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Paraview files fixed
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@krzysg
krzysg committed May 9, 2018
1 parent 90cd009 commit df7b336
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Showing 3 changed files with 17 additions and 18 deletions.
2 changes: 1 addition & 1 deletion src/io/APRWriter.hpp
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Expand Up @@ -314,7 +314,7 @@ class APRWriter {
writeData(AprTypes::ParaviewTypeType, f.objectId, typev, blosc_comp_type, blosc_comp_level, blosc_shuffle);

// TODO: This needs to be able extended to handle more general type, currently it is assuming uint16
write_main_paraview_xdmf_xml(save_loc,file_name,apr_iterator.total_number_particles());
write_main_paraview_xdmf_xml(save_loc,hdf5_file_name, file_name,apr_iterator.total_number_particles());

// ------------- output the file size -------------------
hsize_t file_size;
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31 changes: 15 additions & 16 deletions src/io/hdf5functions_blosc.cpp
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Expand Up @@ -87,39 +87,38 @@ hid_t hdf5_create_file_blosc(std::string file_name){
return H5Fcreate(file_name.c_str(),H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); //this writes over the current file
}

void write_main_paraview_xdmf_xml(std::string save_loc,std::string file_name,uint64_t num_parts){
const std::string hdf5_file_name = file_name + ".h5";
std::ofstream myfile(save_loc + file_name + ".xmf");
void write_main_paraview_xdmf_xml(const std::string &aDestinationDir,const std::string &aHdf5FileName, const std::string &aParaviewFileName, uint64_t aNumOfParticles){
std::ofstream myfile(aDestinationDir + aParaviewFileName + "_paraview.xmf");
myfile << "<?xml version=\"1.0\" ?>\n";
myfile << "<!DOCTYPE Xdmf SYSTEM \"Xdmf.dtd\" []>\n";
myfile << "<Xdmf Version=\"2.0\" xmlns:xi=\"[http://www.w3.org/2001/XInclude]\">\n";
myfile << " <Domain>\n";
myfile << " <Grid Name=\"parts\" GridType=\"Uniform\">\n";
myfile << " <Topology TopologyType=\"Polyvertex\" Dimensions=\"" << num_parts << "\"/>\n";
myfile << " <Topology TopologyType=\"Polyvertex\" Dimensions=\"" << aNumOfParticles << "\"/>\n";
myfile << " <Geometry GeometryType=\"X_Y_Z\">\n";
myfile << " <DataItem Dimensions=\""<< num_parts <<"\" NumberType=\"UInt\" Precision=\"2\" Format=\"HDF\">\n";
myfile << " " << hdf5_file_name << ":/ParticleRepr/t/x\n";
myfile << " <DataItem Dimensions=\""<< aNumOfParticles <<"\" NumberType=\"UInt\" Precision=\"2\" Format=\"HDF\">\n";
myfile << " " << aHdf5FileName << ":/ParticleRepr/t/x\n";
myfile << " </DataItem>\n";
myfile << " <DataItem Dimensions=\""<< num_parts <<"\" NumberType=\"UInt\" Precision=\"2\" Format=\"HDF\">\n";
myfile << " " << hdf5_file_name << ":/ParticleRepr/t/y\n";
myfile << " <DataItem Dimensions=\""<< aNumOfParticles <<"\" NumberType=\"UInt\" Precision=\"2\" Format=\"HDF\">\n";
myfile << " " << aHdf5FileName << ":/ParticleRepr/t/y\n";
myfile << " </DataItem>\n";
myfile << " <DataItem Dimensions=\""<< num_parts <<"\" NumberType=\"UInt\" Precision=\"2\" Format=\"HDF\">\n";
myfile << " " << hdf5_file_name << ":/ParticleRepr/t/z\n";
myfile << " <DataItem Dimensions=\""<< aNumOfParticles <<"\" NumberType=\"UInt\" Precision=\"2\" Format=\"HDF\">\n";
myfile << " " << aHdf5FileName << ":/ParticleRepr/t/z\n";
myfile << " </DataItem>\n";
myfile << " </Geometry>\n";
myfile << " <Attribute Name=\"particle property\" AttributeType=\"Scalar\" Center=\"Node\">\n";
myfile << " <DataItem Dimensions=\""<< num_parts <<"\" NumberType=\"UInt\" Precision=\"2\" Format=\"HDF\">\n";
myfile << " " << hdf5_file_name << ":/ParticleRepr/t/particle property\n";
myfile << " <DataItem Dimensions=\""<< aNumOfParticles <<"\" NumberType=\"UInt\" Precision=\"2\" Format=\"HDF\">\n";
myfile << " " << aHdf5FileName << ":/ParticleRepr/t/particle property\n";
myfile << " </DataItem>\n";
myfile << " </Attribute>\n";
myfile << " <Attribute Name=\"level\" AttributeType=\"Scalar\" Center=\"Node\">\n";
myfile << " <DataItem Dimensions=\""<< num_parts <<"\" NumberType=\"UInt\" Precision=\"1\" Format=\"HDF\">\n";
myfile << " " << hdf5_file_name << ":/ParticleRepr/t/level\n";
myfile << " <DataItem Dimensions=\""<< aNumOfParticles <<"\" NumberType=\"UInt\" Precision=\"1\" Format=\"HDF\">\n";
myfile << " " << aHdf5FileName << ":/ParticleRepr/t/level\n";
myfile << " </DataItem>\n";
myfile << " </Attribute>\n";
myfile << " <Attribute Name=\"type\" AttributeType=\"Scalar\" Center=\"Node\">\n";
myfile << " <DataItem Dimensions=\""<< num_parts <<"\" NumberType=\"UInt\" Precision=\"1\" Format=\"HDF\">\n";
myfile << " " << hdf5_file_name << ":/ParticleRepr/t/type\n";
myfile << " <DataItem Dimensions=\""<< aNumOfParticles <<"\" NumberType=\"UInt\" Precision=\"1\" Format=\"HDF\">\n";
myfile << " " << aHdf5FileName << ":/ParticleRepr/t/type\n";
myfile << " </DataItem>\n";
myfile << " </Attribute>\n";
myfile << " </Grid>\n";
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2 changes: 1 addition & 1 deletion src/io/hdf5functions_blosc.h
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Expand Up @@ -28,7 +28,7 @@ void hdf5_load_data_blosc(hid_t obj_id, void* buff, const char* data_name);
void hdf5_load_data_blosc(hid_t obj_id, hid_t dataType, void* buff, const char* data_name);
void hdf5_write_attribute_blosc(hid_t obj_id,hid_t type_id,const char* attr_name,hsize_t rank,hsize_t* dims, const void * const data );
void hdf5_write_data_blosc(hid_t obj_id,hid_t type_id,const char* ds_name,hsize_t rank,hsize_t* dims, void* data ,unsigned int comp_type,unsigned int comp_level,unsigned int shuffle);
void write_main_paraview_xdmf_xml(std::string save_loc,std::string file_name,uint64_t num_parts);
void write_main_paraview_xdmf_xml(const std::string &aDestinationDir,const std::string &aHdf5FileName, const std::string &aParaviewFileName, uint64_t aNumOfParticles);


#endif

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