Added a first working preset

CMakeLists.txt

@@ -197,12 +197,15 @@ add_library(
         src/IO/sources.cpp
         src/IO/receivers.cpp
         src/IO/mesh.cpp
+        # Fortran 2D part
         src/IO/mesh/impl/fortran/dim2/read_boundaries.cpp
         src/IO/mesh/impl/fortran/dim2/read_elements.cpp
         src/IO/mesh/impl/fortran/dim2/read_material_properties.cpp
         src/IO/mesh/impl/fortran/dim2/read_mesh_database.cpp
         src/IO/mesh/impl/fortran/dim2/read_interfaces.cpp
         src/IO/mesh/impl/fortran/dim2/read_parameters.cpp
+        # Fortran 3D part
+        src/IO/mesh/impl/fortran/dim3/read_parameters.cpp
 )
 
 if (NOT HDF5_CXX_BUILD)

CMakePresets.json

@@ -0,0 +1,26 @@
+{
+  "version": 6,
+  "configurePresets": [
+    {
+      "name": "debug",
+      "displayName": "Debug (Serial)",
+      "binaryDir": "build/debug",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Debug",
+        "BUILD_TESTS": "ON",
+        "ENABLE_SIMD": "OFF",
+        "Kokkos_ARCH_NATIVE": "ON",
+        "Kokkos_ENABLE_AGGRESSIVE_VECTORIZATION": "ON",
+        "Kokkos_ENABLE_ATOMICS_BYPASS": "ON"
+      }
+    }
+  ],
+  "buildPresets": [
+    {
+      "name": "debug",
+      "configurePreset": "debug",
+      "targets": ["all"],
+      "jobs": 8
+    }
+  ]
+}

examples/dim3/homogeneous_halfspace/specfem_config.yaml

@@ -45,6 +45,7 @@ parameters:
   ## databases
   databases:
     mesh-database: "OUTPUT_FILES/DATABASES_MPI/proc000000_external_mesh.bin"
+    mesh-parameters: "OUTPUT_FILES/DATABASES_MPI/mesh_parameters.bin"
 
   ## sources
   sources: "/Users/lsawade/SPECFEMPP/examples/homogeneous-medium-flat-topography/source.yaml"

fortran/meshfem3d/generate_databases/save_parameters.f90

@@ -71,17 +71,17 @@ subroutine save_parameters()
       WRITE(IOUT) NGLLSQUARE
 
       ! Write test parameter
-      WRITE(IOUT) itest
       itest = 9997
+      WRITE(IOUT) itest
 
       WRITE(IOUT) NSPEC_AB ! nspec
       WRITE(IOUT) NSPEC_PORO ! nspec_poro == nspec, if POROELASTIC_SIMULATION
       WRITE(IOUT) NGLOB_AB ! nglob
       WRITE(IOUT) NGLOB_OCEAN
 
       ! Write test parameter
-      WRITE(IOUT) itest
       itest = 9996
+      WRITE(IOUT) itest
 
       WRITE(IOUT) NSPEC2D_BOTTOM
       WRITE(IOUT) NSPEC2D_TOP
@@ -92,8 +92,8 @@ subroutine save_parameters()
       WRITE(IOUT) nspec_irregular
 
       ! Write test parameter
-      WRITE(IOUT) itest
       itest = 9995
+      WRITE(IOUT) itest
 
       WRITE(IOUT) num_neighbors_all
       WRITE(IOUT) nfaces_surface
@@ -107,8 +107,8 @@ subroutine save_parameters()
       WRITE(IOUT) max_nibool_interfaces_ext_mesh
 
       ! Write test parameter
-      WRITE(IOUT) itest
       itest = 9994
+      WRITE(IOUT) itest
 
       WRITE(IOUT) nspec_inner_acoustic
       WRITE(IOUT) nspec_outer_acoustic
@@ -118,8 +118,8 @@ subroutine save_parameters()
       WRITE(IOUT) nspec_outer_poroelastic
 
       ! Write test parameter
-      WRITE(IOUT) itest
       itest = 9993
+      WRITE(IOUT) itest
 
       WRITE(IOUT) num_phase_ispec_acoustic
       WRITE(IOUT) num_phase_ispec_elastic
@@ -130,8 +130,8 @@ subroutine save_parameters()
       WRITE(IOUT) num_colors_outer_elastic
 
       ! Write test parameter
-      WRITE(IOUT) itest
       itest = 9992
+      WRITE(IOUT) itest
   endif
 
 end subroutine save_parameters

include/IO/interface.hpp

@@ -25,7 +25,9 @@ specfem::mesh::mesh<specfem::dimension::type::dim2>
 read_2d_mesh(const std::string filename, const specfem::MPI::MPI *mpi);
 
 specfem::mesh::mesh<specfem::dimension::type::dim3>
-read_3d_mesh(const std::string filename, const specfem::MPI::MPI *mpi);
+read_3d_mesh(const std::string mesh_parameters_file,
+             const std::string mesh_databases_file,
+             const specfem::MPI::MPI *mpi);
 /**
  * @brief Read station file
  *

include/mesh/mesh.hpp

@@ -5,6 +5,7 @@
 #include "coupled_interfaces/coupled_interfaces.hpp"
 #include "elements/axial_elements.hpp"
 #include "elements/tangential_elements.hpp"
+#include "enumerations/dimension.hpp"
 #include "enumerations/interface.hpp"
 #include "materials/materials.hpp"
 #include "mesh/tags/tags.hpp"

include/mesh/parameters/parameters.hpp

@@ -95,6 +95,13 @@ template <> struct parameters<specfem::dimension::type::dim3> {
   bool approximate_ocean_load; ///< Flag for approx. ocean load
   bool use_mesh_coloring;      ///< Flag for mesh coloring
 
+  // Integer Parameters: Dimensions and GLL layouts
+  int ndim;       ///< Number of dimensions
+  int ngllx;      ///< Number of GLL points in x
+  int nglly;      ///< Number of GLL points in y
+  int ngllz;      ///< Number of GLL points in z
+  int ngllsquare; ///< Number of GLL points in square
+
   // Integer Parameters: Elements/Nodes
   int nspec;           ///< Number of spectral elements (SEs)
   int nspec_poro;      ///< Number of poroelastic SEs
@@ -153,6 +160,8 @@ template <> struct parameters<specfem::dimension::type::dim3> {
    * @param approximate_ocean_load Flag for approx. ocean load
    * @param use_mesh_coloring Flag for mesh coloring
    *
+   *
+   *
    * @param nspec Number of spectral elements (SEs)
    * @param nspec_poro Number of poroelastic SEs
    * @param nglob Number of global nodes
@@ -246,7 +255,7 @@ template <> struct parameters<specfem::dimension::type::dim3> {
         num_colors_outer_acoustic(num_colors_outer_acoustic),
         num_colors_inner_elastic(num_colors_inner_elastic),
         num_colors_outer_elastic(num_colors_outer_elastic){};
-
+};
 } // namespace mesh
 } // namespace specfem
 

include/parameter_parser/database_configuration.hpp

@@ -23,6 +23,10 @@ class database_configuration {
   database_configuration(std::string fortran_database)
       : fortran_database(fortran_database){};
 
+  database_configuration(std::string fortran_database,
+                         std::string mesh_parameters)
+      : fortran_database(fortran_database), mesh_parameters(mesh_parameters){};
+
   /**
    * @brief Construct a new run setup object
    *
@@ -32,8 +36,11 @@ class database_configuration {
 
   std::string get_databases() const { return this->fortran_database; }
 
+  std::string get_mesh_parameters() const { return this->mesh_parameters; };
+
 private:
   std::string fortran_database; ///< location of fortran binary database
+  std::string mesh_parameters;  ///< location of mesh parameter file
 };
 
 } // namespace runtime_configuration

include/parameter_parser/setup.hpp

@@ -103,6 +103,9 @@ class setup {
    * to mesh database and source yaml file
    */
   std::string get_databases() const { return databases->get_databases(); }
+  std::string get_mesh_parameters() const {
+    return databases->get_mesh_parameters();
+  }
 
   /**
    * @brief Get the sources YAML object

src/IO/mesh.cpp

@@ -8,6 +8,7 @@
 #include "IO/mesh/impl/fortran/dim2/read_material_properties.hpp"
 #include "IO/mesh/impl/fortran/dim2/read_mesh_database.hpp"
 #include "IO/mesh/impl/fortran/dim2/read_parameters.hpp"
+#include "IO/mesh/impl/fortran/dim3/read_parameters.hpp"
 #include "enumerations/interface.hpp"
 #include "kokkos_abstractions.h"
 #include "medium/material.hpp"
@@ -227,18 +228,19 @@ specfem::IO::read_2d_mesh(const std::string filename,
 }
 
 specfem::mesh::mesh<specfem::dimension::type::dim3>
-specfem::IO::read_3d_mesh(const std::string filename,
+specfem::IO::read_3d_mesh(const std::string mesh_parameters_file,
+                          const std::string mesh_databases_file,
                           const specfem::MPI::MPI *mpi) {
 
   // Declaring empty mesh objects
   specfem::mesh::mesh<specfem::dimension::type::dim3> mesh;
 
   // Open the database file
   std::ifstream stream;
-  stream.open(filename);
+  stream.open(mesh_parameters_file);
 
   if (!stream.is_open()) {
-    throw std::runtime_error("Could not open database file");
+    throw std::runtime_error("Could not open mesh parameter file");
   }
 
   try {
@@ -249,6 +251,18 @@ specfem::IO::read_3d_mesh(const std::string filename,
     throw;
   }
 
+  // Mesh Parameters are populated, closing the parameters file.
+  stream.close();
+
+  // Open the database file
+  stream.open(mesh_databases_file);
+
+  if (!stream.is_open()) {
+    throw std::runtime_error("Could not open mesh database file");
+  }
+
+  stream.close();
+
   // // Mesh class to be populated from the database file.
   // try {
   //   mesh.control_nodes.coord =