Merge pull request #149 from PrincetonUniversity/issue-146

Implements mesh reading as specfem::IO::read_mesh(...)

CMakeLists.txt

@@ -137,6 +137,11 @@ else()
         )
 endif()
 
+target_link_libraries(
+  IO
+  mesh
+)
+
 add_library(
         point
         src/point/coordinates.cpp
@@ -508,31 +513,6 @@ target_link_libraries(
         Boost::program_options
 )
 
-add_executable(
-        homo2d
-        examples/homogeneous-medium-flat-topography/homo2d.cpp
-)
-
-target_link_libraries(
-        homo2d
-        specfem_mpi
-        Kokkos::kokkos
-        mesh
-        quadrature
-        compute
-        source_class
-        parameter_reader
-        receiver_class
-        writer
-        reader
-        domain
-        coupled_interface
-        kernels
-        solver
-        Boost::program_options
-        ${HDF5_LIBRARIES}
-)
-
 # Include tests
 if (BUILD_TESTS)
         message("-- Including tests.")

docs/api/IO/Libraries/index.rst

@@ -39,5 +39,6 @@ The snippet below shows how to use these modules to write and read a Kokkos::Vie
 .. toctree::
     :maxdepth: 1
 
+    mesh/index
     ASCII/index
     HDF5/index

docs/api/IO/Libraries/mesh/index.rst

@@ -0,0 +1,33 @@
+.. _mesh_reader:
+
+Mesh Reader
+===========
+
+.. doxygenfunction:: specfem::IO::read_mesh
+
+
+The above function reads the fortran binary mesh database and the following
+functions are called in the order of appearance in the code:
+
+
+.. doxygenfunction:: specfem::IO::mesh::fortran::read_mesh_database_header
+
+.. doxygenfunction:: specfem::IO::mesh::fortran::read_coorg_elements
+
+.. doxygenfunction:: specfem::IO::mesh::fortran::read_properties
+
+.. doxygenfunction:: specfem::IO::mesh::fortran::read_mesh_database_attenuation
+
+.. doxygenfunction:: specfem::IO::mesh::fortran::read_material_properties
+
+.. doxygenfunction:: specfem::IO::mesh::fortran::read_boundaries
+
+.. doxygenfunction:: specfem::IO::mesh::fortran::read_coupled_interfaces
+
+.. doxygenfunction:: specfem::IO::mesh::fortran::read_tangential_elements
+
+.. doxygenfunction:: specfem::IO::mesh::fortran::read_axial_elements
+
+Finally, we add tags to the :cpp:struct:`specfem::mesh::mesh` using the
+:cpp:struct:`specfem::mesh::tags` struct. The description of which can be found
+here: :ref:`mesh_tags`.

docs/api/IO/index.rst

@@ -6,6 +6,6 @@ Input/Output modules
     :maxdepth: 2
 
     fortran_io
-    Library/index
+    Libraries/index
     writer/index
     reader/index

docs/api/index.rst

@@ -16,6 +16,7 @@ API documentation
     datatypes/index
     assembly/index
     policies/index
+    IO/index
     operators/index
     compute_kernels/index
     coupling_physics/coupled_interface

docs/developer_documentation/tutorials/tutorial1/Chapter1/index.rst

@@ -2,7 +2,7 @@
 .. _Chapter1:
 
 Chapter 1: Generating the mesh, sources and receivers
-====================================================
+=====================================================
 
 Before we start writing the solver, we need to generate an hexahedral mesh, and define our sources and receivers. To do this we will use the Fortran package ``MESHFEM2D``.
 
@@ -11,7 +11,7 @@ Before we start writing the solver, we need to generate an hexahedral mesh, and
     Since ``MESHFEM2D`` is a dependency for SPECFEM++, it is should already be installed as part of the SPECFEM++ installation.
 
 Defining the MESHFEM2D Parameter File
---------------------------------------
+-------------------------------------
 
 Let us generate a Hex mesh for 2D elastic domain using the following parameter file. You will also need a topography file to define the surface topography of the mesh, see :ref:`Topgraphy File <homogeneous-medium-flat-topography-topography-file>`
 

include/IO/mesh/fortran/read_interfaces.hpp

@@ -15,6 +15,15 @@ specfem::mesh::interface_container<medium1, medium2>
 read_interfaces(const int num_interfaces, std::ifstream &stream,
                 const specfem::MPI::MPI *mpi);
 
+/* @brief Read the coupled interfaces from the database file
+ *
+ * @param stream input file stream
+ * @param num_interfaces_elastic_acoustic
+ * @param num_interfaces_acoustic_poroelastic
+ * @param num_interfaces_elastic_poroelastic
+ * @param mpi
+ * @return specfem::mesh::coupled_interfaces
+ */
 specfem::mesh::coupled_interfaces read_coupled_interfaces(
     std::ifstream &stream, const int num_interfaces_elastic_acoustic,
     const int num_interfaces_acoustic_poroelastic,

include/IO/mesh/fortran/read_mesh_database.hpp

@@ -32,8 +32,7 @@ read_mesh_database_header(std::ifstream &stream, const specfem::MPI::MPI *mpi);
  * section
  * @param npgeo Total number of control nodes in simulation box
  * @param mpi Pointer to MPI object
- * @return specfem::kokkos::HostView2d<type_real> coorg values as read from
- * fortran binary database file
+ * @return std::tuple<int, int, int>  nspec, npgeo, nproc values read from
  */
 specfem::kokkos::HostView2d<type_real>
 read_coorg_elements(std::ifstream &stream, const int npgeo,

include/IO/mesh/fortran/read_properties.hpp

@@ -14,7 +14,7 @@ namespace fortran {
  *
  * @param stream Input stream
  * @param mpi MPI object
- * @return specfem::mesh::properties
+ * @return specfem::mesh::properties Property object
  */
 specfem::mesh::properties read_properties(std::ifstream &stream,
                                           const specfem::MPI::MPI *mpi);

include/IO/mesh/read_mesh.hpp

@@ -0,0 +1,21 @@
+#pragma once
+
+#include "mesh/mesh.hpp"
+#include "specfem_mpi/interface.hpp"
+#include "specfem_setup.hpp"
+
+namespace specfem {
+
+namespace IO {
+
+/* @brief Construct a mesh object from a Fortran binary database file
+ *
+ * @param filename Fortran binary database filename
+ * @param mpi pointer to MPI object to manage communication
+ * @return specfem::mesh::mesh Specfem mesh object
+ */
+specfem::mesh::mesh read_mesh(const std::string filename,
+                              const specfem::MPI::MPI *mpi);
+
+} // namespace IO
+} // namespace specfem

include/policies/range.hpp

@@ -6,9 +6,7 @@
 namespace specfem {
 
 namespace iterator {
-
 namespace impl {
-
 /**
  * @brief Index type for the range iterator.
  *
@@ -21,7 +19,7 @@ template <bool UseSIMD> struct range_index_type;
  *
  */
 template <> struct range_index_type<false> {
-  specfem::point::assembly_index index; ///< Assembly index
+  specfem::point::assembly_index<false> index; ///< Assembly index
 
   KOKKOS_INLINE_FUNCTION
   range_index_type(const specfem::point::assembly_index<false> index)

src/IO/mesh/fortran/read_material_properties.cpp

@@ -1,6 +1,7 @@
 #include "IO/mesh/fortran/read_material_properties.hpp"
 #include "IO/fortranio/interface.hpp"
-#include "mesh/materials/materials.hpp"
+// #include "mesh/materials/materials.hpp"
+#include "mesh/materials/materials.tpp"
 #include "specfem_mpi/interface.hpp"
 #include "utilities/interface.hpp"
 #include <memory>
@@ -184,12 +185,12 @@ specfem::mesh::materials specfem::IO::mesh::fortran::read_material_properties(
 
   // Read material properties
   auto index_mapping =
-      read_materials(stream, numat, materials.elastic_isotropic,
-                     materials.acoustic_isotropic, mpi);
+      ::read_materials(stream, numat, materials.elastic_isotropic,
+                       materials.acoustic_isotropic, mpi);
 
   // Read material indices
-  read_material_indices(stream, nspec, numat, index_mapping,
-                        materials.material_index_mapping, knods, mpi);
+  ::read_material_indices(stream, nspec, numat, index_mapping,
+                          materials.material_index_mapping, knods, mpi);
 
   return materials;
 }