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  • mosaic/software/parallel-computing/openfpm/openfpm_io
  • argupta/openfpm_io
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CMakeLists.txt
View file @ 112c3790
...@@ -40,12 +40,15 @@ set(HDF5_PREFER_PARALLEL TRUE) ...@@ -40,12 +40,15 @@ set(HDF5_PREFER_PARALLEL TRUE)
set (ENV{BOOST_ROOT} ${BOOST_ROOT}) set (ENV{BOOST_ROOT} ${BOOST_ROOT})
set (Boost_NO_BOOST_CMAKE OFF) set (Boost_NO_BOOST_CMAKE OFF)
find_package(Boost 1.72.0 REQUIRED COMPONENTS unit_test_framework iostreams program_options OPTIONAL_COMPONENTS fiber context) find_package(Boost 1.72.0 REQUIRED COMPONENTS unit_test_framework iostreams program_options system filesystem
OPTIONAL_COMPONENTS fiber context)
find_package(MPI REQUIRED) find_package(MPI REQUIRED)
find_package(HDF5 REQUIRED) find_package(HDF5 REQUIRED)
find_package(TinyObjLoader) find_package(TinyObjLoader)
find_package(PETSc) find_package(PETSc)
find_package(OpenMP) if (NOT CUDA_ON_BACKEND STREQUAL "HIP")
find_package(OpenMP)
endif()
if (CUDA_ON_BACKEND STREQUAL "HIP" AND NOT HIP_FOUND) if (CUDA_ON_BACKEND STREQUAL "HIP" AND NOT HIP_FOUND)
find_package(HIP) find_package(HIP)
endif() endif()
......
src/CMakeLists.txt
View file @ 112c3790
...@@ -21,17 +21,19 @@ if ( CUDA_ON_BACKEND STREQUAL "HIP" AND HIP_FOUND ) ...@@ -21,17 +21,19 @@ if ( CUDA_ON_BACKEND STREQUAL "HIP" AND HIP_FOUND )
set_source_files_properties(${CUDA_SOURCES} PROPERTIES LANGUAGE CXX) set_source_files_properties(${CUDA_SOURCES} PROPERTIES LANGUAGE CXX)
hip_add_executable(io main.cpp hip_add_executable(io main.cpp
MetaParser/MetaParser_unit_test.cpp MetaParser/MetaParser_unit_test.cpp
${CUDA_SOURCES} ${CUDA_SOURCES}
ObjReader/ObjReader_unit_test.cpp) ObjReader/ObjReader_unit_test.cpp
CSVReader/tests/CSVReader_unit_test.cpp)
else() else()
add_executable(io main.cpp add_executable(io main.cpp
MetaParser/MetaParser_unit_test.cpp MetaParser/MetaParser_unit_test.cpp
${CUDA_SOURCES} ${CUDA_SOURCES}
ObjReader/ObjReader_unit_test.cpp) ObjReader/ObjReader_unit_test.cpp
CSVReader/tests/CSVReader_unit_test.cpp)
set_property(TARGET io PROPERTY CUDA_ARCHITECTURES OFF) set_property(TARGET io PROPERTY CUDA_ARCHITECTURES OFF)
...@@ -107,13 +109,13 @@ endif() ...@@ -107,13 +109,13 @@ endif()
install(FILES RawReader/RawReader.hpp install(FILES RawReader/RawReader.hpp
RawReader/RawReader_unit_tests.hpp RawReader/RawReader_unit_tests.hpp
DESTINATION openfpm_io/include/RawReader DESTINATION openfpm_io/include/RawReader
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES CSVWriter/csv_multiarray.hpp install(FILES CSVWriter/csv_multiarray.hpp
CSVWriter/CSVWriter.hpp CSVWriter/CSVWriter.hpp
CSVWriter/is_csv_writable.hpp CSVWriter/is_csv_writable.hpp
DESTINATION openfpm_io/include/CSVWriter/ DESTINATION openfpm_io/include/CSVWriter/
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES CSVReader/CSVReader.hpp install(FILES CSVReader/CSVReader.hpp
...@@ -121,11 +123,11 @@ install(FILES CSVReader/CSVReader.hpp ...@@ -121,11 +123,11 @@ install(FILES CSVReader/CSVReader.hpp
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES GraphMLWriter/GraphMLWriter.hpp install(FILES GraphMLWriter/GraphMLWriter.hpp
DESTINATION openfpm_io/include/GraphMLWriter DESTINATION openfpm_io/include/GraphMLWriter
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES util/util.hpp util/GBoxes.hpp install(FILES util/util.hpp util/GBoxes.hpp
DESTINATION openfpm_io/include/util DESTINATION openfpm_io/include/util
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES VTKWriter/VTKWriter.hpp install(FILES VTKWriter/VTKWriter.hpp
...@@ -138,11 +140,11 @@ install(FILES VTKWriter/VTKWriter.hpp ...@@ -138,11 +140,11 @@ install(FILES VTKWriter/VTKWriter.hpp
VTKWriter/VTKWriter_grids_util.hpp VTKWriter/VTKWriter_grids_util.hpp
VTKWriter/VTKWriter_vector_box.hpp VTKWriter/VTKWriter_vector_box.hpp
VTKWriter/is_vtk_writable.hpp VTKWriter/is_vtk_writable.hpp
DESTINATION openfpm_io/include/VTKWriter/ DESTINATION openfpm_io/include/VTKWriter/
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES MetaParser/MetaParser.hpp install(FILES MetaParser/MetaParser.hpp
DESTINATION openfpm_io/include/MetaParser/ DESTINATION openfpm_io/include/MetaParser/
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES HDF5_wr/HDF5_wr.hpp install(FILES HDF5_wr/HDF5_wr.hpp
...@@ -164,7 +166,7 @@ install(FILES util/PathsAndFiles.hpp ...@@ -164,7 +166,7 @@ install(FILES util/PathsAndFiles.hpp
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES Plot/GoogleChart.hpp Plot/util.hpp install(FILES Plot/GoogleChart.hpp Plot/util.hpp
DESTINATION openfpm_io/include/Plot DESTINATION openfpm_io/include/Plot
COMPONENT OpenFPM) COMPONENT OpenFPM)
......
src/RawReader/InitGridWithPixel.hpp
View file @ 112c3790
...@@ -113,9 +113,6 @@ void load_pixel_onto_grid(grid_type & grid, std::string file_name, std::vector < ...@@ -113,9 +113,6 @@ void load_pixel_onto_grid(grid_type & grid, std::string file_name, std::vector <
} }
} }
// initialize complete grid including ghost layer with -1
init_grid_and_ghost<Phi_0>(grid, -1.0);
// assign pixel values to domain. For each pixel get factor_refinement number of grid points with corresponding value // assign pixel values to domain. For each pixel get factor_refinement number of grid points with corresponding value
auto dom = grid.getDomainIterator(); auto dom = grid.getDomainIterator();
std::vector<BYTE> pixel_line; // one x-line of the image stack which will be read std::vector<BYTE> pixel_line; // one x-line of the image stack which will be read
......
src/VTKWriter/VTKWriter_point_set.hpp
View file @ 112c3790
...@@ -3,6 +3,7 @@ ...@@ -3,6 +3,7 @@
* *
* Created on: Feb 6, 2016 * Created on: Feb 6, 2016
* Author: i-bird * Author: i-bird
* Modified pvtp writer by: Abhinav
*/ */
#ifndef OPENFPM_IO_SRC_VTKWRITER_POINT_SET_HPP_ #ifndef OPENFPM_IO_SRC_VTKWRITER_POINT_SET_HPP_
...@@ -15,6 +16,8 @@ ...@@ -15,6 +16,8 @@
#include <string> #include <string>
#include "byteswap_portable.hpp" #include "byteswap_portable.hpp"
#include "MetaParser/MetaParser.hpp" #include "MetaParser/MetaParser.hpp"
#include <util/PathsAndFiles.hpp>
/*! \brief Store a reference to the vector position /*! \brief Store a reference to the vector position
* *
...@@ -246,7 +249,7 @@ struct prop_out_v_pvtp ...@@ -246,7 +249,7 @@ struct prop_out_v_pvtp
void lastProp() void lastProp()
{ {
v_out += " <PDataArray type=\"Float32\" Name=\"domain\"/>\n </PPointData>\n"; v_out += " <PDataArray type=\"Float32\" Name=\"domain\"/>\n </PPointData>\n";
} }
}; };
...@@ -619,16 +622,21 @@ public: ...@@ -619,16 +622,21 @@ public:
* \return true if the write complete successfully * \return true if the write complete successfully
* *
*/ */
bool write_pvtp(std::string file,const openfpm::vector<std::string> & prop_names,size_t n,long int timestamp=-1) bool write_pvtp(std::string file,const openfpm::vector<std::string> & prop_names,size_t n,long int timestamp=-1,double time=-1)
{ {
//openfpm::vector< ele_vpp<typename pair::second>> vpp; //openfpm::vector< ele_vpp<typename pair::second>> vpp;
// Header for the vtk // Header for the vtk
create_directory_if_not_exist("VTPDATA",1);
std::string vtk_header; std::string vtk_header;
std::string Name_data; std::string Name_data;
std::string PpointEnd; std::string PpointEnd;
std::string Piece; std::string Piece;
if(time==-1){
vtk_header = "<VTKFile type=\"PPolyData\" version=\"1.0\" byte_order=\"LittleEndian\" header_type=\"UInt64\">\n <PPolyData>\n <PPointData>\n"; vtk_header = "<VTKFile type=\"PPolyData\" version=\"1.0\" byte_order=\"LittleEndian\" header_type=\"UInt64\">\n <PPolyData>\n <PPointData>\n";
}
else{
vtk_header = "<VTKFile type=\"PPolyData\" version=\"1.0\" byte_order=\"LittleEndian\" header_type=\"UInt64\">\n <PPolyData>\n <FieldData> \n <DataArray type=\"Float64\" Name=\"TimeValue\" NumberOfTuples=\"1\" format=\"ASCII\">\n "+std::to_string(time)+"\n </DataArray>\n </FieldData>\n <PPointData>\n";
}
prop_out_v_pvtp< ele_vpp<typename pair::second>, typename pair::first::value_type::coord_type> pp(Name_data,prop_names); prop_out_v_pvtp< ele_vpp<typename pair::second>, typename pair::first::value_type::coord_type> pp(Name_data,prop_names);
boost::mpl::for_each< boost::mpl::range_c<int,0, pair::second::value_type::max_prop> >(pp); boost::mpl::for_each< boost::mpl::range_c<int,0, pair::second::value_type::max_prop> >(pp);
pp.lastProp(); pp.lastProp();
...@@ -637,12 +645,12 @@ public: ...@@ -637,12 +645,12 @@ public:
if (timestamp==-1) { if (timestamp==-1) {
for (int i = 0; i < n; i++) for (int i = 0; i < n; i++)
{ Piece += " <Piece Source=\"" + file.substr(0, file.size()) + "_" +std::to_string(i) + ".vtp\"/>\n";} { Piece += " <Piece Source=\"./VTPDATA/" + file.substr(0, file.size()) + "_" +std::to_string(i) + ".vtp\"/>\n";}
file += ".pvtp"; file += ".pvtp";
} }
else{ else{
for (int i = 0; i < n; i++) for (int i = 0; i < n; i++)
{ Piece += " <Piece Source=\"" + file.substr(0, file.size()) + "_" +std::to_string(i) + "_" + std::to_string(timestamp) + ".vtp\"/>\n";} { Piece += " <Piece Source=\"./VTPDATA/" + file.substr(0, file.size()) + "_" +std::to_string(i) + "_" + std::to_string(timestamp) + ".vtp\"/>\n";}
file += "_" + std::to_string(timestamp) + ".pvtp"; file += "_" + std::to_string(timestamp) + ".pvtp";
} }
std::string closingFile=" </PPolyData>\n</VTKFile>"; std::string closingFile=" </PPolyData>\n</VTKFile>";
...@@ -744,11 +752,12 @@ public: ...@@ -744,11 +752,12 @@ public:
std::string closingFile=" </PointData>\n </Piece>\n </PolyData>\n</VTKFile>"; std::string closingFile=" </PointData>\n </Piece>\n </PolyData>\n</VTKFile>";
// write the file // write the file
std::ofstream ofs(file); create_directory_if_not_exist("VTPDATA",1);
std::ofstream ofs("VTPDATA/"+file);
// Check if the file is open // Check if the file is open
if (ofs.is_open() == false) if (ofs.is_open() == false)
{std::cerr << "Error cannot create the VTK file: " + file + "\n";} {std::cerr << "Error cannot create the VTK/VTP file. Maybe the \"VTPDATA\" folder cannot be created.: " + file + "\n";}
ofs << vtk_header << point_prop_header << point_list << ofs << vtk_header << point_prop_header << point_list <<
vertex_prop_header << vertex_list << point_data_header << point_data << closingFile; vertex_prop_header << vertex_list << point_data_header << point_data << closingFile;
......
src/VTKWriter/VTKWriter_unit_tests.hpp
View file @ 112c3790
...@@ -1114,10 +1114,10 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set ) ...@@ -1114,10 +1114,10 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set )
vtk_v.add(v3ps,v3pp,90); vtk_v.add(v3ps,v3pp,90);
openfpm::vector<std::string> prp_names; openfpm::vector<std::string> prp_names;
vtk_v.write_pvtp("vtk_points",prp_names,2);
vtk_v.write("vtk_points.vtp",prp_names); vtk_v.write("vtk_points.vtp",prp_names);
//auto &v_cl=create_vcluster(); //auto &v_cl=create_vcluster();
//size_t n=v_cl.size(); //size_t n=v_cl.size();
vtk_v.write_pvtp("vtk_points",prp_names,2);
#ifndef SE_CLASS3 #ifndef SE_CLASS3
...@@ -1125,7 +1125,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set ) ...@@ -1125,7 +1125,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set )
bool test = true; bool test = true;
// Check that match // Check that match
test = compare("vtk_points.vtp","test_data/vtk_points_test.vtp"); test = compare("VTPDATA/vtk_points.vtp","test_data/vtk_points_test.vtp");
BOOST_REQUIRE_EQUAL(test,true); BOOST_REQUIRE_EQUAL(test,true);
//It just checks generation of the format and not actual data (File names) //It just checks generation of the format and not actual data (File names)
...@@ -1143,7 +1143,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set ) ...@@ -1143,7 +1143,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set )
#ifndef SE_CLASS3 #ifndef SE_CLASS3
// Check that match // Check that match
test = compare("vtk_points_pp.vtp","test_data/vtk_points_pp_test.vtp"); test = compare("VTPDATA/vtk_points_pp.vtp","test_data/vtk_points_pp_test.vtp");
BOOST_REQUIRE_EQUAL(test,true); BOOST_REQUIRE_EQUAL(test,true);
#endif #endif
...@@ -1160,10 +1160,10 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set ) ...@@ -1160,10 +1160,10 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set )
#ifndef SE_CLASS3 #ifndef SE_CLASS3
// Check that match // Check that match
test = compare("vtk_points_pp_header.vtp","test_data/vtk_points_pp_header_test.vtp"); test = compare("VTPDATA/vtk_points_pp_header.vtp","test_data/vtk_points_pp_header_test.vtp");
BOOST_REQUIRE_EQUAL(test,true); BOOST_REQUIRE_EQUAL(test,true);
test = compare("vtk_points_pp_header_bin.vtp","test_data/vtk_points_pp_header_bin_test.vtp"); test = compare("VTPDATA/vtk_points_pp_header_bin.vtp","test_data/vtk_points_pp_header_bin_test.vtp");
BOOST_REQUIRE_EQUAL(test,true); BOOST_REQUIRE_EQUAL(test,true);
#endif #endif
...@@ -1226,7 +1226,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_properties ) ...@@ -1226,7 +1226,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_properties )
#ifndef SE_CLASS3 #ifndef SE_CLASS3
// Check that match // Check that match
bool test = compare("vtk_points_with_prp_names.vtp","test_data/vtk_points_with_prp_names_test.vtp"); bool test = compare("VTPDATA/vtk_points_with_prp_names.vtp","test_data/vtk_points_with_prp_names_test.vtp");
BOOST_REQUIRE_EQUAL(test,true); BOOST_REQUIRE_EQUAL(test,true);
#endif #endif
...@@ -1285,7 +1285,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_check_out_precision ) ...@@ -1285,7 +1285,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_check_out_precision )
#ifndef SE_CLASS3 #ifndef SE_CLASS3
// Check that match // Check that match
bool test = compare("vtk_points_with_prp_names_prec_check.vtp","test_data/vtk_points_with_prp_names_prec_check_test.vtp"); bool test = compare("VTPDATA/vtk_points_with_prp_names_prec_check.vtp","test_data/vtk_points_with_prp_names_prec_check_test.vtp");
BOOST_REQUIRE_EQUAL(test,true); BOOST_REQUIRE_EQUAL(test,true);
#endif #endif
...@@ -1391,9 +1391,9 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary ) ...@@ -1391,9 +1391,9 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary )
bool test = true; bool test = true;
// Check that match // Check that match
test = compare("vtk_points_bin.vtp","test_data/vtk_points_bin_test.vtp"); test = compare("VTPDATA/vtk_points_bin.vtp","test_data/vtk_points_bin_test.vtp");
BOOST_REQUIRE_EQUAL(test,true); BOOST_REQUIRE_EQUAL(test,true);
test = compare("vtk_points_bin2.vtp","test_data/vtk_points_bin_test.vtp"); test = compare("VTPDATA/vtk_points_bin2.vtp","test_data/vtk_points_bin_test.vtp");
BOOST_REQUIRE_EQUAL(test,true); BOOST_REQUIRE_EQUAL(test,true);
#endif #endif
...@@ -1407,7 +1407,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary ) ...@@ -1407,7 +1407,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary )
#ifndef SE_CLASS3 #ifndef SE_CLASS3
// Check that match // Check that match
test = compare("vtk_points_pp_bin.vtp","test_data/vtk_points_pp_bin_test.vtp"); test = compare("VTPDATA/vtk_points_pp_bin.vtp","test_data/vtk_points_pp_bin_test.vtp");
BOOST_REQUIRE_EQUAL(test,true); BOOST_REQUIRE_EQUAL(test,true);
#endif #endif
...@@ -1505,7 +1505,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary ) ...@@ -1505,7 +1505,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary )
bool test = true; bool test = true;
// Check that match // Check that match
test = compare("vtk_points_2d_bin.vtp","test_data/vtk_points_2d_bin_test.vtp"); test = compare("VTPDATA/vtk_points_2d_bin.vtp","test_data/vtk_points_2d_bin_test.vtp");
BOOST_REQUIRE_EQUAL(test,true); BOOST_REQUIRE_EQUAL(test,true);
#endif #endif
...@@ -1519,7 +1519,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary ) ...@@ -1519,7 +1519,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary )
#ifndef SE_CLASS3 #ifndef SE_CLASS3
// Check that match // Check that match
test = compare("vtk_points_2d_pp_bin.vtp","test_data/vtk_points_2d_pp_bin_test.vtp"); test = compare("VTPDATA/vtk_points_2d_pp_bin.vtp","test_data/vtk_points_2d_pp_bin_test.vtp");
BOOST_REQUIRE_EQUAL(test,true); BOOST_REQUIRE_EQUAL(test,true);
#endif #endif
......
src/util/PathsAndFiles.hpp
View file @ 112c3790
...@@ -100,7 +100,7 @@ static bool check_if_directory_exists(std::string path) ...@@ -100,7 +100,7 @@ static bool check_if_directory_exists(std::string path)
* *
* @param path Std::string that contains path including name of the folder that should be created. * @param path Std::string that contains path including name of the folder that should be created.
*/ */
static void create_directory_if_not_exist(std::string path) static void create_directory_if_not_exist(std::string path,bool silent=0)
{ {
auto & v_cl = create_vcluster(); auto & v_cl = create_vcluster();
if (v_cl.rank() == 0) if (v_cl.rank() == 0)
...@@ -110,7 +110,11 @@ static void create_directory_if_not_exist(std::string path) ...@@ -110,7 +110,11 @@ static void create_directory_if_not_exist(std::string path)
boost::filesystem::create_directory(path); boost::filesystem::create_directory(path);
// BOOST_LOG_TRIVIAL(info) << "Created directory with name: " << path; // BOOST_LOG_TRIVIAL(info) << "Created directory with name: " << path;
} }
else std::cout << "Folder for current settings ( '" << path << "' ) already exists. New files will be saved to this folder." << std::endl; else {
if(!silent){
std::cout << "Folder for current settings ( '" << path << "' ) already exists. New files will be saved to this folder." << std::endl;
}
}
// BOOST_LOG_TRIVIAL(info) << "Folder for current settings ( '" << path << "' ) already exists. New files will be saved to this folder."; // BOOST_LOG_TRIVIAL(info) << "Folder for current settings ( '" << path << "' ) already exists. New files will be saved to this folder.";
} }
} }
......
test_data/pvtp_points_test.pvtp
View file @ 112c3790
...@@ -8,7 +8,7 @@ ...@@ -8,7 +8,7 @@
<PPoints> <PPoints>
<PDataArray type="Float64" Name="Points" NumberOfComponents="3"/> <PDataArray type="Float64" Name="Points" NumberOfComponents="3"/>
</PPoints> </PPoints>
<Piece Source="vtk_points_0.vtp"/> <Piece Source="./VTPDATA/vtk_points_0.vtp"/>
<Piece Source="vtk_points_1.vtp"/> <Piece Source="./VTPDATA/vtk_points_1.vtp"/>
</PPolyData> </PPolyData>
</VTKFile> </VTKFile>
\ No newline at end of file