Deprecate ./setup folder and remove default.yaml dependency

CMakeLists.txt

@@ -181,18 +181,6 @@ else(SPECFEM_ENABLE_DOUBLE_PRECISION)
     set(TYPE_REAL "float")
 endif(SPECFEM_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 configure files to the clean target
-set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_CLEAN_FILES
-    ${CMAKE_BINARY_DIR}/include/specfem_setup.hpp
-    ${CMAKE_BINARY_DIR}/include/constants.hpp
-)
-
 # Add the include directories so that the generated files can be found
 include_directories(core)
 include_directories(${CMAKE_SOURCE_DIR}/include)

core/specfem.cpp

@@ -1,4 +1,4 @@
-#include "constants.hpp"
+#include "specfem/constants.hpp"
 #include "specfem/logger.hpp"
 #include "specfem/program.hpp"
 #include "specfem/program/context.hpp"
@@ -29,9 +29,7 @@ boost::program_options::options_description define_specfem_args() {
   // Add basic options
   desc.add_options()("help,h", "Print this help message")(
       "parameters_file,p", po::value<std::string>()->required(),
-      "Location to parameters file")(
-      "default_file", po::value<std::string>()->default_value(__default_file__),
-      "Location of default parameters file.");
+      "Location to parameters file");
 
   // Add logger options
   desc.add_options()(
@@ -120,11 +118,9 @@ int main(int argc, char **argv) {
     // Extract parameters (dimension is already extracted as positional
     // argument)
     const std::string parameters_file = vm["parameters_file"].as<std::string>();
-    const std::string default_file = vm["default_file"].as<std::string>();
 
-    // Load configuration files
+    // Load configuration file
     const YAML::Node parameter_dict = YAML::LoadFile(parameters_file);
-    const YAML::Node default_dict = YAML::LoadFile(default_file);
 
     // Extract and apply Logger options from parsed arguments
     auto logger_options =
@@ -140,7 +136,7 @@ int main(int argc, char **argv) {
 
     // Execute program with the specified dimension
     const auto success =
-        specfem::program::execute(dimension, parameter_dict, default_dict);
+        specfem::program::execute(dimension, parameter_dict);
 
     // Check execution result
     if (!success) {

core/specfem/CMakeLists.txt

@@ -1,3 +1,12 @@
+# Configure setup.hpp from setup.hpp.in
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup.hpp.in
+               ${CMAKE_BINARY_DIR}/include/specfem/setup.hpp)
+
+# Add the configure file to the clean target
+set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_CLEAN_FILES
+    ${CMAKE_BINARY_DIR}/include/specfem/setup.hpp
+)
+
 # Add existing subdirectories
 add_subdirectory(algorithms)
 add_subdirectory(assembly)

core/specfem/algorithms/gradient.hpp

@@ -1,6 +1,5 @@
 #pragma once
 
-#include "kokkos_abstractions.h"
 #include "specfem/assembly.hpp"
 #include "specfem/data_access.hpp"
 #include "specfem/execution.hpp"

core/specfem/algorithms/interpolate.hpp

@@ -1,9 +1,8 @@
 #pragma once
 
-#include "kokkos_abstractions.h"
 #include "specfem/datatype.hpp"
 #include "specfem/execution.hpp"
-#include "specfem_setup.hpp"
+#include "specfem/setup.hpp"
 #include <Kokkos_Core.hpp>
 
 /**

core/specfem/algorithms/locate_point/dim2/locate_point.cpp

@@ -5,7 +5,7 @@
 #include "specfem/assembly.hpp"
 #include "specfem/jacobian.hpp"
 #include "specfem/point.hpp"
-#include "specfem_setup.hpp"
+#include "specfem/setup.hpp"
 #include <Kokkos_Core.hpp>
 #include <stdexcept>
 

core/specfem/assembly.hpp

@@ -5,6 +5,8 @@
 #include "assembly/boundary_values.hpp"
 #include "assembly/conforming_interfaces.hpp"
 #include "assembly/element_types.hpp"
+#include "assembly/edge_types.hpp"
+#include "assembly/face_types.hpp"
 #include "assembly/fields.hpp"
 #include "assembly/jacobian_matrix.hpp"
 #include "assembly/kernels.hpp"

core/specfem/assembly/compute_source_array.hpp

@@ -1,11 +1,10 @@
 #pragma once
 
-#include "kokkos_abstractions.h"
 #include "specfem/assembly/element_types.hpp"
 #include "specfem/assembly/jacobian_matrix.hpp"
 #include "specfem/assembly/mesh.hpp"
 #include "specfem/source.hpp"
-#include "specfem_setup.hpp"
+#include "specfem/setup.hpp"
 #include <Kokkos_Core.hpp>
 
 namespace specfem::assembly {

core/specfem/assembly/compute_source_array/dim2/compute_source_array.tpp

@@ -4,13 +4,14 @@
 #include "specfem/element.hpp"
 #include "impl/compute_source_array_from_tensor.hpp"
 #include "impl/compute_source_array_from_vector.hpp"
-#include "kokkos_abstractions.h"
+#include "specfem/assembly/compute_source_array.hpp"
+
 #include "specfem/assembly/element_types.hpp"
 #include "specfem/source.hpp"
-#include "specfem_setup.hpp"
+#include "specfem/setup.hpp"
 #include <Kokkos_Core.hpp>
 
-template<typename SourceArrayViewType>
+template <typename SourceArrayViewType>
 void specfem::assembly::compute_source_array(
     const std::shared_ptr<
         specfem::sources::source<specfem::element::dimension_tag::dim2> > &source,
@@ -20,7 +21,8 @@ void specfem::assembly::compute_source_array(
     SourceArrayViewType &source_array) {
 
   // Ensure source_array is a 3D view
-  static_assert(SourceArrayViewType::rank() == 3, "Source array must be in rank 3.");
+  static_assert(SourceArrayViewType::rank() == 3,
+                "Source array must be in rank 3.");
 
   switch (source->get_source_type()) {
   case specfem::sources::source_type::vector_source: {

core/specfem/assembly/compute_source_array/dim2/impl/compute_source_array_from_tensor.cpp

@@ -1,5 +1,5 @@
 #include "compute_source_array_from_tensor.hpp"
-#include "kokkos_abstractions.h"
+
 #include "specfem/algorithms.hpp"
 #include "specfem/assembly/element_types.hpp"
 #include "specfem/assembly/jacobian_matrix.hpp"
@@ -8,7 +8,7 @@
 #include "specfem/point.hpp"
 #include "specfem/quadrature.hpp"
 #include "specfem/source.hpp"
-#include "specfem_setup.hpp"
+#include "specfem/setup.hpp"
 #include <Kokkos_Core.hpp>
 
 namespace specfem::assembly::compute_source_array_impl {

core/specfem/assembly/compute_source_array/dim2/impl/compute_source_array_from_tensor.hpp

@@ -1,5 +1,5 @@
 #pragma once
-#include "kokkos_abstractions.h"
+
 #include "specfem/assembly/jacobian_matrix.hpp"
 #include "specfem/assembly/mesh.hpp"
 #include "specfem/source.hpp"

core/specfem/assembly/compute_source_array/dim2/impl/compute_source_array_from_vector.cpp

@@ -1,5 +1,5 @@
 #include "compute_source_array_from_vector.hpp"
-#include "kokkos_abstractions.h"
+
 #include "specfem/algorithms.hpp"
 #include "specfem/assembly/element_types.hpp"
 #include "specfem/assembly/jacobian_matrix.hpp"
@@ -8,7 +8,7 @@
 #include "specfem/point.hpp"
 #include "specfem/quadrature.hpp"
 #include "specfem/source.hpp"
-#include "specfem_setup.hpp"
+#include "specfem/setup.hpp"
 #include <Kokkos_Core.hpp>
 
 void specfem::assembly::compute_source_array_impl::from_vector(

core/specfem/assembly/compute_source_array/dim2/impl/compute_source_array_from_vector.hpp

@@ -1,5 +1,5 @@
 #pragma once
-#include "kokkos_abstractions.h"
+
 #include "specfem/assembly/mesh.hpp"
 #include "specfem/source.hpp"
 #include <Kokkos_Core.hpp>

core/specfem/assembly/compute_source_array/dim3/compute_source_array.tpp

@@ -4,13 +4,14 @@
 #include "specfem/element.hpp"
 #include "impl/compute_source_array_from_tensor.hpp"
 #include "impl/compute_source_array_from_vector.hpp"
-#include "kokkos_abstractions.h"
+#include "specfem/assembly/compute_source_array.hpp"
+
 #include "specfem/assembly/element_types.hpp"
 #include "specfem/source.hpp"
-#include "specfem_setup.hpp"
+#include "specfem/setup.hpp"
 #include <Kokkos_Core.hpp>
 
-template<typename SourceArrayViewType>
+template <typename SourceArrayViewType>
 void specfem::assembly::compute_source_array(
     const std::shared_ptr<
         specfem::sources::source<specfem::element::dimension_tag::dim3> > &source,
@@ -20,8 +21,8 @@ void specfem::assembly::compute_source_array(
     SourceArrayViewType &source_array) {
 
   // Ensure source_array is a 4D view
-  static_assert(SourceArrayViewType::rank() == 4, "Source array must be in rank 4.");
-
+  static_assert(SourceArrayViewType::rank() == 4,
+                "Source array must be in rank 4.");
 
   switch (source->get_source_type()) {
   case specfem::sources::source_type::vector_source: {

core/specfem/assembly/compute_source_array/dim3/impl/compute_source_array_from_tensor.cpp

@@ -1,5 +1,5 @@
 #include "compute_source_array_from_tensor.hpp"
-#include "kokkos_abstractions.h"
+
 #include "specfem/algorithms.hpp"
 #include "specfem/assembly/element_types.hpp"
 #include "specfem/assembly/jacobian_matrix.hpp"
@@ -8,7 +8,7 @@
 #include "specfem/point.hpp"
 #include "specfem/quadrature.hpp"
 #include "specfem/source.hpp"
-#include "specfem_setup.hpp"
+#include "specfem/setup.hpp"
 
 namespace specfem::assembly::compute_source_array_impl {
 

core/specfem/assembly/compute_source_array/dim3/impl/compute_source_array_from_tensor.hpp

@@ -1,5 +1,5 @@
 #pragma once
-#include "kokkos_abstractions.h"
+
 #include "specfem/assembly/jacobian_matrix.hpp"
 #include "specfem/assembly/mesh.hpp"
 #include "specfem/source.hpp"

core/specfem/assembly/compute_source_array/dim3/impl/compute_source_array_from_vector.cpp

@@ -1,5 +1,5 @@
 #include "compute_source_array_from_vector.hpp"
-#include "kokkos_abstractions.h"
+
 #include "specfem/algorithms.hpp"
 #include "specfem/assembly/element_types.hpp"
 #include "specfem/assembly/jacobian_matrix.hpp"
@@ -8,7 +8,7 @@
 #include "specfem/point.hpp"
 #include "specfem/quadrature.hpp"
 #include "specfem/source.hpp"
-#include "specfem_setup.hpp"
+#include "specfem/setup.hpp"
 #include <Kokkos_Core.hpp>
 
 void specfem::assembly::compute_source_array_impl::from_vector(

core/specfem/assembly/compute_source_array/dim3/impl/compute_source_array_from_vector.hpp

@@ -1,5 +1,5 @@
 #pragma once
-#include "kokkos_abstractions.h"
+
 #include "specfem/assembly/mesh.hpp"
 #include "specfem/source.hpp"
 #include <Kokkos_Core.hpp>