PrincetonUniversity · lsawade · Feb 7, 2025 · Feb 18, 2025 · Feb 20, 2025 · Feb 20, 2025
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -245,6 +245,7 @@ add_library(
         src/IO/mesh/impl/fortran/dim3/read_parameters.cpp
         src/IO/mesh/impl/fortran/dim3/read_coordinates.cpp
         src/IO/mesh/impl/fortran/dim3/read_partial_derivatives.cpp
+        src/IO/mesh/impl/fortran/dim3/utilities.cpp
 )
 
 if (NOT HDF5_CXX_BUILD)
@@ -350,15 +351,22 @@ add_library(
         src/mesh/dim2/tags/tags.cpp
         # 3-D
         src/mesh/dim3/mesh.cpp
+        src/mesh/dim3/boundaries/absorbing_boundary.cpp
+        src/mesh/dim3/boundaries/free_surface.cpp
+        src/mesh/dim3/coupled_interfaces/coupled_interfaces.cpp
+        src/mesh/dim3/element_types/element_types.cpp
         src/mesh/dim3/parameters/parameters.cpp
         src/mesh/dim3/parameters/parameters.cpp
         src/mesh/dim3/mapping/mapping.cpp
+        src/mesh/dim3/materials/materials.cpp
         src/mesh/dim3/coordinates/coordinates.cpp
         src/mesh/dim3/partial_derivatives/partial_derivatives.cpp
+
 )
 
 target_link_libraries(
         mesh
+        enumerations
         Kokkos::kokkos
         specfem_mpi
         # material_class

diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
@@ -502,7 +502,7 @@ NUM_PROC_THREADS       = 1
 # normally produced when WARNINGS is set to YES.
 # The default value is: NO.
 
-EXTRACT_ALL            = NO
+EXTRACT_ALL            = YES
 
 # If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
 # be included in the documentation.
@@ -741,7 +741,7 @@ GENERATE_DEPRECATEDLIST= YES
 # sections, marked by \if <section_label> ... \endif and \cond <section_label>
 # ... \endcond blocks.
 
-ENABLED_SECTIONS       =
+ENABLED_SECTIONS       = NO
 
 # The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
 # initial value of a variable or macro / define can have for it to appear in the
@@ -1222,15 +1222,15 @@ IGNORE_PREFIX          =
 # If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
 # The default value is: YES.
 
-GENERATE_HTML          = YES
+GENERATE_HTML          = NO
 
 # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
 # it.
 # The default directory is: html.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_OUTPUT            = html
+HTML_OUTPUT            = "doxygen/html_doxygen"
 
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
 # generated HTML page (for example: .htm, .php, .asp).
@@ -2146,7 +2146,7 @@ GENERATE_XML           = YES
 # The default directory is: xml.
 # This tag requires that the tag GENERATE_XML is set to YES.
 
-XML_OUTPUT             = xml
+XML_OUTPUT             = doxygen/xml
 
 # If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
 # listings (including syntax highlighting and cross-referencing information) to

diff --git a/docs/api/IO/fortran_io.rst b/docs/api/IO/fortran_io.rst
@@ -5,4 +5,4 @@ Fortran IO
 
 Fortran IO namespace provides a functions to read data stored in unformatted fortran binary files.
 
-.. doxygenfunction:: specfem::fortran_IO::fortran_read_line
+.. doxygenfunction:: specfem::IO::fortran_read_line
diff --git a/docs/api/IO/index.rst b/docs/api/IO/index.rst
@@ -29,8 +29,11 @@ are exposed through the following modules:
     reader/index
 
 
-Read Mesh
----------
+Input for the 2D Solver
++++++++++++++++++++++++
+
+Read the 2D Mesh
+----------------
 
 .. doxygenfunction:: specfem::IO::read_2d_mesh
 
@@ -45,3 +48,35 @@ Read Receivers
 --------------
 
 .. doxygenfunction:: specfem::IO::read_receivers(const std::string stations_file, const type_real angle)
+
+
+
+
+Input for the 3D Solver
++++++++++++++++++++++++
+
+
+Read the 3D Mesh
+----------------
+
+.. doxygenfunction:: specfem::IO::read_3d_mesh
+
+
+Helper functions
+''''''''''''''''
+
+**Reading any values**
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::dim3::try_read_line
+
+**Reading any array**
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::dim3::try_read_array
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::dim3::read_array
+
+**Reading index arrays**
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::dim3::try_read_index_array
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::dim3::read_index_array
diff --git a/docs/api/enumerations/index.rst b/docs/api/enumerations/index.rst
@@ -1,4 +1,4 @@
-.. _enumerations::
+.. _enumerations:
 
 Enumerations
 ============

diff --git a/docs/api/medium/index.rst b/docs/api/medium/index.rst
@@ -1,4 +1,4 @@
-.. _medium::
+.. _medium:
 
 Medium modules
 ==============

diff --git a/.../mesh/boundaries/absorbing_boundaries.rst → .../dim2/boundaries/absorbing_boundaries.rst b/.../mesh/boundaries/absorbing_boundaries.rst → .../dim2/boundaries/absorbing_boundaries.rst
diff --git a/...mesh/boundaries/acoustic_free_surface.rst → ...dim2/boundaries/acoustic_free_surface.rst b/...mesh/boundaries/acoustic_free_surface.rst → ...dim2/boundaries/acoustic_free_surface.rst
diff --git a/docs/api/mesh/boundaries/index.rst → docs/api/mesh/dim2/boundaries/index.rst b/docs/api/mesh/boundaries/index.rst → docs/api/mesh/dim2/boundaries/index.rst
diff --git a/docs/api/mesh/control_nodes/index.rst → docs/api/mesh/dim2/control_nodes/index.rst b/docs/api/mesh/control_nodes/index.rst → docs/api/mesh/dim2/control_nodes/index.rst
diff --git a/docs/api/mesh/coupled_interfaces/index.rst → ...pi/mesh/dim2/coupled_interfaces/index.rst b/docs/api/mesh/coupled_interfaces/index.rst → ...pi/mesh/dim2/coupled_interfaces/index.rst
@@ -4,7 +4,7 @@
 Coupled Interfaces
 ==================
 
-.. doxygenstruct:: specfem::mesh::coupled_interfaces
+.. doxygenstruct:: specfem::mesh::coupled_interfaces< specfem::dimension::type::dim2 >
     :members:
 
 

diff --git a/docs/api/mesh/dim2/index.rst b/docs/api/mesh/dim2/index.rst
@@ -0,0 +1,18 @@
+
+.. _mesh_2D:
+
+SPECFEM++ 2D Mesh
+=================
+
+.. doxygenstruct:: specfem::mesh::mesh< specfem::dimension::type::dim2 >
+    :members:
+
+
+.. toctree::
+    :maxdepth: 1
+
+    boundaries/index
+    control_nodes/index
+    coupled_interfaces/index
+    materials/index
+    tags/index
diff --git a/docs/api/mesh/materials/index.rst → docs/api/mesh/dim2/materials/index.rst b/docs/api/mesh/materials/index.rst → docs/api/mesh/dim2/materials/index.rst
diff --git a/docs/api/mesh/tags/index.rst → docs/api/mesh/dim2/tags/index.rst b/docs/api/mesh/tags/index.rst → docs/api/mesh/dim2/tags/index.rst
diff --git a/docs/api/mesh/dim3/boundaries/index.rst b/docs/api/mesh/dim3/boundaries/index.rst
@@ -0,0 +1,23 @@
+
+.. _mesh_boundaries_3D:
+
+Boundaries
+++++++++++
+
+
+.. doxygenstruct:: specfem::mesh::boundaries< specfem::dimension::type::dim3 >
+    :members:
+
+Absorbing Boundaries
+====================
+
+.. doxygenstruct:: specfem::mesh::absorbing_boundary< specfem::dimension::type::dim3 >
+    :members:
+
+
+
+Free surface boundary
+=====================
+
+.. doxygenstruct:: specfem::mesh::free_surface< specfem::dimension::type::dim3 >
+    :members:
diff --git a/docs/api/mesh/dim3/coordinates/index.rst b/docs/api/mesh/dim3/coordinates/index.rst
@@ -0,0 +1,7 @@
+.. _mesh_coordinates_3D:
+
+Coordinates
++++++++++++
+
+.. doxygenstruct:: specfem::mesh::coordinates< specfem::dimension::type::dim3 >
+    :members:
diff --git a/docs/api/mesh/dim3/coupled_interfaces/index.rst b/docs/api/mesh/dim3/coupled_interfaces/index.rst
@@ -0,0 +1,8 @@
+.. mesh_3D_coupled_interfaces:
+
+Coupled Interfaces
+==================
+
+
+.. doxygenstruct:: specfem::mesh::coupled_interfaces< specfem::dimension::type::dim3 >
+    :members:
diff --git a/docs/api/mesh/dim3/element_types/index.rst b/docs/api/mesh/dim3/element_types/index.rst
@@ -0,0 +1,7 @@
+.. mesh_3D_element_types:
+
+Element Types
+=============
+
+.. doxygenstruct:: specfem::mesh::element_types< specfem::dimension::type::dim3 >
+    :members:
diff --git a/docs/api/mesh/dim3/index.rst b/docs/api/mesh/dim3/index.rst
@@ -0,0 +1,25 @@
+
+.. _mesh_3D:
+
+SPECFEM++ 3D Mesh
+=================
+
+.. doxygenstruct:: specfem::mesh::mesh< specfem::dimension::type::dim3 >
+    :members:
+
+
+What the 3D mesh struct holds
+-----------------------------
+
+.. toctree::
+    :maxdepth: 1
+
+    parameters/index
+    coordinates/index
+    mapping/index
+    partial_derivatives/index
+    element_types/index
+    materials/index
+    mass_matrix/index
+    boundaries/index
+    coupled_interfaces/index
diff --git a/docs/api/mesh/dim3/mapping/index.rst b/docs/api/mesh/dim3/mapping/index.rst
@@ -0,0 +1,7 @@
+.. mesh_3D_mapping:
+
+Mapping
+=======
+
+.. doxygenstruct:: specfem::mesh::mapping< specfem::dimension::type::dim3 >
+    :members:
diff --git a/docs/api/mesh/dim3/mass_matrix/index.rst b/docs/api/mesh/dim3/mass_matrix/index.rst
@@ -0,0 +1,7 @@
+.. mesh_3D_mass_matrix:
+
+Matrix
+======
+
+.. doxygenstruct:: specfem::mesh::mass_matrix< specfem::dimension::type::dim3 >
+    :members:
diff --git a/docs/api/mesh/dim3/materials/index.rst b/docs/api/mesh/dim3/materials/index.rst
@@ -0,0 +1,7 @@
+.. mesh_3D_materials:
+
+Material
+========
+
+.. doxygenstruct:: specfem::mesh::materials< specfem::dimension::type::dim3 >
+    :members:
diff --git a/docs/api/mesh/dim3/parameters/index.rst b/docs/api/mesh/dim3/parameters/index.rst
@@ -0,0 +1,7 @@
+.. mesh_3D_parameters:
+
+Parameters
+==========
+
+.. doxygenstruct:: specfem::mesh::parameters< specfem::dimension::type::dim3 >
+    :members:
diff --git a/docs/api/mesh/dim3/partial_derivatives/index.rst b/docs/api/mesh/dim3/partial_derivatives/index.rst
@@ -0,0 +1,7 @@
+.. mesh_3D_partial_derivatives:
+
+Partial Derivatives
+===================
+
+.. doxygenstruct:: specfem::mesh::partial_derivatives< specfem::dimension::type::dim3 >
+    :members:
diff --git a/docs/api/mesh/index.rst b/docs/api/mesh/index.rst
@@ -11,8 +11,5 @@ SPECFEM++ Mesh
 .. toctree::
     :maxdepth: 1
 
-    boundaries/index
-    control_nodes/index
-    coupled_interfaces/index
-    materials/index
-    tags/index
+    dim2/index
+    dim3/index
diff --git a/docs/conf.py b/docs/conf.py
@@ -14,9 +14,31 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 import subprocess
+import sys
+import os
 
 # Doxygen
-subprocess.call("doxygen Doxyfile.in", shell=True)
+doxygen_cmd = "doxygen Doxyfile.in"  # or Doxyfile.in if that's the correct filename
+
+# Create the doxygen subdirectory if it doesn't exist
+if os.path.exists("_build/doxygen") is False:
+    os.makedirs("_build/doxygen")
+
+if os.environ.get("NODOXYGEN") is not None:
+    print("Skipping Doxygen build as NODOXYGEN environment variable is set")
+    result = 0
+else:
+    result = subprocess.call(doxygen_cmd, shell=True)
+
+if result != 0:
+    print(f"Error: Doxygen command '{doxygen_cmd}' failed with code {result}")
+    sys.exit(1)
+
+# Check if output directory exists
+if not os.path.exists("_build/doxygen/xml"):
+    print("Error: Doxygen XML output directory '_build/doxygen/xml' not found")
+    print("Please check Doxygen configuration and make sure it runs correctly")
+    sys.exit(1)
 
 # -- Project information -----------------------------------------------------
 
@@ -42,10 +64,14 @@
     "sphinx.ext.viewcode",
     "sphinx_sitemap",
     "sphinx.ext.inheritance_diagram",
+    "sphinx_design",
     "breathe",
     "sphinx_copybutton",
 ]
 
+# Adding this to avoid the WARNING: duplicate label warning
+autosectionlabel_prefix_document = True
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -78,7 +104,7 @@
 # }
 # html_logo = ''
 github_url = "https://github.com/PrincetonUniversity/SPECFEMPP"
-# html_baseurl = ''
+html_baseurl = "https://specfem2d-kokkos.readthedocs.io/"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -96,6 +122,6 @@
 
 # -- Breathe configuration -------------------------------------------------
 
-breathe_projects = {"SPECFEM KOKKOS IMPLEMENTATION": "_build/xml"}
+breathe_projects = {"SPECFEM KOKKOS IMPLEMENTATION": "_build/doxygen/xml"}
 breathe_default_project = "SPECFEM KOKKOS IMPLEMENTATION"
 breathe_default_members = ()
diff --git a/docs/developer_documentation/tutorials/tutorial1/Chapter1/index.rst b/docs/developer_documentation/tutorials/tutorial1/Chapter1/index.rst
@@ -172,7 +172,7 @@ Defining sources
 
 Now that we have the mesh and receiver locations, we can define the sources. We will use the following source file to define the sources.
 
-.. code:: yaml
+.. code-block:: yaml
     :caption: sources.yaml
 
     number-of-sources: 1
@@ -189,6 +189,8 @@ Now that we have the mesh and receiver locations, we can define the sources. We
             tshift: 0.0
             f0: 10.0
 
+
+
 Final mesh
 ----------
Original file line number	Diff line number	Diff line change
Expand Up		@@ -5,4 +5,4 @@ Fortran IO

		Fortran IO namespace provides a functions to read data stored in unformatted fortran binary files.

		.. doxygenfunction:: specfem::fortran_IO::fortran_read_line
		.. doxygenfunction:: specfem::IO::fortran_read_line