Issue 463 -- Making header files configuration files

.gitignore

@@ -30,3 +30,4 @@ profiles
 .cache/
 test*.cpp
 test*.hpp
+include/specfem_setup.hpp

.jenkins/gnu_compiler_checks.gvy

@@ -25,7 +25,7 @@ pipeline{
                     }
                     axis{
                         name 'HostSpace'
-                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_ATOMICS_BYPASS=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 10'
+                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_ATOMICS_BYPASS=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 1 -c 10'
                     }
                 }
                 stages {

.jenkins/intel_compiler_checks.gvy

@@ -21,7 +21,7 @@ pipeline{
                     }
                     axis{
                         name 'HostSpace'
-                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_ATOMICS_BYPASS=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 10'
+                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_ATOMICS_BYPASS=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 1 -c 10'
                     }
                     axis{
                         name 'SIMD'

.jenkins/nvidia_compiler_checks.gvy

@@ -21,7 +21,7 @@ pipeline{
                     }
                     axis{
                         name 'HostSpace'
-                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 10'
+                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON; -n 1 -c 10'
                     }
                     axis{
                         name 'DeviceSpace'

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.17.5)
 
-project(SPECFEMPP VERSION 0.1.0)
+project(SPECFEMPP VERSION 0.1.0 LANGUAGES CXX Fortran)
 
 set(CMAKE_CXX_STANDARD 17)
 option(HDF5_CXX_BUILD "Build HDF5 C++" ON)
@@ -11,6 +11,8 @@ option(BUILD_EXAMPLES "Examples included" ON)
 option(ENABLE_SIMD "Enable SIMD" OFF)
 option(ENABLE_PROFILING "Enable profiling" OFF)
 option(SPECFEMPP_BINDING_PYTHON "Enable Python binding" OFF)
+option(ENABLE_DOUBLE_PRECISION "Enable double precision" OFF)
+
 # set(CMAKE_BUILD_TYPE Release)
 set(CHUNK_SIZE 32)
 set(NUM_CHUNKS 1)
@@ -158,14 +160,6 @@ else()
 endif()
 
 
-configure_file(constants.hpp.in constants.hpp)
-
-include_directories(include)
-include_directories(${CMAKE_BINARY_DIR})
-
-add_subdirectory(fortran/meshfem2d)
-add_subdirectory(fortran/meshfem3d)
-
 if (ENABLE_SIMD)
     message("-- Enabling SIMD")
     add_definitions(-DENABLE_SIMD)
@@ -176,6 +170,30 @@ if (ENABLE_PROFILING)
     add_definitions(-DENABLE_PROFILING)
 endif()
 
+if (ENABLE_DOUBLE_PRECISION)
+    message("-- Enabling double precision")
+    set(TYPE_REAL "double")
+else(ENABLE_DOUBLE_PRECISION)
+    message("-- Enabling single precision")
+    set(TYPE_REAL "float")
+endif(ENABLE_DOUBLE_PRECISION)
+
+# Configure the setup headers
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup/specfem_setup.hpp.in
+               ${CMAKE_BINARY_DIR}/include/specfem_setup.hpp)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup/constants.hpp.in
+               ${CMAKE_BINARY_DIR}/include/constants.hpp)
+
+# Add the include directories so that the generated files can be found
+include_directories(include)
+include_directories(${CMAKE_BINARY_DIR}/include)
+
+# ========== MESHFEM ==============
+add_subdirectory(fortran/meshfem2d)
+add_subdirectory(fortran/meshfem3d)
+# =================================
+
+
 # Build specfem2d libraries
 add_library(
         quadrature
@@ -197,12 +215,17 @@ 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
+        src/IO/mesh/impl/fortran/dim3/read_mapping.cpp
+        src/IO/mesh/impl/fortran/dim3/read_coordinates.cpp
 )
 
 if (NOT HDF5_CXX_BUILD)
@@ -304,6 +327,9 @@ add_library(
         src/mesh/coupled_interfaces/interface_container.cpp
         src/mesh/coupled_interfaces/coupled_interfaces.cpp
         src/mesh/tags/tags.cpp
+        src/mesh/parameters/parameters.cpp
+        src/mesh/mapping/mapping.cpp
+        src/mesh/coordinates/coordinates.cpp
         src/mesh/mesh.cpp
 )
 

CMakePresets.json

@@ -0,0 +1,43 @@
+{
+  "version": 6,
+  "configurePresets": [
+    {
+      "name": "release",
+      "displayName": "Default Release -- SIMD enabled",
+      "binaryDir": "build/release",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Release",
+        "BUILD_TESTS": "ON",
+        "ENABLE_SIMD": "ON",
+        "Kokkos_ARCH_NATIVE": "ON",
+        "Kokkos_ENABLE_AGGRESSIVE_VECTORIZATION": "ON",
+        "Kokkos_ENABLE_ATOMICS_BYPASS": "ON"
+      }
+    },
+    {
+      "name": "debug",
+      "displayName": "Default Debug -- SIMD enabled",
+      "binaryDir": "build/debug",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Debug",
+        "BUILD_TESTS": "ON",
+        "ENABLE_SIMD": "ON",
+        "Kokkos_ARCH_NATIVE": "ON",
+        "Kokkos_ENABLE_AGGRESSIVE_VECTORIZATION": "ON",
+        "Kokkos_ENABLE_ATOMICS_BYPASS": "ON"
+      }
+    }
+  ],
+  "buildPresets": [
+    {
+      "name": "release",
+      "configurePreset": "release",
+      "targets": ["all"]
+    },
+    {
+      "name": "debug",
+      "configurePreset": "debug",
+      "targets": ["all"]
+    }
+  ]
+}

docs/developer_documentation/SPECFEM_architecture/architecture.rst

@@ -29,3 +29,7 @@ The code is divided into set of modules (classes and structs), the major of whic
    mesh
    compute
    domain
+
+
+
+CUSTOM_REAL

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/meshfem2d/.gitignore

@@ -0,0 +1,5 @@
+config.h
+constants.h
+precision.h
+config.fh
+version.fh