documentation tweaks

hklion · Dec 17, 2024 · e3c4c66 · e3c4c66
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diff --git a/Docs/sphinx_doc/AMReX.rst b/Docs/sphinx_doc/AMReX.rst
@@ -0,0 +1,18 @@
+
+ .. role:: cpp(code)
+    :language: c++
+
+.. _subsec:AMReX:
+
+AMReX
+==============
+
+REMORAis built on AMReX, a C++--based software framework that supports the development of structured mesh algorithms for solving systems of partial differential equations, with options for adaptive mesh refinement, on machines from laptops to exascale architectures. AMReX was developed in the U.S. Department of Energy’s Exascale Computing Project and is now a member project of the High Performance Software Foundation under the umbrella of the Linux Foundation.
+
+AMReX uses an MPI+X model of hierarchical parallelism where blocks of data are distributed across MPI ranks (typically across multiple nodes).  Fine-grained parallelism at the node level (X) is achieved using
+OpenMP for CPU-only machines, or CUDA, HIP or SYCL for NVIDIA, AMD or Intel GPUs, respectively. AMReX provides extensive support for kernel launching on GPU accelerators (using ParallelFor looping constructs and C++ lambda functions) and the effective use of various memory types, including managed, device, and pinned. Architecture-specific aspects of the software for GPUs are highly localized within the code, and essentially hidden from the application developer or user.
+
+In addition to portability across architectures, AMReX provides data structures and iterators that define, allocate and efficiently operate on distributed multi-dimensional arrays.
+Data is defined on disjoint logically rectangular regions of the domain known as patches (or grids or boxes). Common operations, such as parallel communication and reduction operations, as well as interpolation and averaging operators between levels of refinement, are provided by the AMReX framework.
+
+Finally, REMORA currently leverages, or plans to leverage, AMReX capabilities for effective load balancing, adaptive mesh refinement, memory management, asynchronous I/O, Lagrangian particles with particle-mesh interactions, and linear solvers.
diff --git a/Docs/sphinx_doc/Doxygen.rst b/Docs/sphinx_doc/Doxygen.rst
@@ -0,0 +1,11 @@
+
+ .. role:: cpp(code)
+    :language: c++
+
+.. _doxygen_link:
+
+Doxygen Documentation
+=====================
+
+For details about the REMORA code structure and APIs,
+see the `Doxygen documentation <https://seahorce-scidac.github.io/docs/index.html>`_
diff --git a/Docs/sphinx_doc/MeshRefinement.rst b/Docs/sphinx_doc/MeshRefinement.rst
@@ -7,6 +7,9 @@
 Mesh Refinement
 ===============
 
+.. warning::
+    Mesh refinement in REMORA is currently in beta and an active area of development. Static and dynamic mesh refinement has been verified for scalar advection with flat bathymetry. Other problems are in progress.
+
 REMORA allows both static and dynamic mesh refinement, as well as the choice of one-way or two-way coupling.
 
 Note that any tagged region will be covered by one or more boxes.  The user may

diff --git a/Docs/sphinx_doc/Plotfiles.rst b/Docs/sphinx_doc/Plotfiles.rst
@@ -43,17 +43,18 @@ List of Parameters
 |                                | plot files       |                       |            |
 +--------------------------------+------------------+-----------------------+------------+
 | **remora.plot_vars**           | name of          | list of names         | None       |
-|                                | variables to     |                       |            |
+|                                | variables to     | (see table below)     |            |
 |                                | include in       |                       |            |
-|                                | plotfiles        |                       |            |
+|                                | plotfiles. Not   |                       |            |
+|                                | used for netCDF  |                       |            |
 +--------------------------------+------------------+-----------------------+------------+
 
 .. _notes-5:
 
 Notes
 -----
 
--  The NeTCDF option is only available if REMORA has been built with USE_NETCDF enabled.
+-  The NeTCDF option is only available if REMORA has been built with USE_PNETCDF enabled.
 
 -  The write_history_file option is only available if **plotfile_type = netcdf**
 
@@ -66,6 +67,28 @@ Notes
 
 -  File prefixes can include directories.
 
+Plotfile Field Options
+----------------------
+
++--------------------------------+---------------------------+
+| Field                          | Definition                |
+|                                |                           |
++================================+===========================+
+| **salt**                       | salinity                  |
++--------------------------------+---------------------------+
+| **temp**                       | temperature               |
++--------------------------------+---------------------------+
+| **scalar**                     | passive scalar            |
++--------------------------------+---------------------------+
+| **x_velocity**                 | velocity in x-direction   |
++--------------------------------+---------------------------+
+| **y_velocity**                 | velocity in y-direction   |
++--------------------------------+---------------------------+
+| **z_velocity**                 | velocity in z-direction   |
++--------------------------------+---------------------------+
+| **vorticity**                  | vorticity                 |
++--------------------------------+---------------------------+
+
 .. _examples-of-usage-8:
 
 Examples of Usage

diff --git a/Docs/sphinx_doc/index.rst b/Docs/sphinx_doc/index.rst
@@ -32,6 +32,7 @@ In addition to this documentation, there is API documentation for REMORA generat
    :hidden:
 
    coc
+   Doxygen.rst
 
 .. toctree::
    :caption: USER GUIDE
@@ -41,6 +42,7 @@ In addition to this documentation, there is API documentation for REMORA generat
    GettingStarted.rst
    Inputs.rst
    ProblemSetup.rst
+   testing.rst
 
 .. toctree::
    :caption: THEORY
@@ -56,6 +58,7 @@ In addition to this documentation, there is API documentation for REMORA generat
    :maxdepth: 1
    :hidden:
 
+   AMReX.rst
    ArakawaCGrid.rst
    BoundaryConditions.rst
    Checkpoint.rst