Merge pull request #1584 from PrincetonUniversity/issue-1554

Issue 1554 - Move most code from include/ to core/ (excluding io, medium and enumerations)

Author: icui

CMakeLists.txt

@@ -231,21 +231,6 @@ set(CMAKE_MESSAGE_LOG_LEVEL ${_saved_CMAKE_MESSAGE_LOG_LEVEL})
 # Add module subdirectories
 add_subdirectory(core)
 
-# Build specfem2d libraries
-add_library(
-        quadrature
-        src/quadrature/quadrature.cpp
-        src/quadrature/gll/gll_utils.cpp
-        src/quadrature/gll/gll_library.cpp
-        src/quadrature/gll/lagrange_poly.cpp
-        src/quadrature/gll/gll.cpp
-)
-
-target_link_libraries(
-        quadrature
-        Kokkos::kokkos
-)
-
 add_library(
         io
         # IO libraries
@@ -277,7 +262,7 @@ add_library(
 
 target_link_libraries(
         io
-        mesh
+        specfem::mesh
         source_class
         specfem::receivers
         yaml-cpp
@@ -328,35 +313,6 @@ target_link_libraries(
 #         Kokkos::kokkos
 # )
 
-add_library(
-        mesh
-        # 2-D
-        src/mesh/dim2/boundaries/forcing_boundaries.cpp
-        src/mesh/dim2/boundaries/absorbing_boundaries.cpp
-        src/mesh/dim2/boundaries/acoustic_free_surface.cpp
-        src/mesh/dim2/elements/tangential_elements.cpp
-        src/mesh/dim2/elements/axial_elements.cpp
-        # src/mesh/mpi_interfaces/mpi_interfaces.cpp
-        src/mesh/dim2/tags/tags.cpp
-        src/mesh/dim2/adjacency_graph/assert_symmetry.cpp
-        src/mesh/dim2/mesh.cpp
-        # 3-D
-
-        src/mesh/dim3/adjacency_graph/assert_symmetry.cpp
-        src/mesh/dim3/tags/tags.cpp
-        src/mesh/dim3/mesh.cpp
-)
-
-target_link_libraries(
-        mesh
-        enumerations
-        Kokkos::kokkos
-        specfem::macros
-        # material_class
-        yaml-cpp
-        ${BOOST_LIBS}
-)
-
 add_library(
         read_seismogram
         src/io/seismogram/reader.cpp
@@ -367,16 +323,6 @@ target_link_libraries(
         Kokkos::kokkos
         )
 
-add_library(utilities
-        src/utilities/strings.cpp
-)
-
-target_link_libraries(
-        utilities
-        Kokkos::kokkos
-        ${BOOST_LIBS}
-)
-
 add_library(
         reader
         src/io/property/reader.cpp
@@ -388,49 +334,7 @@ target_link_libraries(
         assembly
         io
         read_seismogram
-        utilities
-)
-
-add_library(
-        algorithms
-        src/algorithms/dim2/locate_point.cpp
-        src/algorithms/dim2/locate_point_impl.cpp
-        src/algorithms/dim3/locate_point.cpp
-        src/algorithms/dim3/locate_point_impl.cpp
-)
-
-target_link_libraries(
-        algorithms
-        Kokkos::kokkos
-        jacobian
-        point
-        assembly
-        ${BOOST_LIBS}
-)
-
-add_library(
-        kokkos_kernels
-        src/kokkos_kernels/impl/compute_mass_matrix.cpp
-        src/kokkos_kernels/impl/invert_mass_matrix.cpp
-        src/kokkos_kernels/impl/divide_mass_matrix.cpp
-        src/kokkos_kernels/impl/compute_seismogram.cpp
-        src/kokkos_kernels/impl/compute_source_interaction.cpp
-        src/kokkos_kernels/impl/compute_stiffness_interaction.cpp
-        src/kokkos_kernels/impl/compute_material_derivatives.cpp
-        src/kokkos_kernels/impl/compute_coupling.cpp
-        src/kokkos_kernels/frechet_kernels.cpp
-)
-
-set_target_properties(kokkos_kernels PROPERTIES
-        UNITY_BUILD $<NOT:$<BOOL:${__APPLE__}>>
-        UNITY_BUILD_BATCH_SIZE $<IF:$<BOOL:${__APPLE__}>,0,4>
-)
-
-target_link_libraries(
-        kokkos_kernels
-        PRIVATE
-        assembly
-        Kokkos::kokkos
+        specfem::utilities
 )
 
 add_library(
@@ -446,43 +350,9 @@ target_link_libraries(
         assembly
         specfem::receivers
         io
-        utilities
-)
-
-
-add_library(
-        parameter_reader
-        src/parameter_parser/run_setup.cpp
-        src/parameter_parser/time_scheme/time_scheme.cpp
-        src/parameter_parser/database_configuration.cpp
-        src/parameter_parser/header.cpp
-        src/parameter_parser/quadrature.cpp
-        src/parameter_parser/elastic_wave.cpp
-        src/parameter_parser/electromagnetic_wave.cpp
-        src/parameter_parser/receivers.cpp
-        src/parameter_parser/writer/seismogram.cpp
-        src/parameter_parser/setup.cpp
-        src/parameter_parser/writer/wavefield.cpp
-        src/parameter_parser/writer/plot_wavefield.cpp
-        src/parameter_parser/writer/kernel.cpp
-        src/parameter_parser/writer/property.cpp
-)
-
-target_link_libraries(
-        parameter_reader
-        quadrature
-        specfem::timescheme
-        specfem::receivers
-        yaml-cpp
-        specfem::periodic_tasks
-        writer
-        reader
-        kokkos_kernels
-        specfem::solver
-        ${BOOST_LIBS}
+        specfem::utilities
 )
 
-
 # specfem2d executable for backward compatibility
 add_executable(specfem2d src/specfem2d.cpp)
 target_link_libraries(specfem2d

core/specfem/CMakeLists.txt

@@ -1,18 +1,24 @@
 # Add existing subdirectories
-add_subdirectory(mpi)
+add_subdirectory(algorithms)
+add_subdirectory(assembly)
+add_subdirectory(jacobian)
+add_subdirectory(kokkos_kernels)
 add_subdirectory(logger)
 add_subdirectory(macros)
-add_subdirectory(assembly)
+add_subdirectory(mesh)
+add_subdirectory(mpi)
+add_subdirectory(periodic_tasks)
 add_subdirectory(point)
+add_subdirectory(program)
+add_subdirectory(quadrature)
 add_subdirectory(receivers)
+add_subdirectory(runtime_configuration)
 add_subdirectory(shape_function)
 add_subdirectory(solver)
 add_subdirectory(source)
 add_subdirectory(source_time_functions)
-add_subdirectory(jacobian)
 add_subdirectory(timescheme)
-add_subdirectory(periodic_tasks)
-add_subdirectory(program)
+add_subdirectory(utilities)
 
 
 
@@ -22,16 +28,26 @@ add_library(specfem::core ALIAS specfem_core_interface)
 
 target_link_libraries(specfem_core_interface
     INTERFACE
+        specfem::algorithms
         specfem::assembly
         specfem::jacobian
+        specfem::kokkos_kernels
+        specfem::logger
+        specfem::macros
+        specfem::mesh
         specfem::mpi
         specfem::periodic_tasks
         specfem::point
         specfem::program
+        specfem::quadrature
         specfem::receivers
+        specfem::runtime_configuration
         specfem::shape_function
+        specfem::solver
         specfem::source
+        specfem::source_time_functions
         specfem::timescheme
+        specfem::utilities
 )
 
 target_include_directories(specfem_core_interface

include/algorithms/interface.hpp core/specfem/algorithms.hppinclude/algorithms/interface.hpp renamed to core/specfem/algorithms.hpp

@@ -20,6 +20,7 @@
  */
 namespace specfem::algorithms {}
 
+#include "algorithms/coupling_integral.hpp"
 #include "algorithms/divergence.hpp"
 #include "algorithms/gradient.hpp"
 #include "algorithms/interpolate.hpp"

core/specfem/algorithms/CMakeLists.txt

@@ -0,0 +1,16 @@
+file(GLOB_RECURSE ALGORITHMS_SOURCE_FILES "./*.cpp" "./**/*.cpp")
+
+add_library(
+        specfem_algorithms
+        ${ALGORITHMS_SOURCE_FILES}
+)
+add_library(specfem::algorithms ALIAS specfem_algorithms)
+
+target_link_libraries(
+        specfem_algorithms
+        Kokkos::kokkos
+        jacobian
+        point
+        assembly
+        ${BOOST_LIBS}
+)

…rithms/integrate/coupling_integral1d.hpp …specfem/algorithms/coupling_integral.hppinclude/algorithms/integrate/coupling_integral1d.hpp renamed to core/specfem/algorithms/coupling_integral.hpp include/algorithms/integrate/coupling_integral1d.hpp renamed to core/specfem/algorithms/coupling_integral.hpp

@@ -1,14 +1,17 @@
 #pragma once
 
 #include "enumerations/interface.hpp"
-#include "execution/for_each_level.hpp"
-#include "execution/team_thread_md_range_iterator.hpp"
-#include "specfem/assembly.hpp"
+#include "specfem/assembly/nonconforming_interfaces.hpp"
+#include "specfem/execution.hpp"
 #include "specfem/point.hpp"
 #include <Kokkos_Core.hpp>
 
+namespace specfem::assembly {
+template <specfem::dimension::type DimensionTag> struct assembly;
+}
+
 /**
- * @file coupling_integral1d.hpp
+ * @file coupling_integral.hpp
  * @brief 1D coupling integrals for interface computations
  * @ingroup AlgorithmsIntegration
  *

include/algorithms/divergence.hpp core/specfem/algorithms/divergence.hppinclude/algorithms/divergence.hpp renamed to core/specfem/algorithms/divergence.hpp

@@ -1,8 +1,7 @@
 #pragma once
 
-#include "datatypes/point_view.hpp"
-#include "execution/for_each_level.hpp"
-#include "specfem/assembly.hpp"
+#include "specfem/datatype.hpp"
+#include "specfem/execution.hpp"
 #include "specfem/point.hpp"
 #include <Kokkos_Core.hpp>
 

include/algorithms/gradient.hpp core/specfem/algorithms/gradient.hppinclude/algorithms/gradient.hpp renamed to core/specfem/algorithms/gradient.hpp

@@ -1,9 +1,9 @@
 #pragma once
 
-#include "execution/for_each_level.hpp"
 #include "kokkos_abstractions.h"
-#include "specfem/assembly.hpp"
+#include "specfem/assembly/jacobian_matrix.hpp"
 #include "specfem/data_access.hpp"
+#include "specfem/execution.hpp"
 #include "specfem/point.hpp"
 #include <Kokkos_Core.hpp>
 

include/algorithms/interpolate.hpp core/specfem/algorithms/interpolate.hppinclude/algorithms/interpolate.hpp renamed to core/specfem/algorithms/interpolate.hpp

@@ -1,8 +1,8 @@
 #pragma once
 
-#include "datatypes/point_view.hpp"
-#include "execution/for_each_level.hpp"
 #include "kokkos_abstractions.h"
+#include "specfem/datatype.hpp"
+#include "specfem/execution.hpp"
 #include "specfem_setup.hpp"
 #include <Kokkos_Core.hpp>
 

include/algorithms/locate_point.hpp core/specfem/algorithms/locate_point.hppinclude/algorithms/locate_point.hpp renamed to core/specfem/algorithms/locate_point.hpp

@@ -1,7 +1,7 @@
-#include "algorithms/locate_point.hpp"
-#include "algorithms/locate_point_impl.hpp"
-#include "algorithms/locate_point_impl.tpp"
+#include "specfem/algorithms/locate_point.hpp"
 #include "enumerations/mesh_entities.hpp"
+#include "specfem/algorithms/locate_point/locate_point_impl.hpp"
+#include "specfem/algorithms/locate_point/locate_point_impl.tpp"
 #include "specfem/assembly.hpp"
 #include "specfem/jacobian.hpp"
 #include "specfem/point.hpp"