prepare for H5 serialization

.github/workflows/build-ci.yml

@@ -23,7 +23,7 @@ jobs:
       run: |
         mkdir -p build &&
         pushd build &&
-        cmake -DBUILD_PYTHON=ON -DBUILD_WFC=ON ../ &&
+        cmake -DBUILD_PYTHON=ON -DBUILD_WFC=ON -DBUILD_TESTS=ON ../ &&
         make &&
         popd
 

CMakeLists.txt

@@ -4,10 +4,16 @@ project(eisvogel)
 
 option(BUILD_PYTHON "Build with python support." OFF)
 option(BUILD_WFC "Also build weighting field creator." OFF)
+option(BUILD_TESTS "Build tests." OFF)
 
 add_subdirectory(cmake)
 add_subdirectory(src)
+add_subdirectory(examples)
+
 if(BUILD_PYTHON)
     add_subdirectory(cpython)
 endif(BUILD_PYTHON)
-add_subdirectory(examples)
+
+if(BUILD_TESTS)
+    add_subdirectory(tests)
+endif(BUILD_TESTS)

README.md

@@ -36,6 +36,12 @@ and to also build the components for the calculation of the Green's function do
 cmake -DBUILD_WFC=ON ..
 ```
 
+If you want to build the C++ unit tests, add
+
+```
+cmake -DBUILD_TESTS=ON ..
+```
+
 ## More information
 
 - P. Windischhofer, C. Welling, C. Deaconu, "Eisvogel: Exact and efficient calculations of radio emissions from in-ice neutrino showers", PoS(ICRC2023)

include/Eisvogel/H5Serialization.hh

@@ -0,0 +1,34 @@
+#ifndef __H5SERIALIZATION_HH
+#define __H5SERIALIZATION_HH
+
+#include "hdf5.h"
+#include <string>
+
+namespace h5stor {
+
+  template <typename T>
+  struct Traits;
+
+  class H5Serializer {
+
+  public:
+    H5Serializer(std::string filepath) {
+      m_file_id = H5Fcreate(filepath.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+    }
+
+    template <typename T>
+    void serialize(const T& value, std::string name) {
+      Traits<T>::serialize(m_file_id, value, name);
+    }
+
+    template <typename T>
+    T deserialize(std::string name) {
+      return Traits<T>::deserialize(m_file_id, name);
+    }
+
+  private:
+    hid_t m_file_id;
+  };
+}
+
+#endif

include/Eisvogel/NDArray.hh

@@ -9,6 +9,10 @@
 
 #include "Serialization.hh"
 
+// ======================================================
+// General n-dimensional array
+// ======================================================
+
 template <class T, std::size_t dims>
 class NDArray {
 
@@ -34,7 +38,9 @@ protected:
 template <class T, std::size_t dims>
 inline NDArray<T, dims>::~NDArray() { }
 
-// ======
+// ======================================================
+// Dense n-dimensional array
+// ======================================================
 
 template <class T, std::size_t dims>
 class DenseNDArray : public NDArray<T, dims> {
@@ -233,4 +239,10 @@ using IndexVector = DenseVector<std::size_t>;
 template <class T>
 using ScalarField3D = DenseNDArray<T, 3>;
 
+// ======================================================
+// Sparse n-dimensional array
+// ======================================================
+
+
+
 #endif

src/CMakeLists.txt

@@ -16,6 +16,7 @@ set_target_properties(eisvogel PROPERTIES
                       LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/eisvogel)
 
 if(BUILD_WFC)
+    find_package(MPI REQUIRED)
     find_package(PkgConfig REQUIRED)
     pkg_check_modules(MEEP REQUIRED meep)
     find_package(HDF5 REQUIRED)
@@ -25,7 +26,7 @@ if(BUILD_WFC)
                 Geometry.cxx
                 Antenna.cxx)
     target_link_directories(eisvogel_wfc PUBLIC ${MEEP_LIBRARY_DIRS} ${HDF_LIBRARY_DIRS})
-    target_link_libraries(eisvogel_wfc PUBLIC eisvogel ${MEEP_LIBRARIES} ${HDF_LIBRARIES})
+    target_link_libraries(eisvogel_wfc PUBLIC eisvogel ${MEEP_LIBRARIES} ${HDF_LIBRARIES} MPI::MPI_CXX)
     target_include_directories(eisvogel_wfc PUBLIC ${PROJECT_SOURCE_DIR}/include ${MEEP_INCLUDE_DIRS} ${HDF_INCLUDE_DIRS})
     target_compile_options(eisvogel_wfc PUBLIC ${MEEP_CFLAGS_OTHER} ${HDF_CFLAGS_OTHER})
 

src/WeightingFieldCalculator.cxx

@@ -97,6 +97,6 @@ void WeightingFieldCalculator::Calculate(double t_end) {
     }
     f -> step();
     f -> loop_in_chunks(meep::saving_chunkloop, (void*)data.c_str(), f -> total_volume());
-    f -> output_hdf5(meep::Ez, gv -> surroundings());
+    // f -> output_hdf5(meep::Ez, gv -> surroundings());
   }
 }