Merge branch 'doc-fixes' into '2.0.0-rc'

ktangsali · ktangsali · commit 8f6ad0ba7f4f · 2025-03-07T14:04:29.000-08:00
Doc fixes

See merge request modulus/modulus-sym!391
diff --git a/docs/api/api_index.rst b/docs/api/api_index.rst
@@ -1,8 +1,8 @@
 
 Welcome to the PhysicsNeMo Sym API documentation.
 
-Core API
-===========
+Fundamental API
+================
 
 .. toctree::
    :maxdepth: 1
diff --git a/docs/api/physicsnemo.sym.domain.constraint.rst b/docs/api/physicsnemo.sym.domain.constraint.rst
@@ -1,5 +1,5 @@
 PhysicsNeMo Sym Constraints
-=======================
+============================
 
 Continuous Constraints
 ------------------------------------------------
diff --git a/docs/api/physicsnemo.sym.domain.inferencer.rst b/docs/api/physicsnemo.sym.domain.inferencer.rst
@@ -1,5 +1,5 @@
 PhysicsNeMo Sym Inferencers
-=======================
+============================
 
 
 Pointwise Inferencer
diff --git a/docs/api/physicsnemo.sym.domain.monitor.rst b/docs/api/physicsnemo.sym.domain.monitor.rst
@@ -1,5 +1,5 @@
 PhysicsNeMo Sym Monitors
-====================
+============================
 
 
 Pointwise Monitor
diff --git a/docs/api/physicsnemo.sym.domain.validator.rst b/docs/api/physicsnemo.sym.domain.validator.rst
@@ -1,5 +1,5 @@
 PhysicsNeMo Sym Validators
-======================
+============================
 
 Continuous Validators
 ------------------------------------------------
diff --git a/docs/api/physicsnemo.sym.eq.rst b/docs/api/physicsnemo.sym.eq.rst
@@ -1,5 +1,5 @@
 PhysicsNeMo Sym Equations and Utils
-================================
+====================================
 
 pde.advection\_diffusion
 ----------------------------------------
diff --git a/docs/api/physicsnemo.sym.geometry.rst b/docs/api/physicsnemo.sym.geometry.rst
diff --git a/docs/api/physicsnemo.sym.hydra.rst b/docs/api/physicsnemo.sym.hydra.rst
diff --git a/docs/api/physicsnemo.sym.loss.rst b/docs/api/physicsnemo.sym.loss.rst
@@ -1,16 +1,16 @@
 PhysicsNeMo Sym Loss
-================
+====================
 
 physicsnemo.sym.loss.loss
-----------------------
+--------------------------
 
 .. automodule:: physicsnemo.sym.loss.loss
    :members:
    :show-inheritance:
 
 
 physicsnemo.sym.loss.aggregator
-----------------------------
+--------------------------------
 
 .. automodule:: physicsnemo.sym.loss.aggregator
    :members:
diff --git a/docs/api/physicsnemo.sym.models.rst b/docs/api/physicsnemo.sym.models.rst
diff --git a/docs/api/physicsnemo.sym.rst b/docs/api/physicsnemo.sym.rst
@@ -2,36 +2,36 @@ PhysicsNeMo Sym
 ===============
 
 physicsnemo.sym.constants
-------------------------
+--------------------------
 
 .. automodule:: physicsnemo.sym.constants
    :members:
    :show-inheritance:
 
 
 physicsnemo.sym.graph
---------------------
+----------------------
 
 .. automodule:: physicsnemo.sym.graph
    :members:
    :show-inheritance:
 
 physicsnemo.sym.key
-------------------
+--------------------
 
 .. automodule:: physicsnemo.sym.key
    :members:
    :show-inheritance:
 
 physicsnemo.sym.node
--------------------
+---------------------
 
 .. automodule:: physicsnemo.sym.node
    :members:
    :show-inheritance:
 
 physicsnemo.sym.trainer
-----------------------
+------------------------
 
 .. automodule:: physicsnemo.sym.trainer
    :members:
diff --git a/docs/api/physicsnemo.sym.utils.rst b/docs/api/physicsnemo.sym.utils.rst
diff --git a/docs/images/user_guide/physicsnemo_architecture.png b/docs/images/user_guide/physicsnemo_architecture.png
diff --git a/docs/images/user_guide/physicsnemo_dev_workflow.png b/docs/images/user_guide/physicsnemo_dev_workflow.png
diff --git a/docs/images/user_guide/physicsnemo_training_loop.png b/docs/images/user_guide/physicsnemo_training_loop.png
diff --git a/docs/user_guide/advanced/fpga.rst b/docs/user_guide/advanced/fpga.rst
@@ -265,42 +265,42 @@ comparison for the loss values from different runs.
 .. table:: Comparison of pressure drop and peak temperatures from various runs
    :align: center
 
-   +---------------------------+----------------------+----------------------+
-   | **Case Description**      | :math:`P_{drop}`     | :math:`T_{peak}`     |
-   |                           | :math:`(Pa)`         | :math:`(^{\circ} C)` |
-   +---------------------------+----------------------+----------------------+
-   | **PhysicsNeMo Sym:** Fully    | 29.24                | 77.90                |
-   | Connected Networks        |                      |                      |
-   +---------------------------+----------------------+----------------------+
-   | **PhysicsNeMo Sym:** Fully    | 28.92                | 90.63                |
-   | Connected Networks        |                      |                      |
-   | with Exact                |                      |                      |
-   | Continuity                |                      |                      |
-   +---------------------------+----------------------+----------------------+
-   | **PhysicsNeMo Sym:** Fourier  | 29.19                | 77.08                |
-   | Networks                  |                      |                      |
-   +---------------------------+----------------------+----------------------+
-   | **PhysicsNeMo Sym:** Modified | 29.23                | 80.96                |
-   | Fourier Networks          |                      |                      |
-   +---------------------------+----------------------+----------------------+
-   | **PhysicsNeMo Sym:** SiReNs   | 29.21                | 76.54                |
-   +---------------------------+----------------------+----------------------+
-   | **PhysicsNeMo Sym:** Fourier  | 29.14                | 78.56                |
-   | Networks with             |                      |                      |
-   | Symmetry                  |                      |                      |
-   +---------------------------+----------------------+----------------------+
-   | **PhysicsNeMo Sym:** DGM      | 29.10                | 76.86                |
-   | Networks with Global      |                      |                      |
-   | LR annealing, Global      |                      |                      |
-   | Adaptive                  |                      |                      |
-   | Activations, and          |                      |                      |
-   | Halton Sequences          |                      |                      |
-   +---------------------------+----------------------+----------------------+
-   | **OpenFOAM Solver**       | 28.03                | 76.67                |
-   +---------------------------+----------------------+----------------------+
-   | **Commercial Solver**     | 28.38                | 84.93                |
-   |                           |                      |                      |
-   +---------------------------+----------------------+----------------------+
+   +-------------------------------+----------------------+--------------------------+
+   | **Case Description**          | :math:`P_{drop}`     | :math:`T_{peak}`         |
+   |                               | :math:`(Pa)`         | :math:`(^{\circ} C)`     |
+   +-------------------------------+----------------------+--------------------------+
+   | **PhysicsNeMo Sym:** Fully    | 29.24                | 77.90                    |
+   | Connected Networks            |                      |                          |
+   +-------------------------------+----------------------+--------------------------+
+   | **PhysicsNeMo Sym:** Fully    | 28.92                | 90.63                    |
+   | Connected Networks            |                      |                          |
+   | with Exact                    |                      |                          |
+   | Continuity                    |                      |                          |
+   +-------------------------------+----------------------+--------------------------+
+   | **PhysicsNeMo Sym:** Fourier  | 29.19                | 77.08                    |
+   | Networks                      |                      |                          |
+   +-------------------------------+----------------------+--------------------------+
+   | **PhysicsNeMo Sym:** Modified | 29.23                | 80.96                    |
+   | Fourier Networks              |                      |                          |
+   +-------------------------------+----------------------+--------------------------+
+   | **PhysicsNeMo Sym:** SiReNs   | 29.21                | 76.54                    |
+   +-------------------------------+----------------------+--------------------------+
+   | **PhysicsNeMo Sym:** Fourier  | 29.14                | 78.56                    |
+   | Networks with                 |                      |                          |
+   | Symmetry                      |                      |                          |
+   +-------------------------------+----------------------+--------------------------+
+   | **PhysicsNeMo Sym:** DGM      | 29.10                | 76.86                    |
+   | Networks with Global          |                      |                          |
+   | LR annealing, Global          |                      |                          |
+   | Adaptive                      |                      |                          |
+   | Activations, and              |                      |                          |
+   | Halton Sequences              |                      |                          |
+   +-------------------------------+----------------------+--------------------------+
+   | **OpenFOAM Solver**           | 28.03                | 76.67                    |
+   +-------------------------------+----------------------+--------------------------+
+   | **Commercial Solver**         | 28.38                | 84.93                    |
+   |                               |                      |                          |
+   +-------------------------------+----------------------+--------------------------+
 
 
 .. _fig-fpga-loss-plots:
diff --git a/docs/user_guide/advanced/industrial_heat_sink.rst b/docs/user_guide/advanced/industrial_heat_sink.rst
@@ -141,39 +141,39 @@ profile is shown in :numref:`fig-limerock_thermal`.
 .. table:: A comparison for the solver and PhysicsNeMo Sym results for NVSwitch pressure drop and peak temperature.
    :align: center
 
-   +----------------------+---------------+---------------+---------------+
+   +----------------------+---------------+---------------+-------------------+
    | Property             | OpenFOAM      | Commercial    | PhysicsNeMo Sym   |
-   |                      |               | Solver        |               |
-   +----------------------+---------------+---------------+---------------+
-   | Pressure Drop        |               |               |               |
-   | :math:`(Pa)`         | :math:`133.96`| :math:`137.50`| :math:`150.25`|
-   +----------------------+---------------+---------------+---------------+
-   | Peak                 | :math:`93.41` | :math:`95.10` | :math:`97.35` |
-   | Temperature          |               |               |               |
-   | :math:`(^{\circ} C)` |               |               |               |
-   +----------------------+---------------+---------------+---------------+
+   |                      |               | Solver        |                   |
+   +----------------------+---------------+---------------+-------------------+
+   | Pressure Drop        |               |               |                   |
+   | :math:`(Pa)`         | :math:`133.96`| :math:`137.50`| :math:`150.25`    |
+   +----------------------+---------------+---------------+-------------------+
+   | Peak                 | :math:`93.41` | :math:`95.10` | :math:`97.35`     |
+   | Temperature          |               |               |                   |
+   | :math:`(^{\circ} C)` |               |               |                   |
+   +----------------------+---------------+---------------+-------------------+
 
 
 .. _table-limerock2:
 
 .. table:: Commercial solver mesh refinement results for NVSwitch pressure drop and peak temperature.
    :align: center
    
-   +--------------------+------------------------------------------+------------------------------------------+
-   | Number of elements | Pressure drop (Pa)                       | Peak temperature :math:`(^{\circ} C)`    |
-   |                    +-------------------+-------------+--------+-------------------+-------------+--------+
+   +--------------------+----------------------------------------------+----------------------------------------------+
+   | Number of elements | Pressure drop (Pa)                           | Peak temperature :math:`(^{\circ} C)`        |
+   |                    +-------------------+-----------------+--------+-------------------+-----------------+--------+
    |                    | Commercial solver | PhysicsNeMo Sym | % diff | Commercial solver | PhysicsNeMo Sym | % diff |
-   +--------------------+-------------------+-------------+--------+-------------------+-------------+--------+
-   | 22.4 M             | 81.27             | 150.25      | 84.88  | 97.40             | 97.35       | 0.05   |
-   +--------------------+-------------------+-------------+--------+-------------------+-------------+--------+
-   | 24.7 M             | 111.76            | 150.25      | 34.44  | 95.50             | 97.35       | 1.94   |
-   +--------------------+-------------------+-------------+--------+-------------------+-------------+--------+
-   | 26.9 M             | 122.90            | 150.25      | 22.25  | 95.10             | 97.35       | 2.36   |
-   +--------------------+-------------------+-------------+--------+-------------------+-------------+--------+
-   | 30.0 M             | 132.80            | 150.25      | 13.14  | -                 | -           | -      |
-   +--------------------+-------------------+-------------+--------+-------------------+-------------+--------+
-   | 32.0 M             | 137.50            | 150.25      | 9.27   | -                 | -           | -      |
-   +--------------------+-------------------+-------------+--------+-------------------+-------------+--------+
+   +--------------------+-------------------+-----------------+--------+-------------------+-----------------+--------+
+   | 22.4 M             | 81.27             | 150.25          | 84.88  | 97.40             | 97.35           | 0.05   |
+   +--------------------+-------------------+-----------------+--------+-------------------+-----------------+--------+
+   | 24.7 M             | 111.76            | 150.25          | 34.44  | 95.50             | 97.35           | 1.94   |
+   +--------------------+-------------------+-----------------+--------+-------------------+-----------------+--------+
+   | 26.9 M             | 122.90            | 150.25          | 22.25  | 95.10             | 97.35           | 2.36   |
+   +--------------------+-------------------+-----------------+--------+-------------------+-----------------+--------+
+   | 30.0 M             | 132.80            | 150.25          | 13.14  | -                 | -               | -      |
+   +--------------------+-------------------+-----------------+--------+-------------------+-----------------+--------+
+   | 32.0 M             | 137.50            | 150.25          | 9.27   | -                 | -               | -      |
+   +--------------------+-------------------+-----------------+--------+-------------------+-----------------+--------+
 
 
 .. _fig-limerock_thermal:
diff --git a/docs/user_guide/basics/lid_driven_cavity_flow.rst b/docs/user_guide/basics/lid_driven_cavity_flow.rst
@@ -186,7 +186,7 @@ we will create a list of nodes to pass to different constraints that need to be
 The constraints include equations, residuals, and boundary conditions.
 
 Using Hydra to Configure PhysicsNeMo Sym
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Hydra configuration files are at the heart of using PhysicsNeMo Sym.
 Each configuration file is a text file in YAML format.
diff --git a/docs/user_guide/basics/physicsnemo_overview.rst b/docs/user_guide/basics/physicsnemo_overview.rst
@@ -1,8 +1,8 @@
 PhysicsNeMo Sym Overview
-====================
+=========================
 
 PhysicsNeMo Sym Building Blocks
----------------------------
+-------------------------------
 
 * **Geometry and Data**
     PhysicsNeMo Sym provides both physics-informed and data-driven machine learning solutions for physics simulation problems.
@@ -54,7 +54,7 @@ PhysicsNeMo Sym Building Blocks
     ``Monitor`` results can also be exported to a text file in comma-separated values (CSV) format.
 
 PhysicsNeMo Sym Development Workflow
---------------------------------
+-------------------------------------
 
 The figure below illustrates a typical workflow when developing in PhysicsNeMo Sym.
 Not all problems will call for exactly this workflow, but it serves as a general guide.
@@ -83,7 +83,7 @@ More details of each step can be found in the :ref:`Introductory Example` chapte
 
 
 PhysicsNeMo Sym Training Algorithm
-------------------------------
+----------------------------------
 
 .. _fig-physicsnemo-training-loop:
 
diff --git a/docs/user_guide/features/configuration.rst b/docs/user_guide/features/configuration.rst
@@ -1,7 +1,7 @@
 .. _config: 
 
 PhysicsNeMo Sym Configuration
-=========================
+=============================
 
 PhysicsNeMo Sym employs an extension of the `Hydra configuration framework <https://hydra.cc/>`_ to offer a highly customizable but user friendly method
 for configuring the majority of PhysicsNeMo Sym' features.
diff --git a/docs/user_guide/features/performance.rst b/docs/user_guide/features/performance.rst
@@ -58,22 +58,22 @@ dramatically reduced training times (:numref:`fig-fpga_tf32_speedup`) without ch
 .. table:: Comparison of results with and without TF32 math mode
    :align: center
 
-   +---------------------------+-----------------------+
-   | **Case Description**      | :math:`P_{drop}`      |
-   |                           | :math:`(Pa)`          |
-   +---------------------------+-----------------------+
+   +-------------------------------+-----------------------+
+   | **Case Description**          | :math:`P_{drop}`      |
+   |                               | :math:`(Pa)`          |
+   +-------------------------------+-----------------------+
    | **PhysicsNeMo Sym:** Fully    | 29.24                 |
-   | Connected Networks        |                       |
-   | with FP32                 |                       |
-   +---------------------------+-----------------------+
+   | Connected Networks            |                       |
+   | with FP32                     |                       |
+   +-------------------------------+-----------------------+
    | **PhysicsNeMo Sym:** Fully    | 29.13                 |
-   | Connected Networks        |                       |
-   | with TF32                 |                       |
-   +---------------------------+-----------------------+
-   | **OpenFOAM Solver**       | 28.03                 |
-   +---------------------------+-----------------------+
-   | **Commercial Solver**     | 28.38                 |
-   +---------------------------+-----------------------+
+   | Connected Networks            |                       |
+   | with TF32                     |                       |
+   +-------------------------------+-----------------------+
+   | **OpenFOAM Solver**           | 28.03                 |
+   +-------------------------------+-----------------------+
+   | **Commercial Solver**         | 28.38                 |
+   +-------------------------------+-----------------------+
    
    
 
diff --git a/docs/user_guide/features/post_processing.rst b/docs/user_guide/features/post_processing.rst
@@ -1,12 +1,12 @@
 
 Post Processing in PhysicsNeMo Sym
-==============================
+==================================
 
 
 .. _tensorboard:
 
 TensorBoard in PhysicsNeMo Sym
---------------------------
+------------------------------
 
 Introduction
 ^^^^^^^^^^^^
@@ -143,7 +143,7 @@ Finally, run the example code. You should automatically see your plots being add
 .. _vtk:
 
 VTK Utilities in PhysicsNeMo Sym
-----------------------------
+--------------------------------
 
 Introduction
 ^^^^^^^^^^^^
diff --git a/docs/user_guide/foundational/inverse_problem.rst b/docs/user_guide/foundational/inverse_problem.rst
@@ -194,15 +194,15 @@ in :numref:`fig-inverse-point-result`.
 .. table:: Comparison of the inverted coefficients with the actual values
    :align: center
 
-   +----------------------+----------------------+--------------------------+
+   +----------------------+----------------------+------------------------------+
    | Property             | OpenFOAM (True)      | PhysicsNeMo Sym (Predicted)  |
-   +----------------------+----------------------+--------------------------+
-   | Kinematic Viscosity  | 1.00 × 10\ :sup:`−2` | 9.87 × 10\ :sup:`−3`     |
-   | :math:`(m^2/s)`      |                      |                          |
-   +----------------------+----------------------+--------------------------+
-   | Thermal Diffusivity  | 2.00 × 10\ :sup:`−3` | 2.53 × 10\ :sup:`−3`     |
-   | :math:`(m^2/s)`      |                      |                          |
-   +----------------------+----------------------+--------------------------+
+   +----------------------+----------------------+------------------------------+
+   | Kinematic Viscosity  | 1.00 × 10\ :sup:`−2` | 9.87 × 10\ :sup:`−3`         |
+   | :math:`(m^2/s)`      |                      |                              |
+   +----------------------+----------------------+------------------------------+
+   | Thermal Diffusivity  | 2.00 × 10\ :sup:`−3` | 2.53 × 10\ :sup:`−3`         |
+   | :math:`(m^2/s)`      |                      |                              |
+   +----------------------+----------------------+------------------------------+
 
 
 .. _fig-inverse-point-result:
diff --git a/docs/user_guide/theory/architectures.rst b/docs/user_guide/theory/architectures.rst
@@ -2,7 +2,7 @@
 .. _architectures:
 
 Architectures In PhysicsNeMo Sym
-============================
+================================
 
 In this section, we discuss some of the advanced and state-of-the-art
 Deep learning architectures and schemes that have become a part of
diff --git a/docs/user_guide/theory/phys_informed.rst b/docs/user_guide/theory/phys_informed.rst
@@ -1,5 +1,5 @@
 Physics Informed Neural Networks in PhysicsNeMo Sym
-===============================================
+====================================================
 
 .. _nn_methodology:
 
diff --git a/docs/user_guide/theory/recommended_practices.rst b/docs/user_guide/theory/recommended_practices.rst
