Merge pull request #348 from PrincetonUniversity/issue-343

Property reader / writer

CMakeLists.txt

@@ -10,7 +10,7 @@ option(BUILD_TESTS "Tests included" OFF)
 option(BUILD_EXAMPLES "Examples included" ON)
 option(ENABLE_SIMD "Enable SIMD" OFF)
 option(ENABLE_PROFILING "Enable profiling" OFF)
-option(SPECFEMPP_ENABLE_PYTHON "Enable Python binding" OFF)
+option(SPECFEMPP_BINDING_PYTHON "Enable Python binding" OFF)
 # set(CMAKE_BUILD_TYPE Release)
 set(CHUNK_SIZE 32)
 set(NUM_CHUNKS 1)
@@ -25,7 +25,7 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 # For external modules that need to be built suppress build output
 set(FETCHCONTENT_QUIET TRUE)
 
-if (SPECFEMPP_ENABLE_PYTHON)
+if (SPECFEMPP_BINDING_PYTHON)
     message("-- Adding -fPIC flag for Python binding.")
     if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
             set(CMAKE_CXX_FLAGS "-fp-model=precise -fPIC")
@@ -36,15 +36,15 @@ if (SPECFEMPP_ENABLE_PYTHON)
     else()
             set(CMAKE_CXX_FLAGS "-fPIC")
     endif()
-else (SPECFEMPP_ENABLE_PYTHON)
+else (SPECFEMPP_BINDING_PYTHON)
     if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
             set(CMAKE_CXX_FLAGS "-fp-model=precise")
     elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
             message("-- Detected Intel classic compiler which will be deprecated soon.")
             message("-- It is recommended you use IntelLLVM compiler.")
             set(CMAKE_CXX_FLAGS "-diag-disable=10441 -fp-model=precise")
     endif()
-endif (SPECFEMPP_ENABLE_PYTHON)
+endif (SPECFEMPP_BINDING_PYTHON)
 
 # Check if MacOS
 if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
@@ -341,7 +341,7 @@ target_link_libraries(
 
 add_library(
         read_seismogram
-        src/reader/seismogram.cpp
+        src/IO/seismogram/reader.cpp
 )
 
 target_link_libraries(
@@ -351,7 +351,8 @@ target_link_libraries(
 
 add_library(
         reader
-        src/reader/wavefield.cpp
+        src/IO/wavefield/reader.cpp
+        src/IO/property/reader.cpp
 )
 
 target_link_libraries(
@@ -535,9 +536,10 @@ target_link_libraries(
 
 add_library(
         writer
-        src/writer/seismogram.cpp
-        src/writer/wavefield.cpp
-        src/writer/kernel.cpp
+        src/IO/seismogram/writer.cpp
+        src/IO/wavefield/writer.cpp
+        src/IO/kernel/writer.cpp
+        src/IO/property/writer.cpp
 )
 
 target_link_libraries(
@@ -589,6 +591,7 @@ add_library(
         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(
@@ -674,7 +677,7 @@ if (SPECFEMPP_USE_SKBUILD AND EXISTS ${SKBUILD_SCRIPTS_DIR})
     install(FILES ${CMAKE_BINARY_DIR}/xmeshfem2D DESTINATION ${SKBUILD_SCRIPTS_DIR} PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE)
 endif ()
 
-if (SPECFEMPP_ENABLE_PYTHON)
+if (SPECFEMPP_BINDING_PYTHON)
     find_package(Python REQUIRED COMPONENTS Interpreter Development.Module)
     find_package(pybind11 CONFIG REQUIRED)
     python_add_library(_core MODULE src/specfem2d.cpp WITH_SOABI)
@@ -689,6 +692,7 @@ if (SPECFEMPP_ENABLE_PYTHON)
         parameter_reader
         receiver_class
         writer
+        plotter
         reader
         domain
         medium
@@ -698,7 +702,7 @@ if (SPECFEMPP_ENABLE_PYTHON)
         ${BOOST_LIBS}
         pybind11::headers
     )
-    target_compile_definitions(_core PRIVATE SPECFEMPP_ENABLE_PYTHON)
+    target_compile_definitions(_core PRIVATE SPECFEMPP_BINDING_PYTHON)
     target_compile_definitions(_core PRIVATE VERSION_INFO=${PROJECT_VERSION})
     install(TARGETS _core DESTINATION specfempp_core)
-endif (SPECFEMPP_ENABLE_PYTHON)
+endif (SPECFEMPP_BINDING_PYTHON)

docs/api/IO/index.rst

@@ -12,9 +12,9 @@ formats for the reading of the mesh is binary, and for sources and receivers it
 is yaml.
 
 In addition to these basic read functions, there are also the two
-reader and writer classes, :cpp:class:`specfem::reader::wavefield` and
-:cpp:class:`specfem::writer::wavefield`, which support both HDF5 and ASCII I/O.
-And, to write seismograms, we can use :cpp:class:`specfem::writer::seismogram`.
+reader and writer classes, :cpp:class:`specfem::IO::wavefield_reader` and
+:cpp:class:`specfem::IO::wavefield_writer`, which support both HDF5 and ASCII I/O.
+And, to write seismograms, we can use :cpp:class:`specfem::IO::seismogram_writer`.
 Seismogram I/O is only supported in ASCII format thus far.
 
 The slightly-lower level functionality to read and write data to and from disk

docs/api/IO/reader/index.rst

@@ -4,7 +4,7 @@ Reader
 
 The ``reader`` class provides interfaces to read simulation data as output files.
 
-.. doxygenclass:: specfem::writer::writer
+.. doxygenclass:: specfem::IO::writer
 
 Types of readers
 ----------------

docs/api/IO/reader/wavefield.rst

@@ -4,5 +4,5 @@
 Wavefield Reader
 ================
 
-.. doxygenclass:: specfem::reader::wavefield
+.. doxygenclass:: specfem::IO::wavefield_reader
     :members:

docs/api/IO/writer/index.rst

@@ -4,7 +4,7 @@ Writer
 
 The ``writer`` class provides interfaces to write simulation data as output files.
 
-.. doxygenclass:: specfem::writer::writer
+.. doxygenclass:: specfem::IO::writer
    :members:
 
 Types of writers

docs/api/IO/writer/seismogram_writer.rst

@@ -4,5 +4,5 @@ Seismogram Writer
 
 The ``seismogram`` provides methods to write seismograms to a file.
 
-.. doxygenclass:: specfem::writer::seismogram
+.. doxygenclass:: specfem::IO::seismogram_writer
     :members:

docs/api/IO/writer/wavefield.rst

@@ -4,5 +4,5 @@
 Wavefield Writer
 ================
 
-.. doxygenclass:: specfem::writer::wavefield
+.. doxygenclass:: specfem::IO::wavefield_writer
     :members:

fortran/meshfem3d/setup/precision.h

@@ -18,9 +18,9 @@ either version 3 of the License,
 !
 ! You should have received a copy of the GNU General Public License along
 ! with this program;
-if
-not, write to the Free Software Foundation, Inc., !51 Franklin Street,
-    Fifth Floor, Boston,
+if not
+, write to the Free Software Foundation, Inc., !51 Franklin Street, Fifth Floor,
+    Boston,
     MA 02110 - 1301 USA.! != == == == == == == == == == == == == == == == == ==
             == == == == == == == == == == == == == == == == ==
 

include/writer/kernel.hpp → include/IO/kernel/writer.hpp

@@ -1,18 +1,17 @@
-#ifndef _SPECFEM_WRITER_KERNEL_HPP
-#define _SPECFEM_WRITER_KERNEL_HPP
+#pragma once
 
 #include "compute/interface.hpp"
 #include "enumerations/interface.hpp"
-#include "writer/writer.hpp"
+#include "IO/writer.hpp"
 
 namespace specfem {
-namespace writer {
+namespace IO {
 /**
  * @brief Writer to output misfit kernel data to disk
  *
  * @tparam OutputLibrary Library to use for output (HDF5, ASCII, etc.)
  */
-template <typename OutputLibrary> class kernel : public writer {
+template <typename OutputLibrary> class kernel_writer : public writer {
 public:
   /**
    * @name Constructors
@@ -26,21 +25,16 @@ template <typename OutputLibrary> class kernel : public writer {
    * @param output_folder Path to output location (will be an .h5 file if using
    * HDF5, and a folder if using ASCII)
    */
-  kernel(const specfem::compute::assembly &assembly,
-         const std::string output_folder);
+  kernel_writer(const std::string output_folder);
 
   /**
    * @brief write the kernel data to disk
    *
    */
-  void write() override;
+  void write(specfem::compute::assembly &assembly) override;
 
 private:
-  std::string output_folder;         ///< Path to output folder
-  specfem::compute::mesh mesh;       ///< Mesh object
-  specfem::compute::kernels kernels; ///< Kernels object
+  std::string output_folder; ///< Path to output folder
 };
-} // namespace writer
+} // namespace IO
 } // namespace specfem
-
-#endif /* _SPECFEM_WRITER_KERNEL_HPP */

include/writer/kernel.tpp → include/IO/kernel/writer.tpp

@@ -1,22 +1,21 @@
-#ifndef _SPECFEM_WRITER_KERNEL_TPP
-#define _SPECFEM_WRITER_KERNEL_TPP
+#pragma once
 
 #include "compute/assembly/assembly.hpp"
 #include "enumerations/dimension.hpp"
 #include "enumerations/medium.hpp"
 #include "kokkos_abstractions.h"
 #include "point/kernels.hpp"
-#include "writer/kernel.hpp"
+#include "IO/kernel/writer.hpp"
 #include <Kokkos_Core.hpp>
 
 template <typename OutputLibrary>
-specfem::writer::kernel<OutputLibrary>::kernel(
-    const specfem::compute::assembly &assembly, const std::string output_folder)
-    : output_folder(output_folder), mesh(assembly.mesh),
-      kernels(assembly.kernels) {}
+specfem::IO::kernel_writer<OutputLibrary>::kernel_writer(const std::string output_folder)
+    : output_folder(output_folder) {}
 
 template <typename OutputLibrary>
-void specfem::writer::kernel<OutputLibrary>::write() {
+void specfem::IO::kernel_writer<OutputLibrary>::write(specfem::compute::assembly &assembly) {
+  const auto &mesh = assembly.mesh;
+  auto &kernels = assembly.kernels;
 
   using DomainView =
       Kokkos::View<type_real ***, Kokkos::LayoutLeft, Kokkos::HostSpace>;
@@ -167,7 +166,7 @@ void specfem::writer::kernel<OutputLibrary>::write() {
           const specfem::point::index<specfem::dimension::type::dim2> index(
               ispec, iz, ix);
           specfem::point::kernels<specfem::dimension::type::dim2,
-                                  specfem::element::medium_tag::elastic,
+                                  specfem::element::medium_tag::acoustic,
                                   specfem::element::property_tag::isotropic,
                                   false>
               point_kernels;
@@ -195,5 +194,3 @@ void specfem::writer::kernel<OutputLibrary>::write() {
   std::cout << "Kernels written to " << output_folder << "/Kernels"
             << std::endl;
 }
-
-#endif /* _SPECFEM_WRITER_KERNEL_TPP */

include/IO/property/reader.hpp

@@ -0,0 +1,42 @@
+#pragma once
+
+#include "compute/interface.hpp"
+#include "enumerations/interface.hpp"
+#include "IO/reader.hpp"
+
+namespace specfem {
+namespace IO {
+/**
+ * @brief Read model property
+ *
+ * @tparam InputLibrary Library to use for output (HDF5, ASCII, etc.)
+ */
+template <typename InputLibrary> class property_reader : public reader {
+public:
+  /**
+   * @name Constructors
+   *
+   */
+  ///@{
+  /**
+   * @brief Construct a reader object
+   *
+   * @param output_folder Path to input location (will be an .h5 file if using
+   * HDF5, and a folder if using ASCII)
+   */
+  property_reader(const std::string input_folder);
+
+  /**
+   * @brief read the property from disk
+   *
+   * @param assembly SPECFEM++ assembly
+   *
+   */
+  void read(specfem::compute::assembly &assembly) override;
+
+private:
+  std::string input_folder;                ///< Path to output folder
+  specfem::compute::properties properties; ///< Properties object
+};
+} // namespace IO
+} // namespace specfem

include/IO/property/reader.tpp

@@ -0,0 +1,57 @@
+#pragma once
+
+#include "compute/assembly/assembly.hpp"
+#include "enumerations/dimension.hpp"
+#include "enumerations/medium.hpp"
+#include "kokkos_abstractions.h"
+#include "point/properties.hpp"
+#include "IO/property/reader.hpp"
+#include <Kokkos_Core.hpp>
+
+template <typename InputLibrary>
+specfem::IO::property_reader<InputLibrary>::property_reader(const std::string input_folder): input_folder(input_folder) {}
+
+template <typename InputLibrary>
+void specfem::IO::property_reader<InputLibrary>::read(specfem::compute::assembly &assembly) {
+  auto &properties = assembly.properties;
+
+  using DomainView =
+      Kokkos::View<type_real ***, Kokkos::LayoutLeft, Kokkos::HostSpace>;
+
+  typename InputLibrary::File file(input_folder + "/Properties");
+
+  {
+    typename InputLibrary::Group elastic = file.openGroup("/ElasticIsotropic");
+
+    elastic.openDataset("rho", properties.elastic_isotropic.h_rho).read();
+    elastic.openDataset("mu", properties.elastic_isotropic.h_mu).read();
+    elastic.openDataset("lambdaplus2mu", properties.elastic_isotropic.h_lambdaplus2mu).read();
+  }
+
+  {
+    typename InputLibrary::Group elastic = file.openGroup("/ElasticAnisotropic");
+
+    elastic.openDataset("rho", properties.elastic_anisotropic.h_rho).read();
+    elastic.openDataset("c11", properties.elastic_anisotropic.h_c11).read();
+    elastic.openDataset("c13", properties.elastic_anisotropic.h_c13).read();
+    elastic.openDataset("c15", properties.elastic_anisotropic.h_c15).read();
+    elastic.openDataset("c33", properties.elastic_anisotropic.h_c33).read();
+    elastic.openDataset("c35", properties.elastic_anisotropic.h_c35).read();
+    elastic.openDataset("c55", properties.elastic_anisotropic.h_c55).read();
+    elastic.openDataset("c12", properties.elastic_anisotropic.h_c12).read();
+    elastic.openDataset("c23", properties.elastic_anisotropic.h_c23).read();
+    elastic.openDataset("c25", properties.elastic_anisotropic.h_c25).read();
+  }
+
+  {
+    typename InputLibrary::Group acoustic = file.openGroup("/Acoustic");
+
+    acoustic.openDataset("rho_inverse", properties.acoustic_isotropic.h_rho_inverse).read();
+    acoustic.openDataset("kappa", properties.acoustic_isotropic.h_kappa).read();
+  }
+
+  std::cout << "Properties read from " << input_folder << "/Properties"
+            << std::endl;
+
+  properties.copy_to_device();
+}