Hdf5

.github/workflows/ci-cmake_tests.yml

@@ -63,7 +63,8 @@ jobs:
         # pyproject.toml as the single source of truth for everything
         # Python.
         run: |
-          mamba install _openmp_mutex=*=*_llvm cmake make boost git compilers blas=*=openblas liblapacke arpack gtest
+          mamba install _openmp_mutex=*=*_llvm cmake make boost git compilers blas=*=openblas liblapacke arpack gtest hdf5
+
 
       - name: CPU info
         run: lscpu

.github/workflows/coverity-scan.yml

@@ -35,10 +35,15 @@ jobs:
     - name: Install dependencies
       shell: bash -l {0}
       run: |
-        mamba install cmake make boost compilers blas=*=mkl pybind11 arpack
+        mamba config append channels conda-forge
 
-        cmake -S ${{github.workspace}} -B ${{github.workspace}}/build -DCMAKE_INSTALL_PREFIX=/home/runner/works/Cytnx_lib --preset=mkl-cpu
+        mamba install cmake make boost compilers hdf5 mkl mkl-include arpack
 
+        cmake -S ${{github.workspace}} -B ${{github.workspace}}/build \
+          -DCMAKE_INSTALL_PREFIX=/home/runner/works/Cytnx_lib \
+          -DCMAKE_PREFIX_PATH=$CONDA_PREFIX \
+          -DHDF5_ROOT=$CONDA_PREFIX \
+          --preset=mkl-cpu -DBUILD_PYTHON=OFF
     - name: Download Coverity Build Tool
       shell: bash -l {0}
       working-directory: ${{github.workspace}}/build

CMakeLists.txt

@@ -286,6 +286,11 @@ find_library(ARPACK_LIB arpack REQUIRED)
 message(STATUS "Found ARPACK_LIB at: ${ARPACK_LIB}")
 target_link_libraries(cytnx PRIVATE ${ARPACK_LIB})
 
+#HDF5
+find_package(HDF5 1.10.0 REQUIRED COMPONENTS CXX)
+target_include_directories(cytnx PRIVATE ${HDF5_INCLUDE_DIRS})
+target_link_libraries(cytnx PRIVATE ${HDF5_LIBRARIES})
+
 
 # #####################################################################
 # ## Get Gtest & benchmark
@@ -375,6 +380,7 @@ IF(BUILD_PYTHON)
   endif()
 
   pybind11_add_module(pycytnx MODULE pybind/cytnx.cpp
+    pybind/io_py.cpp
     pybind/generator_py.cpp
     pybind/storage_py.cpp
     pybind/tensor_py.cpp

benchmarks/linalg/Svd_bm.cpp

@@ -39,7 +39,7 @@ namespace BMTest_Svd {
   BENCHMARK(BM_Tensor_Svd_C128)->Args({1, 1})->Args({10, 10})->Args({100, 100})->Args({1000, 1000});
 
   // DenseUniTensor
-  UniTensor ConstructDenseUT(const int D, const int dtype, const unsigned int device = Device.cpu) {
+  UniTensor ConstructDenseUT(const int D, const int dtype, const int device = Device.cpu) {
     auto bd_vi = Bond(D, BD_IN);
     auto bd_pi = Bond(2, BD_IN);
     auto bd_po = Bond(2, BD_OUT);

benchmarks/linalg/Svd_truncate_bm.cpp

@@ -5,7 +5,7 @@ using namespace cytnx;
 namespace BMTest_Svd_truncate {
 
   // DenseUniTensor
-  UniTensor ConstructDenseUT(const int D, const int dtype, const unsigned int device = Device.cpu) {
+  UniTensor ConstructDenseUT(const int D, const int dtype, const int device = Device.cpu) {
     auto bd_vi = Bond(D, BD_IN);
     auto bd_pi = Bond(2, BD_IN);
     auto bd_po = Bond(2, BD_OUT);

conda_build/meta.yaml

@@ -10,6 +10,9 @@ source:
 
 build:
   number: 0
+  channels:
+    - conda-forge
+    - defaults
   script_env:
     # Refer to : https://github.com/ccache/ccache/discussions/821#discussioncomment-521209
     - CCACHE_NOHASHDIR=1
@@ -39,6 +42,7 @@ requirements:
     - boost >=1.82.0
     - blas=*=mkl            # [x86]
     - blas=*=openblas       # [not x86]
+    - hdf5 >=1.10.0
     - gtest
     - arpack
   run:
@@ -49,6 +53,7 @@ requirements:
     - graphviz
     - blas=*=mkl            # [x86]
     - blas=*=openblas       # [not x86]
+    - hdf5 >=1.10.0
     - beartype
     - arpack
 

cytnx/io_conti.py

@@ -0,0 +1,9 @@
+from typing import Any
+from cytnx import *
+
+def Load(obj: Any, container, name: str, path: str = ""):
+    io.c_Load(obj, container, name, path)
+
+# inject into the submodule
+obj = io
+setattr(obj,"Load",Load)

docs/source/adv_install.rst

@@ -93,7 +93,7 @@ There are two methods how you can set-up all the dependencies before starting th
 
 .. code-block:: shell
 
-    $conda install cmake make boost boost-cpp git compilers numpy openblas arpack pybind11 beartype arpack
+    $conda install cmake make boost boost-cpp git compilers hdf5 numpy openblas arpack pybind11 beartype arpack
 
 
 .. Note::
@@ -103,7 +103,7 @@ There are two methods how you can set-up all the dependencies before starting th
 
         .. code-block:: shell
 
-            $conda install cmake make boost boost-cpp git compilers numpy mkl mkl-include mkl-service arpack pybind11 libblas=*=*mkl beartype arpack
+            $conda install cmake make boost boost-cpp git compilers hdf5 numpy mkl mkl-include mkl-service arpack pybind11 libblas=*=*mkl beartype arpack
 
     3. After the installation, an automated test based on gtest and benchmark can be run. This option needs to be activated in the install script. In this case, gtest needs to be installed as well:
 

include/Bond.hpp

@@ -1,14 +1,18 @@
 #ifndef CYTNX_BOND_H_
 #define CYTNX_BOND_H_
 
-#include "Type.hpp"
-#include "cytnx_error.hpp"
-#include "Symmetry.hpp"
-#include <initializer_list>
-#include <vector>
+#include <algorithm>
+#include <filesystem>
 #include <fstream>
+#include <initializer_list>
 #include <map>
-#include <algorithm>
+#include <vector>
+
+#include "H5Cpp.h"
+
+#include "Symmetry.hpp"
+#include "Type.hpp"
+#include "cytnx_error.hpp"
 #include "intrusive_ptr_base.hpp"
 #include "utils/vec_clone.hpp"
 
@@ -36,6 +40,10 @@ namespace cytnx {
     BD_IN = -1, /*!< -1, same as BD_KET */
     BD_OUT = 1 /*!< 1, same as BD_BRA */
   };
+  static const std::map<bondType, std::string> bondtype_to_string = {
+    {BD_REG, "REG"}, {BD_IN, "IN"}, {BD_OUT, "OUT"}};
+  static const std::map<std::string, bondType> string_to_bondtype = {
+    {"REG", BD_REG}, {"IN", BD_IN}, {"OUT", BD_OUT}};
 
   /// @cond
   class Bond_impl : public intrusive_ptr_base<Bond_impl> {
@@ -848,52 +856,116 @@ namespace cytnx {
     }
 
     /**
-    @brief Save the Bond object to the file.
-    @details Save the Bond object to the file. The file extension will be automatically
-      added as ".cybd".
-          @param[in] fname the file name of the Bond object (exclude the file extension).
-    @see Load(const std::string &fname)
-    */
-    void Save(const std::string &fname) const;
-
+     * @brief Save Bond to file
+     * @details Save the Bond to a file. The file ending should be one of ".h5", ".hdf5", ".H5",
+     * ".HDF5", ".hdf" to save in HDF5 file format. Otherwise, a binary file format is used.
+     * @param[in] fname file name
+     * @param[in] path path inside the file. Only used for HDF5 files. A path '/foo/bar/' will write
+     * the Bond to the group '/foo/bar' in the file.
+     * @param[in] mode the write mode:\n
+     *  `w` Creates a new file. If the given file exists, its contents are destroyed.\n
+     *  `x` Creates a new file. Fails if the given file exists already.\n
+     *  `a` Opens for writing without overwriting any existing content. Creates the file if it
+     *      doesn't exist. Only available for HDF5 files.\n
+     *  `u` Opens for writing. Existing content will be updated(overwritten).
+     *      Creates the file if it doesn't exist. Only available for HDF5 files.
+     * @note The common file ending for saving a Bond in binary format is ".cybd".
+     * @warning HDF5 file format is strongly recommended for compatibility with other libraries,
+     * readability, and future-proofing.
+     * @see Load()
+     */
+    void Save(const std::filesystem::path &fname, const std::string &path = "/Bond/",
+              const char mode = 'w') const;
     /**
-        @see Save(const std::string &fname) const;
-    */
-    void Save(const char *fname) const;
+     * @see Save(const std::filesystem::path &fname, const std::string &path, const char mode)
+     * const;
+     */
+    void Save(const char *fname, const std::string &path = "/Bond/", const char mode = 'w') const;
+
+    /**
+     * @brief Load Bond from file and create new instance
+     * @details This function creates a new Bond and keeps the original Bond unchanged. See Load_()
+     * for loading the Bond to the current Bond.
+     * @param fname[in] file name
+     * @param[in] path path inside the file. Only used for HDF5 files. A path '/foo/bar/' will read
+     * the Bond from the group '/foo/bar' in the file.
+     * @param[in] restore_device whether to try restoring the device on which the data is stored; if
+     * false, the data will be kept on the CPU. Use .to_() to move it to the target device after
+     * loading.
+     * @pre The file must be a Bond object which is saved by Save().
+     * @note For HDF5 file format, one of the file endings ".h5", ".hdf5", ".H5", ".HDF5", ".hdf" is
+     * expected. For binary format, the common file ending for a Bond is ".cybd".
+     */
+    static cytnx::Bond Load(const std::filesystem::path &fname, const std::string &path = "/Bond/");
+    /**
+     * @see Load(const std::filesystem::path &fname, const std::string &path)
+     */
+    static cytnx::Bond Load(const char *fname, const std::string &path = "/Bond/");
 
     /**
-    @brief Load the Bond object from the file.
-          @param[in] fname the file name of the Bond object.
-          @pre The file need to be the file of Bond object, which is saved by the
-      function Bond::Save(const std::string &fname) const.
-    */
-    static cytnx::Bond Load(const std::string &fname);
+     * @brief Load Bond from file and overwrite current instance
+     * @details This function overwrites the existing Bond. See Load() for creating a new Bond.
+     * @see Load()
+     */
+    void Load_(const std::filesystem::path &fname, const std::string &path = "/Bond/");
+    /**
+     * @see Load_(const std::filesystem::path &fname, const std::string &path)
+     */
+    void Load_(const char *fname, const std::string &path = "/Bond/");
 
     /**
-    @see Load(const std::string &fname)
-    */
-    static cytnx::Bond Load(const char *fname);
+     * @brief Save Bond to HDF5 file
+     * @param[in] container the HDF5 parent group.
+     * @param[in] name the subgroup in which the Bond will be saved.
+     * @param[in] overwrite overwrite previous Bond information in the container.
+     * @warning This function is only available in C++. Use Save() for saving to file in C++ or
+     * Python.
+     * @see from_hdf5()
+     */
+    void to_hdf5(H5::Group &container, const std::string &name = "Bond",
+                 const bool overwrite = false) const;
+    /**
+     * @brief Load Bond from HDF5 file (inline)
+     * @param[in] container the HDF5 parent group.
+     * @param[in] name the subgroup from which the Bond will be loaded.
+     * @warning This function is only available in C++. Use Load() for loading from file in C++ or
+     * Python.
+     * @see to_hdf5() const
+     */
+    void from_hdf5(H5::Group &container, const std::string &name = "Bond");
 
-    /// @cond
-    void _Save(std::fstream &f) const;
-    void _Load(std::fstream &f);
-    /// @endcond
+    /**
+     * @brief Save Bond to binary file
+     * @param[in] f the output stream where the Bond will be saved.
+     * @warning This function is only available in C++. In Python, use pickle for the same binary
+     * file format. Use Save() for saving to file in C++ or Python.
+     * @see from_binary()
+     */
+    void to_binary(std::ostream &f) const;
+    /**
+     * @brief Load Bond from binary file
+     * @param[in] f the input stream from which the Bond will be loaded.
+     * @warning This function is only available in C++. In Python, use pickle for the same binary
+     * file format. Use Load() for loading from file in C++ or Python.
+     * @see to_binary() const
+     */
+    void from_binary(std::istream &f);
 
     /**
     @brief The comparison operator 'equal to'.
-    @details The comparison operators to compare two Bonds. If two Bond object are
-          same, return true. Otherwise, return false. This equal to operator will
-    compare all the "value" of the Bond object. Even the Bond object are different
-    object (different address), but they are same "value", it will return true.
-          @see operator!=(const Bond &rhs) const
+    @details The comparison operators to compare two Bonds. If two Bond object are same, return
+    true. Otherwise, return false. This equal to operator will compare all the "value" of the Bond
+    object. Even the Bond object are different object (different address), but they are same
+    "value", it will return true.
+    @see operator!=(const Bond &rhs) const
     */
     bool operator==(const Bond &rhs) const;
 
     /**
     @brief The comparison operator 'not equal to'.
-    @details The comparison operators to compare two Bonds. More precisely, it is
-    the opposite result of the operator==(const Bond &rhs) const.
-          @see operator==(const Bond &rhs) const
+    @details The comparison operators to compare two Bonds. More precisely, it is the opposite
+    result of the operator==(const Bond &rhs) const.
+    @see operator==(const Bond &rhs) const
     */
     bool operator!=(const Bond &rhs) const;