Merge pull request #413 from PrincetonUniversity/issue-278

Issue 278 - Refactor of domain folder.
PrincetonUniversity · Jan 22, 2025 · e41d8df · e41d8df
2 parents fb0e3a0 + bbc92bf
commit e41d8df
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Showing 155 changed files with 2,712 additions and 5,742 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -327,18 +327,6 @@ target_link_libraries(
         point
 )
 
-# add_library(
-#         utilities
-#         src/utilities/utilities.cpp
-# )
-
-# target_link_libraries(
-#         utilities
-#         jacobian
-#         Kokkos::kokkos
-#         specfem_mpi
-# )
-
 add_library(
         read_seismogram
         src/IO/seismogram/reader.cpp
@@ -429,8 +417,7 @@ target_link_libraries(
 add_library(
         compute
         src/compute/compute_mesh.cpp
-        src/compute/impl/element_types.cpp
-        src/compute/impl/value_containers.cpp
+        src/compute/element_types/element_types.cpp
         src/compute/compute_partial_derivatives.cpp
         src/compute/compute_properties.cpp
         src/compute/compute_kernels.cpp
@@ -460,17 +447,14 @@ target_link_libraries(
 )
 
 add_library(
-        domain
-        src/domain/impl/boundary_conditions/boundary_conditions.cpp
-        src/domain/impl/elements/kernel.cpp
-        src/domain/impl/kernels.cpp
-        src/domain/domain.cpp
+        boundary_conditions
+        src/boundary_conditions/boundary_conditions.cpp
 )
 
 target_link_libraries(
-        domain
+        boundary_conditions
         Kokkos::kokkos
-        enumerations
+        ${BOOST_LIBS}
 )
 
 add_library(
@@ -483,7 +467,7 @@ target_link_libraries(
         medium
         Kokkos::kokkos
         compute
-        domain
+        boundary_conditions
         enumerations
 )
 
@@ -498,14 +482,22 @@ target_link_libraries(
 )
 
 add_library(
-        kernels
-        src/kernels/frechet_kernels.cpp
+        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/frechet_kernels.cpp
 )
 
 target_link_libraries(
-        kernels
+        kokkos_kernels
         Kokkos::kokkos
         compute
+        boundary_conditions
 )
 
 add_library(
@@ -530,8 +522,7 @@ target_link_libraries(
         solver
         Kokkos::kokkos
         timescheme
-        domain
-        kernels
+        kokkos_kernels
         medium
 )
 
@@ -603,8 +594,7 @@ target_link_libraries(
         yaml-cpp
         writer
         reader
-        kernels
-        domain
+        kokkos_kernels
         medium
         solver
         ${BOOST_LIBS}
@@ -630,10 +620,9 @@ target_link_libraries(
         writer
         plotter
         reader
-        domain
         medium
         coupled_interface
-        kernels
+        kokkos_kernels
         solver
         ${BOOST_LIBS}
 )
@@ -695,10 +684,9 @@ if (SPECFEMPP_BINDING_PYTHON)
         writer
         plotter
         reader
-        domain
         medium
         coupled_interface
-        kernels
+        kokkos_kernels
         solver
         ${BOOST_LIBS}
         pybind11::headers

diff --git a/include/IO/kernel/writer.hpp b/include/IO/kernel/writer.hpp
@@ -1,8 +1,8 @@
 #pragma once
 
+#include "IO/writer.hpp"
 #include "compute/interface.hpp"
 #include "enumerations/interface.hpp"
-#include "IO/writer.hpp"
 
 namespace specfem {
 namespace IO {

diff --git a/include/IO/kernel/writer.tpp b/include/IO/kernel/writer.tpp
@@ -15,6 +15,7 @@ specfem::IO::kernel_writer<OutputLibrary>::kernel_writer(const std::string outpu
 template <typename OutputLibrary>
 void specfem::IO::kernel_writer<OutputLibrary>::write(specfem::compute::assembly &assembly) {
   const auto &mesh = assembly.mesh;
+  auto &element_types = assembly.element_types;
   auto &kernels = assembly.kernels;
 
   using DomainView =
@@ -35,7 +36,7 @@ void specfem::IO::kernel_writer<OutputLibrary>::write(specfem::compute::assembly
   {
     typename OutputLibrary::Group elastic = file.createGroup("/ElasticIsotropic");
 
-    const auto element_indices = kernels.get_elements_on_host(
+    const auto element_indices = element_types.get_elements_on_host(
         specfem::element::medium_tag::elastic,
         specfem::element::property_tag::isotropic);
     n_elastic_isotropic = element_indices.size();
@@ -89,7 +90,7 @@ void specfem::IO::kernel_writer<OutputLibrary>::write(specfem::compute::assembly
   {
     typename OutputLibrary::Group elastic = file.createGroup("/ElasticAnisotropic");
 
-    const auto element_indices = kernels.get_elements_on_host(
+    const auto element_indices = element_types.get_elements_on_host(
         specfem::element::medium_tag::elastic,
         specfem::element::property_tag::anisotropic);
     n_elastic_anisotropic = element_indices.size();
@@ -146,7 +147,7 @@ void specfem::IO::kernel_writer<OutputLibrary>::write(specfem::compute::assembly
   {
     typename OutputLibrary::Group acoustic = file.createGroup("/Acoustic");
 
-    const auto element_indices = kernels.get_elements_on_host(specfem::element::medium_tag::acoustic);
+    const auto element_indices = element_types.get_elements_on_host(specfem::element::medium_tag::acoustic);
     n_acoustic = element_indices.size();
 
     DomainView x("xcoordinates_acoustic", n_acoustic, ngllz, ngllx);

diff --git a/include/IO/property/writer.tpp b/include/IO/property/writer.tpp
@@ -15,6 +15,7 @@ specfem::IO::property_writer<OutputLibrary>::property_writer(const std::string o
 template <typename OutputLibrary>
 void specfem::IO::property_writer<OutputLibrary>::write(specfem::compute::assembly &assembly) {
   const auto &mesh = assembly.mesh;
+  auto &element_types = assembly.element_types;
   auto &properties = assembly.properties;
 
   using DomainView =
@@ -35,7 +36,7 @@ void specfem::IO::property_writer<OutputLibrary>::write(specfem::compute::assemb
   {
     typename OutputLibrary::Group elastic = file.createGroup("/ElasticIsotropic");
 
-    const auto element_indices = properties.get_elements_on_host(
+    const auto element_indices = element_types.get_elements_on_host(
         specfem::element::medium_tag::elastic,
         specfem::element::property_tag::isotropic);
     n_elastic_isotropic = element_indices.size();
@@ -64,7 +65,7 @@ void specfem::IO::property_writer<OutputLibrary>::write(specfem::compute::assemb
   {
     typename OutputLibrary::Group elastic = file.createGroup("/ElasticAnisotropic");
 
-    const auto element_indices = properties.get_elements_on_host(
+    const auto element_indices = element_types.get_elements_on_host(
         specfem::element::medium_tag::elastic,
         specfem::element::property_tag::anisotropic);
     n_elastic_anisotropic = element_indices.size();
@@ -100,7 +101,7 @@ void specfem::IO::property_writer<OutputLibrary>::write(specfem::compute::assemb
   {
     typename OutputLibrary::Group acoustic = file.createGroup("/Acoustic");
 
-    const auto element_indices = properties.get_elements_on_host(specfem::element::medium_tag::acoustic);
+    const auto element_indices = element_types.get_elements_on_host(specfem::element::medium_tag::acoustic);
     n_acoustic = element_indices.size();
 
     DomainView x("xcoordinates_acoustic", n_acoustic, ngllz, ngllx);

diff --git a/...undary_conditions/boundary_conditions.hpp → ...undary_conditions/boundary_conditions.hpp b/...undary_conditions/boundary_conditions.hpp → ...undary_conditions/boundary_conditions.hpp
@@ -9,8 +9,7 @@
 #include <type_traits>
 
 namespace specfem {
-namespace domain {
-namespace impl {
+
 namespace boundary_conditions {
 template <typename PointBoundaryType, typename PointPropertyType,
           typename PointFieldType, typename PointAccelerationType>
@@ -78,6 +77,4 @@ compute_mass_matrix_terms(const type_real dt, const PointBoundaryType &boundary,
 }
 
 } // namespace boundary_conditions
-} // namespace impl
-} // namespace domain
 } // namespace specfem
diff --git a/..._dirichlet/composite_stacey_dirichlet.hpp → ..._dirichlet/composite_stacey_dirichlet.hpp b/..._dirichlet/composite_stacey_dirichlet.hpp → ..._dirichlet/composite_stacey_dirichlet.hpp
@@ -5,8 +5,6 @@
 #include <Kokkos_Core.hpp>
 
 namespace specfem {
-namespace domain {
-namespace impl {
 namespace boundary_conditions {
 
 using composite_stacey_dirichlet_type = std::integral_constant<
@@ -28,6 +26,4 @@ KOKKOS_FUNCTION void impl_compute_mass_matrix_terms(
     PointMassMatrixType &mass_matrix);
 
 } // namespace boundary_conditions
-} // namespace impl
-} // namespace domain
 } // namespace specfem
diff --git a/..._dirichlet/composite_stacey_dirichlet.tpp → ..._dirichlet/composite_stacey_dirichlet.tpp b/..._dirichlet/composite_stacey_dirichlet.tpp → ..._dirichlet/composite_stacey_dirichlet.tpp
@@ -1,17 +1,17 @@
 #pragma once
 
 #include "composite_stacey_dirichlet.hpp"
-#include "domain/impl/boundary_conditions/boundary_conditions.hpp"
-#include "domain/impl/boundary_conditions/dirichlet/dirichlet.hpp"
-#include "domain/impl/boundary_conditions/stacey/stacey.hpp"
+#include "boundary_conditions/boundary_conditions.hpp"
+#include "boundary_conditions/dirichlet/dirichlet.hpp"
+#include "boundary_conditions/stacey/stacey.hpp"
 #include "enumerations/boundary.hpp"
 #include "point/boundary.hpp"
 #include <Kokkos_Core.hpp>
 
 template <typename PointBoundaryType, typename PointPropertyType,
           typename PointFieldType, typename PointAccelerationType>
 KOKKOS_FUNCTION void
-specfem::domain::impl::boundary_conditions::impl_apply_boundary_conditions(
+specfem::boundary_conditions::impl_apply_boundary_conditions(
     const composite_stacey_dirichlet_type &, const PointBoundaryType &boundary,
     const PointPropertyType &property, const PointFieldType &field,
     PointAccelerationType &acceleration) {
@@ -47,7 +47,7 @@ specfem::domain::impl::boundary_conditions::impl_apply_boundary_conditions(
 template <typename PointBoundaryType, typename PointPropertyType,
           typename PointMassMatrixType>
 KOKKOS_FUNCTION void
-specfem::domain::impl::boundary_conditions::impl_compute_mass_matrix_terms(
+specfem::boundary_conditions::impl_compute_mass_matrix_terms(
     const composite_stacey_dirichlet_type &, const type_real dt,
     const PointBoundaryType &boundary, const PointPropertyType &property,
     PointMassMatrixType &mass_matrix) {

diff --git a/...undary_conditions/dirichlet/dirichlet.hpp → ...undary_conditions/dirichlet/dirichlet.hpp b/...undary_conditions/dirichlet/dirichlet.hpp → ...undary_conditions/dirichlet/dirichlet.hpp
@@ -6,8 +6,6 @@
 #include <Kokkos_SIMD.hpp>
 
 namespace specfem {
-namespace domain {
-namespace impl {
 namespace boundary_conditions {
 
 using acoustic_free_surface_type = std::integral_constant<
@@ -85,6 +83,4 @@ KOKKOS_FORCEINLINE_FUNCTION void impl_compute_mass_matrix_terms(
 };
 
 } // namespace boundary_conditions
-} // namespace impl
-} // namespace domain
 } // namespace specfem
diff --git a/...in/impl/boundary_conditions/none/none.hpp → include/boundary_conditions/none/none.hpp b/...in/impl/boundary_conditions/none/none.hpp → include/boundary_conditions/none/none.hpp
@@ -5,8 +5,6 @@
 #include <Kokkos_Core.hpp>
 
 namespace specfem {
-namespace domain {
-namespace impl {
 namespace boundary_conditions {
 
 using none_type = std::integral_constant<specfem::element::boundary_tag,
@@ -41,6 +39,4 @@ KOKKOS_INLINE_FUNCTION void impl_compute_mass_matrix_terms(
 }
 
 } // namespace boundary_conditions
-} // namespace impl
-} // namespace domain
 } // namespace specfem
diff --git a/...mpl/boundary_conditions/stacey/stacey.hpp → ...ude/boundary_conditions/stacey/stacey.hpp b/...mpl/boundary_conditions/stacey/stacey.hpp → ...ude/boundary_conditions/stacey/stacey.hpp
@@ -5,8 +5,6 @@
 #include <Kokkos_Core.hpp>
 
 namespace specfem {
-namespace domain {
-namespace impl {
 namespace boundary_conditions {
 
 using stacey_type =
@@ -27,6 +25,4 @@ KOKKOS_FUNCTION void impl_compute_mass_matrix_terms(
     const PointPropertyType &property, PointMassMatrixType &mass_matrix);
 
 } // namespace boundary_conditions
-} // namespace impl
-} // namespace domain
 } // namespace specfem
diff --git a/...mpl/boundary_conditions/stacey/stacey.tpp → ...ude/boundary_conditions/stacey/stacey.tpp b/...mpl/boundary_conditions/stacey/stacey.tpp → ...ude/boundary_conditions/stacey/stacey.tpp
@@ -1,7 +1,7 @@
 #pragma once
 
 #include "algorithms/dot.hpp"
-#include "domain/impl/boundary_conditions/boundary_conditions.hpp"
+#include "boundary_conditions/boundary_conditions.hpp"
 #include "enumerations/medium.hpp"
 #include "point/field.hpp"
 #include "stacey.hpp"
@@ -335,7 +335,7 @@ impl_enforce_traction(const elastic_type &, const anisotropic_type &,
 template <typename PointBoundaryType, typename PointPropertyType,
           typename PointFieldType, typename PointAccelerationType>
 KOKKOS_FUNCTION void
-specfem::domain::impl::boundary_conditions::impl_apply_boundary_conditions(
+specfem::boundary_conditions::impl_apply_boundary_conditions(
     const stacey_type &, const PointBoundaryType &boundary,
     const PointPropertyType &property, const PointFieldType &field,
     PointAccelerationType &acceleration) {
@@ -354,7 +354,7 @@ specfem::domain::impl::boundary_conditions::impl_apply_boundary_conditions(
 template <typename PointBoundaryType, typename PointPropertyType,
           typename PointMassMatrixType>
 KOKKOS_FORCEINLINE_FUNCTION void
-specfem::domain::impl::boundary_conditions::impl_compute_mass_matrix_terms(
+specfem::boundary_conditions::impl_compute_mass_matrix_terms(
     const stacey_type &, const type_real dt, const PointBoundaryType &boundary,
     const PointPropertyType &property, PointMassMatrixType &mass_matrix) {
 

diff --git a/include/compute/assembly/assembly.hpp b/include/compute/assembly/assembly.hpp
@@ -34,6 +34,8 @@ namespace compute {
  */
 struct assembly {
   specfem::compute::mesh mesh; ///< Properties of the assembled mesh
+  specfem::compute::element_types element_types; ///< Element tags for every
+                                                 ///< spectral element
   specfem::compute::partial_derivatives partial_derivatives; ///< Partial
                                                              ///< derivatives of
                                                              ///< the basis

diff --git a/include/compute/boundary_values/boundary_values.hpp b/include/compute/boundary_values/boundary_values.hpp
@@ -25,7 +25,7 @@ class boundary_values {
       composite_stacey_dirichlet;
 
   boundary_values(const int nstep, const specfem::compute::mesh mesh,
-                  const specfem::compute::properties properties,
+                  const specfem::compute::element_types element_types,
                   const specfem::compute::boundaries boundaries);
 
   template <specfem::element::boundary_tag BoundaryTag>

diff --git a/include/compute/boundary_values/boundary_values_container.hpp b/include/compute/boundary_values/boundary_values_container.hpp
@@ -33,7 +33,7 @@ class boundary_value_container {
   boundary_value_container() = default;
 
   boundary_value_container(const int nstep, const specfem::compute::mesh mesh,
-                           const specfem::compute::properties properties,
+                           const specfem::compute::element_types element_types,
                            const specfem::compute::boundaries boundaries);
 
   void sync_to_host() {

diff --git a/include/compute/boundary_values/boundary_values_container.tpp b/include/compute/boundary_values/boundary_values_container.tpp
@@ -8,7 +8,7 @@ template <specfem::dimension::type DimensionType,
           specfem::element::boundary_tag BoundaryTag>
 specfem::compute::boundary_value_container<DimensionType, BoundaryTag>::
     boundary_value_container(const int nstep, const specfem::compute::mesh mesh,
-                             const specfem::compute::properties properties,
+                             const specfem::compute::element_types element_types,
                              const specfem::compute::boundaries boundaries)
     : property_index_mapping(
           "specfem::compute::boundary_value_container::property_index_mapping",
@@ -24,11 +24,11 @@ specfem::compute::boundary_value_container<DimensionType, BoundaryTag>::
 
   acoustic = specfem::compute::impl::boundary_medium_container<
       DimensionType, specfem::element::medium_tag::acoustic, BoundaryTag>(
-      nstep, mesh, properties, boundaries, h_property_index_mapping);
+      nstep, mesh, element_types, boundaries, h_property_index_mapping);
 
   elastic = specfem::compute::impl::boundary_medium_container<
       DimensionType, specfem::element::medium_tag::elastic, BoundaryTag>(
-      nstep, mesh, properties, boundaries, h_property_index_mapping);
+      nstep, mesh, element_types, boundaries, h_property_index_mapping);
 
   Kokkos::deep_copy(property_index_mapping, h_property_index_mapping);
 }