packages.biu: add hdf5

packages/biu/CMakeLists.txt

@@ -17,12 +17,13 @@ find_package(Boost REQUIRED COMPONENTS headers iostreams filesystem)
 find_package(range-v3 REQUIRED)
 find_path(NAMEOF_INCLUDE_DIR nameof.hpp REQUIRED)
 find_package(Eigen3 REQUIRED)
+find_package(HighFive REQUIRED)
 
-add_library(biu src/common.cpp)
+add_library(biu src/common.cpp src/hdf5.cpp)
 target_include_directories(biu PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}> ${NAMEOF_INCLUDE_DIR} ${ZPP_BITS_INCLUDE_DIR})
 target_link_libraries(biu PUBLIC magic_enum::magic_enum fmt::fmt Boost::headers Boost::iostreams Boost::filesystem
-  range-v3::range-v3 Eigen3::Eigen)
+  range-v3::range-v3 Eigen3::Eigen HighFive_HighFive)
 set_property(TARGET biu PROPERTY CXX_STANDARD 23 CXX_STANDARD_REQUIRED ON)
 install(TARGETS biu EXPORT biuTargets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
   ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}

packages/biu/biuConfig.cmake

@@ -5,3 +5,4 @@ find_package(Boost REQUIRED COMPONENTS headers iostreams)
 find_package(Eigen3 REQUIRED)
 find_package(range-v3 REQUIRED)
 find_path(NAMEOF_INCLUDE_DIR nameof.hpp REQUIRED)
+find_package(HighFive REQUIRED)

packages/biu/default.nix

@@ -1,11 +1,11 @@
 {
   stdenv, cmake, lib,
-  magic-enum, fmt, boost, eigen, range-v3, nameof, zpp-bits
+  magic-enum, fmt, boost, eigen, range-v3, nameof, zpp-bits, highfive
 }: stdenv.mkDerivation rec
 {
   name = "biu";
   src = ./.;
-  buildInputs = [ magic-enum fmt boost range-v3 nameof zpp-bits eigen ];
+  buildInputs = [ magic-enum fmt boost range-v3 nameof zpp-bits eigen highfive ];
   propagatedBuildInputs = buildInputs;
   nativeBuildInputs = [ cmake ];
   doCheck = true;

packages/biu/include/biu.hpp

@@ -6,6 +6,7 @@
 # include <biu/string.tpp>
 # include <biu/format.tpp>
 # include <biu/eigen.tpp>
+# include <biu/hdf5.tpp>
 // # include <biu/logger.tpp>
 // # include <biu/smartref.tpp>
 

packages/biu/include/biu/hdf5.hpp

@@ -0,0 +1,28 @@
+# pragma once
+# include <highfive/H5File.hpp>
+
+namespace biu
+{
+  namespace hdf5
+  {
+    struct PhonopyComplex { double r, i; };
+    namespace detail_
+    {
+      HighFive::CompoundType create_phonopy_complex();
+    }
+
+    class Hdf5file
+    {
+      public:
+        Hdf5file(std::string filename, bool readonly = false);
+        template <typename T> Hdf5file& read(std::string name, T& object);
+        template <typename T> T read(std::string name);
+        template <typename T> Hdf5file& write(std::string name, const T& object);
+      protected:
+        HighFive::File File_;
+    };
+  }
+  using hdf5::Hdf5file, hdf5::PhonopyComplex;
+}
+
+HIGHFIVE_REGISTER_TYPE(biu::hdf5::PhonopyComplex, biu::hdf5::detail_::create_phonopy_complex)

packages/biu/include/biu/hdf5.tpp

@@ -0,0 +1,12 @@
+# pragma once
+# include <biu/hdf5.hpp>
+
+namespace biu::hdf5
+{
+  template <typename T> Hdf5file& Hdf5file::read(std::string name, T& object)
+    { object = File_.getDataSet(name).read<std::remove_cvref_t<decltype(object)>>(); return *this; }
+  template <typename T> T Hdf5file::read(std::string name)
+    { std::remove_cvref_t<T> object; read(name, object); return object; }
+  template <typename T> Hdf5file& Hdf5file::write(std::string name, const T& object)
+    { File_.createDataSet(name, object); return *this; }
+}

packages/biu/src/hdf5.cpp

@@ -0,0 +1,15 @@
+# include <biu/hdf5.hpp>
+
+namespace biu::hdf5
+{
+  Hdf5file::Hdf5file(std::string filename, bool readonly)
+  : File_
+  (
+    filename, 
+    readonly ? HighFive::File::ReadOnly
+      : HighFive::File::ReadWrite | HighFive::File::Create | HighFive::File::Truncate
+  )
+  {}
+  HighFive::CompoundType detail_::create_phonopy_complex()
+    { return {{ "r", HighFive::AtomicType<double>{}}, {"i", HighFive::AtomicType<double>{}}}; }
+}