec_val
-   tidy3d.LARGE_NUMBER
-   tidy3d.GLANCING_CUTOFF
+   tidy3d.constants.dp_eps
+   tidy3d.constants.fp_eps
+   tidy3d.constants.pec_val
+   tidy3d.constants.LARGE_NUMBER
+   tidy3d.constants.GLANCING_CUTOFF

docs/install.rst

@@ -181,4 +181,4 @@ To see some other examples of Tidy3D being used in large scale photonics simulat
 
 To learn more about the many features of Tidy3D, check out our `Feature Walkthrough <./notebooks/Simulation.html>`_.
 
-Or, if you're interested in the API documentation, see `API Reference <./api.html>`_.
+Or, if you're interested in the API documentation, see `API Reference <./api/index.html>`_.

docs/versions/2_5_to_2_6.json

@@ -1,5 +1,5 @@
 {
   "2.6.0": {
-    "https://docs.flexcompute.com/projects/tidy3d/en/stable/_autosummary": "https://docs.flexcompute.com/projects/tidy3d/en/stable/api/_autosummary"
+    "https://docs.flexcompute.com/projects/tidy3d/en/latest/_autosummary": "https://docs.flexcompute.com/projects/tidy3d/en/latest/api/_autosummary"
   }
 }

tidy3d/components/base_sim/simulation.py

@@ -37,28 +37,6 @@ class AbstractSimulation(Box, ABC):
     )
     """
     Background medium of simulation, defaults to vacuum if not specified.
-
-    See Also
-    --------
-
-    `Material Library <../material_library.html>`_:
-        The material library is a dictionary containing various dispersive models from real world materials.
-
-    `Index <../mediums.html>`_:
-        Dispersive and dispersionless Mediums models.
-
-    **Notebooks:**
-
-    * `Fitting dispersive material models <../../notebooks/Fitting.html>`_
-
-    **Lectures:**
-
-    * `Modeling dispersive material in FDTD <https://www.flexcompute.com/fdtd101/Lecture-5-Modeling-dispersive-material-in-FDTD/>`_
-
-    **GUI:**
-
-    * `Mediums <https://www.flexcompute.com/tidy3d/learning-center/tidy3d-gui/Lecture-2-Mediums/>`_
-
     """
 
     structures: Tuple[Structure, ...] = pd.Field(
@@ -88,72 +66,15 @@ class AbstractSimulation(Box, ABC):
             ],
             ...
         )
-
-    **Usage Caveats**
-
-    It is very important to understand the way the dielectric permittivity of the :class:`Structure` list is resolved
-    by the simulation grid. Without :attr:`subpixel` averaging, the structure geometry in relation to the
-    grid points can lead to its features permittivity not being fully resolved by the
-    simulation.
-
-    For example, in the image below, two silicon slabs with thicknesses 150nm and 175nm centered in a grid with
-    spatial discretization :math:`\\Delta z = 25\\text{nm}` will compute equivalently because that grid does
-    not resolve the feature permittivity in between grid points without :attr:`subpixel` averaging.
-
-    .. image:: ../../_static/img/permittivity_on_yee_grid.png
-
-    See Also
-    --------
-
-    :class:`Structure`:
-        Defines a physical object that interacts with the electromagnetic fields.
-
-    :attr:`subpixel`
-        Subpixel averaging of the permittivity based on structure definition, resulting in much higher
-        accuracy for a given grid size.
-
-    **Notebooks:**
-
-    * `Visualizing geometries in Tidy3D <../../notebooks/VizSimulation.html>`_
-
-    **Lectures:**
-
-    * `Using FDTD to Compute a Transmission Spectrum <https://www.flexcompute.com/fdtd101/Lecture-2-Using-FDTD-to-Compute-a-Transmission-Spectrum/>`_
-    *  `Dielectric constant assignment on Yee grids <https://www.flexcompute.com/fdtd101/Lecture-9-Dielectric-constant-assignment-on-Yee-grids/>`_
-
-    **GUI:**
-
-    * `Structures <https://www.flexcompute.com/tidy3d/learning-center/tidy3d-gui/Lecture-3-Structures/#presentation-slides>`_
     """
 
     symmetry: Tuple[Symmetry, Symmetry, Symmetry] = pd.Field(
         (0, 0, 0),
         title="Symmetries",
         description="Tuple of integers defining reflection symmetry across a plane "
         "bisecting the simulation domain normal to the x-, y-, and z-axis "
-        "at the simulation center of each axis, respectively. "
-        "Each element can be ``0`` (no symmetry), ``1`` (even, i.e. 'PMC' symmetry) or "
-        "``-1`` (odd, i.e. 'PEC' symmetry). "
-        "Note that the vectorial nature of the fields must be taken into account to correctly "
-        "determine the symmetry value.",
+        "at the simulation center of each axis, respectively. ",
     )
-    """
-    You should set the ``symmetry`` parameter in your :class:`Simulation` object using a tuple of integers
-    defining reflection symmetry across a plane bisecting the simulation domain normal to the x-, y-, and z-axis.
-    Each element can be 0 (no symmetry), 1 (even, i.e. :class:`PMC` symmetry) or -1 (odd, i.e. :class:`PEC`
-    symmetry). Note that the vectorial nature of the fields must be considered to determine the symmetry value
-    correctly.
-
-    The figure below illustrates how the electric and magnetic field components transform under :class:`PEC`- and
-    :class:`PMC`-like symmetry planes. You can refer to this figure when considering whether a source field conforms
-    to a :class:`PEC`- or :class:`PMC`-like symmetry axis. This would be helpful, especially when dealing with
-    optical waveguide modes.
-
-    .. image:: ../../notebooks/img/pec_pmc.png
-
-
-    .. TODO maybe resize?
-    """
 
     sources: Tuple[None, ...] = pd.Field(
         (),