[Hdf5] Fix windows compilation

applications/HDF5Application/CMakeLists.txt

@@ -10,7 +10,6 @@ set( KRATOS_HDF5_APPLICATION_CORE
   ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_application_variables.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/custom_io/hdf5_file.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/custom_io/hdf5_nd_data_io.cpp
-  ${CMAKE_CURRENT_SOURCE_DIR}/custom_io/hdf5_points_data.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/custom_io/hdf5_connectivities_data.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/custom_io/hdf5_data_value_container_io.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/custom_io/hdf5_container_component_io.cpp

applications/HDF5Application/custom_io/hdf5_connectivities_data.cpp

@@ -109,7 +109,7 @@ void ConnectivitiesData<TContainerType>::Write(
 {
     KRATOS_TRY;
 
-    if (mpFile->GetDataCommunicator().SumAll(rEntities.size()) == 0) {
+    if (mpFile->GetDataCommunicator().SumAll(static_cast<unsigned int>(rEntities.size())) == 0) {
         // do nothing if the all the ranks have no entities.
         return;
     }

applications/HDF5Application/custom_io/hdf5_container_component_io.cpp

@@ -250,7 +250,7 @@ bool ContainerComponentIO<TContainerType, TContainerDataIO, TComponents...>::Wri
         std::vector<int> shape(value_type_traits::Dimension);
 
         // first we have to check the availability
-        Vector<unsigned char> availability(rLocalContainer.size(), 1);
+        Vector<char> availability(rLocalContainer.size(), 1);
         Internals::DataAvailabilityStatesList container_data_availability = TContainerDataIO::DataAvailability;
 
         // check for the availability. Here we do not check for the case CONSISTENTLY_UNAVAILABLE
@@ -260,11 +260,12 @@ bool ContainerComponentIO<TContainerType, TContainerDataIO, TComponents...>::Wri
         if constexpr(TContainerDataIO::DataAvailability == Internals::DataAvailabilityStatesList::INCONCLUSIVE) {
             // the entities in the rContainer may or may not contain the rComponent. Hence, for this
             // type we need to compute the availability.
-            const auto availability_local_counts_pair = IndexPartition<IndexType>(rLocalContainer.size()).for_each<CombinedReduction<SumReduction<IndexType>, SumReduction<IndexType>>>([&rContainerDataIO, &rLocalContainer, &r_component, &availability](const auto Index) {
+            const std::tuple<char, char> availability_local_counts_pair = IndexPartition<IndexType>(rLocalContainer.size()).for_each<CombinedReduction<SumReduction<IndexType>, SumReduction<IndexType>>>([&rContainerDataIO, &rLocalContainer, &r_component, &availability](const auto Index) {
                 availability[Index] = rContainerDataIO.HasValue(*(rLocalContainer.begin() + Index), r_component);
-                return std::make_tuple<IndexType, IndexType>(availability[Index] == true, availability[Index] == false);
+                return std::make_tuple<char, char>(static_cast<char>(availability[Index] == 1), static_cast<char>(availability[Index] == 0));
             });
-            const auto& availability_global_counts_pair = mpFile->GetDataCommunicator().SumAll(std::vector<IndexType>{std::get<0>(availability_local_counts_pair), std::get<1>(availability_local_counts_pair), rLocalContainer.size()});
+
+            const auto& availability_global_counts_pair = mpFile->GetDataCommunicator().SumAll(std::vector<char>{std::get<0>(availability_local_counts_pair), std::get<1>(availability_local_counts_pair)});
 
             KRATOS_ERROR_IF(availability_global_counts_pair[1] == availability_global_counts_pair[2])
                 << "None of the entities in the container have \"" << rComponentName << "\" defined.";
@@ -290,7 +291,7 @@ bool ContainerComponentIO<TContainerType, TContainerDataIO, TComponents...>::Wri
             value_type value_prototype{};
 
             // identifying the shape of the component by looking at the first entity which has the component defined.
-            auto first_available_pos = std::find(availability.begin(), availability.end(), true);
+            auto first_available_pos = std::find(availability.begin(), availability.end(), 1);
             if (first_available_pos != availability.end()) {
                 // if the value type is not static, then we need to get the shape
                 // of the first element assuming all the entities will have the same

applications/HDF5Application/custom_io/hdf5_file.cpp

@@ -905,7 +905,7 @@ void File::SetFileDriver(const std::string& rDriver, hid_t FaplId) const
     KRATOS_CATCH("");
 }
 
-template<File::DataTransferMode TDataTransferMode, class TDataType, class TIntegerType = unsigned int>
+template<File::DataTransferMode TDataTransferMode, class TDataType, class TIntegerType>
 void File::WriteDataSetImpl(
     const std::string& rPath,
     TDataType const * pData,

applications/HDF5Application/custom_io/hdf5_points_data.h

@@ -24,6 +24,7 @@
 // Application includes
 #include "custom_io/hdf5_file.h"
 #include "hdf5_application_define.h"
+#include "custom_utilities/hdf5_data_set_partition_utility.h"
 
 namespace Kratos
 {
@@ -57,20 +58,71 @@ class PointsData
 
     PointsData(
         const std::string& rPrefix,
-        File::Pointer mpFile);
+        File::Pointer pFile) 
+        : mpFile(pFile),
+          mPrefix(rPrefix) 
+    {
+
+    }
 
     ///@}
     ///@name Operations
     ///@{
 
     Parameters Read(
         typename TContainerDataIO::ContainerType& rContainer,
-        const TContainerDataIO& rContainerDataIO);
+        const TContainerDataIO& rContainerDataIO)
+    {
+        KRATOS_TRY;
+
+        IndexType start_index, block_size;
+        std::tie(start_index, block_size) = StartIndexAndBlockSize(*mpFile, mPrefix);
+
+        Vector<int> ids;
+        Vector<array_1d<double, 3>> coords;
+
+        mpFile->ReadDataSet(mPrefix + "/Ids", ids, start_index, block_size);
+        mpFile->ReadDataSet(mPrefix + "/Coordinates", coords, start_index, block_size);
+        auto attributes = mpFile->ReadAttribute(mPrefix);
+
+        const unsigned num_new_nodes = ids.size();
+        rContainer.reserve(rContainer.size() + num_new_nodes);
+
+        for (unsigned i = 0; i < num_new_nodes; ++i) {
+            rContainerDataIO.AddPoint(rContainer, ids[i], coords[i]);
+        }
+
+        return attributes;
+
+        KRATOS_CATCH("");
+    }
 
     void Write(
         const typename TContainerDataIO::ContainerType& rContainer,
         const TContainerDataIO& rContainerDataIO,
-        const Parameters Attributes);
+        const Parameters Attributes) 
+    {
+        KRATOS_TRY;
+
+        const unsigned num_nodes = rContainer.size();
+
+        Vector<int> ids(num_nodes);
+        Vector<array_1d<double, 3>> coords(num_nodes);
+
+        IndexPartition<IndexType>(num_nodes).for_each([&rContainer, &rContainerDataIO, &ids, &coords](const auto Index) {
+            const auto& r_point = *(rContainer.begin() + Index);
+            rContainerDataIO.GetData(ids[Index], coords[Index], r_point);
+        });
+
+        WriteInfo info;
+        mpFile->WriteDataSet(mPrefix + "/Ids", ids, info);
+        mpFile->WriteDataSet(mPrefix + "/Coordinates", coords, info);
+        mpFile->WriteAttribute(mPrefix, Attributes);
+
+        WritePartitionTable(*mpFile, mPrefix, info);
+
+        KRATOS_CATCH("");
+    }
 
     ///@}
 

applications/HDF5Application/custom_io/hdf5_properties_io.h

@@ -33,12 +33,12 @@ namespace Kratos::HDF5::Internals
 ///@addtogroup HDF5Application
 ///@{
 
-void ReadProperties(
+void KRATOS_API(HDF5_APPLICATION) ReadProperties(
     File& rFile,
     const std::string& rPrefix,
     PropertiesContainerType& rProperties);
 
-void WriteProperties(
+void KRATOS_API(HDF5_APPLICATION) WriteProperties(
     File& rFile,
     const std::string& rPrefix,
     const PropertiesContainerType& rProperties);

applications/HDF5Application/custom_io/hdf5_vertex_container_io.cpp

@@ -25,7 +25,7 @@ namespace HDF5
 
 namespace Internals
 {
-std::string AddMissingAndGetPrefix(Parameters Settings)
+std::string AddMissingAndGetPrefix(Parameters & Settings)
 {
     Parameters default_params(R"(
         {
@@ -44,7 +44,7 @@ VertexContainerCoordinateIO::VertexContainerCoordinateIO(
 {
     KRATOS_TRY
 
-    const std::string prefix = Settings["prefix"].Get<std::string>();
+    const std::string prefix = Settings["prefix"].GetString();
     KRATOS_ERROR_IF(!prefix.empty() && prefix.back() == '/')
         << "The prefix for vertex coordinates assumed to be a group hence no need to have an ending \"/\" [ prefix = \""
         << Settings["prefix"].GetString() << "\" ].\n";