Merge pull request #196 from PrincetonUniversity/issue-192

moved read_mesh/sources/receivers to the IO/interface.hpp

CMakeLists.txt

@@ -129,15 +129,15 @@ add_library(
         src/IO/fortranio/fortran_io.cpp
         src/IO/HDF5/native_type.cpp
         # src/IO/ASCII/native_type.cpp
-        src/IO/mesh/read_mesh.cpp
+        src/IO/sources.cpp
+        src/IO/receivers.cpp
+        src/IO/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)
@@ -163,15 +163,7 @@ endif()
 target_link_libraries(
   IO
   mesh
-)
-
-target_link_libraries(
-  IO
   source_class
-)
-
-target_link_libraries(
-  IO
   receiver_class
 )
 

include/IO/interface.hpp

@@ -0,0 +1,56 @@
+#pragma once
+
+#include "enumerations/simulation.hpp"
+#include "mesh/mesh.hpp"
+#include "receiver/interface.hpp"
+#include "source/interface.hpp"
+#include "specfem_mpi/interface.hpp"
+#include "specfem_setup.hpp"
+
+namespace specfem {
+
+namespace IO {
+
+/**
+ * @brief Construct a mesh object from a Fortran binary database file
+ *
+ * @param filename Fortran binary database filename
+ * @param mpi pointer to MPI object to manage communication
+ * @return specfem::mesh::mesh Specfem mesh object
+ *
+ */
+specfem::mesh::mesh read_mesh(const std::string filename,
+                              const specfem::MPI::MPI *mpi);
+
+/**
+ * @brief Read receiver station file
+ *
+ * Parse receiver stations file and create a vector of
+ * specfem::source::source * object
+ *
+ * @param stations_file Stations file describing receiver locations
+ * @param angle Angle of the receivers
+ * @return std::vector<specfem::receivers::receiver *> vector of instantiated
+ * receiver objects
+ */
+std::vector<std::shared_ptr<specfem::receivers::receiver> >
+read_receivers(const std::string stations_file, const type_real angle);
+
+/**
+ * @brief Read sources file written in .yml format
+ *
+ * Parse source specification file written in yaml format and create a vector of
+ * specfem::source::source * object
+ *
+ * @param sources_file Name of the yml file
+ * @param mpi Pointer to specfem MPI object
+ * @return std::vector<specfem::sources::source *> vector of instantiated source
+ * objects
+ */
+std::tuple<std::vector<std::shared_ptr<specfem::sources::source> >, type_real>
+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 IO
+} // namespace specfem

src/IO/mesh/read_mesh.cpp → src/IO/mesh.cpp

@@ -1,5 +1,7 @@
-#include "IO/mesh/read_mesh.hpp"
+// Internal Includes
+#include "mesh/mesh.hpp"
 #include "IO/fortranio/interface.hpp"
+#include "IO/interface.hpp"
 #include "IO/mesh/impl/fortran/read_boundaries.hpp"
 #include "IO/mesh/impl/fortran/read_elements.hpp"
 #include "IO/mesh/impl/fortran/read_interfaces.hpp"
@@ -9,10 +11,11 @@
 #include "enumerations/specfem_enums.hpp"
 #include "kokkos_abstractions.h"
 #include "material/material.hpp"
-#include "mesh/mesh.hpp"
 #include "mesh/tags/tags.hpp"
 #include "specfem_mpi/interface.hpp"
 #include "specfem_setup.hpp"
+
+// External/Standard Libraries
 #include <Kokkos_Core.hpp>
 #include <algorithm>
 #include <limits>

src/IO/receivers/read_receivers.cpp → src/IO/receivers.cpp

@@ -1,8 +1,11 @@
-#include "IO/receivers/read_receivers.hpp"
+// Internal Includes
+#include "IO/interface.hpp"
 #include "receiver/interface.hpp"
 #include "specfem_setup.hpp"
 #include "utilities/interface.hpp"
 #include "yaml-cpp/yaml.h"
+
+// External Includes
 #include <boost/tokenizer.hpp>
 #include <fstream>
 #include <string>

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

@@ -1,8 +1,11 @@
-#include "IO/sources/read_sources.hpp"
+// Internal Includes
+#include "IO/interface.hpp"
 #include "source/interface.hpp"
 #include "specfem_setup.hpp"
 #include "utilities/interface.hpp"
 #include "yaml-cpp/yaml.h"
+
+// External Includes
 #include <boost/tokenizer.hpp>
 #include <fstream>
 #include <memory>

src/specfem2d.cpp

@@ -1,9 +1,7 @@
 #include "compute/interface.hpp"
 // #include "coupled_interface/interface.hpp"
 // #include "domain/interface.hpp"
-#include "IO/mesh/read_mesh.hpp"
-#include "IO/receivers/read_receivers.hpp"
-#include "IO/sources/read_sources.hpp"
+#include "IO/interface.hpp"
 #include "kokkos_abstractions.h"
 #include "mesh/mesh.hpp"
 #include "parameter_parser/interface.hpp"

tests/unit-tests/algorithms/interpolate_function.cpp

@@ -1,4 +1,4 @@
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "Kokkos_Environment.hpp"
 #include "MPI_environment.hpp"
 #include "algorithms/interpolate.hpp"

tests/unit-tests/algorithms/locate.cpp

@@ -1,4 +1,4 @@
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "Kokkos_Environment.hpp"
 #include "MPI_environment.hpp"
 #include "algorithms/locate_point.hpp"

tests/unit-tests/assembly/test_fixture/test_fixture.cpp

@@ -1,7 +1,5 @@
 #include "test_fixture.hpp"
-#include "IO/mesh/read_mesh.hpp"
-#include "IO/receivers/read_receivers.hpp"
-#include "IO/sources/read_sources.hpp"
+#include "IO/interface.hpp"
 #include "test_fixture.tpp"
 
 // ------------------------------------------------------------------------

tests/unit-tests/assembly/test_fixture/test_fixture.hpp

@@ -1,6 +1,7 @@
 #pragma once
 
 #include "../../MPI_environment.hpp"
+#include "IO/interface.hpp"
 #include "compute/assembly/assembly.hpp"
 #include "enumerations/specfem_enums.hpp"
 #include "mesh/mesh.hpp"

tests/unit-tests/compute/acoustic/compute_properties_tests.cpp

@@ -1,7 +1,7 @@
 #include "../../Kokkos_Environment.hpp"
 #include "../../MPI_environment.hpp"
 #include "../../utilities/include/interface.hpp"
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "material/interface.hpp"
 #include "mesh/mesh.hpp"

tests/unit-tests/compute/coupled_interfaces/coupled_interfaces_tests.cpp

@@ -1,7 +1,7 @@
 #include "../../Kokkos_Environment.hpp"
 #include "../../MPI_environment.hpp"
 #include "../../utilities/include/interface.hpp"
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "edge/interface.hpp"
 #include "material/interface.hpp"

tests/unit-tests/compute/elastic/compute_properties_tests.cpp

@@ -1,7 +1,7 @@
 #include "../../Kokkos_Environment.hpp"
 #include "../../MPI_environment.hpp"
 #include "../../utilities/include/interface.hpp"
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "mesh/mesh.hpp"
 #include "quadrature/interface.hpp"

tests/unit-tests/compute/index/compute_tests.cpp

@@ -1,7 +1,7 @@
 #include "../../Kokkos_Environment.hpp"
 #include "../../MPI_environment.hpp"
 #include "../../utilities/include/interface.hpp"
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "mesh/mesh.hpp"
 #include "quadrature/interface.hpp"

tests/unit-tests/compute/partial_derivatives/compute_partial_derivatives_tests.cpp

@@ -1,7 +1,7 @@
 #include "../../Kokkos_Environment.hpp"
 #include "../../MPI_environment.hpp"
 #include "../../utilities/include/interface.hpp"
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "quadrature/interface.hpp"
 #include "yaml-cpp/yaml.h"

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

@@ -1,7 +1,7 @@
 #include "../../../Kokkos_Environment.hpp"
 #include "../../../MPI_environment.hpp"
 #include "../../../utilities/include/compare_array.h"
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "constants.hpp"
 #include "domain/interface.hpp"

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

@@ -1,7 +1,7 @@
 #include "../../../Kokkos_Environment.hpp"
 #include "../../../MPI_environment.hpp"
 #include "../../../utilities/include/compare_array.h"
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "constants.hpp"
 #include "domain/interface.hpp"

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

@@ -1,9 +1,7 @@
 #include "../../Kokkos_Environment.hpp"
 #include "../../MPI_environment.hpp"
 #include "../../utilities/include/interface.hpp"
-#include "IO/mesh/read_mesh.hpp"
-#include "IO/receivers/read_receivers.hpp"
-#include "IO/sources/read_sources.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "constants.hpp"
 #include "domain/domain.hpp"

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

@@ -1,7 +1,7 @@
 #include "../../Kokkos_Environment.hpp"
 #include "../../MPI_environment.hpp"
 #include "../../utilities/include/compare_array.h"
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "constants.hpp"
 #include "domain/interface.hpp"

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

@@ -1,7 +1,7 @@
 #include "../../Kokkos_Environment.hpp"
 #include "../../MPI_environment.hpp"
 #include "../../utilities/include/compare_array.h"
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "constants.hpp"
 #include "domain/interface.hpp"

tests/unit-tests/domain/rmass_inverse_tests.cpp

@@ -1,7 +1,7 @@
 #include "../Kokkos_Environment.hpp"
 #include "../MPI_environment.hpp"
 #include "../utilities/include/interface.hpp"
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "constants.hpp"
 #include "domain/domain.hpp"

tests/unit-tests/mesh/mesh_tests.cpp

@@ -1,7 +1,7 @@
 #include "../Kokkos_Environment.hpp"
 #include "../MPI_environment.hpp"
+#include "IO/interface.hpp"
 #include "IO/mesh/impl/fortran/read_mesh_database.hpp"
-#include "IO/mesh/read_mesh.hpp"
 #include "mesh/mesh.hpp"
 #include "yaml-cpp/yaml.h"
 #include <fstream>

tests/unit-tests/seismogram/acoustic/seismogram_tests.cpp

@@ -2,8 +2,7 @@
 #include "../../MPI_environment.hpp"
 // #include "../../utilities/include/compare_array.h"
 #include "IO/fortranio/interface.hpp"
-#include "IO/mesh/read_mesh.hpp"
-#include "IO/receivers/read_receivers.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "constants.hpp"
 #include "domain/domain.hpp"

tests/unit-tests/seismogram/elastic/seismogram_tests.cpp

@@ -2,8 +2,7 @@
 #include "../../MPI_environment.hpp"
 // #include "../../utilities/include/compare_array.h"
 #include "IO/fortranio/interface.hpp"
-#include "IO/mesh/read_mesh.hpp"
-#include "IO/receivers/read_receivers.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "constants.hpp"
 #include "domain/domain.hpp"

tests/unit-tests/source/source_location_tests.cpp

@@ -1,6 +1,6 @@
 #include "../Kokkos_Environment.hpp"
 #include "../MPI_environment.hpp"
-#include "IO/mesh/read_mesh.hpp"
+#include "IO/interface.hpp"
 #include "compute/interface.hpp"
 #include "material/interface.hpp"
 #include "mesh/mesh.hpp"