Merge pull request #189 from PrincetonUniversity/issue-185

Issue 185

CMakeLists.txt

@@ -130,12 +130,12 @@ add_library(
         src/IO/HDF5/native_type.cpp
         # src/IO/ASCII/native_type.cpp
         src/IO/mesh/read_mesh.cpp
-        src/IO/mesh/fortran/read_boundaries.cpp
-        src/IO/mesh/fortran/read_elements.cpp
-        src/IO/mesh/fortran/read_material_properties.cpp
-        src/IO/mesh/fortran/read_mesh_database.cpp
-        src/IO/mesh/fortran/read_interfaces.cpp
-        src/IO/mesh/fortran/read_properties.cpp
+        src/IO/mesh/impl/fortran/read_boundaries.cpp
+        src/IO/mesh/impl/fortran/read_elements.cpp
+        src/IO/mesh/impl/fortran/read_material_properties.cpp
+        src/IO/mesh/impl/fortran/read_mesh_database.cpp
+        src/IO/mesh/impl/fortran/read_interfaces.cpp
+        src/IO/mesh/impl/fortran/read_properties.cpp
         src/IO/sources/read_sources.cpp
         src/IO/receivers/read_receivers.cpp
 )

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

@@ -8,23 +8,23 @@ The below functions are helper functions for the Fortran binary mesh database
 reader. The functions are called in :cpp:func:`specfem::IO::read_mesh`
 in sequential order and faciliate the reading of the mesh database.
 
-.. doxygenfunction:: specfem::IO::mesh::fortran::read_mesh_database_header
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_mesh_database_header
 
-.. doxygenfunction:: specfem::IO::mesh::fortran::read_coorg_elements
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_coorg_elements
 
-.. doxygenfunction:: specfem::IO::mesh::fortran::read_properties
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_properties
 
-.. doxygenfunction:: specfem::IO::mesh::fortran::read_mesh_database_attenuation
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_mesh_database_attenuation
 
-.. doxygenfunction:: specfem::IO::mesh::fortran::read_material_properties
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_material_properties
 
-.. doxygenfunction:: specfem::IO::mesh::fortran::read_boundaries
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_boundaries
 
-.. doxygenfunction:: specfem::IO::mesh::fortran::read_coupled_interfaces
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_coupled_interfaces
 
-.. doxygenfunction:: specfem::IO::mesh::fortran::read_tangential_elements
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_tangential_elements
 
-.. doxygenfunction:: specfem::IO::mesh::fortran::read_axial_elements
+.. doxygenfunction:: specfem::IO::mesh::impl::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

include/IO/mesh/fortran/read_boundaries.hpp → include/IO/mesh/impl/fortran/read_boundaries.hpp

@@ -11,6 +11,7 @@
 namespace specfem {
 namespace IO {
 namespace mesh {
+namespace impl {
 namespace fortran {
 
 // /**
@@ -70,6 +71,7 @@ read_boundaries(std::ifstream &stream, const int nspec, const int n_absorbing,
                 const specfem::MPI::MPI *mpi);
 
 } // namespace fortran
+} // namespace impl
 } // namespace mesh
 } // namespace IO
 } // namespace specfem

include/IO/mesh/fortran/read_elements.hpp → include/IO/mesh/impl/fortran/read_elements.hpp

@@ -7,6 +7,7 @@
 namespace specfem {
 namespace IO {
 namespace mesh {
+namespace impl {
 namespace fortran {
 
 /**
@@ -36,6 +37,7 @@ read_axial_elements(std::ifstream &stream, const int nelem_on_the_axis,
                     const int nspec, const specfem::MPI::MPI *mpi);
 
 } // namespace fortran
+} // namespace impl
 } // namespace mesh
 } // namespace IO
 } // namespace specfem

include/IO/mesh/fortran/read_interfaces.hpp → include/IO/mesh/impl/fortran/read_interfaces.hpp

@@ -7,6 +7,7 @@
 namespace specfem {
 namespace IO {
 namespace mesh {
+namespace impl {
 namespace fortran {
 
 template <specfem::element::medium_tag medium1,
@@ -30,6 +31,7 @@ specfem::mesh::coupled_interfaces read_coupled_interfaces(
     const int num_interfaces_elastic_poroelastic, const specfem::MPI::MPI *mpi);
 
 } // namespace fortran
+} // namespace impl
 } // namespace mesh
 } // namespace IO
 } // namespace specfem

include/IO/mesh/fortran/read_material_properties.hpp → include/IO/mesh/impl/fortran/read_material_properties.hpp

@@ -10,6 +10,7 @@
 namespace specfem {
 namespace IO {
 namespace mesh {
+namespace impl {
 namespace fortran {
 
 /**
@@ -28,6 +29,7 @@ specfem::mesh::materials read_material_properties(
     const specfem::kokkos::HostView2d<int> knods, const specfem::MPI::MPI *mpi);
 
 } // namespace fortran
+} // namespace impl
 } // namespace mesh
 } // namespace IO
 } // namespace specfem

include/IO/mesh/fortran/read_mesh_database.hpp → include/IO/mesh/impl/fortran/read_mesh_database.hpp

@@ -10,6 +10,7 @@
 namespace specfem {
 namespace IO {
 namespace mesh {
+namespace impl {
 namespace fortran {
 
 /**
@@ -46,6 +47,7 @@ std::tuple<int, type_real, bool>
 read_mesh_database_attenuation(std::ifstream &stream,
                                const specfem::MPI::MPI *mpi);
 } // namespace fortran
+} // namespace impl
 } // namespace mesh
 } // namespace IO
 } // namespace specfem

include/IO/mesh/fortran/read_properties.hpp → include/IO/mesh/impl/fortran/read_properties.hpp

@@ -7,6 +7,7 @@
 namespace specfem {
 namespace IO {
 namespace mesh {
+namespace impl {
 namespace fortran {
 
 /*
@@ -20,6 +21,7 @@ specfem::mesh::properties read_properties(std::ifstream &stream,
                                           const specfem::MPI::MPI *mpi);
 
 } // namespace fortran
+} // namespace impl
 } // namespace mesh
 } // namespace IO
 } // namespace specfem

src/IO/mesh/fortran/read_boundaries.cpp → src/IO/mesh/impl/fortran/read_boundaries.cpp

@@ -1,4 +1,4 @@
-#include "IO/mesh/fortran/read_boundaries.hpp"
+#include "IO/mesh/impl/fortran/read_boundaries.hpp"
 #include "IO/fortranio/interface.hpp"
 #include "mesh/boundaries/boundaries.hpp"
 #include "specfem_mpi/interface.hpp"
@@ -49,11 +49,13 @@ find_corners(const specfem::kokkos::HostView1d<int> ispec_edge,
   }
 
   specfem::kokkos::HostView1d<int> ispec_corners(
-      "specfem:IO::mesh::fortran::read_boundaries::find_corners::ispec_corners",
+      "specfem:IO::mesh::impl::fortran::read_boundaries::find_corners::ispec_"
+      "corners",
       ncorner);
 
   specfem::kokkos::HostView1d<specfem::enums::boundaries::type> type_corners(
-      "specfem:IO::mesh::fortran::read_boundaries::find_corners::type_corners",
+      "specfem:IO::mesh::impl::fortran::read_boundaries::find_corners::type_"
+      "corners",
       ncorner);
 
   int icorner = 0;
@@ -349,7 +351,7 @@ read_forcing_boundaries(std::ifstream &stream, const int nelement_acforcing,
   return forcing_boundary;
 }
 
-specfem::mesh::boundaries specfem::IO::mesh::fortran::read_boundaries(
+specfem::mesh::boundaries specfem::IO::mesh::impl::fortran::read_boundaries(
     std::ifstream &stream, const int nspec, const int n_absorbing,
     const int n_acoustic_surface, const int n_acforcing,
     const Kokkos::View<int **, Kokkos::HostSpace> knods,

src/IO/mesh/fortran/read_elements.cpp → src/IO/mesh/impl/fortran/read_elements.cpp

@@ -1,14 +1,13 @@
-#include "IO/mesh/fortran/read_elements.hpp"
+#include "IO/mesh/impl/fortran/read_elements.hpp"
 #include "IO/fortranio/interface.hpp"
 #include "mesh/elements/axial_elements.hpp"
 #include "mesh/elements/tangential_elements.hpp"
 #include "specfem_mpi/interface.hpp"
 
 specfem::mesh::elements::axial_elements
-specfem::IO::mesh::fortran::read_axial_elements(std::ifstream &stream,
-                                                const int nelem_on_the_axis,
-                                                const int nspec,
-                                                const specfem::MPI::MPI *mpi) {
+specfem::IO::mesh::impl::fortran::read_axial_elements(
+    std::ifstream &stream, const int nelem_on_the_axis, const int nspec,
+    const specfem::MPI::MPI *mpi) {
 
   int ispec;
 
@@ -26,7 +25,7 @@ specfem::IO::mesh::fortran::read_axial_elements(std::ifstream &stream,
 }
 
 specfem::mesh::elements::tangential_elements
-specfem::IO::mesh::fortran::read_tangential_elements(
+specfem::IO::mesh::impl::fortran::read_tangential_elements(
     std::ifstream &stream, const int nnodes_tangential_curve) {
   type_real xread, yread;
 

src/IO/mesh/fortran/read_interfaces.cpp → src/IO/mesh/impl/fortran/read_interfaces.cpp

@@ -1,4 +1,4 @@
-#include "IO/mesh/fortran/read_interfaces.hpp"
+#include "IO/mesh/impl/fortran/read_interfaces.hpp"
 #include "IO/fortranio/interface.hpp"
 #include "mesh/coupled_interfaces/coupled_interfaces.hpp"
 #include "mesh/coupled_interfaces/interface_container.hpp"
@@ -7,9 +7,9 @@
 template <specfem::element::medium_tag medium1,
           specfem::element::medium_tag medium2>
 specfem::mesh::interface_container<medium1, medium2>
-specfem::IO::mesh::fortran::read_interfaces(const int num_interfaces,
-                                            std::ifstream &stream,
-                                            const specfem::MPI::MPI *mpi) {
+specfem::IO::mesh::impl::fortran::read_interfaces(
+    const int num_interfaces, std::ifstream &stream,
+    const specfem::MPI::MPI *mpi) {
 
   specfem::mesh::interface_container<medium1, medium2> interface(
       num_interfaces);
@@ -33,7 +33,7 @@ specfem::IO::mesh::fortran::read_interfaces(const int num_interfaces,
 template specfem::mesh::interface_container<
     specfem::element::medium_tag::elastic,
     specfem::element::medium_tag::acoustic>
-specfem::IO::mesh::fortran::read_interfaces<
+specfem::IO::mesh::impl::fortran::read_interfaces<
     specfem::element::medium_tag::elastic,
     specfem::element::medium_tag::acoustic>(const int num_interfaces,
                                             std::ifstream &stream,
@@ -43,7 +43,7 @@ specfem::IO::mesh::fortran::read_interfaces<
 template specfem::mesh::interface_container<
     specfem::element::medium_tag::acoustic,
     specfem::element::medium_tag::poroelastic>
-specfem::IO::mesh::fortran::read_interfaces<
+specfem::IO::mesh::impl::fortran::read_interfaces<
     specfem::element::medium_tag::acoustic,
     specfem::element::medium_tag::poroelastic>(const int num_interfaces,
                                                std::ifstream &stream,
@@ -53,30 +53,30 @@ specfem::IO::mesh::fortran::read_interfaces<
 template specfem::mesh::interface_container<
     specfem::element::medium_tag::elastic,
     specfem::element::medium_tag::poroelastic>
-specfem::IO::mesh::fortran::read_interfaces<
+specfem::IO::mesh::impl::fortran::read_interfaces<
     specfem::element::medium_tag::elastic,
     specfem::element::medium_tag::poroelastic>(const int num_interfaces,
                                                std::ifstream &stream,
                                                const specfem::MPI::MPI *mpi);
 
 specfem::mesh::coupled_interfaces
-specfem::IO::mesh::fortran::read_coupled_interfaces(
+specfem::IO::mesh::impl::fortran::read_coupled_interfaces(
     std::ifstream &stream, const int num_interfaces_elastic_acoustic,
     const int num_interfaces_acoustic_poroelastic,
     const int num_interfaces_elastic_poroelastic,
     const specfem::MPI::MPI *mpi) {
 
-  auto elastic_acoustic = specfem::IO::mesh::fortran::read_interfaces<
+  auto elastic_acoustic = specfem::IO::mesh::impl::fortran::read_interfaces<
       specfem::element::medium_tag::elastic,
       specfem::element::medium_tag::acoustic>(num_interfaces_elastic_acoustic,
                                               stream, mpi);
 
-  auto acoustic_poroelastic = specfem::IO::mesh::fortran::read_interfaces<
+  auto acoustic_poroelastic = specfem::IO::mesh::impl::fortran::read_interfaces<
       specfem::element::medium_tag::acoustic,
       specfem::element::medium_tag::poroelastic>(
       num_interfaces_acoustic_poroelastic, stream, mpi);
 
-  auto elastic_poroelastic = specfem::IO::mesh::fortran::read_interfaces<
+  auto elastic_poroelastic = specfem::IO::mesh::impl::fortran::read_interfaces<
       specfem::element::medium_tag::elastic,
       specfem::element::medium_tag::poroelastic>(
       num_interfaces_elastic_poroelastic, stream, mpi);

src/IO/mesh/fortran/read_material_properties.cpp → src/IO/mesh/impl/fortran/read_material_properties.cpp

@@ -1,4 +1,4 @@
-#include "IO/mesh/fortran/read_material_properties.hpp"
+#include "IO/mesh/impl/fortran/read_material_properties.hpp"
 #include "IO/fortranio/interface.hpp"
 // #include "mesh/materials/materials.hpp"
 #include "mesh/materials/materials.tpp"
@@ -175,7 +175,8 @@ void read_material_indices(
 
 } // namespace
 
-specfem::mesh::materials specfem::IO::mesh::fortran::read_material_properties(
+specfem::mesh::materials
+specfem::IO::mesh::impl::fortran::read_material_properties(
     std::ifstream &stream, const int numat, const int nspec,
     const specfem::kokkos::HostView2d<int> knods,
     const specfem::MPI::MPI *mpi) {

src/IO/mesh/fortran/read_mesh_database.cpp → src/IO/mesh/impl/fortran/read_mesh_database.cpp

@@ -1,4 +1,4 @@
-#include "IO/mesh/fortran/read_mesh_database.hpp"
+#include "IO/mesh/impl/fortran/read_mesh_database.hpp"
 #include "IO/fortranio/interface.hpp"
 #include "kokkos_abstractions.h"
 // #include "mesh/IO/fortran/read_material_properties.hpp"
@@ -9,7 +9,8 @@
 #include <iostream>
 #include <tuple>
 
-std::tuple<int, int, int> specfem::IO::mesh::fortran::read_mesh_database_header(
+std::tuple<int, int, int>
+specfem::IO::mesh::impl::fortran::read_mesh_database_header(
     std::ifstream &stream, const specfem::MPI::MPI *mpi) {
   // This subroutine reads header values of the database which are skipped
   std::string dummy_s;
@@ -144,9 +145,8 @@ std::tuple<int, int, int> specfem::IO::mesh::fortran::read_mesh_database_header(
 }
 
 specfem::kokkos::HostView2d<type_real>
-specfem::IO::mesh::fortran::read_coorg_elements(std::ifstream &stream,
-                                                const int npgeo,
-                                                const specfem::MPI::MPI *mpi) {
+specfem::IO::mesh::impl::fortran::read_coorg_elements(
+    std::ifstream &stream, const int npgeo, const specfem::MPI::MPI *mpi) {
 
   int ipoin = 0;
 
@@ -169,7 +169,7 @@ specfem::IO::mesh::fortran::read_coorg_elements(std::ifstream &stream,
 }
 
 std::tuple<int, type_real, bool>
-specfem::IO::mesh::fortran::read_mesh_database_attenuation(
+specfem::IO::mesh::impl::fortran::read_mesh_database_attenuation(
     std::ifstream &stream, const specfem::MPI::MPI *mpi) {
 
   int n_sls;

src/IO/mesh/fortran/read_properties.cpp → src/IO/mesh/impl/fortran/read_properties.cpp

@@ -1,10 +1,9 @@
-#include "IO/mesh/fortran/read_properties.hpp"
+#include "IO/mesh/impl/fortran/read_properties.hpp"
 #include "IO/fortranio/interface.hpp"
 #include "mesh/properties/properties.hpp"
 
-specfem::mesh::properties
-specfem::IO::mesh::fortran::read_properties(std::ifstream &stream,
-                                            const specfem::MPI::MPI *mpi) {
+specfem::mesh::properties specfem::IO::mesh::impl::fortran::read_properties(
+    std::ifstream &stream, const specfem::MPI::MPI *mpi) {
   // ---------------------------------------------------------------------
   // reading mesh properties