diff --git a/build.sh b/build.sh
index a7402af1ccb52673c3203fb4e43d8589262e34a0..281e94a24dcefce2be50ea5894f071d5c655668b 100755
--- a/build.sh
+++ b/build.sh
@@ -17,6 +17,20 @@ git clone git@git.mpi-cbg.de:openfpm/openfpm_data.git openfpm_data
git clone git@git.mpi-cbg.de:openfpm/openfpm_pdata.git openfpm_pdata
git clone git@git.mpi-cbg.de:openfpm/openfpm_vcluster.git openfpm_vcluster
+# Go in the right branch
+
+cd openfpm_pdata
+git checkout Release_0.9.0
+cd ..
+
+cd openfpm_data
+git checkout Release_0.9.0
+cd ..
+
+cd openfpm_vcluster
+git checkout Release_0.9.0
+cd ..
+
cd "$1/openfpm_io"
echo "Compiling on $2"
diff --git a/configure.ac b/configure.ac
index 284a37c97a119d3e914ba9b30f1db02422ada29c..ba69661c99e6395154f65023149e7bf13000450f 100755
--- a/configure.ac
+++ b/configure.ac
@@ -34,6 +34,11 @@ CXXFLAGS+=" -march=native -mtune=native -Wno-unused-local-typedefs -Wextra -Wno-
NVCCFLAGS=" "
INCLUDES_PATH=" "
+AC_LANG_PUSH([C++])
+AC_CHECK_HEADER(mpi.h,[],[echo "mpi.h not found"
+ exit 200])
+AC_LANG_POP([C++])
+
# set default prefix
if test "$prefix" = "NONE"; then
prefix="/usr/local"
diff --git a/gc_out2_test.html b/gc_out2_test.html
index 319e97c1073dc24c7157aa3fb3bafc079bb04826..16f6147e1cae865ac05b60a01a8385b70007554f 100644
--- a/gc_out2_test.html
+++ b/gc_out2_test.html
@@ -38,7 +38,8 @@ vAxis: {title: 'Y Axis'},
hAxis: {title: 'X Axis'},
seriesType: 'bars'};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
-var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
}</script>
</head>
<body>
diff --git a/gc_out3_test.html b/gc_out3_test.html
index 10eb9edf701d0be9d38a031bd44d82fb86325125..3eaf8466eb869c19006628900982ec5dd46783ac 100644
--- a/gc_out3_test.html
+++ b/gc_out3_test.html
@@ -38,7 +38,8 @@ vAxis: {title: 'Y Axis'},
hAxis: {title: 'X Axis'},
seriesType: ''};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
-var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
}</script>
</head>
<body>
diff --git a/gc_out4_test.html b/gc_out4_test.html
index 6c00c1528bd98a9e230b67e500d473a0e35e77f7..f851830c498ab3315b7e8585f9d0cb6ac2e27b47 100644
--- a/gc_out4_test.html
+++ b/gc_out4_test.html
@@ -38,7 +38,8 @@ vAxis: {title: ''},
hAxis: {title: ''},
seriesType: ''};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
-var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
}</script>
</head>
<body>
diff --git a/gc_out5_test.html b/gc_out5_test.html
index d579b983fd6d526304e4da5d47013efe38fd1629..4ef5259fdec336339185223f522efd6d0e93930d 100644
--- a/gc_out5_test.html
+++ b/gc_out5_test.html
@@ -38,7 +38,8 @@ vAxis: {title: ''},
hAxis: {title: ''},
seriesType: ''};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
-var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
}</script>
</head>
<body>
diff --git a/gc_out6_test.html b/gc_out6_test.html
index 2f1de14b260a6846797d77efb8e7918819be2a4e..8b1afbb0f181a8cab8efceb11bc61e786a851d64 100644
--- a/gc_out6_test.html
+++ b/gc_out6_test.html
@@ -38,7 +38,8 @@ vAxis: {title: ''},
hAxis: {title: ''},
seriesType: ''};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
-var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
}</script>
</head>
<body>
diff --git a/gc_out7_test.html b/gc_out7_test.html
index 81d5a5e1310b0ba1fccd09719610b6de48cc88da..b157cd50033ee4c2af1833d719f7d38d4996ea54 100644
--- a/gc_out7_test.html
+++ b/gc_out7_test.html
@@ -79,11 +79,14 @@ hAxis: {title: 'X Axis'},
seriesType: 'bars',
series: {3: {type: 'line'}}};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
-var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
$("#export_svg1").on("click", function (event) {exportToSVG.apply(this,[1]);});
-var chart = new google.visualization.ComboChart(document.getElementById('chart_div1'));chart.draw(data1, options1);
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div1'));
+chart.draw(data1, options1);
$("#export_svg2").on("click", function (event) {exportToSVG.apply(this,[2]);});
-var chart = new google.visualization.ComboChart(document.getElementById('chart_div2'));chart.draw(data2, options2);
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div2'));
+chart.draw(data2, options2);
}</script>
</head>
<body>
diff --git a/gc_out_test.html b/gc_out_test.html
index 60c941aefd4bea476acfda2414a5267a20092f5f..b65719ef3b2d79be7ccad9ed89d3b0fe9ce04126 100644
--- a/gc_out_test.html
+++ b/gc_out_test.html
@@ -39,7 +39,8 @@ hAxis: {title: 'X Axis'},
seriesType: 'bars',
series: {3: {type: 'line'}}};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
-var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
}</script>
</head>
<body>
diff --git a/gc_plot2_out_test.html b/gc_plot2_out_test.html
index 7cf93912e963e4e7fae09443a93d12a72f8a8184..f48dbf2078e27c13cdce1be8f88222b2029c8627 100644
--- a/gc_plot2_out_test.html
+++ b/gc_plot2_out_test.html
@@ -45,7 +45,8 @@ curveType: 'function',
lineWidth: 1,
intervals: { 'style':'area' }};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
-var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
}</script>
</head>
<body>
diff --git a/gc_plot_out_test.html b/gc_plot_out_test.html
index 4a105cd7a115d370f2058780ad75f2951154c370..a52ce00093bec66089e37e2099e7899cc5492169 100644
--- a/gc_plot_out_test.html
+++ b/gc_plot_out_test.html
@@ -47,7 +47,8 @@ intervals: { 'style':'area' },
interval: {'i2': { 'color': '#4374E0', 'style':'bars', 'lineWidth':4, 'fillOpacity':1 } }
};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
-var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
}</script>
</head>
<body>
diff --git a/m4/acx_mpi.m4 b/m4/acx_mpi.m4
old mode 100755
new mode 100644
diff --git a/src/CSVWriter/CSVWriter.hpp b/src/CSVWriter/CSVWriter.hpp
index 974818ac64d0fa9586d5cd449e3b75d7603f50b2..de38b2df7c55c08db99928640b5fa377946624a3 100644
--- a/src/CSVWriter/CSVWriter.hpp
+++ b/src/CSVWriter/CSVWriter.hpp
@@ -16,7 +16,7 @@
#include <boost/mpl/range_c.hpp>
#include <boost/mpl/for_each.hpp>
#include "csv_multiarray.hpp"
-#include "util.hpp"
+#include "util/util.hpp"
#include "is_csv_writable.hpp"
#define CSV_WRITER 0x30000
diff --git a/src/CSVWriter/CSVWriter_unit_tests.hpp b/src/CSVWriter/CSVWriter_unit_tests.hpp
index f1fa26538a009a2a6461c1c6e433a06a769a769a..bacfe6c249cb3604f7bb33852149f0470f792002 100644
--- a/src/CSVWriter/CSVWriter_unit_tests.hpp
+++ b/src/CSVWriter/CSVWriter_unit_tests.hpp
@@ -9,6 +9,11 @@ BOOST_AUTO_TEST_SUITE( csv_writer_test )
BOOST_AUTO_TEST_CASE( csv_writer_particles )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
{
// Allocate a property vector
auto v_prp = allocate_openfpm_prp(16);
@@ -29,7 +34,7 @@ BOOST_AUTO_TEST_CASE( csv_writer_particles )
// Write the CSV
csv_writer.write("csv_out.csv",v_pos,v_prp);
- bool test = compare("csv_out.csv","csv_out_test.csv");
+ bool test = compare("csv_out.csv","test_data/csv_out_test.csv");
BOOST_REQUIRE_EQUAL(true,test);
}
@@ -53,7 +58,7 @@ BOOST_AUTO_TEST_CASE( csv_writer_particles )
// Write the CSV
csv_writer.write("csv_out_unk.csv",v_pos,v_prp);
- bool test = compare("csv_out_unk.csv","csv_out_unk_test.csv");
+ bool test = compare("csv_out_unk.csv","test_data/csv_out_unk_test.csv");
BOOST_REQUIRE_EQUAL(true,test);
}
diff --git a/src/CSVWriter/is_csv_writable.hpp b/src/CSVWriter/is_csv_writable.hpp
index 556fa9e36c0b77e122833af37426687968591432..b7268b09d9cb62b3f9671c146d06147f1f4cd25a 100644
--- a/src/CSVWriter/is_csv_writable.hpp
+++ b/src/CSVWriter/is_csv_writable.hpp
@@ -9,111 +9,132 @@
#define OPENFPM_IO_SRC_CSVWRITER_IS_CSV_WRITABLE_HPP_
-
+//! Indicate if the property T is writable in CSV
template<typename T>
struct is_csv_writable
{
+ //! as default if not recognized is not writable
enum
{
value = false
};
};
+//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<float>
{
+ //! float is writable
enum
{
value = true
};
};
+//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<double>
{
+ //! double is writable
enum
{
value = true
};
};
+//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<char>
{
+ //! char is writable
enum
{
value = true
};
};
+//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<unsigned char>
{
+ //! unsigned char is writable
enum
{
value = true
};
};
+//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<short>
{
+ //! short is writable
enum
{
value = true
};
};
+//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<unsigned short>
{
+ //! unsigned is writable
enum
{
value = true
};
};
-
+//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<int>
{
+ //! int is writable
enum
{
value = true
};
};
+//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<unsigned int>
{
+ //! unsigned int is writable
enum
{
value = true
};
};
+//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<long int>
{
+ //! long int is writable
enum
{
value = true
};
};
+//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<unsigned long int>
{
+ //! unsigned long int is writable
enum
{
value = true
};
};
-
+//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<bool>
{
+ //! bool is writable
enum
{
value = true
diff --git a/src/GraphMLWriter/GraphMLWriter_unit_tests.hpp b/src/GraphMLWriter/GraphMLWriter_unit_tests.hpp
index 8b2a92694ed93d16f923aeda6292d7d675e35459..6c9b8c452f7c6da66a91a38c5acc8100744fe4d9 100644
--- a/src/GraphMLWriter/GraphMLWriter_unit_tests.hpp
+++ b/src/GraphMLWriter/GraphMLWriter_unit_tests.hpp
@@ -12,7 +12,7 @@
#include "GraphMLWriter.hpp"
#include "Graph/CartesianGraphFactory.hpp"
-#include "util.hpp"
+#include "util/util.hpp"
BOOST_AUTO_TEST_SUITE( graphml_writer_test )
@@ -77,6 +77,11 @@ const std::string ne_cp::attributes::name[] = {"x","y","z","double_num","long_nu
BOOST_AUTO_TEST_CASE( graphml_writer_use)
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
Graph_CSR<ne_cp,ne_cp> g_csr2;
// Add 4 vertex and connect
@@ -114,7 +119,7 @@ BOOST_AUTO_TEST_CASE( graphml_writer_use)
// check that match
- bool test = compare("test_graph2.graphml","test_graph2_test.graphml");
+ bool test = compare("test_graph2.graphml","test_data/test_graph2_test.graphml");
BOOST_REQUIRE_EQUAL(true,test);
//! Create a graph
@@ -138,7 +143,7 @@ BOOST_AUTO_TEST_CASE( graphml_writer_use)
// check that match
- test = compare("test_graph.graphml","test_graph_test.graphml");
+ test = compare("test_graph.graphml","test_data/test_graph_test.graphml");
BOOST_REQUIRE_EQUAL(true,test);
}
diff --git a/src/HDF5_wr/HDF5_reader.hpp b/src/HDF5_wr/HDF5_reader.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..d5b4a2ffd0e595220e3048988a5383656f814a0e
--- /dev/null
+++ b/src/HDF5_wr/HDF5_reader.hpp
@@ -0,0 +1,25 @@
+/*
+ * HDF5_loader.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_HPP_
+
+#include "VCluster/VCluster.hpp"
+
+template <unsigned int type>
+class HDF5_reader
+{
+ void load()
+ {
+ std::cerr << __FILE__ << ":" << __LINE__ << " Error: we do not know how to write this type of data" << std::endl;
+ }
+};
+
+#include "HDF5_reader_vd.hpp"
+#include "HDF5_reader_gd.hpp"
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_HPP_ */
diff --git a/src/HDF5_wr/HDF5_reader_gd.hpp b/src/HDF5_wr/HDF5_reader_gd.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..33f34b090c25b7bdc37cc58f1037ae680bb9a278
--- /dev/null
+++ b/src/HDF5_wr/HDF5_reader_gd.hpp
@@ -0,0 +1,249 @@
+/*
+ * HDF5_reader_gr.hpp
+ *
+ * Created on: May 2, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_GD_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_GD_HPP_
+
+
+#include "Packer_Unpacker/Pack_selector.hpp"
+#include "Packer_Unpacker/Packer.hpp"
+#include "Packer_Unpacker/Unpacker.hpp"
+#include "util/GBoxes.hpp"
+
+template <>
+class HDF5_reader<GRID_DIST>
+{
+ template<typename device_grid> void load_block(long int bid,
+ hssize_t mpi_size_old,
+ int * metadata_out,
+ openfpm::vector<size_t> & metadata_accum,
+ hid_t plist_id,
+ hid_t dataset_2,
+ openfpm::vector<device_grid> & loc_grid_old,
+ openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext_old)
+ {
+ hsize_t offset[1];
+ hsize_t block[1];
+
+ if (bid < mpi_size_old && bid != -1)
+ {
+ offset[0] = metadata_accum.get(bid);
+ block[0] = metadata_out[bid];
+ }
+ else
+ {
+ offset[0] = 0;
+ block[0] = 0;
+ }
+
+ hsize_t count[1] = {1};
+
+ //Select file dataspace
+ hid_t file_dataspace_id_2 = H5Dget_space(dataset_2);
+
+ H5Sselect_hyperslab(file_dataspace_id_2, H5S_SELECT_SET, offset, NULL, count, block);
+
+ hsize_t mdim_2[1] = {block[0]};
+
+ //Create data space in memory
+ hid_t mem_dataspace_id_2 = H5Screate_simple(1, mdim_2, NULL);
+
+ // allocate the memory
+ HeapMemory pmem;
+ //pmem.allocate(req);
+ ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(block[0],pmem));
+ mem.incRef();
+
+ // Read the dataset.
+ H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_2, file_dataspace_id_2, plist_id, (char *)mem.getPointer());
+
+ mem.allocate(pmem.size());
+
+ Unpack_stat ps;
+
+ openfpm::vector<device_grid> loc_grid_old_unp;
+ openfpm::vector<GBoxes<device_grid::dims>> gdb_ext_old_unp;
+
+ Unpacker<typename std::remove_reference<decltype(loc_grid_old)>::type,HeapMemory>::unpack(mem,loc_grid_old_unp,ps,1);
+ Unpacker<typename std::remove_reference<decltype(gdb_ext_old)>::type,HeapMemory>::unpack(mem,gdb_ext_old_unp,ps,1);
+
+ for (size_t i = 0; i < loc_grid_old_unp.size(); i++)
+ loc_grid_old.add(loc_grid_old_unp.get(i));
+
+ for (size_t i = 0; i < gdb_ext_old_unp.size(); i++)
+ gdb_ext_old.add(gdb_ext_old_unp.get(i));
+
+ mem.decRef();
+ delete &mem;
+
+ }
+
+public:
+
+ template<typename device_grid> inline void load(const std::string & filename,
+ openfpm::vector<device_grid> & loc_grid_old,
+ openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext_old)
+ {
+ Vcluster & v_cl = create_vcluster();
+
+ MPI_Comm comm = v_cl.getMPIComm();
+ MPI_Info info = MPI_INFO_NULL;
+
+ int mpi_rank = v_cl.getProcessUnitID();
+ //int mpi_size = v_cl.getProcessingUnits();
+
+ // Set up file access property list with parallel I/O access
+ hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ H5Pset_fapl_mpio(plist_id, comm, info);
+
+ //Open a file
+ hid_t file = H5Fopen (filename.c_str(), H5F_ACC_RDONLY, plist_id);
+ H5Pclose(plist_id);
+
+ //Open dataset
+ hid_t dataset = H5Dopen (file, "metadata", H5P_DEFAULT);
+
+ //Create property list for collective dataset read
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+
+ //Select file dataspace
+ hid_t file_dataspace_id = H5Dget_space(dataset);
+
+ hssize_t mpi_size_old = H5Sget_select_npoints (file_dataspace_id);
+
+ //if (mpi_rank == 0)
+ //printf ("\nOld MPI size: %llu\n", mpi_size_old);
+
+ //Where to read metadata
+ int metadata_out[mpi_size_old];
+
+ for (int i = 0; i < mpi_size_old; i++)
+ {
+ metadata_out[i] = 0;
+ }
+
+ //Size for data space in memory
+ hsize_t mdim[1] = {(size_t)mpi_size_old};
+
+ //Create data space in memory
+ hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
+
+/*
+ if (mpi_rank == 0)
+ {
+ hssize_t size;
+
+ size = H5Sget_select_npoints (mem_dataspace_id);
+ printf ("\nmemspace_id size: %llu\n", size);
+ size = H5Sget_select_npoints (file_dataspace_id);
+ printf ("dataspace_id size: %llu\n", size);
+ }
+*/
+ // Read the dataset.
+ H5Dread(dataset, H5T_NATIVE_INT, mem_dataspace_id, file_dataspace_id, plist_id, metadata_out);
+/*
+ if (mpi_rank == 0)
+ {
+ std::cout << "Metadata_out[]: ";
+ for (int i = 0; i < mpi_size_old; i++)
+ {
+ std::cout << metadata_out[i] << " ";
+ }
+ std::cout << " " << std::endl;
+ }
+*/
+
+ openfpm::vector<size_t> metadata_accum;
+ metadata_accum.resize(mpi_size_old);
+
+ metadata_accum.get(0) = 0;
+ for (int i = 1 ; i < mpi_size_old ; i++)
+ metadata_accum.get(i) = metadata_accum.get(i-1) + metadata_out[i-1];
+
+ //Open dataset
+ hid_t dataset_2 = H5Dopen (file, "grid_dist", H5P_DEFAULT);
+
+ //Create property list for collective dataset read
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+
+ /////////////////////////////////////
+
+ openfpm::vector<size_t> n_block;
+ n_block.resize(v_cl.getProcessingUnits());
+
+
+ for(size_t i = 0 ; i < n_block.size() ; i++)
+ n_block.get(i) = mpi_size_old / v_cl.getProcessingUnits();
+
+ size_t rest_block = mpi_size_old % v_cl.getProcessingUnits();
+
+ // std::cout << "MPI size old: " << mpi_size_old << std::endl;
+ //std::cout << "MPI size: " << v_cl.getProcessingUnits() << std::endl;
+
+
+ // std::cout << "Rest block: " << rest_block << std::endl;
+
+ size_t max_block;
+
+ if (rest_block != 0)
+ max_block = n_block.get(0) + 1;
+ else
+ max_block = n_block.get(0);
+
+ //for(size_t i = 0 ; i < n_block.size() ; i++)
+ for(size_t i = 0 ; i < rest_block ; i++)
+ n_block.get(i) += 1;
+
+
+ //for(size_t i = 0 ; i < n_block.size() ; i++)
+ //std::cout << "n_block.get(i): " << n_block.get(i) << std::endl;
+
+ size_t start_block = 0;
+ size_t stop_block = 0;
+
+
+ if (v_cl.getProcessUnitID() != 0)
+ {
+ for(size_t i = 0 ; i < v_cl.getProcessUnitID() ; i++)
+ start_block += n_block.get(i);
+ }
+
+ stop_block = start_block + n_block.get(v_cl.getProcessUnitID());
+
+// std::cout << "ID: " << v_cl.getProcessUnitID() << "; Start block: " << start_block << "; " << "Stop block: " << stop_block << std::endl;
+
+ if (mpi_rank >= mpi_size_old)
+ load_block(start_block,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,loc_grid_old,gdb_ext_old);
+ else
+ {
+ size_t n_bl = 0;
+ size_t lb = start_block;
+ for ( ; lb < stop_block ; lb++, n_bl++)
+ load_block(lb,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,loc_grid_old,gdb_ext_old);
+
+ if (n_bl < max_block)
+ load_block(-1,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,loc_grid_old,gdb_ext_old);
+ }
+
+ ////////////////////////////////////
+
+ //std::cout << "LOAD: sum: " << sum << std::endl;
+
+ // Close the dataset.
+ H5Dclose(dataset);
+ H5Dclose(dataset_2);
+ // Close the file.
+ H5Fclose(file);
+ H5Pclose(plist_id);
+ }
+
+};
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_GD_HPP_ */
diff --git a/src/HDF5_wr/HDF5_reader_vd.hpp b/src/HDF5_wr/HDF5_reader_vd.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..41109782295fdab5d40ac4b042a5c5c6a58519df
--- /dev/null
+++ b/src/HDF5_wr/HDF5_reader_vd.hpp
@@ -0,0 +1,244 @@
+/*
+ * HDF5_reader_vd.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_VD_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_VD_HPP_
+
+
+template <>
+class HDF5_reader<VECTOR_DIST>
+{
+private:
+
+ template<unsigned int dim, typename St,typename prp>
+ bool load_block(long int bid,
+ hssize_t mpi_size_old,
+ int * metadata_out,
+ openfpm::vector<size_t> metadata_accum,
+ hid_t plist_id,
+ hid_t dataset_2,
+ size_t & g_m,
+ openfpm::vector<Point<dim,St>> & v_pos,
+ openfpm::vector<prp> & v_prp)
+ {
+ hsize_t offset[1];
+ hsize_t block[1];
+
+ if (bid < mpi_size_old && bid != -1)
+ {
+ offset[0] = metadata_accum.get(bid);
+ block[0] = metadata_out[bid];
+ }
+ else
+ {
+ offset[0] = 0;
+ block[0] = 0;
+ }
+
+ hsize_t count[1] = {1};
+
+
+ //Select file dataspace
+ hid_t file_dataspace_id_2 = H5Dget_space(dataset_2);
+ if (file_dataspace_id_2 < 0) {return false;}
+
+ herr_t err = H5Sselect_hyperslab(file_dataspace_id_2, H5S_SELECT_SET, offset, NULL, count, block);
+ if (err < 0) {return false;}
+
+ hsize_t mdim_2[1] = {block[0]};
+
+
+ //Create data space in memory
+ hid_t mem_dataspace_id_2 = H5Screate_simple(1, mdim_2, NULL);
+ if (mem_dataspace_id_2 < 0) {return false;}
+
+ size_t sum = 0;
+
+ for (int i = 0; i < mpi_size_old; i++)
+ sum += metadata_out[i];
+
+ // allocate the memory
+ HeapMemory pmem;
+
+ ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(block[0],pmem));
+ mem.incRef();
+
+ // Read the dataset.
+ err = H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_2, file_dataspace_id_2, plist_id, (char *)mem.getPointer());
+ if (err < 0) {return false;}
+
+ mem.allocate(pmem.size());
+
+ Unpack_stat ps;
+
+ openfpm::vector<Point<dim, St>> v_pos_unp;
+
+ openfpm::vector<prp> v_prp_unp;
+
+ Unpacker<decltype(v_pos_unp),HeapMemory>::unpack(mem,v_pos_unp,ps,1);
+ Unpacker<decltype(v_prp_unp),HeapMemory>::unpack(mem,v_prp_unp,ps,1);
+
+ mem.decRef();
+ delete &mem;
+
+ for (size_t i = 0; i < v_pos_unp.size(); i++)
+ v_pos.add(v_pos_unp.get(i));
+
+ for (size_t i = 0; i < v_prp_unp.size(); i++)
+ v_prp.add(v_prp_unp.get(i));
+
+ g_m = v_pos.size();
+
+ H5Sclose(file_dataspace_id_2);
+ H5Sclose(mem_dataspace_id_2);
+
+ return true;
+ }
+
+public:
+
+ template<unsigned int dim, typename St, typename prp> inline bool load(const std::string & filename,
+ openfpm::vector<Point<dim,St>> & v_pos,
+ openfpm::vector<prp> & v_prp,
+ size_t & g_m)
+ {
+ Vcluster & v_cl = create_vcluster();
+
+ v_pos.clear();
+ v_prp.clear();
+
+ g_m = 0;
+
+ MPI_Comm comm = v_cl.getMPIComm();
+ MPI_Info info = MPI_INFO_NULL;
+
+ int mpi_rank = v_cl.getProcessUnitID();
+
+ // Set up file access property list with parallel I/O access
+ hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ if (plist_id == -1) {return false;}
+ herr_t err = H5Pset_fapl_mpio(plist_id, comm, info);
+ if (err < 0)
+ return false;
+
+ //Open a file
+ hid_t file = H5Fopen (filename.c_str(), H5F_ACC_RDONLY, plist_id);
+ if (file < 0) {return false;}
+ H5Pclose(plist_id);
+
+ //Open dataset
+ hid_t dataset = H5Dopen (file, "metadata", H5P_DEFAULT);
+ if (dataset < 0) {return false;}
+
+ //Create property list for collective dataset read
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ if (plist_id == -1) {return false;}
+ H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+
+ //Select file dataspace
+ hid_t file_dataspace_id = H5Dget_space(dataset);
+ if (file_dataspace_id < 0) {return false;}
+
+ hssize_t mpi_size_old = H5Sget_select_npoints (file_dataspace_id);
+ if (mpi_size_old < 0) {return false;}
+
+ //Where to read metadata
+ int metadata_out[mpi_size_old];
+
+ for (int i = 0; i < mpi_size_old; i++)
+ {metadata_out[i] = 0;}
+
+ //Size for data space in memory
+ hsize_t mdim[1] = {(size_t)mpi_size_old};
+
+ //Create data space in memory
+ hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
+ if (mem_dataspace_id < 0) {return false;}
+
+ // Read the dataset.
+ err = H5Dread(dataset, H5T_NATIVE_INT, mem_dataspace_id, file_dataspace_id, plist_id, metadata_out);
+ if (err < 0) {return false;}
+
+ openfpm::vector<size_t> metadata_accum;
+ metadata_accum.resize(mpi_size_old);
+
+ metadata_accum.get(0) = 0;
+ for (int i = 1 ; i < mpi_size_old ; i++)
+ metadata_accum.get(i) = metadata_accum.get(i-1) + metadata_out[i-1];
+
+ //Open dataset
+ hid_t dataset_2 = H5Dopen (file, "vector_dist", H5P_DEFAULT);
+ if (dataset_2 < 0) {return false;}
+
+ //Create property list for collective dataset read
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ if (plist_id == -1) {return false;}
+
+ err = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+ if (err < 0) {return false;}
+
+ openfpm::vector<size_t> n_block;
+ n_block.resize(v_cl.getProcessingUnits());
+
+
+ for(size_t i = 0 ; i < n_block.size() ; i++)
+ n_block.get(i) = mpi_size_old / v_cl.getProcessingUnits();
+
+ size_t rest_block = mpi_size_old % v_cl.getProcessingUnits();
+
+ size_t max_block;
+
+ if (rest_block != 0)
+ max_block = n_block.get(0) + 1;
+ else
+ max_block = n_block.get(0);
+
+ //for(size_t i = 0 ; i < n_block.size() ; i++)
+ for(size_t i = 0 ; i < rest_block ; i++)
+ n_block.get(i) += 1;
+
+ size_t start_block = 0;
+ size_t stop_block = 0;
+
+
+ if (v_cl.getProcessUnitID() != 0)
+ {
+ for(size_t i = 0 ; i < v_cl.getProcessUnitID() ; i++)
+ start_block += n_block.get(i);
+ }
+
+ stop_block = start_block + n_block.get(v_cl.getProcessUnitID());
+
+ if (mpi_rank >= mpi_size_old)
+ load_block(start_block,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,g_m,v_pos,v_prp);
+ else
+ {
+ size_t n_bl = 0;
+ size_t lb = start_block;
+ for ( ; lb < stop_block ; lb++, n_bl++)
+ load_block(lb,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,g_m,v_pos,v_prp);
+
+ if (n_bl < max_block)
+ load_block(-1,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,g_m,v_pos,v_prp);
+ }
+
+ // Close open object
+ H5Sclose(mem_dataspace_id);
+ H5Sclose(file_dataspace_id);
+ // Close the dataset.
+ H5Dclose(dataset);
+ H5Dclose(dataset_2);
+ // Close the file.
+ H5Fclose(file);
+ H5Pclose(plist_id);
+
+ return true;
+ }
+};
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_VD_HPP_ */
diff --git a/src/HDF5_wr/HDF5_wr.hpp b/src/HDF5_wr/HDF5_wr.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..69fa3936cccb8d76065ce8e00812678f6fa21b2a
--- /dev/null
+++ b/src/HDF5_wr/HDF5_wr.hpp
@@ -0,0 +1,19 @@
+/*
+ * HDF5_wr.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_WR_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_WR_HPP_
+
+
+#define VECTOR_DIST 1
+#define GRID_DIST 2
+
+#include "HDF5_writer.hpp"
+#include "HDF5_reader.hpp"
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WR_HPP_ */
diff --git a/src/HDF5_wr/HDF5_writer.hpp b/src/HDF5_wr/HDF5_writer.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..95b686cf9a4867d49d3110dddfef79ba492670c1
--- /dev/null
+++ b/src/HDF5_wr/HDF5_writer.hpp
@@ -0,0 +1,29 @@
+/*
+ * HDF5_writer.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_HPP_
+
+
+#include "VCluster/VCluster.hpp"
+#include <hdf5.h>
+
+template <unsigned int type>
+class HDF5_writer
+{
+
+ void save()
+ {
+ std::cerr << __FILE__ << ":" << __LINE__ << " Error: we do not know how to write this type of data" << std::endl;
+ }
+
+};
+
+#include "HDF5_writer_vd.hpp"
+#include "HDF5_writer_gd.hpp"
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_HPP_ */
diff --git a/src/HDF5_wr/HDF5_writer_gd.hpp b/src/HDF5_wr/HDF5_writer_gd.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..592624b83f52a428e17e551712cecafb825ef8c1
--- /dev/null
+++ b/src/HDF5_wr/HDF5_writer_gd.hpp
@@ -0,0 +1,177 @@
+/*
+ * HDF5_writer_gd.hpp
+ *
+ * Created on: May 2, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_GD_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_GD_HPP_
+
+
+#include "Packer_Unpacker/Pack_selector.hpp"
+#include "Packer_Unpacker/Packer.hpp"
+#include "Packer_Unpacker/Unpacker.hpp"
+#include "util/GBoxes.hpp"
+
+template <>
+class HDF5_writer<GRID_DIST>
+{
+public:
+
+ template<typename device_grid>
+ inline void save(const std::string & filename,
+ const openfpm::vector<device_grid> & loc_grid,
+ const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext) const
+ {
+ Vcluster & v_cl = create_vcluster();
+
+ //Pack_request vector
+ size_t req = 0;
+
+ //Pack request
+ Packer<typename std::remove_reference<decltype(loc_grid)>::type,HeapMemory>::packRequest(loc_grid,req);
+ Packer<typename std::remove_reference<decltype(gdb_ext)>::type,HeapMemory>::packRequest(gdb_ext,req);
+
+ //std::cout << "Req: " << req << std::endl;
+
+ // allocate the memory
+ HeapMemory pmem;
+ //pmem.allocate(req);
+ ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(req,pmem));
+ mem.incRef();
+
+ //Packing
+
+ Pack_stat sts;
+
+ Packer<typename std::remove_reference<decltype(loc_grid)>::type,HeapMemory>::pack(mem,loc_grid,sts);
+ Packer<typename std::remove_reference<decltype(gdb_ext)>::type,HeapMemory>::pack(mem,gdb_ext,sts);
+
+ /*****************************************************************
+ * Create a new file with default creation and access properties.*
+ * Then create a dataset and write data to it and close the file *
+ * and dataset. *
+ *****************************************************************/
+
+ int mpi_rank = v_cl.getProcessUnitID();
+ int mpi_size = v_cl.getProcessingUnits();
+
+ MPI_Comm comm = v_cl.getMPIComm();
+ MPI_Info info = MPI_INFO_NULL;
+
+ // Set up file access property list with parallel I/O access
+
+ hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ H5Pset_fapl_mpio(plist_id, comm, info);
+
+ // Create a new file collectively and release property list identifier.
+ hid_t file = H5Fcreate (filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
+ H5Pclose(plist_id);
+
+ size_t sz = pmem.size();
+ //std::cout << "Pmem.size: " << pmem.size() << std::endl;
+ openfpm::vector<size_t> sz_others;
+ v_cl.allGather(sz,sz_others);
+ v_cl.execute();
+
+ size_t sum = 0;
+
+ for (size_t i = 0; i < sz_others.size(); i++)
+ sum += sz_others.get(i);
+
+ //Size for data space in file
+ hsize_t fdim[1] = {sum};
+
+ //Size for data space in file
+ hsize_t fdim2[1] = {(size_t)mpi_size};
+
+ //Create data space in file
+ hid_t file_dataspace_id = H5Screate_simple(1, fdim, NULL);
+
+ //Create data space in file
+ hid_t file_dataspace_id_2 = H5Screate_simple(1, fdim2, NULL);
+
+ //Size for data space in memory
+ hsize_t mdim[1] = {pmem.size()};
+
+ //Create data space in memory
+ hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
+
+ //if (mpi_rank == 0)
+ //std::cout << "Total object size: " << sum << std::endl;
+
+ //Create data set in file
+ hid_t file_dataset = H5Dcreate (file, "grid_dist", H5T_NATIVE_CHAR, file_dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ //Create data set 2 in file
+ hid_t file_dataset_2 = H5Dcreate (file, "metadata", H5T_NATIVE_INT, file_dataspace_id_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ //H5Pclose(plist_id);
+ H5Sclose(file_dataspace_id);
+ H5Sclose(file_dataspace_id_2);
+
+ hsize_t block[1] = {pmem.size()};
+
+ //hsize_t stride[1] = {1};
+
+ hsize_t count[1] = {1};
+
+ hsize_t offset[1] = {0};
+
+ for (int i = 0; i < mpi_rank; i++)
+ {
+ if (mpi_rank == 0)
+ offset[0] = 0;
+ else
+ offset[0] += sz_others.get(i);
+ }
+
+ // std::cout << "MPI rank: " << mpi_rank << ", MPI size: " << mpi_size << ", Offset: " << offset[0] << ", Block: " << block[0] << std::endl;
+
+ int metadata[mpi_size];
+
+ for (int i = 0; i < mpi_size; i++)
+ metadata[i] = sz_others.get(i);
+
+ //Select hyperslab in the file.
+ file_dataspace_id = H5Dget_space(file_dataset);
+ H5Sselect_hyperslab(file_dataspace_id, H5S_SELECT_SET, offset, NULL, count, block);
+
+ file_dataspace_id_2 = H5Dget_space(file_dataset_2);
+
+
+ //Create property list for collective dataset write.
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+
+ //Write a data set to a file
+ H5Dwrite(file_dataset, H5T_NATIVE_CHAR, mem_dataspace_id, file_dataspace_id, plist_id, (const char *)pmem.getPointer());
+
+ //Write a data set 2 to a file
+ H5Dwrite(file_dataset_2, H5T_NATIVE_INT, H5S_ALL, file_dataspace_id_2, plist_id, metadata);
+/*
+ for (size_t i = 0; i < gdb_ext.size(); i++)
+ {
+ Box<dim,long int> box = gdb_ext.get(i).Dbox;
+ std::cout << "Dboxes saved: (" << box.getLow(0) << "; " << box.getLow(1) << "); (" << box.getHigh(0) << "; " << box.getHigh(1) << ")" << std::endl;
+ }
+
+ for (size_t i = 0; i < loc_grid.size(); i++)
+ {
+ std::cout << "loc_grids saved: (" << loc_grid.get(i).getGrid().getBox().getLow(0) << "; " << loc_grid.get(i).getGrid().getBox().getLow(1) << "); (" << loc_grid.get(i).getGrid().getBox().getHigh(0) << "; " << loc_grid.get(i).getGrid().getBox().getHigh(1) << ")" << std::endl;
+ }
+*/
+ //Close/release resources.
+ H5Dclose(file_dataset);
+ H5Sclose(file_dataspace_id);
+ H5Dclose(file_dataset_2);
+ H5Sclose(file_dataspace_id_2);
+ H5Sclose(mem_dataspace_id);
+ H5Pclose(plist_id);
+ H5Fclose(file);
+ }
+
+};
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_GD_HPP_ */
diff --git a/src/HDF5_wr/HDF5_writer_unit_tests.hpp b/src/HDF5_wr/HDF5_writer_unit_tests.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..0fc72b14825d1864c690158be5b08d51c2cd4028
--- /dev/null
+++ b/src/HDF5_wr/HDF5_writer_unit_tests.hpp
@@ -0,0 +1,115 @@
+/*
+ * HDF5_writer_unit_test.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_UNIT_TESTS_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_UNIT_TESTS_HPP_
+
+#include "HDF5_wr.hpp"
+
+#include "hdf5.h"
+
+BOOST_AUTO_TEST_SUITE( vd_hdf5_chckpnt_rstrt_test )
+
+// Dimensionality
+const size_t dim = 3;
+
+BOOST_AUTO_TEST_CASE( vector_dist_hdf5_save_test )
+{
+ openfpm::vector<Point<3,float>> vpos;
+ openfpm::vector<aggregate<float[dim]>> vprp;
+
+ // Put forces
+
+ for (size_t i = 0 ; i < 1024 ; i++)
+ {
+ Point<3,float> p;
+
+ p.get(0) = i;
+ p.get(1) = i+13;
+ p.get(2) = i+17;
+
+ vpos.add(p);
+
+ vprp.add();
+ vprp.template get<0>(vprp.size()-1)[0] = p.get(0) + 100.0;
+ vprp.template get<0>(vprp.size()-1)[1] = p.get(1) + 200.0;
+ vprp.template get<0>(vprp.size()-1)[2] = p.get(2) + 300.0;
+ }
+
+ HDF5_writer<VECTOR_DIST> h5;
+
+ // Save the vector
+ h5.save("vector_dist.h5",vpos,vprp);
+
+ HDF5_reader<VECTOR_DIST> h5r;
+
+ openfpm::vector<Point<3,float>> vpos2;
+ openfpm::vector<aggregate<float[dim]>> vprp2;
+
+ size_t g_m = 0;
+ h5r.load("vector_dist.h5",vpos2,vprp2,g_m);
+
+ BOOST_REQUIRE_EQUAL(1024ul,vpos2.size());
+ BOOST_REQUIRE_EQUAL(1024ul,vprp2.size());
+
+ BOOST_REQUIRE_EQUAL(1024ul,g_m);
+
+ // Check that vpos == vpos2 and vprp2 == vprp2
+
+ bool check = true;
+ for (size_t i = 0 ; i < vpos.size() ; i++)
+ {
+ check &= (vpos.get(i) == vpos2.get(i));
+ check &= (vprp.get_o(i) == vprp2.get_o(i));
+ }
+
+ BOOST_REQUIRE_EQUAL(check,true);
+}
+
+
+
+BOOST_AUTO_TEST_CASE( vector_dist_hdf5_load_test )
+{
+ Vcluster & v_cl = create_vcluster();
+
+ openfpm::vector<Point<3,float>> vpos;
+ openfpm::vector<aggregate<float[dim]>> vprp;
+
+ HDF5_reader<VECTOR_DIST> h5;
+
+ size_t g_m = 0;
+
+ // Load the vector
+ h5.load("test_data/vector_dist_24.h5",vpos,vprp,g_m);
+
+ /////////////////// Checking data ///////////////////////
+
+ // Check total number of particles
+ size_t n_part = vpos.size();
+ v_cl.sum(n_part);
+ v_cl.execute();
+
+ BOOST_REQUIRE_EQUAL(n_part,1024ul*24ul);
+
+ BOOST_REQUIRE_EQUAL(vpos.size(),vprp.size());
+
+ bool check = true;
+
+ for (size_t i = 0 ; i < vpos.size() ; i++)
+ {
+ check &= (vprp.template get<0>(i)[0] == vpos.template get<0>(i)[0] + 100.0);
+ check &= (vprp.template get<0>(i)[1] == vpos.template get<0>(i)[1] + 200.0);
+ check &= (vprp.template get<0>(i)[2] == vpos.template get<0>(i)[2] + 300.0);
+ }
+
+
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_UNIT_TESTS_HPP_ */
diff --git a/src/HDF5_wr/HDF5_writer_vd.hpp b/src/HDF5_wr/HDF5_writer_vd.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..d4139624679969553eb06d71529e99993e687efe
--- /dev/null
+++ b/src/HDF5_wr/HDF5_writer_vd.hpp
@@ -0,0 +1,161 @@
+/*
+ * HDF5_loader_vector_dist.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_
+
+#include "Packer_Unpacker/Pack_selector.hpp"
+#include "Packer_Unpacker/Packer.hpp"
+#include "Packer_Unpacker/Unpacker.hpp"
+
+template <>
+class HDF5_writer<VECTOR_DIST>
+{
+public:
+
+ template<unsigned int dim, typename St, typename prp>
+ inline void save(const std::string & filename,
+ const openfpm::vector<Point<dim,St>> & v_pos,
+ const openfpm::vector<prp> & v_prp) const
+ {
+ Vcluster & v_cl = create_vcluster();
+
+ //Pack_request vector
+ size_t req = 0;
+
+ //std::cout << "V_pos.size() before save: " << v_pos.size() << std::endl;
+
+ //Pack request
+ Packer<typename std::remove_reference<decltype(v_pos)>::type,HeapMemory>::packRequest(v_pos,req);
+ Packer<typename std::remove_reference<decltype(v_prp)>::type,HeapMemory>::packRequest(v_prp,req);
+
+ // allocate the memory
+ HeapMemory pmem;
+ //pmem.allocate(req);
+ ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(req,pmem));
+ mem.incRef();
+
+ //Packing
+
+ Pack_stat sts;
+
+ Packer<typename std::remove_reference<decltype(v_pos)>::type,HeapMemory>::pack(mem,v_pos,sts);
+ Packer<typename std::remove_reference<decltype(v_prp)>::type,HeapMemory>::pack(mem,v_prp,sts);
+
+ /*****************************************************************
+ * Create a new file with default creation and access properties.*
+ * Then create a dataset and write data to it and close the file *
+ * and dataset. *
+ *****************************************************************/
+
+ int mpi_rank = v_cl.getProcessUnitID();
+ int mpi_size = v_cl.getProcessingUnits();
+
+ MPI_Comm comm = v_cl.getMPIComm();
+ MPI_Info info = MPI_INFO_NULL;
+
+ // Set up file access property list with parallel I/O access
+
+ hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ H5Pset_fapl_mpio(plist_id, comm, info);
+
+ // Create a new file collectively and release property list identifier.
+ hid_t file = H5Fcreate (filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
+ H5Pclose(plist_id);
+
+ size_t sz = pmem.size();
+ //std::cout << "Pmem.size: " << pmem.size() << std::endl;
+ openfpm::vector<size_t> sz_others;
+ v_cl.allGather(sz,sz_others);
+ v_cl.execute();
+
+ size_t sum = 0;
+
+ for (size_t i = 0; i < sz_others.size(); i++)
+ sum += sz_others.get(i);
+
+ //Size for data space in file
+ hsize_t fdim[1] = {sum};
+
+ //Size for data space in file
+ hsize_t fdim2[1] = {(size_t)mpi_size};
+
+ //Create data space in file
+ hid_t file_dataspace_id = H5Screate_simple(1, fdim, NULL);
+
+ //Create data space in file
+ hid_t file_dataspace_id_2 = H5Screate_simple(1, fdim2, NULL);
+
+ //Size for data space in memory
+ hsize_t mdim[1] = {pmem.size()};
+
+ //Create data space in memory
+ hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
+
+ //Create data set in file
+ hid_t file_dataset = H5Dcreate (file, "vector_dist", H5T_NATIVE_CHAR, file_dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ //Create data set 2 in file
+ hid_t file_dataset_2 = H5Dcreate (file, "metadata", H5T_NATIVE_INT, file_dataspace_id_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ //H5Pclose(plist_id);
+ H5Sclose(file_dataspace_id);
+ H5Sclose(file_dataspace_id_2);
+
+ hsize_t block[1] = {pmem.size()};
+
+ //hsize_t stride[1] = {1};
+
+ hsize_t count[1] = {1};
+
+ hsize_t offset[1] = {0};
+
+ for (int i = 0; i < mpi_rank; i++)
+ {
+ if (mpi_rank == 0)
+ offset[0] = 0;
+ else
+ offset[0] += sz_others.get(i);
+ }
+
+ int metadata[mpi_size];
+
+ for (int i = 0; i < mpi_size; i++)
+ metadata[i] = sz_others.get(i);
+
+ //Select hyperslab in the file.
+ file_dataspace_id = H5Dget_space(file_dataset);
+ H5Sselect_hyperslab(file_dataspace_id, H5S_SELECT_SET, offset, NULL, count, block);
+
+ file_dataspace_id_2 = H5Dget_space(file_dataset_2);
+
+
+ //Create property list for collective dataset write.
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+
+ //Write a data set to a file
+ H5Dwrite(file_dataset, H5T_NATIVE_CHAR, mem_dataspace_id, file_dataspace_id, plist_id, (const char *)pmem.getPointer());
+
+ //Write a data set 2 to a file
+ H5Dwrite(file_dataset_2, H5T_NATIVE_INT, H5S_ALL, file_dataspace_id_2, plist_id, metadata);
+
+
+ //Close/release resources.
+ H5Dclose(file_dataset);
+ H5Sclose(file_dataspace_id);
+ H5Dclose(file_dataset_2);
+ H5Sclose(file_dataspace_id_2);
+ H5Sclose(mem_dataspace_id);
+ H5Pclose(plist_id);
+ H5Fclose(file);
+ }
+
+};
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_ */
diff --git a/src/Makefile.am b/src/Makefile.am
index 06d23e47432bcb80329066b221179a897c964bb6..e77305ed8a5f83ee2cf5f52031ed4993d54c2316 100755
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,16 +1,16 @@
-LINKLIBS = $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_IOSTREAMS_LIB) $(BOOST_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_THREAD_LIB) $(HDF5_LDFLAGS) $(HDF5_LIBS)
+LINKLIBS = $(PTHREAD_LIBS) $(HDF5_LDFLAGS) $(HDF5_LIBS) $(OPT_LIBS) $(BOOST_IOSTREAMS_LIB) $(BOOST_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_THREAD_LIB)
noinst_PROGRAMS = io
-io_SOURCES = main.cpp ../../openfpm_vcluster/src/VCluster/VCluster.cpp ../../openfpm_devices/src/memory/HeapMemory.cpp ../../openfpm_devices/src/Memleak_check.cpp
-io_CXXFLAGS = $(AM_CXXFLAGS) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) -I/usr/local/include $(HDF5_CPPFLAGS)
+io_SOURCES = main.cpp ../../openfpm_vcluster/src/VCluster/VCluster.cpp ../../openfpm_devices/src/memory/HeapMemory.cpp ../../openfpm_devices/src/Memleak_check.cpp ../../openfpm_devices/src/memory/PtrMemory.cpp
+io_CXXFLAGS = $(AM_CXXFLAGS) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(HDF5_CPPFLAGS) $(BOOST_CPPFLAGS) -I/usr/local/include
io_CFLAGS = $(CUDA_CFLAGS)
-io_LDADD = $(LINKLIBS)
+io_LDADD = $(LINKLIBS)
-nobase_include_HEADERS = CSVWriter/csv_multiarray.hpp CSVWriter/CSVWriter.hpp CSVWriter/is_csv_writable.hpp \
-GraphMLWriter/GraphMLWriter.hpp util.hpp \
-VTKWriter/VTKWriter.hpp VTKWriter/byteswap_portable.hpp VTKWriter/VTKWriter_dist_graph.hpp VTKWriter/VTKWriter_graph.hpp VTKWriter/VTKWriter_point_set.hpp VTKWriter/VTKWriter_grids.hpp VTKWriter/VTKWriter_grids_st.hpp VTKWriter/VTKWriter_grids_util.hpp VTKWriter/VTKWriter_vector_box.hpp VTKWriter/is_vtk_writable.hpp HDF5_XdmfWriter/HDF5_XdmfWriter.hpp HDF5_XdmfWriter/HDF5_XdmfWriter_point_set.hpp HDF5_XdmfWriter/HDF5_XdmfWriter_util.hpp \
-Plot/GoogleChart.hpp Plot/util.hpp
+nobase_include_HEADERS = RawReader/RawReader.hpp RawReader/RawReader_unit_tests.hpp CSVWriter/csv_multiarray.hpp CSVWriter/CSVWriter.hpp CSVWriter/is_csv_writable.hpp \
+GraphMLWriter/GraphMLWriter.hpp util/util.hpp util/GBoxes.hpp \
+VTKWriter/VTKWriter.hpp VTKWriter/byteswap_portable.hpp VTKWriter/VTKWriter_dist_graph.hpp VTKWriter/VTKWriter_graph.hpp VTKWriter/VTKWriter_point_set.hpp VTKWriter/VTKWriter_grids.hpp VTKWriter/VTKWriter_grids_st.hpp VTKWriter/VTKWriter_grids_util.hpp VTKWriter/VTKWriter_vector_box.hpp VTKWriter/is_vtk_writable.hpp HDF5_wr/HDF5_wr.hpp HDF5_wr/HDF5_writer.hpp HDF5_wr/HDF5_writer_vd.hpp HDF5_wr/HDF5_writer_gd.hpp HDF5_wr/HDF5_reader_gd.hpp HDF5_wr/HDF5_reader.hpp HDF5_wr/HDF5_reader_vd.hpp \
+Plot/GoogleChart.hpp Plot/util.hpp
.cu.o :
diff --git a/src/Plot/GoogleChart.hpp b/src/Plot/GoogleChart.hpp
index 38d20008241ced3d405db5ec8edddf9744942198..136e7b228c4ae2c7d9412616079a209d346f2353 100644
--- a/src/Plot/GoogleChart.hpp
+++ b/src/Plot/GoogleChart.hpp
@@ -68,7 +68,16 @@ struct GCoptions
//! curve type
std::string curveType = "function";
- //! copy operator
+ //! barWD
+ bool barWD = false;
+
+ /*! \brief copy operator
+ *
+ * \param opt object to copy
+ *
+ * \return itself
+ *
+ */
GCoptions & operator=(const GCoptions & opt)
{
title = opt.title;
@@ -87,6 +96,9 @@ struct GCoptions
}
};
+/*! \brief Google Graph
+ *
+ */
struct GGraph
{
//! TypeOfGraph
@@ -98,6 +110,9 @@ struct GGraph
//! option
std::string option;
+ //! view in case we need a view
+ std::string view;
+
//! Google chart option
GCoptions opt;
};
@@ -243,6 +258,35 @@ class GoogleChart
return data.str();
}
+ /*! \brief Construct a view option
+ *
+ * \param opt GoogleChart option
+ *
+ * \return the string
+ *
+ */
+ std::string get_view_bar_option(const GCoptions & opt, size_t n_col)
+ {
+ if (opt.barWD == false)
+ return std::string();
+
+ std::stringstream str;
+
+ str << "[0" << std::endl;
+
+ for (size_t i = 1 ; i < n_col ; i++)
+ {
+ str << "," << i << ",{ calc: \"stringify\"," << std::endl;
+ str << "sourceColumn: " << i << "," << std::endl;
+ str << "type: \"string\"," << std::endl;
+ str << "role: \"annotation\" }"<< std::endl;
+ }
+
+ str << "]" << std::endl;
+
+ return str.str();
+ }
+
std::string get_colums_bar_option(const GCoptions & opt)
{
std::stringstream str;
@@ -311,19 +355,46 @@ class GoogleChart
of << "};\n";
}
+ /*! \brief Add a view data variable
+ *
+ * \param of file out
+ * \param i id
+ * \param view string
+ *
+ */
+ void addView(std::ofstream & of, size_t i, std::string view)
+ {
+ if (view.size() == 0)
+ return;
+
+ of << "var view" << i << " = new google.visualization.DataView(data" << i << ");" << std::endl;
+ of << "view"<< i << ".setColumns(";
+ of << view << ");" << std::endl;
+ }
+
/*! \brief Add a draw div section
*
* \param of file out
* \param i id
+ * \param draw_view draw a chart(true) or view(false)
*
*/
- void addDrawDiv(std::ofstream & of, size_t i)
+ void addDrawDiv(std::ofstream & of, size_t i, bool draw_view)
{
of << "$(\"#export_svg" << i << "\").on(\"click\", function (event) {exportToSVG.apply(this,[" << i << "]);});\n";
of << "var chart = new google.visualization.ComboChart(document.getElementById('chart_div";
of << i;
- of << "'));chart.draw(data";
- of << i;
+ of << "'));" << std::endl;
+ if (draw_view == true)
+ {
+ of << "chart.draw(data";
+ of << i;
+ }
+ else
+ {
+ of << "chart.draw(view";
+ of << i;
+ }
of << ", options";
of << i;
of << ");\n";
@@ -438,6 +509,7 @@ public:
set_of_graphs.last().type = GGRAPH_COLUMS;
set_of_graphs.last().data = get_points_plot_data(x,y,yn,opt,set_of_graphs.size()-1);
set_of_graphs.last().option = get_colums_bar_option(opt);
+ set_of_graphs.last().view = get_view_bar_option(opt,y.get(0).size());
set_of_graphs.last().opt = opt;
}
@@ -599,7 +671,10 @@ public:
addOption(of,i,set_of_graphs.get(i).option);
for (size_t i = 0 ; i < set_of_graphs.size() ; i++)
- addDrawDiv(of,i);
+ addView(of,i,set_of_graphs.get(i).view);
+
+ for (size_t i = 0 ; i < set_of_graphs.size() ; i++)
+ addDrawDiv(of,i,set_of_graphs.get(i).view.size() == 0);
of << begin_div;
diff --git a/src/Plot/Plot_unit_tests.hpp b/src/Plot/Plot_unit_tests.hpp
index 04841b931a9c64fcc29a7b6987ae626ad4d4d1fc..db2d2ecc9db4b35b8d5b10e6fb03d535e9104b9a 100644
--- a/src/Plot/Plot_unit_tests.hpp
+++ b/src/Plot/Plot_unit_tests.hpp
@@ -13,8 +13,72 @@
BOOST_AUTO_TEST_SUITE( plot_unit_test )
+
+BOOST_AUTO_TEST_CASE( google_chart_bar_string )
+{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+ //! [Producing an Histogram graph]
+
+ openfpm::vector<std::string> x;
+ openfpm::vector<openfpm::vector<size_t>> y;
+ openfpm::vector<std::string> yn;
+
+ x.add("colum1");
+ x.add("colum2");
+ x.add("colum3");
+ x.add("colum4");
+ x.add("colum5");
+ x.add("colum6");
+
+ // Each colum can have multiple data set (in this case 4 dataset)
+ // Each dataset can have a name
+ yn.add("dataset1");
+ yn.add("dataset2");
+ yn.add("dataset3");
+ yn.add("dataset4");
+
+ // Each colums can have multiple data-set
+ y.add({2,3,5,6});
+ y.add({5,6,1,6});
+ y.add({2,1,6,9});
+ y.add({1,6,3,2});
+ y.add({3,3,0,6});
+ y.add({2,1,4,6});
+
+ // Google charts options
+ GCoptions options;
+
+ options.title = std::string("Example");
+ options.yAxis = std::string("Y Axis");
+ options.xAxis = std::string("X Axis");
+ options.stype = std::string("bars");
+ options.barWD = true;
+
+ // it say that the colum4 must me represented with a line
+ options.stypeext = std::string("{3: {type: 'line'}}");
+
+ GoogleChart cg;
+ cg.AddHistGraph(x,y,yn,options);
+ cg.write("gc_out_sc.html");
+
+ //! [Producing an Histogram graph]
+
+ bool test = compare("gc_out_sc.html","test_data/gc_out_sc_test.html");
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+
BOOST_AUTO_TEST_CASE( google_chart )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
//! [Producing an Histogram graph]
openfpm::vector<std::string> x;
@@ -66,6 +130,11 @@ BOOST_AUTO_TEST_CASE( google_chart )
BOOST_AUTO_TEST_CASE( google_chart2 )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
openfpm::vector<std::string> x;
openfpm::vector<openfpm::vector<float>> y;
openfpm::vector<std::string> yn;
@@ -110,6 +179,11 @@ BOOST_AUTO_TEST_CASE( google_chart2 )
BOOST_AUTO_TEST_CASE( google_chart3 )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
openfpm::vector<std::string> x;
openfpm::vector<openfpm::vector<float>> y;
openfpm::vector<std::string> yn;
@@ -153,6 +227,11 @@ BOOST_AUTO_TEST_CASE( google_chart3 )
BOOST_AUTO_TEST_CASE( google_chart4 )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
openfpm::vector<std::string> x;
openfpm::vector<openfpm::vector<float>> y;
openfpm::vector<std::string> yn;
@@ -189,6 +268,11 @@ BOOST_AUTO_TEST_CASE( google_chart4 )
BOOST_AUTO_TEST_CASE( google_chart5 )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
openfpm::vector<std::string> x;
openfpm::vector<openfpm::vector<float>> y;
@@ -217,6 +301,11 @@ BOOST_AUTO_TEST_CASE( google_chart5 )
BOOST_AUTO_TEST_CASE( google_chart6 )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
openfpm::vector<openfpm::vector<float>> y;
// Each colums can have multiple data-set
@@ -237,6 +326,11 @@ BOOST_AUTO_TEST_CASE( google_chart6 )
BOOST_AUTO_TEST_CASE( google_chart_with_inject_HTML )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
//! [Producing a set of histograms graphs]
openfpm::vector<std::string> x;
@@ -295,6 +389,11 @@ BOOST_AUTO_TEST_CASE( google_chart_with_inject_HTML )
BOOST_AUTO_TEST_CASE( google_chart_linear_plot )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
//! [Producing lines graph with style]
openfpm::vector<std::string> x;
@@ -357,6 +456,11 @@ BOOST_AUTO_TEST_CASE( google_chart_linear_plot )
BOOST_AUTO_TEST_CASE( google_chart_linear_plot2 )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
//! [Producing lines]
openfpm::vector<std::string> x;
@@ -410,6 +514,11 @@ double f(double x)
BOOST_AUTO_TEST_CASE( plot_util )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
//! [fill a vector]
openfpm::vector<double> x;
diff --git a/src/RawReader/RawReader.hpp b/src/RawReader/RawReader.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..706c84960ac1aa7568957df65fc9f31c5be1fc19
--- /dev/null
+++ b/src/RawReader/RawReader.hpp
@@ -0,0 +1,193 @@
+/*! \brief This class read a Grid raw data format
+ *
+ * A grid row data format is very simple. The first n numbers indicate the
+ * size in every dimension of the grid. The other is the data contained by the grid.
+ * In particular if we are in 3D and we are saving a 45x50x30 grid after the 3 numbers
+ * I am expecting 45x50x30 = 67500 objects of type T. There is no check the dimensionality
+ * is correct, neither the type is correct
+ *
+ * \tparam dim dimensionality of the grid
+ * \tparam T type of the grid
+ *
+ */
+#include <iostream>
+#include <Grid/map_grid.hpp>
+#include <fstream>
+
+#define FORTRAN_STYLE 1
+#define STRUCT_OF_ARRAY 2
+
+/*! \brief This is the scalar case
+ *
+ * \tparam T scalar type
+ *
+ */
+template<unsigned int dim, typename Tg, typename Tr, unsigned int i>
+struct meta_raw_read
+{
+ static inline void read(grid_cpu<dim,Tg> & gr,std::ifstream & raw)
+ {
+ auto it = gr.getIterator();
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ raw.read((char *)&gr.template get<i>(key),sizeof(Tr));
+
+ ++it;
+ }
+ }
+};
+
+/*! \brief This is the vector case
+ *
+ * \tparam T vector type
+ *
+ */
+template<unsigned int dim, typename Tg, typename Tr ,unsigned int i, unsigned int nv>
+struct meta_raw_read<dim,Tg,Tr[nv],i>
+{
+ static inline void read(grid_cpu<dim,Tg> & gr,std::ifstream & raw)
+ {
+ for (size_t k = 0 ; k < nv ; k++)
+ {
+ auto it = gr.getIterator();
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ raw.read((char *)&gr.template get<i>(key)[k],sizeof(Tr));
+
+ ++it;
+ }
+ }
+ }
+};
+
+/*! \brief this class is a functor for "for_each" algorithm
+ *
+ * This class is a functor for "for_each" algorithm. For each
+ * element of the boost::vector the operator() is called.
+ * Is mainly used to read each property
+ *
+ * \tparam ele_g element that store the grid and its attributes
+ * \param St type of space where the grid live
+ *
+ */
+template<unsigned int dim, typename Tg>
+struct raw_read
+{
+ //! Grid out
+ grid_cpu<dim,Tg> & gr;
+
+ //! File stream
+ std::ifstream & fl;
+
+ /*! \brief constructor
+ *
+ * \param gr grid to fill
+ * \param fl file from where to read
+ *
+ */
+ raw_read(grid_cpu<dim,Tg> & gr,std::ifstream & fl)
+ :gr(gr),fl(fl)
+ {};
+
+ //! It read for each property
+ template<typename T>
+ void operator()(T& t) const
+ {
+ typedef typename boost::mpl::at<typename Tg::type,boost::mpl::int_<T::value>>::type Tr;
+
+ meta_raw_read<dim,Tg,Tr,T::value>::read(gr,fl);
+ }
+};
+
+template <unsigned int dim, typename T, typename idx_type>
+class GridRawReader
+{
+public:
+
+ //! Constructor
+ GridRawReader() {};
+
+
+ /*! \brief Read a raw grid
+ *
+ * \param file raw file to read
+ * \param gr grid to fill
+ * \param opt option (FORTRAN_STYLE)
+ * \param skip skip N byte
+ *
+ */
+ bool read(std::string file, grid_cpu<dim,T> & gr, size_t opt = 0, size_t skip = 0)
+ {
+ idx_type tmp;
+ std::ifstream raw;
+ raw.open (file, std::ios::binary );
+
+ if (raw.is_open() == false)
+ {
+ std::cerr << __FILE__ << ":" << __LINE__ << " error in opening the file: " << file << std::endl;
+ return false;
+ }
+
+ // get length of file:
+ raw.seekg (0, std::ios::end);
+ size_t length = raw.tellg();
+ raw.seekg (skip, std::ios::beg);
+
+ if (opt & FORTRAN_STYLE)
+ raw.read((char *)&tmp,sizeof(idx_type));
+
+ size_t sz[dim];
+
+ for (size_t i = 0 ; i < dim ; i++)
+ {
+ sz[i] = 0;
+ raw.read((char *)&sz[i],sizeof(idx_type));
+ }
+
+ if (opt & FORTRAN_STYLE)
+ raw.read((char *)&tmp,sizeof(idx_type));
+
+ if (opt & FORTRAN_STYLE)
+ raw.read((char *)&tmp,sizeof(idx_type));
+
+ grid_sm<dim,void> gs(sz);
+
+ size_t offset = 0;
+ if (opt & FORTRAN_STYLE)
+ offset += 2*sizeof(idx_type)*2;
+
+ // Check the the file size make sense
+ if (length - dim*sizeof(idx_type) - offset - skip != gs.size()*sizeof(T) )
+ {
+ std::cout << __FILE__ << ":" << __LINE__ << " Error the size of the raw file does not match with the calculated one" << std::endl;
+ return false;
+ }
+
+ gr.setMemory();
+
+ // resize the grid
+ gr.resize(sz);
+
+ if (!(opt & STRUCT_OF_ARRAY))
+ {
+ // read the data
+ raw.read((char *)gr.getPointer(),gr.size()*sizeof(T));
+ raw.close();
+ }
+ else
+ {
+ // for each property
+ raw_read<dim,T> rr(gr,raw);
+
+ boost::mpl::for_each< boost::mpl::range_c<int,0, T::max_prop> >(rr);
+ }
+
+ return true;
+ }
+};
diff --git a/src/RawReader/RawReader_unit_tests.hpp b/src/RawReader/RawReader_unit_tests.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..5ad59f0be70ac517586aace706249c863e0eda11
--- /dev/null
+++ b/src/RawReader/RawReader_unit_tests.hpp
@@ -0,0 +1,48 @@
+/*
+ * RawReader_unit_tests.hpp
+ *
+ * Created on: April 16, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_RAW_READER_UNIT_TESTS_HPP_
+#define OPENFPM_IO_RAW_READER_UNIT_TESTS_HPP_
+
+#include "RawReader.hpp"
+
+BOOST_AUTO_TEST_SUITE( raw_reader_unit_test )
+
+
+BOOST_AUTO_TEST_CASE( raw_reader_read_test )
+{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+ grid_cpu<3,aggregate<float,float[3]>> read_bin_test;
+
+ GridRawReader<3,aggregate<float,float[3]>,int> rr;
+ rr.read("test_data/raw_read_sv_test.bin",read_bin_test,FORTRAN_STYLE | STRUCT_OF_ARRAY,12);
+
+ auto it = read_bin_test.getIterator();
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ BOOST_REQUIRE_EQUAL(read_bin_test.template get<0>(key),1.5f);
+
+ BOOST_REQUIRE_EQUAL(read_bin_test.template get<1>(key)[0],1.5f);
+ BOOST_REQUIRE_EQUAL(read_bin_test.template get<1>(key)[1],2.5f);
+ BOOST_REQUIRE_EQUAL(read_bin_test.template get<1>(key)[2],3.5f);
+
+ ++it;
+ }
+}
+
+
+
+BOOST_AUTO_TEST_SUITE_END()
+
+#endif /* OPENFPM_DATA_SRC_PLOT_PLOT_UNIT_TESTS_HPP_ */
diff --git a/src/VTKWriter/VTKWriter_dist_graph.hpp b/src/VTKWriter/VTKWriter_dist_graph.hpp
index b340c6011d846103f6e7e48a0213e694f2a3d19c..d7b7ccdecff641bd085719cd304ed54595ad6a15 100644
--- a/src/VTKWriter/VTKWriter_dist_graph.hpp
+++ b/src/VTKWriter/VTKWriter_dist_graph.hpp
@@ -125,7 +125,11 @@ struct vtk_dist_vertex_node
v_node += std::to_string(x[0]) + " " + std::to_string(x[1]) + " " + std::to_string(x[2]) + "\n";
}
- //! It call the functor for each member
+ /*! \brief It call the functor for each attribute
+ *
+ * \param t attribute id
+ *
+ */
template<typename T>
void operator()(T& t)
{
@@ -173,7 +177,11 @@ struct vtk_dist_vertex_node<G, false>
{
}
- //! It call the functor for each member
+ /*! \brief It call the functor for each attribute
+ *
+ * \param t attribute id
+ *
+ */
template<typename T>
void operator()(T& t)
{
@@ -391,10 +399,11 @@ public:
/*! \brief For each vertex set the value
*
- * \tparam i vertex property to print
*
* \param g graph to output
*
+ * \return get the point data string
+ *
*/
static std::string get_point_data(const Graph & g)
{
@@ -418,11 +427,11 @@ public:
}
/*! \brief For each edge set the value, set 1 on vertices, needed by vtk file format
- *
- * \tparam i edge property to print
*
* \param g graph to output
*
+ * \return the cell-data string
+ *
*/
static std::string get_cell_data(const Graph & g)
@@ -464,6 +473,8 @@ public:
*
* \param prop property id
*
+ * \return the string with the property header
+ *
*/
static std::string get_point_property_header(size_t prop)
{
@@ -601,6 +612,8 @@ class dist_prop_output<false, Graph, i>
*
* \param g graph to print
*
+ * \return the string with the point data
+ *
*/
static std::string get_point_data(Graph & g)
{
@@ -625,10 +638,11 @@ class dist_prop_output<false, Graph, i>
/*! \brief For each edge output the property string
*
- * \param graph to print
+ * \param g graph to print
+ *
+ * \return the string containing cell-data
*
*/
-
static std::string get_cell_data(const Graph & g)
{
//! vertex node output string
@@ -801,7 +815,11 @@ struct dist_prop_out_vertex
{
}
- //! It produce an output for each property
+ /*! \brief It produce an output for each property
+ *
+ * \param t property id
+ *
+ */
template<typename T>
void operator()(T& t) const
{
@@ -846,16 +864,19 @@ struct dist_prop_out_edge
/*! \brief constructor
*
- * \param v_out string to fill with the vertex properties
+ * \param e_out string to fill with the edge properties
+ * \param g graph to write
*
*/
dist_prop_out_edge(std::string & e_out, const Graph & g) :
e_out(e_out), g(g)
- {
- }
- ;
+ {};
- //! It produce an output for each property
+ /*! \brief It produce an output for each property
+ *
+ * \param t index property
+ *
+ */
template<typename T>
void operator()(T& t) const
{
@@ -930,6 +951,11 @@ class VTKWriter<Graph, DIST_GRAPH>
return v_out;
}
+ /*! \brief Get the VTK point info string
+ *
+ * \return the point info string
+ *
+ */
std::string get_point_info()
{
//! vertex property output string
@@ -977,9 +1003,10 @@ class VTKWriter<Graph, DIST_GRAPH>
/*! \brief Create the VTK point definition
*
- * \tparam s_type spatial type of the data
* \tparam attr false x,y,z are set to 0 for each vertex
*
+ * \return the point list string
+ *
*/
template<bool attr> std::string get_point_list()
@@ -1018,11 +1045,11 @@ class VTKWriter<Graph, DIST_GRAPH>
/*! \brief Create the VTK vertex definition
*
- * \tparam s_type spatial type of the data
* \tparam attr false x,y,z are set to 0 for each vertex
*
+ * \return the vertex list string
+ *
*/
-
std::string get_vertex_list()
{
//! vertex node output string
@@ -1114,11 +1141,12 @@ public:
* \tparam prp_out which properties to output [default = -1 (all)]
*
* \param file path where to write
- * \param name of the graph
+ * \param graph_name of the graph
* \param ft specify if it is a VTK BINARY or ASCII file [default = ASCII]
*
+ * \return true if it succeed
+ *
*/
-
template<int prp = -1> bool write(std::string file, std::string graph_name = "Graph", file_type ft = file_type::ASCII)
{
diff --git a/src/VTKWriter/VTKWriter_graph.hpp b/src/VTKWriter/VTKWriter_graph.hpp
index 417a135e4edffb1ace2b565ac3d409aabfdec84e..18d4667808aea9f99c298d72dcadecb16bc78728 100644
--- a/src/VTKWriter/VTKWriter_graph.hpp
+++ b/src/VTKWriter/VTKWriter_graph.hpp
@@ -91,17 +91,19 @@ struct vtk_vertex_node_array_scalar_selector<true>
template<typename G, bool attr>
struct vtk_vertex_node
{
- // Vertex spatial type information
+ //! Vertex spatial type information
typedef typename G::V_type::s_type s_type;
+ //! Indicate if there is the information about the z coordinate
bool z_set;
+ //! point to write
s_type (&x)[3];
- // Vertex object container
+ //! Vertex object container
typename G::V_container & vo;
- // vertex node string
+ //! vertex node string
std::string & v_node;
/*! \brief Constructor
@@ -110,6 +112,7 @@ struct vtk_vertex_node
*
* \param v_node std::string that is filled with the graph properties in the GraphML format
* \param n_obj object container to access its properties for example encapc<...>
+ * \param x temporal buffer to store the point coordinates
*
*/
vtk_vertex_node(std::string & v_node, typename G::V_container & n_obj, s_type (&x)[3])
@@ -123,7 +126,11 @@ struct vtk_vertex_node
v_node += std::to_string(x[0]) + " " + std::to_string(x[1]) + " " + std::to_string(x[2]) + "\n";
}
- //! It call the functor for each member
+ /*! \brief It call the functor for each member
+ *
+ * \param t property id
+ *
+ */
template<typename T>
void operator()(T& t)
{
@@ -152,10 +159,10 @@ struct vtk_vertex_node
template<typename G>
struct vtk_vertex_node<G, false>
{
- // Vertex object container
+ //! Vertex object container
typename G::V_container & vo;
- // vertex node string
+ //! vertex node string
std::string & v_node;
/*! \brief Constructor
@@ -172,7 +179,13 @@ struct vtk_vertex_node<G, false>
}
;
- //! It call the functor for each member
+ /*! \brief It call the functor for each member
+ *
+ * It set the position of vertex to zero
+ *
+ * \param t property id
+ *
+ */
template<typename T>
void operator()(T& t)
{
@@ -192,10 +205,10 @@ struct vtk_vertex_node<G, false>
template<typename G>
struct vtk_edge_node
{
- // Vertex object container
+ //! Vertex object container
typename G::E_container & vo;
- // edge node string
+ //! edge node string
std::string & e_node;
/*! \brief Constructor
@@ -204,7 +217,6 @@ struct vtk_edge_node
*
* \param e_node std::string that is filled with the graph properties in the GraphML format
* \param n_obj object container to access the object properties for example encapc<...>
- * \param n_prop number of properties
*
*/
vtk_edge_node(std::string & e_node, typename G::E_container & n_obj) :
@@ -215,7 +227,9 @@ struct vtk_edge_node
/*! \brief Create a new node
*
- * \param vc node number
+ * \param v_c unused
+ * \param s source of the edge
+ * \param d destination of the edge
*
*/
void new_node(size_t v_c, size_t s, size_t d)
@@ -295,7 +309,7 @@ struct prop_output_array_scalar_selector_edge
*
* \param v_out Buffer to write into
* \param g Graph
- * \param p Property id
+ * \param edge to write
*/
template<typename ele_v, typename Graph, unsigned int i>
static inline void write(std::string &v_out, const Graph &g, const typename Graph::E_container &edge)
@@ -318,7 +332,7 @@ struct prop_output_array_scalar_selector_edge<true>
*
* \param v_out Buffer to write into
* \param g Graph
- * \param p Property id
+ * \param edge to write
*/
template<typename ele_v, typename Graph, unsigned int i>
static inline void write(std::string &v_out, const Graph &g, const typename Graph::E_container &edge)
@@ -388,12 +402,13 @@ class prop_output
{
public:
- /*! \brief For each vertex set the value
+ /*! \brief Get the vtk point data section for a graph g
+ *
+ * \param g graph
*
- * \tparam i vertex property to print
+ * \return point data section string
*
*/
-
static std::string get_point_data(const Graph & g)
{
//! vertex node output string
@@ -415,12 +430,13 @@ public:
return v_out;
}
- /*! \brief For each edge set the value, set 1 on vertices, needed by vtk file format
+ /*! \brief Get the cell data section for a graph g
+ *
+ * \param g graph
*
- * \tparam i edge property to print
+ * \return the cell data section
*
*/
-
static std::string get_cell_data(const Graph & g)
{
//! vertex node output string
@@ -456,16 +472,17 @@ public:
return e_out;
}
- /*! \brief Given a Graph return the point data header for a typename T
+ /*! \brief Return the point header for the property prop
*
- * \tparam T type to write
- * \param n_node number of the node
+ * \param prop property to write
+ *
+ * \return a string containing the header of the properties
*
*/
static std::string get_point_property_header(size_t prop)
{
- //! vertex node output string
+ // vertex node output string
std::string v_out;
// Type of the property
@@ -509,11 +526,11 @@ public:
/*! \brief Given a Graph return the cell data header for a typename T
*
- * \tparam T type to write
- * \param n_node number of the node
+ * \param prop property id
+ *
+ * \return the string with the cell property header
*
*/
-
static std::string get_cell_property_header(size_t prop)
{
//! edge node output string
@@ -558,19 +575,21 @@ public:
return e_out;
}
- /*! \brief Get the attributes name for vertex
+ /*! \brief Get the attributes name for the property i (template parameter)
+ *
+ * \return vertex attribute name
*
*/
-
static std::string get_attributes_vertex()
{
return Graph::V_type::attributes::name[i];
}
- /*! \brief Get the attributes name for edge
+ /*! \brief Get the attributes name for edge property i (template parameter)
+ *
+ * \return edge attribute name
*
*/
-
static std::string get_attributes_edge()
{
return Graph::E_type::attributes::name[i];
@@ -593,12 +612,13 @@ public:
template<typename Graph, unsigned int i>
class prop_output<false, Graph, i>
{
- /*! \brief For each vertex set the value
+ /*! \brief Return the point data section for a graph g
+ *
+ * \param g graph
*
- * \tparam i vertex property to print
+ * \return the point data section string
*
*/
-
static std::string get_point_data(Graph & g)
{
//! vertex node output string
@@ -620,18 +640,20 @@ class prop_output<false, Graph, i>
return v_out;
}
- /*! \brief For each edge set the value
+ /*! \brief Return the cell data section for a graph g
*
- * \tparam i edge property to print
+ * \param g graph
+ *
+ * \return the cell data section
*
*/
static std::string get_cell_data(const Graph & g)
{
- //! vertex node output string
+ // vertex node output string
std::string e_out;
- //! Get a vertex iterator
+ // Get a vertex iterator
auto it_v = g.getVertexIterator();
// if there is the next element
@@ -660,13 +682,12 @@ class prop_output<false, Graph, i>
return e_out;
}
- /*! \brief Given a Graph return the point data header for a typename T
+ /*! \brief Given a Graph return the point data header for the property prop
*
- * \tparam T type to write
- *
- * \param n_node number of the node
* \param prop id of the property
*
+ * \return the string of the property header
+ *
*/
static std::string get_point_property_header(size_t prop)
@@ -695,9 +716,11 @@ class prop_output<false, Graph, i>
return v_out;
}
- /*! \brief Given a Graph return the cell data header for a typename T
+ /*! \brief Given a Graph return the cell data header
*
- * \param n_node number of the node
+ * \param prop property id
+ *
+ * \return the cell property header
*
*/
@@ -746,18 +769,20 @@ class prop_output<false, Graph, i>
}
/*! \brief Get the attributes name for vertex
+ *
+ * \return get attributes vertex name
*
*/
-
static std::string get_attributes_vertex()
{
return Graph::V_type::attributes::name[i];
}
/*! \brief Get the attributes name for edge
+ *
+ * \return get attributes edge name
*
*/
-
static std::string get_attributes_edge()
{
return Graph::E_type::attributes::name[i];
@@ -780,15 +805,16 @@ class prop_output<false, Graph, i>
template<typename Graph>
struct prop_out_vertex
{
- // property output string
+ //! property output string
std::string & v_out;
- // Graph that we are processing
+ //! Graph that we are processing
const Graph & g;
/*! \brief constructor
*
* \param v_out string to fill with the vertex properties
+ * \param g graph to output
*
*/
prop_out_vertex(std::string & v_out, const Graph & g) :
@@ -797,7 +823,11 @@ struct prop_out_vertex
}
;
- //! It produce an output for each property
+ /*! \brief It produce an output for each property
+ *
+ * \param t property id
+ *
+ */
template<typename T>
void operator()(T& t) const
{
@@ -834,15 +864,16 @@ struct prop_out_vertex
template<typename Graph>
struct prop_out_edge
{
- // property output string
+ //! property output string
std::string & e_out;
- // Graph that we are processing
+ //! Graph that we are processing
const Graph & g;
/*! \brief constructor
*
- * \param v_out string to fill with the vertex properties
+ * \param e_out string to fill with the edge properties
+ * \param g graph we are writing
*
*/
prop_out_edge(std::string & e_out, const Graph & g) :
@@ -851,7 +882,11 @@ struct prop_out_edge
}
;
- //! It produce an output for each property
+ /*! \brief It produce an output for each property
+ *
+ * \param t property index
+ *
+ */
template<typename T>
void operator()(T& t) const
{
@@ -883,6 +918,7 @@ struct prop_out_edge
template<typename Graph>
class VTKWriter<Graph, VTK_GRAPH>
{
+ //! graph we are writing
const Graph & g;
/*! \brief It get the vertex properties list
@@ -947,11 +983,11 @@ class VTKWriter<Graph, VTK_GRAPH>
/*! \brief Create the VTK point definition
*
- * \tparam s_type spatial type of the data
* \tparam attr false x,y,z are set to 0 for each vertex
*
+ * \return a string with the point list
+ *
*/
-
template<bool attr> std::string get_point_list()
{
//! VTK spatial information
@@ -988,11 +1024,9 @@ class VTKWriter<Graph, VTK_GRAPH>
/*! \brief Create the VTK vertex definition
*
- * \tparam s_type spatial type of the data
- * \tparam attr false x,y,z are set to 0 for each vertex
+ * \return a string with the vertex definition
*
*/
-
std::string get_vertex_list()
{
//! vertex node output string
@@ -1087,11 +1121,12 @@ public:
* \tparam prp_out which properties to output [default = -1 (all)]
*
* \param file path where to write
- * \param name of the graph
+ * \param graph_name of the graph
* \param ft specify if it is a VTK BINARY or ASCII file [default = ASCII]
*
+ * \return true if it write correctly
+ *
*/
-
template<int prp = -1> bool write(std::string file, std::string graph_name = "Graph", file_type ft = file_type::ASCII)
{
// Check that the Vertex type define x y and z attributes
diff --git a/src/VTKWriter/VTKWriter_graph_util.hpp b/src/VTKWriter/VTKWriter_graph_util.hpp
deleted file mode 100644
index 5729045f2b7eb317eecca9e083b8bbfbefa55285..0000000000000000000000000000000000000000
--- a/src/VTKWriter/VTKWriter_graph_util.hpp
+++ /dev/null
@@ -1,15 +0,0 @@
-/*
- * VTKWriter_graph_util.hpp
- *
- * Created on: Mar 12, 2016
- * Author: i-bird
- */
-
-#ifndef OPENFPM_IO_SRC_VTKWRITER_VTKWRITER_GRAPH_UTIL_HPP_
-#define OPENFPM_IO_SRC_VTKWRITER_VTKWRITER_GRAPH_UTIL_HPP_
-
-
-
-
-
-#endif /* OPENFPM_IO_SRC_VTKWRITER_VTKWRITER_GRAPH_UTIL_HPP_ */
diff --git a/src/VTKWriter/VTKWriter_grids.hpp b/src/VTKWriter/VTKWriter_grids.hpp
index d08b7ba23c7f4b771d36a3e40619088005bbd5bb..46059296bd512cab4ce3d72bd4458ae231b583dc 100644
--- a/src/VTKWriter/VTKWriter_grids.hpp
+++ b/src/VTKWriter/VTKWriter_grids.hpp
@@ -63,26 +63,43 @@ struct prop_out_g
//! grid that we are processing
const openfpm::vector_std< ele_g > & vg;
+ //! File type
+ file_type ft;
+
+ //! list of names for the properties
+ const openfpm::vector<std::string> & prop_names;
+
/*! \brief constructor
*
* \param v_out string to fill with the vertex properties
* \param vg vector of elements to write
+ * \param prop_names properties name
+ * \param ft file type
*
*/
- prop_out_g(std::string & v_out, const openfpm::vector_std< ele_g > & vg)
- :v_out(v_out),vg(vg)
+ prop_out_g(std::string & v_out, const openfpm::vector_std< ele_g > & vg, const openfpm::vector<std::string> & prop_names ,file_type ft)
+ :v_out(v_out),vg(vg),ft(ft),prop_names(prop_names)
{};
- //! It produce an output for each property
+ /*! It produce an output for each propert
+ *
+ * \param t prop-id
+ *
+ */
template<typename T>
void operator()(T& t) const
{
typedef typename boost::mpl::at<typename ele_g::value_type::value_type::type,boost::mpl::int_<T::value>>::type ptype;
typedef typename std::remove_all_extents<ptype>::type base_ptype;
- meta_prop<boost::mpl::int_<T::value> ,ele_g,St, ptype, is_vtk_writable<base_ptype>::value > m(vg,v_out,file_type::ASCII);
+ meta_prop<boost::mpl::int_<T::value> ,ele_g,St, ptype, is_vtk_writable<base_ptype>::value > m(vg,v_out,prop_names,ft);
}
+ /*! \brief Write the last property
+ *
+ *
+ *
+ */
void lastProp()
{
// Create point data properties
@@ -185,9 +202,13 @@ class VTKWriter<pair,VECTOR_GRIDS>
}
/*! \brief Create the VTK point definition
+ *
+ * \param ft file type
+ *
+ * \return the string with the point list
*
*/
- std::string get_point_list()
+ std::string get_point_list(file_type ft)
{
//! vertex node output string
std::stringstream v_out;
@@ -209,10 +230,7 @@ class VTKWriter<pair,VECTOR_GRIDS>
p = it.get().toPoint();
p = pmul(p,vg.get(i).spacing) + vg.get(i).offset;
- if (pair::first::dims == 2)
- v_out << p.toString() << " 0.0" << "\n";
- else
- v_out << p.toString() << "\n";
+ output_point<pair::first::dims,typename pair::second>(p,v_out,ft);
// increment the iterator and counter
++it;
@@ -224,9 +242,11 @@ class VTKWriter<pair,VECTOR_GRIDS>
}
/*! \brief Create the VTK vertex definition
+ *
+ * \param ft file type
*
*/
- std::string get_vertex_list()
+ std::string get_vertex_list(file_type ft)
{
//! vertex node output string
std::string v_out;
@@ -240,7 +260,7 @@ class VTKWriter<pair,VECTOR_GRIDS>
while (it.isNext())
{
- v_out += "1 " + std::to_string(k) + "\n";
+ output_vertex(k,v_out,ft);
++k;
++it;
@@ -280,10 +300,13 @@ public:
* \param g Grid to add
* \param offset grid offset
* \param spacing spacing of the grid
- * \param dom part of the spacethat is the domain
+ * \param dom part of the space that is the domain
*
*/
- void add(const typename pair::first & g, const Point<pair::first::dims,typename pair::second> & offset, const Point<pair::first::dims,typename pair::second> & spacing, const Box<pair::first::dims,typename pair::second> & dom)
+ void add(const typename pair::first & g,
+ const Point<pair::first::dims,typename pair::second> & offset,
+ const Point<pair::first::dims,typename pair::second> & spacing,
+ const Box<pair::first::dims,typename pair::second> & dom)
{
ele_g<typename pair::first,typename pair::second> t(g,offset,spacing,dom);
@@ -296,11 +319,16 @@ public:
*
* \param file path where to write
* \param name of the graph
+ * \param prop_names properties name (can also be a vector of size 0)
* \param ft specify if it is a VTK BINARY or ASCII file [default = ASCII]
*
+ * \return true if the function write successfully
+ *
*/
-
- template<int prp = -1> bool write(std::string file, std::string f_name = "grids" , file_type ft = file_type::ASCII)
+ template<int prp = -1> bool write(std::string file,
+ const openfpm::vector<std::string> & prop_names,
+ std::string f_name = "grids",
+ file_type ft = file_type::ASCII)
{
// Header for the vtk
std::string vtk_header;
@@ -336,20 +364,20 @@ public:
point_prop_header = get_point_properties_list();
// Get point list
- point_list = get_point_list();
+ point_list = get_point_list(ft);
// vertex properties header
vertex_prop_header = get_vertex_properties_list();
// Get vertex list
- vertex_list = get_vertex_list();
+ vertex_list = get_vertex_list(ft);
// Get the point data header
point_data_header = get_point_data_header();
// For each property in the vertex type produce a point data
- prop_out_g< ele_g<typename pair::first,typename pair::second>, typename pair::second > pp(point_data, vg);
+ prop_out_g< ele_g<typename pair::first,typename pair::second>, typename pair::second > pp(point_data, vg, prop_names, ft);
if (prp == -1)
boost::mpl::for_each< boost::mpl::range_c<int,0, pair::first::value_type::max_prop> >(pp);
diff --git a/src/VTKWriter/VTKWriter_grids_util.hpp b/src/VTKWriter/VTKWriter_grids_util.hpp
index be13dbbaeb6baf79f1102b0bf7b7fe3b98726518..8d52da2e223ba24fe6f69add91b3f8d1c4b898d3 100644
--- a/src/VTKWriter/VTKWriter_grids_util.hpp
+++ b/src/VTKWriter/VTKWriter_grids_util.hpp
@@ -12,7 +12,7 @@
#include "is_vtk_writable.hpp"
#include "byteswap_portable.hpp"
-/*! \brief Return the Attributes name (if they have)
+/*! \brief Return the Attributes name from the type
*
*
*/
@@ -23,14 +23,22 @@ struct getAttrName
*
* \param i id of the attribute
* \param oprp post-fix to add
+ * \param prop_names properties name
+ *
+ * \return the string with the property name
*
*/
- static inline std::string get(size_t i, const std::string & oprp)
+ static inline std::string get(size_t i, const openfpm::vector<std::string> & prop_names, const std::string & oprp)
{
return ele_g::value_type::value_type::attributes::name[i] + oprp;
}
};
+/*! \brief Return the Attributes name from the type
+ *
+ * This is the case when the type has no name
+ *
+ */
template<typename ele_g>
struct getAttrName<ele_g,false>
{
@@ -38,11 +46,21 @@ struct getAttrName<ele_g,false>
*
* \param i id of the attribute
* \param oprp post-fix to add
+ * \param prop_names properties name
+ *
+ * \return return the string with the property name
*
*/
- static inline std::string get(size_t i, const std::string & oprp)
+ static inline std::string get(size_t i, const openfpm::vector<std::string> & prop_names, const std::string & oprp)
{
- return std::string("attr" + std::to_string(i) + oprp);
+ if (i >= prop_names.size())
+ {
+ return std::string("attr" + std::to_string(i) + oprp);
+ }
+ else
+ {
+ return prop_names.get(i) + oprp;
+ }
}
};
@@ -52,7 +70,7 @@ struct getAttrName<ele_g,false>
* \param oprp prefix
*
*/
-template<unsigned int i, typename ele_g, bool has_attributes> std::string get_point_property_header_impl(const std::string & oprp)
+template<unsigned int i, typename ele_g, bool has_attributes> std::string get_point_property_header_impl(const std::string & oprp, const openfpm::vector<std::string> & prop_names)
{
//! vertex node output string
std::string v_out;
@@ -76,7 +94,7 @@ template<unsigned int i, typename ele_g, bool has_attributes> std::string get_po
}
// Create point data properties
- v_out += "VECTORS " + getAttrName<ele_g,has_attributes>::get(i,oprp) + " " + type + "\n";
+ v_out += "VECTORS " + getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp) + " " + type + "\n";
}
}
else
@@ -94,16 +112,16 @@ template<unsigned int i, typename ele_g, bool has_attributes> std::string get_po
// We check if it is a vector or scalar like type
if (vtk_dims<ctype>::value == 1)
- v_out += "SCALARS " + getAttrName<ele_g,has_attributes>::get(i,oprp) + " " + type + "\n";
+ v_out += "SCALARS " + getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp) + " " + type + "\n";
else
- v_out += "VECTORS " + getAttrName<ele_g,has_attributes>::get(i,oprp) + " " + type + "\n";
+ v_out += "VECTORS " + getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp) + " " + type + "\n";
}
return v_out;
}
// Create point data properties
- v_out += "SCALARS " + getAttrName<ele_g,has_attributes>::get(i,oprp) + " " + type + "\n";
+ v_out += "SCALARS " + getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp) + " " + type + "\n";
// Default lookup table
v_out += "LOOKUP_TABLE default\n";
@@ -142,16 +160,19 @@ public:
}
else
{
+ typedef decltype(vg.get(k).g.get_o(it.get()).template get<I::value>().get_vtk(0)) ctype_;
+ typedef typename std::remove_reference<ctype_>::type ctype;
+
// Print the properties
for (size_t i1 = 0 ; i1 < vtk_dims<T>::value ; i1++)
{
- auto tmp = vg.get(k).g.get_o(it.get()).template get<I::value>().get_vtk(i1);
+ typename is_vtk_writable<ctype>::base tmp = vg.get(k).g.get_o(it.get()).template get<I::value>().get_vtk(i1);
tmp = swap_endian_lt(tmp);
v_out.append((const char *)&tmp,sizeof(tmp));
}
if (vtk_dims<T>::value == 2)
{
- decltype(vg.get(k).g.get_o(it.get()).template get<I::value>().get_vtk(0)) zero = 0.0;
+ typename is_vtk_writable<ctype>::base zero = 0.0;
zero = swap_endian_lt(zero);
v_out.append((const char *)&zero,sizeof(zero));
}
@@ -168,8 +189,20 @@ class prop_write_out<1,T>
{
public:
+ /*! \brief Write the property
+ *
+ * \param v_out output string of the property
+ * \param vg vector of properties
+ * \param k data-set to output
+ * \param it iterator with the point to output
+ * \param ft output type BINARY or ASCII
+ *
+ */
template<typename vector, typename iterator, typename I> static void write(std::string & v_out, vector & vg, size_t k, iterator & it, file_type ft)
{
+ typedef decltype(vg.get(k).g.get_o(it.get()).template get<I::value>()) ctype_;
+ typedef typename std::remove_reference<ctype_>::type ctype;
+
if (ft == file_type::ASCII)
{
// Print the property
@@ -177,7 +210,7 @@ public:
}
else
{
- auto tmp = vg.get(k).g.get_o(it.get()).template get<I::value>();
+ typename is_vtk_writable<ctype>::base tmp = vg.get(k).g.get_o(it.get()).template get<I::value>();
tmp = swap_endian_lt(tmp);
v_out.append((const char *)&tmp,sizeof(tmp));
}
@@ -201,16 +234,17 @@ struct meta_prop
*
* \param vg array of elements to write
* \param v_out string containing the string
+ * \param prop_names property names
* \param ft ASCII or BINARY
*
*/
- inline meta_prop(const openfpm::vector< ele_g > & vg, std::string & v_out, file_type ft)
+ inline meta_prop(const openfpm::vector< ele_g > & vg, std::string & v_out, const openfpm::vector<std::string> & prop_names, file_type ft)
{
// actual string size
size_t sz = v_out.size();
// Produce the point properties header
- v_out += get_point_property_header_impl<I::value,ele_g,has_attributes<typename ele_g::value_type::value_type>::value>("");
+ v_out += get_point_property_header_impl<I::value,ele_g,has_attributes<typename ele_g::value_type::value_type>::value>("",prop_names);
// If the output has changed, we have to write the properties
if (v_out.size() != sz)
@@ -246,16 +280,17 @@ struct meta_prop<I, ele_g,St,T[N1],is_writable>
*
* \param vg array of elements to write
* \param v_out string containing the string
+ * \param prop_names properties name
* \param ft ASCII or BINARY
*
*/
- inline meta_prop(const openfpm::vector< ele_g > & vg, std::string & v_out, file_type ft)
+ inline meta_prop(const openfpm::vector< ele_g > & vg, std::string & v_out, const openfpm::vector<std::string> & prop_names , file_type ft)
{
// actual string size
size_t sz = v_out.size();
// Produce the point properties header
- v_out += get_point_property_header_impl<I::value,ele_g,has_attributes<typename ele_g::value_type::value_type>::value>("");
+ v_out += get_point_property_header_impl<I::value,ele_g,has_attributes<typename ele_g::value_type::value_type>::value>("",prop_names);
// If the output has changed, we have to write the properties
if (v_out.size() != sz)
@@ -321,10 +356,11 @@ struct meta_prop<I, ele_g,St, T[N1][N2],is_writable>
*
* \param vg array of elements to write
* \param v_out string containing the string
+ * \param prop_names property names
* \param ft ASCII or BINARY
*
*/
- inline meta_prop(const openfpm::vector< ele_g > & vg, std::string & v_out, file_type ft)
+ inline meta_prop(const openfpm::vector< ele_g > & vg, std::string & v_out, const openfpm::vector<std::string> & prop_names, file_type ft)
{
for (size_t i1 = 0 ; i1 < N1 ; i1++)
{
@@ -334,7 +370,7 @@ struct meta_prop<I, ele_g,St, T[N1][N2],is_writable>
size_t sz = v_out.size();
// Produce the point properties header
- v_out += get_point_property_header_impl<I::value,ele_g,has_attributes<typename ele_g::value_type::value_type>::value>("_" + std::to_string(i1) + "_" + std::to_string(i2));
+ v_out += get_point_property_header_impl<I::value,ele_g,has_attributes<typename ele_g::value_type::value_type>::value>("_" + std::to_string(i1) + "_" + std::to_string(i2),prop_names);
// If the output has changed, we have to write the properties
if (v_out.size() != sz)
@@ -381,12 +417,50 @@ struct meta_prop<I,ele_g,St,T,false>
*
* \param vg array of elements to write
* \param v_out string containing the string
+ * \param prop_names properties name
* \param ft ASCII or BINARY
*
*/
- inline meta_prop(const openfpm::vector< ele_g > & vg, std::string & v_out, file_type ft)
+ inline meta_prop(const openfpm::vector< ele_g > & vg, std::string & v_out, const openfpm::vector<std::string> & prop_names, file_type ft)
{
}
};
+template<unsigned int dims,typename T> inline void output_point(Point<dims,T> & p,std::stringstream & v_out, file_type ft)
+{
+ if (ft == file_type::ASCII)
+ {
+ if (dims == 2)
+ v_out << p.toString() << " 0.0" << "\n";
+ else
+ v_out << p.toString() << "\n";
+ }
+ else
+ {
+ for (size_t i = 0 ; i < dims ; i++)
+ {
+ // we use float so we have to convert to float
+ float tmp = p.get(i);
+ tmp = swap_endian_lt(tmp);
+ v_out.write((const char *)&tmp,sizeof(tmp));
+ }
+ }
+}
+
+inline void output_vertex(size_t k,std::string & v_out, file_type ft)
+{
+ if (ft == file_type::ASCII)
+ v_out += "1 " + std::to_string(k) + "\n";
+ else
+ {
+ int tmp;
+ tmp = 1;
+ tmp = swap_endian_lt(tmp);
+ v_out.append((const char *)&tmp,sizeof(int));
+ tmp = k;
+ tmp = swap_endian_lt(tmp);
+ v_out.append((const char *)&tmp,sizeof(int));
+ }
+}
+
#endif /* SRC_VTKWRITER_GRIDS_UTIL_HPP_ */
diff --git a/src/VTKWriter/VTKWriter_point_set.hpp b/src/VTKWriter/VTKWriter_point_set.hpp
index 0c173c95ca008bf800a8b8fbb6d36db5c1c21ee7..50a96f46b0f0ec18e382c8393571e9d007d101cf 100644
--- a/src/VTKWriter/VTKWriter_point_set.hpp
+++ b/src/VTKWriter/VTKWriter_point_set.hpp
@@ -91,6 +91,9 @@ struct prop_out_v
//! vector that we are processing
const openfpm::vector_std< ele_v > & vv;
+ //! properties names
+ const openfpm::vector<std::string> & prop_names;
+
/*! \brief constructor
*
* \param v_out string to fill with the vertex properties
@@ -98,18 +101,25 @@ struct prop_out_v
* \param ft ASCII or BINARY format
*
*/
- prop_out_v(std::string & v_out, const openfpm::vector_std< ele_v > & vv, file_type ft)
- :ft(ft),v_out(v_out),vv(vv)
+ prop_out_v(std::string & v_out,
+ const openfpm::vector_std< ele_v > & vv,
+ const openfpm::vector<std::string> & prop_names,
+ file_type ft)
+ :ft(ft),v_out(v_out),vv(vv),prop_names(prop_names)
{};
- //! It produce an output for each property
+ /*! \brief It produce an output for each property
+ *
+ * \param t property id
+ *
+ */
template<typename T>
void operator()(T& t) const
{
typedef typename boost::mpl::at<typename ele_v::value_type::value_type::type,boost::mpl::int_<T::value>>::type ptype;
typedef typename std::remove_all_extents<ptype>::type base_ptype;
- meta_prop<boost::mpl::int_<T::value> ,ele_v,St, ptype, is_vtk_writable<base_ptype>::value > m(vv,v_out,ft);
+ meta_prop<boost::mpl::int_<T::value> ,ele_v,St, ptype, is_vtk_writable<base_ptype>::value > m(vv,v_out,prop_names,ft);
}
void lastProp()
@@ -258,30 +268,7 @@ class VTKWriter<pair,VECTOR_POINTS>
Point<pair::first::value_type::dims,typename pair::first::value_type::coord_type> p;
p = vps.get(i).g.get(it.get());
- if (ft == file_type::ASCII)
- {
- if (pair::first::value_type::dims == 2)
- v_out << p.toString() << " 0.0" << "\n";
- else
- v_out << p.toString() << "\n";
- }
- else
- {
- for (size_t i = 0 ; i < pair::first::value_type::dims ; i++)
- {
- // we use float so we have to convert to float
- float tmp = p.get(i);
- tmp = swap_endian_lt(tmp);
- v_out.write((const char *)&tmp,sizeof(tmp));
- }
-
- if (pair::first::value_type::dims == 2)
- {
- float tmp = 0.0;
- tmp = swap_endian_lt(tmp);
- v_out.write((const char *)&tmp,sizeof(tmp));
- }
- }
+ output_point<pair::first::value_type::dims,typename pair::first::value_type::coord_type>(p,v_out,ft);
// increment the iterator and counter
++it;
@@ -317,18 +304,7 @@ class VTKWriter<pair,VECTOR_POINTS>
while (it.isNext())
{
- if (ft == file_type::ASCII)
- v_out += "1 " + std::to_string(k) + "\n";
- else
- {
- int tmp;
- tmp = 1;
- tmp = swap_endian_lt(tmp);
- v_out.append((const char *)&tmp,sizeof(int));
- tmp = k;
- tmp = swap_endian_lt(tmp);
- v_out.append((const char *)&tmp,sizeof(int));
- }
+ output_vertex(k,v_out,ft);
++k;
++it;
@@ -371,11 +347,13 @@ public:
*
* \param vps vector of positions
* \param vpp vector of properties
- * \param mark additional information that divide the dataset into 2
- * (in general is used to mark real from ghost information)
+ * \param mark additional information that divide the dataset into 2 (in general is used to mark real from ghost information)
+ * \param opt_names optional parameter that indicate the names of the properties
*
*/
- void add(const typename pair::first & vps, const typename pair::second & vpp,size_t mark)
+ void add(const typename pair::first & vps,
+ const typename pair::second & vpp,
+ size_t mark)
{
ele_vps<typename pair::first> t1(vps,mark);
ele_vpp<typename pair::second> t2(vpp,mark);
@@ -390,10 +368,16 @@ public:
*
* \param file path where to write
* \param f_name name of the dataset
+ * \param prop_names properties names
* \param ft specify if it is a VTK BINARY or ASCII file [default = ASCII]
*
+ * \return true if the write complete successfully
+ *
*/
- template<int prp = -1> bool write(std::string file, std::string f_name = "points" , file_type ft = file_type::ASCII)
+ template<int prp = -1> bool write(std::string file,
+ const openfpm::vector<std::string> & prop_names,
+ std::string f_name = "points" ,
+ file_type ft = file_type::ASCII)
{
// Header for the vtk
std::string vtk_header;
@@ -442,7 +426,7 @@ public:
// For each property in the vertex type produce a point data
- prop_out_v< ele_vpp<typename pair::second>, typename pair::first::value_type::coord_type> pp(point_data, vpp, ft);
+ prop_out_v< ele_vpp<typename pair::second>, typename pair::first::value_type::coord_type> pp(point_data, vpp, prop_names,ft);
if (prp == -1)
boost::mpl::for_each< boost::mpl::range_c<int,0, pair::second::value_type::max_prop> >(pp);
diff --git a/src/VTKWriter/VTKWriter_unit_tests.hpp b/src/VTKWriter/VTKWriter_unit_tests.hpp
index 2c798ce8e2ff0cf5ba64c348418e2e73fb3eda50..e73d5400e2682f841443b2121aab1e24cd7aa740 100644
--- a/src/VTKWriter/VTKWriter_unit_tests.hpp
+++ b/src/VTKWriter/VTKWriter_unit_tests.hpp
@@ -127,6 +127,11 @@ const std::string vertex2::attributes::name[] = {"x","prp1","prp2"};
BOOST_AUTO_TEST_CASE( vtk_writer_use_graph3D )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
// Create some graphs and output them
// Graph
@@ -199,12 +204,17 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph3D )
// check that match
- bool test = compare("vtk_graph_v2.vtk","vtk_graph_v2_test.vtk");
+ bool test = compare("vtk_graph_v2.vtk","test_data/vtk_graph_v2_test.vtk");
BOOST_REQUIRE_EQUAL(true,test);
}
BOOST_AUTO_TEST_CASE( vtk_writer_use_graph3D_edge )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
// Create some graphs and output them
// Graph
@@ -277,7 +287,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph3D_edge )
// check that match
- bool test = compare("vtk_graph_v4.vtk","vtk_graph_v4_test.vtk");
+ bool test = compare("vtk_graph_v4.vtk","test_data/vtk_graph_v4_test.vtk");
BOOST_REQUIRE_EQUAL(true,test);
}
@@ -334,6 +344,11 @@ const std::string vertex3::attributes::name[] = {"x","prp1","prp2"};
BOOST_AUTO_TEST_CASE( vtk_writer_use_graph2D )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
// Create some graphs and output them
// Graph
@@ -359,12 +374,17 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph2D )
// check that match
- bool test = compare("vtk_graph_v3.vtk","vtk_graph_v3_test.vtk");
+ bool test = compare("vtk_graph_v3.vtk","test_data/vtk_graph_v3_test.vtk");
BOOST_REQUIRE_EQUAL(true,test);
}
BOOST_AUTO_TEST_CASE( vtk_writer_use_graph)
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
// Create some graphs and output them
std::cout << "Graph unit test start" << "\n";
@@ -439,12 +459,17 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph)
// check that match
- bool test = compare("vtk_graph.vtk","vtk_graph_test.vtk");
+ bool test = compare("vtk_graph.vtk","test_data/vtk_graph_test.vtk");
BOOST_REQUIRE_EQUAL(true,test);
}
BOOST_AUTO_TEST_CASE( vtk_writer_use_vector_box)
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
// Create a vector of boxes
openfpm::vector<Box<2,float>> vb;
@@ -461,7 +486,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_vector_box)
vtk_box.write("vtk_box.vtk");
// Check that match
- bool test = compare("vtk_box.vtk","vtk_box_test.vtk");
+ bool test = compare("vtk_box.vtk","test_data/vtk_box_test.vtk");
BOOST_REQUIRE_EQUAL(test,true);
// Create a vector of boxes
@@ -480,7 +505,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_vector_box)
vtk_box2.write("vtk_box_3D.vtk");
// Check that match
- test = compare("vtk_box_3D.vtk","vtk_box_3D_test.vtk");
+ test = compare("vtk_box_3D.vtk","test_data/vtk_box_3D_test.vtk");
BOOST_REQUIRE_EQUAL(test,true);
// Create a vector of boxes
@@ -499,7 +524,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_vector_box)
vtk_box3.write("vtk_box_3D_2.vtk");
// Check that match
- test = compare("vtk_box_3D_2.vtk","vtk_box_3D_2_test.vtk");
+ test = compare("vtk_box_3D_2.vtk","test_data/vtk_box_3D_2_test.vtk");
BOOST_REQUIRE_EQUAL(test,true);
}
@@ -596,6 +621,11 @@ void fill_grid_some_data_scal(grid_cpu<2,Point_test_scal<float>> & g)
BOOST_AUTO_TEST_CASE( vtk_writer_use_grids)
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
{
// Create box grids
Point<2,float> offset1({0.0,0.0});
@@ -638,10 +668,11 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_grids)
vtk_g.add(g3,offset3,spacing3,d3);
vtk_g.add(g4,offset4,spacing4,d4);
- vtk_g.write("vtk_grids.vtk");
+ openfpm::vector<std::string> prp_names;
+ vtk_g.write("vtk_grids.vtk",prp_names);
// Check that match
- bool test = compare("vtk_grids.vtk","vtk_grids_test.vtk");
+ bool test = compare("vtk_grids.vtk","test_data/vtk_grids_test.vtk");
BOOST_REQUIRE_EQUAL(test,true);
}
@@ -696,7 +727,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_grids)
vtk_g.write("vtk_grids_st.vtk");
// Check that match
- bool test = compare("vtk_grids_st.vtk","vtk_grids_st_test.vtk");
+ bool test = compare("vtk_grids_st.vtk","test_data/vtk_grids_st_test.vtk");
BOOST_REQUIRE_EQUAL(test,true);
}
@@ -742,10 +773,11 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_grids)
vtk_g.add(g3,offset3,spacing3,d3);
vtk_g.add(g4,offset4,spacing4,d4);
- vtk_g.write("vtk_grids_prp.vtk");
+ openfpm::vector<std::string> prp_names;
+ vtk_g.write("vtk_grids_prp.vtk",prp_names);
// Check that match
- bool test = compare("vtk_grids_prp.vtk","vtk_grids_prp_test.vtk");
+ bool test = compare("vtk_grids_prp.vtk","test_data/vtk_grids_prp_test.vtk");
BOOST_REQUIRE_EQUAL(test,true);
}
@@ -791,10 +823,11 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_grids)
vtk_g.add(g3,offset3,spacing3,d3);
vtk_g.add(g4,offset4,spacing4,d4);
- vtk_g.write("vtk_grids_unk.vtk");
+ openfpm::vector<std::string> prp_names;
+ vtk_g.write("vtk_grids_unk.vtk",prp_names);
// Check that match
- bool test = compare("vtk_grids_unk.vtk","vtk_grids_test.vtk");
+ bool test = compare("vtk_grids_unk.vtk","test_data/vtk_grids_test.vtk");
BOOST_REQUIRE_EQUAL(test,true);
}
@@ -818,6 +851,11 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_grids)
BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
{
// Create 3 vectors with random particles
openfpm::vector<Point<3,double>> v1ps;
@@ -883,10 +921,11 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set )
vtk_v.add(v2ps,v2pp,88);
vtk_v.add(v3ps,v3pp,90);
- vtk_v.write("vtk_points.vtk");
+ openfpm::vector<std::string> prp_names;
+ vtk_v.write("vtk_points.vtk",prp_names);
// Check that match
- bool test = compare("vtk_points.vtk","vtk_points_test.vtk");
+ bool test = compare("vtk_points.vtk","test_data/vtk_points_test.vtk");
BOOST_REQUIRE_EQUAL(test,true);
@@ -894,18 +933,70 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set )
VTKWriter<boost::mpl::pair<openfpm::vector<Point<3,double>>,openfpm::vector<aggregate<float,Point<3,float>>>>,VECTOR_POINTS> vtk_v2;
vtk_v2.add(v1ps,v4pp,75);
- vtk_v2.write("vtk_points_pp.vtk");
+ vtk_v2.write("vtk_points_pp.vtk",prp_names);
// Check that match
- test = compare("vtk_points_pp.vtk","vtk_points_pp_test.vtk");
+ test = compare("vtk_points_pp.vtk","test_data/vtk_points_pp_test.vtk");
BOOST_REQUIRE_EQUAL(test,true);
}
}
+BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_properties )
+{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+ {
+ // Create 3 vectors with random particles
+ openfpm::vector<Point<3,double>> v1ps;
+ openfpm::vector<aggregate<float,float[3]>> v1pp;
+
+ // set the seed
+ // create the random generator engine
+ SimpleRNG rng;
+
+ // fill the vector with random data
+ v1ps.resize(100);
+ v1pp.resize(100);
+
+ for (size_t i = 0 ; i < v1ps.size(); i++)
+ {
+ v1ps.template get<0>(i)[0] = rng.GetUniform();
+ v1ps.template get<0>(i)[1] = rng.GetUniform();
+ v1ps.template get<0>(i)[2] = rng.GetUniform();
+
+
+ v1pp.template get<0>(i) = rng.GetUniform();
+ v1pp.template get<1>(i)[0] = rng.GetUniform();
+ v1pp.template get<1>(i)[1] = rng.GetUniform();
+ v1pp.template get<1>(i)[2] = rng.GetUniform();
+ }
+
+ openfpm::vector<std::string> prop_names;
+
+ // Create a writer and write adding names to the properties
+ VTKWriter<boost::mpl::pair<openfpm::vector<Point<3,double>>,openfpm::vector<aggregate<float,float[3]>>>,VECTOR_POINTS> vtk_v;
+ vtk_v.add(v1ps,v1pp,75);
+ openfpm::vector<std::string> prp_names({"scalar","vector"});
+ vtk_v.write("vtk_points_with_prp_names.vtk",prp_names);
+
+ // Check that match
+ bool test = compare("vtk_points_with_prp_names.vtk","test_data/vtk_points_with_prp_names_test.vtk");
+ BOOST_REQUIRE_EQUAL(test,true);
+
+ }
+}
BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary )
{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
{
// Create 3 vectors with random particles
openfpm::vector<Point<3,double>> v1ps;
@@ -971,21 +1062,25 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary )
vtk_v.add(v2ps,v2pp,88);
vtk_v.add(v3ps,v3pp,90);
- vtk_v.write("vtk_points_bin.vtk","vtk output",file_type::BINARY);
+ openfpm::vector<std::string> prp_names;
+ vtk_v.write("vtk_points_bin.vtk",prp_names,"vtk output",file_type::BINARY);
+ vtk_v.write("vtk_points_bin2.vtk",prp_names,"vtk output",file_type::BINARY);
+
// Check that match
- bool test = compare("vtk_points_bin.vtk","vtk_points_bin_test.vtk");
+ bool test = compare("vtk_points_bin.vtk","test_data/vtk_points_bin_test.vtk");
+ BOOST_REQUIRE_EQUAL(test,true);
+ test = compare("vtk_points_bin2.vtk","test_data/vtk_points_bin_test.vtk");
BOOST_REQUIRE_EQUAL(test,true);
-
// Create a writer and write
VTKWriter<boost::mpl::pair<openfpm::vector<Point<3,double>>,openfpm::vector<aggregate<float,Point<3,float>>>>,VECTOR_POINTS> vtk_v2;
vtk_v2.add(v1ps,v4pp,75);
- vtk_v2.write("vtk_points_pp_bin.vtk","vtk output",file_type::BINARY);
+ vtk_v2.write("vtk_points_pp_bin.vtk",prp_names,"vtk output",file_type::BINARY);
// Check that match
- test = compare("vtk_points_pp_bin.vtk","vtk_points_pp_bin_test.vtk");
+ test = compare("vtk_points_pp_bin.vtk","test_data/vtk_points_pp_bin_test.vtk");
BOOST_REQUIRE_EQUAL(test,true);
}
diff --git a/src/VTKWriter/VTKWriter_vector_box.hpp b/src/VTKWriter/VTKWriter_vector_box.hpp
index 368c451c7cffa19de92ea98efa5a2acc345c761f..2786f21375bd13cffb1ed6147fb5aaa303759f63 100644
--- a/src/VTKWriter/VTKWriter_vector_box.hpp
+++ b/src/VTKWriter/VTKWriter_vector_box.hpp
@@ -11,7 +11,7 @@
#include <boost/math/special_functions/pow.hpp>
#include "Space/Shape/HyperCube.hpp"
#include <random>
-#include "util.hpp"
+#include "util/util.hpp"
template <typename vector>
class v_box
diff --git a/src/VTKWriter/is_vtk_writable.hpp b/src/VTKWriter/is_vtk_writable.hpp
index 44a5b9c6148f38bcc334dcb940f2b29cecbe160b..ec21bfc0dcd70465466ebaa8ce4e112db1111341 100644
--- a/src/VTKWriter/is_vtk_writable.hpp
+++ b/src/VTKWriter/is_vtk_writable.hpp
@@ -83,6 +83,8 @@ struct is_vtk_vector_dims<ObjType, typename Void< decltype(ObjType::dims) >::typ
template<typename T>
struct is_vtk_writable
{
+ typedef T base;
+
//! It check if the object is vtk compatible
enum
{
@@ -94,6 +96,8 @@ struct is_vtk_writable
template<>
struct is_vtk_writable<float>
{
+ typedef float base;
+
//! float is vtk writable
enum
{
@@ -105,6 +109,8 @@ struct is_vtk_writable<float>
template<>
struct is_vtk_writable<double>
{
+ typedef double base;
+
//! double is vtk writable
enum
{
@@ -116,6 +122,8 @@ struct is_vtk_writable<double>
template<>
struct is_vtk_writable<char>
{
+ typedef char base;
+
//! char is vtk writable
enum
{
@@ -127,6 +135,8 @@ struct is_vtk_writable<char>
template<>
struct is_vtk_writable<unsigned char>
{
+ typedef unsigned char base;
+
//! unsigned char is vtk writable
enum
{
@@ -138,6 +148,8 @@ struct is_vtk_writable<unsigned char>
template<>
struct is_vtk_writable<short>
{
+ typedef short base;
+
//! short is vtk writable
enum
{
@@ -149,6 +161,8 @@ struct is_vtk_writable<short>
template<>
struct is_vtk_writable<unsigned short>
{
+ typedef unsigned short base;
+
//! unsigned short is vtk writable
enum
{
@@ -160,6 +174,8 @@ struct is_vtk_writable<unsigned short>
template<>
struct is_vtk_writable<int>
{
+ typedef int base;
+
//! int is vtk writable
enum
{
@@ -171,6 +187,8 @@ struct is_vtk_writable<int>
template<>
struct is_vtk_writable<unsigned int>
{
+ typedef unsigned int base;
+
//! unsigned int is vtk writable
enum
{
@@ -182,6 +200,8 @@ struct is_vtk_writable<unsigned int>
template<>
struct is_vtk_writable<long int>
{
+ typedef long base;
+
//! long int is vtk writable
enum
{
@@ -193,6 +213,8 @@ struct is_vtk_writable<long int>
template<>
struct is_vtk_writable<unsigned long int>
{
+ typedef unsigned long base;
+
//! unsigned long int is vtk writable
enum
{
@@ -204,6 +226,8 @@ struct is_vtk_writable<unsigned long int>
template<>
struct is_vtk_writable<bool>
{
+ typedef bool base;
+
//! bool is vtk writable
enum
{
diff --git a/src/HDF5_XdmfWriter/HDF5_XdmfWriter.hpp b/src/garbage/HDF5_XdmfWriter.hpp
similarity index 100%
rename from src/HDF5_XdmfWriter/HDF5_XdmfWriter.hpp
rename to src/garbage/HDF5_XdmfWriter.hpp
diff --git a/src/HDF5_XdmfWriter/HDF5_XdmfWriter_point_set.hpp b/src/garbage/HDF5_XdmfWriter_point_set.hpp
similarity index 81%
rename from src/HDF5_XdmfWriter/HDF5_XdmfWriter_point_set.hpp
rename to src/garbage/HDF5_XdmfWriter_point_set.hpp
index 4d6d5b3dec1ec6b8b073fa5712eb11cafe321227..5be3e3a5cb7554d8f4732ec151f5327c55981953 100644
--- a/src/HDF5_XdmfWriter/HDF5_XdmfWriter_point_set.hpp
+++ b/src/garbage/HDF5_XdmfWriter_point_set.hpp
@@ -27,13 +27,13 @@
template<typename ele_v, bool has_name>
struct H5_prop_out
{
- // HDF5 file
+ //! HDF5 file
hid_t file_id;
- // vector that we are processing
+ //! vector that we are processing
ele_v & vv;
- // Up to which element to write
+ //! Up to which element to write
size_t stop;
/*! \brief constructor
@@ -45,7 +45,11 @@ struct H5_prop_out
:file_id(file_id),vv(vv),stop(stop)
{};
- //! It produce an output for each property
+ /*! \brief It produce an output for each property
+ *
+ * \param t property id
+ *
+ */
template<typename T>
void operator()(T& t) const
{
@@ -71,25 +75,31 @@ struct H5_prop_out
template<typename ele_v>
struct H5_prop_out<ele_v,false>
{
- // HDF5 file
+ //! HDF5 file
hid_t file_id;
- // vector that we are processing
+ //! vector that we are processing
ele_v & vv;
- // Up to which element to write
+ //! Up to which element to write
size_t stop;
/*! \brief constructor
*
- * \param v_out string to fill with the vertex properties
+ * \param file_id handle of the file
+ * \param vv element to write
+ * \param stop up to which element to write
*
*/
H5_prop_out(hid_t file_id, ele_v & vv, size_t stop)
:file_id(file_id),vv(vv),stop(stop)
{};
- //! It produce an output for each property
+ /*! \brief It produce an output for each property
+ *
+ * \param t property id
+ *
+ */
template<typename T>
void operator()(T& t) const
{
@@ -99,6 +109,10 @@ struct H5_prop_out<ele_v,false>
}
};
+/*! \brief HDF5 writer for a point set
+ *
+ *
+ */
template <>
class HDF5_XdmfWriter<H5_POINTSET>
{
@@ -118,18 +132,23 @@ public:
/*!
*
- * \brief Write a set of particle position and properties into HDF5
+ * \brief Write a set of particle positions and properties into HDF5
*
* \tparam Pos Vector of positions type
* \taparam Prp Vector of properties type
* \tparam prp list of properties to output
*
- * \param pos Vector with the positions
- * \param prp Vector with the properties
+ * \param file output file
+ * \param v_pos Vector with the positions
+ * \param v_prp Vector with the properties
* \param stop size of the vector to output
*
*/
- template<typename VPos, typename VPrp, int ... prp > bool write(const std::string & file, openfpm::vector<VPos> & v_pos, openfpm::vector<VPrp> & v_prp, size_t stop)
+ template<typename VPos, typename VPrp, int ... prp >
+ bool write(const std::string & file,
+ openfpm::vector<VPos> & v_pos,
+ openfpm::vector<VPrp> & v_prp,
+ size_t stop)
{
Vcluster & v_cl = create_vcluster();
diff --git a/src/HDF5_XdmfWriter/HDF5_XdmfWriter_unit_tests.hpp b/src/garbage/HDF5_XdmfWriter_unit_tests.hpp
similarity index 100%
rename from src/HDF5_XdmfWriter/HDF5_XdmfWriter_unit_tests.hpp
rename to src/garbage/HDF5_XdmfWriter_unit_tests.hpp
diff --git a/src/HDF5_XdmfWriter/HDF5_XdmfWriter_util.hpp b/src/garbage/HDF5_XdmfWriter_util.hpp
similarity index 100%
rename from src/HDF5_XdmfWriter/HDF5_XdmfWriter_util.hpp
rename to src/garbage/HDF5_XdmfWriter_util.hpp
diff --git a/src/main.cpp b/src/main.cpp
index 12dbfcdf249309083e41306d5c09239367572c0d..795d036046b93972c66a76dac173ac6eed465481 100755
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -5,13 +5,17 @@
#define BOOST_DISABLE_ASSERTS
-
#define BOOST_TEST_MODULE "C++ test module for OpenFPM_io project"
#include <boost/test/included/unit_test.hpp>
+#include "VCluster/VCluster.hpp"
+#include "unit_test_init_cleanup_io.hpp"
+
#include "VCluster/VCluster.hpp"
#include "CSVWriter/CSVWriter_unit_tests.hpp"
#include "GraphMLWriter/GraphMLWriter_unit_tests.hpp"
#include "VTKWriter/VTKWriter_unit_tests.hpp"
//#include "HDF5_XdmfWriter/HDF5_XdmfWriter_unit_tests.hpp"
#include "Plot/Plot_unit_tests.hpp"
+#include "RawReader/RawReader_unit_tests.hpp"
+#include "HDF5_wr/HDF5_writer_unit_tests.hpp"
diff --git a/src/unit_test_init_cleanup_io.hpp b/src/unit_test_init_cleanup_io.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..c4fbc1b3d5c133d6b96579c5fbac529947f52115
--- /dev/null
+++ b/src/unit_test_init_cleanup_io.hpp
@@ -0,0 +1,34 @@
+/*
+ * unit_test_init_cleanup.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_UNIT_TEST_INIT_CLEANUP_IO_HPP_
+#define OPENFPM_IO_SRC_UNIT_TEST_INIT_CLEANUP_IO_HPP_
+
+
+struct ut_start
+{
+ //!
+ ut_start()
+ {
+ BOOST_TEST_MESSAGE("Initialize global VCluster");
+
+ openfpm_init(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv);
+ }
+
+ ~ut_start()
+ {
+ BOOST_TEST_MESSAGE("Delete global VClster");
+ openfpm_finalize();
+ }
+};
+
+//____________________________________________________________________________//
+
+BOOST_GLOBAL_FIXTURE( ut_start );
+
+
+#endif /* OPENFPM_IO_SRC_UNIT_TEST_INIT_CLEANUP_IO_HPP_ */
diff --git a/src/util/GBoxes.hpp b/src/util/GBoxes.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..b63033b3f636e81eef8522661dabca1daf7b94a0
--- /dev/null
+++ b/src/util/GBoxes.hpp
@@ -0,0 +1,50 @@
+/*
+ * Gboxes.hpp
+ *
+ * Created on: May 2, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_UTIL_GBOXES_HPP_
+#define OPENFPM_IO_SRC_UTIL_GBOXES_HPP_
+
+
+/*! \brief This structure store the Box that define the domain inside the Ghost + domain box
+ *
+ \verbatim
+
+ (Ghost + Domain)
+ +------------------+
+ | |
+ | +------------+ <---------- (Domain)
+ | | | |
+ | | Domain | |
+ | | Box | |
+ | | | |
+ | | | |
+ | +------------+ |
+ | |
+ +------------------+
+(0,0) local coordinate ---> ( x, y )
+
+ \endverbatim
+
+ *
+ * * Domain
+ *
+ * \tparam dim dimensionality
+ *
+ */
+template<unsigned int dim>
+struct GBoxes
+{
+ //! Ghost + Domain ghost
+ Box<dim,long int> GDbox;
+ //! Domain box
+ Box<dim,long int> Dbox;
+ //! origin of GDbox in global grid coordinates
+ Point<dim,long int> origin;
+};
+
+
+#endif /* OPENFPM_IO_SRC_UTIL_GBOXES_HPP_ */
diff --git a/src/util.hpp b/src/util/util.hpp
similarity index 100%
rename from src/util.hpp
rename to src/util/util.hpp
diff --git a/csv_out_test.csv b/test_data/csv_out_test.csv
similarity index 100%
rename from csv_out_test.csv
rename to test_data/csv_out_test.csv
diff --git a/csv_out_unk_test.csv b/test_data/csv_out_unk_test.csv
similarity index 100%
rename from csv_out_unk_test.csv
rename to test_data/csv_out_unk_test.csv
diff --git a/test_data/gc_out_sc_test.html b/test_data/gc_out_sc_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..c704abb8a4653bbb95e732b3eed2d6ba78eb67ba
--- /dev/null
+++ b/test_data/gc_out_sc_test.html
@@ -0,0 +1,65 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(this).attr({'href': svgData,'target': '_blank'});
+}
+
+ function drawVisualization() {
+var data0 = new google.visualization.DataTable();
+data0.addColumn('string','X Axis');
+data0.addColumn('number','dataset1');
+data0.addColumn('number','dataset2');
+data0.addColumn('number','dataset3');
+data0.addColumn('number','dataset4');
+data0.addRows([
+['colum1',2,3,5,6],
+['colum2',5,6,1,6],
+['colum3',2,1,6,9],
+['colum4',1,6,3,2],
+['colum5',3,3,0,6],
+['colum6',2,1,4,6],
+]);
+var options0= {
+title : 'Example',
+vAxis: {title: 'Y Axis'},
+hAxis: {title: 'X Axis'},
+seriesType: 'bars',
+series: {3: {type: 'line'}}};
+var view0 = new google.visualization.DataView(data0);
+view0.setColumns([0
+,1,{ calc: "stringify",
+sourceColumn: 1,
+type: "string",
+role: "annotation" }
+,2,{ calc: "stringify",
+sourceColumn: 2,
+type: "string",
+role: "annotation" }
+,3,{ calc: "stringify",
+sourceColumn: 3,
+type: "string",
+role: "annotation" }
+]
+);
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(view0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/test_data/raw_read_sv_test.bin b/test_data/raw_read_sv_test.bin
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diff --git a/vtk_box_3D_2_test.vtk b/test_data/vtk_box_3D_2_test.vtk
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similarity index 100%
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diff --git a/vtk_graph_v4_test.vtk b/test_data/vtk_graph_v4_test.vtk
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diff --git a/vtk_grids_prp_test.vtk b/test_data/vtk_grids_prp_test.vtk
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similarity index 100%
rename from vtk_grids_test.vtk
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diff --git a/vtk_points_bin_test.vtk b/test_data/vtk_points_bin_test.vtk
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rename from vtk_points_bin_test.vtk
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diff --git a/vtk_points_pp_bin_test.vtk b/test_data/vtk_points_pp_bin_test.vtk
similarity index 100%
rename from vtk_points_pp_bin_test.vtk
rename to test_data/vtk_points_pp_bin_test.vtk
diff --git a/vtk_points_pp_test.vtk b/test_data/vtk_points_pp_test.vtk
similarity index 100%
rename from vtk_points_pp_test.vtk
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diff --git a/vtk_points_test.vtk b/test_data/vtk_points_test.vtk
similarity index 100%
rename from vtk_points_test.vtk
rename to test_data/vtk_points_test.vtk