Merge pull request #371 from PrincetonUniversity/issue-370

Refactor reader / writer to IO namespace

CMakeLists.txt

@@ -341,7 +341,7 @@ target_link_libraries(
 
 add_library(
         read_seismogram
-        src/reader/seismogram.cpp
+        src/IO/seismogram/reader.cpp
 )
 
 target_link_libraries(
@@ -351,8 +351,8 @@ target_link_libraries(
 
 add_library(
         reader
-        src/reader/wavefield.cpp
-        src/reader/property.cpp
+        src/IO/wavefield/reader.cpp
+        src/IO/property/reader.cpp
 )
 
 target_link_libraries(
@@ -536,10 +536,10 @@ target_link_libraries(
 
 add_library(
         writer
-        src/writer/seismogram.cpp
-        src/writer/wavefield.cpp
-        src/writer/kernel.cpp
-        src/writer/property.cpp
+        src/IO/seismogram/writer.cpp
+        src/IO/wavefield/writer.cpp
+        src/IO/kernel/writer.cpp
+        src/IO/property/writer.cpp
 )
 
 target_link_libraries(

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
@@ -26,7 +25,7 @@ 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 std::string output_folder);
+  kernel_writer(const std::string output_folder);
 
   /**
    * @brief write the kernel data to disk
@@ -37,7 +36,5 @@ template <typename OutputLibrary> class kernel : public writer {
 private:
   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

@@ -1,20 +1,19 @@
-#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 std::string output_folder)
+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(specfem::compute::assembly &assembly) {
+void specfem::IO::kernel_writer<OutputLibrary>::write(specfem::compute::assembly &assembly) {
   const auto &mesh = assembly.mesh;
   auto &kernels = assembly.kernels;
 
@@ -195,5 +194,3 @@ void specfem::writer::kernel<OutputLibrary>::write(specfem::compute::assembly &a
   std::cout << "Kernels written to " << output_folder << "/Kernels"
             << std::endl;
 }
-
-#endif /* _SPECFEM_WRITER_KERNEL_TPP */

include/reader/property.hpp → include/IO/property/reader.hpp

@@ -2,16 +2,16 @@
 
 #include "compute/interface.hpp"
 #include "enumerations/interface.hpp"
-#include "reader/reader.hpp"
+#include "IO/reader.hpp"
 
 namespace specfem {
-namespace reader {
+namespace IO {
 /**
  * @brief Read model property
  *
  * @tparam InputLibrary Library to use for output (HDF5, ASCII, etc.)
  */
-template <typename InputLibrary> class property : public reader {
+template <typename InputLibrary> class property_reader : public reader {
 public:
   /**
    * @name Constructors
@@ -24,7 +24,7 @@ template <typename InputLibrary> class property : public reader {
    * @param output_folder Path to input location (will be an .h5 file if using
    * HDF5, and a folder if using ASCII)
    */
-  property(const std::string input_folder);
+  property_reader(const std::string input_folder);
 
   /**
    * @brief read the property from disk
@@ -38,5 +38,5 @@ template <typename InputLibrary> class property : public reader {
   std::string input_folder;                ///< Path to output folder
   specfem::compute::properties properties; ///< Properties object
 };
-} // namespace reader
+} // namespace IO
 } // namespace specfem

include/reader/property.tpp → include/IO/property/reader.tpp

@@ -5,14 +5,14 @@
 #include "enumerations/medium.hpp"
 #include "kokkos_abstractions.h"
 #include "point/properties.hpp"
-#include "reader/property.hpp"
+#include "IO/property/reader.hpp"
 #include <Kokkos_Core.hpp>
 
 template <typename InputLibrary>
-specfem::reader::property<InputLibrary>::property(const std::string input_folder): input_folder(input_folder) {}
+specfem::IO::property_reader<InputLibrary>::property_reader(const std::string input_folder): input_folder(input_folder) {}
 
 template <typename InputLibrary>
-void specfem::reader::property<InputLibrary>::read(specfem::compute::assembly &assembly) {
+void specfem::IO::property_reader<InputLibrary>::read(specfem::compute::assembly &assembly) {
   auto &properties = assembly.properties;
 
   using DomainView =

include/writer/property.hpp → include/IO/property/writer.hpp

@@ -2,16 +2,16 @@
 
 #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 model property data to disk
  *
  * @tparam OutputLibrary Library to use for output (HDF5, ASCII, etc.)
  */
-template <typename OutputLibrary> class property : public writer {
+template <typename OutputLibrary> class property_writer : public writer {
 public:
   /**
    * @name Constructors
@@ -24,7 +24,7 @@ template <typename OutputLibrary> class property : public writer {
    * @param output_folder Path to output location (will be an .h5 file if using
    * HDF5, and a folder if using ASCII)
    */
-  property(const std::string output_folder);
+  property_writer(const std::string output_folder);
 
   /**
    * @brief write the property data to disk

include/writer/property.tpp → include/IO/property/writer.tpp

@@ -5,15 +5,15 @@
 #include "enumerations/medium.hpp"
 #include "kokkos_abstractions.h"
 #include "point/properties.hpp"
-#include "writer/property.hpp"
+#include "IO/property/writer.hpp"
 #include <Kokkos_Core.hpp>
 
 template <typename OutputLibrary>
-specfem::writer::property<OutputLibrary>::property(const std::string output_folder)
+specfem::IO::property_writer<OutputLibrary>::property_writer(const std::string output_folder)
     : output_folder(output_folder) {}
 
 template <typename OutputLibrary>
-void specfem::writer::property<OutputLibrary>::write(specfem::compute::assembly &assembly) {
+void specfem::IO::property_writer<OutputLibrary>::write(specfem::compute::assembly &assembly) {
   const auto &mesh = assembly.mesh;
   auto &properties = assembly.properties;
 

include/reader/reader.hpp → include/IO/reader.hpp

@@ -7,7 +7,7 @@ class assembly;
 } // namespace specfem
 
 namespace specfem {
-namespace reader {
+namespace IO {
 /**
  * @brief Base reader class
  *
@@ -22,5 +22,5 @@ class reader {
    */
   virtual void read(specfem::compute::assembly &assembly) = 0;
 };
-} // namespace reader
+} // namespace IO
 } // namespace specfem

include/reader/seismogram.hpp → include/IO/seismogram/reader.hpp

@@ -2,7 +2,7 @@
 #define SPECFEM_READER_SEISMOGRAM_HPP
 
 #include "enumerations/specfem_enums.hpp"
-#include "reader/reader.hpp"
+#include "IO/reader.hpp"
 
 namespace specfem {
 namespace forcing_function {
@@ -11,17 +11,17 @@ class external;
 } // namespace specfem
 
 namespace specfem {
-namespace reader {
+namespace IO {
 
-class seismogram {
+class seismogram_reader {
 public:
-  seismogram(){};
-  seismogram(const char *filename,
+  seismogram_reader(){};
+  seismogram_reader(const char *filename,
              const specfem::enums::seismogram::format type,
              specfem::kokkos::HostView2d<type_real> source_time_function)
       : filename(filename), type(type),
         source_time_function(source_time_function) {}
-  seismogram(const std::string &filename,
+  seismogram_reader(const std::string &filename,
              const specfem::enums::seismogram::format type,
              specfem::kokkos::HostView2d<type_real> source_time_function)
       : filename(filename), type(type),
@@ -34,7 +34,7 @@ class seismogram {
   specfem::enums::seismogram::format type;
   specfem::kokkos::HostView2d<type_real> source_time_function;
 };
-} // namespace reader
+} // namespace IO
 } // namespace specfem
 
 #endif /* SPECFEM_READER_SEISMOGRAM_HPP */

include/writer/seismogram.hpp → include/IO/seismogram/writer.hpp

@@ -1,20 +1,19 @@
-#ifndef _SEISMOGRAM_WRITER_HPP
-#define _SEISMOGRAM_WRITER_HPP
+#pragma once
 
 #include "compute/interface.hpp"
 #include "constants.hpp"
 #include "receiver/interface.hpp"
 #include "specfem_setup.hpp"
-#include "writer.hpp"
+#include "IO/writer.hpp"
 #include <vector>
 
 namespace specfem {
-namespace writer {
+namespace IO {
 /**
  * @brief Seismogram writer class to write seismogram to a file
  *
  */
-class seismogram : public writer {
+class seismogram_writer : public writer {
 
 public:
   /**
@@ -27,7 +26,7 @@ class seismogram : public writer {
    * @param nstep_between_samples number of timesteps between seismogram
    * sampling (seismogram sampling frequency)
    */
-  seismogram(const specfem::enums::seismogram::format type,
+  seismogram_writer(const specfem::enums::seismogram::format type,
              const std::string output_folder, const type_real dt,
              const type_real t0, const int nstep_between_samples)
       : type(type), output_folder(output_folder), dt(dt), t0(t0),
@@ -51,7 +50,5 @@ class seismogram : public writer {
                              ///< sampling (seismogram sampling frequency)
 };
 
-} // namespace writer
+} // namespace IO
 } // namespace specfem
-
-#endif