Merge branch 'devel' into issue-160

.github/pull_request_template.md

@@ -1,18 +1,18 @@
 # Description
 
-Please describe the changes/features in this pull request. 
+Please describe the changes/features in this pull request.
 
 # Issue Number
 
 If there is an issue created for these changes, link it here
 
 # Checklist
 
-Please make sure to check developer documentation on specfem docs. 
+Please make sure to check developer documentation on specfem docs.
 
-[] I ran the code through pre-commit to check style
-[] My code passes all the integration tests
-[] I have added sufficient unittests to test my changes
-[] I have added/updated documentation for the changes I am proposing
-[] I have updated CMakeLists to ensure my code builds
-[] My code builds across all platforms 
+- [ ] I ran the code through pre-commit to check style
+- [ ] My code passes all the integration tests
+- [ ] I have added sufficient unittests to test my changes
+- [ ] I have added/updated documentation for the changes I am proposing
+- [ ] I have updated CMakeLists to ensure my code builds
+- [ ] My code builds across all platforms

.gitignore

@@ -8,6 +8,7 @@ firebase*.yml
 *.out
 debug.sh
 output.log
+output.txt
 results/
 timing.sh
 examples/*/*_config.yaml

.jenkins/gnu_compiler_checks.gvy

@@ -68,8 +68,8 @@ pipeline{
                                     sh """
                                         module load boost/1.73.0
                                         module load ${GNU_COMPILER_MODULE}
-                                        cmake3 -S . -B build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} -DBUILD_TESTS=ON
-                                        cmake3 --build build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}
+                                        cmake3 -S . -B build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} -DBUILD_TESTS=ON
+                                        cmake3 --build build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}
                                     """
                                     echo ' Build completed '
                                 }
@@ -80,7 +80,7 @@ pipeline{
                                     sh """
                                         module load boost/1.73.0
                                         module load ${GNU_COMPILER_MODULE}
-                                        cd build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}/tests/unit-tests
+                                        cd build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}/tests/unit-tests
                                         srun -N 1 -t 00:20:00 ${HOST_RUN_FLAGS} --constraint=skylake bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest --verbose;'
                                     """
                                     echo ' Testing completed '
@@ -90,7 +90,7 @@ pipeline{
                         post {
                             always {
                                 echo ' Cleaning '
-                                sh "rm -rf build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}"
+                                sh "rm -rf build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}"
                             }
                         }
                     }

.jenkins/intel_compiler_checks.gvy

@@ -69,8 +69,8 @@ pipeline{
                                         module load ${INTEL_MODULE}
                                         export CC=icx
                                         export CXX=icpx
-                                        cmake3 -S . -B build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} -D BUILD_TESTS=ON
-                                        cmake3 --build build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}
+                                        cmake3 -S . -B build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} -D BUILD_TESTS=ON
+                                        cmake3 --build build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}
                                     """
                                     echo ' Build completed '
                                 }
@@ -81,7 +81,7 @@ pipeline{
                                     sh """
                                         module load boost/1.73.0
                                         module load ${INTEL_MODULE}
-                                        cd build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}/tests/unit-tests
+                                        cd build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}/tests/unit-tests
                                         srun -N 1 -t 00:20:00 ${HOST_RUN_FLAGS} --constraint=skylake bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest --verbose;'
                                     """
                                     echo ' Testing completed '
@@ -91,7 +91,7 @@ pipeline{
                         post {
                             always {
                                 echo ' Cleaning '
-                                sh "rm -rf build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}"
+                                sh "rm -rf build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}"
                             }
                         }
                     }

.jenkins/nvidia_compiler_checks.gvy

@@ -83,8 +83,8 @@ pipeline{
                                     sh """
                                         module load boost/1.73.0
                                         module load ${CUDA_MODULE}
-                                        cmake3 -S . -B build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.GIT_COMMIT} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${CMAKE_DEVICE_FLAGS} ${SIMD_FLAGS} -D BUILD_TESTS=ON
-                                        cmake3 --build build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}
+                                        cmake3 -S . -B build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${CMAKE_DEVICE_FLAGS} ${SIMD_FLAGS} -D BUILD_TESTS=ON
+                                        cmake3 --build build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG}
                                     """
                                     echo ' Build completed '
                                 }
@@ -95,7 +95,7 @@ pipeline{
                                     sh """
                                         module load boost/1.73.0
                                         module load ${CUDA_MODULE}
-                                        cd build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}/tests/unit-tests
+                                        cd build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG}/tests/unit-tests
                                         srun -N 1 -t 00:20:00 ${HOST_RUN_FLAGS} ${DEVICE_RUN_FLAGS} bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest --verbose;'
                                     """
                                     echo ' Testing completed '
@@ -105,7 +105,7 @@ pipeline{
                         post {
                             always {
                                 echo ' Cleaning '
-                                sh "rm -rf build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}"
+                                sh "rm -rf build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG}"
                             }
                         }
                     }

CMakeLists.txt

@@ -4,6 +4,7 @@ project(specfem2d_kokkos VERSION 0.1.0)
 
 set(CMAKE_CXX_STANDARD 17)
 option(HDF5_CXX_BUILD "Build HDF5 C++" ON)
+option(VTK_CXX_BUILD "Build VTK C++" ON)
 option(MPI_PARALLEL "MPI enabled" OFF)
 option(BUILD_TESTS "Tests included" OFF)
 option(BUILD_EXAMPLES "Examples included" OFF)
@@ -48,6 +49,26 @@ FetchContent_MakeAvailable(yaml)
 
 include_directories(BEFORE SYSTEM ${yaml_BINARY_DIR} ${yaml_SOURCE_DIR}/include)
 
+find_package(VTK COMPONENTS
+CommonColor
+CommonCore
+FiltersSources
+InteractionStyle
+RenderingContextOpenGL2
+RenderingCore
+RenderingFreeType
+RenderingGL2PSOpenGL2
+RenderingOpenGL2
+)
+
+if (NOT VTK_FOUND)
+  message("VTK not found: ${VTK_NOT_FOUND_MESSAGE}")
+  set(VTK_CXX_BUILD OFF)
+else ()
+  message(STATUS "    VTK:   ${VTK_LIBRARIES}")
+endif()
+
+
 # Try finding boost and if not found install.
 find_package(Boost 1.73.0 COMPONENTS program_options filesystem system)
 
@@ -107,7 +128,16 @@ add_library(
         IO
         src/IO/fortranio/fortran_io.cpp
         src/IO/HDF5/native_type.cpp
-        src/IO/ASCII/native_type.cpp
+        # src/IO/ASCII/native_type.cpp
+        src/IO/mesh/read_mesh.cpp
+        src/IO/mesh/impl/fortran/read_boundaries.cpp
+        src/IO/mesh/impl/fortran/read_elements.cpp
+        src/IO/mesh/impl/fortran/read_material_properties.cpp
+        src/IO/mesh/impl/fortran/read_mesh_database.cpp
+        src/IO/mesh/impl/fortran/read_interfaces.cpp
+        src/IO/mesh/impl/fortran/read_properties.cpp
+        src/IO/sources/read_sources.cpp
+        src/IO/receivers/read_receivers.cpp
 )
 
 if (NOT HDF5_CXX_BUILD)
@@ -130,6 +160,21 @@ else()
         )
 endif()
 
+target_link_libraries(
+  IO
+  mesh
+)
+
+target_link_libraries(
+  IO
+  source_class
+)
+
+target_link_libraries(
+  IO
+  receiver_class
+)
+
 add_library(
         point
         src/point/coordinates.cpp
@@ -141,6 +186,11 @@ target_link_libraries(
         Kokkos::kokkos
 )
 
+add_library(
+        enumerations
+        src/enumerations/medium.cpp
+)
+
 add_library(
         edge
         src/edge/interface.cpp
@@ -180,14 +230,12 @@ endif(MPI_PARALLEL)
 
 add_library(
         mesh
-        src/mesh/IO/fortran/read_mesh_database.cpp
         src/mesh/boundaries/forcing_boundaries.cpp
         src/mesh/boundaries/absorbing_boundaries.cpp
         src/mesh/boundaries/acoustic_free_surface.cpp
         src/mesh/elements/tangential_elements.cpp
         src/mesh/elements/axial_elements.cpp
-        src/mesh/properties/properties.cpp
-        src/mesh/mpi_interfaces/mpi_interfaces.cpp
+        # src/mesh/mpi_interfaces/mpi_interfaces.cpp
         src/mesh/materials/materials.cpp
         src/mesh/coupled_interfaces/interface_container.cpp
         src/mesh/coupled_interfaces/coupled_interfaces.cpp
@@ -200,7 +248,6 @@ target_link_libraries(
         Kokkos::kokkos
         specfem_mpi
         # material_class
-        IO
         yaml-cpp
 )
 
@@ -228,16 +275,26 @@ target_link_libraries(
 #         specfem_mpi
 # )
 
+add_library(
+        read_seismogram
+        src/reader/seismogram.cpp
+)
+
+target_link_libraries(
+        read_seismogram
+        Kokkos::kokkos
+        )
+
 add_library(
         reader
         src/reader/wavefield.cpp
-        src/reader/seismogram.cpp
 )
 
 target_link_libraries(
         reader
         compute
         IO
+        read_seismogram
 )
 
 add_library(
@@ -261,7 +318,7 @@ add_library(
 
 target_link_libraries(
         source_time_function
-        reader
+        read_seismogram
         Kokkos::kokkos
         point
 )
@@ -273,7 +330,6 @@ add_library(
         src/source/moment_tensor_source.cpp
         src/source/adjoint_source.cpp
         src/source/external.cpp
-        src/source/read_sources.cpp
 )
 
 target_link_libraries(
@@ -292,7 +348,6 @@ target_link_libraries(
 add_library(
         receiver_class
         src/receiver/receiver.cpp
-        src/receiver/read_receiver.cpp
 )
 
 target_link_libraries(
@@ -319,7 +374,8 @@ add_library(
         src/compute/boundaries/boundaries.cpp
         src/compute/fields/fields.cpp
         src/compute/compute_boundary_values.cpp
-        src/compute/compute_assembly.cpp
+        src/compute/assembly/assembly.cpp
+        src/compute/assembly/compute_wavefield.cpp
 )
 
 target_link_libraries(
@@ -359,6 +415,7 @@ add_library(
 target_link_libraries(
         domain
         Kokkos::kokkos
+        enumerations
 )
 
 add_library(coupled_interface
@@ -448,6 +505,29 @@ target_link_libraries(
         IO
 )
 
+add_library(
+        plotter
+        src/plotter/plot_wavefield.cpp
+)
+
+if (NOT VTK_CXX_BUILD)
+        target_compile_definitions(
+                plotter
+                PUBLIC -DNO_VTK
+        )
+
+        target_link_libraries(
+                plotter
+                compute
+        )
+else ()
+        target_link_libraries(
+                plotter
+                compute
+                ${VTK_LIBRARIES}
+        )
+endif()
+
 add_library(
         parameter_reader
         src/parameter_parser/run_setup.cpp
@@ -460,6 +540,7 @@ add_library(
         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
 )
 
@@ -482,6 +563,8 @@ add_executable(
         src/specfem2d.cpp
 )
 
+
+
 target_link_libraries(
         specfem2d
         specfem_mpi
@@ -493,6 +576,7 @@ target_link_libraries(
         parameter_reader
         receiver_class
         writer
+        plotter
         reader
         domain
         coupled_interface

docs/api/IO/Libraries/index.rst

@@ -39,5 +39,7 @@ The snippet below shows how to use these modules to write and read a Kokkos::Vie
 .. toctree::
     :maxdepth: 1
 
+    sources/index
+    mesh/index
     ASCII/index
     HDF5/index

docs/api/IO/Libraries/mesh/index.rst

@@ -0,0 +1,31 @@
+.. _mesh_reader:
+
+Mesh Reader
+===========
+
+
+The below functions are helper functions for the Fortran binary mesh database
+reader. The functions are called in :cpp:func:`specfem::IO::read_mesh`
+in sequential order and faciliate the reading of the mesh database.
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_mesh_database_header
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_coorg_elements
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_properties
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_mesh_database_attenuation
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_material_properties
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_boundaries
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_coupled_interfaces
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_tangential_elements
+
+.. doxygenfunction:: specfem::IO::mesh::impl::fortran::read_axial_elements
+
+Finally, we add tags to the :cpp:struct:`specfem::mesh::mesh` using the
+:cpp:struct:`specfem::mesh::tags` struct. The description of which can be found
+here: :ref:`mesh_tags`.