Issue 150 -- Implements read sources under the IO module.

CMakeLists.txt

@@ -107,14 +107,16 @@ 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/fortran/read_boundaries.cpp
         src/IO/mesh/fortran/read_elements.cpp
         src/IO/mesh/fortran/read_material_properties.cpp
         src/IO/mesh/fortran/read_mesh_database.cpp
         src/IO/mesh/fortran/read_interfaces.cpp
         src/IO/mesh/fortran/read_properties.cpp
+        src/IO/sources/read_sources.cpp
+        # src/IO/receivers/read_receivers.cpp
 )
 
 if (NOT HDF5_CXX_BUILD)
@@ -142,6 +144,11 @@ target_link_libraries(
   mesh
 )
 
+target_link_libraries(
+  IO
+  source_class
+)
+
 add_library(
         point
         src/point/coordinates.cpp
@@ -210,7 +217,6 @@ target_link_libraries(
         Kokkos::kokkos
         specfem_mpi
         # material_class
-        IO
         yaml-cpp
 )
 
@@ -238,16 +244,26 @@ 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(
@@ -271,7 +287,7 @@ add_library(
 
 target_link_libraries(
         source_time_function
-        reader
+        read_seismogram
         Kokkos::kokkos
         point
 )
@@ -283,7 +299,6 @@ 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(

docs/api/IO/Libraries/index.rst

@@ -39,6 +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/index.rst

@@ -2,10 +2,22 @@
 Input/Output modules
 ====================
 
+There are three high-level functions that are essential for the SPECFEM++
+codebase: :cpp:function:`specfem::IO::mesh::read_mesh`,
+:cpp:function:`specfem::IO::sources::read_sources`, and
+:cpp:function:`specfem::IO::receivers::read_receivers`. These functions are
+used to read the mesh, sources and receivers from disk. The undelying
+implementations are not expose to the user. Currently supporte
+formats for the reading of the mesh is binary, and for sources and receivers it
+is yaml.
+
+The slightly-lower level functions to read and write data to and from disk are
+exposed through the following abstractions.
+
 .. toctree::
     :maxdepth: 2
 
-    fortran_io
     Libraries/index
+    fortran_io
     writer/index
     reader/index

docs/api/sources/index.rst

@@ -19,8 +19,3 @@ Types of sources
 
     force_source
     moment_tensor_source
-
-Auxiliary functions
--------------------
-
-.. doxygenfunction:: specfem::sources::read_sources

docs/developer_documentation/tutorials/tutorial1/Chapter11/index.rst

@@ -29,7 +29,7 @@ Finally, we have all the components that we need to put together to create a com
         specfem::mesh::mesh mesh("OUTPUT_FILES/database.bin", mpi);
 
         // Read the sources
-        const auto sources = specfem::sources::read_sources(
+        const auto sources = specfem::IO::sources::read_sources(
                                         "OUTPUT_FILES/sources.yaml",
                                         simulation_params.nsteps,
                                         simulation_params.t0,

docs/developer_documentation/tutorials/tutorial1/Chapter2/index.rst

@@ -61,7 +61,7 @@ Next we will read the sources and receivers generated in :ref:`Chapter1 <Chapter
         const auto simulation_type = specfem::simulation::type::forward;
 
         // Read the sources and receivers
-        const auto sources = specfem::sources::read_sources(sources_filename, nsteps, t0, dt, simulation_type);
+        const auto sources = specfem::IO::sources::read_sources(sources_filename, nsteps, t0, dt, simulation_type);
         const auto receivers = specfem::receivers::read_receivers(receivers_filename, angle);
 
         // Output source information

include/source/read_sources.hpp → include/IO/sources/read_sources.hpp

@@ -2,11 +2,11 @@
 #define _READ_SOURCES_HPP
 
 #include "enumerations/simulation.hpp"
-#include "source.hpp"
+#include "source/interface.hpp"
 #include <memory>
 
 namespace specfem {
-namespace sources {
+namespace IO {
 /**
  * @brief Read sources file written in .yml format
  *
@@ -23,7 +23,7 @@ read_sources(const std::string sources_file, const int nsteps,
              const type_real user_t0, const type_real dt,
              const specfem::simulation::type simulation_type);
 
-} // namespace sources
+} // namespace IO
 } // namespace specfem
 
 #endif

include/enumerations/simulation.hpp

@@ -1,4 +1,5 @@
 #pragma once
+#include <string>
 
 namespace specfem {
 namespace simulation {

include/reader/seismogram.hpp

@@ -15,6 +15,7 @@ namespace reader {
 
 class seismogram : public reader {
 public:
+  seismogram(){};
   seismogram(const char *filename,
              const specfem::enums::seismogram::format type,
              specfem::kokkos::HostView2d<type_real> source_time_function)

include/source/interface.hpp

@@ -5,7 +5,6 @@
 #include "external.hpp"
 #include "force_source.hpp"
 #include "moment_tensor_source.hpp"
-#include "read_sources.hpp"
 #include "source.hpp"
 
 #endif

src/source/read_sources.cpp → src/IO/sources/read_sources.cpp

@@ -1,3 +1,4 @@
+#include "IO/sources/read_sources.hpp"
 #include "source/interface.hpp"
 #include "specfem_setup.hpp"
 #include "utilities/interface.hpp"
@@ -9,9 +10,9 @@
 #include <vector>
 
 std::tuple<std::vector<std::shared_ptr<specfem::sources::source> >, type_real>
-specfem::sources::read_sources(
-    const std::string sources_file, const int nsteps, const type_real user_t0,
-    const type_real dt, const specfem::simulation::type simulation_type) {
+specfem::IO::read_sources(const std::string sources_file, const int nsteps,
+                          const type_real user_t0, const type_real dt,
+                          const specfem::simulation::type simulation_type) {
 
   const bool user_defined_start_time =
       (std::abs(user_t0) > std::numeric_limits<type_real>::epsilon());

src/specfem2d.cpp

@@ -1,13 +1,8 @@
 #include "compute/interface.hpp"
 // #include "coupled_interface/interface.hpp"
 // #include "domain/interface.hpp"
-#include "IO/mesh/fortran/read_boundaries.hpp"
-#include "IO/mesh/fortran/read_elements.hpp"
-#include "IO/mesh/fortran/read_interfaces.hpp"
-#include "IO/mesh/fortran/read_material_properties.hpp"
-#include "IO/mesh/fortran/read_mesh_database.hpp"
-#include "IO/mesh/fortran/read_properties.hpp"
 #include "IO/mesh/read_mesh.hpp"
+#include "IO/sources/read_sources.hpp"
 #include "kokkos_abstractions.h"
 #include "mesh/mesh.hpp"
 #include "parameter_parser/interface.hpp"
@@ -113,7 +108,7 @@ void execute(const std::string &parameter_file, const std::string &default_file,
   // --------------------------------------------------------------
   const int nsteps = setup.get_nsteps();
   const specfem::simulation::type simulation_type = setup.get_simulation_type();
-  auto [sources, t0] = specfem::sources::read_sources(
+  auto [sources, t0] = specfem::IO::read_sources(
       source_filename, nsteps, setup.get_t0(), setup.get_dt(), simulation_type);
   setup.update_t0(t0); // Update t0 in case it was changed
 

tests/unit-tests/CMakeLists.txt

@@ -101,6 +101,7 @@ target_link_libraries(
   mpi_environment
   kokkos_environment
   yaml-cpp
+  IO
   # material_class
   -lpthread -lm
 )
@@ -175,6 +176,7 @@ target_link_libraries(
   kokkos_environment
   yaml-cpp
   compare_arrays
+  IO
   Boost::filesystem
   # material_class
   -lpthread -lm
@@ -192,6 +194,7 @@ target_link_libraries(
   compute
   quadrature
   mpi_environment
+  IO
   kokkos_environment
   yaml-cpp
   Boost::filesystem
@@ -213,6 +216,7 @@ target_link_libraries(
   kokkos_environment
   algorithms
   point
+  IO
   Boost::filesystem
 )
 
@@ -229,6 +233,7 @@ target_link_libraries(
   mpi_environment
   kokkos_environment
   algorithms
+  IO
   Boost::filesystem
   point
 )
@@ -288,6 +293,7 @@ target_link_libraries(
   point
   algorithms
   domain
+  IO
   coupled_interface
   -lpthread -lm
 )

tests/unit-tests/assembly/test_fixture.hpp

@@ -2,6 +2,7 @@
 
 #include "../MPI_environment.hpp"
 #include "IO/mesh/read_mesh.hpp"
+#include "IO/sources/read_sources.hpp"
 #include "compute/assembly/assembly.hpp"
 #include "enumerations/specfem_enums.hpp"
 #include "mesh/mesh.hpp"
@@ -148,7 +149,7 @@ class ASSEMBLY : public ::testing::Test {
           Test.get_databases();
       specfem::mesh::mesh mesh = specfem::IO::read_mesh(database_file, mpi);
 
-      const auto [sources, t0] = specfem::sources::read_sources(
+      const auto [sources, t0] = specfem::IO::read_sources(
           sources_file, 0, 0, 0, specfem::simulation::type::forward);
 
       const auto receivers =

tests/unit-tests/displacement_tests/Newmark/acoustic/newmark_tests.cpp

@@ -69,7 +69,7 @@ TEST(DISPLACEMENT_TESTS, newmark_scheme_tests) {
   //    if start time is not explicitly specified then t0 is determined using
   //    source frequencies and time shift
   auto [sources, t0] =
-      specfem::sources::read_sources(sources_file, setup.get_dt(), mpi);
+      specfem::IO::read_sources(sources_file, setup.get_dt(), mpi);
 
   // Generate compute structs to be used by the solver
   specfem::compute::compute compute(mesh.coorg, mesh.material_ind.knods, gllx,

tests/unit-tests/displacement_tests/Newmark/elastic/newmark_tests.cpp

@@ -69,7 +69,7 @@ TEST(DISPLACEMENT_TESTS, newmark_scheme_tests) {
   //    if start time is not explicitly specified then t0 is determined using
   //    source frequencies and time shift
   auto [sources, t0] =
-      specfem::sources::read_sources(sources_file, setup.get_dt(), mpi);
+      specfem::IO::read_sources(sources_file, setup.get_dt(), mpi);
 
   // Generate compute structs to be used by the solver
   specfem::compute::compute compute(mesh.coorg, mesh.material_ind.knods, gllx,

tests/unit-tests/displacement_tests/Newmark/newmark_tests.cpp

@@ -2,6 +2,7 @@
 #include "../../MPI_environment.hpp"
 #include "../../utilities/include/interface.hpp"
 #include "IO/mesh/read_mesh.hpp"
+#include "IO/sources/read_sources.hpp"
 #include "compute/interface.hpp"
 #include "constants.hpp"
 #include "domain/domain.hpp"
@@ -182,7 +183,7 @@ TEST(DISPLACEMENT_TESTS, newmark_scheme_tests) {
     // Read sources
     //    if start time is not explicitly specified then t0 is determined using
     //    source frequencies and time shift
-    auto [sources, t0] = specfem::sources::read_sources(
+    auto [sources, t0] = specfem::IO::read_sources(
         sources_file, nsteps, setup.get_t0(), dt, setup.get_simulation_type());
 
     for (auto &source : sources) {

tests/unit-tests/domain/acoustic/rmass_inverse_tests.cpp

@@ -65,7 +65,7 @@ TEST(DOMAIN_TESTS, rmass_inverse_elastic_test) {
   // Read sources
   //    if start time is not explicitly specified then t0 is determined using
   //    source frequencies and time shift
-  auto [sources, t0] = specfem::sources::read_sources(sources_file, 1e-5, mpi);
+  auto [sources, t0] = specfem::IO::read_sources(sources_file, 1e-5, mpi);
 
   // Generate compute structs to be used by the solver
   specfem::compute::compute compute(mesh.coorg, mesh.material_ind.knods, gllx,

tests/unit-tests/domain/elastic/rmass_inverse_tests.cpp

@@ -65,7 +65,7 @@ TEST(DOMAIN_TESTS, rmass_inverse_elastic_test) {
   // Read sources
   //    if start time is not explicitly specified then t0 is determined using
   //    source frequencies and time shift
-  auto [sources, t0] = specfem::sources::read_sources(sources_file, 1e-5, mpi);
+  auto [sources, t0] = specfem::IO::read_sources(sources_file, 1e-5, mpi);
 
   // Generate compute structs to be used by the solver
   specfem::compute::compute compute(mesh.coorg, mesh.material_ind.knods, gllx,

tests/unit-tests/source/source_location_tests.cpp

@@ -167,7 +167,7 @@ TEST(SOURCE_LOCATION_TESTS, compute_source_locations) {
 
   // read sources file
   auto [sources, t0] =
-      specfem::sources::read_sources(test_config.sources_file, 1.0, mpi);
+      specfem::IO::read_sources(test_config.sources_file, 1.0, mpi);
 
   // setup compute struct for future use
   specfem::compute::compute compute(mesh.coorg, mesh.material_ind.knods, gllx,