diff --git a/.gitignore b/.gitignore
index 1399389afcbdd97743d9c51bf7b4a32237e26828..3affdd38e54123c27b697377e6d500ce0025aa1c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -38,9 +38,6 @@ Thumbs.db
###### Other
-*.vtk
-*.swp
-install-sh
AUTHORS
COPYING
ChangeLog
@@ -50,21 +47,15 @@ README
Makefile
Makefile.in
config.status
-config.guess
-config.sub
configure
numerics
**/.deps
**/src/config
aclocal.m4
**/autom4te.cache
-compile
-depcomp
-missing
-src/mem_map
-#**/performance/
-previous_measure
-previous_measureg
-previous_measurev
+src/io
+csv_out.csv
+test_graph.graphml
+test_graph2.graphml
*.html
-test_save
+
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 36bd74d4b25325e09cdedffac562e4dcc20ad3c3..6280a89b71e9b698942a560f15d4fa4c37aceed2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,7 +4,12 @@ centos_build:
- centos
artifacts:
paths:
+<<<<<<< HEAD
- ./openfpm_data/build/src/mem_map
+=======
+ - ./openfpm_io/build/src/io
+ - ./openfpm_io/test_data
+>>>>>>> origin/master
script:
- ./build.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS NO $CI_COMMIT_REF_NAME
@@ -15,7 +20,11 @@ centos_run:
dependencies:
- centos_build
script:
+<<<<<<< HEAD
- ./openfpm_data/build/src/mem_map
+=======
+ - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS NO $CI_COMMIT_REF_NAME
+>>>>>>> origin/master
mac_build:
stage: build
@@ -23,7 +32,12 @@ mac_build:
- mac
artifacts:
paths:
+<<<<<<< HEAD
- ./openfpm_data/build/src/mem_map
+=======
+ - ./openfpm_io/build/src/io
+ - ./openfpm_io/test_data
+>>>>>>> origin/master
script:
- ./build.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS NO $CI_COMMIT_REF_NAME
@@ -34,7 +48,11 @@ mac_run:
dependencies:
- mac_build
script:
+<<<<<<< HEAD
- ./openfpm_data/build/src/mem_map
+=======
+ - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS NO $CI_COMMIT_REF_NAME
+>>>>>>> origin/master
ubuntu_build:
stage: build
@@ -42,7 +60,12 @@ ubuntu_build:
- ubuntu
artifacts:
paths:
+<<<<<<< HEAD
- ./openfpm_data/build/src/mem_map
+=======
+ - ./openfpm_io/build/src/io
+ - ./openfpm_io/test_data
+>>>>>>> origin/master
script:
- ./build.sh $CI_PROJECT_DIR $CI_RUNNER_EXECUTABLE_TAGS NO $CI_COMMIT_REF_NAME
@@ -53,5 +76,9 @@ ubuntu_run:
dependencies:
- ubuntu_build
script:
+<<<<<<< HEAD
- ./openfpm_data/build/src/mem_map
+=======
+ - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS NO $CI_COMMIT_REF_NAME
+>>>>>>> origin/master
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1ddf767cd6567232e0372285c018f0011b986615..39610d7e7df4cc9cb2ac5a7449ea8ded343acd36 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -5,6 +5,7 @@ if (POLICY CMP0074)
cmake_policy(SET CMP0074 OLD)
endif ()
+<<<<<<< HEAD
list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake_modules/ /opt/rocm/hip/cmake)
set(BOOST_INCLUDE ${Boost_INCLUDE_DIR} CACHE PATH "Include directory for BOOST")
@@ -17,6 +18,26 @@ set(HIP_ENABLE CACHE BOOL "Enable HIP compiler")
set(AMD_ARCH_COMPILE "gfx900" CACHE STRING "AMD gpu architecture used to compile kernels")
add_subdirectory (../openfpm_devices/ openfpm_devices)
+=======
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake_modules/)
+
+if (POLICY CMP0074)
+ cmake_policy(SET CMP0074 NEW)
+endif()
+
+set(BOOST_INCLUDE ${Boost_INCLUDE_DIR} CACHE PATH "Include directory for BOOST")
+set(HDF5_ROOT CACHE PATH "HDF5 root path")
+set(SE_CLASS1 CACHE BOOL "Activate compilation with SE_CLASS1")
+set(SE_CLASS3 CACHE BOOL "Activate compilation with SE_CLASS3")
+set(ENV{HDF5_ROOT} ${HDF5_ROOT})
+set(OPENFPM_PDATA_DIR CACHE PATH "OpenFPM_pdata dirs")
+set(PETSC_ROOT CACHE PATH "If compiling with linear algebra indicate the PETSC root directory")
+set(ENV{PETSC_DIR} ${PETSC_ROOT})
+set(HIP_ENABLE CACHE BOOL "Enable HIP compiler")
+set(AMD_ARCH_COMPILE "gfx900" CACHE STRING "AMD gpu architecture used to compile kernels")
+
+add_subdirectory (../openfpm_vcluster openfpm_vcluster)
+>>>>>>> origin/master
if (CUDA_ON_BACKEND STREQUAL "CUDA")
enable_language(CUDA)
@@ -25,6 +46,7 @@ endif()
set (CMAKE_CXX_STANDARD 14)
set (CMAKE_CUDA_STANDARD 14)
+<<<<<<< HEAD
set(Vc_DIR "${Vc_ROOT}/lib/cmake/Vc/")
message("Searching Vc in ${Vc_DIR}")
@@ -39,6 +61,43 @@ endif()
if (NOT CUDA_ON_BACKEND STREQUAL "HIP")
find_package(OpenMP)
+=======
+if(NOT TINYOBJLOADER_FOUND)
+ set(TINYOBJLOADER_ROOT CACHE PATH "TinyObjLoader library path")
+endif()
+
+set(ENV{PATH} "$ENV{PATH}:${HDF5_ROOT}/bin")
+set(HDF5_PREFER_PARALLEL TRUE)
+
+set (ENV{BOOST_ROOT} ${BOOST_ROOT})
+set (Boost_NO_BOOST_CMAKE OFF)
+find_package(Boost 1.72.0 REQUIRED COMPONENTS unit_test_framework iostreams program_options system filesystem
+ OPTIONAL_COMPONENTS fiber context)
+find_package(MPI REQUIRED)
+find_package(HDF5 REQUIRED)
+find_package(TinyObjLoader)
+find_package(PETSc)
+if (NOT CUDA_ON_BACKEND STREQUAL "HIP")
+ find_package(OpenMP)
+endif()
+if (CUDA_ON_BACKEND STREQUAL "HIP" AND NOT HIP_FOUND)
+ find_package(HIP)
+endif()
+
+if(HIP_FOUND)
+ set(DEFINE_HIP_GPU "#define HIP_GPU")
+ set(DEFINE_CUDIFY_USE_HIP "#define CUDIFY_USE_HIP")
+endif()
+
+if(HIP_FOUND)
+ set(DEFINE_CUDA_GPU "#define CUDA_GPU")
+endif()
+
+if(CUDA_FOUND)
+ set(OPENFPM_INIT_FILE "initialize/initialize_wrapper_cuda.cu")
+else()
+ set(OPENFPM_INIT_FILE "initialize/initialize_wrapper_cuda.cpp")
+>>>>>>> origin/master
endif()
###### CONFIG.h FILE ######
@@ -51,6 +110,7 @@ if(SE_CLASS3)
set(DEFINE_SE_CLASS3 "#define SE_CLASS3")
endif()
+<<<<<<< HEAD
if(TEST_PERFORMANCE)
set(DEFINE_PERFORMANCE_TEST "#define PERFORMANCE_TEST")
endif()
@@ -94,10 +154,44 @@ if(LIBHILBERT_FOUND)
set(DEFINE_HAVE_LIBHILBERT "#define HAVE_LIBHILBERT 1")
else()
message( FATAL_ERROR "LibHilbert is required in order to install OpenFPM")
+=======
+if(CUDA_FOUND)
+ set(DEFINE_CUDA_GPU "#define CUDA_GPU")
+endif()
+
+if(MPI_FOUND)
+ set(DEFINE_HAVE_MPI "#define HAVE_MPI")
+else()
+ message( FATAL_ERROR "MPI is required in order to install OpenFPM" )
+endif()
+
+if(PETSC_FOUND)
+ set(DEFINE_HAVE_PETSC "#define HAVE_PETSC")
+endif()
+
+if(HDF5_FOUND)
+ if (HDF5_IS_PARALLEL)
+ set(DEFINE_HAVE_HDF5 "#define HAVE_HDF5")
+ else()
+ message( STATUS "HDF5 found ${HDF5_INCLUDE_DIRS} does not have parallel support, OpenFPM require it" )
+ endif()
+else()
+ message( FATAL_ERROR "HDF5 with parallel support is required in order to install OpenFPM" )
+endif()
+
+if(TINYOBJLOADER_FOUND)
+ set(DEFINE_HAVE_TINYOBJLOADER "#define HAVE_TINYOBJLOADER 1")
+>>>>>>> origin/master
endif()
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/src/config/config_cmake.h.in ${CMAKE_CURRENT_SOURCE_DIR}/src/config/config.h)
+<<<<<<< HEAD
+=======
+include_directories(SYSTEM ${MPI_INCLUDE_PATH})
+
+
+>>>>>>> origin/master
add_subdirectory (src)
get_directory_property(hasParent PARENT_DIRECTORY)
diff --git a/Jenkinsfile b/Jenkinsfile
new file mode 100644
index 0000000000000000000000000000000000000000..207c3da88a038af26f4f5422b227a379499634c5
--- /dev/null
+++ b/Jenkinsfile
@@ -0,0 +1,100 @@
+#!groovy
+
+parallel (
+
+"nyu" : {node ('nyu')
+ {
+ deleteDir()
+
+ int ntry = 5
+ while (ntry != 0)
+ {
+ try {
+ checkout scm
+ ntry = 0
+ }
+ catch (IOException e)
+ {
+ ntry--
+ sleep(50)
+ }
+ }
+
+ stage ('build_nyu')
+ {
+ sh "./build.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+ }
+
+ stage ('run_nyu')
+ {
+ sh "cd openfpm_io && ./run.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+ sh "cd openfpm_io && ./success.sh 2 nyu openfpm_io"
+ }
+ }
+ },
+
+
+"sb15" : {node ('sbalzarini-mac-15')
+ {
+ deleteDir()
+ env.PATH = "/usr/local/bin:${env.PATH}"
+
+ int ntry = 5
+ while (ntry != 0)
+ {
+ try {
+ checkout scm
+ ntry = 0
+ }
+ catch (IOException e)
+ {
+ ntry--
+ sleep(50)
+ }
+ }
+
+ stage ('build_sb15')
+ {
+ sh "echo $PATH && ./build.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+ }
+
+ stage ('run_sb15')
+ {
+ sh "cd openfpm_io && ./run.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+ sh "cd openfpm_io && ./success.sh 2 sbalzarini-mac-15 openfpm_io"
+ }
+ }
+ },
+
+"gin" : {node ('gin')
+ {
+ deleteDir()
+
+ int ntry = 5
+ while (ntry != 0)
+ {
+ try {
+ checkout scm
+ ntry = 0
+ }
+ catch (IOException e)
+ {
+ ntry--
+ sleep(50)
+ }
+ }
+
+ stage ('build_gin')
+ {
+ sh "echo $PATH && ./build.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+ }
+
+ stage ('run_gin')
+ {
+ sh "cd openfpm_io && ./run.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+ sh "cd openfpm_io && ./success.sh 2 gin openfpm_io"
+ }
+ }
+ }
+)
+
diff --git a/Jenkinsfile_mpi b/Jenkinsfile_mpi
index 642cb804a86c79955edee8d3ecaf5ce27a1f1cef..0cab6265950aff48f31c50821e3c9832870a2401 100644
--- a/Jenkinsfile_mpi
+++ b/Jenkinsfile_mpi
@@ -2,7 +2,11 @@
parallel (
+<<<<<<< HEAD
"ubuntu" : {node ('cifarm-ubuntu-node')
+=======
+"cifarm-ubuntu-node" : {node ('cifarm-ubuntu-node')
+>>>>>>> origin/master
{
deleteDir()
@@ -16,6 +20,7 @@ parallel (
catch (IOException e)
{
ntry--
+<<<<<<< HEAD
sleep(10)
}
}
@@ -29,13 +34,64 @@ parallel (
{
sh "cd openfpm_data && ./run.sh $WORKSPACE $NODE_NAME NO"
sh "cd openfpm_data && ./success.sh 2 ubuntu openfpm_data"
+=======
+ sleep(50)
+ }
+ }
+
+ stage ('build ubuntu')
+ {
+ sh "./build.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+ }
+
+ stage ('run ubuntu')
+ {
+ sh "cd openfpm_io && ./run.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+ sh "cd openfpm_io && ./success.sh 2 ubuntu openfpm_io"
+>>>>>>> origin/master
}
}
},
+<<<<<<< HEAD
"macosx" : {node ('cifarm-mac-node')
+=======
+"cifarm-mac-node" : {node ('cifarm-mac-node')
+ {
+ deleteDir()
+ env.PATH = "/usr/local/bin:${env.PATH}"
+
+ int ntry = 5
+ while (ntry != 0)
+ {
+ try {
+ checkout scm
+ ntry = 0
+ }
+ catch (IOException e)
+ {
+ ntry--
+ sleep(50)
+ }
+ }
+
+ stage ('build mac')
+ {
+ sh "echo $PATH && ./build.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+ }
+
+ stage ('run mac')
+ {
+ sh "cd openfpm_io && ./run.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+ sh "cd openfpm_io && ./success.sh 2 mac openfpm_io"
+ }
+ }
+ },
+
+"cifarm-centos-node" : {node ('cifarm-centos-node')
+>>>>>>> origin/master
{
deleteDir()
@@ -49,6 +105,7 @@ parallel (
catch (IOException e)
{
ntry--
+<<<<<<< HEAD
sleep(10)
}
}
@@ -99,5 +156,23 @@ parallel (
+=======
+ sleep(50)
+ }
+ }
+
+ stage ('build_gin')
+ {
+ sh "echo $PATH && ./build.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+ }
+
+ stage ('run_gin')
+ {
+ sh "cd openfpm_io && ./run.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+ sh "cd openfpm_io && ./success.sh 2 centos openfpm_io"
+ }
+ }
+ }
+>>>>>>> origin/master
)
diff --git a/Makefile.am b/Makefile.am
new file mode 100755
index 0000000000000000000000000000000000000000..bad0185690207b20c536ceace77718261a0f6833
--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,7 @@
+SUBDIRS = src
+
+bin_PROGRAMS =
+
+test:
+ cd src && make test
+
diff --git a/build.sh b/build.sh
index 2b80de126c3064c3d6c4e32bae5e87e6895ddc63..48406c1a45a9e4eb16ed095472137ce25970bcce 100755
--- a/build.sh
+++ b/build.sh
@@ -1,5 +1,6 @@
#! /bin/bash
+<<<<<<< HEAD
# Make a directory in /tmp/openfpm_data
workspace=$1
@@ -94,5 +95,88 @@ if [ $? -ne 0 ]; then
fi
ls build/src/mem_map
+=======
+workspace=$1
+hostname=$(hostname)
+branch=$3
+
+echo "Directory: $workspace"
+echo "Machine: $hostname"
+echo "Branch name: $branch"
+
+echo "Branch: $3"
+
+# Make a directory in /tmp/openfpm_data
+
+mkdir /tmp/openfpm_io
+mv * .[^.]* /tmp/openfpm_io
+mv /tmp/openfpm_io openfpm_io
+
+git clone git@git.mpi-cbg.de:openfpm/openfpm_devices.git openfpm_devices
+cd openfpm_devices
+git checkout develop
+cd ..
+git clone git@git.mpi-cbg.de:openfpm/openfpm_data.git openfpm_data
+cd openfpm_data
+git checkout develop
+cd ..
+git clone git@git.mpi-cbg.de:openfpm/openfpm_pdata.git openfpm_pdata
+cd openfpm_pdata
+git checkout develop
+cd ..
+git clone git@git.mpi-cbg.de:openfpm/openfpm_vcluster.git openfpm_vcluster
+cd openfpm_vcluster
+git checkout develop
+cd ..
+
+cd "$1/openfpm_io"
+
+#rm -rf $HOME/openfpm_dependencies/openfpm_io/$branch/MPI
+#rm -rf $HOME/openfpm_dependencies/openfpm_io/$branch/HDF5
+#rm -rf $HOME/openfpm_dependencies/openfpm_io/$branch/BOOST
+
+
+if [ x"$hostname" == x"cifarm-centos-node.mpi-cbg.de" ]; then
+ source /opt/rh/devtoolset-7/enable
+ ./install_MPI.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4
+ export PATH="$HOME/openfpm_dependencies/openfpm_io/$branch/MPI/bin/:$PATH"
+ ./install_BOOST.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4
+ ./install_HDF5.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4
+ ./install_LIBHILBERT.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4
+ ./install_VCDEVEL.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4 gcc g++
+fi
+
+if [ x"$hostname" == x"cifarm-ubuntu-node" ]; then
+ ./install_MPI.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4
+ export PATH="/opt/bin:$HOME/openfpm_dependencies/openfpm_io/$branch/MPI/bin/:$PATH"
+ ./install_BOOST.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4
+ ./install_HDF5.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4
+ ./install_LIBHILBERT.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4
+ ./install_VCDEVEL.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4 gcc g++
+fi
+
+if [ x"$hostname" == x"cifarm-mac-node.mpi-cbg.de" ]; then
+ export PATH="/usr/local/bin:$PATH"
+ ./install_MPI.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4
+ export PATH="$HOME/openfpm_dependencies/openfpm_io/$branch/MPI/bin/:$PATH"
+ ./install_BOOST.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4
+ ./install_HDF5.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4
+ ./install_LIBHILBERT.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4
+ ./install_VCDEVEL.sh $HOME/openfpm_dependencies/openfpm_io/$branch/ 4 gcc g++
+fi
+
+# Go in the right branch
+
+echo "Compiling on $2"
+
+sh ./autogen.sh
+if [ x"$hostname" == x"cifarm-mac-node.mpi-cbg.de" ]; then
+ sh ./configure CXX=mpic++ --with-vcdevel=$HOME/openfpm_dependencies/openfpm_io/$branch/VCDEVEL --with-libhilbert=$HOME/openfpm_dependencies/openfpm_io/$branch/LIBHILBERT --with-hdf5=$HOME/openfpm_dependencies/openfpm_io/$branch/HDF5 --with-boost=$HOME/openfpm_dependencies/openfpm_io/$branch/BOOST --with-pdata=../../openfpm_pdata/ --enable-cuda-on-cpu
+else
+ sh ./configure CXX=mpic++ --with-vcdevel=$HOME/openfpm_dependencies/openfpm_io/$branch/VCDEVEL --with-libhilbert=$HOME/openfpm_dependencies/openfpm_io/$branch/LIBHILBERT --with-hdf5=$HOME/openfpm_dependencies/openfpm_io/$branch/HDF5 --with-boost=$HOME/openfpm_dependencies/openfpm_io/$branch/BOOST --with-pdata=../../openfpm_pdata/ --with-cuda-on-backend=OpenMP
+fi
+
+make VERBOSE=1 -j 4
+>>>>>>> origin/master
diff --git a/build_io.sh b/build_io.sh
new file mode 100755
index 0000000000000000000000000000000000000000..fc419ca8a28b1ef699f36cb03e1a306cdf1dbb2b
--- /dev/null
+++ b/build_io.sh
@@ -0,0 +1,45 @@
+#! /bin/bash
+
+source $HOME/.bashrc
+
+echo "$PATH"
+
+# Make a directory in /tmp/openfpm_data
+
+mkdir /tmp/openfpm_io
+mv * .[^.]* /tmp/openfpm_io
+mv /tmp/openfpm_io openfpm_io
+
+mkdir openfpm_io/src/config
+
+git clone git@ppmcore.mpi-cbg.de:incardon/openfpm_devices.git openfpm_devices
+git clone git@ppmcore.mpi-cbg.de:incardon/openfpm_data.git openfpm_data
+git clone git@ppmcore.mpi-cbg.de:incardon/openfpm_pdata.git openfpm_pdata
+git clone git@ppmcore.mpi-cbg.de:incardon/openfpm_vcluster.git openfpm_vcluster
+
+cd "$1/openfpm_io"
+
+echo "Compiling on $2"
+
+sh ./autogen.sh
+if [ "$2" == "master" ]
+then
+ sh ./configure CXX=mpic++ --with-hdf5=$HOME/HDF5/bin/h5pcc --disable-gpu
+elif [ "$2" == "gin" ]
+then
+ module load gcc/4.8.2
+ module load boost/1.54.0
+ sh ./configure CXX=mpic++ --with-boost=/sw/apps/boost/1.54.0/ --with-hdf5=$HOME/HDF5/bin/h5pcc
+else
+ sh ./configure CXX=mpic++ --with-hdf5=$HOME/HDF5/bin/h5pcc
+fi
+make
+
+./src/io
+if [ $? -ne 0 ]; then
+ curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_io test \" }] }" https://hooks.slack.com/services/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
+ exit 1 ;
+fi
+
+curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Info:\", \"color\": \"#00FF00\", \"text\":\"$2 completed succeffuly the openfpm_io test \" }] }" https://hooks.slack.com/services/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
+
diff --git a/cmake_modules/CorrectWindowsPaths.cmake b/cmake_modules/CorrectWindowsPaths.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..09bcdd67dcd04fd001d2b7acbd904b5014ebe42b
--- /dev/null
+++ b/cmake_modules/CorrectWindowsPaths.cmake
@@ -0,0 +1,14 @@
+# CorrectWindowsPaths - this module defines one macro
+#
+# CONVERT_CYGWIN_PATH( PATH )
+# This uses the command cygpath (provided by cygwin) to convert
+# unix-style paths into paths useable by cmake on windows
+
+macro (CONVERT_CYGWIN_PATH _path)
+ if (WIN32)
+ EXECUTE_PROCESS(COMMAND cygpath.exe -m ${${_path}}
+ OUTPUT_VARIABLE ${_path})
+ string (STRIP ${${_path}} ${_path})
+ endif (WIN32)
+endmacro (CONVERT_CYGWIN_PATH)
+
diff --git a/cmake_modules/FindPETSc.cmake b/cmake_modules/FindPETSc.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..f8ea15b67fbb5a237169411fe37fa5227e6b7aee
--- /dev/null
+++ b/cmake_modules/FindPETSc.cmake
@@ -0,0 +1,349 @@
+# - Try to find PETSc
+# Once done this will define
+#
+# PETSC_FOUND - system has PETSc
+# PETSC_INCLUDES - the PETSc include directories
+# PETSC_LIBRARIES - Link these to use PETSc
+# PETSC_COMPILER - Compiler used by PETSc, helpful to find a compatible MPI
+# PETSC_DEFINITIONS - Compiler switches for using PETSc
+# PETSC_MPIEXEC - Executable for running MPI programs
+# PETSC_VERSION - Version string (MAJOR.MINOR.SUBMINOR)
+#
+# Usage:
+# find_package(PETSc COMPONENTS CXX) - required if build --with-clanguage=C++ --with-c-support=0
+# find_package(PETSc COMPONENTS C) - standard behavior of checking build using a C compiler
+# find_package(PETSc) - same as above
+#
+# Setting these changes the behavior of the search
+# PETSC_DIR - directory in which PETSc resides
+# PETSC_ARCH - build architecture
+#
+# Redistribution and use is allowed according to the terms of the BSD license.
+# For details see the accompanying COPYING-CMAKE-SCRIPTS file.
+#
+
+cmake_policy(VERSION 3.3)
+
+set(PETSC_VALID_COMPONENTS
+ C
+ CXX)
+
+if(NOT PETSc_FIND_COMPONENTS)
+ get_property (_enabled_langs GLOBAL PROPERTY ENABLED_LANGUAGES)
+ if ("C" IN_LIST _enabled_langs)
+ set(PETSC_LANGUAGE_BINDINGS "C")
+ else ()
+ set(PETSC_LANGUAGE_BINDINGS "CXX")
+ endif ()
+else()
+ # Right now, this is designed for compatability with the --with-clanguage option, so
+ # only allow one item in the components list.
+ list(LENGTH ${PETSc_FIND_COMPONENTS} components_length)
+ if(${components_length} GREATER 1)
+ message(FATAL_ERROR "Only one component for PETSc is allowed to be specified")
+ endif()
+ # This is a stub for allowing multiple components should that time ever come. Perhaps
+ # to also test Fortran bindings?
+ foreach(component ${PETSc_FIND_COMPONENTS})
+ list(FIND PETSC_VALID_COMPONENTS ${component} component_location)
+ if(${component_location} EQUAL -1)
+ message(FATAL_ERROR "\"${component}\" is not a valid PETSc component.")
+ else()
+ list(APPEND PETSC_LANGUAGE_BINDINGS ${component})
+ endif()
+ endforeach()
+endif()
+
+function (petsc_get_version)
+ if (EXISTS "${PETSC_DIR}/include/petscversion.h")
+ file (STRINGS "${PETSC_DIR}/include/petscversion.h" vstrings REGEX "#define PETSC_VERSION_(RELEASE|MAJOR|MINOR|SUBMINOR|PATCH) ")
+ foreach (line ${vstrings})
+ string (REGEX REPLACE " +" ";" fields ${line}) # break line into three fields (the first is always "#define")
+ list (GET fields 1 var)
+ list (GET fields 2 val)
+ set (${var} ${val} PARENT_SCOPE)
+ set (${var} ${val}) # Also in local scope so we have access below
+ endforeach ()
+ if (PETSC_VERSION_RELEASE)
+ if ($(PETSC_VERSION_PATCH) GREATER 0)
+ set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}p${PETSC_VERSION_PATCH}" CACHE INTERNAL "PETSc version")
+ else ()
+ set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}" CACHE INTERNAL "PETSc version")
+ endif ()
+ else ()
+ # make dev version compare higher than any patch level of a released version
+ set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}.99" CACHE INTERNAL "PETSc version")
+ endif ()
+ else ()
+ message (SEND_ERROR "PETSC_DIR can not be used, ${PETSC_DIR}/include/petscversion.h does not exist")
+ endif ()
+endfunction ()
+
+# Debian uses versioned paths e.g /usr/lib/petscdir/3.5/
+file (GLOB DEB_PATHS "/usr/lib/petscdir/*")
+
+find_path (PETSC_DIR include/petsc.h
+ HINTS ENV PETSC_DIR
+ PATHS
+ /usr/lib/petsc
+ # Debian paths
+ ${DEB_PATHS}
+ # Arch Linux path
+ /opt/petsc/linux-c-opt
+ # MacPorts path
+ /opt/local/lib/petsc
+ $ENV{HOME}/petsc
+ DOC "PETSc Directory")
+
+find_program (MAKE_EXECUTABLE NAMES make gmake)
+
+if (PETSC_DIR AND NOT PETSC_ARCH)
+ set (_petsc_arches
+ $ENV{PETSC_ARCH} # If set, use environment variable first
+ linux-gnu-c-debug linux-gnu-c-opt # Debian defaults
+ x86_64-unknown-linux-gnu i386-unknown-linux-gnu)
+ set (petscconf "NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
+ foreach (arch ${_petsc_arches})
+ if (NOT PETSC_ARCH)
+ find_path (petscconf petscconf.h
+ HINTS ${PETSC_DIR}
+ PATH_SUFFIXES ${arch}/include bmake/${arch}
+ NO_DEFAULT_PATH)
+ if (petscconf)
+ set (PETSC_ARCH "${arch}" CACHE STRING "PETSc build architecture")
+ endif (petscconf)
+ endif (NOT PETSC_ARCH)
+ endforeach (arch)
+ set (petscconf "NOTFOUND" CACHE INTERNAL "Scratch variable" FORCE)
+endif (PETSC_DIR AND NOT PETSC_ARCH)
+
+set (petsc_slaves LIBRARIES_SYS LIBRARIES_VEC LIBRARIES_MAT LIBRARIES_DM LIBRARIES_KSP LIBRARIES_SNES LIBRARIES_TS
+ INCLUDE_DIR INCLUDE_CONF)
+include (FindPackageMultipass)
+find_package_multipass (PETSc petsc_config_current
+ STATES DIR ARCH
+ DEPENDENTS INCLUDES LIBRARIES COMPILER MPIEXEC ${petsc_slaves})
+
+# Determine whether the PETSc layout is old-style (through 2.3.3) or
+# new-style (>= 3.0.0)
+if (EXISTS "${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/petscvariables") # > 3.5
+ set (petsc_conf_rules "${PETSC_DIR}/lib/petsc/conf/rules")
+ set (petsc_conf_variables "${PETSC_DIR}/lib/petsc/conf/variables")
+elseif (EXISTS "${PETSC_DIR}/${PETSC_ARCH}/include/petscconf.h") # > 2.3.3
+ set (petsc_conf_rules "${PETSC_DIR}/conf/rules")
+ set (petsc_conf_variables "${PETSC_DIR}/conf/variables")
+elseif (EXISTS "${PETSC_DIR}/bmake/${PETSC_ARCH}/petscconf.h") # <= 2.3.3
+ set (petsc_conf_rules "${PETSC_DIR}/bmake/common/rules")
+ set (petsc_conf_variables "${PETSC_DIR}/bmake/common/variables")
+elseif (PETSC_DIR)
+ message (SEND_ERROR "The pair PETSC_DIR=${PETSC_DIR} PETSC_ARCH=${PETSC_ARCH} do not specify a valid PETSc installation")
+endif ()
+
+if (petsc_conf_rules AND petsc_conf_variables AND NOT petsc_config_current)
+ petsc_get_version()
+
+ # Put variables into environment since they are needed to get
+ # configuration (petscvariables) in the PETSc makefile
+ set (ENV{PETSC_DIR} "${PETSC_DIR}")
+ set (ENV{PETSC_ARCH} "${PETSC_ARCH}")
+
+ # A temporary makefile to probe the PETSc configuration
+ set (petsc_config_makefile "${PROJECT_BINARY_DIR}/Makefile.petsc")
+ file (WRITE "${petsc_config_makefile}"
+"## This file was autogenerated by FindPETSc.cmake
+# PETSC_DIR = ${PETSC_DIR}
+# PETSC_ARCH = ${PETSC_ARCH}
+include ${petsc_conf_rules}
+include ${petsc_conf_variables}
+show :
+\t-@echo -n \${\${VARIABLE}}
+")
+
+ macro (PETSC_GET_VARIABLE name var)
+ set (${var} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+ execute_process (COMMAND ${MAKE_EXECUTABLE} --no-print-directory -f ${petsc_config_makefile} show VARIABLE=${name}
+ OUTPUT_VARIABLE ${var}
+ RESULT_VARIABLE petsc_return)
+ endmacro (PETSC_GET_VARIABLE)
+ petsc_get_variable (PETSC_LIB_DIR petsc_lib_dir)
+ petsc_get_variable (PETSC_EXTERNAL_LIB_BASIC petsc_libs_external)
+ petsc_get_variable (PETSC_CCPPFLAGS petsc_cpp_line)
+ petsc_get_variable (PETSC_INCLUDE petsc_include)
+ petsc_get_variable (PCC petsc_cc)
+ petsc_get_variable (PCC_FLAGS petsc_cc_flags)
+ petsc_get_variable (MPIEXEC petsc_mpiexec)
+ # We are done with the temporary Makefile, calling PETSC_GET_VARIABLE after this point is invalid!
+ file (REMOVE ${petsc_config_makefile})
+
+ execute_process(COMMAND ${MPI_C_COMPILER} --showme:compile OUTPUT_VARIABLE mpi_compile_options ERROR_VARIABLE mpi_compile_error)
+ set(petsc_cpp_line ${petsc_cpp_line} ${mpi_compile_options})
+
+ include (ResolveCompilerPaths)
+ # Extract include paths and libraries from compile command line
+ resolve_includes (petsc_includes_all "${petsc_cpp_line}")
+
+ #on windows we need to make sure we're linking against the right
+ #runtime library
+ if (WIN32)
+ if (petsc_cc_flags MATCHES "-MT")
+ set(using_md False)
+ foreach(flag_var
+ CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
+ CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO
+ CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
+ CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO)
+ if(${flag_var} MATCHES "/MD")
+ set(using_md True)
+ endif(${flag_var} MATCHES "/MD")
+ endforeach(flag_var)
+ if(${using_md} MATCHES "True")
+ message(WARNING "PETSc was built with /MT, but /MD is currently set.
+ See http://www.cmake.org/Wiki/CMake_FAQ#How_can_I_build_my_MSVC_application_with_a_static_runtime.3F")
+ endif(${using_md} MATCHES "True")
+ endif (petsc_cc_flags MATCHES "-MT")
+ endif (WIN32)
+
+ include (CorrectWindowsPaths)
+ convert_cygwin_path(petsc_lib_dir)
+ message (STATUS "petsc_lib_dir ${petsc_lib_dir}")
+
+ macro (PETSC_FIND_LIBRARY suffix name)
+ set (PETSC_LIBRARY_${suffix} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE) # Clear any stale value, if we got here, we need to find it again
+ if (WIN32)
+ set (libname lib${name}) #windows expects "libfoo", linux expects "foo"
+ else (WIN32)
+ set (libname ${name})
+ endif (WIN32)
+ find_library (PETSC_LIBRARY_${suffix} NAMES ${libname} HINTS ${petsc_lib_dir} NO_DEFAULT_PATH)
+ set (PETSC_LIBRARIES_${suffix} "${PETSC_LIBRARY_${suffix}}")
+ mark_as_advanced (PETSC_LIBRARY_${suffix})
+ endmacro (PETSC_FIND_LIBRARY suffix name)
+
+ # Look for petscvec first, if it doesn't exist, we must be using single-library
+ petsc_find_library (VEC petscvec)
+ if (PETSC_LIBRARY_VEC)
+ petsc_find_library (SYS "petscsys;petsc") # libpetscsys is called libpetsc prior to 3.1 (when single-library was introduced)
+ petsc_find_library (MAT petscmat)
+ petsc_find_library (DM petscdm)
+ petsc_find_library (KSP petscksp)
+ petsc_find_library (SNES petscsnes)
+ petsc_find_library (TS petscts)
+ macro (PETSC_JOIN libs deps)
+ list (APPEND PETSC_LIBRARIES_${libs} ${PETSC_LIBRARIES_${deps}})
+ endmacro (PETSC_JOIN libs deps)
+ petsc_join (VEC SYS)
+ petsc_join (MAT VEC)
+ petsc_join (DM MAT)
+ petsc_join (KSP DM)
+ petsc_join (SNES KSP)
+ petsc_join (TS SNES)
+ petsc_join (ALL TS)
+ else ()
+ set (PETSC_LIBRARY_VEC "NOTFOUND" CACHE INTERNAL "Cleared" FORCE) # There is no libpetscvec
+ petsc_find_library (SINGLE petsc)
+ # Debian 9/Ubuntu 16.04 uses _real and _complex extensions when using libraries in /usr/lib/petsc.
+ if (NOT PETSC_LIBRARY_SINGLE)
+ petsc_find_library (SINGLE petsc_real)
+ endif()
+ if (NOT PETSC_LIBRARY_SINGLE)
+ petsc_find_library (SINGLE petsc_complex)
+ endif()
+ foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
+ set (PETSC_LIBRARIES_${pkg} "${PETSC_LIBRARY_SINGLE}")
+ endforeach ()
+ endif ()
+ if (PETSC_LIBRARY_TS)
+ message (STATUS "Recognized PETSc install with separate libraries for each package")
+ else ()
+ message (STATUS "Recognized PETSc install with single library for all packages")
+ endif ()
+
+ include(Check${PETSC_LANGUAGE_BINDINGS}SourceRuns)
+ macro (PETSC_TEST_RUNS includes libraries runs)
+ if (PETSC_VERSION VERSION_GREATER 3.1)
+ set (_PETSC_TSDestroy "TSDestroy(&ts)")
+ else ()
+ set (_PETSC_TSDestroy "TSDestroy(ts)")
+ endif ()
+
+ set(_PETSC_TEST_SOURCE "
+static const char help[] = \"PETSc test program.\";
+#include <petscts.h>
+int main(int argc,char *argv[]) {
+ PetscErrorCode ierr;
+ TS ts;
+
+ ierr = PetscInitialize(&argc,&argv,0,help);CHKERRQ(ierr);
+ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
+ ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
+ ierr = ${_PETSC_TSDestroy};CHKERRQ(ierr);
+ ierr = PetscFinalize();CHKERRQ(ierr);
+ return 0;
+}
+")
+ multipass_source_runs ("${includes}" "${libraries}" "${_PETSC_TEST_SOURCE}" ${runs} "${PETSC_LANGUAGE_BINDINGS}")
+ if (${${runs}})
+ set (PETSC_EXECUTABLE_RUNS "YES" CACHE BOOL
+ "Can the system successfully run a PETSc executable? This variable can be manually set to \"YES\" to force CMake to accept a given PETSc configuration, but this will almost always result in a broken build. If you change PETSC_DIR, PETSC_ARCH, or PETSC_CURRENT you would have to reset this variable." FORCE)
+ endif (${${runs}})
+ endmacro (PETSC_TEST_RUNS)
+
+
+ find_path (PETSC_INCLUDE_DIR petscts.h HINTS "${PETSC_DIR}" PATH_SUFFIXES include NO_DEFAULT_PATH)
+ find_path (PETSC_INCLUDE_CONF petscconf.h HINTS "${PETSC_DIR}" PATH_SUFFIXES "${PETSC_ARCH}/include" "bmake/${PETSC_ARCH}" NO_DEFAULT_PATH)
+ mark_as_advanced (PETSC_INCLUDE_DIR PETSC_INCLUDE_CONF)
+ set (petsc_includes_minimal ${PETSC_INCLUDE_CONF} ${PETSC_INCLUDE_DIR})
+
+ petsc_test_runs ("${petsc_includes_minimal}" "${PETSC_LIBRARIES_TS}" petsc_works_minimal)
+ if (petsc_works_minimal)
+ message (STATUS "Minimal PETSc includes and libraries work. This probably means we are building with shared libs.")
+ set (petsc_includes_needed "${petsc_includes_minimal}")
+ else (petsc_works_minimal) # Minimal includes fail, see if just adding full includes fixes it
+ petsc_test_runs ("${petsc_includes_all}" "${PETSC_LIBRARIES_TS}" petsc_works_allincludes)
+ if (petsc_works_allincludes) # It does, we just need all the includes (
+ message (STATUS "PETSc requires extra include paths, but links correctly with only interface libraries. This is an unexpected configuration (but it seems to work fine).")
+ set (petsc_includes_needed ${petsc_includes_all})
+ else (petsc_works_allincludes) # We are going to need to link the external libs explicitly
+ resolve_libraries (petsc_libraries_external "${petsc_libs_external}")
+ foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
+ list (APPEND PETSC_LIBRARIES_${pkg} ${petsc_libraries_external})
+ endforeach (pkg)
+ petsc_test_runs ("${petsc_includes_minimal}" "${PETSC_LIBRARIES_TS}" petsc_works_alllibraries)
+ if (petsc_works_alllibraries)
+ message (STATUS "PETSc only need minimal includes, but requires explicit linking to all dependencies. This is expected when PETSc is built with static libraries.")
+ set (petsc_includes_needed ${petsc_includes_minimal})
+ else (petsc_works_alllibraries)
+ # It looks like we really need everything, should have listened to Matt
+ set (petsc_includes_needed ${petsc_includes_all})
+ petsc_test_runs ("${petsc_includes_all}" "${PETSC_LIBRARIES_TS}" petsc_works_all)
+ if (petsc_works_all) # We fail anyways
+ message (STATUS "PETSc requires extra include paths and explicit linking to all dependencies. This probably means you have static libraries and something unexpected in PETSc headers.")
+ else (petsc_works_all) # We fail anyways
+ message (STATUS "PETSc could not be used, maybe the install is broken.")
+ endif (petsc_works_all)
+ endif (petsc_works_alllibraries)
+ endif (petsc_works_allincludes)
+ endif (petsc_works_minimal)
+
+ # We do an out-of-source build so __FILE__ will be an absolute path, hence __INSDIR__ is superfluous
+ if (${PETSC_VERSION} VERSION_LESS 3.1)
+ set (PETSC_DEFINITIONS "-D__SDIR__=\"\"" CACHE STRING "PETSc definitions" FORCE)
+ else ()
+ set (PETSC_DEFINITIONS "-D__INSDIR__=" CACHE STRING "PETSc definitions" FORCE)
+ endif ()
+ # Sometimes this can be used to assist FindMPI.cmake
+ set (PETSC_MPIEXEC ${petsc_mpiexec} CACHE FILEPATH "Executable for running PETSc MPI programs" FORCE)
+ set (PETSC_INCLUDES ${petsc_includes_needed} CACHE STRING "PETSc include path" FORCE)
+ set (PETSC_LIBRARIES ${PETSC_LIBRARIES_ALL} CACHE STRING "PETSc libraries" FORCE)
+ set (PETSC_COMPILER ${petsc_cc} CACHE FILEPATH "PETSc compiler" FORCE)
+ # Note that we have forced values for all these choices. If you
+ # change these, you are telling the system to trust you that they
+ # work. It is likely that you will end up with a broken build.
+ mark_as_advanced (PETSC_INCLUDES PETSC_LIBRARIES PETSC_COMPILER PETSC_DEFINITIONS PETSC_MPIEXEC PETSC_EXECUTABLE_RUNS)
+endif ()
+
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (PETSc
+ REQUIRED_VARS PETSC_INCLUDES PETSC_LIBRARIES PETSC_EXECUTABLE_RUNS
+ VERSION_VAR PETSC_VERSION
+ FAIL_MESSAGE "PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH.")
diff --git a/cmake_modules/FindPackageMultipass.cmake b/cmake_modules/FindPackageMultipass.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..fbf06a7f0fc3aa20a0387f091eac4f74e7ffdab2
--- /dev/null
+++ b/cmake_modules/FindPackageMultipass.cmake
@@ -0,0 +1,106 @@
+# PackageMultipass - this module defines two macros
+#
+# FIND_PACKAGE_MULTIPASS (Name CURRENT
+# STATES VAR0 VAR1 ...
+# DEPENDENTS DEP0 DEP1 ...)
+#
+# This function creates a cache entry <UPPERCASED-Name>_CURRENT which
+# the user can set to "NO" to trigger a reconfiguration of the package.
+# The first time this function is called, the values of
+# <UPPERCASED-Name>_VAR0, ... are saved. If <UPPERCASED-Name>_CURRENT
+# is false or if any STATE has changed since the last time
+# FIND_PACKAGE_MULTIPASS() was called, then CURRENT will be set to "NO",
+# otherwise CURRENT will be "YES". IF not CURRENT, then
+# <UPPERCASED-Name>_DEP0, ... will be FORCED to NOTFOUND.
+# Example:
+# find_path (FOO_DIR include/foo.h)
+# FIND_PACKAGE_MULTIPASS (Foo foo_current
+# STATES DIR
+# DEPENDENTS INCLUDES LIBRARIES)
+# if (NOT foo_current)
+# # Make temporary files, run programs, etc, to determine FOO_INCLUDES and FOO_LIBRARIES
+# endif (NOT foo_current)
+#
+# MULTIPASS_SOURCE_RUNS (Name INCLUDES LIBRARIES SOURCE RUNS LANGUAGE)
+# Always runs the given test, use this when you need to re-run tests
+# because parent variables have made old cache entries stale. The LANGUAGE
+# variable is either C or CXX indicating which compiler the test should
+# use.
+# MULTIPASS_C_SOURCE_RUNS (Name INCLUDES LIBRARIES SOURCE RUNS)
+# DEPRECATED! This is only included for backwards compatability. Use
+# the more general MULTIPASS_SOURCE_RUNS instead.
+# Always runs the given test, use this when you need to re-run tests
+# because parent variables have made old cache entries stale.
+
+macro (FIND_PACKAGE_MULTIPASS _name _current)
+ string (TOUPPER ${_name} _NAME)
+ set (_args ${ARGV})
+ list (REMOVE_AT _args 0 1)
+
+ set (_states_current "YES")
+ list (GET _args 0 _cmd)
+ if (_cmd STREQUAL "STATES")
+ list (REMOVE_AT _args 0)
+ list (GET _args 0 _state)
+ while (_state AND NOT _state STREQUAL "DEPENDENTS")
+ # The name of the stored value for the given state
+ set (_stored_var PACKAGE_MULTIPASS_${_NAME}_${_state})
+ if (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
+ set (_states_current "NO")
+ endif (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
+ set (${_stored_var} "${${_NAME}_${_state}}" CACHE INTERNAL "Stored state for ${_name}." FORCE)
+ list (REMOVE_AT _args 0)
+ list (GET _args 0 _state)
+ endwhile (_state AND NOT _state STREQUAL "DEPENDENTS")
+ endif (_cmd STREQUAL "STATES")
+
+ set (_stored ${_NAME}_CURRENT)
+ if (NOT ${_stored})
+ set (${_stored} "YES" CACHE BOOL "Is the configuration for ${_name} current? Set to \"NO\" to reconfigure." FORCE)
+ set (_states_current "NO")
+ endif (NOT ${_stored})
+
+ set (${_current} ${_states_current})
+ if (NOT ${_current} AND PACKAGE_MULTIPASS_${_name}_CALLED)
+ message (STATUS "Clearing ${_name} dependent variables")
+ # Clear all the dependent variables so that the module can reset them
+ list (GET _args 0 _cmd)
+ if (_cmd STREQUAL "DEPENDENTS")
+ list (REMOVE_AT _args 0)
+ foreach (dep ${_args})
+ set (${_NAME}_${dep} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+ endforeach (dep)
+ endif (_cmd STREQUAL "DEPENDENTS")
+ set (${_NAME}_FOUND "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+ endif ()
+ set (PACKAGE_MULTIPASS_${name}_CALLED YES CACHE INTERNAL "Private" FORCE)
+endmacro (FIND_PACKAGE_MULTIPASS)
+
+
+macro (MULTIPASS_SOURCE_RUNS includes libraries source runs language)
+ include (Check${language}SourceRuns)
+ # This is a ridiculous hack. CHECK_${language}_SOURCE_* thinks that if the
+ # *name* of the return variable doesn't change, then the test does
+ # not need to be re-run. We keep an internal count which we
+ # increment to guarantee that every test name is unique. If we've
+ # gotten here, then the configuration has changed enough that the
+ # test *needs* to be rerun.
+ if (NOT MULTIPASS_TEST_COUNT)
+ set (MULTIPASS_TEST_COUNT 00)
+ endif (NOT MULTIPASS_TEST_COUNT)
+ math (EXPR _tmp "${MULTIPASS_TEST_COUNT} + 1") # Why can't I add to a cache variable?
+ set (MULTIPASS_TEST_COUNT ${_tmp} CACHE INTERNAL "Unique test ID")
+ set (testname MULTIPASS_TEST_${MULTIPASS_TEST_COUNT}_${runs})
+ set (CMAKE_REQUIRED_INCLUDES ${includes})
+ set (CMAKE_REQUIRED_LIBRARIES ${libraries})
+ if(${language} STREQUAL "C")
+ check_c_source_runs ("${source}" ${testname})
+ elseif(${language} STREQUAL "CXX")
+ check_cxx_source_runs ("${source}" ${testname})
+ endif()
+ set (${runs} "${${testname}}")
+endmacro (MULTIPASS_SOURCE_RUNS)
+
+macro (MULTIPASS_C_SOURCE_RUNS includes libraries source runs)
+ multipass_source_runs("${includes}" "${libraries}" "${source}" ${runs} "C")
+endmacro (MULTIPASS_C_SOURCE_RUNS)
diff --git a/cmake_modules/FindTinyObjLoader.cmake b/cmake_modules/FindTinyObjLoader.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..3410fb89255b171376592f8a3aa4ccaf0a8bc9e9
--- /dev/null
+++ b/cmake_modules/FindTinyObjLoader.cmake
@@ -0,0 +1,99 @@
+# - Try to find LibHilbert
+# Once done this will define
+#
+# TINYOBJLOADER_FOUND - system has TinyObjLoader
+# TINYOBJLOADER_INCLUDE_DIRS - include directories for TinyObjLoader
+# TINYOBJLOADER_LIBRARY_DIRS - library directories for TinyObjLoader
+# TINYOBJLOADER_LIBRARIES - libraries for TinyObjLoader
+#
+#=============================================================================
+# Copyright (C) 2010-2016 Pietro Incardona
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in
+# the documentation and/or other materials provided with the
+# distribution.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#=============================================================================
+
+
+if (TINYOBJLOADER_FOUND OR TARGET tinyobjloader)
+ return()
+endif()
+
+add_library(tinyobjloader INTERFACE IMPORTED)
+
+# Add libraries (static)
+set(_libs "-L${TINYOBJLOADER_ROOT}/lib64 -ltinyobjloader")
+set_property(TARGET tinyobjloader PROPERTY INTERFACE_LINK_LIBRARIES "${_libs}")
+
+
+# Create LibHilbert test program
+set(TINYOBJLOADER_TEST_LIB_CPP
+ "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/tinyobjloader_test_lib.cpp")
+
+
+file(WRITE ${TINYOBJLOADER_TEST_LIB_CPP} "
+#define TINYOBJLOADER_IMPLEMENTATION
+#include \"tiny_obj_loader.h\"
+
+
+int main()
+{
+ std::string inputfile = \"null.obj\";
+ tinyobj::attrib_t attrib;
+ std::vector<tinyobj::shape_t> shapes;
+ std::vector<tinyobj::material_t> materials;
+
+ std::string err;
+ bool ret = tinyobj::LoadObj(&attrib, &shapes, &materials, &err, inputfile.c_str());
+
+ return 0;
+}
+")
+
+# Try to run test program (static linking)
+try_run(
+ TINYOBJLOADER_TEST_LIB_EXITCODE
+ TINYOBJLOADER_TEST_LIB_COMPILED
+ ${CMAKE_CURRENT_BINARY_DIR}
+ ${TINYOBJLOADER_TEST_LIB_CPP}
+ CMAKE_FLAGS
+ "-DINCLUDE_DIRECTORIES:STRING=${TINYOBJLOADER_ROOT}/include"
+ "-DLINK_LIBRARIES:STRING=${TINYOBJLOADER_ROOT}/lib"
+ LINK_LIBRARIES tinyobjloader
+ COMPILE_OUTPUT_VARIABLE TINYOBJLOADER_TEST_LIB_COMPILE_OUTPUT
+ RUN_OUTPUT_VARIABLE TINYOBJLOADER_TEST_LIB_OUTPUT)
+
+
+if (TINYOBJLOADER_TEST_LIB_COMPILED AND TINYOBJLOADER_TEST_LIB_EXITCODE EQUAL 0)
+ message(STATUS "Test TinyObjLoader_TEST_RUNS static linking - Success")
+ set(TINYOBJLOADER_TEST_RUNS TRUE)
+ set(TINYOBJLOADER_FOUND TRUE)
+ set(TINYOBJLOADER_INCLUDE_DIRS ${TINYOBJLOADER_ROOT}/include)
+ set(TINYOBJLOADER_LIBRARY_DIRS ${TINYOBJLOADER_ROOT}/lib64)
+ set(TINYOBJLOADER_LIBRARIES -ltinyobjloader)
+else()
+ message(STATUS "Test TinyObjLoader_TEST_RUNS static linking - Failed")
+ set(TINYOBJLOADER_TEST_RUNS FALSE)
+endif()
+
diff --git a/cmake_modules/ResolveCompilerPaths.cmake b/cmake_modules/ResolveCompilerPaths.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..54787fa38ffa50136414e6c788c50fb3c63746b8
--- /dev/null
+++ b/cmake_modules/ResolveCompilerPaths.cmake
@@ -0,0 +1,105 @@
+# ResolveCompilerPaths - this module defines two macros
+#
+# RESOLVE_LIBRARIES (XXX_LIBRARIES LINK_LINE)
+# This macro is intended to be used by FindXXX.cmake modules.
+# It parses a compiler link line and resolves all libraries
+# (-lfoo) using the library path contexts (-L/path) in scope.
+# The result in XXX_LIBRARIES is the list of fully resolved libs.
+# Example:
+#
+# RESOLVE_LIBRARIES (FOO_LIBRARIES "-L/A -la -L/B -lb -lc -ld")
+#
+# will be resolved to
+#
+# FOO_LIBRARIES:STRING="/A/liba.so;/B/libb.so;/A/libc.so;/usr/lib/libd.so"
+#
+# if the filesystem looks like
+#
+# /A: liba.so libc.so
+# /B: liba.so libb.so
+# /usr/lib: liba.so libb.so libc.so libd.so
+#
+# and /usr/lib is a system directory.
+#
+# Note: If RESOLVE_LIBRARIES() resolves a link line differently from
+# the native linker, there is a bug in this macro (please report it).
+#
+# RESOLVE_INCLUDES (XXX_INCLUDES INCLUDE_LINE)
+# This macro is intended to be used by FindXXX.cmake modules.
+# It parses a compile line and resolves all includes
+# (-I/path/to/include) to a list of directories. Other flags are ignored.
+# Example:
+#
+# RESOLVE_INCLUDES (FOO_INCLUDES "-I/A -DBAR='\"irrelevant -I/string here\"' -I/B")
+#
+# will be resolved to
+#
+# FOO_INCLUDES:STRING="/A;/B"
+#
+# assuming both directories exist.
+# Note: as currently implemented, the -I/string will be picked up mistakenly (cry, cry)
+include (CorrectWindowsPaths)
+
+macro (RESOLVE_LIBRARIES LIBS LINK_LINE)
+ string (REGEX MATCHALL "((-L|-l|-Wl)([^\" ]+|\"[^\"]+\")|[^\" ]+\\.(a|so|dll|lib))" _all_tokens "${LINK_LINE}")
+ set (_libs_found "")
+ set (_directory_list "")
+ foreach (token ${_all_tokens})
+ if (token MATCHES "-L([^\" ]+|\"[^\"]+\")")
+ # If it's a library path, add it to the list
+ string (REGEX REPLACE "^-L" "" token ${token})
+ string (REGEX REPLACE "//" "/" token ${token})
+ convert_cygwin_path(token)
+ list (APPEND _directory_list ${token})
+ elseif (token MATCHES "^(-l([^\" ]+|\"[^\"]+\")|[^\" ]+\\.(a|so|dll|lib))")
+ # It's a library, resolve the path by looking in the list and then (by default) in system directories
+ if (WIN32) #windows expects "libfoo", linux expects "foo"
+ string (REGEX REPLACE "^-l" "lib" token ${token})
+ else (WIN32)
+ string (REGEX REPLACE "^-l" "" token ${token})
+ endif (WIN32)
+ set (_root "")
+ if (token MATCHES "^/") # We have an absolute path
+ #separate into a path and a library name:
+ string (REGEX MATCH "[^/]*\\.(a|so|dll|lib)$" libname ${token})
+ string (REGEX MATCH ".*[^${libname}$]" libpath ${token})
+ convert_cygwin_path(libpath)
+ set (_directory_list ${_directory_list} ${libpath})
+ set (token ${libname})
+ endif (token MATCHES "^/")
+ set (_lib "NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
+ find_library (_lib ${token} HINTS ${_directory_list} ${_root})
+ if (_lib)
+ string (REPLACE "//" "/" _lib ${_lib})
+ list (APPEND _libs_found ${_lib})
+ else (_lib)
+ message (STATUS "Unable to find library ${token}")
+ endif (_lib)
+ endif (token MATCHES "-L([^\" ]+|\"[^\"]+\")")
+ endforeach (token)
+ set (_lib "NOTFOUND" CACHE INTERNAL "Scratch variable" FORCE)
+ # only the LAST occurence of each library is required since there should be no circular dependencies
+ if (_libs_found)
+ list (REVERSE _libs_found)
+ list (REMOVE_DUPLICATES _libs_found)
+ list (REVERSE _libs_found)
+ endif (_libs_found)
+ set (${LIBS} "${_libs_found}")
+endmacro (RESOLVE_LIBRARIES)
+
+macro (RESOLVE_INCLUDES INCS COMPILE_LINE)
+ string (REGEX MATCHALL "-I([^\" ]+|\"[^\"]+\")" _all_tokens "${COMPILE_LINE}")
+ set (_incs_found "")
+ foreach (token ${_all_tokens})
+ string (REGEX REPLACE "^-I" "" token ${token})
+ string (REGEX REPLACE "//" "/" token ${token})
+ convert_cygwin_path(token)
+ if (EXISTS ${token})
+ list (APPEND _incs_found ${token})
+ else (EXISTS ${token})
+ message (STATUS "Include directory ${token} does not exist")
+ endif (EXISTS ${token})
+ endforeach (token)
+ list (REMOVE_DUPLICATES _incs_found)
+ set (${INCS} "${_incs_found}")
+endmacro (RESOLVE_INCLUDES)
diff --git a/image/g_graph_hist.jpg b/image/g_graph_hist.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..eb94c8098ca8b8ad40ff25fb9857f80801c754e3
Binary files /dev/null and b/image/g_graph_hist.jpg differ
diff --git a/image/g_graph_plot.jpg b/image/g_graph_plot.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..3c174a15cbfa7bb868d38cdec76b7b197db686e2
Binary files /dev/null and b/image/g_graph_plot.jpg differ
diff --git a/image/g_graph_plot2.jpg b/image/g_graph_plot2.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..320553d86c3f8059fb301629c9a3dc408a7ebd46
Binary files /dev/null and b/image/g_graph_plot2.jpg differ
diff --git a/install_HDF5.sh b/install_HDF5.sh
new file mode 100755
index 0000000000000000000000000000000000000000..6477e1869f69f6904cff24b7229249e0a5ff2725
--- /dev/null
+++ b/install_HDF5.sh
@@ -0,0 +1,57 @@
+#! /bin/bash
+
+source script/discover_os
+
+discover_os
+
+# check if the directory $1/HDF5 exist
+
+if [ -d "$1/HDF5" -a -f "$1/HDF5/include/hdf5.h" ]; then
+ echo "HDF5 is already installed"
+ exit 0
+fi
+
+if [ ! -d "$1/ZLIB" -a x"$platform" != x"cygwin" ]; then
+ rm zlib-1.2.11.tar.gz
+ rm -rf zlib-1.2.11
+ wget https://zlib.net/zlib-1.2.11.tar.gz
+ if [ $? -ne 0 ]; then
+ echo -e "\033[91;5;1m FAILED! Installation requires an Internet connection \033[0m"
+ exit 1
+ fi
+ tar -xf zlib-1.2.11.tar.gz
+ cd zlib-1.2.11
+
+ CC=mpicc ./configure --prefix=$1/ZLIB
+ make -j $2
+ cd ..
+ if [ $? -eq 0 ]; then
+ make check install
+ else
+ echo -e "\033[91;5;1m ZLIB Installation FAILED \033[0m"
+ exit 1
+ fi
+
+else
+ echo "ZLIB is already installed"
+fi
+
+### 1.8.19 does not compile on CYGWIN
+wget http://ppmcore.mpi-cbg.de/upload/hdf5-1.10.7.tar.gz
+tar -xf hdf5-1.10.7.tar.gz
+cd hdf5-1.10.7
+
+if [ x"$platform" != x"cygwin" ]; then
+ CC=mpicc ./configure --with-zlib=$1/ZLIB --enable-parallel --prefix=$1/HDF5
+ make -j $2
+else
+ CC=mpicc ./configure --enable-parallel --prefix=$1/HDF5
+ make CFLAGS=-D_POSIX_C_SOURCE -j $2
+fi
+mkdir $1/HDF5
+make install
+if [ $? -ne 0 ]; then
+ echo "HDF5 error installing"
+ exit 0
+fi
+echo 3 > $1/HDF5/version
diff --git a/install_MPI.sh b/install_MPI.sh
new file mode 100755
index 0000000000000000000000000000000000000000..66fa52740360c63d247543d9664dc41d8006b642
--- /dev/null
+++ b/install_MPI.sh
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+# check if the directory $1/MPI exist
+
+if [ -d "$1/MPI" ]; then
+ echo "MPI already installed"
+ exit 0
+fi
+
+./script/download_MPI.sh
+cd openmpi-4.1.1
+
+if [ -f ../mpi_add_options ]; then
+ mpi_options=$(cat ../mpi_add_options)
+ echo "Adding MPI options: $mpi_options"
+fi
+
+if [ x"$3" == x"1" ]; then
+ echo "Installing MPI with GPU support"
+
+ # Detect where is nvcc
+ cuda_location=$(dirname $(dirname $(which nvcc)) )
+
+ ./configure --with-hwloc=internal --with-libevent=internal $mpi_options --with-cuda=$cuda_location --prefix=$1/MPI --enable-mpi-fortran=yes CC=$4 CXX=$5 F77=$6 FC=$7 $8
+else
+ echo "Installing MPI without GPU support"
+ ./configure --with-hwloc=internal --with-libevent=internal $mpi_options --prefix=$1/MPI --enable-mpi-fortran=yes CC=$4 CXX=$5 F77=$6 FC=$7 $8
+fi
+make -j $2
+make install
+
+# Mark the installation
+echo 10 > $1/MPI/version
+
diff --git a/install_MPI_mpich.sh b/install_MPI_mpich.sh
new file mode 100755
index 0000000000000000000000000000000000000000..07fe079cf3697ff9dac49428a8a622364c053dca
--- /dev/null
+++ b/install_MPI_mpich.sh
@@ -0,0 +1,41 @@
+#!/bin/bash
+
+# check if the directory $1/MPI exist
+
+if [ -d "$1/MPI" ]; then
+ echo "MPI already installed"
+ exit 0
+fi
+rm -rf mpich-3.4.2
+rm mpich-3.4.2.tar.gz
+wget http://ppmcore.mpi-cbg.de/upload/mpich-3.4.2.tar.gz
+tar -xvf mpich-3.4.2.tar.gz
+cd mpich-3.4.2
+
+#
+# --disable-mca-dso \
+# --disable-sysv-shmem \
+# --enable-cxx-exceptions \
+# --with-threads=posix \
+# --without-cs-fs \
+# --with-mpi-param_check=always \
+# --enable-contrib-no-build=vt,libompitrace \
+#
+#--enable-mca-no-build=paffinity,installdirs-windows,timer-windows,shmem-sysv
+#
+#
+
+
+if [ x"$6" == x"1" ]; then
+ echo "Installing MPI with GPU support"
+ ./configure --prefix=$1/MPI --enable-fortran CC=$3 CXX=$4 F77=$5 FC=$5 FFLAGS=-fallow-argument-mismatch
+else
+ echo "Installing MPI without GPU support"
+ ./configure --prefix=$1/MPI --enable-fortran CC=$3 CXX=$4 F77=$5 FC=$5 FFLAGS=-fallow-argument-mismatch
+fi
+make -j $2
+make install
+
+# Mark the installation
+echo 4 > $1/MPI/version
+
diff --git a/install_VCDEVEL.sh b/install_VCDEVEL.sh
index 671db944275766f0bda85f90f402504e82e6ebf6..fe67aa8f1fdccc9b266c4d266fdf89a5aa40a639 100755
--- a/install_VCDEVEL.sh
+++ b/install_VCDEVEL.sh
@@ -2,7 +2,11 @@
# check if the directory $1/VCDEVEL exist
+<<<<<<< HEAD
if [ -d "$1/VCDEVEL" && -f "$1/VCDEVEL/include/Vc/Vc" ]; then
+=======
+if [ -d "$1/VCDEVEL" -a -f "$1/VCDEVEL/include/Vc/Vc" ]; then
+>>>>>>> origin/master
echo "VCDEVEL already installed"
exit 0
fi
@@ -13,7 +17,11 @@ tar -xf Vc-1.4.1.tar.gz
cd Vc-1.4.1
mkdir build
cd build
+<<<<<<< HEAD
cmake -DCMAKE_INSTALL_PREFIX:PATH=$1/VCDEVEL ..
+=======
+cmake -DCMAKE_INSTALL_PREFIX:PATH=$1/VCDEVEL -DCMAKE_C_COMPILER=$3 -DCMAKE_CXX_COMPILER=$4 ..
+>>>>>>> origin/master
make
make install
diff --git a/openfpm_io.doc b/openfpm_io.doc
new file mode 100644
index 0000000000000000000000000000000000000000..a8340ae302cf064df6b549895504f17f83193847
--- /dev/null
+++ b/openfpm_io.doc
@@ -0,0 +1,2303 @@
+# Doxyfile 1.8.6
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project.
+#
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
+# The format is:
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all text
+# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
+# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
+# for the list of possible encodings.
+# The default value is: UTF-8.
+
+DOXYFILE_ENCODING = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
+
+PROJECT_NAME = "OpenFPM_io"
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
+
+PROJECT_NUMBER = 0.2.0
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer a
+# quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF = "Project that contain the implementation and interfaces for basic structure like vectors, grids, graph ... ."
+
+# With the PROJECT_LOGO tag one can specify an logo or icon that is included in
+# the documentation. The maximum height of the logo should not exceed 55 pixels
+# and the maximum width should not exceed 200 pixels. Doxygen will copy the logo
+# to the output directory.
+
+PROJECT_LOGO =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. If a relative path is
+# entered, it will be relative to the location where doxygen was started. If
+# left blank the current directory will be used.
+
+OUTPUT_DIRECTORY = doxygen/
+
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub-
+# directories (in 2 levels) under the output directory of each output format and
+# will distribute the generated files over these directories. Enabling this
+# option can be useful when feeding doxygen a huge amount of source files, where
+# putting all generated files in the same directory would otherwise causes
+# performance problems for the file system.
+# The default value is: NO.
+
+CREATE_SUBDIRS = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
+# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
+# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
+# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
+# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
+# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
+# Ukrainian and Vietnamese.
+# The default value is: English.
+
+OUTPUT_LANGUAGE = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES doxygen will include brief member
+# descriptions after the members that are listed in the file and class
+# documentation (similar to Javadoc). Set to NO to disable this.
+# The default value is: YES.
+
+BRIEF_MEMBER_DESC = YES
+
+# If the REPEAT_BRIEF tag is set to YES doxygen will prepend the brief
+# description of a member or function before the detailed description
+#
+# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+# The default value is: YES.
+
+REPEAT_BRIEF = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator that is
+# used to form the text in various listings. Each string in this list, if found
+# as the leading text of the brief description, will be stripped from the text
+# and the result, after processing the whole list, is used as the annotated
+# text. Otherwise, the brief description is used as-is. If left blank, the
+# following values are used ($name is automatically replaced with the name of
+# the entity):The $name class, The $name widget, The $name file, is, provides,
+# specifies, contains, represents, a, an and the.
+
+ABBREVIATE_BRIEF =
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# doxygen will generate a detailed section even if there is only a brief
+# description.
+# The default value is: NO.
+
+ALWAYS_DETAILED_SEC = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+# The default value is: NO.
+
+INLINE_INHERITED_MEMB = NO
+
+# If the FULL_PATH_NAMES tag is set to YES doxygen will prepend the full path
+# before files name in the file list and in the header files. If set to NO the
+# shortest path that makes the file name unique will be used
+# The default value is: YES.
+
+FULL_PATH_NAMES = YES
+
+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
+# Stripping is only done if one of the specified strings matches the left-hand
+# part of the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the path to
+# strip.
+#
+# Note that you can specify absolute paths here, but also relative paths, which
+# will be relative from the directory where doxygen is started.
+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
+
+STRIP_FROM_PATH =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
+# path mentioned in the documentation of a class, which tells the reader which
+# header file to include in order to use a class. If left blank only the name of
+# the header file containing the class definition is used. Otherwise one should
+# specify the list of include paths that are normally passed to the compiler
+# using the -I flag.
+
+STRIP_FROM_INC_PATH =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
+# less readable) file names. This can be useful is your file systems doesn't
+# support long names like on DOS, Mac, or CD-ROM.
+# The default value is: NO.
+
+SHORT_NAMES = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
+# first line (until the first dot) of a Javadoc-style comment as the brief
+# description. If set to NO, the Javadoc-style will behave just like regular Qt-
+# style comments (thus requiring an explicit @brief command for a brief
+# description.)
+# The default value is: NO.
+
+JAVADOC_AUTOBRIEF = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
+# line (until the first dot) of a Qt-style comment as the brief description. If
+# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
+# requiring an explicit \brief command for a brief description.)
+# The default value is: NO.
+
+QT_AUTOBRIEF = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
+# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
+# a brief description. This used to be the default behavior. The new default is
+# to treat a multi-line C++ comment block as a detailed description. Set this
+# tag to YES if you prefer the old behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
+# documentation from any documented member that it re-implements.
+# The default value is: YES.
+
+INHERIT_DOCS = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce a
+# new page for each member. If set to NO, the documentation of a member will be
+# part of the file/class/namespace that contains it.
+# The default value is: NO.
+
+SEPARATE_MEMBER_PAGES = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
+# uses this value to replace tabs by spaces in code fragments.
+# Minimum value: 1, maximum value: 16, default value: 4.
+
+TAB_SIZE = 4
+
+# This tag can be used to specify a number of aliases that act as commands in
+# the documentation. An alias has the form:
+# name=value
+# For example adding
+# "sideeffect=@par Side Effects:\n"
+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". You can put \n's in the value part of an alias to insert
+# newlines.
+
+ALIASES =
+
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding "class=itcl::class"
+# will allow you to use the command class in the itcl::class meaning.
+
+TCL_SUBST =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
+# only. Doxygen will then generate output that is more tailored for C. For
+# instance, some of the names that are used will be different. The list of all
+# members will be omitted, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_FOR_C = YES
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_JAVA = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
+
+OPTIMIZE_FOR_FORTRAN = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for VHDL.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_VHDL = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension, and
+# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
+# C#, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL. For instance to make
+# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
+# (default is Fortran), use: inc=Fortran f=C.
+#
+# Note For files without extension you can use no_extension as a placeholder.
+#
+# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
+# the files are not read by doxygen.
+
+EXTENSION_MAPPING =
+
+# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
+# according to the Markdown format, which allows for more readable
+# documentation. See http://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you can
+# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
+# case of backward compatibilities issues.
+# The default value is: YES.
+
+MARKDOWN_SUPPORT = YES
+
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by by putting a % sign in front of the word
+# or globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+
+AUTOLINK_SUPPORT = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
+
+BUILTIN_STL_SUPPORT = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+# The default value is: NO.
+
+CPP_CLI_SUPPORT = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
+
+SIP_SUPPORT = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
+
+IDL_PROPERTY_SUPPORT = NO
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES, then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+# The default value is: NO.
+
+DISTRIBUTE_GROUP_DOC = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
+
+SUBGROUPING = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
+
+INLINE_SIMPLE_STRUCTS = NO
+
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
+
+EXTRACT_ALL = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIVATE = YES
+
+# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE = YES
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
+
+EXTRACT_STATIC = YES
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# This flag is only useful for Objective-C code. When set to YES local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO only methods in the interface are
+# included.
+# The default value is: NO.
+
+EXTRACT_LOCAL_METHODS = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
+
+EXTRACT_ANON_NSPACES = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO these classes will be included in the various overviews. This option has
+# no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO these declarations will be
+# included in the documentation.
+# The default value is: NO.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
+
+HIDE_IN_BODY_DOCS = NO
+
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+# The default value is: system dependent.
+
+CASE_SENSE_NAMES = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES the
+# scope will be hidden.
+# The default value is: NO.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO the members will appear in declaration order.
+# The default value is: YES.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING = NO
+
+# The GENERATE_TODOLIST tag can be used to enable ( YES) or disable ( NO) the
+# todo list. This list is created by putting \todo commands in the
+# documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable ( YES) or disable ( NO) the
+# test list. This list is created by putting \test commands in the
+# documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST = YES
+
+# The GENERATE_BUGLIST tag can be used to enable ( YES) or disable ( NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable ( YES) or disable ( NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES the list
+# will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE = DoxygenLayout.xml
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. Do not use file names with spaces, bibtex cannot handle them. See
+# also \cite for info how to create references.
+
+CITE_BIB_FILES =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error ( stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
+WARNINGS = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES, then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO doxygen will only warn about wrong or incomplete parameter
+# documentation, but not about the absence of documentation.
+# The default value is: NO.
+
+WARN_NO_PARAMDOC = YES
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces.
+# Note: If this tag is empty the current directory is searched.
+
+INPUT = src
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: http://www.gnu.org/software/libiconv) for the list of
+# possible encodings.
+# The default value is: UTF-8.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank the
+# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii,
+# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp,
+# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown,
+# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
+# *.qsf, *.as and *.js.
+
+FILE_PATTERNS = *.hpp *.cpp *.ipp *.h
+
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
+
+RECURSIVE = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE =
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =*/map_units_test/* */for_each_ref.hpp
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+EXAMPLE_PATH = src
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
+
+EXAMPLE_PATTERNS =
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
+
+EXAMPLE_RECURSIVE = YES
+
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+IMAGE_PATH = image
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER ) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
+
+FILTER_SOURCE_FILES = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
+
+SOURCE_BROWSER = YES
+
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
+
+REFERENCES_RELATION = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES, then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see http://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
+
+VERBATIM_HEADERS = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
+
+ALPHABETICAL_INDEX = YES
+
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES doxygen will generate HTML output
+# The default value is: YES.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional user-
+# defined cascading style sheet that is included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefor more robust against future updates.
+# Doxygen will copy the style sheet file to the output directory. For an example
+# see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the stylesheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_TIMESTAMP = NO
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_SECTIONS = YES
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: http://developer.apple.com/tools/xcode/), introduced with
+# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_DOCSET = NO
+
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDNAME = "OpenFPM data"
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_BUNDLE_ID = ppcore.mpi-cbg.de
+
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_ID = ppmcore.mpi-cbg.de
+
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_NAME = Pietro Incardona
+
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_HTMLHELP = NO
+
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
+# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler ( hhc.exe). If non-empty
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated (
+# YES) or that it should be included in the master .chm file ( NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+GENERATE_CHI = NO
+
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index ( hhk), content ( hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated (
+# YES) or a normal table of contents ( NO) in the .chm file.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_NAMESPACE = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
+# folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS =
+
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_ECLIPSEHELP = NO
+
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
+
+ECLIPSE_DOC_ID = ppmcore.mpi-cbg.de
+
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+DISABLE_INDEX = YES
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom stylesheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW = YES
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+ENUM_VALUES_PER_LINE = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+TREEVIEW_WIDTH = 250
+
+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+EXT_LINKS_IN_WINDOW = NO
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_FONTSIZE = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_TRANSPARENT = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# http://www.mathjax.org) which uses client side Javascript for the rendering
+# instead of using prerendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+USE_MATHJAX = YES
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from http://www.mathjax.org before deployment.
+# The default value is: http://cdn.mathjax.org/mathjax/latest.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS =
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SEARCHENGINE = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript. There
+# are two flavours of web server based searching depending on the
+# EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for
+# searching and an index file used by the script. When EXTERNAL_SEARCH is
+# enabled the indexing and searching needs to be provided by external tools. See
+# the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SERVER_BASED_SEARCH = NO
+
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer ( doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer ( doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
+# The default value is: YES.
+
+GENERATE_LATEX = YES
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when enabling USE_PDFLATEX this option is only used for generating
+# bitmaps for formulas in the HTML output, but not in the Makefile that is
+# written to the output directory.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PAPER_TYPE = a4
+
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. To get the times font for
+# instance you can specify
+# EXTRA_PACKAGES=times
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+EXTRA_PACKAGES =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber. Doxygen will
+# replace them by respectively the title of the page, the current date and time,
+# only the current date, the version number of doxygen, the project name (see
+# PROJECT_NAME), or the project number (see PROJECT_NUMBER).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HEADER =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_FOOTER =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PDF_HYPERLINKS = YES
+
+# If the LATEX_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES to get a
+# higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+USE_PDFLATEX = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BATCHMODE = NO
+
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HIDE_INDICES = NO
+
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_SOURCE_CODE = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BIB_STYLE = plain
+
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_HYPERLINKS = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's config
+# file, i.e. a series of assignments. You only have to provide replacements,
+# missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_EXTENSIONS_FILE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_EXTENSION = .3
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
+
+GENERATE_XML = YES
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_OUTPUT = xml
+
+# The XML_SCHEMA tag can be used to specify a XML schema, which can be used by a
+# validating XML parser to check the syntax of the XML files.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_SCHEMA =
+
+# The XML_DTD tag can be used to specify a XML DTD, which can be used by a
+# validating XML parser to check the syntax of the XML files.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_DTD =
+
+# If the XML_PROGRAMLISTING tag is set to YES doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT = docbook
+
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES doxygen will generate an AutoGen
+# Definitions (see http://autogen.sf.net) file that captures the structure of
+# the code including all documentation. Note that this feature is still
+# experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES doxygen will expand all macro names
+# in the source code. If set to NO only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES the includes files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+PREDEFINED =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all refrences to function-like macros that are alone on a line, have an
+# all uppercase name, and do not end with a semicolon. Such function macros are
+# typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have an unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
+
+TAGFILES =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
+
+GENERATE_TAGFILE =
+
+# If the ALLEXTERNALS tag is set to YES all external class will be listed in the
+# class index. If set to NO only the inherited external classes will be listed.
+# The default value is: NO.
+
+ALLEXTERNALS = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed in
+# the modules index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
+
+EXTERNAL_GROUPS = YES
+
+# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
+
+EXTERNAL_PAGES = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of 'which perl').
+# The default file (with absolute path) is: /usr/bin/perl.
+
+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES doxygen will generate a class diagram
+# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
+# NO turns the diagrams off. Note that this option also works with HAVE_DOT
+# disabled, but it is recommended to install and use dot, since it yields more
+# powerful graphs.
+# The default value is: YES.
+
+CLASS_DIAGRAMS = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see:
+# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH =
+
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_PATH =
+
+# If set to YES, the inheritance and collaboration graphs will hide inheritance
+# and usage relations if the target is undocumented or is not a class.
+# The default value is: YES.
+
+HIDE_UNDOC_RELATIONS = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz (see:
+# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# Bell Labs. The other options in this section have no effect if this option is
+# set to NO
+# The default value is: NO.
+
+HAVE_DOT = NO
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
+# to run in parallel. When set to 0 doxygen will base this on the number of
+# processors available in the system. You can set it explicitly to a value
+# larger than 0 to get control over the balance between CPU load and processing
+# speed.
+# Minimum value: 0, maximum value: 32, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_NUM_THREADS = 0
+
+# When you want a differently looking font n the dot files that doxygen
+# generates you can specify the font name using DOT_FONTNAME. You need to make
+# sure dot is able to find the font, which can be done by putting it in a
+# standard location or by setting the DOTFONTPATH environment variable or by
+# setting DOT_FONTPATH to the directory containing the font.
+# The default value is: Helvetica.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTNAME = Helvetica
+
+# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
+# dot graphs.
+# Minimum value: 4, maximum value: 24, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTSIZE = 10
+
+# By default doxygen will tell dot to use the default font as specified with
+# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
+# the path where dot can find it using this tag.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTPATH =
+
+# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
+# each documented class showing the direct and indirect inheritance relations.
+# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
+# graph for each documented class showing the direct and indirect implementation
+# dependencies (inheritance, containment, and class references variables) of the
+# class with other documented classes.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+COLLABORATION_GRAPH = YES
+
+# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
+# groups, showing the direct groups dependencies.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GROUP_GRAPHS = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+UML_LOOK = NO
+
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
+# class node. If there are many fields or methods and many nodes the graph may
+# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
+# number of items for each type to make the size more manageable. Set this to 0
+# for no limit. Note that the threshold may be exceeded by 50% before the limit
+# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
+# but if the number exceeds 15, the total amount of fields shown is limited to
+# 10.
+# Minimum value: 0, maximum value: 100, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+UML_LIMIT_NUM_FIELDS = 10
+
+# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
+# collaboration graphs will show the relations between templates and their
+# instances.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+TEMPLATE_RELATIONS = NO
+
+# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
+# YES then doxygen will generate a graph for each documented file showing the
+# direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INCLUDE_GRAPH = YES
+
+# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
+# set to YES then doxygen will generate a graph for each documented file showing
+# the direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INCLUDED_BY_GRAPH = YES
+
+# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable call graphs for selected
+# functions only using the \callgraph command.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CALL_GRAPH = NO
+
+# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable caller graphs for selected
+# functions only using the \callergraph command.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CALLER_GRAPH = NO
+
+# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
+# hierarchy of all classes instead of a textual one.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GRAPHICAL_HIERARCHY = YES
+
+# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
+# dependencies a directory has on other directories in a graphical way. The
+# dependency relations are determined by the #include relations between the
+# files in the directories.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DIRECTORY_GRAPH = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot.
+# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
+# to make the SVG files visible in IE 9+ (other browsers do not have this
+# requirement).
+# Possible values are: png, jpg, gif and svg.
+# The default value is: png.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_IMAGE_FORMAT = png
+
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+# enable generation of interactive SVG images that allow zooming and panning.
+#
+# Note that this requires a modern browser other than Internet Explorer. Tested
+# and working are Firefox, Chrome, Safari, and Opera.
+# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
+# the SVG files visible. Older versions of IE do not have SVG support.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INTERACTIVE_SVG = NO
+
+# The DOT_PATH tag can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_PATH =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the \dotfile
+# command).
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOTFILE_DIRS =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the \mscfile
+# command).
+
+MSCFILE_DIRS =
+
+# The DIAFILE_DIRS tag can be used to specify one or more directories that
+# contain dia files that are included in the documentation (see the \diafile
+# command).
+
+DIAFILE_DIRS =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
+# that will be shown in the graph. If the number of nodes in a graph becomes
+# larger than this value, doxygen will truncate the graph, which is visualized
+# by representing a node as a red box. Note that doxygen if the number of direct
+# children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
+# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# Minimum value: 0, maximum value: 10000, default value: 50.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_GRAPH_MAX_NODES = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
+# generated by dot. A depth value of 3 means that only nodes reachable from the
+# root by following a path via at most 3 edges will be shown. Nodes that lay
+# further from the root node will be omitted. Note that setting this option to 1
+# or 2 may greatly reduce the computation time needed for large code bases. Also
+# note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+# Minimum value: 0, maximum value: 1000, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+MAX_DOT_GRAPH_DEPTH = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not seem
+# to support this out of the box.
+#
+# Warning: Depending on the platform used, enabling this option may lead to
+# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
+# read).
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_TRANSPARENT = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10) support
+# this, this feature is disabled by default.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_MULTI_TARGETS = NO
+
+# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
+# explaining the meaning of the various boxes and arrows in the dot generated
+# graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GENERATE_LEGEND = YES
+
+# If the DOT_CLEANUP tag is set to YES doxygen will remove the intermediate dot
+# files that are used to generate the various graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_CLEANUP = YES
diff --git a/run.sh b/run.sh
index 185d155748e08ffba78e8b7478e8fa1d37b1501c..43c500db52885f6756d48ae7b5d4fef3f95cff5c 100755
--- a/run.sh
+++ b/run.sh
@@ -1,3 +1,4 @@
+<<<<<<< HEAD
#! \bin\bash
$pre_command ./build/src/mem_map
@@ -7,3 +8,37 @@ if [ $? -ne 0 ]; then
fi
+=======
+#! /bin/bash
+
+hostname=$(hostname)
+branch=$3
+
+# Make a directory in /tmp/openfpm_data
+
+cd "openfpm_io"
+
+echo "CHECKING MACHINE"
+if [ x"$hostname" == x"cifarm-centos-node.mpi-cbg.de" ]; then
+ echo "CENTOS"
+ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/HDF5/lib"
+ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/BOOST/lib"
+fi
+
+if [ x"$hostname" == x"cifarm-ubuntu-node" ]; then
+ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/HDF5/lib"
+ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/BOOST/lib"
+fi
+
+if [ x"$hostname" == x"cifarm-mac-node.mpi-cbg.de" ]; then
+ echo "MACOS X"
+ export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/HDF5/lib"
+ export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/BOOST/lib"
+fi
+
+pwd
+
+./build/src/io
+
+
+>>>>>>> origin/master
diff --git a/script/discover_os b/script/discover_os
new file mode 100755
index 0000000000000000000000000000000000000000..b80dda2b84e5d61b919a8d92e65e5661602337c2
--- /dev/null
+++ b/script/discover_os
@@ -0,0 +1,37 @@
+#! /bin/bash
+
+function discover_os() {
+platform=unknown
+
+
+ if [[ "$OSTYPE" == "linux-gnu" ]]; then
+ echo -e "We are on\033[1;34m LINUX \033[0m"
+ platform=linux
+ elif [[ "$OSTYPE" == "linux" ]]; then
+ echo -e "We are on\033[1;34m LINUX \033[0m"
+ platform=linux
+ elif [[ "$OSTYPE" == "darwin"* ]]; then
+ echo -e "We are on\033[1;34m MAC OSX \033[0m"
+ platform=osx
+ elif [[ "$OSTYPE" == "cygwin" ]]; then
+ echo -e "We are on\033[1;34m CYGWIN \033[0m"
+ platform=cygwin
+ elif [[ "$OSTYPE" == "msys" ]]; then
+ echo -e "We are on\033[1;34m Microsoft Window \033[0m"
+ echo "This platform is not supported"
+ exit 1
+ elif [[ "$OSTYPE" == "win32" ]]; then
+ echo -e "We are on\033[1;34m Microsoft Window \033[0m"
+ echo "This platform is not supported"
+ exit 1
+ elif [[ "$OSTYPE" == "freebsd"* ]]; then
+ echo -e "We are on\033[1;34m FREEBSD \033[0m"
+ echo "This platform is not supported"
+ exit 1
+ else
+ echo -e "We are on an\033[1;34m unknown OS \033[0m"
+ echo "This platform is not supported"
+ exit 1
+ fi
+}
+
diff --git a/script/download_MPI.sh b/script/download_MPI.sh
new file mode 100755
index 0000000000000000000000000000000000000000..87c15208e4449bf7ca1a8b0a74bcf82f1c7a880f
--- /dev/null
+++ b/script/download_MPI.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+# check if the directory $1/MPI exist
+
+rm -rf openmpi-4.1.1
+rm openmpi-4.1.1.tar.gz
+wget http://ppmcore.mpi-cbg.de/upload/openmpi-4.1.1.tar.gz
+tar -xvf openmpi-4.1.1.tar.gz
+
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index cc9991a00e7c7bede93c56623d7b557727d496ff..e2eaa93b97f24610d2afb1d0cadcd7160805fb36 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,5 +1,6 @@
cmake_minimum_required(VERSION 3.8 FATAL_ERROR)
+<<<<<<< HEAD
########################### Executables
@@ -52,10 +53,17 @@ if (CUDA_ON_BACKEND STREQUAL "OpenMP" OR CUDA_ON_BACKEND STREQUAL "SEQUENTIAL")
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang" OR CMAKE_CXX_COMPILER_ID STREQUAL "Clang" OR CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
add_definitions("-x c++")
endif()
+=======
+########################### Executables
+
+if(NOT CUDA_ON_BACKEND STREQUAL "None")
+ set(CUDA_SOURCES HDF5_wr/HDF5_writer_cuda.cu)
+>>>>>>> origin/master
endif()
if ( CUDA_ON_BACKEND STREQUAL "HIP" AND HIP_FOUND )
+<<<<<<< HEAD
list(APPEND HIP_HIPCC_FLAGS ${CMAKE_CXX_FLAGS_DEBUG})
if (CMAKE_BUILD_TYPE STREQUAL "Debug")
@@ -77,10 +85,30 @@ if ( CUDA_ON_BACKEND STREQUAL "HIP" AND HIP_FOUND )
SparseGrid/SparseGrid_chunk_copy_unit_tests.cpp
Grid/copy_grid_unit_test.cpp NN/Mem_type/Mem_type_unit_tests.cpp
Grid/Geometry/tests/grid_smb_tests.cpp)
+=======
+ list(APPEND HIP_HIPCC_FLAGS ${CMAKE_CXX_FLAGS_DEBUG})
+
+ if (CMAKE_BUILD_TYPE STREQUAL "Debug")
+ list(APPEND HIP_HIPCC_FLAGS -O0)
+ endif()
+
+# set(CMAKE_CXX_COMPILER ${HIP_HIPCC_EXECUTABLE})
+
+ list(APPEND HIP_HIPCC_FLAGS -D__NVCC__ -D__HIP__ -DCUDART_VERSION=11000 -D__CUDACC__ -D__CUDACC_VER_MAJOR__=11 -D__CUDACC_VER_MINOR__=0 -D__CUDACC_VER_BUILD__=0)
+
+ set_source_files_properties(${CUDA_SOURCES} PROPERTIES LANGUAGE CXX)
+
+ hip_add_executable(io main.cpp
+ MetaParser/MetaParser_unit_test.cpp
+ ${CUDA_SOURCES}
+ ObjReader/ObjReader_unit_test.cpp
+ CSVReader/tests/CSVReader_unit_test.cpp)
+>>>>>>> origin/master
else()
+<<<<<<< HEAD
add_executable(mem_map ${CUDA_SOURCES}
main.cpp
data_type/aggregate_unit_tests.cpp
@@ -133,11 +161,33 @@ if (CMAKE_COMPILER_IS_GNUCC)
target_compile_options(mem_map PRIVATE $<$<COMPILE_LANGUAGE:CXX>: -fprofile-arcs -ftest-coverage>)
endif ()
endif ()
+=======
+ add_executable(io main.cpp
+ MetaParser/MetaParser_unit_test.cpp
+ ${CUDA_SOURCES}
+ ObjReader/ObjReader_unit_test.cpp
+ CSVReader/tests/CSVReader_unit_test.cpp)
+
+ set_property(TARGET io PROPERTY CUDA_ARCHITECTURES OFF)
+
+endif()
+
+add_dependencies(io ofpmmemory)
+add_dependencies(io vcluster)
+
+if ( CMAKE_COMPILER_IS_GNUCC )
+ target_compile_options(io PRIVATE "-Wno-deprecated-declarations")
+ if (TEST_COVERAGE)
+ target_compile_options(io PRIVATE $<$<COMPILE_LANGUAGE:CXX>: -fprofile-arcs -ftest-coverage>)
+ endif()
+endif()
+>>>>>>> origin/master
if (CMAKE_CUDA_COMPILER_ID STREQUAL "Clang")
add_definitions(-D__STRICT_ANSI__)
endif()
+<<<<<<< HEAD
###########################
@@ -530,6 +580,125 @@ install(FILES util/cuda/moderngpu/context.hxx
DESTINATION openfpm_data/include/util/cuda/moderngpu/
COMPONENT OpenFPM)
+=======
+###########################
+
+if (CUDA_FOUND)
+ target_include_directories (io PUBLIC ${MPI_C_INCLUDE_DIRS})
+
+ if( CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0 )
+ add_compile_options( "-fabi-version=6" )
+ endif()
+
+ if (TEST_COVERAGE)
+ target_compile_options(io PRIVATE $<$<COMPILE_LANGUAGE:CUDA>: -Xcompiler "-fprofile-arcs -ftest-coverage" >)
+ endif()
+endif()
+
+target_include_directories (io PUBLIC ${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES})
+target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_devices/src/)
+target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_vcluster/src/)
+target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_data/src/)
+target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../src/)
+target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/config)
+target_include_directories (io PUBLIC ${HDF5_ROOT}/include)
+target_include_directories (io PUBLIC ${TINYOBJLOADER_INCLUDE_DIRS} )
+target_include_directories (io PUBLIC ${Boost_INCLUDE_DIRS})
+target_include_directories (io PUBLIC ${OPENFPM_PDATA_DIR}/src)
+target_include_directories (io PUBLIC ${ALPAKA_ROOT}/include)
+
+if (PETSC_FOUND)
+ target_include_directories(io PUBLIC ${PETSC_INCLUDES})
+endif()
+
+target_link_libraries(io ${Boost_LIBRARIES})
+target_link_libraries(io ${HDF5_LIBRARIES})
+target_link_libraries(io ${TINYOBJLOADER_LIBRARIES} )
+target_link_libraries(io vcluster)
+target_link_libraries(io ofpmmemory)
+if (OPENMP_FOUND)
+ target_link_libraries(io OpenMP::OpenMP_CXX)
+endif()
+
+if (PETSC_FOUND)
+ target_link_libraries(io ${PETSC_LIBRARIES})
+endif()
+
+# Request that particles be built with -std=c++11
+# As this is a public compile feature anything that links to particles
+# will also build with -std=c++11
+target_compile_features(io PUBLIC cxx_std_11)
+target_link_libraries(io ${MPI_C_LIBRARIES})
+target_link_libraries(io ${MPI_CXX_LIBRARIES})
+if (TEST_COVERAGE)
+ target_link_libraries(io -lgcov)
+endif()
+
+install(FILES RawReader/RawReader.hpp
+ RawReader/RawReader_unit_tests.hpp
+ DESTINATION openfpm_io/include/RawReader
+ COMPONENT OpenFPM)
+
+install(FILES CSVWriter/csv_multiarray.hpp
+ CSVWriter/CSVWriter.hpp
+ CSVWriter/is_csv_writable.hpp
+ DESTINATION openfpm_io/include/CSVWriter/
+ COMPONENT OpenFPM)
+
+install(FILES CSVReader/CSVReader.hpp
+ DESTINATION openfpm_io/include/CSVReader/
+ COMPONENT OpenFPM)
+
+install(FILES GraphMLWriter/GraphMLWriter.hpp
+ DESTINATION openfpm_io/include/GraphMLWriter
+ COMPONENT OpenFPM)
+
+install(FILES util/util.hpp util/GBoxes.hpp
+ DESTINATION openfpm_io/include/util
+ COMPONENT OpenFPM)
+
+install(FILES 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
+ DESTINATION openfpm_io/include/VTKWriter/
+ COMPONENT OpenFPM)
+
+install(FILES MetaParser/MetaParser.hpp
+ DESTINATION openfpm_io/include/MetaParser/
+ COMPONENT OpenFPM)
+
+install(FILES 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
+ DESTINATION openfpm_io/include/HDF5_wr
+ COMPONENT OpenFPM)
+
+install(FILES RawReader/InitGridWithPixel.hpp
+ DESTINATION openfpm_io/include/RawReader/
+ COMPONENT OpenFPM)
+
+install(FILES util/PathsAndFiles.hpp
+ DESTINATION openfpm_io/include/util
+ COMPONENT OpenFPM)
+
+install(FILES Plot/GoogleChart.hpp Plot/util.hpp
+ DESTINATION openfpm_io/include/Plot
+ COMPONENT OpenFPM)
+
+
+>>>>>>> origin/master
#if(BUILD_TESTING)
# add_executable(particle_test test.cu)
@@ -541,9 +710,17 @@ install(FILES util/cuda/moderngpu/context.hxx
# add_test(NAME particles_256k COMMAND particle_test 256000 )
# if(APPLE)
+<<<<<<< HEAD
# We need to add the default path to the driver (libcuda.dylib) as an rpath,
# so that the static cuda runtime can find it at runtime.
# set_property(TARGET particle_test PROPERTY BUILD_RPATH ${CMAKE_CUDA_IMPLICIT_LINK_DIRECTORIES})
# endif()
#endif()
+=======
+ # We need to add the default path to the driver (libcuda.dylib) as an rpath,
+ # so that the static cuda runtime can find it at runtime.
+ # set_property(TARGET particle_test PROPERTY BUILD_RPATH ${CMAKE_CUDA_IMPLICIT_LINK_DIRECTORIES})
+ # endif()
+ #endif()
+>>>>>>> origin/master
diff --git a/src/CSVReader/CSVReader.hpp b/src/CSVReader/CSVReader.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..b83a2eea57424a388ef066c8ca4a19d1f8aeb968
--- /dev/null
+++ b/src/CSVReader/CSVReader.hpp
@@ -0,0 +1,87 @@
+//
+// Created by jstark on 23.12.21.
+//
+
+#ifndef OPENFPM_IO_CSVREADER_HPP
+#define OPENFPM_IO_CSVREADER_HPP
+
+#include <iostream>
+#include <sstream>
+#include <string>
+
+#include "Vector/map_vector.hpp"
+#include "util/PathsAndFiles.hpp"
+#include "VCluster/VCluster.hpp"
+
+/**@brief Converts string into template type T.
+ *
+ * @tparam T Destination type.
+ * @param string_to_convert String that will be streamed into a variable of type T
+ * @return T-type variable storing the content of string_to_convert
+ */
+template <typename T>
+T string_to_type(const std::string & string_to_convert)
+{
+ T x_new_type;
+ std::istringstream istream_string_to_convert(string_to_convert);
+ istream_string_to_convert >> x_new_type;
+ return x_new_type;
+}
+
+
+/**@brief Csv file is read by process rank 0 and the elements are saved into a linearized vector. The vector is
+ * broadcasted to the other processes.
+ *
+ * @tparam T Type that elements from csv file shall be converted to.
+ * @param input_file std::string containing the path to the input csv file.
+ * @param output_vector Empty openfpm::vector<T> to which linearized matrix from csv file will be written.
+ * @param m Size_t variable to which number of rows of the csv file will be returned.
+ * @param n Size_t variable to which number of columns of the csv file will be returned.
+ */
+template <typename T>
+void read_csv_to_vector(const std::string & input_file, openfpm::vector<T> & output_vector, size_t & m, size_t & n)
+{
+ size_t total_size = 0;
+ m = 0;
+ n = 0;
+ auto & v_cl = create_vcluster();
+ // File is accessed and read only by one process
+ if (v_cl.rank() == 0)
+ {
+ if(!check_if_file_exists(input_file))
+ {
+ std::cout << "Cannot find < " << input_file << " >. Please check path specification. Aborting..."
+ << std::endl;
+ abort();
+ }
+ std::ifstream file(input_file); // Create file pointer and open file
+ std::string line, element;
+ while (getline(file, line)) // Read entire row and store as one string in line
+ {
+ std::stringstream stream_line(line); // Needed to break line into elements later one
+ while (getline(stream_line, element, ',')) // Read every column of line and store content as string in element
+ {
+ output_vector.add(string_to_type<T>(element)); // Convert element from string to type T and append to
+ // output_vector
+ total_size += 1; // Increase n by one for each element read
+ }
+ m += 1; // Increase m by one for each row read
+ }
+ if(m >= 1) n = total_size / m; // If at least one row present, divide number of elements read by number of rows to get
+ // the number of columns
+ }
+ // Distribute size of the lin. vector to all other processes s.t. their output_vector can be resized accordingly.
+ MPI_Bcast(&total_size,1,MPI_UNSIGNED,0,MPI_COMM_WORLD);
+ MPI_Bcast(&m,1,MPI_UNSIGNED,0,MPI_COMM_WORLD);
+ MPI_Bcast(&n,1,MPI_UNSIGNED,0,MPI_COMM_WORLD);
+
+ if (v_cl.rank() != 0)
+ {
+ output_vector.resize(total_size);
+ }
+ // After the output_vector has been resized to correct size, it can receive the content from process 0.
+ v_cl.Bcast(output_vector, 0);
+ v_cl.execute();
+}
+
+#endif //OPENFPM_IO_CSVREADER_HPP
diff --git a/src/CSVReader/tests/CSVReader_unit_test.cpp b/src/CSVReader/tests/CSVReader_unit_test.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..c8d2fbee9d9c57d52048aa4a30c00df8aa908981
--- /dev/null
+++ b/src/CSVReader/tests/CSVReader_unit_test.cpp
@@ -0,0 +1,62 @@
+//
+// Created by jstark on 28.12.21.
+//
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+#include "CSVReader/CSVReader.hpp"
+
+BOOST_AUTO_TEST_SUITE(CSVReaderTestSuite)
+BOOST_AUTO_TEST_CASE(csv_reader_int_test)
+ {
+#ifdef OPENFPM_PDATA
+ std::string csv_file = std::string("openfpm_io/test_data/integer.csv");
+#else
+ std::string csv_file = std::string("test_data/integer.csv");
+#endif
+ // Read csv file into vector while linearizing
+ openfpm::vector<int> v_lin; // Vector to which csv file will be read to
+ size_t m, n; // Number of rows m and columns n
+
+ read_csv_to_vector(csv_file, v_lin, m, n);
+
+ BOOST_CHECK(m == 4);
+ BOOST_CHECK(n == 3);
+ BOOST_CHECK(m * n == v_lin.size());
+
+ for(int i = 0; i < v_lin.size() / n; ++i)
+ {
+ BOOST_CHECK( v_lin.get(i * n) == i + 1);
+ BOOST_CHECK( v_lin.get(i * n + 1) == (i + 1) * 2);
+ BOOST_CHECK( v_lin.get(i * n + 2) == v_lin.get(i * n) * v_lin.get(i * n + 1));
+ }
+ }
+
+
+BOOST_AUTO_TEST_CASE(csv_reader_char_test)
+ {
+#ifdef OPENFPM_PDATA
+ std::string csv_file = std::string("openfpm_io/test_data/char.csv");
+#else
+ std::string csv_file = std::string("test_data/char.csv");
+#endif
+ // Read csv file into vector while linearizing
+ openfpm::vector<std::string> v_lin; // Vector to which csv file will be read to
+ size_t m, n; // Number of rows m and columns n
+
+ read_csv_to_vector(csv_file, v_lin, m, n);
+
+ BOOST_CHECK(m == 5);
+ BOOST_CHECK(n == 2);
+ BOOST_CHECK(m * n == v_lin.size());
+
+ openfpm::vector<std::string> col1 = {"a", "b", "c", "d", "e"};
+ openfpm::vector<std::string> col2 = {"antilope", "ballena", "camel", "dackel", "elefant"};
+
+ for(int i = 0; i < v_lin.size() / n; ++i)
+ {
+ BOOST_CHECK(col1.get(i) == v_lin.get(i * n));
+ BOOST_CHECK(col2.get(i) == v_lin.get(i * n + 1));
+ }
+
+ }
+BOOST_AUTO_TEST_SUITE_END()
diff --git a/src/CSVWriter/CSVWriter.hpp b/src/CSVWriter/CSVWriter.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..c7abc933923e4115cf88a2e057ff287cc6279924
--- /dev/null
+++ b/src/CSVWriter/CSVWriter.hpp
@@ -0,0 +1,281 @@
+/*
+ * CSVWriter.hpp
+ *
+ * Created on: Dec 15, 2014
+ * Author: Pietro Incardona
+ */
+
+#ifndef CSVWRITER_HPP_
+#define CSVWRITER_HPP_
+
+#include <iostream>
+#include <boost/fusion/include/mpl.hpp>
+#include <boost/fusion/include/for_each.hpp>
+#include <fstream>
+#include "util/common.hpp"
+#include <boost/mpl/range_c.hpp>
+#include "util/for_each_ref_host.hpp"
+#include "csv_multiarray.hpp"
+#include "util/util.hpp"
+#include "is_csv_writable.hpp"
+
+#define CSV_WRITER 0x30000
+
+/*! \brief this class is a functor for "for_each" algorithm
+ *
+ * For each element of the boost::vector the operator() is called.
+ * Is mainly used to create a string containing all the properties of the object
+ *
+ * \tparam Tobj object
+ *
+ */
+
+template<typename Tobj>
+struct csv_prp
+{
+ //! String containing the csv line constructed from an object
+ std::stringstream & str;
+
+ //! Object to write
+ Tobj & obj;
+
+ /*! \brief Constructor
+ *
+ * Create a vertex properties list
+ *
+ * \param str streamstring
+ * \param obj object to write
+ *
+ */
+ csv_prp(std::stringstream & str, Tobj & obj)
+ :str(str),obj(obj)
+ {
+ };
+
+ //! It call the functor for each member
+ template<typename T>
+ void operator()(T& t)
+ {
+ // This is the type of the csv column
+ typedef typename boost::mpl::at<typename Tobj::type,T>::type col_type;
+
+ // Remove the reference from the column type
+ typedef typename boost::remove_reference<col_type>::type col_rtype;
+ typedef typename std::remove_all_extents<col_rtype>::type base_col_rtype;
+
+ csv_value_str<col_rtype, is_csv_writable<base_col_rtype>::value >(obj.template get<T::value>(),str);
+ }
+};
+
+/*! \brief this class is a functor for "for_each" algorithm
+ *
+ * For each element of the boost::vector the operator() is called.
+ * Is mainly used to create a string containing all the properties of the object
+ *
+ * \tparam T object
+ *
+ */
+
+template<typename Tobj, bool attr>
+struct csv_col
+{
+ //! String containing the colums list as string
+ std::stringstream & str;
+
+ /*! \brief Constructor
+ *
+ * \str String where to put the colum list
+ *
+ */
+ csv_col(std::stringstream & str)
+ :str(str)
+ {
+ };
+
+ //! It call the functor for each member
+ template<typename T>
+ inline void operator()(T& t)
+ {
+ // This is the type of the csv column
+ typedef typename boost::mpl::at<typename Tobj::type,boost::mpl::int_<T::value>>::type col_type;
+
+ csv_col_str<col_type>(std::string(Tobj::attributes::name[T::value]),str);
+ }
+};
+
+/*! \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 create a string containing all the vertex
+ * properties
+ *
+ * Specialization when we do not have vertex attributes
+ *
+ * \tparam G graph type
+ *
+ */
+
+template<typename Tobj>
+struct csv_col<Tobj,false>
+{
+ //! String containing the colums list as string
+ std::stringstream & str;
+
+ /*! \brief Constructor
+ *
+ * \str String where to put the colum list
+ *
+ */
+ csv_col(std::stringstream & str)
+ :str(str)
+ {
+ };
+
+ //! It call the functor for each member
+ template<typename T>
+ void operator()(T& t)
+ {
+ // This is the type of the csv column
+ typedef typename boost::fusion::result_of::at_c<typename Tobj::type,T::value>::type col_type;
+
+ // Remove the reference from the column type
+ typedef typename boost::remove_reference<col_type>::type col_rtype;
+
+ std::stringstream str2;
+ str2 << "column_" << T::value;
+
+ csv_col_str<col_rtype>(str2.str(),str);
+ }
+};
+
+//#define VECTOR 1
+
+/*! \brief CSV Writer
+ *
+ * It write in CSV format vector of objects living into an N-dimensional space
+ *
+ * \tparam v_pos Positional vector
+ * \tparam v_prp Property vector
+ *
+ */
+template <typename v_pos, typename v_prp, unsigned int impl = 1>
+class CSVWriter
+{
+ /*! \brief Get the colums name (also the positional name)
+ *
+ */
+ std::string get_csv_colums()
+ {
+ std::stringstream str;
+
+ // write positional columns
+ for (size_t i = 0 ; i < v_pos::value_type::dims ; i++)
+ {
+ if (i == 0)
+ str << "x[" << i << "]";
+ else
+ str << "," << "x[" << i << "]";
+ }
+
+ // write positional information
+
+ csv_col<typename v_prp::value_type,has_attributes<typename v_prp::value_type>::value> col(str);
+
+ // Iterate through all the vertex and create the vertex list
+ boost::mpl::for_each_ref_host< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(col);
+
+ str << "\n";
+
+ return str.str();
+ }
+
+ /*! \brief Get the csv data section
+ *
+ * \param vp vector that contain the positional information
+ * \param vpr vector that contain the property information
+ * \param offset from where to start
+ *
+ */
+ std::string get_csv_data(v_pos & vp, v_prp & vpr, size_t offset)
+ {
+ std::stringstream str;
+
+ // The position and property vector size must match
+ if (vp.size() != vpr.size())
+ {
+ std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " position vector and property vector must have the same size \n";
+ return std::string("");
+ }
+
+ // Write the data
+ for (size_t i = offset ; i < vp.size() ; i++)
+ {
+ for (size_t j = 0 ; j < v_pos::value_type::dims ; j++)
+ {
+ if (j == 0)
+ str << vp.template get<0>(i)[j];
+ else
+ str << "," << vp.template get<0>(i)[j];
+ }
+
+ // Object to write
+ auto obj = vpr.get(i);
+
+ csv_prp<decltype(obj)> c_prp(str,obj);
+
+ // write the properties to the stream string
+ boost::mpl::for_each_ref_host< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(c_prp);
+
+ str << "\n";
+ }
+
+ return str.str();
+ }
+
+public:
+
+ /*! \brief It write a CSV file
+ *
+ * \tparam prp which properties to output [default = -1 (all)]
+ *
+ * \param file path where to write
+ * \param v positional vector
+ * \param prp properties vector
+ * \param offset from where to start to write
+ *
+ */
+ bool write(std::string file, v_pos & v , v_prp & prp, size_t offset=0)
+ {
+ // Header for csv (colums name)
+ std::string csv_header;
+ // Data point
+ std::string point_data;
+
+ // Get csv columns
+ csv_header = get_csv_colums();
+
+ // For each property in the vertex type produce a point data
+ point_data = get_csv_data(v,prp,offset);
+
+ // write the file
+ std::ofstream ofs(file);
+
+ // Check if the file is open
+ if (ofs.is_open() == false)
+ {std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " cannot create the CSV file: " << file << std::endl;}
+
+ ofs << csv_header << point_data;
+
+ // Close the file
+
+ ofs.close();
+
+ // Completed succefully
+ return true;
+ }
+};
+
+
+#endif /* CSVWRITER_HPP_ */
+
diff --git a/src/CSVWriter/CSVWriter_unit_tests.hpp b/src/CSVWriter/CSVWriter_unit_tests.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..ed01d3c21ce130fcc7311556a926648e72752c64
--- /dev/null
+++ b/src/CSVWriter/CSVWriter_unit_tests.hpp
@@ -0,0 +1,87 @@
+#ifndef CSVWRITER_UNIT_TESTS_HPP_
+#define CSVWRITER_UNIT_TESTS_HPP_
+
+#include "CSVWriter.hpp"
+#include "Vector/vector_test_util.hpp"
+
+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;
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/csv_out_test.csv");
+ std::string c3 = std::string("openfpm_io/test_data/csv_out_unk_test.csv");
+
+
+#else
+
+ std::string c2 = std::string("test_data/csv_out_test.csv");
+ std::string c3 = std::string("test_data/csv_out_unk_test.csv");
+
+#endif
+
+ {
+ // Allocate a property vector
+ auto v_prp = allocate_openfpm_prp(16);
+ // Vector of position
+ openfpm::vector<Point<3,float>> v_pos;
+
+ // create a positional vector
+ for (size_t i = 0 ; i < v_prp.size() ; i++)
+ {
+ Point<3,float> p({1.0,2.0,3.0});
+
+ v_pos.add(p);
+ }
+
+ // CSVWriter test
+ CSVWriter<openfpm::vector<Point<3,float>>, openfpm::vector<Point_test_prp<float>> > csv_writer;
+
+ // Write the CSV
+ csv_writer.write("csv_out.csv",v_pos,v_prp);
+
+ bool test = compare("csv_out.csv",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+ }
+
+ {
+ // Allocate a property vector
+ auto v_prp = allocate_openfpm_aggregate_with_complex(16);
+ // Vector of position
+ openfpm::vector<Point<3,float>> v_pos;
+
+ // create a positional vector
+ for (size_t i = 0 ; i < v_prp.size() ; i++)
+ {
+ Point<3,float> p({1.0,2.0,3.0});
+
+ v_pos.add(p);
+ }
+
+ // CSVWriter test
+ CSVWriter<openfpm::vector<Point<3,float>>, openfpm::vector< aggregate<float,float,float,float,float[3],float[3][3],openfpm::vector<int>> > > csv_writer;
+
+ // Write the CSV
+ csv_writer.write("csv_out_unk.csv",v_pos,v_prp);
+
+ // In case of SE_CLASS3 enabled the number of properties change
+
+#ifndef SE_CLASS3
+ bool test = compare("csv_out_unk.csv",c3);
+ BOOST_REQUIRE_EQUAL(true,test);
+#endif
+ }
+
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+
+#endif
diff --git a/src/CSVWriter/csv_multiarray.hpp b/src/CSVWriter/csv_multiarray.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..6d91899f626798730a0dc77fed1a953ee44c2e78
--- /dev/null
+++ b/src/CSVWriter/csv_multiarray.hpp
@@ -0,0 +1,218 @@
+/*
+ * csv_multiarray_copy.hpp
+ *
+ * Created on: Jun 20, 2015
+ * Author: i-bird
+ */
+
+#ifndef CSV_MULTIARRAY_COPY_HPP_
+#define CSV_MULTIARRAY_COPY_HPP_
+
+
+
+/*! \brief This class is an helper to produce csv headers from multi-array
+ *
+ * Usage:
+ *
+ * \code{.cpp}
+ *
+ * float src[3];
+ *
+ * std::stringstream str;
+ * csv_col_str<float[3]> cp(std::string("test"),str);
+ *
+ * std::cout << str.str() << "\n";
+ *
+ * \endcode
+ *
+ * Will produce ",test[0],test[1],test[2]"
+ *
+ */
+template<typename T>
+struct csv_col_str
+{
+ inline csv_col_str(std::string prp, std::stringstream & str)
+ {
+ str << "," << prp;
+ }
+};
+
+//! Partial specialization for N=1 1D-Array
+template<typename T,size_t N1>
+struct csv_col_str<T[N1]>
+{
+ inline csv_col_str(std::string prp, std::stringstream & str)
+ {
+ for (size_t i = 0 ; i < N1 ; i++)
+ str << "," << prp << "_" << "[" << i << "]";
+ }
+};
+
+//! Partial specialization for N=2 2D-Array
+template<typename T,size_t N1,size_t N2>
+struct csv_col_str<T[N1][N2]>
+{
+ inline csv_col_str(std::string prp, std::stringstream & str)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ str << "," << prp << "_" << "[" << i1 << "]" << "[" << i2 << "]";
+ }
+ }
+ }
+};
+
+//! Partial specialization for N=3
+template<typename T,size_t N1,size_t N2,size_t N3>
+struct csv_col_str<T[N1][N2][N3]>
+{
+ inline csv_col_str(std::string prp, std::stringstream & str)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ for (size_t i3 = 0 ; i3 < N3 ; i3++)
+ {
+ str << "," << prp << "_" << "[" << i1 << "]" << "[" << i2 << "]" << "[" << i3 << "]";
+ }
+ }
+ }
+ }
+};
+
+//! Partial specialization for N=4
+template<typename T,size_t N1,size_t N2,size_t N3,size_t N4>
+struct csv_col_str<T[N1][N2][N3][N4]>
+{
+ inline csv_col_str(std::string prp, std::stringstream & str)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ for (size_t i3 = 0 ; i3 < N3 ; i3++)
+ {
+ for (size_t i4 = 0 ; i4 < N4 ; i4++)
+ {
+ str << "," << prp << "_" << "[" << i1 << "]" << "[" << i2 << "]" << "[" << i3 << "]" << "[" << i4 << "]";
+ }
+ }
+ }
+ }
+ }
+};
+
+
+/*! \brief This class is an helper to produce csv data from multi-array
+ *
+ * Usage:
+ *
+ * \code{.cpp}
+ *
+ * float src[3] = {1.0,2.0,3.0};
+ *
+ * std::stringstream str;
+ * csv_value_str<float[3]> cp(src,str);
+ *
+ * std::cout << str.str() << "\n";
+ *
+ * \endcode
+ *
+ * Will produce ",1.0,2.0,3.0"
+ *
+ */
+template<typename T, bool is_writable>
+struct csv_value_str
+{
+ inline csv_value_str(T & v, std::stringstream & str)
+ {
+ str << "," << v;
+ }
+};
+
+//! Partial specialization for N=1 1D-Array
+template<typename T,size_t N1, bool is_writable>
+struct csv_value_str<T[N1], is_writable>
+{
+ template<typename ArrObject>
+ inline csv_value_str(const ArrObject v, std::stringstream & str)
+ {
+ for (size_t i = 0 ; i < N1 ; i++)
+ str << "," << v[i];
+ }
+};
+
+//! Partial specialization for N=2 2D-Array
+template<typename T,size_t N1,size_t N2, bool is_writable>
+struct csv_value_str<T[N1][N2], is_writable>
+{
+ template<typename ArrObject>
+ inline csv_value_str(const ArrObject v, std::stringstream & str)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ str << "," << v[i1][i2];
+ }
+ }
+ }
+};
+
+//! Partial specialization for N=3
+template<typename T,size_t N1,size_t N2,size_t N3, bool is_writable>
+struct csv_value_str<T[N1][N2][N3], is_writable>
+{
+ template<typename ArrObject>
+ inline csv_value_str(const ArrObject v, std::stringstream & str)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ for (size_t i3 = 0 ; i3 < N3 ; i3++)
+ {
+ str << "," << v[i1][i2][i3];
+ }
+ }
+ }
+ }
+};
+
+//! Partial specialization for N=4
+template<typename T,size_t N1,size_t N2,size_t N3,size_t N4, bool is_writable>
+struct csv_value_str<T[N1][N2][N3][N4],is_writable>
+{
+ template<typename ArrObject>
+ inline csv_value_str(const ArrObject v, std::stringstream & str)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ for (size_t i3 = 0 ; i3 < N3 ; i3++)
+ {
+ for (size_t i4 = 0 ; i4 < N4 ; i4++)
+ {
+ str << "," << v[i1][i2][i3][i4];
+ }
+ }
+ }
+ }
+ }
+};
+
+//! Partial specialization for unknown property
+template<typename T>
+struct csv_value_str<T,false>
+{
+ inline csv_value_str(const T v, std::stringstream & str)
+ {
+ str << "," << 0.0;
+ }
+};
+
+#endif /* CSV_MULTIARRAY_COPY_HPP_ */
diff --git a/src/CSVWriter/is_csv_writable.hpp b/src/CSVWriter/is_csv_writable.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..48beba760ab6169b962bc252a6ba38f615d57e05
--- /dev/null
+++ b/src/CSVWriter/is_csv_writable.hpp
@@ -0,0 +1,177 @@
+/*
+ * is_csv_writable.hpp
+ *
+ * Created on: Jul 18, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_CSVWRITER_IS_CSV_WRITABLE_HPP_
+#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
+ };
+};
+
+//! Indicate if the property T is writable in CSV
+template<typename T, unsigned int N1>
+struct is_csv_writable<T[N1]>
+{
+ //! bool is writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! Indicate if the property T is writable in CSV
+template<typename T, unsigned int N1, unsigned int N2>
+struct is_csv_writable<T[N1][N2]>
+{
+ //! bool is writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! Indicate if the property T is writable in CSV
+template<typename T, unsigned int N1, unsigned int N2, unsigned int N3>
+struct is_csv_writable<T[N1][N2][N3]>
+{
+ //! bool is writable
+ enum
+ {
+ value = true
+ };
+};
+
+#endif /* OPENFPM_IO_SRC_CSVWRITER_IS_CSV_WRITABLE_HPP_ */
diff --git a/src/GraphMLWriter/GraphMLWriter.hpp b/src/GraphMLWriter/GraphMLWriter.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..d34504e9220116119f086da98002418a606b61ed
--- /dev/null
+++ b/src/GraphMLWriter/GraphMLWriter.hpp
@@ -0,0 +1,764 @@
+#ifndef GRAPHML_WRITER_HPP
+#define GRAPHML_WRITER_HPP
+
+#include "Graph/map_graph.hpp"
+#include <iostream>
+#include <fstream>
+#include "util/common.hpp"
+
+
+/*! \brief Create properties name starting from a type T
+ *
+ * if T has defined some properties name that name are used otherwise
+ * default name are created
+ *
+ * \tparam T vertex type
+ *
+ */
+
+template <typename T>
+void create_prop(std::string * str)
+{
+ // if T has attributes defined
+ if (has_attributes<T>::value )
+ {
+ // Create properties names based on the attributes name defined
+ for (size_t i = 0 ; i < T::max_prop ; i++)
+ {
+ str[i] = std::string(T::attributes::name[i]);
+ }
+ }
+ else
+ {
+ // Create default properties name
+ for (size_t i = 0 ; i < T::max_prop ; i++)
+ {
+ str[i] = "attr" + std::to_string(i);
+ }
+ }
+}
+
+/*! \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 create a string containing all the vertex
+ * properties
+ *
+ */
+
+template<typename G>
+struct vertex_prop
+{
+ //! Properties counter
+ int cnt = 0;
+
+ //! vertex properties
+ std::string & v_prop;
+
+ //! Attribute names
+ std::string * attributes_names;
+
+ //! Number of attributes name defined into the vertex
+ int n_attr = 0;
+
+ //! indicate if attributes_names is to destroy
+ bool to_destroy = false;
+
+ /*! \brief Constructor
+ *
+ * Create a vertex properties list
+ *
+ * \param v_prop std::string that is filled with the graph properties in the GraphML format
+ * \param a_name array with the names of the properties
+ *
+ */
+ vertex_prop(std::string & v_prop, typename G::V_type::attributes & a_name)
+ :v_prop(v_prop),attributes_names(a_name.name)
+ {
+ // Calculate the number of attributes name
+ n_attr = sizeof(a_name.name)/sizeof(std::string);
+ };
+
+ /*! \brief Constructor
+ *
+ * Create a vertex properties list
+ *
+ * \param v_prop std::string that is filled with the graph properties in the GraphML format
+ *
+ */
+ vertex_prop(std::string & v_prop)
+ :v_prop(v_prop),attributes_names(NULL)
+ {
+ // Calculate the number of attributes
+ n_attr = G::V_type::max_prop;
+
+ // Create default property names
+ attributes_names = new std::string[G::V_type::max_prop];
+ to_destroy = true;
+
+ // Create default property names
+ create_prop<typename G::V_type>(attributes_names);
+ };
+
+ //! destructor
+ ~vertex_prop()
+ {
+ if (to_destroy == true)
+ {delete [] attributes_names;}
+ }
+
+ /*! It call the functor for each member
+ *
+ * \param t each member
+ *
+ */
+ template<typename T>
+ void operator()(T& t)
+ {
+ //! Create an entry for the attribute
+ if (cnt < n_attr)
+ {
+ // if it is a yFile extension property name, does not process it
+ if (attributes_names[cnt] == "x" || attributes_names[cnt] == "y"
+ || attributes_names[cnt] == "z" || attributes_names[cnt] == "shape" )
+ {cnt++; return ;}
+
+ // Create a property string based on the type of the property
+ if (std::is_same<T,float>::value)
+ v_prop += "<key id=\"vk" + std::to_string(cnt) + "\" for=\"node\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"float\"/>\n";
+ else if (std::is_same<T,double>::value)
+ v_prop += "<key id=\"vk" + std::to_string(cnt) + "\" for=\"node\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"double\"/>\n";
+ else if (std::is_same<T,int>::value)
+ v_prop += "<key id=\"vk" + std::to_string(cnt) + "\" for=\"node\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"int\"/>\n";
+ else if (std::is_same<T,long int>::value)
+ v_prop += "<key id=\"vk" + std::to_string(cnt) + "\" for=\"node\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"long\"/>\n";
+ else if (std::is_same<T,bool>::value)
+ v_prop += "<key id=\"vk" + std::to_string(cnt) + "\" for=\"node\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"boolean\"/>\n";
+ else if (std::is_same<T,std::string>::value)
+ v_prop += "<key id=\"vk" + std::to_string(cnt) + "\" for=\"node\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"string\"/>\n";
+ }
+
+ cnt++;
+ }
+};
+
+/*! \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 create a string containing all the vertex
+ * properties
+ *
+ */
+
+template<typename G>
+struct vertex_node
+{
+ //! Vertex object container
+ const typename G::V_container & vo;
+
+ //! Properties counter
+ int cnt = 0;
+
+ //! vertex node string
+ std::string & v_node;
+
+ //! Attribute names
+ std::string * attributes_names;
+
+ //! Number of attributes name defined into the vertex
+ int n_attr = 0;
+
+ //! indicate if attributes_names is to destroy
+ bool to_destroy = false;
+
+ /*! \brief Constructor
+ *
+ * Create a vertex node
+ *
+ * \param v_node std::string that is filled with the graph node definition in the GraphML format
+ * \param n_obj object container to access its properties for example encapc<...>
+ * \param a_name stub SFINAE, it basically check if G has properties names defined, if yes this
+ * constructor is selected over the other one
+ *
+ */
+ inline vertex_node(std::string & v_node, const typename G::V_container & n_obj, typename G::V_type::attributes & a_name)
+ :vo(n_obj),v_node(v_node),attributes_names(a_name.name)
+ {
+ // Calculate the number of attributes name
+ n_attr = sizeof(a_name.name)/sizeof(std::string);
+ };
+
+#ifdef DEBUG
+ /*! \brief Constructor
+ *
+ * Calling this constructor produce an error. This class store the reference of the object,
+ * this mean that the object passed must not be a temporal object
+ *
+ */
+ inline vertex_node(std::string & v_node, const typename G::V_container && n_obj, typename G::V_type::attributes & a_name)
+ :vo(n_obj),v_node(v_node),attributes_names(a_name.name)
+ {std::cerr << "Error: " <<__FILE__ << ":" << __LINE__ << " Passing a temporal object\n";};
+#endif
+
+ /*! \brief Constructor
+ *
+ * Create a vertex properties list
+ *
+ * \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<...>
+ *
+ */
+ inline vertex_node(std::string & v_node, const typename G::V_container & n_obj)
+ :vo(n_obj),v_node(v_node),attributes_names(NULL)
+ {
+ // Calculate the number of attributes
+ n_attr = G::V_type::max_prop;
+
+ // Create default property names
+ attributes_names = new std::string[G::V_type::max_prop];
+ to_destroy = true;
+
+ // Create default property names
+ create_prop<typename G::V_type>(attributes_names);
+ };
+
+ inline ~vertex_node()
+ {
+ if (to_destroy == true)
+ {delete [] attributes_names;}
+ }
+
+#ifdef DEBUG
+ /*! \brief Constructor
+ *
+ * Calling this constructor produce an error. This class store the reference of the object,
+ * this mean that the object passed must not be a temporal object
+ *
+ */
+ inline vertex_node(std::string & v_node, const typename G::V_container && n_obj)
+ :vo(n_obj),v_node(v_node),attributes_names(NULL)
+ {std::cerr << "Error: " <<__FILE__ << ":" << __LINE__ << " Passing a temporal object\n";};
+#endif
+
+ /*! \brief Create a new node
+ *
+ * \param v_c id of the node
+ *
+ */
+ void new_node(size_t v_c)
+ {
+ // start a new node
+ v_node += "<node id=\"n"+ std::to_string(v_c) + "\">\n";
+
+ // reset the counter properties
+ cnt = 0;
+ }
+
+ /*! \brief Close a node
+ *
+ * Close a node
+ *
+ */
+ void end_node()
+ {
+ // close a node
+ v_node += "</node>\n";
+ }
+
+ /*! \brief It call the functor for each member
+ *
+ * \param t each member
+ *
+ */
+ template<typename T>
+ void operator()(T& t)
+ {
+ //! Create an entry for the attribute
+ if (T::value < n_attr)
+ {
+ typedef typename std::remove_reference<decltype(vo.template get<T::value>())>::type type_get;
+
+ // Create a property string based on the type of the property
+ if (std::is_same<type_get,float>::value)
+ v_node += " <data key=\"vk" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
+ else if (std::is_same<type_get,double>::value)
+ v_node += " <data key=\"vk" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
+ else if (std::is_same<type_get,int>::value )
+ v_node += " <data key=\"vk" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
+ else if (std::is_same<type_get,long int>::value)
+ v_node += " <data key=\"vk" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
+ else if (std::is_same<type_get,bool>::value)
+ v_node += " <data key=\"vk" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
+ else if (std::is_same<type_get,std::string>::value)
+ v_node += " <data key=\"vk" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
+ }
+
+ cnt++;
+ }
+};
+
+/*! \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 create a string containing all the edge
+ * properties
+ *
+ */
+
+template<typename G>
+struct edge_prop
+{
+ //! Properties counter
+ int cnt = 0;
+
+ //! edge properties
+ std::string & e_prop;
+
+ //! Attribute names
+ std::string * attributes_names;
+
+ //! Number of attributes name defined into the vertex
+ int n_attr = 0;
+
+ //! indicate if attributes_names is to destroy
+ bool to_destroy = false;
+
+ /*! \brief Constructor
+ *
+ * Create an edge properties list
+ *
+ * \param e_prop std::string that is filled with the graph properties in the GraphML format
+ * \param a_name stub SFINAE, it basically check if G::E_type has properties names defined, if yes this
+ * constructor is selected over the other one
+ *
+ */
+ edge_prop(std::string & e_prop, typename G::E_type::attributes & a_name)
+ :e_prop(e_prop),attributes_names(a_name.name)
+ {
+ // Calculate the number of attributes name
+ n_attr = sizeof(a_name.name)/sizeof(std::string);
+ };
+
+ /*! \brief Constructor
+ *
+ * Create an edge properties list
+ *
+ * \param e_prop std::string that is filled with the graph properties in the GraphML format
+ *
+ */
+ edge_prop(std::string & e_prop)
+ :e_prop(e_prop),attributes_names(NULL)
+ {
+ // Calculate the number of attributes
+ n_attr = G::E_type::max_prop;
+
+ // Create default property names
+ attributes_names = new std::string[G::E_type::max_prop];
+ to_destroy = true;
+
+ // Create default property names
+ create_prop<typename G::E_type>(attributes_names);
+ };
+
+ inline ~edge_prop()
+ {
+ if (to_destroy == true)
+ {delete [] attributes_names;}
+ }
+
+ /*! \brief It call the functor for each member
+ *
+ * \param t each member
+ *
+ */
+ template<typename T>
+ void operator()(T& t)
+ {
+ //! Create an entry for the attribute
+ if (cnt < n_attr)
+ {
+ // Create a property string based on the type of the property
+ if (std::is_same<T,float>::value)
+ e_prop += "<key id=\"ek" + std::to_string(cnt) + "\" for=\"edge\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"float\"/>\n";
+ else if (std::is_same<T,double>::value)
+ e_prop += "<key id=\"ek" + std::to_string(cnt) + "\" for=\"edge\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"double\"/>\n";
+ else if (std::is_same<T,int>::value)
+ e_prop += "<key id=\"ek" + std::to_string(cnt) + "\" for=\"edge\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"int\"/>\n";
+ else if (std::is_same<T,long int>::value)
+ e_prop += "<key id=\"ek" + std::to_string(cnt) + "\" for=\"edge\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"long\"/>\n";
+ else if (std::is_same<T,bool>::value)
+ e_prop += "<key id=\"ek" + std::to_string(cnt) + "\" for=\"edge\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"boolean\"/>\n";
+ else if (std::is_same<T,std::string>::value)
+ e_prop += "<key id=\"ek" + std::to_string(cnt) + "\" for=\"edge\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"string\"/>\n";
+ }
+
+ cnt++;
+ }
+};
+
+/*! \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 create a string containing all the edge
+ * properties
+ *
+ */
+
+template<typename G>
+struct edge_node
+{
+ //! Vertex object container
+ typename G::E_container & vo;
+
+ //! Properties counter
+ int cnt = 0;
+
+ //! edge node string
+ std::string & e_node;
+
+ //! Attribute names
+ std::string * attributes_names;
+
+ //! Number of attributes name defined into the vertex
+ int n_attr = 0;
+
+ //! indicate if attributes_names is to destroy
+ bool to_destroy = false;
+
+ /*! \brief Constructor
+ *
+ * Create an edge node
+ *
+ * \param e_node std::string that is filled with the graph node definition in the GraphML format
+ * \param n_obj object container to access the object properties for example encapc<...>
+ * \param a_name attributes names
+ *
+ */
+ edge_node(std::string & e_node, typename G::E_container & n_obj, typename G::E_type::attributes & a_name)
+ :vo(n_obj),e_node(e_node),attributes_names(a_name.name)
+ {
+ // Calculate the number of attributes name
+ n_attr = sizeof(a_name.name)/sizeof(std::string);
+ };
+
+ /*! \brief Constructor
+ *
+ * Create an 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<...>
+ *
+ */
+ edge_node(std::string & e_node, typename G::E_container & n_obj)
+ :vo(n_obj),e_node(e_node),attributes_names(NULL)
+ {
+ // Calculate the number of attributes
+ n_attr = G::E_type::max_prop;
+
+ // Create a number of default properties name
+ attributes_names = new std::string[G::E_type::max_prop];
+ to_destroy = true;
+
+ // Create default property names
+ create_prop<typename G::E_type>(attributes_names);
+
+ };
+
+ inline ~edge_node()
+ {
+ if (to_destroy == true)
+ {delete [] attributes_names;}
+ }
+
+ /*! \brief Create a new node
+ *
+ * \param v_c node number
+ * \param s source node id
+ * \param d destination node id
+ *
+ */
+ void new_node(size_t v_c, size_t s, size_t d)
+ {
+ // start a new node
+ e_node += "<edge id=\"e"+ std::to_string(v_c) + "\" source=\"n" + std::to_string(s) + "\" target=\"n" + std::to_string(d) + "\">\n";
+
+ // reset the counter properties
+ cnt = 0;
+ }
+
+ /*! \brief Close a node
+ *
+ * Close a node
+ *
+ */
+ void end_node()
+ {
+ // close a node
+ e_node += "</edge>\n";
+ }
+
+ /*! It call the functor for each member
+ *
+ * \param t each member
+ *
+ */
+ template<typename T>
+ void operator()(T& t)
+ {
+ //! Create an entry for the attribute
+ if (T::value < n_attr)
+ {
+ typedef typename std::remove_reference<decltype(vo.template get<T::value>())>::type type_get;
+
+ // Create a property string based on the type of the property
+ if (std::is_same<type_get,float>::value)
+ e_node += " <data key=\"ek" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
+ else if (std::is_same<type_get,double>::value)
+ e_node += " <data key=\"ek" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
+ else if (std::is_same<type_get,int>::value)
+ e_node += " <data key=\"ek" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
+ else if (std::is_same<type_get,long int>::value)
+ e_node += " <data key=\"ek" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
+ else if (std::is_same<type_get,bool>::value)
+ e_node += " <data key=\"ek" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
+ else if (std::is_same<type_get,std::string>::value)
+ e_node += " <data key=\"ek" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
+ }
+
+ cnt++;
+ }
+};
+
+/*!
+ *
+ * From a Graphbasic structure it write a GraphML format file
+ *
+ */
+
+template <typename Graph>
+class GraphMLWriter
+{
+ //! Graph to write
+ Graph & g;
+
+ /*! \brief It get the vertex properties list
+ *
+ * It get the vertex properties list of the vertex defined as a GraphML header
+ * and
+ * define position and shape of the node
+ *
+ * \return a string that define the vertex properties in graphML format
+ *
+ */
+ std::string get_vertex_properties_list()
+ {
+ //! vertex property output string
+ std::string v_out("");
+
+ // create a vertex property functor
+ vertex_prop<Graph> vp(v_out);
+
+ // Iterate through all the vertex and create the vertex list
+ boost::mpl::for_each_ref< typename Graph::V_type::type >(vp);
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief It get the edge properties list
+ *
+ * It get the edge properties list of the edge defined as a GraphML header
+ *
+ * \return a string that define the edge properties in graphML format
+ *
+ */
+ std::string get_edge_properties_list()
+ {
+ //! edge property output string
+ std::string e_out;
+
+ // create a vertex property functor
+ edge_prop<Graph> ep(e_out);
+
+ // Iterate through all the vertex and create the vertex list
+ boost::mpl::for_each_ref< typename Graph::E_type::type >(ep);
+
+ // return the edge properties string
+ return e_out;
+ }
+
+ /*! \brief Get the string containing the set of vertices
+ *
+ * \return the set of vertices as string
+ *
+ */
+ std::string get_vertex_list()
+ {
+ // node counter
+ size_t nc = 0;
+
+ //! vertex node output string
+ std::string v_out;
+
+ //! Get a vertex iterator
+ auto it = g.getVertexIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ auto v = g.vertex(it.get());
+
+ // create a vertex list functor
+ vertex_node<Graph> vn(v_out,v);
+
+ // create new node
+ vn.new_node(nc);
+
+ // Iterate through all the vertex and create the vertex list
+ boost::mpl::for_each_ref< boost::mpl::range_c<int,0,Graph::V_type::max_prop> >(vn);
+
+ // end node
+ vn.end_node();
+
+ // increment the iterator and counter
+ ++it;
+ nc++;
+ }
+
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief return the edge list as a string
+ *
+ * \return the edge list as string
+ *
+ */
+ std::string get_edge_list()
+ {
+ // node counter
+ size_t nc = 0;
+
+ //! edge node output string
+ std::string e_out;
+
+ //! Get an edge iterator
+ auto it = g.getEdgeIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ // Get the edge object
+ auto obj = g.edge(it.get());
+
+ // create an edge list functor
+ edge_node<Graph> en(e_out,obj);
+
+ // create a new node
+ en.new_node(nc,it.source(),it.target());
+
+ // Iterate through all the edges and create the edge list
+ boost::mpl::for_each_ref< boost::mpl::range_c<int,0,Graph::E_type::max_prop> >(en);
+
+ // end new node
+ en.end_node();
+
+ // increment the operator
+ ++it;
+ nc++;
+ }
+
+ // return the edge list
+ return e_out;
+ }
+
+public:
+
+ /*!
+ *
+ * GraphMLWriter constructor, it take a graph and write a GraphML format
+ *
+ * \param g Graph to write
+ *
+ */
+ GraphMLWriter(Graph & g)
+ :g(g)
+ {}
+
+ /*! \brief It write a GraphML file from a graph
+ *
+ * \param file path where to write
+ * \param name of the graph
+ *
+ */
+ bool write(std::string file, std::string graph_name="Graph")
+ {
+ // Header for the GraphML
+ std::string gml_header;
+ // Vertex list of the GraphML
+ std::string vertex_list;
+ // End for the GraphML
+ std::string gml_header_end;
+ // Graph header
+ std::string graph_header;
+ // Graph header end
+ std::string graph_header_end;
+ // Edge list of the GraphML
+ std::string edge_list;
+ // vertex properties header
+ std::string vertex_prop_header;
+ // edge properties header
+ std::string edge_prop_header;
+
+ // GraphML header
+ gml_header = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n\
+ <graphml xmlns=\"http://graphml.graphdrawing.org/xmlns\"\n\
+ xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n\
+ xsi:schemaLocation=\"http://graphml.graphdrawing.org/xmlns\n\
+ http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd\">\n";
+
+ // Graph header to define an header
+ graph_header = "<graph id=\"" + graph_name + "\" edgedefault=\"undirected\">\n";
+ // Graph header end
+ graph_header_end = "</graph>\n";
+
+ // Vertex properties header
+ vertex_prop_header = get_vertex_properties_list();
+
+ // Edge properties header
+ edge_prop_header = get_edge_properties_list();
+
+ // Get the node graph list
+ vertex_list = get_vertex_list();
+
+ // Get the edge graph list
+ edge_list = get_edge_list();
+
+ // Header end
+ gml_header_end = "</graphml>";
+
+ // write the file
+
+ std::ofstream ofs(file);
+
+ // Check if the file is open
+ if (ofs.is_open() == false)
+ {std::cerr << "Error cannot creare the graphML file: " + file;}
+
+ ofs << gml_header << graph_header << vertex_prop_header << edge_prop_header <<
+ vertex_list << edge_list << graph_header_end << gml_header_end;
+
+ // Close the file
+
+ ofs.close();
+
+ // Completed succefully
+ return true;
+ }
+};
+
+#endif
diff --git a/src/GraphMLWriter/GraphMLWriter_unit_tests.hpp b/src/GraphMLWriter/GraphMLWriter_unit_tests.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..953cfc7cfb043a438f77af622d08d50d40175e55
--- /dev/null
+++ b/src/GraphMLWriter/GraphMLWriter_unit_tests.hpp
@@ -0,0 +1,171 @@
+/*
+ * GraphMLWriter_unit_tests.hpp
+ *
+ * Created on: Dec 9, 2014
+ * Author: i-bird
+ */
+
+#ifndef GRAPHMLWRITER_UNIT_TESTS_HPP_
+#define GRAPHMLWRITER_UNIT_TESTS_HPP_
+
+#define GS_SIZE 8
+
+#include "GraphMLWriter.hpp"
+#include "Graph/CartesianGraphFactory.hpp"
+#include "util/util.hpp"
+
+BOOST_AUTO_TEST_SUITE( graphml_writer_test )
+
+/*!
+ *
+ * Test node and edge
+ *
+ */
+
+struct ne_cp
+{
+ //! The node contain several properties
+ typedef boost::fusion::vector<float,float,float,double,long int,int,std::string> type;
+
+ //! The data
+ type data;
+
+ //! x property id in boost::fusion::vector
+ static const unsigned int x = 0;
+ //! y property id in boost::fusion::vector
+ static const unsigned int y = 1;
+ //! z property id in boost::fusion::vector
+ static const unsigned int z = 2;
+ //! double_num property id in boost::fusion::vector
+ static const unsigned int double_num = 3;
+ //! long_num property id in boost::fusion::vector
+ static const unsigned int long_num = 4;
+ //! integer property id in boost::fusion::vector
+ static const unsigned int integer = 5;
+ //! string property id in boost::fusion::vector
+ static const unsigned int string = 6;
+ //! total number of properties boost::fusion::vector
+ static const unsigned int max_prop = 7;
+
+ //! get x
+ float & get_x() {return boost::fusion::at_c<x>(data);}
+ //! get y
+ float & get_y() {return boost::fusion::at_c<y>(data);}
+ //! get z
+ float & get_z() {return boost::fusion::at_c<z>(data);}
+ //! get double number
+ double & get_dn() {return boost::fusion::at_c<double_num>(data);}
+ //! get long number
+ long int & get_ln() {return boost::fusion::at_c<long_num>(data);}
+ //! get integer
+ int & get_i() {return boost::fusion::at_c<integer>(data);}
+ //! get string
+ std::string & get_str() {return boost::fusion::at_c<string>(data);}
+
+ //! define attributes names
+ struct attributes
+ {
+ static const std::string name[max_prop];
+ };
+
+ static inline bool noPointers()
+ {
+ return true;
+ }
+
+ //! type of the spatial information
+ typedef float s_type;
+};
+
+// Initialize the attributes strings array
+const std::string ne_cp::attributes::name[] = {"x","y","z","double_num","long_num","integer","string"};
+
+BOOST_AUTO_TEST_CASE( graphml_writer_use)
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/test_graph2_test.graphml");
+ std::string c3 = std::string("openfpm_io/test_data/test_graph_test.graphml");
+
+#else
+
+ std::string c2 = std::string("test_data/test_graph2_test.graphml");
+ std::string c3 = std::string("test_data/test_graph_test.graphml");
+
+#endif
+
+ Graph_CSR<ne_cp,ne_cp> g_csr2;
+
+ // Add 4 vertex and connect
+
+ struct ne_cp n1;
+ n1.get_x() = 1.0;
+ n1.get_y() = 2.0;
+ n1.get_z() = 3.0;
+ n1.get_dn() = 4.0;
+ n1.get_ln() = 5.0;
+ n1.get_i() = 6.0;
+ n1.get_str() = std::string("test");
+ g_csr2.addVertex(n1);
+ n1.get_str() = std::string("tes2");
+ g_csr2.addVertex(n1);
+ n1.get_str() = std::string("test3");
+ g_csr2.addVertex(n1);
+ n1.get_str() = std::string("test4");
+ g_csr2.addVertex(n1);
+ n1.get_str() = std::string("test5");
+
+ g_csr2.addEdge(0,1,n1);
+ n1.get_str() = std::string("test6");
+ g_csr2.addEdge(2,1,n1);
+ n1.get_str() = std::string("test7");
+ g_csr2.addEdge(3,1,n1);
+ n1.get_str() = std::string("test8");
+ g_csr2.addEdge(2,0,n1);
+ n1.get_str() = std::string("test9");
+ g_csr2.addEdge(3,2,n1);
+
+ // Create a graph ML
+ GraphMLWriter<Graph_CSR<ne_cp,ne_cp>> gv2(g_csr2);
+ gv2.write("test_graph2.graphml");
+
+ // check that match
+
+ bool test = compare("test_graph2.graphml",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+
+ //! Create a graph
+
+ CartesianGraphFactory<3,Graph_CSR<ne_cp,ne_cp>> g_factory;
+
+ // Cartesian grid
+ size_t sz[] = {GS_SIZE,GS_SIZE,GS_SIZE};
+
+ // Box
+ Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});
+
+ // Boundary conditions, non periodic
+ size_t bc[] = {NON_PERIODIC,NON_PERIODIC,NON_PERIODIC};
+
+ Graph_CSR<ne_cp,ne_cp> g_csr = g_factory.construct<5,NO_VERTEX_ID,float,2,ne_cp::x,ne_cp::y,ne_cp::z>(sz,box,bc);
+
+ // Create a graph ML
+ GraphMLWriter<Graph_CSR<ne_cp,ne_cp>> gw(g_csr);
+ gw.write("test_graph.graphml");
+
+
+ // check that match
+ test = compare("test_graph.graphml",c3);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+
+
+#endif /* GRAPHMLWRITER_UNIT_TESTS_HPP_ */
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..500f9715b3cdb76a685f1c4eb49243b950bdeb3e
--- /dev/null
+++ b/src/HDF5_wr/HDF5_reader_gd.hpp
@@ -0,0 +1,248 @@
+/*
+ * 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,
+ long 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};
+
+ // allocate the memory
+ HeapMemory pmem;
+ //pmem.allocate(req);
+ ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(block[0],pmem));
+ mem.incRef();
+
+ //Select file dataspace
+ hid_t file_dataspace_id_2 = H5Dget_space(dataset_2);
+
+ size_t to_read = block[0];
+ size_t coffset = 0;
+
+ auto & v_cl = create_vcluster();
+
+ int read_test = (to_read != 0);
+ v_cl.max(read_test);
+ v_cl.execute();
+
+ while (read_test)
+ {
+ hsize_t block_c[1];
+ block_c[0] = std::min((size_t)(to_read),(size_t)0x7FFFFFFF);
+
+ hsize_t offset_c[1] = {offset[0] + coffset};
+ H5Sselect_hyperslab(file_dataspace_id_2, H5S_SELECT_SET, offset_c, NULL, count, block_c);
+
+ hsize_t mdim_2[1] = {block_c[0]};
+
+ //Create data space in memory
+ hid_t mem_dataspace_id_2 = H5Screate_simple(1, mdim_2, NULL);
+
+ // Read the dataset.
+ H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_2, file_dataspace_id_2, plist_id, (char *)mem.getPointer() + coffset);
+
+ coffset += std::min((size_t)(to_read),(size_t)0x7FFFFFFF);
+ to_read -= std::min((size_t)(to_read),(size_t)0x7FFFFFFF);
+
+ read_test = (to_read != 0);
+ v_cl.max(read_test);
+ v_cl.execute();
+ }
+
+ 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.last().swap(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
+ long 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);
+
+ // Read the dataset.
+ H5Dread(dataset, H5T_NATIVE_LLONG, mem_dataspace_id, file_dataspace_id, plist_id, metadata_out);
+
+
+ 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();
+
+ 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..34497d46f5505e760617ad254326c5d6536d7204
--- /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<typename vector_pos_type, typename vector_prp_type>
+ 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,
+ vector_pos_type & v_pos,
+ vector_prp_type & 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;
+
+ vector_pos_type v_pos_unp;
+
+ vector_prp_type 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<typename vector_pos_type, typename vector_prp_type> inline bool load(const std::string & filename,
+ vector_pos_type & v_pos,
+ vector_prp_type & 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..d0c2b673ddaf6efaddc1efe063f9bebe92f3fefc
--- /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_cuda.cu b/src/HDF5_wr/HDF5_writer_cuda.cu
new file mode 100644
index 0000000000000000000000000000000000000000..5dfd6862322423485f7a870e9db9a9ab7afc226a
--- /dev/null
+++ b/src/HDF5_wr/HDF5_writer_cuda.cu
@@ -0,0 +1,101 @@
+#include "config.h"
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+#include "HDF5_wr.hpp"
+
+#include "hdf5.h"
+
+BOOST_AUTO_TEST_SUITE( vd_hdf5_chckpnt_rstrt_test_gpu )
+
+// Dimensionality
+const size_t dim = 3;
+
+BOOST_AUTO_TEST_CASE( vector_dist_hdf5_save_test_gpu )
+{
+ openfpm::vector_gpu<Point<3,float>> vpos;
+ openfpm::vector_gpu<aggregate<double,float[dim],size_t,float[dim][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) = p.get(0) + 113.0;
+
+ vprp.template get<1>(vprp.size()-1)[0] = p.get(0) + 100.0;
+ vprp.template get<1>(vprp.size()-1)[1] = p.get(1) + 200.0;
+ vprp.template get<1>(vprp.size()-1)[2] = p.get(2) + 300.0;
+
+ vprp.template get<2>(vprp.size()-1) = p.get(0) + 10013.0;
+
+ vprp.template get<3>(vprp.size()-1)[0][0] = p.get(0) + 600.0;
+ vprp.template get<3>(vprp.size()-1)[0][1] = p.get(0) + 900.0;
+ vprp.template get<3>(vprp.size()-1)[0][2] = p.get(0) + 1600.0;
+ vprp.template get<3>(vprp.size()-1)[1][0] = p.get(0) + 5600.0;
+ vprp.template get<3>(vprp.size()-1)[1][1] = p.get(0) + 6900.0;
+ vprp.template get<3>(vprp.size()-1)[1][2] = p.get(0) + 7600.0;
+ vprp.template get<3>(vprp.size()-1)[2][0] = p.get(0) + 9600.0;
+ vprp.template get<3>(vprp.size()-1)[2][1] = p.get(0) + 1900.0;
+ vprp.template get<3>(vprp.size()-1)[2][2] = p.get(0) + 101600.0;
+ }
+
+ HDF5_writer<VECTOR_DIST> h5;
+
+ // Save the vector
+ h5.save("vector_dist.h5",vpos,vprp);
+
+ HDF5_reader<VECTOR_DIST> h5r;
+
+ openfpm::vector_gpu<Point<3,float>> vpos2;
+ openfpm::vector_gpu<aggregate<double,float[dim],size_t,float[dim][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++)
+ {
+ Point<3,float> p1 = vpos.get(i);
+ Point<3,float> p2 = vpos2.get(i);
+
+ check &= (p1 == p2);
+
+ check &= (vprp.template get<1>(i)[0] == vprp2.template get<1>(i)[0]);
+ check &= (vprp.template get<1>(i)[1] == vprp2.template get<1>(i)[1]);
+ check &= (vprp.template get<1>(i)[2] == vprp2.template get<1>(i)[2]);
+
+ check &= (vprp.template get<0>(i) == vprp2.template get<0>(i));
+ check &= (vprp.template get<2>(i) == vprp2.template get<2>(i));
+
+ check &= (vprp.template get<3>(i)[0][0] == vprp2.template get<3>(i)[0][0]);
+ check &= (vprp.template get<3>(i)[0][1] == vprp2.template get<3>(i)[0][1]);
+ check &= (vprp.template get<3>(i)[0][2] == vprp2.template get<3>(i)[0][2]);
+ check &= (vprp.template get<3>(i)[1][0] == vprp2.template get<3>(i)[1][0]);
+ check &= (vprp.template get<3>(i)[1][1] == vprp2.template get<3>(i)[1][1]);
+ check &= (vprp.template get<3>(i)[1][2] == vprp2.template get<3>(i)[1][2]);
+ check &= (vprp.template get<3>(i)[2][0] == vprp2.template get<3>(i)[2][0]);
+ check &= (vprp.template get<3>(i)[2][1] == vprp2.template get<3>(i)[2][1]);
+ check &= (vprp.template get<3>(i)[2][2] == vprp2.template get<3>(i)[2][2]);
+ }
+
+ BOOST_REQUIRE_EQUAL(check,true);
+}
+
+BOOST_AUTO_TEST_SUITE_END()
diff --git a/src/HDF5_wr/HDF5_writer_gd.hpp b/src/HDF5_wr/HDF5_writer_gd.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..f41de0fec8f6c888a78e2f2118c7f1b0e6048576
--- /dev/null
+++ b/src/HDF5_wr/HDF5_writer_gd.hpp
@@ -0,0 +1,183 @@
+/*
+ * 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);
+
+ //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_LLONG, 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)
+ {
+ /* coverity[dead_error_line] */
+ 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;
+
+ long 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);
+
+ //Create property list for collective dataset write.
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+
+ // We slipt the write in chunk of 2GB maximum
+ size_t to_write = block[0];
+ size_t coffset = 0;
+ while (to_write)
+ {
+ hsize_t block_c[1];
+ block_c[0] = std::min((size_t)(to_write),(size_t)0x7FFFFFFF);
+
+ //Create data space in memory
+ hid_t mem_dataspace_id = H5Screate_simple(1, block_c, NULL);
+
+ hsize_t offset_c[1] = {offset[0] + coffset};
+ H5Sselect_hyperslab(file_dataspace_id, H5S_SELECT_SET, offset_c, NULL, count, block_c);
+
+ //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() + coffset);
+
+ coffset += std::min((size_t)(to_write),(size_t)0x7FFFFFFF);
+ to_write -= std::min((size_t)(to_write),(size_t)0x7FFFFFFF);
+
+ H5Sclose(mem_dataspace_id);
+ }
+
+ file_dataspace_id_2 = H5Dget_space(file_dataset_2);
+
+ //Write a data set 2 to a file
+ H5Dwrite(file_dataset_2, H5T_NATIVE_LLONG, 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);
+ H5Pclose(plist_id);
+ H5Fclose(file);
+
+ mem.decRef();
+ delete &mem;
+ }
+
+};
+
+#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..4a3106781fb2ad2b24ad41a927a3150654581b5c
--- /dev/null
+++ b/src/HDF5_wr/HDF5_writer_unit_tests.hpp
@@ -0,0 +1,125 @@
+/*
+ * 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_io )
+
+// 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();
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/vector_dist_24.h5");
+
+#else
+
+ std::string c2 = std::string("test_data/vector_dist_24.h5");
+
+#endif
+
+ 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(c2,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..f6bd869a75ee2bb1897f6cb9ab982ca85ab50a9e
--- /dev/null
+++ b/src/HDF5_wr/HDF5_writer_vd.hpp
@@ -0,0 +1,236 @@
+/*
+ * 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<typename vector_pos_type, typename vector_prp_type>
+ inline void save(const std::string & filename,
+ const vector_pos_type & v_pos,
+ const vector_prp_type & 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)
+ {
+ /* coverity[dead_error_line] */
+ 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);
+ mem.decRef();
+ delete &mem;
+ }
+
+ /*! \brief Return the equivalent HDF5 type for T
+ *
+ * \return The HDF5 type equivalent to T
+ *
+ */
+ template<typename T>
+ hid_t getType()
+ {
+ if (std::is_same<T,float>::value)
+ {return H5T_IEEE_F32LE;}
+ else if (std::is_same<T,double>::value)
+ {return H5T_IEEE_F64LE;}
+ else if (std::is_same<T,char>::value || std::is_same<T,unsigned char>::value)
+ {return H5T_STD_I8LE;}
+ else if (std::is_same<T,short>::value || std::is_same<T,unsigned short>::value)
+ {return H5T_STD_I16LE;}
+ else if (std::is_same<T,int>::value || std::is_same<T,unsigned int>::value)
+ {return H5T_STD_I32LE;}
+ else if (std::is_same<T,long int>::value || std::is_same<T,unsigned long int>::value)
+ {return H5T_STD_I64LE;}
+ }
+
+ /*! \brief It add an attribute to an already opened file
+ *
+ * \param dataset_id dataset_id
+ * \param name_ name of the attribute
+ * \param att_ attribute value
+ */
+ template<typename value_type>
+ void addAttributeHDF5(hid_t dataset_id, std::string name_, value_type att_)
+ {
+ //create the data space for the scalar attibute
+ hid_t dataspace_id = H5Screate(H5S_SCALAR);
+
+ //create the dataset attribute (H5T_IEEE_F64BE: 64-bit float little endian)
+ hid_t attribute_id = H5Acreate2(dataset_id, name_.c_str(), H5T_IEEE_F32LE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT);
+ //write the attibute data
+ herr_t status = H5Awrite(attribute_id,H5T_NATIVE_DOUBLE, &att_);
+ //close the attribute
+ status = H5Aclose(attribute_id);
+ //close the dataspace
+ status = H5Sclose(dataspace_id);
+ }
+
+ /*! \brief It add an attribute to an already opened file
+ *
+ * \param dataset_id dataset_id
+ * \param name_ name of the attribute
+ * \param att_ attribute value
+ */
+ template<typename value_type>
+ void addAttributeHDF5(std::string filename, std::string name_, value_type att_)
+ {
+ Vcluster<> & v_cl = create_vcluster();
+ 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);
+
+ hid_t file_id = H5Fopen(filename.c_str(),H5F_ACC_RDWR, plist_id);
+ hid_t dataset_id = H5Dopen2(file_id,"/vector_dist", H5P_DEFAULT);
+
+ addAttributeHDF5(dataset_id,name_.c_str(),att_);
+
+ //close the dataset
+ herr_t status = H5Dclose(dataset_id);
+ //close the file
+ status = H5Fclose(file_id);
+ }
+
+};
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_ */
diff --git a/src/Makefile.am b/src/Makefile.am
new file mode 100755
index 0000000000000000000000000000000000000000..a32d6ef4025c2340ef0c4f5eb2380a5b3b85663a
--- /dev/null
+++ b/src/Makefile.am
@@ -0,0 +1,21 @@
+
+LINKLIBS = $(PTHREAD_LIBS) $(HDF5_LDFLAGS) $(HDF5_LIBS) $(OPT_LIBS) $(BOOST_IOSTREAMS_LIB) $(BOOST_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_THREAD_LIB) $(CUDA_LIBS)
+
+noinst_PROGRAMS = io
+io_SOURCES = main.cpp ../../openfpm_vcluster/src/VCluster/VCluster.cpp ../../openfpm_devices/src/memory/CudaMemory.cu ../../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)
+
+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 :
+ $(NVCC) $(NVCCFLAGS) -o $@ -c $<
+
+test: io
+ source $(HOME)/openfpm_vars && cd .. && ./src/io
+
diff --git a/src/MatLabWriter.hpp b/src/MatLabWriter.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..a50d3a1e3c7e676446f6c3137cdb8ce6a7f3f225
--- /dev/null
+++ b/src/MatLabWriter.hpp
@@ -0,0 +1,111 @@
+#ifndef MATLABWRITER_HPP
+#define MATLABWRITER_HPP
+
+#include <iostream>
+#include "tiffio.h"
+#include "map_grid.hpp"
+#include <string>
+
+/*! \brief This class is able to save grid into tiff files
+ *
+ * This class is able to save grid into tiff files
+ *
+ */
+
+template<unsigned int dim, typename T>
+class MatLabWriter
+{
+ /*! \brief Save grid into tiff files
+ *
+ * Save grid into tiff files
+ *
+ */
+
+ template<typename grid, typename Mem> int operator<<(grid data, std::string file)
+ {
+ // Grid can have several properties we can save only scalar fields
+ // for each properties save one scalar fields
+
+ // Tiff files can be saved up to 5D
+
+ if (dim > 5)
+ {
+ std::cerr << "Error Tiff writer support until 5D images" << "\n";
+ }
+
+ // Open the tiff image
+
+ uint32 width;
+ uint32 height;
+ TIFF *tif = TIFFOpen(file.c_str(),"w");
+
+ // if the file is open
+
+ if(tif)
+ {
+ // set width and height for 2D
+
+ width = data.getGrid().size(0);
+ height = data.getGrid().size(1);
+
+ TIFFSetField(tif,TIFFTAG_IMAGEWIDTH, &width);
+ TIFFSetField(tif,TIFFTAG_IMAGELENGTH, &height);
+
+ // Create the tiff line, in case the grid is CPU, we have only
+ // one property and is a scalar, we can directly copy the line
+
+ typename boost::fusion::result_of::at<T::type,0>::type first_element_type;
+
+ if (typeid(grid).name() == "grid_cpu" && T::num_prop == 1 && boost::is_array<first_element_type>::type::value == true)
+ {
+ // Get the grid key iterator
+
+ grid_key_dx_iterator<dim> key = data.getIterator();
+
+ // write all lines
+
+ for(int i = 0; i < height ; i++)
+ {
+ // select the correct lines
+
+ key.set(1,i);
+
+ // we have only one scalar properties, get the buffer pointer
+ void * buf = &data.template get<0>(key);
+
+ TIFFWriteScanline(tif,buf,i, 0);
+ }
+ }
+ else
+ {
+ // we have to create the a scan line for each properties and index array
+ // each property and index array became a channel
+
+ // Get the grid key iterator
+
+ grid_key_dx_iterator<dim> key = data.getIterator();
+
+ // count how many properties and how many indexes we have
+
+ const int n_prp = total_prop<T>;
+
+ // write all lines
+
+ for(int i = 0; i < height ; i++)
+ {
+ // select the correct lines
+
+ key.set(1,i);
+
+ // we have only one scalar properties, get the buffer pointer
+ void * buf = &data.template get<0>(key);
+
+ TIFFWriteScanline(tif,buf,i, 0);
+ }
+ }
+ }
+ }
+
+};
+
+#endif
diff --git a/src/MetaParser/MetaParser.hpp b/src/MetaParser/MetaParser.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..7ce43539daf7fd2a7e1114e3bb5327ff9f2851e0
--- /dev/null
+++ b/src/MetaParser/MetaParser.hpp
@@ -0,0 +1,84 @@
+/*
+ * MetaParser.hpp
+ *
+ * Created on: Mar 3, 2019
+ * Author: i-bird
+ */
+
+#ifndef METAPARSER_HPP_
+#define METAPARSER_HPP_
+
+#include <algorithm>
+#include <iostream>
+#include <iterator>
+#include <string>
+#include <vector>
+
+#include <boost/bind/bind.hpp>
+#include <boost/program_options.hpp>
+#include <boost/tokenizer.hpp>
+
+typedef boost::program_options::options_description MetaParser_options;
+namespace MetaParser_def = boost::program_options;
+
+class MetaParser
+{
+ boost::program_options::options_description desc;
+
+ boost::program_options::variables_map vm;
+
+public:
+
+ explicit MetaParser(boost::program_options::options_description & desc)
+ :desc(desc)
+ {
+ }
+
+ /*! \brief Parse the string of options
+ *
+ * \param string of options
+ *
+ */
+ bool parse(std::string & opts)
+ {
+ std::istringstream iss(opts);
+
+ // Parse mocked up input.
+ boost::program_options::store(boost::program_options::parse_config_file(iss,desc), vm);
+ boost::program_options::notify(vm);
+
+ return true;
+ }
+
+ /*! \brief Return the option opt in value
+ *
+ * \param opt option to check
+ * \param value where to store the value of the option
+ *
+ * \return true if the option has been set
+ *
+ */
+ template<typename T>
+ bool getOption(std::string opt,T & value)
+ {
+ if (vm.count(opt))
+ {
+ value = vm[opt].as<T>();
+ return true;
+ }
+
+ return false;
+ }
+
+ /*! \brief clear everything you parsed so far
+ *
+ *
+ */
+ void clear()
+ {
+ vm.clear();
+ }
+};
+
+
+#endif /* METAPARSER_HPP_ */
diff --git a/src/MetaParser/MetaParser_unit_test.cpp b/src/MetaParser/MetaParser_unit_test.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..a02a9c2d05806df230770856719429f208e99488
--- /dev/null
+++ b/src/MetaParser/MetaParser_unit_test.cpp
@@ -0,0 +1,117 @@
+/*
+ * MetaParser_unit_test.cpp
+ *
+ * Created on: Mar 3, 2019
+ * Author: i-bird
+ */
+
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+#include "MetaParser.hpp"
+
+BOOST_AUTO_TEST_SUITE( vtk_writer_tests )
+
+BOOST_AUTO_TEST_CASE( vtk_writer_meta_parser_use )
+{
+ std::string test_options("time = 5.0");
+ std::string test_options2("time=6.0");
+ std::string test_options3("time =7.0");
+ std::string test_options4("time= 8.0");
+ std::string test_options5("time= 9.0");
+
+ double time = 1.0;
+
+ MetaParser_options opts;
+ opts.add_options()
+ ("time", MetaParser_def::value<double>(&time));
+
+ MetaParser mp(opts);
+ mp.parse(test_options);
+
+ BOOST_REQUIRE_EQUAL(time,5.0);
+
+ time = 0.0;
+ bool exist = mp.getOption("time",time);
+
+ BOOST_REQUIRE_EQUAL(exist,true);
+ BOOST_REQUIRE_EQUAL(time,5.0);
+
+ exist = mp.getOption("invalid",time);
+ BOOST_REQUIRE_EQUAL(exist,false);
+
+ // parse another
+
+ mp.clear();
+
+ time = 0.0;
+ mp.parse(test_options2);
+
+ BOOST_REQUIRE_EQUAL(time,6.0);
+
+ time = 0.0;
+ exist = mp.getOption("time",time);
+
+ BOOST_REQUIRE_EQUAL(exist,true);
+ BOOST_REQUIRE_EQUAL(time,6.0);
+
+ exist = mp.getOption("invalid",time);
+ BOOST_REQUIRE_EQUAL(exist,false);
+
+ // parse another
+
+ mp.clear();
+
+ time = 0.0;
+ mp.parse(test_options3);
+
+ BOOST_REQUIRE_EQUAL(time,7.0);
+
+ time = 0.0;
+ exist = mp.getOption("time",time);
+
+ BOOST_REQUIRE_EQUAL(exist,true);
+ BOOST_REQUIRE_EQUAL(time,7.0);
+
+ exist = mp.getOption("invalid",time);
+ BOOST_REQUIRE_EQUAL(exist,false);
+
+ // parse another
+
+ mp.clear();
+
+ time = 0.0;
+ mp.parse(test_options4);
+
+ BOOST_REQUIRE_EQUAL(time,8.0);
+
+ time = 0.0;
+ exist = mp.getOption("time",time);
+
+ BOOST_REQUIRE_EQUAL(exist,true);
+ BOOST_REQUIRE_EQUAL(time,8.0);
+
+ exist = mp.getOption("invalid",time);
+ BOOST_REQUIRE_EQUAL(exist,false);
+
+ // parse another
+
+ mp.clear();
+
+ time = 0.0;
+ mp.parse(test_options5);
+
+ BOOST_REQUIRE_EQUAL(time,9.0);
+
+ time = 0.0;
+ exist = mp.getOption("time",time);
+
+ BOOST_REQUIRE_EQUAL(exist,true);
+ BOOST_REQUIRE_EQUAL(time,9.0);
+
+ exist = mp.getOption("invalid",time);
+ BOOST_REQUIRE_EQUAL(exist,false);
+
+}
+
+BOOST_AUTO_TEST_SUITE_END()
diff --git a/src/ObjReader/ObjReader.hpp b/src/ObjReader/ObjReader.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..a62d1dec61a3b660a5c3d30a87aa7793a24bb7e5
--- /dev/null
+++ b/src/ObjReader/ObjReader.hpp
@@ -0,0 +1,188 @@
+/*
+ * ObjReader.hpp
+ *
+ * Created on: Oct 31, 2018
+ * Author: i-bird
+ */
+
+#ifndef OBJREADER_HPP_
+#define OBJREADER_HPP_
+
+#include "config.h"
+#include "Space/Shape/Point.hpp"
+
+#ifdef HAVE_TINYOBJLOADER
+#include "tiny_obj_loader.h"
+
+/*! \brief Wavefront obj File reader
+ *
+ * \tparam T precision of the 3D space
+ *
+ */
+template<typename T>
+class ObjReader
+{
+ size_t shape_counter;
+ size_t face_counter;
+ size_t index_offset;
+
+ tinyobj::attrib_t attrib;
+ std::vector<tinyobj::shape_t> shapes;
+ std::vector<tinyobj::material_t> materials;
+
+ size_t end_shape;
+
+ public:
+
+ /*! \brief Constructor
+ *
+ *
+ */
+ ObjReader()
+ {}
+
+ /*! \brief Read an Wavefront obj file
+ *
+ * \param file to open
+ *
+ * \return true if the read succeed
+ */
+ bool read(std::string file)
+ {
+ shape_counter = 0;
+ face_counter = 0;
+ index_offset = 0;
+
+ shapes.clear();
+ materials.clear();
+
+ std::string err;
+ bool ret = tinyobj::LoadObj(&attrib, &shapes, &materials, &err, file.c_str());
+
+ if (!err.empty())
+ {std::cerr << err << std::endl;}
+
+ if (!ret)
+ {return false;}
+
+ end_shape = shapes.size();
+
+ return true;
+ }
+
+
+ /*! \brief Next triangle
+ *
+ * \return itself
+ *
+ */
+ ObjReader & operator++()
+ {
+ index_offset += getFaceNVertex();
+ ++face_counter;
+
+ if (face_counter >= shapes[shape_counter].mesh.num_face_vertices.size())
+ {
+ face_counter = 0;
+ index_offset = 0;
+ ++shape_counter;
+ }
+
+ return *this;
+ }
+
+ /*! \brief Return true if we have another face
+ *
+ * \return true if we have next face
+ */
+ inline bool isNext()
+ {
+ return shape_counter < end_shape;
+ }
+
+ /*! \brief Iterate only on a partucular object faces
+ *
+ * \param i object to iterate
+ *
+ * \return
+ */
+ inline void setObject(int i)
+ {
+ if (i >= shapes.size())
+ {
+ std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " you selected object " << i << " but the file contain " << shapes.size() << " objects" << std::endl;
+ }
+
+ shape_counter = i;
+ end_shape = i+1;
+ }
+
+
+ /*! \brief Get the number of vertices in the face
+ *
+ * \return number of vertices a face has
+ */
+ unsigned int getFaceNVertex()
+ {
+ return shapes[shape_counter].mesh.num_face_vertices[face_counter];
+ }
+
+ /*! \brief return the vertex v of the actual face
+ *
+ * \param v vertex
+ * \return the position of such vertex
+ */
+ inline Point<3,T> getVertex(unsigned int v)
+ {
+ Point<3,T> p;
+
+ tinyobj::index_t idx = shapes[shape_counter].mesh.indices[index_offset + v];
+
+ p.get(0) = attrib.vertices[3*idx.vertex_index+0];
+ p.get(1) = attrib.vertices[3*idx.vertex_index+1];
+ p.get(2) = attrib.vertices[3*idx.vertex_index+2];
+
+ return p;
+ }
+
+ /*! \brief return the vertex v of the actual face
+ *
+ * \param v vertex
+ * \return the position of such vertex
+ */
+ inline Point<3,T> getNormal(unsigned int v)
+ {
+ Point<3,T> p;
+
+ tinyobj::index_t idx = shapes[shape_counter].mesh.indices[index_offset + v];
+
+ p.get(0) = attrib.normals[3*idx.normal_index+0];
+ p.get(1) = attrib.normals[3*idx.normal_index+1];
+ p.get(2) = attrib.normals[3*idx.normal_index+2];
+
+ return p;
+ }
+
+ /*! \brief Get the texture coordinates
+ *
+ * \param v vertex
+ *
+ * \return The texture coordinates of the vertex v
+ *
+ */
+ inline Point<2,T> getTexCoord(unsigned int v)
+ {
+ Point<2,T> p;
+
+ tinyobj::index_t idx = shapes[shape_counter].mesh.indices[index_offset + v];
+
+ p.get(0) = attrib.texcoords[2*idx.texcoord_index+0];
+ p.get(1) = attrib.texcoords[2*idx.texcoord_index+1];
+
+ return p;
+ }
+};
+
+#endif
+
+#endif /* OBJREADER_HPP_ */
diff --git a/src/ObjReader/ObjReader_unit_test.cpp b/src/ObjReader/ObjReader_unit_test.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..79c2b6644e7438d6f1f81007c2ef2047fa42afcf
--- /dev/null
+++ b/src/ObjReader/ObjReader_unit_test.cpp
@@ -0,0 +1,20 @@
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+#include "ObjReader.hpp"
+
+#ifdef HAVE_TINYOBJLOADER
+
+BOOST_AUTO_TEST_SUITE( obj_reader_test_suite )
+
+BOOST_AUTO_TEST_CASE( obj_reader_test_use)
+{
+ ObjReader<float> reader;
+
+ reader.read("");
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+
+
+#endif
diff --git a/src/Plot/GoogleChart.hpp b/src/Plot/GoogleChart.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..ef0a9af292ee01d70fa07f1327f42c8082a436c5
--- /dev/null
+++ b/src/Plot/GoogleChart.hpp
@@ -0,0 +1,1001 @@
+/*
+ * GoogleChart.hpp
+ *
+ * Created on: Jan 9, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_DATA_SRC_PLOT_GOOGLECHART_HPP_
+#define OPENFPM_DATA_SRC_PLOT_GOOGLECHART_HPP_
+
+#include <fstream>
+#include "Vector/map_vector.hpp"
+#include <cmath>
+
+#define GGRAPH_COLUMS 1
+#define GGRAPH_POINTS 2
+
+#define GC_ZOOM std::string("explorer: {actions: ['dragToZoom', 'rightClickToReset'],axis: 'horizontal,vertical',keepInBounds: true, maxZoomIn: 128.0}")
+#define GC_X_LOG std::string("hAxis: { logScale: true }")
+#define GC_Y_LOG std::string("vAxis: { logScale: true }")
+
+/*! \brief Google chart options
+ *
+ */
+struct GCoptions
+{
+ //! Title of the chart
+ std::string title;
+ //! Y axis name
+ std::string yAxis;
+ //! X axis name
+ std::string xAxis;
+
+ //! Type of chart (list of the option can be founded in Google Chart API for seriesType)
+ //! Possible options are:
+ //! 'line', 'area', 'bars', 'candlesticks', and 'steppedArea'
+ //! default: line
+ std::string stype;
+
+ //! Extended series options
+ //! Example {5: {type: 'line'}} specify that the series number 5 must be represented
+ //! with a line
+ std::string stypeext;
+
+ //! width of the graph in pixels
+ size_t width=900;
+
+ //! height of the graph in pixels
+ size_t heigh=500;
+
+ //! Flag that specify if the colums are stacked
+ //! Check in Google Chart for is stacked option
+ bool isStacked = false;
+
+ //! Width of the line
+ size_t lineWidth = 4;
+
+ //! Style for all the intervals
+ //! Check Google Chart API intervals option
+ std::string intervalsext;
+
+ //! Style for each interval
+ //! Check Google Chart API interval option
+ std::string intervalext;
+
+ //! more
+ std::string more;
+
+ //! curve type
+ std::string curveType = "function";
+
+ //! barWD
+ bool barWD = false;
+
+ /*! \brief copy operator
+ *
+ * \param opt object to copy
+ *
+ * \return itself
+ *
+ */
+ GCoptions & operator=(const GCoptions & opt)
+ {
+ title = opt.title;
+ yAxis = opt.yAxis;
+ xAxis = opt.xAxis;
+ stype = opt.stype;
+ stypeext = opt.stypeext;
+ width=opt.width;
+ heigh=opt.heigh;
+
+ lineWidth = opt.lineWidth;
+ intervalsext = opt.intervalsext;
+ more = opt.more;
+
+ return *this;
+ }
+};
+
+/*! \brief Google Graph
+ *
+ */
+struct GGraph
+{
+ //! TypeOfGraph
+ size_t type;
+
+ //! data
+ std::string data;
+
+ //! option
+ std::string option;
+
+ //! view in case we need a view
+ std::string view;
+
+ //! Google chart option
+ GCoptions opt;
+};
+
+/////////////////// Constants strings usefull to construct the HTML page //////////
+
+const std::string begin_data ="<html>\n\
+ <head>\n\
+ <script type=\"text/javascript\" src=\"https://www.gstatic.com/charts/loader.js\"></script>\n\
+ <script src=\"https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js\"></script>\n\
+ <script type=\"text/javascript\">\n\
+ google.charts.load('current', {'packages':['corechart']});\n\
+ google.charts.setOnLoadCallback(drawVisualization);\n\
+\n\
+function exportToSVG(i)\n\
+{\n\
+var e = document.getElementById('chart_div'+i);\n\
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;\n\
+var pos = svg.lastIndexOf(\"</svg>\");\n\
+pos += 6;\n\
+svg = svg.substring(0,4) + \" xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' \" + svg.substring(4,pos);\n\
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);\n\
+$(this).attr({'href': svgData,'target': '_blank'});\n\
+}\n\
+\n\
+ function drawVisualization() {\n";
+
+const std::string end_data="]);\n\n";
+
+const std::string begin_div = "}</script>\n\
+</head>\n\
+<body>\n";
+
+const std::string div_end = "</body>\n\
+</html>\n";
+
+const std::string saving_javascript = "function save(i)\n\
+ var e = document.getElementById('chart_')\n\
+ e.getElementsByTagName('svg')[0].parentNode.innerHTML";
+
+template<typename T>
+struct check_nan
+{
+ static bool check(const T & n)
+ {
+ return false;
+ }
+};
+
+template<>
+struct check_nan<float>
+{
+ static bool check(const float & n)
+ {
+ return std::isnan(n);
+ }
+};
+
+template<>
+struct check_nan<double>
+{
+ static bool check(const double & n)
+ {
+ return std::isnan(n);
+ }
+};
+
+/////////////////////////////////////////////////////////////////////
+
+/*! \brief Small class to produce graph with Google chart in HTML
+ *
+ * This Class can produce several graph using google chart
+ *
+ * ### Create Histogram graph
+ *
+ * \image html g_graph_hist.jpg
+ *
+ * This code produce the graph above
+ *
+ * \snippet Plot_unit_tests.hpp Producing an Histogram graph
+ *
+ * ### Create Lines
+ *
+ * \image html g_graph_plot2.jpg
+ *
+ * This code produce the graph above
+ *
+ * \snippet Plot_unit_tests.hpp Producing lines
+ *
+ * ### Create lines with different styles
+ *
+ * \image html g_graph_plot.jpg
+ *
+ * This code produce the graph above
+ *
+ * \snippet Plot_unit_tests.hpp Producing lines graph with style
+ *
+ */
+class GoogleChart
+{
+ template<typename arg_0, typename ... args>
+ struct get_value_type
+ {
+ typedef typename arg_0::value_type type;
+ };
+
+ //! set of graphs
+ openfpm::vector<GGraph> set_of_graphs;
+
+ //! set inject HTML;
+ openfpm::vector<std::string> injectHTML;
+
+ //! Data has holes
+ bool holes = false;
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param x vector with x
+ * \param y vector with y
+ * \param xy all the other vectors
+ *
+ */
+ template<typename X, typename ... Xs>
+ void recursive_sort(X & x,X & y,Xs& ... xy)
+ {
+ struct srt_xy
+ {
+ typename X::value_type x;
+ unsigned int id;
+
+ bool operator<(const srt_xy & tmp) const
+ {
+ return x < tmp.x;
+ }
+ };
+
+ openfpm::vector<srt_xy> reord;
+ X y_tmp;
+
+ reord.resize(x.size());
+ y_tmp.resize(x.size());
+
+ for (size_t i = 0 ; i < x.size() ; i++)
+ {
+ reord.get(i).x = x.get(i);
+ reord.get(i).id = i;
+ }
+
+ reord.sort();
+
+ // reorder x and y
+
+ for (size_t i = 0 ; i < x.size() ; i++)
+ {
+ x.get(i) = reord.get(i).x;
+ y_tmp.get(i) = y.get(reord.get(i).id);
+ }
+
+ y_tmp.swap(y);
+
+ // sort x
+
+ recursive_sort(xy ...);
+ }
+
+ //! terminator for recursive sort
+ void recursive_sort()
+ {}
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param counters indexes
+ * \param x vector with x
+ * \param y vector with y
+ * \param xy all the other vectors
+ *
+ */
+ template<typename X, typename ... Xs>
+ bool isNext(size_t * counters,X & x,X & y,Xs& ... xy)
+ {
+ if (counters[0] < x.size())
+ {
+ return true;
+ }
+ return isNext(&counters[1],xy ...);
+ }
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param counters indexes
+ *
+ */
+ bool isNext(size_t * counters)
+ {
+ return false;
+ }
+
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param counters indexes
+ * \param x vector with x
+ * \param y vector with y
+ * \param xy all the other vectors
+ *
+ */
+ template<typename T, typename X, typename ... Xs>
+ T get_low(size_t * counters,X & x,X & y,Xs& ... xy)
+ {
+ if (sizeof...(Xs) != 0)
+ {
+ T low1;
+ if (counters[0] >= x.size())
+ {low1 = std::numeric_limits<typename X::value_type>::infinity();}
+ else
+ {low1 = x.get(counters[0]);}
+
+ T low2 = get_low<T>(&counters[1],xy ...);
+ return (low1 < low2)?low1:low2;
+ }
+
+ if (counters[0] >= x.size())
+ {return std::numeric_limits<typename X::value_type>::infinity();}
+ return x.get(counters[0]);
+ }
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param counters indexes
+ *
+ */
+ template<typename T>
+ T get_low(size_t * counters)
+ {
+ return 0.0;
+ }
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param x vector with x
+ * \param y vector with y
+ * \param xy all the other vectors
+ *
+ */
+ template<typename X, typename ... Xs>
+ void get_point(typename X::value_type low,
+ typename X::value_type * point,
+ size_t * counters,
+ X & x,
+ X & y,
+ Xs& ... xy)
+ {
+ if (counters[0] < x.size() && low == x.get(counters[0]))
+ {
+ point[0] = y.get(counters[0]);
+ counters[0]++;
+ }
+ else
+ {
+ point[0] = std::numeric_limits<typename X::value_type>::quiet_NaN();
+ }
+
+ get_point(low,&point[1],&counters[1],xy...);
+ }
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param x vector with x
+ * \param y vector with y
+ * \param xy all the other vectors
+ *
+ */
+ template<typename T>
+ void get_point(T low,
+ T * point,
+ size_t * counters)
+ {
+ return;
+ }
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param x vector with x
+ * \param y vector with y
+ * \param xy all the other vectors
+ *
+ */
+ template<typename ... Xs>
+ bool get_v(typename get_value_type<Xs...>::type & x,
+ typename get_value_type<Xs...>::type * point,
+ size_t * counters,
+ Xs& ... xy)
+ {
+ // if exist the next element
+ if (isNext(counters,xy...) == false)
+ {return false;}
+
+ // get lowest x
+ typename get_value_type<Xs...>::type low = get_low<typename get_value_type<Xs...>::type>(counters,xy...);
+
+ x = low;
+
+ get_point(low,point,counters,xy...);
+
+ return true;
+ }
+
+ /*! \brief Given X and Y vector return the string representing the data section of the Google Chart
+ *
+ * \tparam X type for the X coordinates
+ * \tparam Y type for the Y coordinates
+ *
+ * \param x vector of points on x
+ * \param y vector of points on y
+ * \param yn vector containing the name of each graph
+ * \param opt options to draw the graph
+ * \param i index of the graph we are drawing
+ *
+ * \return string with the data section
+ *
+ */
+ template<typename X, typename Y> std::string get_points_plot_data(const openfpm::vector<X> & x, const openfpm::vector<Y> & y, const openfpm::vector<std::string> & yn, const GCoptions & opt, size_t i)
+ {
+ std::stringstream data;
+
+ size_t interval = 0;
+
+ // we require that the number of x elements are the same as y elements
+
+ if (x.size() != y.size())
+ {std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " vector x and the vector y must have the same number of elements " << x.size() << "!=" << y.size() << "\n";}
+
+ // Google chart visualization
+ data << "var data" << i << " = new google.visualization.DataTable();\n";
+ if (std::is_same<X,typename std::string>::value == true)
+ data << "data" << i << ".addColumn(" << "'string'" << "," << "'" << opt.xAxis <<"');\n";
+ else
+ data << "data" << i << ".addColumn(" << "'number'" << "," << "'" << opt.xAxis <<"');\n";
+
+ for (size_t j = 0 ; j < y.last().size() ; j++)
+ {
+ if (yn.get(j) == std::string("interval"))
+ {
+ data << "data" << i << ".addColumn({id:'i" << interval/2 << "', type:'number', role:'interval'});\n";
+ interval++;
+ }
+ else
+ data << "data" << i << ".addColumn(" << "'number'" << "," << "'" << yn.get(j) <<"');\n";
+ }
+
+ data << "data" << i << ".addRows([\n";
+ for (size_t i = 0 ; i < y.size() && x.size() ; i++)
+ {
+
+ for (size_t j = 0 ; j < y.get(i).size()+1 ; j++)
+ {
+ // the first is x
+ if (j == 0)
+ {
+ if (std::is_same<X,typename std::string>::value == true)
+ data << "['" << x.get(i) << "'";
+ else
+ data << "[" << x.get(i);
+ }
+ else
+ {
+ if (check_nan<typename Y::value_type>::check(y.get(i).get(j-1)) == false)
+ {
+ data << "," << y.get(i).get(j-1);
+ }
+ else
+ {
+ holes = true;
+ data << "," << "null";
+ }
+ }
+ }
+ data << "],\n";
+ }
+
+ 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;
+ str << "title : '" << opt.title << "'";
+ str << ",\nvAxis: {title: '" << opt.yAxis << "'}";
+ str << ",\nhAxis: {title: '" << opt.xAxis << "'}";
+ str << ",\nseriesType: '" << opt.stype << "'";
+ if (opt.stypeext.size() != 0)
+ str << ",\nseries: " << opt.stypeext;
+ if (opt.more.size() != 0)
+ str << ",\n" <<opt.more;
+
+ return str.str();
+ }
+
+ std::string get_points_plot_option(const GCoptions & opt)
+ {
+ std::stringstream str;
+ str << "title : '" << opt.title << "'";
+ str << ",\nvAxis: {title: '" << opt.yAxis << "'}";
+ str << ",\nhAxis: {title: '" << opt.xAxis << "'}";
+ str << ",\ncurveType: '"<< opt.curveType << "'";
+
+ str << ",\nlineWidth: " << opt.lineWidth;
+ if (opt.intervalsext.size() != 0)
+ str << ",\nintervals: " << opt.intervalsext;
+ else
+ str << ",\nintervals: " << "{ 'style':'area' }";
+
+ if (opt.intervalext.size() != 0)
+ str << ",\ninterval: " << opt.intervalext << "\n";
+
+ if (opt.more.size() != 0)
+ str << ",\n" << opt.more;
+
+ return str.str();
+ }
+
+ /*! \brief Add a graph data variable
+ *
+ * \param of file out
+ * \param i id
+ * \param data string
+ *
+ */
+ void addData(std::ofstream & of, size_t i, const std::string & data)
+ {
+
+ of << data;
+ of << "]);\n";
+ }
+
+ /*! \brief Add an option data variable
+ *
+ * \param of file out
+ * \param i id
+ * \param opt string
+ *
+ */
+ void addOption(std::ofstream & of, size_t i, const std::string & opt)
+ {
+ of << "var options";
+ of << i;
+ of << "= {\n";
+ if (holes == true)
+ {of << "interpolateNulls : true,\n";}
+ of << opt;
+ 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, 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 << "'));" << 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";
+ }
+
+ /*! \brief Add a div section
+ *
+ * \param of file ofstream
+ * \param i id of the graph
+ * \param gc GoogleChart option
+ *
+ */
+ void addDiv(std::ofstream & of, size_t i, const GCoptions & gc)
+ {
+ of << "<a href=\"#\" download=\"graph1.svg\" id=\"export_svg" << i << "\"><button>Export data into svg</button></a>";
+ of << "<div id=\"chart_div";
+ of << i;
+ of << "\" style=\"width: ";
+ of << gc.width;
+ of << "px; height: ";
+ of << gc.heigh;
+ of << "px;\"></div>\n";
+ }
+
+public:
+
+ GoogleChart()
+ {
+ injectHTML.add();
+ }
+
+ /*! \brief Add an histogram graph
+ *
+ * \param y A vector of vectors the size of y indicate how many values we have on x
+ * each x value can have multiple values or datasets
+ *
+ */
+ template<typename Y> void AddHistGraph(openfpm::vector<Y> & y)
+ {
+ openfpm::vector<std::string> x;
+ x.resize(y.size());
+
+ AddHistGraph<std::string,Y>(x,y);
+ }
+
+ /*! \brief Add an histogram graph
+ *
+ * \param y A vector of vectors the size of y indicate how many values we have on x
+ * each x value can have multiple values or datasets
+ *
+ * \param x Give a name or number to each colums. Can be a string or a number
+ *
+ */
+ template<typename X, typename Y> void AddHistGraph(openfpm::vector<X> & x, openfpm::vector<Y> & y)
+ {
+ GCoptions opt;
+
+ openfpm::vector<std::string> yn;
+
+ if (y.size() != 0)
+ yn.resize(y.get(0).size());
+
+ AddHistGraph<X,Y,std::string>(x,y,yn,opt);
+ }
+
+ /*! \brief Add an histogram graph
+ *
+ * \param y A vector of vectors the size of y indicate how many values we have on x
+ * each x value can have multiple values or datasets
+ *
+ * \param x Give a name or number to each colums. Can be a string or a number
+ *
+ * \param yn Give a name to each dataset
+ *
+ */
+ template<typename X, typename Y, typename Yn> void AddHistGraph(openfpm::vector<X> & x, openfpm::vector<Y> & y, openfpm::vector<Yn> & yn)
+ {
+ GCoptions opt;
+
+ AddHistGraph(x,y,yn,opt);
+ }
+
+ /*! \brief Add an histogram graph
+ *
+ * \param y A vector of vectors the size of y indicate how many values we have on x
+ * each x value can have multiple values or datasets
+ *
+ * \param x Give a name or number to each colums. Can be a string or a number
+ *
+ * \param yn Give a name to each dataset
+ *
+ * \param opt Graph options
+ *
+ */
+ template<typename X, typename Y, typename Yn> void AddHistGraph(openfpm::vector<X> & x, openfpm::vector<Y> & y, openfpm::vector<Yn> & yn , const GCoptions & opt)
+ {
+ set_of_graphs.add();
+ injectHTML.add();
+
+ // Check that all the internal vector has the same number of elements
+
+ if (y.size() != 0)
+ {
+ size_t sz = y.get(0).size();
+ for (size_t i = 0; i < y.size() ; i++)
+ {
+ if (y.get(i).size() != sz)
+ std::cerr << __FILE__ << ":" << __LINE__ << " error all the elements in the y vector must have the same numbers, element " << i << ": " << y.get(i).size() << " " << " mismatch the numbers of elements at 0: " << sz << "/n";
+ }
+ }
+
+ 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;
+ }
+
+
+ /*! \brief Add lines graph
+ *
+ * \param xy list of vectors like openfpm::vector<float> or openfpm::vector<double>. Suppose you have a dataset of points x1,y1
+ * and a dataset x2,y2 and you want to display all these points in one graph. Than you call this function with
+ * AddLines(x1,y1,x2,y2,opt)
+ *
+ * \param opt Graph options
+ *
+ */
+ template<typename ... X> void AddLines(const openfpm::vector<std::string> & yn,
+ const GCoptions & opt,
+ X ... xy)
+ {
+ // first we sort the vectors
+ recursive_sort(xy ... );
+
+ size_t counters[sizeof...(X)];
+ memset(&counters,0,sizeof(counters));
+
+ typename get_value_type<X...>::type point[sizeof...(X)];
+ typename get_value_type<X...>::type xe;
+
+ openfpm::vector<typename get_value_type<X...>::type> x;
+
+ openfpm::vector<openfpm::vector<typename get_value_type<X...>::type>> y;
+
+
+ while (get_v(xe,point,counters,xy...))
+ {
+ y.add();
+ x.add(xe);
+
+ for (size_t i = 0 ; i < sizeof...(X)/2 ; i++)
+ {
+ y.last().add(point[i]);
+ }
+ }
+
+ AddLinesGraph(x,y,yn,opt);
+ }
+
+ /*! \brief Add lines graph
+ *
+ * If the x vector contain 0.0,0.1,0.2,0.3,0.4 and you want to draw two lines you specifying two y values for each of the x points
+ * you create an openfpm::vector<openfpm::vector<float>> y such that
+ *
+ * \verbatim
+ ------ j ------- |
+ y.get(i).get(j) = 3.2 3.4 5.4 1.3 2.3 i
+ 1.4 5.3 3.2 2.1 1.1 |
+
+ \endverbatim
+ *
+ * \param y A vector of vectors of values. each vector contain the graph points, compared to AddLinesGraph the points are stored
+ *
+ *
+ * \param x axis values
+ *
+ * \param opt Graph options
+ *
+ */
+ template<typename X, typename Y> void AddLinesGraphT(openfpm::vector<X> & x, openfpm::vector<Y> & y , const GCoptions & opt)
+ {
+ openfpm::vector<std::string> yn;
+
+ if (y.size() == 0)
+ {
+ std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " vector y must be filled" << std::endl;
+ return;
+ }
+
+ for (size_t i = 0 ; i < y.last().size() ; i++)
+ yn.add(std::string("line") + std::to_string(i));
+
+ if (y.size() == 0)
+ return;
+
+ // number of points
+ size_t np = y.last().size();
+
+ for (size_t j = 0 ; j < y.size() ; j++)
+ {
+ if (y.get(j).size() != np)
+ std::cerr << __FILE__ << ":" << __LINE__ << " Error all the graph must have the same number of points " << np << "!=" << y.get(j).size() << std::endl;
+ }
+
+ openfpm::vector<openfpm::vector<X>> swap;
+
+
+ // swap the vector
+ // Each vector is a graph
+ // It is different from the other call where each vector
+ // has multiple value for the same point
+ for (size_t i = 0 ; i < np ; i++)
+ {
+ swap.add();
+ for (size_t j = 0 ; j < y.size() ; j++)
+ {
+ swap.last().add(y.get(j).get(i));
+ }
+ }
+
+ AddLinesGraph(x,swap,yn,opt);
+ }
+
+ /*! \brief Add a simple lines graph
+ *
+ * If the x vector contain 0.0,0.1,0.2,0.3,0.4 and you want to draw two lines you specifying two y values for each of the x points
+ * you create an openfpm::vector<openfpm::vector<float>> y such that
+ *
+ * \verbatim
+ -- j --
+ y.get(i).get(j) = 3.2 3.4
+ 1.4 5.3 |
+ 5.4 3.2 i
+ 1.3 2.2 |
+ 2.3 1.1
+ \endverbatim
+ *
+ * \param y A vector of vectors of values. The size of y indicate how many x values
+ * we have, while the internal vector can store multiple value of the same point,
+ * for example error bar
+ *
+ * \param x Give a name or number to each x value, so can be a string or a number
+ *
+ * \param opt Graph options
+ *
+ */
+ template<typename X, typename Y> void AddLinesGraph(openfpm::vector<X> & x, openfpm::vector<Y> & y , const GCoptions & opt)
+ {
+ openfpm::vector<std::string> yn;
+
+ if (y.size() == 0)
+ {
+ std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " vector y must be filled";
+ return;
+ }
+
+ for (size_t i = 0 ; i < y.last().size() ; i++)
+ yn.add(std::string("line") + std::to_string(i));
+
+ AddLinesGraph(x,y,yn,opt);
+ }
+
+ /*! \brief Add a simple plot graph
+ *
+ * \param y A vector of vector of values (numbers) the size of y indicate how many x values
+ * or colums we have, while the internal vector store multiple lines,
+ * or error bars
+ *
+ * \param x Give a name or number to each colums, so can be a string or a number
+ *
+ * \param yn Give a name to each line, or specify an error bar
+ *
+ * \param opt Graph options
+ *
+ */
+ template<typename X, typename Y> void AddLinesGraph(openfpm::vector<X> & x, openfpm::vector<Y> & y , const openfpm::vector<std::string> & yn, const GCoptions & opt)
+ {
+ if (y.size() == 0)
+ {
+ std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " vector y must be filled\n";
+ return;
+ }
+
+ set_of_graphs.add();
+ injectHTML.add();
+
+ // Check that all the internal vectors has the same number of elements
+
+ if (y.size() != 0)
+ {
+ size_t sz = y.get(0).size();
+ for (size_t i = 0; i < y.size() ; i++)
+ {
+ if (y.get(i).size() != sz)
+ std::cerr << __FILE__ << ":" << __LINE__ << " error all the elements in the y vector must have the same numbers of elements " << y.get(i).size() << " != " << sz << "\n";
+ }
+ }
+
+ set_of_graphs.last().type = GGRAPH_POINTS;
+ set_of_graphs.last().data = get_points_plot_data(x,y,yn,opt,set_of_graphs.size()-1);
+ set_of_graphs.last().option = get_points_plot_option(opt);
+ set_of_graphs.last().opt = opt;
+ }
+
+ /*! \brief Add HTML text
+ *
+ * \param html add html text in the page
+ *
+ */
+ void addHTML(const std::string & html)
+ {
+ injectHTML.last() = html;
+ }
+
+ /*! \brief It write the graphs on file in html format using Google charts
+ *
+ * \param file output file
+ *
+ */
+ void write(std::string file)
+ {
+ // Open a file
+
+ std::ofstream of(file);
+
+ // Check if the file is open
+ if (of.is_open() == false)
+ {std::cerr << "Error cannot create the HTML file: " + file + "\n";}
+
+ // write the file
+
+ of << begin_data;
+
+ for (size_t i = 0 ; i < set_of_graphs.size() ; i++)
+ addData(of,i,set_of_graphs.get(i).data);
+
+ for (size_t i = 0 ; i < set_of_graphs.size() ; i++)
+ addOption(of,i,set_of_graphs.get(i).option);
+
+ for (size_t i = 0 ; i < set_of_graphs.size() ; 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;
+
+ of << injectHTML.get(0);
+
+ for (size_t i = 0 ; i < set_of_graphs.size() ; i++)
+ {
+ addDiv(of,i,set_of_graphs.get(i).opt);
+ of << injectHTML.get(i+1);
+ }
+
+ of << div_end;
+
+ of.close();
+ }
+};
+
+#endif /* OPENFPM_DATA_SRC_PLOT_GOOGLECHART_HPP_ */
diff --git a/src/Plot/Plot_unit_tests.hpp b/src/Plot/Plot_unit_tests.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..3d261ab81c15e1ba675bdec99f9406b26826a761
--- /dev/null
+++ b/src/Plot/Plot_unit_tests.hpp
@@ -0,0 +1,793 @@
+/*
+ * Plot_unit_tests.hpp
+ *
+ * Created on: Jan 9, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_DATA_SRC_PLOT_PLOT_UNIT_TESTS_HPP_
+#define OPENFPM_DATA_SRC_PLOT_PLOT_UNIT_TESTS_HPP_
+
+#include "GoogleChart.hpp"
+#include "Plot/util.hpp"
+
+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;
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/gc_out_sc_test.html");
+
+#else
+
+ std::string c2 = std::string("test_data/gc_out_sc_test.html");
+
+#endif
+
+ //! [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",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+
+BOOST_AUTO_TEST_CASE( google_chart )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/gc_out_test.html");
+
+#else
+
+ std::string c2 = std::string("test_data/gc_out_test.html");
+
+#endif
+
+ //! [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");
+
+ // 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.html");
+
+ //! [Producing an Histogram graph]
+
+ bool test = compare("gc_out.html",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_CASE( google_chart2 )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/gc_out2_test.html");
+
+#else
+
+ std::string c2 = std::string("test_data/gc_out2_test.html");
+
+#endif
+
+ openfpm::vector<std::string> x;
+ openfpm::vector<openfpm::vector<float>> 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({2.2,1.3,4.5,0.6});
+ y.add({5.0,6.1,1.3,2.6});
+ y.add({2.1,1.0,6.1,9.3});
+ y.add({1.1,6.1,3.0,2.0});
+ y.add({3.3,0.3,0.0,6.2});
+ y.add({2.0,1.1,4.0,6.1});
+
+ // 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");
+
+ GoogleChart cg;
+ cg.AddHistGraph(x,y,yn,options);
+ cg.write("gc_out2.html");
+
+ bool test = compare("gc_out2.html",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_CASE( google_chart3 )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/gc_out3_test.html");
+
+#else
+
+ std::string c2 = std::string("test_data/gc_out3_test.html");
+
+#endif
+
+ openfpm::vector<std::string> x;
+ openfpm::vector<openfpm::vector<float>> 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({2.2,1.3,4.5,0.6});
+ y.add({5.0,6.1,1.3,2.6});
+ y.add({2.1,1.0,6.1,9.3});
+ y.add({1.1,6.1,3.0,2.0});
+ y.add({3.3,0.3,0.0,6.2});
+ y.add({2.0,1.1,4.0,6.1});
+
+ // Google charts options
+ GCoptions options;
+
+ options.title = std::string("Example");
+ options.yAxis = std::string("Y Axis");
+ options.xAxis = std::string("X Axis");
+
+ GoogleChart cg;
+ cg.AddHistGraph(x,y,yn,options);
+ cg.write("gc_out3.html");
+
+ bool test = compare("gc_out3.html",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_CASE( google_chart4 )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/gc_out4_test.html");
+
+#else
+
+ std::string c2 = std::string("test_data/gc_out4_test.html");
+
+#endif
+
+ openfpm::vector<std::string> x;
+ openfpm::vector<openfpm::vector<float>> 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({2.2,1.3,4.5,0.6});
+ y.add({5.0,6.1,1.3,2.6});
+ y.add({2.1,1.0,6.1,9.3});
+ y.add({1.1,6.1,3.0,2.0});
+ y.add({3.3,0.3,0.0,6.2});
+ y.add({2.0,1.1,4.0,6.1});
+
+ GoogleChart cg;
+ cg.AddHistGraph(x,y,yn);
+ cg.write("gc_out4.html");
+
+ bool test = compare("gc_out4.html",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_CASE( google_chart5 )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/gc_out5_test.html");
+
+#else
+
+ std::string c2 = std::string("test_data/gc_out5_test.html");
+
+#endif
+
+ openfpm::vector<std::string> x;
+ openfpm::vector<openfpm::vector<float>> y;
+
+ x.add("colum1");
+ x.add("colum2");
+ x.add("colum3");
+ x.add("colum4");
+ x.add("colum5");
+ x.add("colum6");
+
+ // Each colums can have multiple data-set
+ y.add({2.2,1.3,4.5,0.6});
+ y.add({5.0,6.1,1.3,2.6});
+ y.add({2.1,1.0,6.1,9.3});
+ y.add({1.1,6.1,3.0,2.0});
+ y.add({3.3,0.3,0.0,6.2});
+ y.add({2.0,1.1,4.0,6.1});
+
+ GoogleChart cg;
+ cg.AddHistGraph(x,y);
+ cg.write("gc_out5.html");
+
+ bool test = compare("gc_out5.html",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_CASE( google_chart6 )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/gc_out6_test.html");
+
+#else
+
+ std::string c2 = std::string("test_data/gc_out6_test.html");
+
+#endif
+
+ openfpm::vector<openfpm::vector<float>> y;
+
+ // Each colums can have multiple data-set
+ y.add({2.2,1.3,4.5,0.6});
+ y.add({5.0,6.1,1.3,2.6});
+ y.add({2.1,1.0,6.1,9.3});
+ y.add({1.1,6.1,3.0,2.0});
+ y.add({3.3,0.3,0.0,6.2});
+ y.add({2.0,1.1,4.0,6.1});
+
+ GoogleChart cg;
+ cg.AddHistGraph(y);
+ cg.write("gc_out6.html");
+
+ bool test = compare("gc_out6.html",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_CASE( google_chart_with_inject_HTML )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/gc_out7_test.html");
+
+#else
+
+ std::string c2 = std::string("test_data/gc_out7_test.html");
+
+#endif
+
+ //! [Producing a set of histograms graphs]
+
+ 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");
+
+ // it say that the colum4 must me represented with a line
+ options.stypeext = std::string("{3: {type: 'line'}}");
+
+ GoogleChart cg;
+ //
+ cg.addHTML("<h2>Before first graph</h2>");
+ cg.AddHistGraph(x,y,yn,options);
+ cg.addHTML("<h2>Before second graph</h2>");
+ cg.AddHistGraph(x,y,yn,options);
+ cg.addHTML("<h2>Before third graph</h2>");
+ cg.AddHistGraph(x,y,yn,options);
+ cg.addHTML("<h2>At the end</h2>");
+ cg.write("gc_out7.html");
+
+ //! [Producing a set of histograms graphs]
+
+ bool test = compare("gc_out7.html",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_CASE( google_chart_number )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/gc_num_plot_test.html");
+
+#else
+
+ std::string c2 = std::string("test_data/gc_num_plot_test.html");
+
+#endif
+
+ //! [Producing a set of histograms graphs]
+
+ openfpm::vector<float> x;
+ openfpm::vector<openfpm::vector<size_t>> y;
+ openfpm::vector<std::string> yn;
+
+ x.add(0.1);
+ x.add(0.2);
+ x.add(0.3);
+ x.add(0.4);
+ x.add(0.5);
+ x.add(0.6);
+
+ // 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("line");
+
+ GoogleChart cg;
+ //
+ cg.AddLinesGraph(x,y,yn,options);
+ cg.write("gc_num_plot.html");
+
+ //! [Producing a set of histograms graphs]
+
+ bool test = compare("gc_num_plot.html",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_CASE( google_chart_number_lines_different_x )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/gc_num_ydif_plot_test.html");
+
+#else
+
+ std::string c2 = std::string("test_data/gc_num_ydif_plot_test.html");
+
+#endif
+
+ //! [Producing a set of histograms graphs]
+
+ openfpm::vector<float> x1;
+ openfpm::vector<float> y1;
+ openfpm::vector<float> x2;
+ openfpm::vector<float> y2;
+ openfpm::vector<float> x3;
+ openfpm::vector<float> y3;
+ openfpm::vector<std::string> yn;
+
+ x1.add(0.1); y1.add(4.5);
+ x1.add(0.2); y1.add(3.0);
+ x1.add(0.3); y1.add(5.5);
+ x1.add(0.4); y1.add(3.3);
+ x1.add(0.5); y1.add(1.0);
+ x1.add(0.6); y1.add(7.0);
+
+ x2.add(0.15); y2.add(1.5);
+ x2.add(0.2); y2.add(4.5);
+ x2.add(0.35); y2.add(2.5);
+ x2.add(0.45); y2.add(6.5);
+
+ x3.add(0.1); y3.add(3.5);
+ x3.add(0.2); y3.add(6.5);
+ x3.add(0.63); y3.add(1.5);
+ x3.add(0.37); y3.add(1.5);
+ x3.add(0.7); y3.add(3.5);
+ x3.add(0.82); y3.add(2.5);
+ x3.add(0.4); y3.add(2.5);
+ x3.add(1.0); y3.add(1.5);
+ x3.add(0.5); y3.add(7.5);
+ x3.add(0.91); y3.add(5.5);
+
+ // 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");
+
+
+ // 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("line");
+
+ GoogleChart cg;
+
+ cg.AddLines(yn,options,x1,y1,x2,y2,x3,y3);
+ cg.write("gc_num_ydif_plot.html");
+
+ //! [Producing a set of histograms graphs]
+
+ bool test = compare("gc_num_ydif_plot.html",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_CASE( google_chart_linear_plot )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/gc_plot_out_test.html");
+
+#else
+
+ std::string c2 = std::string("test_data/gc_plot_out_test.html");
+
+#endif
+
+ //! [Producing lines graph with style]
+
+ openfpm::vector<std::string> x;
+ openfpm::vector<openfpm::vector<double>> y;
+ openfpm::vector<std::string> yn;
+
+ x.add("colum1");
+ x.add("colum2");
+ x.add("colum3");
+ x.add("colum4");
+ x.add("colum5");
+ x.add("colum6");
+
+ // Here we specify how many lines we have
+ // first Line
+ yn.add("line1");
+
+ // second line + 2 intervals (Error bands)
+ yn.add("line2");
+ yn.add("interval");
+ yn.add("interval");
+ yn.add("interval");
+ yn.add("interval");
+
+ // third line + 1 interval (Error bands)
+ yn.add("line3");
+ yn.add("interval");
+ yn.add("interval");
+
+ // Each line can have multiple intervals or error bars
+ // The first number specify the bottom line
+ // The last three numbers specify the top line + error band (min, max)
+ // The middle 5 line specify the middle lines + one external error band + one internal error band
+
+ y.add({0.10,0.20,0.19,0.22,0.195,0.215,0.35,0.34,0.36});
+ y.add({0.11,0.21,0.18,0.22,0.19,0.215,0.36,0.35,0.37});
+ y.add({0.12,0.22,0.21,0.23,0.215,0.225,0.35,0.34,0.36});
+ y.add({0.15,0.25,0.20,0.26,0.22,0.255,0.36,0.35,0.37});
+ y.add({0.09,0.29,0.25,0.30,0.26,0.295,0.35,0.34,0.36});
+ y.add({0.08,0.28,0.27,0.29,0.275,0.285,0.36,0.35,0.37});
+
+ // Google charts options
+ GCoptions options;
+
+ options.title = std::string("Example");
+ options.yAxis = std::string("Y Axis");
+ options.xAxis = std::string("X Axis");
+ options.lineWidth = 1.0;
+ options.intervalext = std::string("{'i2': { 'color': '#4374E0', 'style':'bars', 'lineWidth':4, 'fillOpacity':1 } }");
+
+ GoogleChart cg;
+ cg.AddLinesGraph(x,y,yn,options);
+ cg.write("gc_plot_out.html");
+
+ //! [Producing lines graph with style]
+
+ bool test = compare("gc_plot_out.html",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_CASE( google_chart_linear_plot2 )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ std::string c2 = std::string("openfpm_io/test_data/gc_plot2_out_test.html");
+
+#else
+
+ std::string c2 = std::string("test_data/gc_plot2_out_test.html");
+
+#endif
+
+ //! [Producing lines]
+
+ openfpm::vector<std::string> x;
+ openfpm::vector<openfpm::vector<double>> y;
+
+ x.add("colum1");
+ x.add("colum2");
+ x.add("colum3");
+ x.add("colum4");
+ x.add("colum5");
+ x.add("colum6");
+
+ // Each line can have multiple intervals or error bars
+ // The first number specify the bottom line
+ // The last three numbers specify the top line + error band (min, max)
+ // The middle 5 line specify the middle lines + one external error band + one internal error band
+
+ y.add({0.10,0.20,0.19,0.22,0.195,0.215,0.35,0.34,0.36});
+ y.add({0.11,0.21,0.18,0.22,0.19,0.215,0.36,0.35,0.37});
+ y.add({0.12,0.22,0.21,0.23,0.215,0.225,0.35,0.34,0.36});
+ y.add({0.15,0.25,0.20,0.26,0.22,0.255,0.36,0.35,0.37});
+ y.add({0.09,0.29,0.25,0.30,0.26,0.295,0.35,0.34,0.36});
+ y.add({0.08,0.28,0.27,0.29,0.275,0.285,0.36,0.35,0.37});
+
+ // Google charts options
+ GCoptions options;
+
+ options.title = std::string("Example");
+ options.yAxis = std::string("Y Axis");
+ options.xAxis = std::string("X Axis");
+ options.lineWidth = 1.0;
+
+ GoogleChart cg;
+ cg.AddLinesGraph(x,y,options);
+ cg.write("gc_plot2_out.html");
+
+ //! [Producing lines]
+
+ bool test = compare("gc_plot2_out.html",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+//! [Definition of a function]
+
+double f(double x)
+{
+ return x*x;
+}
+
+//! [Definition of a function]
+
+BOOST_AUTO_TEST_CASE( plot_util )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+ //! [fill a vector]
+
+ openfpm::vector<double> x;
+
+ Fill1D(0.0,2.0,5,x);
+
+ BOOST_REQUIRE_EQUAL(x.get(0),0.0);
+ BOOST_REQUIRE_EQUAL(x.get(1),0.5);
+ BOOST_REQUIRE_EQUAL(x.get(2),1.0);
+ BOOST_REQUIRE_EQUAL(x.get(3),1.5);
+ BOOST_REQUIRE_EQUAL(x.get(4),2.0);
+
+ //! [fill a vector]
+
+ x.clear();
+
+ //! [fill a vector with a function]
+
+ Fill1D(0.0,2.0,5,x,f);
+
+ BOOST_REQUIRE_EQUAL(x.get(0),0.0);
+ BOOST_REQUIRE_EQUAL(x.get(1),0.25);
+ BOOST_REQUIRE_EQUAL(x.get(2),1.0);
+ BOOST_REQUIRE_EQUAL(x.get(3),2.25);
+ BOOST_REQUIRE_EQUAL(x.get(4),4.0);
+
+ //! [fill a vector function]
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+
+#endif /* OPENFPM_DATA_SRC_PLOT_PLOT_UNIT_TESTS_HPP_ */
diff --git a/src/Plot/util.hpp b/src/Plot/util.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..b9a53c529877493353f35f4e9f56d030e2425ba4
--- /dev/null
+++ b/src/Plot/util.hpp
@@ -0,0 +1,45 @@
+/*
+ * util.hpp
+ *
+ * Created on: Feb 23, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_PLOT_UTIL_HPP_
+#define OPENFPM_IO_SRC_PLOT_UTIL_HPP_
+
+/*! \brief It fill the vector x with function values
+ *
+ * ### Define a function
+ * \snippet Plot_unit_tests.hpp Definition of a function
+ * ### Example vector with points on a specified range
+ * \snippet Plot_unit_tests.hpp fill a vector with a function
+ *
+ */
+template<typename T> static inline void Fill1D(T start, T stop, size_t np, openfpm::vector<T> & x,T f(T x))
+{
+ x.resize(np);
+
+ T spacing = (stop - start) / (np - 1);
+
+ for (size_t i = 0 ; i < np ; i++)
+ x.get(i) = f(start + i*spacing);
+}
+
+/*! \brief It fill the vector x with uniformly distributed set of points
+ *
+ * ### Example vector with points on a specified range
+ * \snippet Plot_unit_tests.hpp fill a vector
+ *
+ */
+template<typename T> static inline void Fill1D(T start, T stop, size_t np, openfpm::vector<T> & x)
+{
+ x.resize(np);
+
+ T spacing = (stop - start) / (np - 1);
+
+ for (size_t i = 0 ; i < np ; i++)
+ x.get(i) = start + i*spacing;
+}
+
+#endif /* OPENFPM_IO_SRC_PLOT_UTIL_HPP_ */
diff --git a/src/RawReader/InitGridWithPixel.hpp b/src/RawReader/InitGridWithPixel.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..c4acf96ca9c9cc3451b05fa8348cfcdcbe690fb3
--- /dev/null
+++ b/src/RawReader/InitGridWithPixel.hpp
@@ -0,0 +1,190 @@
+//
+// Created by jstark on 2019-11-07.
+//
+/**
+ * @file InitGridWithPixel.hpp
+ *
+ * @brief Header file containing functions for loading pixel values from 2D image or 3D image stack (volume) stored
+ * in a binary file onto an openFPM grid.
+ *
+ * @details Can be run in parallel.
+ *
+ * @author Justina Stark & Pietro Incardona
+ * @date November 2019 - August 2020
+ */
+#ifndef IMAGE_BASED_RECONSTRUCTION_GETINITIALGRID_HPP
+#define IMAGE_BASED_RECONSTRUCTION_GETINITIALGRID_HPP
+
+#include <iostream>
+#include <typeinfo>
+#include <cmath>
+#include <sys/stat.h>
+
+#include "Vector/vector_dist.hpp"
+#include "Grid/grid_dist_id.hpp"
+#include "data_type/aggregate.hpp"
+#include "Decomposition/CartDecomposition.hpp"
+
+#include "level_set/redistancing_Sussman/HelpFunctionsForGrid.hpp"
+typedef signed char BYTE;
+
+inline bool exists_test (const std::string& name) {
+ struct stat buffer;
+ return (stat (name.c_str(), &buffer) == 0);
+}
+
+
+
+/**@brief Read the number of pixels per dimension from a csv-file in order to create a grid with the same size.
+ *
+ * @param path_to_file Std::string containing the path to the csv file that holds the image/volume size in
+ * #pixels per dimension.
+ * @return Std::vector containing the count of pixels for each dimension as it was read from the csv file.
+ */
+std::vector<int> get_size(const std::string & path_to_file)
+{
+ std::vector<int> stack_dimst_1d;
+ // check if file exists and stream input csv file
+ if(!exists_test(path_to_file)){
+ std::cout << "------------------------------------------------------------------------" << std::endl;
+ std::cout << "Error: file " << path_to_file << " does not exist. Aborting..." << std::endl;
+ std::cout << "------------------------------------------------------------------------" << std::endl;
+ abort();
+ }
+ std::ifstream file(path_to_file);
+
+
+ // get its size
+ std::streampos fileSize;
+ file.seekg(0, std::ios::end);
+ fileSize = file.tellg();
+ file.seekg(0, std::ios::beg);
+
+ // reserve capacity
+ stack_dimst_1d.reserve(fileSize);
+
+ std::string field;
+ while ( getline(file, field) ) // 1 field per axis
+ {
+ std::istringstream iss(field);
+ int val;
+ iss >> val;
+ stack_dimst_1d.push_back(val); // add the #pixels for current axis to the array
+ }
+
+ // reverse order to compensate reverse reading
+ std::reverse(std::begin(stack_dimst_1d), std::end(stack_dimst_1d));
+
+ return stack_dimst_1d;
+}
+
+
+/**@brief Converts the pixel values stored in a binary file into doubles and loads them onto an OpenFPM grid.
+ *
+ * @tparam Phi_0 Index of property in which pixel value should be stored.
+ * @tparam grid_type Type of OpenFPM grid.
+ * @param grid Grid of type grid_type, on which image / image-stack should be loaded.
+ * @param file_name Std::string containing the path + name of the binary file that stores the pixel values.
+ * @param stack_dims Size_t variable that contains the dimensionality of the image / image stack. Can be given
+ * manually or loaded from a csv file before (see: #get_size())
+ */
+template <size_t Phi_0, typename grid_type>
+void load_pixel_onto_grid(grid_type & grid, std::string file_name, std::vector <int> & stack_dims)
+{
+ constexpr size_t x = 0;
+ constexpr size_t y = 1;
+ constexpr size_t z = 2;
+
+ // check if file exists and stream input file
+ if(!exists_test(file_name)){
+ std::cout << "------------------------------------------------------------------------" << std::endl;
+ std::cout << "Error: file " << file_name << " does not exist. Aborting..." << std::endl;
+ std::cout << "------------------------------------------------------------------------" << std::endl;
+ abort();
+ }
+ std::ifstream file_stream (file_name, std::ifstream::binary);
+
+ auto & v_cl = create_vcluster();
+ if (v_cl.rank() == 0)
+ {
+ for (int d = 0; d < grid_type::dims; d++)
+ {
+ std::cout << "# grid points in dimension " << d << " = " << grid.size(d) << std::endl;
+ }
+ }
+
+ // assign pixel values to domain. For each pixel get factor_refinement number of grid points with corresponding value
+ auto dom = grid.getDomainIterator();
+ std::vector<BYTE> pixel_line; // one x-line of the image stack which will be read
+
+ size_t sz_img[grid_type::dims];
+ for (int d = 0; d < grid_type::dims; d++)
+ {
+ sz_img[d] = stack_dims[d];
+ }
+ grid_sm<grid_type::dims,void> ginfo_image(sz_img); // in order to get the image related key later on
+
+ double refinement[grid_type::dims];
+ for (int d = 0; d < grid_type::dims; d++)
+ {
+ refinement[d] = (double) grid.size(d) / (double)stack_dims[d]; // get the factor, by which the grid resolution differs from the image stack resolution
+ if (v_cl.rank() == 0) std::cout << "effective refinement in dimension " << d << " = " << refinement[d] << std::endl;
+ }
+
+ while(dom.isNext())
+ {
+ auto key = dom.get();
+ auto gkey = grid.getGKey(key);
+
+ // In case a patch starts within a group of nodes to which same pixel-value should be assigned, get the
+ // respective rest-offset
+ int rest_offset = (int) (fmod(gkey.get(0), refinement[x])); // get the remainder
+
+
+ // get l as the length of one x-line of the original image stack for the specific patch on the processor
+ auto & gbox = grid.getLocalGridsInfo();
+ auto & DomBox = gbox.get(key.getSub()).Dbox;
+ size_t patch_size = DomBox.getHigh(0) - DomBox.getLow(0) + 1;
+
+ size_t l = (size_t) ceil( (patch_size + rest_offset) / refinement[x]);
+
+ // in case that the grid has a different resolution than the underlying image stack:
+ // create a key which is used to get the offset for the file reading
+ // the indices in this key are corrected by the refinement factor
+ for (int d = 0; d < grid_type::dims; d++)
+ {
+ gkey.set_d(d, floor(gkey.get(d) / refinement[d]));
+ }
+
+ // the offset matches the pixel from the image stack to the corresponding current position of the iterator
+ // in the grid
+ size_t offset = ginfo_image.LinId(gkey);
+ file_stream.seekg(offset); // jump to the correct position in the file
+
+ // prepare space for the pixel values of one x-line in the original image stack
+ pixel_line.resize(l);
+ // stream the file and fill pixel values into pixel_line
+ file_stream.read((char*) & pixel_line[0], l);
+
+ // run over a whole grid-line in x and assign pixel values from pixel_line to grid nodes
+ // if the grid is finer in x as the image stack, the same pixel value from pixel_line is
+ // assigned refinement[x] times
+ for (int k = 0; k < patch_size; ++k)
+ {
+ auto key = dom.get();
+ // get the correct index of the pixel to be read from pixel_line by considering a potential rest-offset,
+ // when the patch divides group of nodes that belong to the same pixel
+ size_t i = (size_t) floor((k + rest_offset) / refinement[x]);
+ grid.template get<Phi_0>(key) = (double) pixel_line[i];
+ ++dom;
+ }
+ // now one grid line in x is finished and the iterator dom has advanced accordingly s.t. next loop continues
+ // with next line, meaning that y increased by 1 (or z respectivley, when y = ymax + 1)
+ }
+
+ grid.template ghost_get<Phi_0>();
+}
+
+
+
+#endif //IMAGE_BASED_RECONSTRUCTION_GETINITIALGRID_HPP
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..97443d04eadb4608b7b488ebe6bcfff826698eef
--- /dev/null
+++ b/src/RawReader/RawReader_unit_tests.hpp
@@ -0,0 +1,64 @@
+/*
+ * 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;
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/raw_read_sv_test.bin");
+
+#else
+
+ std::string c2 = std::string("test_data/raw_read_sv_test.bin");
+
+#endif
+
+ grid_cpu<3,aggregate<float,float[3]>> read_bin_test;
+
+ GridRawReader<3,aggregate<float,float[3]>,int> rr;
+
+#ifndef SE_CLASS3
+
+ rr.read(c2,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;
+ }
+
+#endif
+}
+
+
+
+BOOST_AUTO_TEST_SUITE_END()
+
+#endif /* OPENFPM_DATA_SRC_PLOT_PLOT_UNIT_TESTS_HPP_ */
diff --git a/src/SparseGridGpu/SparseGridGpu.hpp b/src/SparseGridGpu/SparseGridGpu.hpp
index 00a31a272a0d8a56fc5e333fbbab9bb64b2cdc67..1d6f32b7a979ed16d4ac0eb067116432de165d96 100644
--- a/src/SparseGridGpu/SparseGridGpu.hpp
+++ b/src/SparseGridGpu/SparseGridGpu.hpp
@@ -718,6 +718,8 @@ public:
typedef sparse_grid_gpu_index<self> base_key;
+ typedef indexT indexT_;
+
typedef decltype(std::declval<BMG>().toKernel().insertBlock(0)) insert_encap;
/*! \brief return the size of the grid
@@ -2775,12 +2777,37 @@ public:
typedef BlockMapGpu<AggregateInternalT, threadBlockSize, indexT, layout_base> BMG;
- auto block_data = this->insertBlockFlush(block_id);
+ auto block_data = BlockMapGpu<AggregateInternalT, threadBlockSize, indexT, layout_base>::insertBlockFlush(block_id);
block_data.template get<BMG::pMask>()[local_id] = 1;
return block_data.template get<p>()[local_id];
}
+ /*! \brief Insert the point on host side and flush directly
+ *
+ * First you have to move everything on host with deviceToHost, insertFlush and than move to GPU again
+ *
+ * \param grid point where to insert
+ *
+ * \return a reference to the data to fill
+ *
+ *
+ */
+ template<typename CoordT>
+ auto insertBlockFlush(const grid_key_dx<dim,CoordT> &coord, indexT & local_id) -> decltype(BlockMapGpu<AggregateInternalT, threadBlockSize, indexT, layout_base>::insertBlockFlush(0))
+ {
+ auto lin = gridGeometry.LinId(coord);
+ indexT block_id = lin / blockSize;
+ local_id = lin % blockSize;
+
+ typedef BlockMapGpu<AggregateInternalT, threadBlockSize, indexT, layout_base> BMG;
+
+ auto block_data = BlockMapGpu<AggregateInternalT, threadBlockSize, indexT, layout_base>::insertBlockFlush(block_id);
+ block_data.template get<BMG::pMask>()[local_id] = 1;
+
+ return block_data;
+ }
+
/*! \brief Insert the point on host side and flush directly
*
* First you have to move everything on host with deviceToHost, insertFlush and than move to GPU again
@@ -2801,7 +2828,7 @@ public:
typedef BlockMapGpu<AggregateInternalT, threadBlockSize, indexT, layout_base> BMG;
- auto block_data = this->insertBlockFlush(block_id);
+ auto block_data = BlockMapGpu<AggregateInternalT, threadBlockSize, indexT, layout_base>::insertBlockFlush(block_id);
block_data.template get<BMG::pMask>()[local_id] = 1;
return block_data.template get<p>()[local_id];
diff --git a/src/TiffWriter.hpp b/src/TiffWriter.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..241eef6e79cecaa6f70ee9fdcbe180001a783d26
--- /dev/null
+++ b/src/TiffWriter.hpp
@@ -0,0 +1,111 @@
+#ifndef TIFFWRITER_HPP
+#define TIFFWRITER_HPP
+
+#include <iostream>
+#include "tiffio.h"
+#include "map_grid.hpp"
+#include <string>
+
+/*! \brief This class is able to save grid into tiff files
+ *
+ * This class is able to save grid into tiff files
+ *
+ */
+
+template<unsigned int dim, typename T>
+class TiffWriter
+{
+ /*! \brief Save grid into tiff files
+ *
+ * Save grid into tiff files
+ *
+ */
+
+ template<typename grid, typename Mem> int write(grid data, std::string file)
+ {
+ // Grid can have several properties we can save only scalar fields
+ // for each properties save one scalar fields
+
+ // Tiff files can be saved up to 5D
+
+ if (dim > 5)
+ {
+ std::cerr << "Error Tiff writer support until 5D images" << "\n";
+ }
+
+ // Open the tiff image
+
+ uint32 width;
+ uint32 height;
+ TIFF *tif = TIFFOpen(file.c_str(),"w");
+
+ // if the file is open
+
+ if(tif)
+ {
+ // set width and height for 2D
+
+ width = data.getGrid().size(0);
+ height = data.getGrid().size(1);
+
+ TIFFSetField(tif,TIFFTAG_IMAGEWIDTH, &width);
+ TIFFSetField(tif,TIFFTAG_IMAGELENGTH, &height);
+
+ // Create the tiff line, in case the grid is CPU, we have only
+ // one property and is a scalar, we can directly copy the line
+
+ typename boost::fusion::result_of::at<T::type,0>::type first_element_type;
+
+ if (typeid(grid).name() == "grid_cpu" && T::num_prop == 1 && boost::is_array<first_element_type>::type::value == true)
+ {
+ // Get the grid key iterator
+
+ grid_key_dx_iterator<dim> key = data.getIterator();
+
+ // write all lines
+
+ for(int i = 0; i < height ; i++)
+ {
+ // select the correct lines
+
+ key.set(1,i);
+
+ // we have only one scalar properties, get the buffer pointer
+ void * buf = &data.template get<0>(key);
+
+ TIFFWriteScanline(tif,buf,i, 0);
+ }
+ }
+ else
+ {
+ // we have to create the a scan line for each properties and index array
+ // each property and index array became a channel
+
+ // Get the grid key iterator
+
+ grid_key_dx_iterator<dim> key = data.getIterator();
+
+ // count how many properties and how many indexes we have
+
+ const int n_prp = total_prop<T>;
+
+ // write all lines
+
+ for(int i = 0; i < height ; i++)
+ {
+ // select the correct lines
+
+ key.set(1,i);
+
+ // we have only one scalar properties, get the buffer pointer
+ void * buf = &data.template get<0>(key);
+
+ TIFFWriteScanline(tif,buf,i, 0);
+ }
+ }
+ }
+ }
+
+};
+
+#endif
diff --git a/src/VTKWriter/VTKWriter.hpp b/src/VTKWriter/VTKWriter.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..a5bfcd5bca4fcd12a7b38f37bb8474e2dd7326f6
--- /dev/null
+++ b/src/VTKWriter/VTKWriter.hpp
@@ -0,0 +1,164 @@
+/*
+ * VTKWriter.hpp
+ *
+ * Created on: Dec 15, 2014
+ * Author: Pietro Incardona
+ */
+
+#ifndef VTKWRITER_HPP_
+#define VTKWRITER_HPP_
+
+#include "Graph/map_graph.hpp"
+#include <iostream>
+#include <boost/fusion/include/mpl.hpp>
+#include <boost/fusion/include/for_each.hpp>
+#include <fstream>
+#include "util/common.hpp"
+
+/*! \brief Get the type Old
+ *
+ * It convert T to a string identify the corrispondent type in VTK format
+ *
+ */
+
+template <typename T> std::string getType()
+{
+ // Create a property string based on the type of the property
+ if (std::is_same<T,float>::value)
+ return "float";
+ else if (std::is_same<T,double>::value)
+ return "double";
+ else if (std::is_same<T,char>::value)
+ return "char";
+ else if (std::is_same<T,unsigned char>::value)
+ return "unsigned_char";
+ else if (std::is_same<T,short>::value)
+ return "short";
+ else if (std::is_same<T,unsigned short>::value)
+ return "unsigned_short";
+ else if (std::is_same<T,int>::value)
+ return "int";
+ else if (std::is_same<T,unsigned int>::value)
+ return "unsigned_int";
+ else if (std::is_same<T,long int>::value)
+ return "int";
+ else if (std::is_same<T,unsigned long int>::value )
+ return "unsigned_int";
+ else if (std::is_same<T,bool>::value )
+ return "bit";
+
+ return "";
+}
+
+
+
+/*! \brief Get the type
+ *
+ * It convert T to a string identify the corrispondent type in VTK format
+ *
+ */
+
+template <typename T> std::string getTypeNew()
+{
+ // Create a property string based on the type of the property
+ if (std::is_same<T,float>::value)
+ return "Float32";
+ else if (std::is_same<T,double>::value)
+ return "Float64";
+ else if (std::is_same<T,char>::value)
+ return "Int8";
+ else if (std::is_same<T,unsigned char>::value)
+ return "Uint8";
+ else if (std::is_same<T,short>::value)
+ return "Int16";
+ else if (std::is_same<T,unsigned short>::value)
+ return "Uint16";
+ else if (std::is_same<T,int>::value)
+ return "Int32";
+ else if (std::is_same<T,unsigned int>::value)
+ return "Uint32";
+ else if (std::is_same<T,long int>::value)
+ return "Int64";
+ else if (std::is_same<T,unsigned long int>::value )
+ return "Uint64";
+ else if (std::is_same<T,bool>::value )
+ return "Int8";
+
+ return "";
+}
+
+/*! \brief Set a conversion map between A and B
+ *
+ * Convert A to B
+ *
+ * \tparam B destination type
+ * \tparam A source type
+ *
+ */
+
+template<typename A>
+class convert
+{
+public:
+ template<typename B> static B to(const A & data)
+ {
+ return static_cast<B>(data);
+ }
+};
+
+/*! \brief Partial specialization when A is a string
+ *
+ *
+ */
+
+template<>
+class convert<std::string>
+{
+public:
+ template<typename B> static B to(const std::string & data)
+ {
+ return atof(data.c_str());
+ }
+};
+
+/*! \brief It specify the VTK output file type
+ *
+ */
+
+enum file_type
+{
+ BINARY,
+ ASCII
+};
+
+#define VTK_GRAPH 1
+#define VECTOR_BOX 2
+#define VECTOR_GRIDS 3
+#define VECTOR_ST_GRIDS 4
+#define DIST_GRAPH 5
+#define VECTOR_POINTS 6
+#define VTK_WRITER 0x10000
+#define FORMAT_ASCII 0x0
+#define FORMAT_BINARY 0x10000000
+#define PRINT_GHOST 1
+
+template <typename Object, unsigned int imp>
+class VTKWriter
+{
+
+};
+
+#include "VTKWriter_graph.hpp"
+#include "VTKWriter_vector_box.hpp"
+#include "VTKWriter_grids.hpp"
+#include "VTKWriter_grids_st.hpp"
+
+// This is only active if MPI compiler work
+
+#ifndef DISABLE_MPI_WRITTERS
+#include "VTKWriter_dist_graph.hpp"
+#endif
+
+#include "VTKWriter_point_set.hpp"
+
+#endif /* VTKWRITER_HPP_ */
diff --git a/src/VTKWriter/VTKWriter_dist_graph.hpp b/src/VTKWriter/VTKWriter_dist_graph.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..b059be9336c3135d857fd35e194d8475801fe3d4
--- /dev/null
+++ b/src/VTKWriter/VTKWriter_dist_graph.hpp
@@ -0,0 +1,1289 @@
+/*
+ * VTKWriter_graph.hpp
+ *
+ * Created on: May 5, 2015
+ * Author: Pietro Incardona
+ */
+
+#ifndef VTKWRITER_DIST_GRAPH_HPP_
+#define VTKWRITER_DIST_GRAPH_HPP_
+
+#include "VCluster/VCluster.hpp"
+
+/*! Property data store for scalar and vector
+ *
+ */
+template<bool is_array>
+struct vtk_dist_vertex_node_array_scalar_selector
+{
+ /*! /brief Print the geometric informations in case it is not an array
+ *
+ * \tparam T Type of the vertex
+ * \tparam ele_v Attribute element to check
+ * \tparam G Graph of reference
+ * \tparam s_type Vertex spatial type information
+ *
+ * \param vo Vertex object container
+ * \param x Array to store geometric informations
+ * \param z_set Value set to true id z axis is in use
+ */
+ template<typename T, typename ele_v, typename G, typename s_type>
+ static inline void move(typename G::V_container &vo, s_type (&x)[3], bool &z_set)
+ {
+ if (G::V_type::attributes::name[T::value] == "x")
+ {
+ x[0] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>())>::type>::template to<s_type>(vo.template get<T::value>());
+ }
+ else if (G::V_type::attributes::name[T::value] == "y")
+ {
+ x[1] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>())>::type>::template to<s_type>(vo.template get<T::value>());
+ }
+ else if (G::V_type::attributes::name[T::value] == "z")
+ {
+ x[2] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>())>::type>::template to<s_type>(vo.template get<T::value>());
+ z_set = true;
+ }
+ }
+};
+
+/*! Template specialization in the case of array type attribute
+ *
+ */
+template<>
+struct vtk_dist_vertex_node_array_scalar_selector<true>
+{
+ /*! \brief Store the geometric informations in case it is an array
+ *
+ * \tparam T Type of the vertex
+ * \tparam ele_v Attribute element to check
+ * \tparam G Graph of reference
+ * \tparam s_type Vertex spatial type information
+ *
+ * \param vo Vertex object container
+ * \param x Array to store geometric informations
+ * \param z_set Value set to true id z axis is in use
+ */
+ template<typename T, typename ele_v, typename G, typename s_type>
+ static inline void move(typename G::V_container &vo, s_type (&x)[3], bool &z_set)
+ {
+ if (std::extent<ele_v>::value == 3)
+ z_set = true;
+
+ for (size_t i = 0; i < std::extent<ele_v>::value; i++)
+ x[i] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>()[i])>::type>::template to<s_type>(vo.template get<T::value>()[i]);
+
+ }
+};
+
+/*! \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 create a string containing all the vertex
+ * properties
+ *
+ * \tparam G graph type
+ * \tparam attr has the vertex attributes
+ *
+ */
+
+template<typename G, bool attr>
+struct vtk_dist_vertex_node
+{
+ //! Vertex spatial type information
+ typedef typename G::V_type::s_type s_type;
+
+ //! indicate if the z coordinate has been set
+ bool z_set;
+
+ //! coordinate of the vertex node
+ s_type (&x)[3];
+
+ //! Vertex object container
+ typename G::V_container & vo;
+
+ //! vertex position converted to string
+ std::string & v_node;
+
+ /*! \brief Constructor
+ *
+ * Create a vertex properties list
+ *
+ * \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 position of the vertex
+ *
+ */
+ vtk_dist_vertex_node(std::string & v_node, typename G::V_container & n_obj, s_type (&x)[3])
+ :z_set(false),x(x), vo(n_obj), v_node(v_node)
+ {
+ }
+
+ //! \brief Write collected information
+ void write()
+ {
+ v_node += std::to_string(x[0]) + " " + std::to_string(x[1]) + " " + std::to_string(x[2]) + "\n";
+ }
+
+ /*! \brief It call the functor for each attribute
+ *
+ * \param t attribute id
+ *
+ */
+ template<typename T>
+ void operator()(T& t)
+ {
+ typedef typename boost::mpl::at<typename G::V_type::type, boost::mpl::int_<T::value>>::type ele_v;
+
+ // if the attribute name is x y or z, create a string with the value of the properties and store it
+
+ vtk_dist_vertex_node_array_scalar_selector<std::is_array<ele_v>::value>::template move<T, ele_v, G, s_type>(vo, x, z_set);
+
+ }
+};
+
+/*! \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 create a string containing all the vertex
+ * properties
+ *
+ * Specialization when we do not have vertex attributes
+ *
+ * \tparam G graph type
+ *
+ */
+
+template<typename G>
+struct vtk_dist_vertex_node<G, false>
+{
+ //! Vertex object container
+ typename G::V_container & vo;
+
+ //! vertex position string
+ std::string & v_node;
+
+ /*! \brief Constructor
+ *
+ * Create a vertex properties list
+ *
+ * \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<...>
+ *
+ */
+ vtk_dist_vertex_node(std::string & v_node, typename G::V_container & n_obj) :
+ vo(n_obj), v_node(v_node)
+ {
+ }
+
+ /*! \brief It call the functor for each attribute
+ *
+ * \param t attribute id
+ *
+ */
+ template<typename T>
+ void operator()(T& t)
+ {
+ v_node += "0 0 0\n";
+ }
+};
+
+/*! \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 create a string containing all the edge
+ * properties
+ *
+ */
+
+template<typename G>
+struct vtk_dist_edge_node
+{
+ //! Vertex object container
+ typename G::E_container & vo;
+
+ //! edge node string
+ std::string & e_node;
+
+ /*! \brief Constructor
+ *
+ * Create an 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<...>
+ *
+ */
+ vtk_dist_edge_node(std::string & e_node, typename G::E_container & n_obj)
+ :vo(n_obj), e_node(e_node)
+ {
+ }
+
+ /*! \brief Create an edge
+ *
+ * \param vc node id
+ * \param s source node
+ * \param d destination node
+ *
+ */
+ void new_node(size_t vc, size_t s, size_t d)
+ {
+ // start a new node
+ e_node += "2 " + std::to_string(s) + " " + std::to_string(d) + "\n";
+ }
+};
+
+/*! \brief Property writer for scalar and vector
+ *
+ */
+template<bool is_array>
+struct dist_prop_output_array_scalar_selector_vertex
+{
+ /*! \brief Writer in case the property is not an array
+ *
+ * \tparam ele_v Property element
+ * \tparam Graph Graph of reference
+ * \tparam i Property id
+ *
+ * \param v_out Buffer to write into
+ * \param g Graph
+ * \param p Property id
+ */
+ template<typename ele_v, typename Graph, unsigned int i>
+ static inline void write(std::string &v_out, const Graph &g, size_t p)
+ {
+ v_out += std::to_string(g.vertex(p).template get<i>()) + "\n";
+ }
+};
+
+/*! \brief Property writer for vector
+ *
+ */
+template<>
+struct dist_prop_output_array_scalar_selector_vertex<true>
+{
+ /*! \brief Writer in case the property is an array
+ *
+ * \tparam ele_v Property element
+ * \tparam Graph Graph of reference
+ * \tparam i Property id
+ *
+ * \param v_out Buffer to write into
+ * \param g Graph
+ * \param p Property id
+ */
+ template<typename ele_v, typename Graph, unsigned int i>
+ static inline void write(std::string &v_out, const Graph &g, size_t p)
+ {
+ for (size_t j = 0; j < 2; j++)
+ {
+ v_out += std::to_string(g.vertex(p).template get<i>()[j]) + " ";
+ }
+
+ if (std::extent<ele_v>::value == 2)
+ v_out += "0";
+ else
+ v_out += std::to_string(g.vertex(p).template get<i>()[2]);
+
+ v_out += "\n";
+ }
+};
+
+/*! \brief Property writer for scalar and vector
+ *
+ */
+template<bool is_array>
+struct dist_prop_output_array_scalar_selector_edge
+{
+ /*! \brief Writer in case the property is not an array
+ *
+ * \tparam ele_v Property element
+ * \tparam Graph Graph of reference
+ * \tparam i Property id for the edge
+ *
+ * \param v_out Buffer to write into
+ * \param g Graph
+ * \param edge edge object
+ */
+ 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)
+ {
+ v_out += std::to_string(edge.template get<i>()) + "\n";
+ }
+};
+
+/*! \brief Property writer for vector
+ *
+ */
+template<>
+struct dist_prop_output_array_scalar_selector_edge<true>
+{
+ /*! \brief Writer in case the property is an array
+ *
+ * \tparam ele_v Property element
+ * \tparam Graph Graph of reference
+ * \tparam i Property id
+ *
+ * \param v_out Buffer to write into
+ * \param g Graph
+ * \param edge edge object
+ */
+ 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)
+ {
+ for (size_t j = 0; j < 2; j++)
+ {
+ v_out += std::to_string(edge.template get<i>()[j]) + " ";
+ }
+
+ if (std::extent<ele_v>::value == 2)
+ v_out += "0";
+ else
+ v_out += std::to_string(edge.template get<i>()[2]);
+
+ v_out += "\n";
+ }
+};
+
+/*! \brief Property writer for scalar and vector, it fill the vertex data (needed for edge representation in vtk)
+ *
+ */
+template<bool is_array>
+struct dist_prop_output_array_scalar_selector_edge_fill_vertex
+{
+ /*! \brief Writer in case the property is not an array
+ *
+ * \param v_out Buffer to write into
+ */
+ static inline void write(std::string &v_out)
+ {
+ v_out += "0\n";
+ }
+};
+
+/*! \brief Property writer for vector
+ *
+ */
+template<>
+struct dist_prop_output_array_scalar_selector_edge_fill_vertex<true>
+{
+ /*! \brief Writer in case the property is an array
+ *
+ * \param v_out Buffer to write into
+ */
+ static inline void write(std::string &v_out)
+ {
+ v_out += "0 0 0\n";
+ }
+};
+
+/*! \brief This class specialize functions in the case the type T
+ * has or not defined attributes
+ *
+ * In C++ partial specialization of a function is not allowed so we have to
+ * encapsulate this function in a class
+ *
+ * \tparam has_attributes parameter that specialize the function in case the vertex
+ * define or not attributes name
+ *
+ * \tparam Graph type of graph we are processing
+ * \tparam i the property we are going to write
+ *
+ */
+
+template<bool has_attributes, typename Graph, unsigned int i>
+class dist_prop_output
+{
+public:
+
+ /*! \brief For each vertex set the value
+ *
+ *
+ * \param g graph to output
+ *
+ * \return get the point data string
+ *
+ */
+ static std::string get_point_data(const Graph & g)
+ {
+ //! vertex node output string
+ std::string v_out;
+
+ //! Get a vertex iterator
+ auto it = g.getVertexIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ typedef typename boost::mpl::at<typename Graph::V_type::type, boost::mpl::int_<i>>::type ele_v;
+ dist_prop_output_array_scalar_selector_vertex<std::is_array<ele_v>::value>::template write<ele_v, Graph, i>(v_out, g, it.get());
+
+ // increment the iterator and counter
+ ++it;
+ }
+
+ return v_out;
+ }
+
+ /*! \brief For each edge set the value, set 1 on vertices, needed by vtk file format
+ *
+ * \param g graph to output
+ *
+ * \return the cell-data string
+ *
+ */
+
+ static std::string get_cell_data(const Graph & g)
+ {
+ //! vertex node output string
+ std::string e_out;
+
+ //! Get a vertex iterator
+ auto it_v = g.getVertexIterator();
+
+ // if there is the next element
+ while (it_v.isNext())
+ {
+ // Print the property
+ typedef typename boost::mpl::at<typename Graph::E_type::type, boost::mpl::int_<i>>::type ele_v;
+ dist_prop_output_array_scalar_selector_edge_fill_vertex<std::is_array<ele_v>::value>::write(e_out);
+
+ // increment the iterator and counter
+ ++it_v;
+ }
+
+ //! Get an edge iterator
+ auto it_e = g.getEdgeIterator();
+
+ // if there is the next element
+ while (it_e.isNext())
+ {
+ typedef typename boost::mpl::at<typename Graph::E_type::type, boost::mpl::int_<i>>::type ele_v;
+ dist_prop_output_array_scalar_selector_edge<std::is_array<ele_v>::value>::template write<ele_v, Graph, i>(e_out, g, g.edge(it_e.get()));
+
+ // increment the iterator and counter
+ ++it_e;
+ }
+
+ return e_out;
+ }
+
+ /*! \brief Given a Graph return the point data header for a typename T
+ *
+ * \param prop property id
+ *
+ * \return the string with the property header
+ *
+ */
+ static std::string get_point_property_header(size_t prop)
+ {
+ //! vertex node output string
+ std::string v_out;
+
+ // Type of the property
+ std::string type;
+
+ typedef typename boost::mpl::at<typename Graph::V_type::type, boost::mpl::int_<i>>::type T;
+
+ // Check if T is a supported format
+ // for now we support only scalar of native type
+ if (std::is_array<T>::value == true && std::is_array<typename std::remove_extent<T>::type>::value == false)
+ {
+ //Get type of the property
+ type = getType<typename std::remove_all_extents<T>::type>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ return v_out;
+
+ // Create point data properties
+ v_out += "VECTORS " + get_attributes_vertex() + " " + type + "\n";
+ }
+ else
+ {
+ type = getType<T>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ return v_out;
+
+ // Create point data properties
+ v_out += "SCALARS " + get_attributes_vertex() + " " + type + "\n";
+
+ // Default lookup table
+ v_out += "LOOKUP_TABLE default\n";
+
+ }
+
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Given a Graph return the cell data header for a typename T
+ *
+ * \param prop property number
+ *
+ * \return the cell string header
+ *
+ */
+ static std::string get_cell_property_header(size_t prop)
+ {
+ //! edge node output string
+ std::string e_out;
+
+ // Type of the property
+ std::string type;
+
+ typedef typename boost::mpl::at<typename Graph::E_type::type, boost::mpl::int_<i>>::type T;
+
+ // Check if T is a supported format
+ // for now we support only scalar of native type
+ if (std::is_array<T>::value == true && std::is_array<typename std::remove_extent<T>::type>::value == false)
+ {
+ //Get type of the property
+ type = getType<typename std::remove_all_extents<T>::type>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ return e_out;
+
+ // Create point data properties
+ e_out += "VECTORS " + get_attributes_edge() + " " + type + "\n";
+ }
+ else
+ {
+ type = getType<T>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ return e_out;
+
+ // Create point data properties
+ e_out += "SCALARS " + get_attributes_edge() + " " + type + "\n";
+
+ // Default lookup table
+ e_out += "LOOKUP_TABLE default\n";
+
+ }
+
+ // return the vertex list
+ return e_out;
+ }
+
+ /*! \brief Get the attributes name for vertex
+ *
+ * \return string with the attribute name
+ *
+ */
+ static std::string get_attributes_vertex()
+ {
+ return Graph::V_type::attributes::name[i];
+ }
+
+ /*! \brief Get the attributes name for edge
+ *
+ * \return the attribute name for the edge
+ *
+ */
+ static std::string get_attributes_edge()
+ {
+ return Graph::E_type::attributes::name[i];
+ }
+};
+
+/*! \brief This class specialize functions in the case the type T
+ * has not defined attributes
+ *
+ * In C++ partial specialization of a function is not allowed so we have to
+ * encapsulate this function in a class
+ *
+ * \tparam has_attributes parameter that specialize the function in case the vertex
+ * define or not attributes name
+ *
+ * \tparam i id of the property we are going to write
+ *
+ */
+
+template<typename Graph, unsigned int i>
+class dist_prop_output<false, Graph, i>
+{
+ /*! \brief For each vertex output the property string
+ *
+ * \param g graph to print
+ *
+ * \return the string with the point data
+ *
+ */
+ static std::string get_point_data(Graph & g)
+ {
+ //! vertex node output string
+ std::string v_out;
+
+ //! Get a vertex iterator
+ auto it = g.getVertexIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ // Print the property
+ v_out += std::to_string(g.vertex(it.get()).template get<i>()) + "\n";
+
+ // increment the iterator and counter
+ ++it;
+ }
+
+ return v_out;
+ }
+
+ /*! \brief For each edge output the property string
+ *
+ * \param g graph to print
+ *
+ * \return the string containing cell-data
+ *
+ */
+ static std::string get_cell_data(const Graph & g)
+ {
+ //! vertex node output string
+ std::string e_out;
+
+ //! Get a vertex iterator
+ auto it_v = g.getVertexIterator();
+
+ // if there is the next element
+ while (it_v.isNext())
+ {
+ // Print the property
+ e_out += std::to_string(0) + "\n";
+
+ // increment the iterator and counter
+ ++it_v;
+ }
+
+ //! Get an edge iterator
+ auto it_e = g.getEdgeIterator();
+
+ // if there is the next element
+ while (it_e.isNext())
+ {
+ // Print the property
+ e_out += std::to_string(g.edge(it_e.get()).template get<i>()) + "\n";
+
+ // increment the iterator and counter
+ ++it_e;
+ }
+
+ return e_out;
+ }
+
+ /*! \brief Given a Graph return the point data header for a typename T
+ *
+ * \param prop id of the property
+ *
+ * \return the string containing the header
+ *
+ */
+ static std::string get_point_property_header(size_t prop)
+ {
+ //! vertex node output string
+ std::string v_out;
+
+ // Check if T is a supported format
+ // for now we support only scalar of native type
+
+ std::string type = getType<boost::fusion::result_of::at<typename Graph::V_type::type, boost::mpl::int_<i>>>("attr" + std::to_string(prop));
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ {
+ return v_out;
+ }
+
+ // Create point data properties
+ v_out += "SCALARS " + get_attributes_vertex() + " " + type + "\n";
+
+ // Default lookup table
+ v_out += "LOOKUP_TABLE default\n";
+
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Given a Graph return the cell data header for a typename T
+ *
+ * \param prop property id
+ *
+ * \return the string containing the header
+ *
+ */
+ static std::string get_cell_property_header(size_t prop)
+ {
+ //! edge node output string
+ std::string e_out;
+
+ // Type of the property
+ std::string type;
+
+ typedef typename boost::mpl::at<typename Graph::E_type::type, boost::mpl::int_<i>>::type T;
+
+ // Check if T is a supported format
+ // for now we support only scalar of native type
+ if (std::is_array<T>::value == true && std::is_array<typename std::remove_extent<T>::type>::value == false)
+ {
+ //Get type of the property
+ type = getType<typename std::remove_all_extents<T>::type>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ return e_out;
+
+ // Create point data properties
+ e_out += "VECTORS " + get_attributes_edge() + " " + type + "\n";
+ }
+ else
+ {
+ type = getType<T>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ return e_out;
+
+ // Create point data properties
+ e_out += "SCALARS " + get_attributes_edge() + " " + type + "\n";
+
+ // Default lookup table
+ e_out += "LOOKUP_TABLE default\n";
+
+ }
+
+ // return the vertex list
+ return e_out;
+ }
+
+ /*! \brief Get the attributes name for vertex
+ *
+ * \return the string containing the vertex attribute name
+ *
+ */
+ static std::string get_attributes_vertex()
+ {
+ return Graph::V_type::attributes::name[i];
+ }
+
+ /*! \brief Get the attributes name for edge
+ *
+ * \return the edge attribute name
+ *
+ */
+ static std::string get_attributes_edge()
+ {
+ return Graph::E_type::attributes::name[i];
+ }
+};
+
+/*! \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 produce at output for each property
+ *
+ * \tparam Graph graph we are processing
+ *
+ * \param dim Dimensionality
+ * \param S type of grid
+ *
+ */
+
+template<typename Graph>
+struct dist_prop_out_vertex
+{
+ //! property output string
+ std::string & v_out;
+
+ //! Graph that we are processing
+ const Graph & g;
+
+ /*! \brief constructor
+ *
+ * \param v_out string to fill with the vertex properties
+ * \param g graph to process
+ *
+ */
+ dist_prop_out_vertex(std::string & v_out, const Graph & g)
+ :v_out(v_out), g(g)
+ {
+ }
+
+ /*! \brief It produce an output for each property
+ *
+ * \param t property id
+ *
+ */
+ template<typename T>
+ void operator()(T& t) const
+ {
+ // actual string size
+ size_t sz = v_out.size();
+
+ // Produce the point properties header
+ v_out += dist_prop_output<has_attributes<typename Graph::V_type>::value, Graph, T::value>::get_point_property_header(t);
+
+ // If the output has changed, we have to write the properties
+ if (v_out.size() != sz)
+ {
+ std::string attr = dist_prop_output<has_attributes<typename Graph::V_type>::value, Graph, T::value>::get_attributes_vertex();
+
+ // Produce point data
+ v_out += dist_prop_output<has_attributes<typename Graph::V_type>::value, Graph, T::value>::get_point_data(g);
+ }
+ }
+};
+
+/*! \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 produce at output for each property
+ *
+ * \tparam Graph graph we are processing
+ *
+ * \param dim Dimensionality
+ * \param S type of grid
+ *
+ */
+
+template<typename Graph>
+struct dist_prop_out_edge
+{
+ //! property output string
+ std::string & e_out;
+
+ //! Graph that we are processing
+ const Graph & g;
+
+ /*! \brief constructor
+ *
+ * \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)
+ {};
+
+ /*! \brief It produce an output for each property
+ *
+ * \param t index property
+ *
+ */
+ template<typename T>
+ void operator()(T& t) const
+ {
+ // actual string size
+ size_t sz = e_out.size();
+
+ // Produce the point properties header
+ e_out += dist_prop_output<has_attributes<typename Graph::E_type>::value, Graph, T::value>::get_cell_property_header(t);
+
+ // If the output has changed, we have to write the properties
+ if (e_out.size() != sz)
+ {
+ std::string attr = dist_prop_output<has_attributes<typename Graph::E_type>::value, Graph, T::value>::get_attributes_edge();
+
+ // Produce cell data
+ e_out += dist_prop_output<has_attributes<typename Graph::E_type>::value, Graph, T::value>::get_cell_data(g);
+ }
+ }
+};
+
+/*!
+ *
+ * It write a VTK format file in case for a graph
+ *
+ * \tparam Type of graph
+ *
+ */
+
+template<typename Graph>
+class VTKWriter<Graph, DIST_GRAPH>
+{
+ //! Graph to output
+ Graph & g;
+
+ /*! \brief It get the vertex properties list
+ *
+ * It get the vertex properties list of the vertex defined as VTK header
+ *
+ * \return a string that define the vertex properties in graphML format
+ *
+ */
+
+ std::string get_vertex_properties_list()
+ {
+ //! vertex property output string
+ std::string v_out;
+
+ // write the number of vertex
+ v_out += "VERTICES " + std::to_string(g.getNVertex()) + " " + std::to_string(g.getNVertex() * 2) + "\n";
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief It get the vertex properties list
+ *
+ * It get the vertex properties list of the vertex defined as a VTK header
+ *
+ * \return a string that define the vertex properties in graphML format
+ *
+ */
+
+ std::string get_point_properties_list()
+ {
+ //! vertex property output string
+ std::string v_out;
+
+ // write the number of vertex
+ v_out += "POINTS " + std::to_string(g.getNVertex()) + " float" + "\n";
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief Get the VTK point info string
+ *
+ * \return the point info string
+ *
+ */
+ std::string get_point_info()
+ {
+ //! vertex property output string
+ std::string v_out;
+
+ // write the ids
+ v_out += "SCALARS id unsigned_long\nLOOKUP_TABLE default\n";
+
+ for (size_t i = 0; i < g.getNVertex(); ++i)
+ {
+ v_out += std::to_string(g.getVertexId(i)) + "\n";
+ }
+
+ // write the ids
+ v_out += "SCALARS gid unsigned_long\nLOOKUP_TABLE default\n";
+
+ for (size_t i = 0; i < g.getNVertex(); ++i)
+ {
+ v_out += std::to_string(g.getVertexGlobalId(i)) + "\n";
+ }
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief It get the edge properties list
+ *
+ * It get the edge properties list of the edge defined as a GraphML header
+ *
+ * \return a string that define the edge properties in graphML format
+ *
+ */
+
+ std::string get_edge_properties_list()
+ {
+ //! vertex property output string
+ std::string e_out;
+
+ // write the number of lines
+ e_out += "LINES " + std::to_string(g.getNEdge()) + " " + std::to_string(3 * g.getNEdge()) + "\n";
+
+ // return the vertex properties string
+ return e_out;
+ }
+
+ /*! \brief Create the VTK point definition
+ *
+ * \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()
+ {
+ //! VTK spatial information
+ typename Graph::V_type::s_type x[3] = { 0, 0, 0 };
+
+ //! vertex node output string
+ std::string v_out;
+
+ //! Get a vertex iterator
+ auto it = g.getVertexIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ // Get vtk vertex node
+ auto obj = g.vertex(it.get());
+
+ // create a vertex list functor
+ vtk_dist_vertex_node<Graph, attr> vn(v_out, obj, x);
+
+ // Iterate through all the vertex and create the vertex list
+ boost::mpl::for_each<boost::mpl::range_c<int, 0, Graph::V_type::max_prop> >(vn);
+
+ // write the node string
+ vn.write();
+
+ // increment the iterator and counter
+ ++it;
+ }
+
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Create the VTK vertex definition
+ *
+ * \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
+ std::string v_out;
+
+ //! For each point create a vertex
+ for (size_t i = 0; i < g.getNVertex(); i++)
+ {
+ v_out += "1 " + std::to_string(i) + "\n";
+ }
+
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Get the point data header
+ *
+ * \return a string with the point data header for VTK format
+ *
+ */
+
+ std::string get_point_data_header()
+ {
+ std::string v_out;
+
+ v_out += "POINT_DATA " + std::to_string(g.getNVertex()) + "\n";
+
+ return v_out;
+ }
+
+ /*! \brief Get the point data header
+ *
+ * \return a string with the point data header for VTK format
+ *
+ */
+
+ std::string get_cell_data_header()
+ {
+ std::string v_out;
+
+ v_out += "CELL_DATA " + std::to_string(g.getNVertex() + g.getNEdge()) + "\n";
+
+ return v_out;
+ }
+
+ /*! \brief Return the edge list
+ *
+ * \return the edge list
+ *
+ */
+
+ std::string get_edge_list()
+ {
+ //! edge node output string
+ std::string e_out;
+
+ //! Get an edge iterator
+ auto it = g.getEdgeIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ e_out += "2 " + std::to_string(it.source()) + " " + std::to_string(g.nodeById(it.target())) + "\n";
+
+ // increment the operator
+ ++it;
+ }
+
+ // return the edge list
+ return e_out;
+ }
+
+public:
+
+ /*!
+ *
+ * VTKWriter constructor, it take a graph and write a GraphML format
+ *
+ * \param g Graph to write
+ *
+ */
+ VTKWriter(Graph & g) :
+ g(g)
+ {
+ }
+
+ /*! \brief It write a VTK file from a graph
+ *
+ * \tparam prp_out which properties to output [default = -1 (all)]
+ *
+ * \param file path where to write
+ * \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)
+ {
+
+ Vcluster<> & v_cl = create_vcluster();
+
+ g.deleteGhosts();
+
+ if (v_cl.getProcessUnitID() == 0)
+ {
+ for (size_t i = 0; i < g.getTotNVertex(); ++i)
+ {
+ g.reqVertex(i);
+ }
+ }
+
+ g.sync();
+
+ if (v_cl.getProcessUnitID() == 0)
+ {
+ // Check that the Vertex type define x y and z attributes
+
+ if (has_attributes<typename Graph::V_type>::value == false)
+ {
+ std::cerr << "Error writing a graph: Vertex must has defines x,y,z properties" << "\n";
+ return false;
+ }
+
+ // Header for the vtk
+ std::string vtk_header;
+ // Point list of the VTK
+ std::string point_list;
+ // Vertex list of the VTK
+ std::string vertex_list;
+ // Graph header
+ std::string vtk_binary_or_ascii;
+ // Edge list of the GraphML
+ std::string edge_list;
+ // vertex properties header
+ std::string point_prop_header;
+ // edge properties header
+ std::string vertex_prop_header;
+ // edge properties header
+ std::string edge_prop_header;
+ // Data point header
+ std::string point_data_header;
+ // Ids point
+ std::string point_ids;
+ // Data point
+ std::string point_data;
+ // Cell data header
+ std::string cell_data_header;
+ // Cell data
+ std::string cell_data;
+
+ // VTK header
+ vtk_header = "# vtk DataFile Version 3.0\n" + graph_name + "\n";
+
+ // Choose if binary or ASCII
+ if (ft == file_type::ASCII)
+ {
+ vtk_header += "ASCII\n";
+ }
+ else
+ {
+ vtk_header += "BINARY\n";
+ }
+
+ // Data type for graph is DATASET POLYDATA
+ vtk_header += "DATASET POLYDATA\n";
+
+ // point properties header
+ point_prop_header = get_point_properties_list();
+
+ // Get point list
+ point_list = get_point_list<has_attributes<typename Graph::V_type>::value>();
+
+ // vertex properties header
+ vertex_prop_header = get_vertex_properties_list();
+
+ // Get vertex list
+ vertex_list = get_vertex_list();
+
+ // Edge properties header
+ edge_prop_header = get_edge_properties_list();
+
+ // Get the edge graph list
+ edge_list = get_edge_list();
+
+ // Get the point data header
+ point_data_header = get_point_data_header();
+
+ // Get the point info
+ point_ids = get_point_info();
+
+ // Get the cell data header
+ cell_data_header = get_cell_data_header();
+
+ // For each property in the vertex type produce a point data
+
+ dist_prop_out_vertex<Graph> pp(point_data, g);
+
+ if (prp == -1)
+ boost::mpl::for_each<boost::mpl::range_c<int, 0, Graph::V_type::max_prop> >(pp);
+ else
+ boost::mpl::for_each<boost::mpl::range_c<int, prp, prp> >(pp);
+
+ // For each property in the edge type produce a point data
+
+ dist_prop_out_edge<Graph> ep(cell_data, g);
+
+ if (prp == -1)
+ boost::mpl::for_each<boost::mpl::range_c<int, 0, Graph::E_type::max_prop> >(ep);
+ else
+ boost::mpl::for_each<boost::mpl::range_c<int, prp, prp> >(ep);
+
+ // write the file
+ std::ofstream ofs(file);
+
+ // Check if the file is open
+ if (ofs.is_open() == false)
+ {
+ std::cerr << "Error cannot create the VTK file: " + file;
+ }
+
+ ofs << vtk_header << point_prop_header << point_list << vertex_prop_header << vertex_list << edge_prop_header << edge_list << point_data_header << point_ids << point_data << cell_data_header << cell_data;
+
+ // Close the file
+
+ ofs.close();
+
+ }
+
+ g.deleteGhosts();
+
+ // Completed succefully
+ return true;
+ }
+};
+
+#endif /* VTKWRITER_GRAPH_HPP_ */
diff --git a/src/VTKWriter/VTKWriter_graph.hpp b/src/VTKWriter/VTKWriter_graph.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..3b4bb1e61a00b564d4c0cd902b030c588915cd29
--- /dev/null
+++ b/src/VTKWriter/VTKWriter_graph.hpp
@@ -0,0 +1,1243 @@
+/*
+ * VTKWriter_graph.hpp
+ *
+ * Created on: May 5, 2015
+ * Author: Pietro Incardona
+ */
+
+#ifndef VTKWRITER_GRAPH_HPP_
+#define VTKWRITER_GRAPH_HPP_
+
+/*! Property data store for scalar and vector
+ *
+ */
+template<bool is_array>
+struct vtk_vertex_node_array_scalar_selector
+{
+ /*! /brief Print the geometric informations in case it is not an array
+ *
+ * \tparam T Type of the vertex
+ * \tparam ele_v Attribute element to check
+ * \tparam G Graph of reference
+ * \tparam s_type Vertex spatial type information
+ *
+ * \param vo Vertex object container
+ * \param x Array to store geometric informations
+ * \param z_set Value set to true id z axis is in use
+ */
+ template<typename T, typename ele_v, typename G, typename s_type>
+ static inline void move(typename G::V_container &vo, s_type (&x)[3], bool &z_set)
+ {
+ if (G::V_type::attributes::name[T::value] == "x")
+ {
+ x[0] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>())>::type>::template to<s_type>(vo.template get<T::value>());
+ }
+ else if (G::V_type::attributes::name[T::value] == "y")
+ {
+ x[1] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>())>::type>::template to<s_type>(vo.template get<T::value>());
+ }
+ else if (G::V_type::attributes::name[T::value] == "z")
+ {
+ x[2] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>())>::type>::template to<s_type>(vo.template get<T::value>());
+ z_set = true;
+ }
+ }
+};
+
+/*! Template specialization in the case of array type attribute
+ *
+ */
+template<>
+struct vtk_vertex_node_array_scalar_selector<true>
+{
+ /*! \brief Store the geometric informations in case it is an array
+ *
+ * \tparam T Type of the vertex
+ * \tparam ele_v Attribute element to check
+ * \tparam G Graph of reference
+ * \tparam s_type Vertex spatial type information
+ *
+ * \param vo Vertex object container
+ * \param x Array to store geometric informations
+ * \param z_set Value set to true id z axis is in use
+ */
+ template<typename T, typename ele_v, typename G, typename s_type>
+ static inline void move(typename G::V_container &vo, s_type (&x)[3], bool &z_set)
+ {
+ if (G::V_type::attributes::name[T::value] != "x")
+ {return;}
+
+ if (std::extent<ele_v>::value == 3)
+ {z_set = true;}
+
+ for (size_t i = 0; i < std::extent<ele_v>::value; i++)
+ {x[i] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>()[i])>::type>::template to<s_type>(vo.template get<T::value>()[i]);}
+ }
+};
+
+/*! \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 create a string containing all the vertex
+ * properties
+ *
+ * \tparam G graph type
+ * \tparam attr has the vertex attributes
+ *
+ */
+
+template<typename G, bool attr>
+struct vtk_vertex_node
+{
+ //! 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
+ typename G::V_container & vo;
+
+ //! vertex node string
+ std::string & v_node;
+
+ /*! \brief Constructor
+ *
+ * Create a vertex properties list
+ *
+ * \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])
+ :z_set(false),x(x),vo(n_obj),v_node(v_node)
+ {
+ }
+
+ //! \brief Write collected information
+ void write()
+ {
+ v_node += std::to_string(x[0]) + " " + std::to_string(x[1]) + " " + std::to_string(x[2]) + "\n";
+ }
+
+ /*! \brief It call the functor for each member
+ *
+ * \param t property id
+ *
+ */
+ template<typename T>
+ void operator()(T& t)
+ {
+ typedef typename boost::mpl::at<typename G::V_type::type, boost::mpl::int_<T::value>>::type ele_v;
+
+ // if the attribute name is x y or z, create a string with the value of the properties and store it
+
+ vtk_vertex_node_array_scalar_selector<std::is_array<ele_v>::value>::template move<T, ele_v, G, s_type>(vo, x, z_set);
+
+ }
+};
+
+/*! \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 create a string containing all the vertex
+ * properties
+ *
+ * Specialization when we do not have vertex attributes
+ *
+ * \tparam G graph type
+ *
+ */
+
+template<typename G>
+struct vtk_vertex_node<G, false>
+{
+ //! Vertex object container
+ typename G::V_container & vo;
+
+ //! vertex node string
+ std::string & v_node;
+
+ /*! \brief Constructor
+ *
+ * Create a vertex properties list
+ *
+ * \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<...>
+ *
+ */
+ vtk_vertex_node(std::string & v_node, typename G::V_container & n_obj) :
+ vo(n_obj), v_node(v_node)
+ {
+ }
+ ;
+
+ /*! \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)
+ {
+ v_node += "0 0 0\n";
+ }
+};
+
+/*! \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 create a string containing all the edge
+ * properties
+ *
+ */
+
+template<typename G>
+struct vtk_edge_node
+{
+ //! Vertex object container
+ typename G::E_container & vo;
+
+ //! edge node string
+ std::string & e_node;
+
+ /*! \brief Constructor
+ *
+ * Create an 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<...>
+ *
+ */
+ vtk_edge_node(std::string & e_node, typename G::E_container & n_obj) :
+ vo(n_obj), e_node(e_node)
+ {
+ }
+ ;
+
+ /*! \brief Create a new node
+ *
+ * \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)
+ {
+ // start a new node
+ e_node += "2 " + std::to_string(s) + " " + std::to_string(d) + "\n";
+ }
+};
+
+/*! \brief Property writer for scalar and vector
+ *
+ */
+template<bool is_array>
+struct prop_output_array_scalar_selector_vertex
+{
+ /*! \brief Writer in case the property is not an array
+ *
+ * \tparam ele_v Property element
+ * \tparam Graph Graph of reference
+ * \tparam i Property id
+ *
+ * \param v_out Buffer to write into
+ * \param g Graph
+ * \param p Property id
+ */
+ template<typename ele_v, typename Graph, unsigned int i>
+ static inline void write(std::string &v_out, const Graph &g, size_t p)
+ {
+ v_out += std::to_string(g.vertex(p).template get<i>()) + "\n";
+ }
+};
+
+/*! \brief Property writer for vector
+ *
+ */
+template<>
+struct prop_output_array_scalar_selector_vertex<true>
+{
+ /*! \brief Writer in case the property is an array
+ *
+ * \tparam ele_v Property element
+ * \tparam Graph Graph of reference
+ * \tparam i Property id
+ *
+ * \param v_out Buffer to write into
+ * \param g Graph
+ * \param p Property id
+ */
+ template<typename ele_v, typename Graph, unsigned int i>
+ static inline void write(std::string &v_out, const Graph &g, size_t p)
+ {
+ for (size_t j = 0; j < 2; j++)
+ {
+ v_out += std::to_string(g.vertex(p).template get<i>()[j]) + " ";
+ }
+
+ if (std::extent<ele_v>::value == 2)
+ v_out += "0";
+ else
+ v_out += std::to_string(g.vertex(p).template get<i>()[2]);
+
+ v_out += "\n";
+ }
+};
+
+/*! \brief Property writer for scalar and vector
+ *
+ */
+template<bool is_array>
+struct prop_output_array_scalar_selector_edge
+{
+ /*! \brief Writer in case the property is not an array
+ *
+ * \tparam ele_v Property element
+ * \tparam Graph Graph of reference
+ * \tparam i Property id
+ *
+ * \param v_out Buffer to write into
+ * \param g Graph
+ * \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)
+ {
+ v_out += std::to_string(edge.template get<i>()) + "\n";
+ }
+};
+
+/*! \brief Property writer for vector
+ *
+ */
+template<>
+struct prop_output_array_scalar_selector_edge<true>
+{
+ /*! \brief Writer in case the property is an array
+ *
+ * \tparam ele_v Property element
+ * \tparam Graph Graph of reference
+ * \tparam i Property id
+ *
+ * \param v_out Buffer to write into
+ * \param g Graph
+ * \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)
+ {
+ for (size_t j = 0; j < 2; j++)
+ {
+ v_out += std::to_string(edge.template get<i>()[j]) + " ";
+ }
+
+ if (std::extent<ele_v>::value == 2)
+ v_out += "0";
+ else
+ v_out += std::to_string(edge.template get<i>()[2]);
+
+ v_out += "\n";
+ }
+};
+
+/*! \brief Property writer for scalar and vector, it fill the vertex data (needed for edge representation in vtk)
+ *
+ */
+template<bool is_array>
+struct prop_output_array_scalar_selector_edge_fill_vertex
+{
+ /*! \brief Writer in case the property is not an array
+ *
+ * \param v_out Buffer to write into
+ */
+ static inline void write(std::string &v_out)
+ {
+ v_out += "0\n";
+ }
+};
+
+/*! \brief Property writer for vector
+ *
+ */
+template<>
+struct prop_output_array_scalar_selector_edge_fill_vertex<true>
+{
+ /*! \brief Writer in case the property is an array
+ *
+ * \param v_out Buffer to write into
+ */
+ static inline void write(std::string &v_out)
+ {
+ v_out += "0 0 0\n";
+ }
+};
+
+/*! \brief This class specialize functions in the case the type T
+ * has or not defined attributes
+ *
+ * In C++ partial specialization of a function is not allowed so we have to
+ * encapsulate this function in a class
+ *
+ * \tparam has_attributes parameter that specialize the function in case the vertex
+ * define or not attributes name
+ *
+ * \tparam Graph type of graph we are processing
+ * \tparam i the property we are going to write
+ *
+ */
+
+template<bool has_attributes, typename Graph, unsigned int i>
+class prop_output
+{
+public:
+
+ /*! \brief Get the vtk point data section for a graph g
+ *
+ * \param g graph
+ *
+ * \return point data section string
+ *
+ */
+ static std::string get_point_data(const Graph & g)
+ {
+ //! vertex node output string
+ std::string v_out;
+
+ //! Get a vertex iterator
+ auto it = g.getVertexIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ typedef typename boost::mpl::at<typename Graph::V_type::type, boost::mpl::int_<i>>::type ele_v;
+ prop_output_array_scalar_selector_vertex<std::is_array<ele_v>::value>::template write<ele_v, Graph, i>(v_out, g, it.get());
+
+ // increment the iterator and counter
+ ++it;
+ }
+
+ return v_out;
+ }
+
+ /*! \brief Get the cell data section for a graph g
+ *
+ * \param g graph
+ *
+ * \return the cell data section
+ *
+ */
+ static std::string get_cell_data(const Graph & g)
+ {
+ //! vertex node output string
+ std::string e_out;
+
+ //! Get a vertex iterator
+ auto it_v = g.getVertexIterator();
+
+ // if there is the next element
+ while (it_v.isNext())
+ {
+ // Print the property
+ typedef typename boost::mpl::at<typename Graph::E_type::type, boost::mpl::int_<i>>::type ele_v;
+ prop_output_array_scalar_selector_edge_fill_vertex<std::is_array<ele_v>::value>::write(e_out);
+
+ // increment the iterator and counter
+ ++it_v;
+ }
+
+ //! Get an edge iterator
+ auto it_e = g.getEdgeIterator();
+
+ // if there is the next element
+ while (it_e.isNext())
+ {
+ typedef typename boost::mpl::at<typename Graph::E_type::type, boost::mpl::int_<i>>::type ele_v;
+ prop_output_array_scalar_selector_edge<std::is_array<ele_v>::value>::template write<ele_v, Graph, i>(e_out, g, g.edge(it_e.get()));
+
+ // increment the iterator and counter
+ ++it_e;
+ }
+
+ return e_out;
+ }
+
+ /*! \brief Return the point header for the property prop
+ *
+ * \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
+ std::string v_out;
+
+ // Type of the property
+ std::string type;
+
+ typedef typename boost::mpl::at<typename Graph::V_type::type, boost::mpl::int_<i>>::type T;
+
+ // Check if T is a supported format
+ // for now we support only scalar of native type
+ if (std::rank<T>::value == 1)
+ {
+ //Get type of the property
+ type = getType<typename std::remove_all_extents<T>::type>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ return v_out;
+
+ // Create point data properties
+ v_out += "VECTORS " + get_attributes_vertex() + " " + type + "\n";
+ }
+ else
+ {
+ type = getType<T>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ return v_out;
+
+ // Create point data properties
+ v_out += "SCALARS " + get_attributes_vertex() + " " + type + "\n";
+
+ // Default lookup table
+ v_out += "LOOKUP_TABLE default\n";
+
+ }
+
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Given a Graph return the cell data header for a typename T
+ *
+ * \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
+ std::string e_out;
+
+ // Type of the property
+ std::string type;
+
+ typedef typename boost::mpl::at<typename Graph::E_type::type, boost::mpl::int_<i>>::type T;
+
+ // Check if T is a supported format
+ // for now we support only scalar of native type
+ if (std::is_array<T>::value == true && std::is_array<typename std::remove_extent<T>::type>::value == false)
+ {
+ //Get type of the property
+ type = getType<typename std::remove_all_extents<T>::type>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ return e_out;
+
+ // Create point data properties
+ e_out += "VECTORS " + get_attributes_edge() + " " + type + "\n";
+ }
+ else
+ {
+ type = getType<T>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ return e_out;
+
+ // Create point data properties
+ e_out += "SCALARS " + get_attributes_edge() + " " + type + "\n";
+
+ // Default lookup table
+ e_out += "LOOKUP_TABLE default\n";
+
+ }
+
+ // return the vertex list
+ return e_out;
+ }
+
+ /*! \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 property i (template parameter)
+ *
+ * \return edge attribute name
+ *
+ */
+ static std::string get_attributes_edge()
+ {
+ return Graph::E_type::attributes::name[i];
+ }
+};
+
+/*! \brief This class specialize functions in the case the type T
+ * has not defined attributes
+ *
+ * In C++ partial specialization of a function is not allowed so we have to
+ * encapsulate this function in a class
+ *
+ * \tparam has_attributes parameter that specialize the function in case the vertex
+ * define or not attributes name
+ *
+ * \tparam i id of the property we are going to write
+ *
+ */
+
+template<typename Graph, unsigned int i>
+class prop_output<false, Graph, i>
+{
+public:
+ /*! \brief Return the point data section for a graph g
+ *
+ * \param g graph
+ *
+ * \return the point data section string
+ *
+ */
+ static std::string get_point_data(Graph & g)
+ {
+ //! vertex node output string
+ std::string v_out;
+
+ //! Get a vertex iterator
+ auto it = g.getVertexIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ // Print the property
+ v_out += std::to_string(g.vertex(it.get()).template get<i>()) + "\n";
+
+ // increment the iterator and counter
+ ++it;
+ }
+
+ return v_out;
+ }
+
+ /*! \brief Return the cell data section for a graph g
+ *
+ * \param g graph
+ *
+ * \return the cell data section
+ *
+ */
+
+ static std::string get_cell_data(const Graph & g)
+ {
+ // vertex node output string
+ std::string e_out;
+
+ // Get a vertex iterator
+ auto it_v = g.getVertexIterator();
+
+ // if there is the next element
+ while (it_v.isNext())
+ {
+ // Print the property
+ e_out += std::to_string(0) + "\n";
+
+ // increment the iterator and counter
+ ++it_v;
+ }
+
+ //! Get an edge iterator
+ auto it_e = g.getEdgeIterator();
+
+ // if there is the next element
+ while (it_e.isNext())
+ {
+ // Print the property
+ e_out += std::to_string(g.edge(it_e.get()).template get<i>()) + "\n";
+
+ // increment the iterator and counter
+ ++it_e;
+ }
+
+ return e_out;
+ }
+
+ /*! \brief Given a Graph return the point data header for the property prop
+ *
+ * \param prop id of the property
+ *
+ * \return the string of the property header
+ *
+ */
+
+ static std::string get_point_property_header(size_t prop)
+ {
+ //! vertex node output string
+ std::string v_out;
+
+ // Check if T is a supported format
+ // for now we support only scalar of native type
+
+ std::string type = getType<boost::fusion::result_of::at<typename Graph::V_type::type, boost::mpl::int_<i>>>("attr" + std::to_string(prop));
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ {
+ return v_out;
+ }
+
+ // Create point data properties
+ v_out += "SCALARS " + get_attributes_vertex() + " " + type + "\n";
+
+ // Default lookup table
+ v_out += "LOOKUP_TABLE default\n";
+
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Given a Graph return the cell data header
+ *
+ * \param prop property id
+ *
+ * \return the cell property header
+ *
+ */
+
+ static std::string get_cell_property_header(size_t prop)
+ {
+ //! edge node output string
+ std::string e_out;
+
+ // Type of the property
+ std::string type;
+
+ typedef typename boost::mpl::at<typename Graph::E_type::type, boost::mpl::int_<i>>::type T;
+
+ // Check if T is a supported format
+ // for now we support only scalar of native type
+ if (std::is_array<T>::value == true && std::is_array<typename std::remove_extent<T>::type>::value == false)
+ {
+ //Get type of the property
+ type = getType<typename std::remove_all_extents<T>::type>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ return e_out;
+
+ // Create point data properties
+ e_out += "VECTORS " + get_attributes_edge() + " " + type + "\n";
+ }
+ else
+ {
+ type = getType<T>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ return e_out;
+
+ // Create point data properties
+ e_out += "SCALARS " + get_attributes_edge() + " " + type + "\n";
+
+ // Default lookup table
+ e_out += "LOOKUP_TABLE default\n";
+
+ }
+
+ // return the vertex list
+ return e_out;
+ }
+
+ /*! \brief Get the attributes name for vertex
+ *
+ * \return get attributes vertex name
+ *
+ */
+ static std::string get_attributes_vertex()
+ {
+ return std::string("attr" + std::to_string(i));
+ }
+
+ /*! \brief Get the attributes name for edge
+ *
+ * \return get attributes edge name
+ *
+ */
+ static std::string get_attributes_edge()
+ {
+ return std::string("attr" + std::to_string(i));
+ }
+};
+
+/*! \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 produce at output for each property
+ *
+ * \tparam Graph graph we are processing
+ *
+ * \param dim Dimensionality
+ * \param S type of grid
+ *
+ */
+
+template<typename Graph>
+struct prop_out_vertex
+{
+ //! property output string
+ std::string & v_out;
+
+ //! 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) :
+ v_out(v_out), g(g)
+ {
+ }
+ ;
+
+ /*! \brief It produce an output for each property
+ *
+ * \param t property id
+ *
+ */
+ template<typename T>
+ void operator()(T& t) const
+ {
+ // actual string size
+ size_t sz = v_out.size();
+
+ // Produce the point properties header
+ v_out += prop_output<has_attributes<typename Graph::V_type>::value, Graph, T::value>::get_point_property_header(t);
+
+ // If the output has changed, we have to write the properties
+ if (v_out.size() != sz)
+ {
+ std::string attr = prop_output<has_attributes<typename Graph::V_type>::value, Graph, T::value>::get_attributes_vertex();
+
+ // Produce point data
+ v_out += prop_output<has_attributes<typename Graph::V_type>::value, Graph, T::value>::get_point_data(g);
+ }
+ }
+};
+
+/*! \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 produce at output for each property
+ *
+ * \tparam Graph graph we are processing
+ *
+ * \param dim Dimensionality
+ * \param S type of grid
+ *
+ */
+
+template<typename Graph>
+struct prop_out_edge
+{
+ //! property output string
+ std::string & e_out;
+
+ //! Graph that we are processing
+ const Graph & g;
+
+ /*! \brief constructor
+ *
+ * \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) :
+ e_out(e_out), g(g)
+ {
+ }
+ ;
+
+ /*! \brief It produce an output for each property
+ *
+ * \param t property index
+ *
+ */
+ template<typename T>
+ void operator()(T& t) const
+ {
+ // actual string size
+ size_t sz = e_out.size();
+
+ // Produce the point properties header
+ e_out += prop_output<has_attributes<typename Graph::E_type>::value, Graph, T::value>::get_cell_property_header(t);
+
+ // If the output has changed, we have to write the properties
+ if (e_out.size() != sz)
+ {
+ std::string attr = prop_output<has_attributes<typename Graph::E_type>::value, Graph, T::value>::get_attributes_edge();
+
+ // Produce cell data
+ e_out += prop_output<has_attributes<typename Graph::E_type>::value, Graph, T::value>::get_cell_data(g);
+ }
+ }
+};
+
+/*!
+ *
+ * It write a VTK format file in case for a graph
+ *
+ * \tparam Type of graph
+ *
+ */
+
+template<typename Graph>
+class VTKWriter<Graph, VTK_GRAPH>
+{
+ //! graph we are writing
+ const Graph & g;
+
+ /*! \brief It get the vertex properties list
+ *
+ * It get the vertex properties list of the vertex defined as VTK header
+ *
+ * \return a string that define the vertex properties in graphML format
+ *
+ */
+
+ std::string get_vertex_properties_list()
+ {
+ //! vertex property output string
+ std::string v_out;
+
+ // write the number of vertex
+ v_out += "VERTICES " + std::to_string(g.getNVertex()) + " " + std::to_string(g.getNVertex() * 2) + "\n";
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief It get the vertex properties list
+ *
+ * It get the vertex properties list of the vertex defined as a VTK header
+ *
+ * \return a string that define the vertex properties in graphML format
+ *
+ */
+
+ std::string get_point_properties_list()
+ {
+ //! vertex property output string
+ std::string v_out;
+
+ // write the number of vertex
+ v_out += "POINTS " + std::to_string(g.getNVertex()) + " float" + "\n";
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief It get the edge properties list
+ *
+ * It get the edge properties list of the edge defined as a GraphML header
+ *
+ * \return a string that define the edge properties in graphML format
+ *
+ */
+
+ std::string get_edge_properties_list()
+ {
+ //! vertex property output string
+ std::string e_out;
+
+ // write the number of lines
+ e_out += "LINES " + std::to_string(g.getNEdge()) + " " + std::to_string(3 * g.getNEdge()) + "\n";
+
+ // return the vertex properties string
+ return e_out;
+ }
+
+ /*! \brief Create the VTK point definition
+ *
+ * \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
+ typename Graph::V_type::s_type x[3] = { 0, 0, 0 };
+
+ //! vertex node output string
+ std::string v_out;
+
+ //! Get a vertex iterator
+ auto it = g.getVertexIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ // Get vtk vertex node
+ auto obj = g.vertex(it.get());
+
+ // create a vertex list functor
+ vtk_vertex_node<Graph, attr> vn(v_out, obj, x);
+
+ // Iterate through all the vertex and create the vertex list
+ boost::mpl::for_each<boost::mpl::range_c<int, 0, Graph::V_type::max_prop > >(vn);
+
+ // write the node string
+ vn.write();
+
+ // increment the iterator and counter
+ ++it;
+ }
+
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Create the VTK vertex definition
+ *
+ * \return a string with the vertex definition
+ *
+ */
+ std::string get_vertex_list()
+ {
+ //! vertex node output string
+ std::string v_out;
+
+ //! For each point create a vertex
+ for (size_t i = 0; i < g.getNVertex(); i++)
+ {
+ v_out += "1 " + std::to_string(i) + "\n";
+ }
+
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Get the point data header
+ *
+ * \return a string with the point data header for VTK format
+ *
+ */
+
+ std::string get_point_data_header()
+ {
+ std::string v_out;
+
+ v_out += "POINT_DATA " + std::to_string(g.getNVertex()) + "\n";
+
+ return v_out;
+ }
+
+ /*! \brief Get the point data header
+ *
+ * \return a string with the point data header for VTK format
+ *
+ */
+
+ std::string get_cell_data_header()
+ {
+ std::string v_out;
+
+ v_out += "CELL_DATA " + std::to_string(g.getNVertex() + g.getNEdge()) + "\n";
+
+ return v_out;
+ }
+
+ /*! \brief Return the edge list
+ *
+ * \return the edge list
+ *
+ */
+
+ std::string get_edge_list()
+ {
+ //! edge node output string
+ std::string e_out;
+
+ //! Get an edge iterator
+ auto it = g.getEdgeIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ // create an edge list functor
+// edge_node<Graph> en(e_out,g.edge(it.get()));
+
+ e_out += "2 " + std::to_string(it.source()) + " " + std::to_string(it.target()) + "\n";
+
+ // increment the operator
+ ++it;
+ }
+
+ // return the edge list
+ return e_out;
+ }
+
+public:
+
+ /*!
+ *
+ * VTKWriter constructor, it take a graph and write a GraphML format
+ *
+ * \param g Graph to write
+ *
+ */
+ VTKWriter(const Graph & g) :
+ g(g)
+ {
+ }
+
+ /*! \brief It write a VTK file from a graph
+ *
+ * \tparam prp_out which properties to output [default = -1 (all)]
+ *
+ * \param file path where to write
+ * \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
+
+ if (has_attributes<typename Graph::V_type>::value == false)
+ {
+ std::cerr << "Error writing a graph: Vertex must has defines x,y,z properties" << "\n";
+ return false;
+ }
+
+ // Header for the vtk
+ std::string vtk_header;
+ // Point list of the VTK
+ std::string point_list;
+ // Vertex list of the VTK
+ std::string vertex_list;
+ // Graph header
+ std::string vtk_binary_or_ascii;
+ // Edge list of the GraphML
+ std::string edge_list;
+ // vertex properties header
+ std::string point_prop_header;
+ // edge properties header
+ std::string vertex_prop_header;
+ // edge properties header
+ std::string edge_prop_header;
+ // Data point header
+ std::string point_data_header;
+ // Data point
+ std::string point_data;
+ // Cell data header
+ std::string cell_data_header;
+ // Cell data
+ std::string cell_data;
+
+ // VTK header
+ vtk_header = "# vtk DataFile Version 3.0\n" + graph_name + "\n";
+
+ // Choose if binary or ASCII
+ if (ft == file_type::ASCII)
+ {
+ vtk_header += "ASCII\n";
+ }
+ else
+ {
+ vtk_header += "BINARY\n";
+ }
+
+ // Data type for graph is DATASET POLYDATA
+ vtk_header += "DATASET POLYDATA\n";
+
+ // point properties header
+ point_prop_header = get_point_properties_list();
+
+ // Get point list
+ point_list = get_point_list<has_attributes<typename Graph::V_type>::value>();
+
+ // vertex properties header
+ vertex_prop_header = get_vertex_properties_list();
+
+ // Get vertex list
+ vertex_list = get_vertex_list();
+
+ // Edge properties header
+ edge_prop_header = get_edge_properties_list();
+
+ // Get the edge graph list
+ edge_list = get_edge_list();
+
+ // Get the point data header
+ point_data_header = get_point_data_header();
+
+ // Get the cell data header
+ cell_data_header = get_cell_data_header();
+
+ // For each property in the vertex type produce a point data
+
+ prop_out_vertex<Graph> pp(point_data, g);
+
+ if (prp == -1)
+ boost::mpl::for_each<boost::mpl::range_c<int, 0, Graph::V_type::max_prop> >(pp);
+ else
+ boost::mpl::for_each<boost::mpl::range_c<int, prp, prp> >(pp);
+
+ // For each property in the edge type produce a point data
+
+ prop_out_edge<Graph> ep(cell_data, g);
+
+ if (prp == -1)
+ boost::mpl::for_each<boost::mpl::range_c<int, 0, Graph::E_type::max_prop> >(ep);
+ else
+ boost::mpl::for_each<boost::mpl::range_c<int, prp, prp> >(ep);
+
+ // write the file
+ std::ofstream ofs(file);
+
+ // Check if the file is open
+ if (ofs.is_open() == false)
+ {
+ std::cerr << "Error cannot create the VTK file: " + file;
+ }
+
+ ofs << vtk_header << point_prop_header << point_list << vertex_prop_header << vertex_list << edge_prop_header << edge_list << point_data_header << point_data << cell_data_header << cell_data;
+
+ // Close the file
+
+ ofs.close();
+
+ // Completed succefully
+ return true;
+ }
+};
+
+#endif /* VTKWRITER_GRAPH_HPP_ */
diff --git a/src/VTKWriter/VTKWriter_grids.hpp b/src/VTKWriter/VTKWriter_grids.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..2616af75e78e70abf7be5861b29abe4ed1685c14
--- /dev/null
+++ b/src/VTKWriter/VTKWriter_grids.hpp
@@ -0,0 +1,444 @@
+/*
+ * VTKWriter_grids.hpp
+ *
+ * Created on: May 5, 2015
+ * Author: Pietro Incardona
+ */
+
+#ifndef VTKWRITER_GRIDS_HPP_
+#define VTKWRITER_GRIDS_HPP_
+
+#include <boost/mpl/pair.hpp>
+#include "VTKWriter_grids_util.hpp"
+#include "is_vtk_writable.hpp"
+
+/*! \brief It store one grid
+ *
+ * \tparam Grid type of grid
+ * \tparam St type of space where the grid is defined
+ *
+ */
+template <typename Grid, typename St>
+class ele_g
+{
+public:
+
+ typedef Grid value_type;
+
+ ele_g(const Grid & g, const Point<Grid::dims,St> & offset, const Point<Grid::dims,St> & spacing, const Box<Grid::dims,St> & dom)
+ :g(g),offset(offset),spacing(spacing),dom(dom)
+ {}
+
+ //! Dataset name
+ std::string dataset;
+ //! Grid
+ const Grid & g;
+ //! offset where it start
+ Point<Grid::dims,St> offset;
+ // spacing of the grid
+ Point<Grid::dims,St> spacing;
+ // Part of the grid that is real domain
+ Box<Grid::dims,size_t> dom;
+};
+
+
+
+/*! \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 produce at output for each property
+ *
+ * \tparam ele_g element that store the grid and its attributes
+ * \param St type of space where the grid live
+ *
+ */
+
+template<typename ele_g, typename St>
+struct prop_out_g
+{
+ //! property output string
+ std::string & v_out;
+
+ //! 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, 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 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,prop_names,ft);
+ }
+
+ /*! \brief Write the last property
+ *
+ *
+ *
+ */
+ void lastProp()
+ {
+ // Create point data properties
+ v_out += "SCALARS domain float\n";
+
+ // Default lookup table
+ v_out += "LOOKUP_TABLE default\n";
+
+ // Produce point data
+ for (size_t k = 0 ; k < vg.size() ; k++)
+ {
+ //! Get a vertex iterator
+ auto it = vg.get(k).g.getIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ if (ft == file_type::ASCII)
+ {
+ if (vg.get(k).dom.isInside(it.get().toPoint()) == true)
+ {
+ float flag = 1.0;
+ flag += vg.get(k).g.getFlag(it.get()) * 2;
+ v_out += std::to_string(flag) + "\n";
+ }
+ else
+ {
+ float flag = 0.0;
+ flag += vg.get(k).g.getFlag(it.get()) * 2;
+ v_out += std::to_string(flag) + "\n";
+ }
+ }
+ else
+ {
+ if (vg.get(k).dom.isInside(it.get().toPoint()) == true)
+ {
+ float flag = 1.0;
+ flag = swap_endian_lt(flag);
+ v_out.append((const char *)&flag,sizeof(flag));
+ }
+ else
+ {
+ float flag = 0.0;
+ flag = swap_endian_lt(flag);
+ v_out.append((const char *)&flag,sizeof(flag));
+ }
+ }
+
+ // increment the iterator and counter
+ ++it;
+ }
+ }
+ }
+};
+
+/*!
+ *
+ * It write a VTK format file in case of grids defined on a space
+ *
+ * \tparam boost::mpl::pair<G,S>
+ *
+ * where G is the type of grid S is the type of space, float, double ...
+ *
+ */
+template <typename pair>
+class VTKWriter<pair,VECTOR_GRIDS>
+{
+ //! Vector of grids
+
+ openfpm::vector< ele_g<typename pair::first,typename pair::second> > vg;
+ /*! \brief Get the total number of points
+ *
+ * \return the total number
+ *
+ */
+ size_t get_total()
+ {
+ size_t tot = 0;
+
+ //! Calculate the full number of vertices
+ for (size_t i = 0 ; i < vg.size() ; i++)
+ {
+ tot += vg.get(i).g.size();
+ }
+ return tot;
+ }
+
+ /*! \brief It get the vertex properties list
+ *
+ * It get the vertex properties list of the vertex defined as VTK header
+ *
+ * \return a string that define the vertex properties in graphML format
+ *
+ */
+
+ std::string get_vertex_properties_list()
+ {
+ //! vertex property output string
+ std::string v_out;
+
+ // write the number of vertex
+ v_out += "VERTICES " + std::to_string(get_total()) + " " + std::to_string(get_total() * 2) + "\n";
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief It get the vertex properties list
+ *
+ * It get the vertex properties list of the vertex defined as a VTK header
+ *
+ * \return a string that define the vertex properties in graphML format
+ *
+ */
+ std::string get_point_properties_list()
+ {
+ //! vertex property output string
+ std::string v_out;
+
+ // write the number of vertex
+ if (std::is_same<typename pair::second,float>::value == true)
+ {v_out += "POINTS " + std::to_string(get_total()) + " float" + "\n";}
+ else
+ {v_out += "POINTS " + std::to_string(get_total()) + " double" + "\n";}
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief Create the VTK point definition
+ *
+ * \param ft file type
+ *
+ * \return the string with the point list
+ *
+ */
+ std::string get_point_list(file_type ft)
+ {
+ //! vertex node output string
+ std::stringstream v_out;
+
+ if (std::is_same<typename pair::second,float>::value == true)
+ {v_out << std::setprecision(7);}
+ else
+ {v_out << std::setprecision(16);}
+
+ //! For each defined grid
+
+ for (size_t i = 0 ; i < vg.size() ; i++)
+ {
+ //! Get the iterator
+ auto it = vg.get(i).g.getIterator();
+
+ //! Where the grid is defined
+ Box<pair::first::dims,typename pair::second> dom;
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ Point<pair::first::dims,typename pair::second> p;
+ p = it.get().toPoint();
+ p = pmul(p,vg.get(i).spacing) + vg.get(i).offset;
+
+ output_point<pair::first::dims,typename pair::second>(p,v_out,ft);
+
+ // increment the iterator and counter
+ ++it;
+ }
+ }
+
+ // return the vertex list
+ return v_out.str();
+ }
+
+ /*! \brief Create the VTK vertex definition
+ *
+ * \param ft file type
+ *
+ */
+ std::string get_vertex_list(file_type ft)
+ {
+ //! vertex node output string
+ std::string v_out;
+
+ size_t k = 0;
+
+ for (size_t i = 0 ; i < vg.size() ; i++)
+ {
+ //! For each grid point create a vertex
+ auto it = vg.get(i).g.getIterator();
+
+ while (it.isNext())
+ {
+ output_vertex(k,v_out,ft);
+
+ ++k;
+ ++it;
+ }
+ }
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Get the point data header
+ *
+ * \return a string with the point data header for VTK format
+ *
+ */
+
+ std::string get_point_data_header()
+ {
+ std::string v_out;
+
+ v_out += "POINT_DATA " + std::to_string(get_total()) + "\n";
+
+ return v_out;
+ }
+
+public:
+
+ /*!
+ *
+ * VTKWriter constructor
+ *
+ */
+ VTKWriter()
+ {}
+
+ /*! \brief Add grid dataset
+ *
+ * \param g Grid to add
+ * \param offset grid offset
+ * \param spacing spacing of the grid
+ * \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)
+ {
+ ele_g<typename pair::first,typename pair::second> t(g,offset,spacing,dom);
+
+ vg.add(t);
+ }
+
+ /*! \brief It write a VTK file from a graph
+ *
+ * \tparam prp_out which properties to output [default = -1 (all)]
+ *
+ * \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,
+ 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;
+ // Point list of the VTK
+ std::string point_list;
+ // Vertex list of the VTK
+ std::string vertex_list;
+ // Graph header
+ std::string vtk_binary_or_ascii;
+ // vertex properties header
+ std::string point_prop_header;
+ // edge properties header
+ std::string vertex_prop_header;
+ // Data point header
+ std::string point_data_header;
+ // Data point
+ std::string point_data;
+
+ // VTK header
+ vtk_header = "# vtk DataFile Version 3.0\n"
+ + f_name + "\n";
+
+ // Choose if binary or ASCII
+ if (ft == file_type::ASCII)
+ {vtk_header += "ASCII\n";}
+ else
+ {vtk_header += "BINARY\n";}
+
+ // Data type for graph is DATASET POLYDATA
+ vtk_header += "DATASET POLYDATA\n";
+
+ // point properties header
+ point_prop_header = get_point_properties_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(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_names, ft);
+
+ if (prp == -1)
+ {boost::mpl::for_each< boost::mpl::range_c<int,0, pair::first::value_type::max_prop> >(pp);}
+ else
+ {boost::mpl::for_each< boost::mpl::range_c<int,prp, prp> >(pp);}
+
+ // Add the last property
+ pp.lastProp();
+
+
+ // write the file
+ std::ofstream ofs(file);
+
+ // Check if the file is open
+ if (ofs.is_open() == false)
+ {std::cerr << "Error cannot create the VTK file: " + file + "\n";}
+
+ ofs << vtk_header << point_prop_header << point_list <<
+ vertex_prop_header << vertex_list << point_data_header << point_data;
+
+ // Close the file
+
+ ofs.close();
+
+ // Completed succefully
+ return true;
+ }
+};
+
+
+#endif /* VTKWRITER_GRAPH_HPP_ */
diff --git a/src/VTKWriter/VTKWriter_grids_st.hpp b/src/VTKWriter/VTKWriter_grids_st.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..b6b523a83e1f843f00aca92d44c541237e75f25d
--- /dev/null
+++ b/src/VTKWriter/VTKWriter_grids_st.hpp
@@ -0,0 +1,727 @@
+/*
+ * VTKWriter_grids_st.hpp
+ *
+ * Created on: Sep 3, 2015
+ * Author: Pietro Incardona
+ */
+
+#ifndef SRC_VTKWRITER_GRIDS_ST_HPP_
+#define SRC_VTKWRITER_GRIDS_ST_HPP_
+
+
+#include <boost/mpl/pair.hpp>
+#include "VTKWriter_grids_util.hpp"
+#include "util/util_debug.hpp"
+#include "util/convert.hpp"
+
+/*! \brief for each combination in the cell grid you can have different grids
+ *
+ * \tparam Grid type of grid
+ *
+ */
+template <typename Grid>
+struct cell_grid
+{
+ //! vector of fused grids
+ openfpm::vector<const Grid *> grids;
+
+ //! combination
+ //! (used to calculate the grid shift from the starting point of the cell)
+ comb<Grid::dims> cmb;
+
+ cell_grid() {}
+
+ /*! \brief construct a cell grid
+ *
+ * \param cmb in which position this grid live
+ *
+ */
+ cell_grid(const comb<Grid::dims> & cmb)
+ :cmb(cmb)
+ {}
+
+ /*! \brief copy contructor
+ *
+ * \param cg element to copy
+ *
+ */
+ cell_grid(const cell_grid<Grid> & cg)
+ {
+ this->operator=(cg);
+ }
+
+ /*! \brief copy constructor
+ *
+ * \param cg element to copy
+ *
+ */
+ cell_grid(cell_grid<Grid> && cg)
+ {
+ this->operator=(cg);
+ }
+
+ /*! \brief Copy the cell grid
+ *
+ * \param cg cell_grid to copy
+ *
+ * \return itself
+ *
+ */
+ cell_grid<Grid> & operator=(const cell_grid<Grid> & cg)
+ {
+ cmb = cg.cmb;
+ grids = cg.grids;
+
+ return *this;
+ }
+
+ /*! \brief Copy the cell grid
+ *
+ * \param cg cell_grid to copy
+ *
+ * \return itself
+ *
+ */
+ cell_grid<Grid> & operator=(cell_grid<Grid> && cg)
+ {
+ cmb = cg.cmb;
+ grids = cg.grids;
+
+ return *this;
+ }
+};
+
+/*! \brief convert a staggered element into a string for vtk write
+ *
+ * \tparam Grid type of the grid
+ * \tparam St space type
+ *
+ */
+template <typename Grid, typename St>
+class ele_g_st
+{
+public:
+
+ //! grid type
+ typedef Grid value_type;
+
+ //! constructor
+ ele_g_st(){};
+
+ /*! \brief convert a staggered grid property into a string
+ *
+ * \param offset shift of the staggered element
+ * \param spacing of the grid
+ * \param dom Part of the grid that is real domain
+ *
+ */
+ ele_g_st(const Point<Grid::dims,St> & offset,
+ const Point<Grid::dims,St> & spacing,
+ const Box<Grid::dims,St> & dom)
+ :offset(offset),spacing(spacing),dom(dom)
+ {}
+
+ //! output string
+ std::string dataset;
+ //! fused grids
+ openfpm::vector<cell_grid<Grid>> g;
+ //! offset where it start the grid
+ Point<Grid::dims,St> offset;
+ //! spacing of the grid
+ Point<Grid::dims,St> spacing;
+ //! Part of the grid that is real domain
+ Box<Grid::dims,size_t> dom;
+
+ /*! \brief Copy constructor
+ *
+ * \param ele element to copy
+ *
+ */
+ inline ele_g_st(const ele_g_st & ele)
+ {
+ this->operator=(ele);
+ }
+
+ /*! \brief Copy constructor
+ *
+ * \param ele element to copy
+ *
+ */
+ inline ele_g_st(ele_g_st && ele)
+ {
+ this->operator=(ele);
+ }
+
+ /*! \brief Copy the object
+ *
+ * \param ele ele_g_st to copy
+ *
+ * \return itself
+ *
+ */
+ ele_g_st<Grid,St> & operator=(const ele_g_st & ele)
+ {
+ dataset = ele.dataset;
+ g = ele.g;
+ offset = ele.offset;
+ spacing = ele.spacing;
+ dom = ele.dom;
+
+ return *this;
+ }
+
+ /*! \brief Copy the object
+ *
+ * \param ele ele_g_st to copy
+ *
+ * \return itself
+ *
+ */
+ ele_g_st<Grid,St> & operator=(ele_g_st && ele)
+ {
+ dataset = ele.dataset;
+ g = ele.g;
+ offset = ele.offset;
+ spacing = ele.spacing;
+ dom = ele.dom;
+
+ return *this;
+ }
+};
+
+/*!
+ *
+ * It write a VTK format file in case of grids defined on a space
+ *
+ * \tparam boost::mpl::pair<G,S>
+ *
+ * where G is the type of grid S is the type of space, float, double ...
+ *
+ */
+template <typename pair>
+class VTKWriter<pair,VECTOR_ST_GRIDS>
+{
+ //! Vector of grids
+ openfpm::vector< ele_g_st<typename pair::first,typename pair::second> > vg;
+
+ /*! \brief Get the total number of points
+ *
+ * \return the total number
+ *
+ */
+ size_t get_total()
+ {
+ size_t tot = 0;
+
+ //! Calculate the full number of vertices
+ for (size_t i = 0 ; i < vg.size() ; i++)
+ {
+ for (size_t j = 0 ; j < vg.get(i).g.size() ; j++)
+ {
+ if (vg.get(i).g.get(j).grids.size() != 0)
+ tot += vg.get(i).g.get(j).grids.get(0)->size();
+ }
+ }
+ return tot;
+ }
+
+ /*! \brief It get the vertex properties list
+ *
+ * It get the vertex properties list of the vertex defined as VTK header
+ *
+ * \return a string that define the vertex properties in graphML format
+ *
+ */
+
+ std::string get_vertex_properties_list()
+ {
+ //! vertex property output string
+ std::string v_out;
+
+ // write the number of vertex
+ v_out += "VERTICES " + std::to_string(get_total()) + " " + std::to_string(get_total() * 2) + "\n";
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief It get the vertex properties list
+ *
+ * It get the vertex properties list of the vertex defined as a VTK header
+ *
+ * \return a string that define the vertex properties in graphML format
+ *
+ */
+
+ std::string get_point_properties_list()
+ {
+ //! vertex property output string
+ std::string v_out;
+
+ // write the number of vertex
+ v_out += "POINTS " + std::to_string(get_total()) + " float" + "\n";
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief Create the VTK point definition
+ *
+ * \return the list of points
+ *
+ */
+ std::string get_point_list()
+ {
+ //! vertex node output string
+ std::stringstream v_out;
+
+ //! For each sub-domain
+ for (size_t i = 0 ; i < vg.size() ; i++)
+ {
+ // For each position in the cell
+ for (size_t j = 0 ; j < vg.get(i).g.size() ; j++)
+ {
+ // If there are no grid in this position
+ if (vg.get(i).g.get(j).grids.size() == 0)
+ continue;
+
+ //! Get the iterator
+ auto it = vg.get(i).g.get(j).grids.get(0)->getIterator();
+
+ //! Where the grid is defined
+ Box<pair::first::dims,typename pair::second> dom;
+
+ // Calculate the offset of the grid considering its cell position
+ Point<pair::first::dims,typename pair::second> middle = vg.get(i).spacing / 2;
+ Point<pair::first::dims,typename pair::second> one;
+ one.one();
+ one = one + toPoint<pair::first::dims,typename pair::second>::convert(vg.get(i).g.get(j).cmb);
+ Point<pair::first::dims,typename pair::second> offset = pmul(middle,one) + vg.get(i).offset;
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ Point<pair::first::dims,typename pair::second> p;
+ p = it.get().toPoint();
+ p = pmul(p,vg.get(i).spacing) + offset;
+
+ if (pair::first::dims == 2)
+ v_out << p.toString() << " 0.0" << "\n";
+ else
+ v_out << p.toString() << "\n";
+
+ // increment the iterator
+ ++it;
+ }
+ }
+ }
+
+ // return the vertex list
+ return v_out.str();
+ }
+
+ /*! \brief It generate a name for the property cell component
+ *
+ * \param k component in the cell
+ *
+ * \return property name
+ *
+ */
+ std::string get_prop_components(size_t k)
+ {
+ std::stringstream v_out;
+
+ //! For each sub-domain
+ for (size_t i = 0 ; i < vg.size() ; i++)
+ {
+ // For each position in the cell
+ for (size_t j = 0 ; j < vg.get(i).g.size() ; j++)
+ {
+ if (k < vg.get(i).g.get(j).grids.size())
+ {
+ // get the combination string
+ v_out << vg.get(i).g.get(j).cmb.to_string();
+ }
+ }
+ }
+
+ return v_out.str();
+ }
+
+ /*! \brief Create the VTK properties output
+ *
+ * \param k component
+ * \param prop_name property name
+ *
+ * \return the property output string for the grid
+ *
+ */
+ std::string get_properties_output(size_t k, std::string prop_name)
+ {
+ //! vertex node output string
+ std::stringstream v_out;
+
+ // Check if T is a supported format
+ // for now we support only scalar of native type
+
+ typedef typename boost::mpl::at<typename pair::first::value_type::type,boost::mpl::int_<0>>::type ctype;
+
+ std::string type = getType<ctype>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ {
+#ifndef DISABLE_ALL_RTTI
+ std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " the type " << demangle(typeid(ctype).name()) << " is not supported by vtk\n";
+#endif
+ return "";
+ }
+
+ std::string prp_cp = get_prop_components(k);
+
+ // Create point data properties
+ v_out << "SCALARS " << prop_name << "_" << prp_cp << " " << type + "\n";
+
+ // Default lookup table
+ v_out << "LOOKUP_TABLE default\n";
+
+ //! For each sub-domain
+ for (size_t i = 0 ; i < vg.size() ; i++)
+ {
+ // For each position in the cell
+ for (size_t j = 0 ; j < vg.get(i).g.size() ; j++)
+ {
+ // If there are no grid in this position
+ if (vg.get(i).g.get(j).grids.size() == 0)
+ continue;
+
+ if (k < vg.get(i).g.get(j).grids.size())
+ {
+ // Grid source
+ auto & g_src = *vg.get(i).g.get(j).grids.get(k);
+
+ //! Get the iterator
+ auto it = g_src.getIterator();
+
+ //! Where the grid is defined
+ Box<pair::first::dims,typename pair::second> dom;
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ v_out << std::to_string(g_src.template get<0>(key)) << "\n";
+
+ // increment the iterator
+ ++it;
+ }
+ }
+ else
+ {
+ // Grid source
+ auto & g_src = *vg.get(i).g.get(j).grids.get(0);
+
+ //! Get the iterator
+ auto it = g_src.getIterator();
+
+ //! Where the grid is defined
+ Box<pair::first::dims,typename pair::second> dom;
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ v_out << "0\n";
+
+ // increment the iterator
+ ++it;
+ }
+ }
+ }
+ }
+
+ // return the vertex list
+ return v_out.str();
+ }
+
+ /*! \brief Return the output of the domain property
+ *
+ * \return vtk output
+ *
+ */
+ std::string lastProp()
+ {
+ //! vertex node output string
+ std::stringstream v_out;
+
+ // Create point data properties
+ v_out << "SCALARS domain float\n";
+
+ // Default lookup table
+ v_out << "LOOKUP_TABLE default\n";
+
+ //! For each sub-domain
+ for (size_t i = 0 ; i < vg.size() ; i++)
+ {
+ // For each position in the cell
+ for (size_t j = 0 ; j < vg.get(i).g.size() ; j++)
+ {
+ // If there are no grid in this position
+ if (vg.get(i).g.get(j).grids.size() == 0)
+ continue;
+
+ //! Get the iterator
+ auto it = vg.get(i).g.get(j).grids.get(0)->getIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ if (vg.get(i).dom.isInside(it.get().toPoint()) == true)
+ v_out << "1.0\n";
+ else
+ v_out << "0.0\n";
+
+ // increment the iterator and counter
+ ++it;
+ }
+ }
+ }
+
+ return v_out.str();
+ }
+
+ /*! \brief Get the maximum number of fused grid
+ *
+ * \return the maximum number of fused grids
+ *
+ */
+ size_t getMaxFused()
+ {
+ size_t max = 0;
+
+ //! For each sub-domain
+ for (size_t i = 0 ; i < vg.size() ; i++)
+ {
+ // For each position in the cell
+ for (size_t j = 0 ; j < vg.get(i).g.size() ; j++)
+ {
+ // If there are no grid in this position
+ if (vg.get(i).g.get(j).grids.size() > max)
+ max = vg.get(i).g.get(j).grids.size();
+ }
+ }
+
+ return max;
+ }
+
+ /*! \brief Create the VTK vertex definition
+ *
+ * \return the string with the vertices as string
+ *
+ */
+ std::string get_vertex_list()
+ {
+ //! vertex node output string
+ std::string v_out;
+
+ size_t k = 0;
+
+ //! For each sub-domain
+ for (size_t i = 0 ; i < vg.size() ; i++)
+ {
+ // For each position in the cell
+ for (size_t j = 0 ; j < vg.get(i).g.size() ; j++)
+ {
+ // If there are no grid in this position
+ if (vg.get(i).g.get(j).grids.size() == 0)
+ continue;
+ //! For each grid point create a vertex
+ auto it = vg.get(i).g.get(j).grids.get(0)->getIterator();
+
+ while (it.isNext())
+ {
+ v_out += "1 " + std::to_string(k) + "\n";
+
+ ++k;
+ ++it;
+ }
+ }
+ }
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Get the point data header
+ *
+ * \return a string with the point data header for VTK format
+ *
+ */
+
+ std::string get_point_data_header()
+ {
+ std::string v_out;
+
+ v_out += "POINT_DATA " + std::to_string(get_total()) + "\n";
+
+ return v_out;
+ }
+
+ /*! \brief Append the grid to the sub-domain, if for a sub-domain we have a grid that is overlapping
+ * fuse them, otherwise create a new combination and grid
+ *
+ * \param id sub-domain id
+ * \param g grid to output
+ * \param cmb position of the grid
+ *
+ * \return a valid slot, if does not exist it append the grid at the end with the new combination
+ *
+ */
+ void append_grid(size_t id, const typename pair::first & g, const comb<pair::first::dims> & cmb)
+ {
+ for(size_t i = 0 ; i < vg.get(id).g.size() ; i++)
+ {
+ // for each defined grid if exist the combination fuse
+ if (cmb == vg.get(id).g.get(i).cmb)
+ {
+ vg.get(id).g.get(i).grids.add(&g);
+ return;
+ }
+ }
+
+ // if the combination does not exist add the grid
+ cell_grid< typename pair::first> cg(cmb);
+ vg.get(id).g.add(cg);
+ vg.get(id).g.last().grids.add(&g);
+ }
+
+public:
+
+ /*!
+ *
+ * VTKWriter constructor
+ *
+ */
+ VTKWriter()
+ {}
+
+ /*! \brief Add grid dataset
+ *
+ * \param i sub-domain id
+ * \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 cmb position of the grid
+ *
+ */
+ void add(size_t i,
+ 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,
+ const comb<pair::first::dims> & cmb)
+ {
+ //! Increase the size
+ if (i >= vg.size())
+ vg.resize(i+1);
+
+ vg.get(i).offset = offset;
+ vg.get(i).spacing = spacing;
+ vg.get(i).dom = dom;
+
+ // append the grid
+ append_grid(i,g,cmb);
+ }
+
+ /*! \brief It write a VTK file from a graph
+ *
+ * \tparam prp_out which properties to output [default = -1 (all)]
+ *
+ * \param file path where to write
+ * \param g_name of the set of grids
+ * \param ft specify if it is a VTK BINARY or ASCII file [default = ASCII]
+ *
+ * \return true if the file is succeful written
+ *
+ */
+
+ template<int prp = -1> bool write(std::string file,
+ std::string g_name = "grids",
+ file_type ft = file_type::ASCII)
+ {
+ // Header for the vtk
+ std::string vtk_header;
+ // Point list of the VTK
+ std::string point_list;
+ // Vertex list of the VTK
+ std::string vertex_list;
+ // Graph header
+ std::string vtk_binary_or_ascii;
+ // vertex properties header
+ std::string point_prop_header;
+ // edge properties header
+ std::string vertex_prop_header;
+ // Data point header
+ std::string point_data_header;
+ // Data point
+ std::string point_data;
+
+ // VTK header
+ vtk_header = "# vtk DataFile Version 3.0\n"
+ + g_name + "\n";
+
+ // Choose if binary or ASCII
+ if (ft == file_type::ASCII)
+ {vtk_header += "ASCII\n";}
+ else
+ {vtk_header += "BINARY\n";}
+
+ // Data type for graph is DATASET POLYDATA
+ vtk_header += "DATASET POLYDATA\n";
+
+ // point properties header
+ point_prop_header = get_point_properties_list();
+
+ // Get point list
+ point_list = get_point_list();
+
+ // vertex properties header
+ vertex_prop_header = get_vertex_properties_list();
+
+ // Get vertex list
+ vertex_list = get_vertex_list();
+
+ // Get the point data header
+ point_data_header = get_point_data_header();
+
+ // Get the maximum number of fused grids
+ size_t mf = getMaxFused();
+
+ // For each property in the vertex type produce a point data
+ for (size_t i = 0 ; i < mf ; i++)
+ point_data += get_properties_output(i,g_name);
+
+ lastProp();
+
+
+ // write the file
+ std::ofstream ofs(file);
+
+ // Check if the file is open
+ if (ofs.is_open() == false)
+ {std::cerr << "Error cannot create the VTK file: " + file + "\n";}
+
+ ofs << vtk_header << point_prop_header << point_list <<
+ vertex_prop_header << vertex_list << point_data_header << point_data;
+
+ // Close the file
+
+ ofs.close();
+
+ // Completed succefully
+ return true;
+ }
+};
+
+
+#endif /* SRC_VTKWRITER_GRIDS_ST_HPP_ */
diff --git a/src/VTKWriter/VTKWriter_grids_util.hpp b/src/VTKWriter/VTKWriter_grids_util.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..cf95d89dd9411af3f5bc19605637156d5272a433
--- /dev/null
+++ b/src/VTKWriter/VTKWriter_grids_util.hpp
@@ -0,0 +1,1117 @@
+/*
+ * VTKWriter_grids_util.hpp
+ *
+ * Created on: Aug 10, 2015
+ * Author: Pietro Incardona
+ */
+
+#ifndef SRC_VTKWRITER_GRIDS_UTIL_HPP_
+#define SRC_VTKWRITER_GRIDS_UTIL_HPP_
+
+#include "util/util_debug.hpp"
+#include "is_vtk_writable.hpp"
+#include "byteswap_portable.hpp"
+
+/*! \brief Return the Attributes name from the type
+ *
+ *
+ */
+template<typename ele_g, bool has_attributes>
+struct getAttrName
+{
+ /*! \brief Get attribute name
+ *
+ * \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 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>
+{
+ /*! \brief Get attribute name
+ *
+ * \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 openfpm::vector<std::string> & prop_names, const std::string & oprp)
+ {
+ if (i >= prop_names.size())
+ {
+ return std::string("attr" + std::to_string(i) + oprp);
+ }
+ else
+ {
+ return prop_names.get(i) + oprp;
+ }
+ }
+};
+
+/*! \brief Get the vtk properties header appending a prefix at the end
+ *
+ * \tparam has_attributes indicate if the properties have attributes name
+ * \param oprp prefix
+ *
+ */
+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;
+
+ typedef typename boost::mpl::at<typename ele_g::value_type::value_type::type,boost::mpl::int_<i>>::type ctype;
+
+ // Check if T is a supported format
+ // for now we support only scalar of native type
+ if (std::rank<ctype>::value == 1)
+ {
+ if (std::extent<ctype>::value <= 3)
+ {
+ //Get type of the property
+ std::string type = getType<typename std::remove_all_extents<ctype>::type>();
+
+ // if the type is not supported skip-it
+ if (type.size() == 0)
+ {
+#ifndef DISABLE_ALL_RTTI
+ std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " the type " << demangle(typeid(ctype).name()) << " is not supported by vtk\n";
+#endif
+ return "";
+ }
+
+ // Create point data properties
+ v_out += "VECTORS " + getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp) + " " + type + "\n";
+ }
+ }
+ else
+ {
+ std::string type = getType<typename std::remove_all_extents<ctype>::type>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ {
+ // We check if is a custom vtk writable object
+
+ if (is_vtk_writable<ctype>::value == true)
+ {
+ type = getType<typename vtk_type<ctype,is_custom_vtk_writable<ctype>::value>::type >();
+
+ // 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,prop_names,oprp) + " " + type + "\n";
+ v_out += "LOOKUP_TABLE default\n";
+ }
+ else
+ 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,prop_names,oprp) + " " + type + "\n";
+
+ // Default lookup table
+ v_out += "LOOKUP_TABLE default\n";
+
+ }
+
+ // return the vertex list
+ return v_out;
+}
+
+
+
+/*! \brief Get the vtp properties header appending a prefix at the end
+ *
+ * \tparam has_attributes indicate if the properties have attributes name
+ * \param oprp prefix
+ *
+ */
+template<unsigned int i, typename ele_g, bool has_attributes> std::string get_point_property_header_impl_new_pvtp(const std::string & oprp, const openfpm::vector<std::string> & prop_names)
+{
+ //! vertex node output string
+ std::string v_out;
+
+ typedef typename boost::mpl::at<typename ele_g::value_type::value_type::type,boost::mpl::int_<i>>::type ctype;
+
+ // Check if T is a supported format
+ // for now we support only scalar of native type
+ if (std::rank<ctype>::value == 1)
+ {
+ if (std::extent<ctype>::value <= 3)
+ {
+ //Get type of the property
+ std::string type = getTypeNew<typename std::remove_all_extents<ctype>::type>();
+
+ // if the type is not supported skip-it
+ if (type.size() == 0)
+ {
+#ifndef DISABLE_ALL_RTTI
+ std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " the type " << demangle(typeid(ctype).name()) << " is not supported by vtp\n";
+#endif
+ return "";
+ }
+
+ // Create point data properties
+ v_out += " <PDataArray type=\""+type+"\" Name=\""+getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp)+"\""+" NumberOfComponents=\"3\"/>\n";
+ //v_out += "VECTORS " + getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp) + " " + type + "\n";
+ }
+ }
+ else
+ {
+ std::string type = getTypeNew<typename std::remove_all_extents<ctype>::type>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ {
+ // We check if is a custom vtk writable object
+
+ if (is_vtk_writable<ctype>::value == true)
+ {
+ type = getTypeNew<typename vtk_type<ctype,is_custom_vtk_writable<ctype>::value>::type >();
+
+ // We check if it is a vector or scalar like type
+ if (vtk_dims<ctype>::value == 1) {
+ v_out += " <PDataArray type=\"" + type + "\" Name=\"" +
+ getAttrName<ele_g, has_attributes>::get(i, prop_names, oprp) + "\"/>\n";
+ //v_out += "SCALARS " + getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp) + " " + type + "\n";
+ }
+ else{
+ v_out += " <PDataArray type=\""+type+"\" Name=\""+getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp)+"\""+" NumberOfComponents=\"3\"/>\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 += " <PDataArray type=\"" + type + "\" Name=\"" +
+ getAttrName<ele_g, has_attributes>::get(i, prop_names, oprp) + "\"/>\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";
+
+ }
+
+ // return the vertex list
+ return v_out;
+}
+
+
+/*! \brief Get the vtk properties header appending a prefix at the end
+ *
+ * \tparam has_attributes indicate if the properties have attributes name
+ * \param oprp prefix
+ *
+ */
+template<unsigned int i, typename ele_g, bool has_attributes> std::string get_point_property_header_impl_new(const std::string & oprp, const openfpm::vector<std::string> & prop_names,file_type ft)
+{
+ //! vertex node output string
+ std::string v_out;
+
+ typedef typename boost::mpl::at<typename ele_g::value_type::value_type::type,boost::mpl::int_<i>>::type ctype;
+
+ // Check if T is a supported format
+ // for now we support only scalar of native type
+ if (std::rank<ctype>::value == 1)
+ {
+ if (std::extent<ctype>::value <= 3)
+ {
+ //Get type of the property
+ std::string type = getTypeNew<typename std::remove_all_extents<ctype>::type>();
+
+ // if the type is not supported skip-it
+ if (type.size() == 0)
+ {
+#ifndef DISABLE_ALL_RTTI
+ std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " the type " << demangle(typeid(ctype).name()) << " is not supported by vtk\n";
+#endif
+ return "";
+ }
+
+ // Create point data properties
+ v_out += " <DataArray type=\""+type+"\" Name=\""+getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp)+"\""+" NumberOfComponents=\"3\"";
+ if(ft==file_type::ASCII){
+ v_out+=" format=\"ascii\">\n";
+ }
+ else{
+ v_out+=" format=\"binary\">\n";
+ }
+
+ //v_out += "VECTORS " + getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp) + " " + type + "\n";
+ }
+ }
+ else
+ {
+ std::string type = getTypeNew<typename std::remove_all_extents<ctype>::type>();
+
+ // if the type is not supported return
+ if (type.size() == 0)
+ {
+ // We check if is a custom vtk writable object
+
+ if (is_vtk_writable<ctype>::value == true)
+ {
+ type = getTypeNew<typename vtk_type<ctype,is_custom_vtk_writable<ctype>::value>::type >();
+
+ // We check if it is a vector or scalar like type
+ if (vtk_dims<ctype>::value == 1) {
+ v_out += " <DataArray type=\"" + type + "\" Name=\"" +
+ getAttrName<ele_g, has_attributes>::get(i, prop_names, oprp) + "\"";
+ if (ft == file_type::ASCII) {
+ v_out += " format=\"ascii\">\n";
+ } else {
+ v_out += " format=\"binary\">\n";
+ }
+ //v_out += "SCALARS " + getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp) + " " + type + "\n";
+ }
+ else{
+ v_out += " <DataArray type=\""+type+"\" Name=\""+getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp)+"\""+" NumberOfComponents=\"3\"";
+ if(ft==file_type::ASCII){
+ v_out+=" format=\"ascii\">\n";
+ }
+ else{
+ v_out+=" format=\"binary\">\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 += " <DataArray type=\"" + type + "\" Name=\"" +getAttrName<ele_g, has_attributes>::get(i, prop_names, oprp) + "\"";
+ if (ft == file_type::ASCII) {
+ v_out += " format=\"ascii\">\n";
+ }
+ else {
+ v_out += " format=\"binary\">\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";
+
+ }
+
+ // return the vertex list
+ return v_out;
+}
+
+/*! \brief Write the vectror property
+ *
+ * \tparam dim Dimensionality of the property
+ *
+ */
+template<unsigned int dim, typename T>
+class prop_write_out
+{
+public:
+
+ template<typename vector, typename iterator, typename I> static void write(std::ostringstream & v_out, vector & vg, size_t k, iterator & it, file_type ft)
+ {
+ if (ft == file_type::ASCII)
+ {
+ // Print the properties
+ for (size_t i1 = 0 ; i1 < vtk_dims<T>::value ; i1++)
+ {
+ v_out << vg.get(k).g.get_o(it.get()).template get<I::value>().get_vtk(i1) << " ";
+ }
+ if (vtk_dims<T>::value == 2)
+ {
+ v_out << "0.0";
+ }
+ v_out << "\n";
+ }
+ 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++)
+ {
+ 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.write((const char *)&tmp,sizeof(tmp));
+ }
+ if (vtk_dims<T>::value == 2)
+ {
+ typename is_vtk_writable<ctype>::base zero = 0.0;
+ zero = swap_endian_lt(zero);
+ v_out.write((const char *)&zero,sizeof(zero));
+ }
+ }
+ }
+};
+
+/*! \brief Write the scalar property
+ *
+ *
+ */
+template<typename T>
+class prop_write_out<0,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::ostringstream & v_out, vector & vg, size_t k, iterator & it, file_type ft)
+ {
+ typedef decltype(vg.get(k).g.template get<I::value>(it.get())) ctype_;
+ typedef typename std::remove_const<typename std::remove_reference<ctype_>::type>::type ctype;
+
+ if (ft == file_type::ASCII)
+ {
+ // Print the property
+ v_out << vg.get(k).g.template get<I::value>(it.get()) << "\n";
+ }
+ else
+ {
+ typename is_vtk_writable<ctype>::base tmp = vg.get(k).g.template get<I::value>(it.get());
+ tmp = swap_endian_lt(tmp);
+ v_out.write((const char *)&tmp,sizeof(tmp));
+ }
+ }
+};
+
+/*! \brief Write the vectror property
+ *
+ * \tparam dim Dimensionality of the property
+ *
+ */
+template<unsigned int dim, typename T>
+class prop_write_out_new
+{
+public:
+
+ template<typename vector, typename iterator, typename I> static void write(std::ostringstream & v_out, vector & vg, size_t k, iterator & it, file_type ft)
+ {
+
+ if (ft == file_type::ASCII)
+ {
+ // Print the properties
+ for (size_t i1 = 0 ; i1 < vtk_dims<T>::value ; i1++)
+ {
+ v_out << vg.get(k).g.get_o(it.get()).template get<I::value>().get_vtk(i1) << " ";
+ }
+ if (vtk_dims<T>::value == 2)
+ {
+ v_out << "0.0";
+ }
+ v_out << "\n";
+ }
+ 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++)
+ {
+ typename is_vtk_writable<ctype>::base tmp = vg.get(k).g.get_o(it.get()).template get<I::value>().get_vtk(i1);
+ v_out.write((const char *)&tmp,sizeof(tmp));
+ }
+ if (vtk_dims<T>::value == 2)
+ {
+ typename is_vtk_writable<ctype>::base zero = 0.0;
+ v_out.write((const char *)&zero,sizeof(zero));
+ }
+ }
+ }
+};
+
+/*! \brief Write the scalar property
+ *
+ *
+ */
+template<typename T>
+class prop_write_out_new<0,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::ostringstream & v_out, vector & vg, size_t k, iterator & it, file_type ft)
+ {
+ typedef decltype(vg.get(k).g.template get<I::value>(it.get())) ctype_;
+ typedef typename std::remove_const<typename std::remove_reference<ctype_>::type>::type ctype;
+
+ if (ft == file_type::ASCII)
+ {
+ // Print the property
+ v_out << vg.get(k).g.template get<I::value>(it.get()) << "\n";
+ }
+ else
+ {
+ typename is_vtk_writable<ctype>::base tmp = vg.get(k).g.template get<I::value>(it.get());
+ v_out.write((const char *)&tmp,sizeof(tmp));
+ }
+ }
+};
+
+
+/*! \brief This class is an helper to create properties output from scalar and compile-time array elements
+ *
+ * \tparam I It is an boost::mpl::int_ that indicate which property we are writing
+ * \tparam ele_g element type that store the grid information
+ * \tparam St type of space where the grid live
+ * \tparam T the type of the property
+ * \tparam is_writable flag that indicate if a property is writable
+ *
+ */
+template<typename I, typename ele_g, typename St, typename T, bool is_writable>
+struct meta_prop
+{
+ /*! \brief Write a vtk compatible type into vtk format
+ *
+ * \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, 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>("",prop_names);
+
+ // If the output has changed, we have to write the properties
+ if (v_out.size() != sz)
+ {
+ std::ostringstream stream_out;
+ if (std::is_same<T,float>::value == true)
+ {stream_out << std::setprecision(7);}
+ else
+ {stream_out << std::setprecision(16);}
+
+ // Produce point data
+
+ for (size_t k = 0 ; k < vg.size() ; k++)
+ {
+ //! Get a vertex iterator
+ auto it = vg.get(k).g.getIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ prop_write_out<vtk_dims<T>::value != 1,T>::template write<decltype(vg),decltype(it),I>(stream_out,vg,k,it,ft);
+
+ // increment the iterator and counter
+ ++it;
+ }
+ }
+
+ v_out += stream_out.str();
+
+ if (ft == file_type::BINARY)
+ v_out += "\n";
+ }
+ }
+};
+
+//! Partial specialization for N=1 1D-Array
+template<typename I, typename ele_g, typename St, typename T, size_t N1, bool is_writable>
+struct meta_prop<I, ele_g,St,T[N1],is_writable>
+{
+ /*! \brief Write a vtk compatible type into vtk format
+ *
+ * \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, 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>("",prop_names);
+
+ // If the output has changed, we have to write the properties
+ if (v_out.size() != sz)
+ {
+ std::ostringstream stream_out;
+ if (std::is_same<T,float>::value == true)
+ {stream_out << std::setprecision(7);}
+ else
+ {stream_out << std::setprecision(16);}
+
+ // Produce point data
+
+ for (size_t k = 0 ; k < vg.size() ; k++)
+ {
+ //! Get a vertex iterator
+ auto it = vg.get(k).g.getIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ if (ft == file_type::ASCII)
+ {
+ // Print the properties
+ stream_out << vg.get(k).g.template get<I::value>(it.get())[0];
+ for (size_t i1 = 1 ; i1 < N1 ; i1++)
+ {stream_out << " " << vg.get(k).g.template get<I::value>(it.get())[i1];}
+
+ if (N1 == 2)
+ {stream_out << " " << (decltype(vg.get(k).g.template get<I::value>(it.get())[0])) 0;}
+
+ stream_out << "\n";
+ }
+ else
+ {
+ T tmp;
+
+ // Print the properties
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ tmp = vg.get(k).g.template get<I::value>(it.get())[i1];
+ tmp = swap_endian_lt(tmp);
+ stream_out.write((const char *)&tmp,sizeof(T));
+ }
+ if (N1 == 2)
+ {
+ tmp = 0.0;
+ tmp = swap_endian_lt(tmp);
+ stream_out.write((const char *)&tmp,sizeof(T));
+ }
+ }
+
+ // increment the iterator and counter
+ ++it;
+ }
+ }
+
+ v_out += stream_out.str();
+
+ if (ft == file_type::BINARY)
+ {v_out += "\n";}
+ }
+ }
+};
+
+//! Partial specialization for N=2 2D-Array
+template<typename I, typename ele_g, typename St ,typename T,size_t N1,size_t N2, bool is_writable>
+struct meta_prop<I, ele_g,St, T[N1][N2],is_writable>
+{
+
+ /*! \brief Write a vtk compatible type into vtk format
+ *
+ * \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, const openfpm::vector<std::string> & prop_names, file_type ft)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ std::ostringstream stream_out;
+ if (std::is_same<T,float>::value == true)
+ {stream_out << std::setprecision(7);}
+ else
+ {stream_out << std::setprecision(16);}
+
+ // 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>("_" + 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)
+ {
+ // Produce point data
+
+ for (size_t k = 0 ; k < vg.size() ; k++)
+ {
+ //! Get a vertex iterator
+ auto it = vg.get(k).g.getIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ T tmp;
+
+ if (ft == file_type::ASCII)
+ {
+ // Print the property
+ stream_out << vg.get(k).g.template get<I::value>(it.get())[i1][i2] << "\n";
+ }
+ else
+ {
+ tmp = vg.get(k).g.template get<I::value>(it.get())[i1][i2];
+ tmp = swap_endian_lt(tmp);
+ stream_out.write((const char *)&tmp,sizeof(tmp));
+ }
+
+ // increment the iterator and counter
+ ++it;
+ }
+ }
+
+ v_out += stream_out.str();
+
+ if (ft == file_type::BINARY)
+ v_out += "\n";
+ }
+ }
+ }
+ }
+};
+
+
+//! Specialication when is not writable
+template<typename I, typename ele_g, typename St, typename T>
+struct meta_prop<I,ele_g,St,T,false>
+{
+
+ /*! \brief Write a vtk compatible type into vtk format
+ *
+ * \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, const openfpm::vector<std::string> & prop_names, file_type ft)
+ {
+ }
+};
+
+
+/*! \brief This class is an helper to create properties output from scalar and compile-time array elements
+ *
+ * \tparam I It is an boost::mpl::int_ that indicate which property we are writing
+ * \tparam ele_g element type that store the grid information
+ * \tparam St type of space where the grid live
+ * \tparam T the type of the property
+ * \tparam is_writable flag that indicate if a property is writable
+ *
+ */
+template<typename I, typename ele_g, typename St, typename T, bool is_writable>
+struct meta_prop_new
+{
+ /*! \brief Write a vtk compatible type into vtk format
+ *
+ * \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_new(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();
+ std::ostringstream v_outToEncode_;
+ std::string v_Encoded;
+
+ if (std::is_same<T,float>::value == true)
+ {v_outToEncode_ << std::setprecision(7);}
+ else
+ {v_outToEncode_ << std::setprecision(16);}
+
+ // Produce the point properties header
+ v_out += get_point_property_header_impl_new<I::value,ele_g,has_attributes<typename ele_g::value_type::value_type>::value>("",prop_names,ft);
+
+ // If the output has changed, we have to write the properties
+ if (v_out.size() != sz)
+ {
+ if (ft == file_type::BINARY) {
+ size_t pp;
+ v_outToEncode_.write((char *)&pp,8);
+ }
+ // Produce point data
+ for (size_t k = 0 ; k < vg.size() ; k++)
+ {
+ //! Get a vertex iterator
+ auto it = vg.get(k).g.getIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ prop_write_out_new<vtk_dims<T>::value != 1,T>::template write<decltype(vg),decltype(it),I>(v_outToEncode_,vg,k,it,ft);
+
+ // increment the iterator and counter
+ ++it;
+ }
+ }
+
+ if (ft == file_type::BINARY)
+ {
+ std::string v_outToEncode = v_outToEncode_.str();
+ *(size_t *) &v_outToEncode[0] = v_outToEncode.size()-sizeof(size_t);
+ v_Encoded.resize(v_outToEncode.size()/3*4+4);
+ size_t sz=EncodeToBase64((const unsigned char*)&v_outToEncode[0],v_outToEncode.size(),(unsigned char *)&v_Encoded[0],0);
+ v_Encoded.resize(sz);
+ v_out += v_Encoded + "\n";
+ }
+ else{
+ v_out += v_outToEncode_.str();
+ };
+ v_out += " </DataArray>\n";
+
+ }
+ }
+ static inline void get_pvtp_out(std::string & v_out, const openfpm::vector<std::string> & prop_names){
+
+ v_out += get_point_property_header_impl_new_pvtp<I::value,ele_g,has_attributes<typename ele_g::value_type::value_type>::value>("",prop_names);
+
+ }
+};
+
+//! Partial specialization for N=1 1D-Array
+template<typename I, typename ele_g, typename St, typename T, size_t N1, bool is_writable>
+struct meta_prop_new<I, ele_g,St,T[N1],is_writable>
+{
+ /*! \brief Write a vtk compatible type into vtk format
+ *
+ * \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_new(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();
+ std::ostringstream v_outToEncode_;
+ std::string v_Encoded;
+
+ if (std::is_same<T,float>::value == true)
+ {v_outToEncode_ << std::setprecision(7);}
+ else
+ {v_outToEncode_ << std::setprecision(16);}
+
+ // Produce the point properties header
+ v_out += get_point_property_header_impl_new<I::value,ele_g,has_attributes<typename ele_g::value_type::value_type>::value>("",prop_names,ft);
+
+ // If the output has changed, we have to write the properties
+ if (v_out.size() != sz)
+ {
+ if (ft == file_type::BINARY) {
+ size_t pp = 0;
+ v_outToEncode_.write((char *)&pp,8);
+ }
+ // Produce point data
+
+ for (size_t k = 0 ; k < vg.size() ; k++)
+ {
+ //! Get a vertex iterator
+ auto it = vg.get(k).g.getIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ if (ft == file_type::ASCII)
+ {
+ // Print the properties
+ v_outToEncode_ << vg.get(k).g.template get<I::value>(it.get())[0];
+ for (size_t i1 = 1 ; i1 < N1 ; i1++)
+ {v_outToEncode_ << " " << vg.get(k).g.template get<I::value>(it.get())[i1];}
+
+ if (N1 == 2)
+ {v_outToEncode_ << " "<< (decltype(vg.get(k).g.template get<I::value>(it.get())[0])) 0;}
+
+ v_outToEncode_ << "\n";
+ }
+ else
+ {
+ T tmp;
+
+ // Print the properties
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ tmp = vg.get(k).g.template get<I::value>(it.get())[i1];
+ //tmp = swap_endian_lt(tmp);
+ v_outToEncode_.write((const char *)&tmp,sizeof(T));
+ }
+ if (N1 == 2)
+ {
+ tmp = 0.0;
+ //tmp = swap_endian_lt(tmp);
+ v_outToEncode_.write((const char *)&tmp,sizeof(T));
+ }
+ }
+
+ // increment the iterator and counter
+ ++it;
+ }
+ }
+ if (ft == file_type::BINARY)
+ {
+ std::string v_outToEncode = v_outToEncode_.str();
+ *(size_t *) &v_outToEncode[0] = v_outToEncode.size()-sizeof(size_t);
+ v_Encoded.resize(v_outToEncode.size()/3*4+4);
+ size_t sz=EncodeToBase64((const unsigned char*)&v_outToEncode[0],v_outToEncode.size(),(unsigned char *)&v_Encoded[0],0);
+ v_Encoded.resize(sz);
+ v_out += v_Encoded + "\n";
+ }
+ else{
+ v_out += v_outToEncode_.str();
+ };
+ v_out += " </DataArray>\n";
+ }
+ }
+
+ static inline void get_pvtp_out(std::string & v_out, const openfpm::vector<std::string> & prop_names){
+
+ v_out += get_point_property_header_impl_new_pvtp<I::value,ele_g,has_attributes<typename ele_g::value_type::value_type>::value>("",prop_names);
+
+ }
+};
+
+//! Partial specialization for N=2 2D-Array
+template<typename I, typename ele_g, typename St ,typename T,size_t N1,size_t N2, bool is_writable>
+struct meta_prop_new<I, ele_g,St, T[N1][N2],is_writable>
+{
+
+ /*! \brief Write a vtk compatible type into vtk format
+ *
+ * \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_new(const openfpm::vector< ele_g > & vg, std::string & v_out, const openfpm::vector<std::string> & prop_names, file_type ft)
+ {
+ std::string v_outToEncode,v_Encoded;
+
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ v_outToEncode.clear();
+ // actual string size
+ size_t sz = v_out.size();
+
+ // Produce the point properties header
+ v_out += get_point_property_header_impl_new<I::value,ele_g,has_attributes<typename ele_g::value_type::value_type>::value>("_" + std::to_string(i1) + "_" + std::to_string(i2),prop_names, ft);
+
+ // If the output has changed, we have to write the properties
+ if (v_out.size() != sz)
+ {
+ if (ft == file_type::BINARY) {
+ v_outToEncode.append(8,0);
+ }
+ // Produce point data
+
+ for (size_t k = 0 ; k < vg.size() ; k++)
+ {
+ //! Get a vertex iterator
+ auto it = vg.get(k).g.getIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ T tmp;
+
+ if (ft == file_type::ASCII)
+ {
+ // Print the property
+ v_outToEncode += std::to_string(vg.get(k).g.template get<I::value>(it.get())[i1][i2]) + "\n";
+ }
+ else
+ {
+ tmp = vg.get(k).g.template get<I::value>(it.get())[i1][i2];
+ //tmp = swap_endian_lt(tmp);
+ v_outToEncode.append((const char *)&tmp,sizeof(tmp));
+ }
+
+ // increment the iterator and counter
+ ++it;
+ }
+ }
+ if (ft == file_type::BINARY)
+ {
+ *(size_t *) &v_outToEncode[0] = v_outToEncode.size()-sizeof(size_t);
+ v_Encoded.resize(v_outToEncode.size()/3*4+4);
+ size_t sz=EncodeToBase64((const unsigned char*)&v_outToEncode[0],v_outToEncode.size(),(unsigned char *)&v_Encoded[0],0);
+ v_Encoded.resize(sz);
+ v_out += v_Encoded + "\n";
+ }
+ else{
+ v_out += v_outToEncode;
+ };
+ v_out += " </DataArray>\n";
+
+ }
+ }
+ }
+ }
+
+ static inline void get_pvtp_out(std::string & v_out, const openfpm::vector<std::string> & prop_names)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ v_out += get_point_property_header_impl_new_pvtp<I::value,ele_g,has_attributes<typename ele_g::value_type::value_type>::value>("_" + std::to_string(i1) + "_" + std::to_string(i2),prop_names);
+ }
+ }
+ }
+};
+
+
+//! Specialication when is not writable
+template<typename I, typename ele_g, typename St, typename T>
+struct meta_prop_new<I,ele_g,St,T,false>
+{
+
+ /*! \brief Write a vtk compatible type into vtk format
+ *
+ * \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_new(const openfpm::vector< ele_g > & vg, std::string & v_out, const openfpm::vector<std::string> & prop_names, file_type ft)
+ {
+ }
+
+ static inline void get_pvtp_out(std::string & v_out, const openfpm::vector<std::string> & prop_names)
+ {}
+};
+
+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)
+ {
+ v_out << p[0];
+ for (int i = 1 ; i < dims ; i++)
+ {v_out << " " << p[i];}
+ size_t i = dims;
+ for ( ; i < 3 ; i++)
+ {v_out << " 0.0";}
+ v_out << "\n";
+ }
+ else
+ {
+ size_t i = 0;
+ for ( ; i < dims ; i++)
+ {
+ // we use float so we have to convert to float
+ auto tmp = p.get(i);
+ tmp = swap_endian_lt(tmp);
+ v_out.write((const char *)&tmp,sizeof(tmp));
+ }
+ for ( ; i < 3 ; i++)
+ {
+ // we use float so we have to convert to float
+
+ /* coverity[dead_error_begin] */
+ T tmp = 0.0;
+ tmp = swap_endian_lt(tmp);
+ v_out.write((const char *)&tmp,sizeof(tmp));
+ }
+ }
+}
+
+
+template<unsigned int dims,typename T> inline void output_point_new(Point<dims,T> & p,std::stringstream & v_out, file_type ft)
+{
+ if (ft == file_type::ASCII)
+ {
+ v_out << p[0];
+ for (int i = 1 ; i < dims ; i++)
+ {v_out << " " << p[i];}
+ size_t i = dims;
+ for ( ; i < 3 ; i++)
+ {v_out << " 0.0";}
+ v_out << "\n";
+ }
+ else
+ {
+ size_t i = 0;
+ for ( ; i < dims ; i++)
+ {
+ // we use float so we have to convert to float
+ auto tmp = p.get(i);
+ v_out.write((const char *)&tmp,sizeof(tmp));
+ }
+ for ( ; i < 3 ; i++)
+ {
+ // we use float so we have to convert to float
+
+ /* coverity[dead_error_begin] */
+ T tmp = 0.0;
+ 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));
+ }
+}
+
+inline void output_vertex_new(size_t k,std::string & v_out, file_type ft)
+{
+ if (ft == file_type::ASCII)
+ {v_out += std::to_string(k) + "\n";}
+ else
+ {
+ size_t tmp;
+ tmp = k;
+ v_out.append((const char *)&tmp,sizeof(size_t));
+ }
+}
+
+#endif /* SRC_VTKWRITER_GRIDS_UTIL_HPP_ */
diff --git a/src/VTKWriter/VTKWriter_point_set.hpp b/src/VTKWriter/VTKWriter_point_set.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..4c1fae250972a99e26d6eba7c53529bf0aad42a6
--- /dev/null
+++ b/src/VTKWriter/VTKWriter_point_set.hpp
@@ -0,0 +1,770 @@
+/*
+ * VTKWriter_point_set.hpp
+ *
+ * Created on: Feb 6, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_VTKWRITER_POINT_SET_HPP_
+#define OPENFPM_IO_SRC_VTKWRITER_POINT_SET_HPP_
+
+#include <cstddef>
+#include <boost/mpl/pair.hpp>
+#include "VTKWriter_grids_util.hpp"
+#include "is_vtk_writable.hpp"
+#include <string>
+#include "byteswap_portable.hpp"
+#include "MetaParser/MetaParser.hpp"
+
+/*! \brief Store a reference to the vector position
+ *
+ * \tparam Vps Type of vector that store the position of the particles
+ *
+ */
+template <typename Vps>
+class ele_vps
+{
+public:
+
+ //! type of vector that store the particle position
+ typedef Vps value_type;
+
+ //! particle position vector
+ const Vps & g;
+
+ //! ghost marker
+ size_t mark;
+
+ //! constructor
+ ele_vps(const Vps & g, size_t mark)
+ :g(g),mark(mark)
+ {}
+
+};
+
+/*! \brief Store a reference to the vector properties
+ *
+ * \tparam Vpp Type of vector that store the property of the particles
+ *
+ */
+template <typename Vpp>
+class ele_vpp
+{
+public:
+
+ //! type of vector that store the particle properties
+ typedef Vpp value_type;
+
+
+ //! Reference to the particle properties
+ const Vpp & g;
+
+ //! ghost marker
+ size_t mark;
+
+ //! constructor
+ ele_vpp(const Vpp & vpp, size_t mark)
+ :g(vpp),mark(mark)
+ {}
+
+};
+
+
+/*! \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 produce an output for each property
+ *
+ * \tparam ele_v It is the class ele_v that store the couple vector of position and property
+ *
+ *
+ */
+template<typename ele_v, typename St>
+struct prop_out_v
+{
+ //! Binary or ASCII
+ file_type ft;
+
+ //! property output string
+ std::string & v_out;
+
+ //! 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
+ * \param vv vector we are processing
+ * \param ft ASCII or BINARY format
+ *
+ */
+ 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)
+ {};
+
+ /*! \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_new<boost::mpl::int_<T::value> ,ele_v,St, ptype, is_vtk_writable<base_ptype>::value > m(vv,v_out,prop_names,ft);
+ }
+
+ void lastProp()
+ {
+ std::string v_outToEncode,v_Encoded;
+ // Create point data properties
+ //v_out += "SCALARS domain float\n";
+ // Default lookup table
+ //v_out += "LOOKUP_TABLE default\n";
+ v_out += " <DataArray type=\"Float32\" Name=\"domain\"";
+ if (ft == file_type::ASCII) {
+ v_out += " format=\"ascii\">\n";
+ }
+ else {
+ v_out += " format=\"binary\">\n";
+ }
+
+ if (ft == file_type::BINARY) {
+ v_outToEncode.append(8,0);
+ }
+ // Produce point data
+ for (size_t k = 0 ; k < vv.size() ; k++)
+ {
+ //! Get a vertex iterator
+ auto it = vv.get(k).g.getIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ if (ft == file_type::ASCII)
+ {
+ if (it.get() < vv.get(k).mark)
+ v_outToEncode += "1.0\n";
+ else
+ v_outToEncode += "0.0\n";
+ }
+ else
+ {
+ if (it.get() < vv.get(k).mark)
+ {
+ float one = 1;
+ //one = swap_endian_lt(one);
+ v_outToEncode.append((const char *)&one,sizeof(int));
+ }
+ else
+ {
+ float zero = 0;
+ //zero = swap_endian_lt(zero);
+ v_outToEncode.append((const char *)&zero,sizeof(int));
+ }
+ }
+
+ // increment the iterator and counter
+ ++it;
+ }
+ }
+ if (ft == file_type::BINARY)
+ {
+ *(size_t *) &v_outToEncode[0] = v_outToEncode.size()-sizeof(size_t);
+ v_Encoded.resize(v_outToEncode.size()/3*4+4);
+ size_t sz=EncodeToBase64((const unsigned char*)&v_outToEncode[0],v_outToEncode.size(),(unsigned char *)&v_Encoded[0],0);
+ v_Encoded.resize(sz);
+ v_out += v_Encoded + "\n";
+ }
+ else{
+ v_out += v_outToEncode;
+ };
+ v_out+=" </DataArray>\n";
+ }
+
+};
+
+
+/*! \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 produce an output for each property
+ *
+ * \tparam ele_v It is the class ele_v that store the couple vector of position and property
+ *
+ *
+ */
+template<typename ele_v, typename St>
+struct prop_out_v_pvtp
+{
+ //! property output string
+ std::string & v_out;
+
+ //! properties names
+ const openfpm::vector<std::string> & prop_names;
+
+ /*! \brief constructor
+ *
+ * \param v_out string to fill with the vertex properties
+ * \param vv vector we are processing
+ * \param ft ASCII or BINARY format
+ *
+ */
+ prop_out_v_pvtp(std::string & v_out,
+ const openfpm::vector<std::string> & prop_names)
+ :v_out(v_out),prop_names(prop_names)
+ {
+ //meta_prop_new<boost::mpl::int_<T::value> ,ele_v,St, ptype, is_vtk_writable<base_ptype>::value > m(vv,v_out,prop_names,ft);
+ };
+
+ /*! \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;
+
+ //std::string type = getTypeNew<base_ptype>();
+ meta_prop_new<boost::mpl::int_<T::value> ,ele_v,St, ptype, is_vtk_writable<base_ptype>::value >::get_pvtp_out(v_out,prop_names);
+ //v_out += " <PDataArray type=\""+type+"\" Name=\""+getAttrName<ele_g,has_attributes>::get(i,prop_names,oprp)+"\""+" NumberOfComponents=\"3\"";
+ }
+
+
+ void lastProp()
+ {
+v_out += " <PDataArray type=\"Float32\" Name=\"domain\"/>\n </PPointData>\n";
+ }
+};
+
+/*!
+ *
+ * It write a VTK format file for a list of grids defined on a space
+ *
+ * \tparam boost::mpl::pair<G,S>
+ *
+ * where G is the type of the vector containing the properties, S is the
+ * type of vector containing the particle positions
+ *
+ */
+template <typename pair>
+class VTKWriter<pair,VECTOR_POINTS>
+{
+ //! Vector of position
+ openfpm::vector< ele_vps<typename pair::first >> vps;
+ //! Vector of properties
+ openfpm::vector< ele_vpp<typename pair::second>> vpp;
+
+ /*! \brief Get the total number of points
+ *
+ * \return the total number
+ *
+ */
+ size_t get_total()
+ {
+ size_t tot = 0;
+
+ //! Calculate the full number of vertices
+ for (size_t i = 0 ; i < vps.size() ; i++)
+ {
+ tot += vps.get(i).g.size();
+ }
+ return tot;
+ }
+
+ /*! \brief It get the vertex properties list
+ *
+ * It get the vertex properties list of the vertex defined as VTK header
+ *
+ * \return a string that define the vertex properties in graphML format
+ *
+ */
+ std::string get_vertex_properties_list(file_type & opt)
+ {
+ //! vertex property output string
+ std::string v_out;
+
+ v_out += " <Verts>\n";
+ if (opt == file_type::ASCII)
+
+ {
+ v_out+=" <DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">\n";
+ }
+ else
+ {
+ v_out+=" <DataArray type=\"Int64\" Name=\"connectivity\" format=\"binary\">\n";
+ }
+
+ // write the number of vertex
+ //v_out += "VERTICES " + std::to_string(get_total()) + " " + std::to_string(get_total() * 2) + "\n";
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief It get the point position header string
+ *
+ * It get the vertex position header of the vertex defined as a VTK header
+ *
+ * \return a string that define the vertex position format
+ *
+ */
+ std::string get_point_properties_list(file_type ft)
+ {
+ //! vertex property output string
+ std::string v_out;
+
+ // write the number of vertex
+
+ v_out += " <Piece NumberOfPoints=\"" + std::to_string(get_total()) + "\" " +"NumberOfVerts=\"" + std::to_string(get_total()) + "\">\n";
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief Create the VTK point list
+ *
+ * \param ft file_type
+ *
+ * \return the list of points
+ *
+ */
+ std::string get_point_list(file_type & opt)
+ {
+ //! vertex node output string
+ std::stringstream v_out;
+
+ v_out<<" <Points>\n";
+
+ if (std::is_same<float,typename pair::first::value_type::coord_type>::value == true)
+ {
+ if (opt == file_type::ASCII)
+ {
+ v_out<<" <DataArray type=\"Float32\" Name=\"Points\" NumberOfComponents=\"3\" format=\"ascii\">\n";
+ }
+ else
+ {
+ v_out<<" <DataArray type=\"Float32\" Name=\"Points\" NumberOfComponents=\"3\" format=\"binary\">\n";
+ }
+ }
+ else
+ {
+ if (opt == file_type::ASCII)
+ {
+ v_out<<" <DataArray type=\"Float64\" Name=\"Points\" NumberOfComponents=\"3\" format=\"ascii\">\n";
+ }
+ else
+ {
+ v_out<<" <DataArray type=\"Float64\" Name=\"Points\" NumberOfComponents=\"3\" format=\"binary\">\n";
+ }
+ }
+
+ std::stringstream binaryToEncode;
+ if (std::is_same<float,typename pair::first::value_type::coord_type>::value == true)
+ {
+ binaryToEncode << std::setprecision(7);
+ }
+ else
+ {
+ binaryToEncode << std::setprecision(16);
+ }
+
+ //! For each defined grid
+ if (opt == file_type::BINARY)
+ {
+ size_t tmp=0;
+ binaryToEncode.write((const char *)&tmp,sizeof(tmp));
+ }
+
+ for (size_t i = 0 ; i < vps.size() ; i++)
+ {
+ //! write the particle position
+ auto it = vps.get(i).g.getIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ Point<pair::first::value_type::dims,typename pair::first::value_type::coord_type> p;
+ p = vps.get(i).g.get(it.get());
+
+ output_point_new<pair::first::value_type::dims,typename pair::first::value_type::coord_type>(p,binaryToEncode,opt);
+
+ // increment the iterator and counter
+ ++it;
+ }
+ }
+ //! In case of binary we have to add a new line at the end of the list
+ if (opt == file_type::BINARY){
+ std::string buffer_out,buffer_bin;
+ buffer_bin=binaryToEncode.str();
+ *(size_t *)&buffer_bin[0]=buffer_bin.size()-8;
+ buffer_out.resize(buffer_bin.size()/3*4+4);
+ unsigned long sz = EncodeToBase64((const unsigned char*)&buffer_bin[0],buffer_bin.size(),(unsigned char*)&buffer_out[0],0);
+ buffer_out.resize(sz);
+ v_out << buffer_out<<std::endl;
+ }
+ else
+ {
+ v_out<<binaryToEncode.str();
+ }
+ v_out<<" </DataArray>\n";
+ v_out<<" </Points>\n";
+ // return the vertex list
+ return v_out.str();
+ }
+
+ /*! \brief Create the VTK vertex list
+ *
+ * \param ft file_type
+ *
+ * \return the list of vertices
+ *
+ */
+ std::string get_vertex_list(file_type ft)
+ {
+ // vertex node output string
+ std::string v_out,v_outToEncode,v_Encoded;
+
+ size_t k = 0;
+ if (ft == file_type::BINARY) {
+ v_outToEncode.append(8,0);
+ }
+ for (size_t i = 0 ; i < vps.size() ; i++)
+ {
+ //! For each grid point create a vertex
+ auto it = vps.get(i).g.getIterator();
+
+ while (it.isNext())
+ {
+ output_vertex_new(k,v_outToEncode,ft);
+
+ ++k;
+ ++it;
+ }
+ }
+ //! In case of binary we have to add a new line at the end of the list
+ if (ft == file_type::BINARY)
+ {
+ *(size_t *) &v_outToEncode[0] = v_outToEncode.size()-sizeof(size_t);
+ v_Encoded.resize(v_outToEncode.size()/3*4+4);
+ size_t sz=EncodeToBase64((const unsigned char*)&v_outToEncode[0],v_outToEncode.size(),(unsigned char *)&v_Encoded[0],0);
+ v_Encoded.resize(sz);
+ v_out += v_Encoded + "\n";
+ }
+ else{
+ v_out += v_outToEncode;
+ };
+ v_out += " </DataArray>\n";
+ v_out += " <DataArray type=\"Int64\" Name=\"offsets\" ";
+
+ if (ft == file_type::ASCII)
+ {
+ v_out += "format=\"ascii\">\n";
+ }
+ else{
+ v_out += "format=\"binary\">\n";
+ }
+
+ k=0;
+ v_outToEncode.clear();
+ if (ft == file_type::BINARY) {
+ v_outToEncode.append(8,0);
+ }
+
+ for (size_t i = 0 ; i < vps.size() ; i++)
+ {
+ //! For each grid point create a vertex
+ auto it = vps.get(i).g.getIterator();
+ while (it.isNext())
+ {
+ output_vertex_new(k+1,v_outToEncode,ft);
+
+ ++k;
+ ++it;
+ }
+ }
+ if (ft == file_type::BINARY)
+ {
+ *(size_t *) &v_outToEncode[0] = v_outToEncode.size()-sizeof(size_t);
+ v_Encoded.resize(v_outToEncode.size()/3*4+4);
+ size_t sz=EncodeToBase64((const unsigned char*)&v_outToEncode[0],v_outToEncode.size(),(unsigned char *)&v_Encoded[0],0);
+ v_Encoded.resize(sz);
+ v_out += v_Encoded + "\n";
+ }
+ else{
+ v_out += v_outToEncode;
+ };
+ v_out += " </DataArray>\n";
+ v_out += " </Verts>\n";
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Get the point data header
+ *
+ * \return a string with the point data header for VTK format
+ *
+ */
+ std::string get_point_data_header()
+ {
+ std::string v_out;
+
+ v_out += " <PointData>\n";
+
+ return v_out;
+ }
+ struct doubleint{
+ long int i;
+ double d;
+ };
+ /*! \brief return the meta data string
+ *
+ * \param meta_data string with the meta-data to add
+ *
+ */
+ std::string add_meta_data(std::string & meta_data, file_type & opt)
+ {
+ std::string meta_string;
+
+ // check for time metadata
+ MetaParser_options opts;
+ opts.add_options()
+ ("time", MetaParser_def::value<double>());
+
+ MetaParser mp(opts);
+ mp.parse(meta_data);
+
+ double time = 0.0;
+ bool exist = mp.getOption("time",time);
+
+ if (exist == true)
+ {
+ //<DataArray type="Float64" Name="TimeValue" NumberOfTuples="1" format="ascii" RangeMin="2" RangeMax="2">
+ //meta_string += "";
+ meta_string += " <FieldData>\n";
+
+ if (opt == file_type::ASCII)
+ { meta_string += " <DataArray type=\"Float64\" Name=\"TimeValue\" NumberOfTuples=\"1\" format=\"ascii\">\n";
+ meta_string += std::to_string(time);
+ }
+ else
+ {
+ meta_string += " <DataArray type=\"Float64\" Name=\"TimeValue\" NumberOfTuples=\"1\" format=\"binary\">\n";
+
+ //time = swap_endian_lt(time);
+ unsigned char time_string[24];//= base64_encode((const unsigned char*)&time,6);
+ //const unsigned char Time=(const unsigned char)time;
+ doubleint timeInit;
+ timeInit.i=8;
+ timeInit.d=time;
+ size_t sz=EncodeToBase64((const unsigned char*)&timeInit,16,time_string,0);
+ //meta_string.append((const char *)&time,sizeof(double));
+ //meta_string += time_string;
+ meta_string.append((const char *)time_string,sz);
+ }
+ meta_string += "\n";
+ meta_string += " </DataArray>\n";
+ meta_string += " </FieldData>\n";
+ }
+
+
+ return meta_string;
+ }
+
+public:
+
+ /*!
+ *
+ * VTKWriter constructor
+ *
+ */
+ VTKWriter()
+ {}
+
+ /*! \brief Add a vector dataset
+ *
+ * \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 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)
+ {
+ ele_vps<typename pair::first> t1(vps,mark);
+ ele_vpp<typename pair::second> t2(vpp,mark);
+
+ this->vps.add(t1);
+ this->vpp.add(t2);
+ }
+
+/*! \brief It write a Merged VTP type file from a vector of points
+ *
+ * \tparam prp_out which properties to output [default = -1 (all)]
+ *
+ * \return true if the write complete successfully
+ *
+ */
+ bool write_pvtp(std::string file,const openfpm::vector<std::string> & prop_names,size_t n,long int timestamp=-1,double time=-1)
+ {
+ //openfpm::vector< ele_vpp<typename pair::second>> vpp;
+ // Header for the vtk
+ std::string vtk_header;
+ std::string Name_data;
+ std::string PpointEnd;
+ std::string Piece;
+ if(time==-1){
+ vtk_header = "<VTKFile type=\"PPolyData\" version=\"1.0\" byte_order=\"LittleEndian\" header_type=\"UInt64\">\n <PPolyData>\n <PPointData>\n";
+ }
+ else{
+ vtk_header = "<VTKFile type=\"PPolyData\" version=\"1.0\" byte_order=\"LittleEndian\" header_type=\"UInt64\">\n <PPolyData>\n <FieldData> \n <DataArray type=\"Float64\" Name=\"TimeValue\" NumberOfTuples=\"1\" format=\"ASCII\">\n "+std::to_string(time)+"\n </DataArray>\n </FieldData>\n <PPointData>\n";
+ }
+ prop_out_v_pvtp< ele_vpp<typename pair::second>, typename pair::first::value_type::coord_type> pp(Name_data,prop_names);
+ boost::mpl::for_each< boost::mpl::range_c<int,0, pair::second::value_type::max_prop> >(pp);
+ pp.lastProp();
+ PpointEnd += " <PPoints>\n <PDataArray type=\""+getTypeNew<typename decltype(vps)::value_type::value_type::value_type::coord_type>()+"\" Name=\"Points\" NumberOfComponents=\"3\"/>\n </PPoints>\n";
+
+
+ if (timestamp==-1) {
+ for (int i = 0; i < n; i++)
+ { Piece += " <Piece Source=\"" + file.substr(0, file.size()) + "_" +std::to_string(i) + ".vtp\"/>\n";}
+ file += ".pvtp";
+ }
+ else{
+ for (int i = 0; i < n; i++)
+ { Piece += " <Piece Source=\"" + file.substr(0, file.size()) + "_" +std::to_string(i) + "_" + std::to_string(timestamp) + ".vtp\"/>\n";}
+ file += "_" + std::to_string(timestamp) + ".pvtp";
+ }
+ std::string closingFile=" </PPolyData>\n</VTKFile>";
+
+ // write the file
+ std::ofstream ofs(file);
+
+ // Check if the file is open
+ if (ofs.is_open() == false)
+ {std::cerr << "Error cannot create the PVTP file: " + file + "\n";}
+
+ ofs << vtk_header << Name_data <<PpointEnd<< Piece << closingFile;
+
+ // Close the file
+
+ ofs.close();
+
+ return true;
+ }
+
+ /*! \brief It write a VTK file from a vector of points
+ *
+ * \tparam prp_out which properties to output [default = -1 (all)]
+ *
+ * \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,
+ const openfpm::vector<std::string> & prop_names,
+ std::string f_name = "points" ,
+ std::string meta_data = "",
+ file_type ft = file_type::ASCII)
+ {
+ // Header for the vtk
+ std::string vtk_header;
+ // Point list of the VTK
+ std::string point_list;
+ // Vertex list of the VTK
+ std::string vertex_list;
+ // Graph header
+ std::string vtk_binary_or_ascii;
+ // vertex properties header
+ std::string point_prop_header;
+ // edge properties header
+ std::string vertex_prop_header;
+ // Data point header
+ std::string point_data_header;
+ // Data point
+ std::string point_data;
+
+ // VTK header
+ vtk_header = "<VTKFile type=\"PolyData\" version=\"1.0\" byte_order=\"LittleEndian\" header_type=\"UInt64\">\n";
+
+ vtk_header +=" <PolyData>\n";
+
+ // Choose if binary or ASCII
+/* if (ft == file_type::ASCII)
+ {vtk_header += "ASCII\n";}
+ else
+ {vtk_header += "BINARY\n";}*/
+
+ // Data type for graph is DATASET POLYDATA
+ //vtk_header += "DATASET POLYDATA\n";
+
+ vtk_header += add_meta_data(meta_data,ft);
+
+ // point properties header
+ point_prop_header = get_point_properties_list(ft);
+
+ // Get point list
+ point_list = get_point_list(ft);
+
+ // vertex properties header
+ vertex_prop_header = get_vertex_properties_list(ft);
+
+ // 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_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);}
+ else
+ {boost::mpl::for_each< boost::mpl::range_c<int,prp, prp> >(pp);}
+
+ // Add the last property
+ pp.lastProp();
+
+ std::string closingFile=" </PointData>\n </Piece>\n </PolyData>\n</VTKFile>";
+
+ // write the file
+ std::ofstream ofs(file);
+
+ // Check if the file is open
+ if (ofs.is_open() == false)
+ {std::cerr << "Error cannot create the VTK file: " + file + "\n";}
+
+ ofs << vtk_header << point_prop_header << point_list <<
+ vertex_prop_header << vertex_list << point_data_header << point_data << closingFile;
+
+ // Close the file
+
+ ofs.close();
+
+ // Completed succefully
+ return true;
+ }
+};
+
+
+#endif /* OPENFPM_IO_SRC_VTKWRITER_POINT_SET_HPP_ */
diff --git a/src/VTKWriter/VTKWriter_unit_tests.hpp b/src/VTKWriter/VTKWriter_unit_tests.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..a909c31da497a743986e83794633b87f73d1423a
--- /dev/null
+++ b/src/VTKWriter/VTKWriter_unit_tests.hpp
@@ -0,0 +1,1531 @@
+/*
+ * VTKWriter_unit_tests.hpp
+ *
+ * Created on: May 6, 2015
+ * Author: Pietro Incardona
+ *
+ * Modified by Abhinav Singh May 17, 2021
+ */
+
+#ifndef VTKWRITER_UNIT_TESTS_HPP_
+#define VTKWRITER_UNIT_TESTS_HPP_
+
+#include "data_type/aggregate.hpp"
+#include <random>
+#include "VTKWriter.hpp"
+#include "util/SimpleRNG.hpp"
+
+BOOST_AUTO_TEST_SUITE( vtk_writer_test )
+
+/*! \brief Sub-domain vertex graph node
+ *
+ */
+struct vertex
+{
+ //! The node contain 3 unsigned long integer for communication computation memory and id
+ typedef boost::fusion::vector<float,float,float,float,size_t,double,unsigned char,long int> type;
+
+ //! type of the positional field
+ typedef float s_type;
+
+ //! Attributes name
+ struct attributes
+ {
+ static const std::string name[];
+ };
+
+ //! The data
+ type data;
+
+ //! x
+ static const unsigned int x = 0;
+ //! y
+ static const unsigned int y = 1;
+ //! z
+ static const unsigned int z = 2;
+ //! property 1
+ static const unsigned int prp1 = 3;
+ //! property 2
+ static const unsigned int prp2 = 4;
+ //! property 3
+ static const unsigned int prp3 = 5;
+ //! property 4
+ static const unsigned int prp4 = 6;
+ //! property 5
+ static const unsigned int prp5 = 7;
+
+ //! total number of properties boost::fusion::vector
+ static const unsigned int max_prop = 8;
+
+ /*!
+ * Default constructor
+ *
+ */
+ vertex()
+ {
+
+ }
+
+ static inline bool noPointers()
+ {
+ return true;
+ }
+
+ /*! \brief Initialize the VTKVertex
+ *
+ * \param x coordinate x
+ * \param y coordinate y
+ * \param z coordinate z
+ *
+ */
+ vertex(float x, float y, float z)
+ {
+ boost::fusion::at_c<vertex::x>(data) = x;
+ boost::fusion::at_c<vertex::y>(data) = y;
+ boost::fusion::at_c<vertex::z>(data) = z;
+ }
+};
+
+const std::string vertex::attributes::name[] = {"x","y","z","prp1","prp2","prp3","prp4","prp5"};
+
+struct vertex2
+{
+ //! The node contain 3 unsigned long integer for communication computation memory and id
+ typedef boost::fusion::vector<float[3],size_t,double> type;
+
+ //! type of the positional field
+ typedef float s_type;
+
+ //! Attributes name
+ struct attributes
+ {
+ static const std::string name[];
+ };
+
+ //! The data
+ type data;
+
+ //! computation property id in boost::fusion::vector
+ static const unsigned int x = 0;
+ static const unsigned int prp1 = 1;
+ static const unsigned int prp2 = 2;
+
+ //! total number of properties boost::fusion::vector
+ static const unsigned int max_prop = 3;
+
+ /*!
+ * Default constructor
+ *
+ */
+ vertex2()
+ {
+
+ }
+
+ static inline bool noPointers()
+ {
+ return true;
+ }
+
+ /*! \brief Initialize the VTKVertex
+ *
+ * \param x coordinate x
+ * \param y coordinate y
+ * \param z coordinate z
+ *
+ */
+ vertex2(float x, float y, float z)
+ {
+ boost::fusion::at_c<vertex::x>(data)[0] = x;
+ boost::fusion::at_c<vertex::x>(data)[1] = y;
+ boost::fusion::at_c<vertex::x>(data)[2] = z;
+ }
+};
+
+// use the vertex like the edge
+typedef vertex edge;
+
+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
+
+ Graph_CSR<vertex2,edge> gr;
+
+ // Create a cube graph
+
+ gr.addVertex(vertex2(0.0,0.0,0.0));
+ gr.addVertex(vertex2(0.0,0.0,1.0));
+ gr.addVertex(vertex2(0.0,1.0,0.0));
+ gr.addVertex(vertex2(0.0,1.0,1.0));
+ gr.addVertex(vertex2(1.0,0.0,0.0));
+ gr.addVertex(vertex2(1.0,0.0,1.0));
+ gr.addVertex(vertex2(1.0,1.0,0.0));
+ gr.addVertex(vertex2(1.0,1.0,1.0));
+
+ gr.addEdge(0,6);
+ gr.addEdge(6,4);
+ gr.addEdge(4,0);
+
+ gr.addEdge(0,2);
+ gr.addEdge(2,6);
+ gr.addEdge(6,0);
+
+ gr.addEdge(0,3);
+ gr.addEdge(3,2);
+ gr.addEdge(2,0);
+
+ gr.addEdge(0,1);
+ gr.addEdge(1,3);
+ gr.addEdge(3,0);
+
+ gr.addEdge(2,7);
+ gr.addEdge(7,6);
+ gr.addEdge(6,2);
+
+ gr.addEdge(2,3);
+ gr.addEdge(3,7);
+ gr.addEdge(7,2);
+
+ gr.addEdge(4,6);
+ gr.addEdge(6,7);
+ gr.addEdge(7,4);
+
+ gr.addEdge(4,7);
+ gr.addEdge(7,5);
+ gr.addEdge(5,4);
+
+ gr.addEdge(0,4);
+ gr.addEdge(4,5);
+ gr.addEdge(5,0);
+
+ gr.addEdge(0,5);
+ gr.addEdge(5,1);
+ gr.addEdge(1,0);
+
+ gr.addEdge(1,5);
+ gr.addEdge(5,7);
+ gr.addEdge(7,1);
+
+ gr.addEdge(1,7);
+ gr.addEdge(7,3);
+ gr.addEdge(3,1);
+
+ // Write the VTK file
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/vtk_graph_v2_test.vtk");
+
+#else
+
+ std::string c2 = std::string("test_data/vtk_graph_v2_test.vtk");
+
+#endif
+
+ VTKWriter<Graph_CSR<vertex2,edge>,VTK_GRAPH> vtk(gr);
+ vtk.write("vtk_graph_v2.vtk");
+
+ // check that match
+
+ bool test = compare("vtk_graph_v2.vtk",c2);
+ 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
+
+ Graph_CSR<vertex2,vertex2> gr;
+
+ // Create a cube graph
+
+ gr.addVertex(vertex2(0.0,0.0,0.0));
+ gr.addVertex(vertex2(0.0,0.0,1.0));
+ gr.addVertex(vertex2(0.0,1.0,0.0));
+ gr.addVertex(vertex2(0.0,1.0,1.0));
+ gr.addVertex(vertex2(1.0,0.0,0.0));
+ gr.addVertex(vertex2(1.0,0.0,1.0));
+ gr.addVertex(vertex2(1.0,1.0,0.0));
+ gr.addVertex(vertex2(1.0,1.0,1.0));
+
+ gr.addEdge(0,6,vertex2(0.0,0.0,1.0));
+ gr.addEdge(6,4,vertex2(0.0,0.0,1.0));
+ gr.addEdge(4,0,vertex2(0.0,0.0,1.0));
+
+ gr.addEdge(0,2,vertex2(0.0,0.0,1.0));
+ gr.addEdge(2,6,vertex2(0.0,0.0,1.0));
+ gr.addEdge(6,0,vertex2(0.0,0.0,1.0));
+
+ gr.addEdge(0,3,vertex2(0.0,0.0,1.0));
+ gr.addEdge(3,2,vertex2(0.0,0.0,1.0));
+ gr.addEdge(2,0,vertex2(0.0,0.0,1.0));
+
+ gr.addEdge(0,1,vertex2(0.0,0.0,1.0));
+ gr.addEdge(1,3,vertex2(0.0,0.0,1.0));
+ gr.addEdge(3,0,vertex2(0.0,0.0,1.0));
+
+ gr.addEdge(2,7,vertex2(0.0,0.0,1.0));
+ gr.addEdge(7,6,vertex2(0.0,0.0,1.0));
+ gr.addEdge(6,2,vertex2(0.0,0.0,1.0));
+
+ gr.addEdge(2,3,vertex2(0.0,0.0,1.0));
+ gr.addEdge(3,7,vertex2(0.0,0.0,1.0));
+ gr.addEdge(7,2,vertex2(0.0,0.0,1.0));
+
+ gr.addEdge(4,6,vertex2(0.0,0.0,1.0));
+ gr.addEdge(6,7,vertex2(0.0,0.0,1.0));
+ gr.addEdge(7,4,vertex2(0.0,0.0,1.0));
+
+ gr.addEdge(4,7,vertex2(0.0,0.0,1.0));
+ gr.addEdge(7,5,vertex2(0.0,0.0,1.0));
+ gr.addEdge(5,4,vertex2(0.0,0.0,1.0));
+
+ gr.addEdge(0,4,vertex2(0.0,0.0,1.0));
+ gr.addEdge(4,5,vertex2(0.0,0.0,1.0));
+ gr.addEdge(5,0,vertex2(0.0,0.0,1.0));
+
+ gr.addEdge(0,5,vertex2(0.0,0.0,1.0));
+ gr.addEdge(5,1,vertex2(0.0,0.0,1.0));
+ gr.addEdge(1,0,vertex2(0.0,0.0,1.0));
+
+ gr.addEdge(1,5,vertex2(0.0,0.0,1.0));
+ gr.addEdge(5,7,vertex2(0.0,0.0,1.0));
+ gr.addEdge(7,1,vertex2(0.0,0.0,1.0));
+
+ gr.addEdge(1,7,vertex2(0.0,0.0,1.0));
+ gr.addEdge(7,3,vertex2(0.0,0.0,1.0));
+ gr.addEdge(3,1,vertex2(0.0,0.0,1.0));
+
+ // Write the VTK file
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/vtk_graph_v4_test.vtk");
+
+#else
+
+ std::string c2 = std::string("test_data/vtk_graph_v4_test.vtk");
+
+#endif
+
+ VTKWriter<Graph_CSR<vertex2,vertex2>,VTK_GRAPH> vtk(gr);
+ vtk.write("vtk_graph_v4.vtk");
+
+ // check that match
+
+ bool test = compare("vtk_graph_v4.vtk",c2);
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+struct vertex3
+{
+ //! The node contain 3 unsigned long integer for communication computation memory and id
+ typedef boost::fusion::vector<float[2],size_t,double> type;
+
+ //! type of the positional field
+ typedef float s_type;
+
+ //! Attributes name
+ struct attributes
+ {
+ static const std::string name[];
+ };
+
+ //! The data
+ type data;
+
+ //! computation property id in boost::fusion::vector
+ static const unsigned int x = 0;
+ static const unsigned int prp1 = 1;
+ static const unsigned int prp2 = 2;
+
+ //! total number of properties boost::fusion::vector
+ static const unsigned int max_prop = 3;
+
+ /*!
+ * Default constructor
+ *
+ */
+ vertex3()
+ {
+
+ }
+
+ static inline bool noPointers()
+ {
+ return true;
+ }
+
+ /*! \brief Initialize the VTKVertex
+ *
+ * \param
+ *
+ */
+ vertex3(float x, float y)
+ {
+ boost::fusion::at_c<vertex::x>(data)[0] = x;
+ boost::fusion::at_c<vertex::x>(data)[1] = y;
+ }
+};
+
+// use the vertex like the edge
+typedef vertex edge;
+
+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
+
+ Graph_CSR<vertex3,edge> gr;
+
+ // Create a cube graph
+
+ gr.addVertex(vertex3(0.0,0.0));
+ gr.addVertex(vertex3(0.0,1.0));
+ gr.addVertex(vertex3(1.0,0.0));
+ gr.addVertex(vertex3(1.0,1.0));
+
+ gr.addEdge(0,1);
+ gr.addEdge(1,3);
+ gr.addEdge(3,2);
+ gr.addEdge(2,0);
+
+ // Write the VTK file
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/vtk_graph_v3_test.vtk");
+
+#else
+
+ std::string c2 = std::string("test_data/vtk_graph_v3_test.vtk");
+
+#endif
+
+ VTKWriter<Graph_CSR<vertex3,edge>,VTK_GRAPH> vtk(gr);
+ vtk.write("vtk_graph_v3.vtk");
+
+ // check that match
+
+ bool test = compare("vtk_graph_v3.vtk",c2);
+ 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";
+
+ // Graph
+
+ Graph_CSR<vertex,edge> gr;
+
+ // Create a cube graph
+
+ gr.addVertex(vertex(0.0,0.0,0.0));
+ gr.addVertex(vertex(0.0,0.0,1.0));
+ gr.addVertex(vertex(0.0,1.0,0.0));
+ gr.addVertex(vertex(0.0,1.0,1.0));
+ gr.addVertex(vertex(1.0,0.0,0.0));
+ gr.addVertex(vertex(1.0,0.0,1.0));
+ gr.addVertex(vertex(1.0,1.0,0.0));
+ gr.addVertex(vertex(1.0,1.0,1.0));
+
+ gr.addEdge(0,6);
+ gr.addEdge(6,4);
+ gr.addEdge(4,0);
+
+ gr.addEdge(0,2);
+ gr.addEdge(2,6);
+ gr.addEdge(6,0);
+
+ gr.addEdge(0,3);
+ gr.addEdge(3,2);
+ gr.addEdge(2,0);
+
+ gr.addEdge(0,1);
+ gr.addEdge(1,3);
+ gr.addEdge(3,0);
+
+ gr.addEdge(2,7);
+ gr.addEdge(7,6);
+ gr.addEdge(6,2);
+
+ gr.addEdge(2,3);
+ gr.addEdge(3,7);
+ gr.addEdge(7,2);
+
+ gr.addEdge(4,6);
+ gr.addEdge(6,7);
+ gr.addEdge(7,4);
+
+ gr.addEdge(4,7);
+ gr.addEdge(7,5);
+ gr.addEdge(5,4);
+
+ gr.addEdge(0,4);
+ gr.addEdge(4,5);
+ gr.addEdge(5,0);
+
+ gr.addEdge(0,5);
+ gr.addEdge(5,1);
+ gr.addEdge(1,0);
+
+ gr.addEdge(1,5);
+ gr.addEdge(5,7);
+ gr.addEdge(7,1);
+
+ gr.addEdge(1,7);
+ gr.addEdge(7,3);
+ gr.addEdge(3,1);
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/vtk_graph_test.vtk");
+
+#else
+
+ std::string c2 = std::string("test_data/vtk_graph_test.vtk");
+
+#endif
+
+ // Write the VTK file
+
+ VTKWriter<Graph_CSR<vertex,edge>,VTK_GRAPH> vtk(gr);
+ vtk.write("vtk_graph.vtk");
+
+ // check that match
+
+ bool test = compare("vtk_graph.vtk",c2);
+ 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;
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/vtk_box_test.vtk");
+ std::string c3 = std::string("openfpm_io/test_data/vtk_box_3D_test.vtk");
+ std::string c4 = std::string("openfpm_io/test_data/vtk_box_3D_2_test.vtk");
+
+#else
+
+ std::string c2 = std::string("test_data/vtk_box_test.vtk");
+ std::string c3 = std::string("test_data/vtk_box_3D_test.vtk");
+ std::string c4 = std::string("test_data/vtk_box_3D_2_test.vtk");
+
+#endif
+
+ // Create a vector of boxes
+ openfpm::vector<Box<2,float>> vb;
+
+ vb.add(Box<2,float>({0.2,0.2},{1.0,0.5}));
+ vb.add(Box<2,float>({0.0,0.0},{0.2,0.2}));
+ vb.add(Box<2,float>({0.2,0.0},{0.5,0.2}));
+ vb.add(Box<2,float>({0.5,0.0},{1.0,0.2}));
+ vb.add(Box<2,float>({0.0,0.2},{0.2,0.5}));
+ vb.add(Box<2,float>({0.0,0.5},{1.0,1.0}));
+
+ // Create a writer and write
+ VTKWriter<openfpm::vector<Box<2,float>>,VECTOR_BOX> vtk_box;
+ vtk_box.add(vb);
+ vtk_box.write("vtk_box.vtk");
+
+ // Check that match
+ bool test = compare("vtk_box.vtk",c2);
+ BOOST_REQUIRE_EQUAL(test,true);
+
+ // Create a vector of boxes
+ openfpm::vector<Box<3,float>> vb2;
+
+ vb2.add(Box<3,float>({0.2,0.2,0.0},{1.0,0.5,0.5}));
+ vb2.add(Box<3,float>({0.0,0.0,0.0},{0.2,0.2,0.5}));
+ vb2.add(Box<3,float>({0.2,0.0,0.0},{0.5,0.2,0.5}));
+ vb2.add(Box<3,float>({0.5,0.0,0.0},{1.0,0.2,0.5}));
+ vb2.add(Box<3,float>({0.0,0.2,0.0},{0.2,0.5,0.5}));
+ vb2.add(Box<3,float>({0.0,0.5,0.0},{1.0,1.0,0.5}));
+
+ // Create a writer and write
+ VTKWriter<openfpm::vector<Box<3,float>>,VECTOR_BOX> vtk_box2;
+ vtk_box2.add(vb2);
+ vtk_box2.write("vtk_box_3D.vtk");
+
+ // Check that match
+ test = compare("vtk_box_3D.vtk",c3);
+ BOOST_REQUIRE_EQUAL(test,true);
+
+ // Create a vector of boxes
+ openfpm::vector<Box<3,float>> vb3;
+ vb3.add(Box<3,float>({0.2,0.2,0.5},{1.0,0.5,1.0}));
+ vb3.add(Box<3,float>({0.0,0.0,0.5},{0.2,0.2,1.0}));
+ vb3.add(Box<3,float>({0.2,0.0,0.5},{0.5,0.2,1.0}));
+ vb3.add(Box<3,float>({0.5,0.0,0.5},{1.0,0.2,1.0}));
+ vb3.add(Box<3,float>({0.0,0.2,0.5},{0.2,0.5,1.0}));
+ vb3.add(Box<3,float>({0.0,0.5,0.5},{1.0,1.0,1.0}));
+
+ // Create a writer and write
+ VTKWriter<openfpm::vector<Box<3,float>>,VECTOR_BOX> vtk_box3;
+ vtk_box3.add(vb2);
+ vtk_box3.add(vb3);
+ vtk_box3.write("vtk_box_3D_2.vtk");
+
+ // Check that match
+ test = compare("vtk_box_3D_2.vtk",c4);
+ BOOST_REQUIRE_EQUAL(test,true);
+}
+
+/*! \brief fill the grid with some random data
+ *
+ * \param g Grid to fill
+ *
+ */
+template<typename grid_type> void fill_grid_some_data(grid_type & g)
+{
+ typedef Point_test<float> p;
+
+ auto it = g.getIterator();
+
+ while (it.isNext())
+ {
+ g.template get<p::x>(it.get()) = it.get().get(0);
+ if (grid_type::dims != 1)
+ {g.template get<p::y>(it.get()) = it.get().get(1);}
+ else
+ {g.template get<p::y>(it.get()) = 0.0;}
+ g.template get<p::z>(it.get()) = 0;
+ g.template get<p::s>(it.get()) = 1.0;
+ g.template get<p::v>(it.get())[0] = g.getGrid().LinId(it.get());
+ g.template get<p::v>(it.get())[1] = g.getGrid().LinId(it.get());
+ g.template get<p::v>(it.get())[2] = g.getGrid().LinId(it.get());
+
+ g.template get<p::t>(it.get())[0][0] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[0][1] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[0][2] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[1][0] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[1][1] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[1][2] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[2][0] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[2][1] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[2][2] = g.getGrid().LinId(it.get());
+
+ ++it;
+ }
+}
+
+/*! \brief fill the grid with some random data
+ *
+ * \param g Grid to fill
+ *
+ */
+void fill_grid_some_data_prp(grid_cpu<2,Point_test_prp<float>> & g)
+{
+ typedef Point_test<float> p;
+
+ auto it = g.getIterator();
+
+ while (it.isNext())
+ {
+ g.template get<p::x>(it.get()) = it.get().get(0);
+ g.template get<p::y>(it.get()) = it.get().get(1);
+ g.template get<p::z>(it.get()) = 0;
+ g.template get<p::s>(it.get()) = 1.0;
+ g.template get<p::v>(it.get())[0] = g.getGrid().LinId(it.get());
+ g.template get<p::v>(it.get())[1] = g.getGrid().LinId(it.get());
+ g.template get<p::v>(it.get())[2] = g.getGrid().LinId(it.get());
+
+ g.template get<p::t>(it.get())[0][0] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[0][1] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[0][2] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[1][0] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[1][1] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[1][2] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[2][0] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[2][1] = g.getGrid().LinId(it.get());
+ g.template get<p::t>(it.get())[2][2] = g.getGrid().LinId(it.get());
+
+ ++it;
+ }
+}
+
+/*! \brief fill the grid with some random data
+ *
+ *
+ */
+void fill_grid_some_data_scal(grid_cpu<2,Point_test_scal<float>> & g)
+{
+ typedef Point_test<float> p;
+
+ auto it = g.getIterator();
+
+ while (it.isNext())
+ {
+ g.template get<p::x>(it.get()) = it.get().get(0);
+ g.template get<p::y>(it.get()) = it.get().get(1);
+ g.template get<p::z>(it.get()) = 0;
+ g.template get<p::s>(it.get()) = 1.0;
+
+ ++it;
+ }
+}
+
+BOOST_AUTO_TEST_CASE( vtk_writer_use_grids)
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ {return;}
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/vtk_grids_test_1d.vtk");
+ std::string c3 = std::string("openfpm_io/test_data/vtk_grids_test.vtk");
+ std::string c4 = std::string("openfpm_io/test_data/vtk_grids_st_test.vtk");
+ std::string c5 = std::string("openfpm_io/test_data/vtk_grids_prp_test.vtk");
+ std::string c6 = std::string("openfpm_io/test_data/vtk_grids_test.vtk");
+
+#else
+
+ std::string c2 = std::string("test_data/vtk_grids_test_1d.vtk");
+ std::string c3 = std::string("test_data/vtk_grids_test.vtk");
+ std::string c4 = std::string("test_data/vtk_grids_st_test.vtk");
+ std::string c5 = std::string("test_data/vtk_grids_prp_test.vtk");
+ std::string c6 = std::string("test_data/vtk_grids_test.vtk");
+
+#endif
+
+ {
+
+ // Create box grids
+ Point<1,double> offset1({0.0});
+ Point<1,double> spacing1({0.1});
+ Box<1,size_t> d1({1},{14});
+
+ // Create box grids
+ Point<1,double> offset2({5.0});
+ Point<1,float> spacing2({0.2});
+ Box<1,size_t> d2({2},{13});
+
+ // Create box grids
+ Point<1,double> offset3({0.0});
+ Point<1,double> spacing3({0.05});
+ Box<1,size_t> d3({3},{11});
+
+ // Create box grids
+ Point<1,double> offset4({5.0});
+ Point<1,double> spacing4({0.1});
+ Box<1,size_t> d4({1},{7});
+
+ size_t sz[] = {16};
+ grid_cpu<1,Point_test<double>> g1(sz);
+ g1.setMemory();
+ fill_grid_some_data(g1);
+ grid_cpu<1,Point_test<double>> g2(sz);
+ g2.setMemory();
+ fill_grid_some_data(g2);
+ grid_cpu<1,Point_test<double>> g3(sz);
+ g3.setMemory();
+ fill_grid_some_data(g3);
+ grid_cpu<1,Point_test<double>> g4(sz);
+ g4.setMemory();
+ fill_grid_some_data(g4);
+
+ g4.template get<Point_test<double>::s>(0) = 1.0/3.0;
+
+ // Create a writer and write
+ VTKWriter<boost::mpl::pair<grid_cpu<1,Point_test<double>>,double>,VECTOR_GRIDS> vtk_g;
+ vtk_g.add(g1,offset1,spacing1,d1);
+ vtk_g.add(g2,offset2,spacing2,d2);
+ vtk_g.add(g3,offset3,spacing3,d3);
+ vtk_g.add(g4,offset4,spacing4,d4);
+
+ openfpm::vector<std::string> prp_names;
+ vtk_g.write("vtk_grids_1d.vtk",prp_names);
+
+ #ifndef SE_CLASS3
+
+ // Check that match
+ bool test = compare("vtk_grids_1d.vtk",c2);
+ BOOST_REQUIRE_EQUAL(test,true);
+
+ #endif
+ }
+
+ {
+
+ // Create box grids
+ Point<2,float> offset1({0.0,0.0});
+ Point<2,float> spacing1({0.1,0.2});
+ Box<2,size_t> d1({1,2},{14,15});
+
+ // Create box grids
+ Point<2,float> offset2({5.0,7.0});
+ Point<2,float> spacing2({0.2,0.1});
+ Box<2,size_t> d2({2,1},{13,15});
+
+ // Create box grids
+ Point<2,float> offset3({0.0,7.0});
+ Point<2,float> spacing3({0.05,0.07});
+ Box<2,size_t> d3({3,2},{11,10});
+
+ // Create box grids
+ Point<2,float> offset4({5.0,0.0});
+ Point<2,float> spacing4({0.1,0.1});
+ Box<2,size_t> d4({1,1},{7,7});
+
+ size_t sz[] = {16,16};
+ grid_cpu<2,Point_test<float>> g1(sz);
+ g1.setMemory();
+ fill_grid_some_data(g1);
+ grid_cpu<2,Point_test<float>> g2(sz);
+ g2.setMemory();
+ fill_grid_some_data(g2);
+ grid_cpu<2,Point_test<float>> g3(sz);
+ g3.setMemory();
+ fill_grid_some_data(g3);
+ grid_cpu<2,Point_test<float>> g4(sz);
+ g4.setMemory();
+ fill_grid_some_data(g4);
+
+ // Create a writer and write
+ VTKWriter<boost::mpl::pair<grid_cpu<2,Point_test<float>>,float>,VECTOR_GRIDS> vtk_g;
+ vtk_g.add(g1,offset1,spacing1,d1);
+ vtk_g.add(g2,offset2,spacing2,d2);
+ vtk_g.add(g3,offset3,spacing3,d3);
+ vtk_g.add(g4,offset4,spacing4,d4);
+
+ openfpm::vector<std::string> prp_names;
+ vtk_g.write("vtk_grids.vtk",prp_names);
+
+ #ifndef SE_CLASS3
+
+ // Check that match
+ bool test = compare("vtk_grids.vtk",c3);
+ BOOST_REQUIRE_EQUAL(test,true);
+
+ #endif
+ }
+
+ {
+ // Create box grids
+ Point<2,float> offset1({0.0,0.0});
+ Point<2,float> spacing1({0.1,0.1});
+ Box<2,size_t> d1({1,2},{14,15});
+
+ // Create box grids
+ Point<2,float> offset2({0.0,0.0});
+ Point<2,float> spacing2({0.1,0.1});
+ Box<2,size_t> d2({2,1},{13,15});
+
+ // Create box grids
+ Point<2,float> offset3({5.0,5.0});
+ Point<2,float> spacing3({0.1,0.1});
+ Box<2,size_t> d3({3,2},{11,10});
+
+ // Create box grids
+ Point<2,float> offset4({5.0,5.0});
+ Point<2,float> spacing4({0.1,0.1});
+ Box<2,size_t> d4({1,1},{7,7});
+
+ size_t sz[] = {16,16};
+ grid_cpu<2,Point_test<float>> g1(sz);
+ g1.setMemory();
+ fill_grid_some_data(g1);
+ grid_cpu<2,Point_test<float>> g2(sz);
+ g2.setMemory();
+ fill_grid_some_data(g2);
+ grid_cpu<2,Point_test<float>> g3(sz);
+ g3.setMemory();
+ fill_grid_some_data(g3);
+ grid_cpu<2,Point_test<float>> g4(sz);
+ g4.setMemory();
+ fill_grid_some_data(g4);
+
+ comb<2> cmb;
+ cmb.zero();
+
+ comb<2> cmb2;
+ cmb2.mone();
+
+ // Create a writer and write
+ VTKWriter<boost::mpl::pair<grid_cpu<2,Point_test<float>>,float>,VECTOR_ST_GRIDS> vtk_g;
+ vtk_g.add(0,g1,offset1,spacing1,d1,cmb);
+ vtk_g.add(0,g2,offset2,spacing2,d2,cmb);
+ vtk_g.add(1,g3,offset3,spacing3,d3,cmb);
+ vtk_g.add(1,g4,offset4,spacing4,d4,cmb2);
+
+ vtk_g.write("vtk_grids_st.vtk");
+
+ // Check that match
+ bool test = compare("vtk_grids_st.vtk",c4);
+ BOOST_REQUIRE_EQUAL(test,true);
+ }
+
+ {
+ // Create box grids
+ Point<2,float> offset1({0.0,0.0});
+ Point<2,float> spacing1({0.1,0.1});
+ Box<2,size_t> d1({1,2},{14,15});
+
+ // Create box grids
+ Point<2,float> offset2({0.0,0.0});
+ Point<2,float> spacing2({0.1,0.1});
+ Box<2,size_t> d2({2,1},{13,15});
+
+ // Create box grids
+ Point<2,float> offset3({5.0,5.0});
+ Point<2,float> spacing3({0.1,0.1});
+ Box<2,size_t> d3({3,2},{11,10});
+
+ // Create box grids
+ Point<2,float> offset4({5.0,5.0});
+ Point<2,float> spacing4({0.1,0.1});
+ Box<2,size_t> d4({1,1},{7,7});
+
+ size_t sz[] = {16,16};
+ grid_cpu<2,Point_test_scal<float>> g1(sz);
+ g1.setMemory();
+ fill_grid_some_data_scal(g1);
+ grid_cpu<2,Point_test_scal<float>> g2(sz);
+ g2.setMemory();
+ fill_grid_some_data_scal(g2);
+ grid_cpu<2,Point_test_scal<float>> g3(sz);
+ g3.setMemory();
+ fill_grid_some_data_scal(g3);
+ grid_cpu<2,Point_test_scal<float>> g4(sz);
+ g4.setMemory();
+ fill_grid_some_data_scal(g4);
+
+ // Create a writer and write
+ VTKWriter<boost::mpl::pair<grid_cpu<2,Point_test_scal<float>>,float>,VECTOR_GRIDS> vtk_g;
+ vtk_g.add(g1,offset1,spacing1,d1);
+ vtk_g.add(g2,offset2,spacing2,d2);
+ vtk_g.add(g3,offset3,spacing3,d3);
+ vtk_g.add(g4,offset4,spacing4,d4);
+
+ 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",c5);
+ BOOST_REQUIRE_EQUAL(test,true);
+ }
+
+ {
+ // Create box grids
+ Point<2,float> offset1({0.0,0.0});
+ Point<2,float> spacing1({0.1,0.2});
+ Box<2,size_t> d1({1,2},{14,15});
+
+ // Create box grids
+ Point<2,float> offset2({5.0,7.0});
+ Point<2,float> spacing2({0.2,0.1});
+ Box<2,size_t> d2({2,1},{13,15});
+
+ // Create box grids
+ Point<2,float> offset3({0.0,7.0});
+ Point<2,float> spacing3({0.05,0.07});
+ Box<2,size_t> d3({3,2},{11,10});
+
+ // Create box grids
+ Point<2,float> offset4({5.0,0.0});
+ Point<2,float> spacing4({0.1,0.1});
+ Box<2,size_t> d4({1,1},{7,7});
+
+ size_t sz[] = {16,16};
+ grid_cpu<2,aggregate<float,float,float,float,float[3],float[3][3],openfpm::vector<int>> > g1(sz);
+ g1.setMemory();
+ fill_grid_some_data(g1);
+ grid_cpu<2,aggregate<float,float,float,float,float[3],float[3][3],openfpm::vector<int>> > g2(sz);
+ g2.setMemory();
+ fill_grid_some_data(g2);
+ grid_cpu<2,aggregate<float,float,float,float,float[3],float[3][3],openfpm::vector<int>> > g3(sz);
+ g3.setMemory();
+ fill_grid_some_data(g3);
+ grid_cpu<2,aggregate<float,float,float,float,float[3],float[3][3],openfpm::vector<int>> > g4(sz);
+ g4.setMemory();
+ fill_grid_some_data(g4);
+
+ // Create a writer and write
+ VTKWriter<boost::mpl::pair<grid_cpu<2,aggregate<float,float,float,float,float[3],float[3][3],openfpm::vector<int>> >,float>,VECTOR_GRIDS> vtk_g;
+ vtk_g.add(g1,offset1,spacing1,d1);
+ vtk_g.add(g2,offset2,spacing2,d2);
+ vtk_g.add(g3,offset3,spacing3,d3);
+ vtk_g.add(g4,offset4,spacing4,d4);
+
+ openfpm::vector<std::string> prp_names;
+ vtk_g.write("vtk_grids_unk.vtk",prp_names);
+
+#ifndef SE_CLASS3
+
+ // Check that match
+ bool test = compare("vtk_grids_unk.vtk",c6);
+ BOOST_REQUIRE_EQUAL(test,true);
+
+#endif
+
+ }
+
+ // Try
+
+ {
+ bool ret = is_vtk_writable<Point<3,float>>::value;
+ BOOST_REQUIRE_EQUAL(ret,true);
+ ret = is_vtk_writable<Point<3,double>>::value;
+ BOOST_REQUIRE_EQUAL(ret,true);
+
+ int dims = vtk_dims<Point<3,float>>::value;
+ BOOST_REQUIRE_EQUAL(dims,3);
+
+ dims = vtk_dims<long int>::value;
+ BOOST_REQUIRE_EQUAL(dims,1);
+ }
+
+}
+
+
+BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/vtk_points_test.vtk");
+ std::string c3 = std::string("openfpm_io/test_data/vtk_points_pp_test.vtk");
+ std::string c4 = std::string("openfpm_io/test_data/vtk_points_pp_header_test.vtk");
+
+#else
+
+ std::string c2 = std::string("test_data/vtk_points_test.vtk");
+ std::string c3 = std::string("test_data/vtk_points_pp_test.vtk");
+ std::string c4 = std::string("test_data/vtk_points_pp_header_test.vtk");
+
+#endif
+
+ {
+ // Create 3 vectors with random particles
+ openfpm::vector<Point<3,double>> v1ps;
+ openfpm::vector<Point<3,double>> v2ps;
+ openfpm::vector<Point<3,double>> v3ps;
+ openfpm::vector<aggregate<float,float[3]>> v1pp;
+ openfpm::vector<aggregate<float,float[3]>> v2pp;
+ openfpm::vector<aggregate<float,float[3]>> v3pp;
+ openfpm::vector<aggregate<float,Point<3,float>>> v4pp;
+
+ // set the seed
+ // create the random generator engine
+ SimpleRNG rng;
+
+ // fill the vector with random data
+ v1ps.resize(100);
+ v2ps.resize(100);
+ v3ps.resize(100);
+
+ v1pp.resize(100);
+ v2pp.resize(100);
+ v3pp.resize(100);
+ v4pp.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();
+
+ v2ps.template get<0>(i)[0] = rng.GetUniform()*0.5;
+ v2ps.template get<0>(i)[1] = rng.GetUniform()*0.5;
+ v2ps.template get<0>(i)[2] = rng.GetUniform()*0.5;
+
+ v3ps.template get<0>(i)[0] = rng.GetUniform()*0.3;
+ v3ps.template get<0>(i)[1] = rng.GetUniform()*0.3;
+ v3ps.template get<0>(i)[2] = rng.GetUniform()*0.3;
+
+ 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();
+
+ v2pp.template get<0>(i) = rng.GetUniform();
+ v2pp.template get<1>(i)[0] = rng.GetUniform();
+ v2pp.template get<1>(i)[1] = rng.GetUniform();
+ v2pp.template get<1>(i)[2] = rng.GetUniform();
+
+ v3pp.template get<0>(i) = rng.GetUniform();
+ v3pp.template get<1>(i)[0] = rng.GetUniform();
+ v3pp.template get<1>(i)[1] = rng.GetUniform();
+ v3pp.template get<1>(i)[2] = rng.GetUniform();
+
+ v4pp.template get<0>(i) = rng.GetUniform();
+ v4pp.template get<1>(i).get(0) = rng.GetUniform();
+ v4pp.template get<1>(i).get(1) = rng.GetUniform();
+ v4pp.template get<1>(i).get(2) = rng.GetUniform();
+ }
+
+ // Create a writer and write
+ 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);
+ vtk_v.add(v2ps,v2pp,88);
+ vtk_v.add(v3ps,v3pp,90);
+
+ openfpm::vector<std::string> prp_names;
+ vtk_v.write("vtk_points.vtp",prp_names);
+ //auto &v_cl=create_vcluster();
+ //size_t n=v_cl.size();
+ vtk_v.write_pvtp("vtk_points",prp_names,2);
+
+
+#ifndef SE_CLASS3
+
+ bool test = true;
+
+ // Check that match
+ test = compare("vtk_points.vtp","test_data/vtk_points_test.vtp");
+ BOOST_REQUIRE_EQUAL(test,true);
+
+ //It just checks generation of the format and not actual data (File names)
+ test = compare("vtk_points.pvtp","test_data/pvtp_points_test.pvtp");
+ BOOST_REQUIRE_EQUAL(test,true);
+
+#endif
+
+ // 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.vtp",prp_names);
+
+#ifndef SE_CLASS3
+
+ // Check that match
+ test = compare("vtk_points_pp.vtp","test_data/vtk_points_pp_test.vtp");
+ BOOST_REQUIRE_EQUAL(test,true);
+
+#endif
+
+ // Create a writer and write
+ VTKWriter<boost::mpl::pair<openfpm::vector<Point<3,double>>,openfpm::vector<aggregate<float,Point<3,float>>>>,VECTOR_POINTS> vtk_v3;
+ vtk_v3.add(v1ps,v4pp,75);
+
+ vtk_v3.write("vtk_points_pp_header.vtp",prp_names,"points","time=5.123");
+
+ // We try binary
+ vtk_v3.write("vtk_points_pp_header_bin.vtp",prp_names,"points","time=5.123",file_type::BINARY);
+
+#ifndef SE_CLASS3
+
+ // Check that match
+ test = compare("vtk_points_pp_header.vtp","test_data/vtk_points_pp_header_test.vtp");
+ BOOST_REQUIRE_EQUAL(test,true);
+
+ test = compare("vtk_points_pp_header_bin.vtp","test_data/vtk_points_pp_header_bin_test.vtp");
+ BOOST_REQUIRE_EQUAL(test,true);
+
+#endif
+
+ }
+}
+
+BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_properties )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/vtk_points_with_prp_names_test.vtk");
+
+#else
+
+ std::string c2 = std::string("test_data/vtk_points_with_prp_names_test.vtk");
+
+#endif
+
+ {
+ // 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.vtp",prp_names);
+
+#ifndef SE_CLASS3
+
+ // Check that match
+ bool test = compare("vtk_points_with_prp_names.vtp","test_data/vtk_points_with_prp_names_test.vtp");
+ BOOST_REQUIRE_EQUAL(test,true);
+
+#endif
+
+ }
+}
+
+BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_check_out_precision )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/vtk_points_with_prp_names_prec_check_test.vtk");
+
+#else
+
+ std::string c2 = std::string("test_data/vtk_points_with_prp_names_prec_check_test.vtk");
+
+#endif
+
+ {
+ // Create 3 vectors with random particles
+ openfpm::vector<Point<3,double>> v1ps;
+ openfpm::vector<aggregate<float,double[3]>> v1pp;
+
+ // 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] = std::numeric_limits<double>::max();
+ v1ps.template get<0>(i)[1] = std::numeric_limits<double>::max();
+ v1ps.template get<0>(i)[2] = std::numeric_limits<double>::max();
+
+
+ v1pp.template get<0>(i) = std::numeric_limits<float>::max();
+ v1pp.template get<1>(i)[0] = std::numeric_limits<double>::max();
+ v1pp.template get<1>(i)[1] = std::numeric_limits<double>::max();
+ v1pp.template get<1>(i)[2] = std::numeric_limits<double>::max();
+ }
+
+ 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,double[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_prec_check.vtp",prp_names);
+
+#ifndef SE_CLASS3
+
+ // Check that match
+ bool test = compare("vtk_points_with_prp_names_prec_check.vtp","test_data/vtk_points_with_prp_names_prec_check_test.vtp");
+ BOOST_REQUIRE_EQUAL(test,true);
+
+#endif
+
+ }
+}
+
+BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+#ifdef OPENFPM_PDATA
+
+ if (v_cl.rank() != 0) {return;}
+ std::string c2 = std::string("openfpm_io/test_data/vtk_points_bin_test.vtk");
+ std::string c3 = std::string("openfpm_io/test_data/vtk_points_pp_bin_test.vtk");
+ std::string c4 = std::string("openfpm_io/test_data/vtk_points_2d_bin_test.vtk");
+ std::string c5 = std::string("openfpm_io/test_data/vtk_points_2d_pp_bin_test.vtk");
+
+#else
+
+ std::string c2 = std::string("test_data/vtk_points_bin_test.vtk");
+ std::string c3 = std::string("test_data/vtk_points_pp_bin_test.vtk");
+ std::string c4 = std::string("test_data/vtk_points_2d_bin_test.vtk");
+ std::string c5 = std::string("test_data/vtk_points_2d_pp_bin_test.vtk");
+
+#endif
+
+ {
+ // Create 3 vectors with random particles
+ openfpm::vector<Point<3,double>> v1ps;
+ openfpm::vector<Point<3,double>> v2ps;
+ openfpm::vector<Point<3,double>> v3ps;
+ openfpm::vector<aggregate<float,float[3]>> v1pp;
+ openfpm::vector<aggregate<float,float[3]>> v2pp;
+ openfpm::vector<aggregate<float,float[3]>> v3pp;
+ openfpm::vector<aggregate<float,Point<3,float>>> v4pp;
+
+ // set the seed
+ // create the random generator engine
+ SimpleRNG rng;
+
+ // fill the vector with random data
+ v1ps.resize(100);
+ v2ps.resize(100);
+ v3ps.resize(100);
+
+ v1pp.resize(100);
+ v2pp.resize(100);
+ v3pp.resize(100);
+ v4pp.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();
+
+ v2ps.template get<0>(i)[0] = rng.GetUniform()*0.5;
+ v2ps.template get<0>(i)[1] = rng.GetUniform()*0.5;
+ v2ps.template get<0>(i)[2] = rng.GetUniform()*0.5;
+
+ v3ps.template get<0>(i)[0] = rng.GetUniform()*0.3;
+ v3ps.template get<0>(i)[1] = rng.GetUniform()*0.3;
+ v3ps.template get<0>(i)[2] = rng.GetUniform()*0.3;
+
+ 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();
+
+ v2pp.template get<0>(i) = rng.GetUniform();
+ v2pp.template get<1>(i)[0] = rng.GetUniform();
+ v2pp.template get<1>(i)[1] = rng.GetUniform();
+ v2pp.template get<1>(i)[2] = rng.GetUniform();
+
+ v3pp.template get<0>(i) = rng.GetUniform();
+ v3pp.template get<1>(i)[0] = rng.GetUniform();
+ v3pp.template get<1>(i)[1] = rng.GetUniform();
+ v3pp.template get<1>(i)[2] = rng.GetUniform();
+
+ v4pp.template get<0>(i) = rng.GetUniform();
+ v4pp.template get<1>(i).get(0) = rng.GetUniform();
+ v4pp.template get<1>(i).get(1) = rng.GetUniform();
+ v4pp.template get<1>(i).get(2) = rng.GetUniform();
+ }
+
+ // Create a writer and write
+ 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);
+ vtk_v.add(v2ps,v2pp,88);
+ vtk_v.add(v3ps,v3pp,90);
+
+ openfpm::vector<std::string> prp_names;
+ vtk_v.write("vtk_points_bin.vtp",prp_names,"vtk output","",file_type::BINARY);
+ vtk_v.write("vtk_points_bin2.vtp",prp_names,"vtk output","",file_type::BINARY);
+
+#ifndef SE_CLASS3
+
+ bool test = true;
+
+ // Check that match
+ test = compare("vtk_points_bin.vtp","test_data/vtk_points_bin_test.vtp");
+ BOOST_REQUIRE_EQUAL(test,true);
+ test = compare("vtk_points_bin2.vtp","test_data/vtk_points_bin_test.vtp");
+ BOOST_REQUIRE_EQUAL(test,true);
+
+#endif
+
+ // 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.vtp",prp_names,"vtk output","",file_type::BINARY);
+
+#ifndef SE_CLASS3
+
+ // Check that match
+ test = compare("vtk_points_pp_bin.vtp","test_data/vtk_points_pp_bin_test.vtp");
+ BOOST_REQUIRE_EQUAL(test,true);
+
+#endif
+
+ }
+
+
+ {
+ // Create 3 vectors with random particles
+ openfpm::vector<Point<2,double>> v1ps;
+ openfpm::vector<Point<2,double>> v2ps;
+ openfpm::vector<Point<2,double>> v3ps;
+ openfpm::vector<aggregate<float,float[3][3]>> v1pp;
+ openfpm::vector<aggregate<float,float[3][3]>> v2pp;
+ openfpm::vector<aggregate<float,float[3][3]>> v3pp;
+ openfpm::vector<aggregate<float[3],double[2]>> v4pp;
+
+ // set the seed
+ // create the random generator engine
+ SimpleRNG rng;
+
+ // fill the vector with random data
+ v1ps.resize(100);
+ v2ps.resize(100);
+ v3ps.resize(100);
+
+ v1pp.resize(100);
+ v2pp.resize(100);
+ v3pp.resize(100);
+ v4pp.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();
+
+ v2ps.template get<0>(i)[0] = rng.GetUniform()*0.5;
+ v2ps.template get<0>(i)[1] = rng.GetUniform()*0.5;
+
+ v3ps.template get<0>(i)[0] = rng.GetUniform()*0.3;
+ v3ps.template get<0>(i)[1] = rng.GetUniform()*0.3;
+
+ v1pp.template get<0>(i) = rng.GetUniform();
+ v1pp.template get<1>(i)[0][0] = rng.GetUniform();
+ v1pp.template get<1>(i)[0][1] = rng.GetUniform();
+ v1pp.template get<1>(i)[0][2] = rng.GetUniform();
+ v1pp.template get<1>(i)[1][0] = rng.GetUniform();
+ v1pp.template get<1>(i)[1][1] = rng.GetUniform();
+ v1pp.template get<1>(i)[1][2] = rng.GetUniform();
+ v1pp.template get<1>(i)[2][0] = rng.GetUniform();
+ v1pp.template get<1>(i)[2][1] = rng.GetUniform();
+ v1pp.template get<1>(i)[2][2] = rng.GetUniform();
+
+ v2pp.template get<0>(i) = rng.GetUniform();
+ v2pp.template get<1>(i)[0][0] = rng.GetUniform();
+ v2pp.template get<1>(i)[0][1] = rng.GetUniform();
+ v2pp.template get<1>(i)[0][2] = rng.GetUniform();
+ v2pp.template get<1>(i)[1][0] = rng.GetUniform();
+ v2pp.template get<1>(i)[1][1] = rng.GetUniform();
+ v2pp.template get<1>(i)[1][2] = rng.GetUniform();
+ v2pp.template get<1>(i)[2][0] = rng.GetUniform();
+ v2pp.template get<1>(i)[2][1] = rng.GetUniform();
+ v2pp.template get<1>(i)[2][2] = rng.GetUniform();
+
+ v3pp.template get<0>(i) = rng.GetUniform();
+ v3pp.template get<1>(i)[0][0] = rng.GetUniform();
+ v3pp.template get<1>(i)[0][1] = rng.GetUniform();
+ v3pp.template get<1>(i)[0][2] = rng.GetUniform();
+ v3pp.template get<1>(i)[1][0] = rng.GetUniform();
+ v3pp.template get<1>(i)[1][1] = rng.GetUniform();
+ v3pp.template get<1>(i)[1][2] = rng.GetUniform();
+ v3pp.template get<1>(i)[2][0] = rng.GetUniform();
+ v3pp.template get<1>(i)[2][1] = rng.GetUniform();
+ v3pp.template get<1>(i)[2][2] = rng.GetUniform();
+
+ v4pp.template get<0>(i)[0] = rng.GetUniform();
+ v4pp.template get<0>(i)[1] = rng.GetUniform();
+ v4pp.template get<0>(i)[2] = rng.GetUniform();
+ v4pp.template get<1>(i)[0] = rng.GetUniform();
+ v4pp.template get<1>(i)[1] = rng.GetUniform();
+ }
+
+ // Create a writer and write
+ VTKWriter<boost::mpl::pair<openfpm::vector<Point<2,double>>,openfpm::vector<aggregate<float,float[3][3]>>>,VECTOR_POINTS> vtk_v;
+ vtk_v.add(v1ps,v1pp,75);
+ vtk_v.add(v2ps,v2pp,88);
+ vtk_v.add(v3ps,v3pp,90);
+
+ openfpm::vector<std::string> stub;
+
+ vtk_v.write("vtk_points_2d_bin.vtp",stub,"vtk output","",file_type::BINARY);
+
+#ifndef SE_CLASS3
+
+ bool test = true;
+
+ // Check that match
+ test = compare("vtk_points_2d_bin.vtp","test_data/vtk_points_2d_bin_test.vtp");
+ BOOST_REQUIRE_EQUAL(test,true);
+
+#endif
+
+ // Create a writer and write
+ VTKWriter<boost::mpl::pair<openfpm::vector<Point<2,double>>,openfpm::vector<aggregate<float[3],double[2]>>>,VECTOR_POINTS> vtk_v2;
+ vtk_v2.add(v1ps,v4pp,75);
+
+ vtk_v2.write("vtk_points_2d_pp_bin.vtp",stub,"vtk output","",file_type::BINARY);
+
+#ifndef SE_CLASS3
+
+ // Check that match
+ test = compare("vtk_points_2d_pp_bin.vtp","test_data/vtk_points_2d_pp_bin_test.vtp");
+ BOOST_REQUIRE_EQUAL(test,true);
+
+#endif
+ }
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+
+#endif /* VTKWRITER_UNIT_TESTS_HPP_ */
diff --git a/src/VTKWriter/VTKWriter_vector_box.hpp b/src/VTKWriter/VTKWriter_vector_box.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..136ff16dbf6df5d96ba70084cca03e2d7b7020d8
--- /dev/null
+++ b/src/VTKWriter/VTKWriter_vector_box.hpp
@@ -0,0 +1,466 @@
+/*
+ * VTKWriter_vector_box.hpp
+ *
+ * Created on: May 5, 2015
+ * Author: i-bird
+ */
+
+#ifndef VTKWRITER_VECTOR_BOX_HPP_
+#define VTKWRITER_VECTOR_BOX_HPP_
+
+#include <boost/math/special_functions/pow.hpp>
+#include "Space/Shape/HyperCube.hpp"
+#include <random>
+#include "util/util.hpp"
+
+template <typename vector>
+class v_box
+{
+public:
+
+ /*! \brief Constructor
+ *
+ * \param v
+ *
+ */
+ v_box(const vector & v)
+ :v(v)
+ {}
+
+ //! dataset-name
+ std::string dataset;
+
+ //! vector
+ const vector & v;
+};
+
+/*!
+ *
+ * From a basic structure it write a VTK format file in case of a vector of Boxes
+ *
+ * \tparam vector type
+ *
+ */
+
+template <typename vector>
+class VTKWriter<vector,VECTOR_BOX>
+{
+ //! data to write
+ openfpm::vector<v_box<vector>> v;
+
+ /*! \brief It get the vertex properties list
+ *
+ * It get the vertex properties list of the vertex defined as a VTK header
+ *
+ * \return a string that define the vertex properties in graphML format
+ *
+ */
+
+ std::string get_point_properties_list()
+ {
+ //! vertex property output string
+ std::string v_out;
+
+ // number of points
+ size_t np = 0;
+
+ // count the number of points
+ for (size_t i = 0 ; i < v.size() ; i++)
+ {
+ np += v.get(i).v.size() * boost::math::pow<vector::value_type::dims>(2);
+ }
+
+ // write the number of vertex
+ v_out += "POINTS " + std::to_string(np) + " float" + "\n";
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief It get the edge properties list
+ *
+ * It get the edge properties list of the edge defined as a GraphML header
+ *
+ * \return a string that define the edge properties in graphML format
+ *
+ */
+
+ std::string get_cell_properties_list()
+ {
+ //! vertex property output string
+ std::string e_out;
+
+ //! number of cells and box
+ size_t nc = 0;
+ size_t nb = 0;
+
+ // count the number of cells
+ for (size_t i = 0 ; i < v.size() ; i++)
+ {
+ nb += v.get(i).v.size();
+ }
+
+ nc = nb * (boost::math::pow<vector::value_type::dims>(2) + 1);
+
+ // write the number of lines
+ e_out += "CELLS " + std::to_string(nb) + " " + std::to_string(nc) + "\n";
+
+ // return the vertex properties string
+ return e_out;
+ }
+
+ /*! \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
+ *
+ */
+
+ std::string get_point_list()
+ {
+ //! vertex node output string
+ std::string v_out;
+
+ //! for each vertex dataset
+
+ for (size_t i = 0 ; i < v.size() ; i++)
+ {
+ auto it = v.get(i).v.getIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ // Get the box
+ auto box = v.get(i).v.get(it.get());
+
+ // Create an hyper-cube and get the vertex combinations
+
+ HyperCube<vector::value_type::dims> hyp;
+ std::vector<comb<vector::value_type::dims>> comb = hyp.getCombinations_R(0);
+
+ // Create the box vertex points
+
+ for (size_t j = 0; j < comb.size() ; j++)
+ {
+ Point<vector::value_type::dims,float> p;
+
+ for (size_t k = 0 ; k < 3 ; k++)
+ {
+ if (k < vector::value_type::dims)
+ {
+ if (comb[j].value(k) < 0)
+ v_out += std::to_string(box.template get<vector::value_type::p1>()[k]) + " ";
+ else
+ v_out += std::to_string(box.template get<vector::value_type::p2>()[k]) + " ";
+ }
+ else
+ {
+ /* coverity[dead_error_line] */
+ v_out += "0.0";
+ }
+ }
+ v_out += "\n";
+ }
+
+ // increment the iterator and counter
+ ++it;
+ }
+ }
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Create the VTK vertex definition
+ *
+ *
+ * \return the string with the vertex definition
+ *
+ */
+ std::string get_cell_list()
+ {
+ // base
+ size_t base = 0;
+
+ //! vertex node output string
+ std::string v_out;
+
+ //! for each vector in the dataset
+
+ for (size_t i = 0 ; i < v.size() ; i++)
+ {
+ auto it = v.get(i).v.getIterator();
+
+ // for each box
+ while (it.isNext())
+ {
+ // Output the box vertex id
+ v_out += std::to_string((size_t)boost::math::pow<vector::value_type::dims>(2)) + " ";
+ for (size_t k = 0 ; k < boost::math::pow<vector::value_type::dims>(2) ; k++)
+ {
+ v_out += " " + std::to_string(base+k);
+ }
+ base += boost::math::pow<vector::value_type::dims>(2);
+ v_out += "\n";
+
+ ++it;
+ }
+ v_out += "\n";
+ }
+
+ // return the vertex list
+ return v_out;
+ }
+
+ /*! \brief Get the point data header
+ *
+ * \return a string with the point data header for VTK format
+ *
+ */
+
+ std::string get_point_data_header()
+ {
+ std::string v_out;
+
+ // number of points
+ size_t np = 0;
+
+ // count the number of points
+ for (size_t i = 0 ; i < v.size() ; i++)
+ {
+ np += v.get(i).v.size() * boost::math::pow<vector::value_type::dims>(2);
+ }
+
+
+ v_out += "POINT_DATA " + std::to_string(np) + "\n";
+
+ return v_out;
+ }
+
+ std::string get_cell_types_header()
+ {
+ //! vertex property output string
+ std::string e_out;
+
+ //! number of cells and box
+ size_t nb = 0;
+
+ // count the number of cells
+ for (size_t i = 0 ; i < v.size() ; i++)
+ {
+ nb += v.get(i).v.size();
+ }
+
+ // write the number of lines
+ e_out += "CELL_TYPES " + std::to_string(nb) + "\n";
+
+ // return the vertex properties string
+ return e_out;
+ }
+
+ std::string get_cell_types_list()
+ {
+ // Cell id
+ size_t cell_id;
+ if (vector::value_type::dims == 2)
+ cell_id = 8;
+ else
+ cell_id = 11;
+
+ //! vertex node output string
+ std::string v_out;
+
+ //! for each vector in the dataset
+
+ for (size_t i = 0 ; i < v.size() ; i++)
+ {
+ auto it = v.get(i).v.getIterator();
+
+ // for each box
+ while (it.isNext())
+ {
+ v_out += std::to_string(cell_id) + "\n";
+
+ ++it;
+ }
+ }
+
+ // return the vertex list
+ return v_out;
+ }
+
+
+ std::string get_cell_data_header()
+ {
+ //! vertex property output string
+ std::string e_out;
+
+ //! number of cells and box
+ size_t nb = 0;
+
+ // count the number of cells
+ for (size_t i = 0 ; i < v.size() ; i++)
+ {
+ nb += v.get(i).v.size();
+ }
+
+ // write the number of lines
+ e_out += "CELL_DATA " + std::to_string(nb) + "\n";
+ e_out += "COLOR_SCALARS data 4\n";
+
+ // return the vertex properties string
+ return e_out;
+ }
+
+ std::string get_cell_data_list()
+ {
+ // random engine
+ SimpleRNG rng;
+
+ //! vertex node output string
+ std::string v_out;
+
+ size_t col_group = 0;
+
+ //! for each vector in the dataset
+ for (size_t i = 0 ; i < v.size() ; i++)
+ {
+ auto it = v.get(i).v.getIterator();
+
+ // for each box
+ while (it.isNext())
+ {
+ // write a color
+ v_out += getColor(col_group,rng).toString() + " 1.0" + "\n";
+
+ ++it;
+ }
+ v_out += "\n";
+ col_group++;
+ }
+
+ // return the vertex list
+ return v_out;
+ }
+
+public:
+
+ /*!
+ *
+ * VTKWriter constructor
+ *
+ */
+ VTKWriter()
+ {}
+
+ /*! \brief Add box vector dataset
+ *
+ * \param v vector to add
+ *
+ */
+ void add(const vector & vc)
+ {
+ v_box<vector> t(vc);
+
+ v.add(t);
+ }
+
+ /*! \brief It write a VTK file from a graph
+ *
+ * \tparam prp_out which properties to output [default = -1 (all)]
+ *
+ * \param file path where to write
+ * \param name of the graph
+ * \param ft specify if it is a VTK BINARY or ASCII file [default = ASCII]
+ *
+ */
+
+ template<int prp = -1> bool write(std::string file, std::string graph_name="Graph", file_type ft = file_type::ASCII)
+ {
+ // Header for the vtk
+ std::string vtk_header;
+ // Point list of the VTK
+ std::string point_list;
+ // Vertex list of the VTK
+ std::string cell_list;
+ // Graph header
+ std::string vtk_binary_or_ascii;
+ // Edge list of the GraphML
+ std::string edge_list;
+ // vertex properties header
+ std::string point_prop_header;
+ // edge properties header
+ std::string cell_prop_header;
+ // edge properties header
+ std::string edge_prop_header;
+ // Data point header
+ std::string point_data_header;
+ // Data point
+ std::string point_data;
+ // Cell type header
+ std::string cell_types_header;
+ // Cell type list
+ std::string cell_types_list;
+ // Cell data header
+ std::string cell_data_header;
+ // Cell data list
+ std::string cell_data_list;
+
+ // VTK header
+ vtk_header = "# vtk DataFile Version 3.0\n"
+ + graph_name + "\n";
+
+ // Choose if binary or ASCII
+ if (ft == file_type::ASCII)
+ {vtk_header += "ASCII\n";}
+ else
+ {vtk_header += "BINARY\n";}
+
+ // Data type for graph is DATASET POLYDATA
+ vtk_header += "DATASET UNSTRUCTURED_GRID\n";
+
+ // point properties header
+ point_prop_header = get_point_properties_list();
+
+ // Get point list
+ point_list = get_point_list();
+
+ // cell properties header
+ cell_prop_header = get_cell_properties_list();
+
+ // Get cell list
+ cell_list = get_cell_list();
+
+ // Get cell types
+ cell_types_header = get_cell_types_header();
+
+ // Get cell type list
+ cell_types_list = get_cell_types_list();
+
+ // Get cell data header
+ cell_data_header = get_cell_data_header();
+
+ // Get cell data list
+ cell_data_list = get_cell_data_list();
+
+ // write the file
+ std::ofstream ofs(file);
+
+ // Check if the file is open
+ if (ofs.is_open() == false)
+ {std::cerr << "Error cannot create the VTK file: " + file + "\n";}
+
+ ofs << vtk_header << point_prop_header << point_list <<
+ cell_prop_header << cell_list << cell_types_header << cell_types_list << cell_data_header << cell_data_list;
+
+ // Close the file
+
+ ofs.close();
+
+ // Completed succefully
+ return true;
+ }
+};
+
+
+
+#endif /* VTKWRITER_VECTOR_BOX_HPP_ */
diff --git a/src/VTKWriter/byteswap_portable.hpp b/src/VTKWriter/byteswap_portable.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..32182636efe1c6c67cbd7fe7dbee10a88118c632
--- /dev/null
+++ b/src/VTKWriter/byteswap_portable.hpp
@@ -0,0 +1,41 @@
+/*
+ * byteswap_portable.hpp
+ *
+ * Created on: Feb 20, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_VTKWRITER_BYTESWAP_PORTABLE_HPP_
+#define OPENFPM_IO_SRC_VTKWRITER_BYTESWAP_PORTABLE_HPP_
+
+#include <climits>
+
+/*! \brief This function swap byte from little endian to big endian format
+ *
+ * \warning in the case of big-endian machine this function should do nothing.
+ * Unfortunately this is not the case because I never had the bad luck
+ * of getting one
+ *
+ * \param T value to convert
+ *
+ */
+template <typename T>
+T swap_endian_lt(T u)
+{
+ static_assert (CHAR_BIT == 8, "CHAR_BIT != 8");
+
+ union
+ {
+ T u;
+ unsigned char u8[sizeof(T)];
+ } source, dest;
+
+ source.u = u;
+
+ for (size_t k = 0; k < sizeof(T); k++)
+ {dest.u8[k] = source.u8[sizeof(T) - k - 1];}
+
+ return dest.u;
+}
+
+#endif /* OPENFPM_IO_SRC_VTKWRITER_BYTESWAP_PORTABLE_HPP_ */
diff --git a/src/VTKWriter/is_vtk_writable.hpp b/src/VTKWriter/is_vtk_writable.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..a7484a3f5b57dc5b59c744a502487e1f4c5d7631
--- /dev/null
+++ b/src/VTKWriter/is_vtk_writable.hpp
@@ -0,0 +1,238 @@
+/*
+ * is_vtk_writable.hpp
+ *
+ * Created on: Jul 18, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_VTKWRITER_IS_VTK_WRITABLE_HPP_
+#define OPENFPM_IO_SRC_VTKWRITER_IS_VTK_WRITABLE_HPP_
+
+//! the vtk type
+template<typename T, bool is_w>
+struct vtk_type
+{
+ //! get the vtk type for the property
+ typedef decltype(std::declval<T>().get_vtk(0)) type;
+};
+
+//! the vtk type
+template<typename T>
+struct vtk_type<T,false>
+{
+ //! non writable vtk property (so void)
+ typedef void type;
+};
+
+/*! \brief it check if the type is vtk writable
+ *
+ *
+ */
+template<typename ObjType, typename Sfinae = void>
+struct is_custom_vtk_writable: std::false_type {};
+
+/*! \brief it check if the type is vtk writable
+ *
+ * \tparam ObjType check the type
+ *
+ */
+template<typename ObjType>
+struct is_custom_vtk_writable <ObjType, typename Void< typename ObjType::is_vtk_writable >::type> : std::true_type
+{};
+
+/*! \brief it check if the type is vtk writable
+ *
+ *
+ */
+template<typename ObjType, typename Sfinae = void>
+struct is_vtk_vector_dims: std::false_type {};
+
+//! If it has not dims property defined the object is considered scalar
+template<typename ObjType, bool has_dims = is_vtk_vector_dims<ObjType>::value >
+struct vtk_dims
+{
+ //! dimensionality of the vtk property (scalar)
+ enum
+ {
+ value = 1
+ };
+};
+
+//! return the dimansionality of the object
+template<typename ObjType >
+struct vtk_dims<ObjType,true>
+{
+ //! dimansionality of the vtk proverty (vector) in case of an object point
+ //! or an object that define dimansionality
+ enum
+ {
+ value = ObjType::dims
+ };
+};
+
+/*! \brief it check if the type is vtk writable
+ *
+ * \tparam ObjType check the type
+ *
+ */
+template<typename ObjType>
+struct is_vtk_vector_dims<ObjType, typename Void< decltype(ObjType::dims) >::type> : std::true_type
+{};
+
+//! check for T to be writable
+template<typename T>
+struct is_vtk_writable
+{
+ typedef T base;
+
+ //! It check if the object is vtk compatible
+ enum
+ {
+ value = is_custom_vtk_writable<T>::value
+ };
+};
+
+//! check float
+template<>
+struct is_vtk_writable<float>
+{
+ typedef float base;
+
+ //! float is vtk writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! check double
+template<>
+struct is_vtk_writable<double>
+{
+ typedef double base;
+
+ //! double is vtk writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! check char
+template<>
+struct is_vtk_writable<char>
+{
+ typedef char base;
+
+ //! char is vtk writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! check unsigned char
+template<>
+struct is_vtk_writable<unsigned char>
+{
+ typedef unsigned char base;
+
+ //! unsigned char is vtk writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! check short
+template<>
+struct is_vtk_writable<short>
+{
+ typedef short base;
+
+ //! short is vtk writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! check unsigned short
+template<>
+struct is_vtk_writable<unsigned short>
+{
+ typedef unsigned short base;
+
+ //! unsigned short is vtk writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! check int
+template<>
+struct is_vtk_writable<int>
+{
+ typedef int base;
+
+ //! int is vtk writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! check unsigned int
+template<>
+struct is_vtk_writable<unsigned int>
+{
+ typedef unsigned int base;
+
+ //! unsigned int is vtk writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! check long int
+template<>
+struct is_vtk_writable<long int>
+{
+ typedef int base;
+
+ //! long int is vtk writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! check unsigned long int
+template<>
+struct is_vtk_writable<unsigned long int>
+{
+ typedef unsigned int base;
+
+ //! unsigned long int is vtk writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! check bool
+template<>
+struct is_vtk_writable<bool>
+{
+ typedef bool base;
+
+ //! bool is vtk writable
+ enum
+ {
+ value = true
+ };
+};
+
+#endif /* OPENFPM_IO_SRC_VTKWRITER_IS_VTK_WRITABLE_HPP_ */
diff --git a/src/config/config_cmake.h.in b/src/config/config_cmake.h.in
index b15e33f40c557f801cc251b997c2876e21f71e08..8c9545e0bd8d61f151ca60fb26d8024b57d7bce5 100644
--- a/src/config/config_cmake.h.in
+++ b/src/config/config_cmake.h.in
@@ -1,6 +1,15 @@
/* Coverty scan */
${DEFINE_COVERTY_SCAN}
+<<<<<<< HEAD
+=======
+/* HIP GPU support */
+${DEFINE_HIP_GPU}
+
+/* HIP Cudify GPU support */
+${DEFINE_CUDIFY_USE_HIP}
+
+>>>>>>> origin/master
/* GPU support */
${DEFINE_CUDA_GPU}
@@ -198,3 +207,7 @@ ${DEFINE_TEST_COVERAGE_MODE}
/* Version number of package */
#define VERSION "1.0.0"
+<<<<<<< HEAD
+=======
+#define OPENFPM_IO
+>>>>>>> origin/master
diff --git a/src/garbage/HDF5_XdmfWriter.hpp b/src/garbage/HDF5_XdmfWriter.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..597c69b92eb18877741c75e0723dc0e9340a5973
--- /dev/null
+++ b/src/garbage/HDF5_XdmfWriter.hpp
@@ -0,0 +1,24 @@
+/*
+ * H5PartWriter.hpp
+ *
+ * Created on: Feb 7, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_HPP_
+#define OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_HPP_
+
+#define H5PART_WRITER 0x20000
+
+#define H5_POINTSET 1
+
+template <unsigned int imp>
+class HDF5_XdmfWriter
+{
+
+};
+
+#include "HDF5_XdmfWriter_point_set.hpp"
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_HPP_ */
diff --git a/src/garbage/HDF5_XdmfWriter_point_set.hpp b/src/garbage/HDF5_XdmfWriter_point_set.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..5be3e3a5cb7554d8f4732ec151f5327c55981953
--- /dev/null
+++ b/src/garbage/HDF5_XdmfWriter_point_set.hpp
@@ -0,0 +1,193 @@
+/*
+ * H5PartWriter_point_set.hpp
+ *
+ * Created on: Feb 7, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_POINT_SET_HPP_
+#define OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_POINT_SET_HPP_
+
+#include "HDF5_XdmfWriter_util.hpp"
+#include "Vector/map_vector.hpp"
+#include "VCluster/VCluster.hpp"
+
+/*! \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 produce write each property in H5Part
+ *
+ * \tparam ele_v is the vector of properties
+ * \tparam seq, sequence of property to output
+ * \tparam has_name define if the structure define names for the properties
+ *
+ */
+
+template<typename ele_v, bool has_name>
+struct H5_prop_out
+{
+ //! HDF5 file
+ hid_t file_id;
+
+ //! vector that we are processing
+ ele_v & vv;
+
+ //! Up to which element to write
+ size_t stop;
+
+ /*! \brief constructor
+ *
+ * \param v_out string to fill with the vertex properties
+ *
+ */
+ H5_prop_out(hid_t file_id, ele_v & vv, size_t stop)
+ :file_id(file_id),vv(vv),stop(stop)
+ {};
+
+ /*! \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;
+
+ H5_write<ptype,T::value,ele_v>::write(file_id,std::string(ele_v::value_type::attributes::names[T::value]),vv,stop);
+ }
+};
+
+
+
+/*! \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 produce an output for each property
+ *
+ * \tparam ele_v is the vector of properties
+ * \tparam seq, sequence of property to output
+ * \tparam has_name define if the structure define names
+ *
+ */
+template<typename ele_v>
+struct H5_prop_out<ele_v,false>
+{
+ //! HDF5 file
+ hid_t file_id;
+
+ //! vector that we are processing
+ ele_v & vv;
+
+ //! Up to which element to write
+ size_t stop;
+
+ /*! \brief constructor
+ *
+ * \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)
+ {};
+
+ /*! \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::type,boost::mpl::int_<T::value>>::type ptype;
+
+ H5_write<ptype,T::value,ele_v>::write(file_id,std::string("attr") + std::to_string(T::value),vv,stop);
+ }
+};
+
+/*! \brief HDF5 writer for a point set
+ *
+ *
+ */
+template <>
+class HDF5_XdmfWriter<H5_POINTSET>
+{
+ //! HDF5 file
+ hid_t file_id;
+
+public:
+
+ /*!
+ *
+ * H5PartWriter constructor
+ *
+ */
+ HDF5_XdmfWriter()
+ {}
+
+
+ /*!
+ *
+ * \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 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)
+ {
+ Vcluster & v_cl = create_vcluster();
+
+ // Open and HDF5 file in parallel
+
+ hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ H5Pset_fapl_mpio(plist_id, v_cl.getMPIComm(), MPI_INFO_NULL);
+ file_id = H5Fcreate(file.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
+ H5Pclose(plist_id);
+
+ // Single coordinate positional vector
+ openfpm::vector<typename VPos::coord_type> x_n;
+ x_n.resize(stop);
+
+ //for each component, fill x_n
+ for (size_t i = 0 ; i < VPos::dims ; i++)
+ {
+ //
+ for (size_t j = 0 ; j < stop ; j++)
+ x_n.get(j) = v_pos.template get<0>(j)[i];
+
+ std::stringstream str;
+ str << "x" << i;
+
+ HDF5CreateDataSet<typename VPos::coord_type>(file_id,str.str(),x_n.getPointer(),stop*sizeof(typename VPos::coord_type));
+ }
+
+ // Now we write the properties
+
+ typedef typename to_boost_vmpl<prp ... >::type v_prp_seq;
+ H5_prop_out<openfpm::vector<VPrp>,has_attributes<VPrp>::value> f(file_id,v_prp,stop);
+
+ boost::mpl::for_each_ref<v_prp_seq>(f);
+
+ H5Fclose(file_id);
+
+ return true;
+ }
+};
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_POINT_SET_HPP_ */
diff --git a/src/garbage/HDF5_XdmfWriter_unit_tests.hpp b/src/garbage/HDF5_XdmfWriter_unit_tests.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..86bd879f3da0f221c1f3e6fa675d1fc00587de3f
--- /dev/null
+++ b/src/garbage/HDF5_XdmfWriter_unit_tests.hpp
@@ -0,0 +1,64 @@
+/*
+ * H5PartWriter_unit_tests.hpp
+ *
+ * Created on: Feb 22, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UNIT_TESTS_HPP_
+#define OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UNIT_TESTS_HPP_
+
+#include "VCluster.hpp"
+#include "util/SimpleRNG.hpp"
+#include "HDF5_XdmfWriter.hpp"
+
+BOOST_AUTO_TEST_SUITE( HDF5_writer_test )
+
+
+BOOST_AUTO_TEST_CASE( HDF5_writer_use)
+{
+ openfpm::vector<Point<3,double>> pv;
+ openfpm::vector<Point_test<double>> pvp;
+
+ SimpleRNG rng;
+
+ Vcluster & v_cl = *global_v_cluster;
+
+ if (v_cl.getProcessingUnits() != 3)
+ return;
+
+ double z_base = v_cl.getProcessUnitID();
+
+ // fill 1000 particles for each processors
+
+ for (size_t i = 0 ; i < 1000 ; i++)
+ {
+ Point<3,double> p;
+ p[0] = rng.GetUniform();
+ p[1] = rng.GetUniform();
+ p[2] = z_base+rng.GetUniform();
+
+ pv.add(p);
+
+ p[0] += 2.0;
+
+ Point_test<double> pt;
+ pt.fill();
+
+ pvp.add(pt);
+ }
+
+ HDF5_XdmfWriter<H5_POINTSET> h5p;
+ h5p.template write<Point<3,double>,Point_test<double>,0,1,4,5>("h5part.h5",pv,pvp,1000);
+
+ // check that match
+
+ bool test = compare("test_h5part.h5part","test_h5part_test.h5part");
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UNIT_TESTS_HPP_ */
diff --git a/src/garbage/HDF5_XdmfWriter_util.hpp b/src/garbage/HDF5_XdmfWriter_util.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..db7acd59b26ee8da0ed7e25da3a7071f17e6f3ff
--- /dev/null
+++ b/src/garbage/HDF5_XdmfWriter_util.hpp
@@ -0,0 +1,300 @@
+/*
+ * H5PartWriteData_meta.hpp
+ *
+ * Created on: Feb 22, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UTIL_HPP_
+#define OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UTIL_HPP_
+
+#include "hdf5.h"
+#include "Vector/map_vector.hpp"
+
+/*! \brief HDF5 Create the data-set in the file
+ *
+ * \tparam type Type to write
+ *
+ * \param file_id Id of the file
+ * \param filespace id where to write
+ * \param str dataset to write
+ * \param ptr pointer with the data to write
+ * \param sz size of the data to write
+ *
+ * \return true if the function succeed
+ *
+ */
+template<typename type> bool HDF5CreateDataSet(hid_t file_id, const std::string & str ,void * ptr, size_t sz)
+{
+ hid_t plist_id = H5Pcreate(H5P_DATASET_XFER);
+ if (plist_id < 0)
+ return false;
+
+ /* Create the dataspace for the position dataset. */
+ hsize_t dimsf[1] = {sz};
+ hid_t filespace = H5Screate_simple(1, dimsf, NULL);
+ if (filespace < 0)
+ return false;
+
+ if (std::is_same<type,char>::value == true)
+ {
+ hid_t dset_id = H5Dcreate(file_id, str.c_str(), H5T_NATIVE_CHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ if (dset_id < 0)
+ return false;
+
+ herr_t status = H5Dwrite(dset_id, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, plist_id, ptr);
+ if (status < 0)
+ return false;
+
+ H5Dclose(dset_id);
+ H5Dclose(filespace);
+ return true;
+ }
+/* else if (std::is_same<type,signed char>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_SCHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ H5Dclose(dset_id);
+ return status;
+ }
+ else if (std::is_same<type,unsigned char>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_UCHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,short>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_SHORT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,unsigned short>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_USHORT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,int>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_INT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,unsigned int>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_UINT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,long>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_LONG, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,unsigned long>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_ULONG, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,long long>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_LLONG, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,unsigned long long>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_ULLONG, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,float>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_FLOAT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }*/
+ else if (std::is_same<type,double>::value == true)
+ {
+ hid_t dset_id = H5Dcreate(file_id, str.c_str(), H5T_NATIVE_DOUBLE, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ if (dset_id < 0)
+ return false;
+
+ herr_t status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, plist_id, ptr);
+ if (status < 0)
+ return false;
+
+ H5Dclose(dset_id);
+ H5Dclose(filespace);
+ return true;
+ }
+ /*else if (std::is_same<type,long double>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_LDOUBLE, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }*/
+
+ return true;
+}
+
+
+/*! \brief Write an HDF5 dataset in case of scalars and vectors
+ *
+ * \tparam T type to write
+ * \tparam pid Property id
+ * \tparam V Vector containing the information
+ *
+ */
+template<typename T,size_t pid, typename V>
+struct H5_write
+{
+ /*! \brief write
+ *
+ * \param file_id HDF5 file
+ * \param str dataset name
+ * \param v Vector containing the information
+ * \param stop size to store
+ *
+ */
+ static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
+ {
+ // Create the buffer
+ openfpm::vector<T> buffer;
+ buffer.resize(stop);
+
+ for (size_t j = 0 ; j < stop ; j++)
+ buffer.get(j) = v.template get<pid>(j);
+
+ HDF5CreateDataSet<T>(file_id,str.c_str(),buffer.getPointer(),stop*sizeof(T));
+ }
+};
+
+//! Partial specialization for N=1 1D-Array
+template<typename T,size_t pid, typename V,size_t N1>
+struct H5_write<T[N1],pid,V>
+{
+
+ /*! \brief write
+ *
+ * \param file_id HDF5 file
+ * \param str dataset name
+ * \param v Vector containing the information
+ * \param stop size to store
+ *
+ */
+ static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ // Create the buffer
+ openfpm::vector<T> buffer;
+ buffer.resize(stop);
+
+ for (size_t j = 0 ; j < stop ; j++)
+ buffer.get(j) = v.template get<pid>(j)[i1];
+
+ std::stringstream sstr;
+ sstr << "_" << i1;
+
+ HDF5CreateDataSet<T>(file_id,std::string(str) + sstr.str(),v.getPointer(),stop*sizeof(T));
+ }
+ }
+};
+
+//! Partial specialization for N=2 2D-Array
+template<typename T, size_t pid, typename V,size_t N1,size_t N2>
+struct H5_write<T[N1][N2],pid,V>
+{
+
+ /*! \brief write
+ *
+ * \param file_id HDF5 file
+ * \param str dataset name
+ * \param v Vector containing the information
+ * \param stop size to store
+ *
+ */
+ static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ // Create the buffer
+ openfpm::vector<T> buffer;
+ buffer.resize(stop);
+
+ for (size_t j = 0 ; j < stop ; j++)
+ buffer.get(j) = v.template get<pid>(j)[i1][i2];
+
+ std::stringstream sstr;
+ sstr << "_" << i1 << "_" << i2;
+
+ HDF5CreateDataSet<T>(file_id,std::string(str) + sstr.str(),v.getPointer(),stop*sizeof(T));
+ }
+ }
+ }
+};
+
+//! Partial specialization for N=3
+template<typename T, size_t pid, typename V,size_t N1,size_t N2,size_t N3>
+struct H5_write<T[N1][N2][N3],pid,V>
+{
+
+ /*! \brief write
+ *
+ * \param file_id HDF5 file
+ * \param str dataset name
+ * \param v Vector containing the information
+ * \param stop size to store
+ *
+ */
+ static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ for (size_t i3 = 0 ; i3 < N3 ; i3++)
+ {
+ // Create the buffer
+ openfpm::vector<T> buffer;
+ buffer.resize(stop);
+
+ for (size_t j = 0 ; j < stop ; j++)
+ buffer.get(j) = v.template get<pid>(j)[i1][i2][i3];
+
+ std::stringstream sstr;
+ sstr << "_" << i1 << "_" << i2 << "_" << i3;
+
+ HDF5CreateDataSet<T>(file_id,std::string(str) + sstr.str(),v.getPointer(),stop*sizeof(T));
+ }
+ }
+ }
+ }
+};
+
+//! Partial specialization for N=4
+template<typename T, size_t pid, typename V ,size_t N1,size_t N2,size_t N3,size_t N4>
+struct H5_write<T[N1][N2][N3][N4],pid,V>
+{
+
+ /*! \brief write
+ *
+ * \param file_id HDF5 file
+ * \param str dataset name
+ * \param v Vector containing the information
+ * \param stop size to store
+ *
+ */
+ static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ for (size_t i3 = 0 ; i3 < N3 ; i3++)
+ {
+ for (size_t i4 = 0 ; i4 < N4 ; i4++)
+ {
+ // Create the buffer
+ openfpm::vector<T> buffer;
+ buffer.resize(stop);
+
+ for (size_t j = 0 ; j < stop ; j++)
+ buffer.get(j) = v.template get<pid>(j)[i1][i2][i3][i4];
+
+
+ std::stringstream sstr;
+ sstr << "_" << i1 << "_" << i2 << "_" << i3 << "_" << i4;
+
+ HDF5CreateDataSet<T>(file_id,std::string(str) + sstr.str(),v.getPointer(),stop*sizeof(T));
+ }
+ }
+ }
+ }
+ }
+};
+
+#endif /* OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UTIL_HPP_ */
diff --git a/src/main.cpp b/src/main.cpp
index 893167fb884a3377a884127ce7e013bade27a617..fbcfde254e740d902f1346d57d2bfbd5458a0ee9 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -1,3 +1,4 @@
+<<<<<<< HEAD
#define BOOST_DISABLE_ASSERTS
#define FUSION_MAX_VECTOR_SIZE 20
@@ -45,6 +46,23 @@
#ifdef PERFORMANCE_TEST
#include "performance.hpp"
#endif
+=======
+#include "config.h"
+#undef VERSION
+
+#include <iostream>
+
+#ifdef OPENFPM_PDATA
+#include "VCluster/VCluster.hpp"
+#endif
+
+#define BOOST_DISABLE_ASSERTS
+
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+#include "VCluster/VCluster.hpp"
+>>>>>>> origin/master
#ifndef NO_INIT_AND_MAIN
@@ -54,6 +72,7 @@ bool init_unit_test()
return true;
}
+<<<<<<< HEAD
std::vector<int> sieve_spf;
// entry point:
@@ -70,3 +89,23 @@ int main(int argc, char* argv[])
+=======
+// entry point:
+int main(int argc, char* argv[])
+{
+ return boost::unit_test::unit_test_main( &init_unit_test, argc, argv );
+}
+
+#include "unit_test_init_cleanup_io.hpp"
+
+#endif
+
+#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"
+>>>>>>> origin/master
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..8ece35653eded808bbf8aa4911b8f0bb30fafc85
--- /dev/null
+++ b/src/util/GBoxes.hpp
@@ -0,0 +1,64 @@
+/*
+ * 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;
+
+ //! In case the grid is not defined everywhere but is defined by a set of boxes
+ //! indicate from which box it come from
+ size_t k;
+
+ /*! \brief Indicate that this structure has no pointers inside
+ *
+ * \return true
+ *
+ */
+ static bool noPointers()
+ {
+ return true;
+ }
+};
+
+
+#endif /* OPENFPM_IO_SRC_UTIL_GBOXES_HPP_ */
diff --git a/src/util/PathsAndFiles.hpp b/src/util/PathsAndFiles.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..41e4ad8772afedf7d1b94f05c1a28ae93fcb3cca
--- /dev/null
+++ b/src/util/PathsAndFiles.hpp
@@ -0,0 +1,123 @@
+//
+// Created by jstark on 2019-12-03.
+//
+/**
+ * @file PathsAndFiles.hpp
+ *
+ * @brief Header file containing functions for creating files and folders.
+ *
+ * @author Justina Stark
+ * @date December 2019
+ */
+
+#ifndef FILES_READ_AND_WRITE_PATHSANDFILES_HPP
+#define FILES_READ_AND_WRITE_PATHSANDFILES_HPP
+#include <unistd.h>
+#include <iostream>
+#include <fstream>
+#include <boost/filesystem.hpp>
+#include "VCluster/VCluster.hpp"
+/**@brief Gets the current working directory and returns path as string.
+ *
+ * @return Std::string of path to current working directory.
+ */
+static std::string get_cwd()
+{
+ char *cwd = nullptr;
+ size_t size;
+ cwd = getcwd(cwd, size);
+
+ // convert current directory to string
+ std::string s_cwd;
+ s_cwd = cwd;
+
+ // std::cout << "The current working directory is: " << dir << std::endl;
+ return s_cwd;
+}
+/**@brief Checks if a file already exists.
+ *
+ * @param path Std::string with path of file for which existence should be checked.
+ * @return True, if file exists, false if not.
+ */
+static bool check_if_file_exists(std::string path)
+{
+ try
+ {
+ // Create a filesystem::path object from given path string
+ boost::filesystem::path pathObj(path);
+ if (boost::filesystem::exists(pathObj) && boost::filesystem::is_regular_file(pathObj))
+ {
+ return true;
+// BOOST_LOG_TRIVIAL(info) << path << " -> File exists.";
+ }
+
+ }
+ catch (boost::filesystem::filesystem_error & e)
+ {
+ std::cerr << e.what() << std::endl;
+// BOOST_LOG_TRIVIAL(error) << "Error when checking existence of file ( " << path << " ): " << e.what();
+ }
+ return false;
+}
+/**@brief Creates a file if not already existent.
+ *
+ * @param path Std::string that contains path including filename of the file that should be created.
+ */
+static void create_file_if_not_exist(std::string path)
+{
+ auto & v_cl = create_vcluster();
+ if (v_cl.rank() == 0)
+ {
+ if ( ! check_if_file_exists(path))
+ {
+ std::ofstream outfile (path);
+// BOOST_LOG_TRIVIAL(info) << "Created file with name: " << path;
+ }
+ }
+}
+
+
+/**@brief Checks if a directory already exists.
+ *
+ * @param path Std::string with path of directory for which existence should be checked.
+ * @return True, if directory exists, false if not.
+ */
+static bool check_if_directory_exists(std::string path)
+{
+ try
+ {
+ // Create a filesystem::path object from given path string
+ boost::filesystem::path pathObj(path);
+ if (boost::filesystem::exists(pathObj) && boost::filesystem::is_directory(pathObj)) return true;
+ }
+ catch (boost::filesystem::filesystem_error & e)
+ {
+ std::cerr << e.what() << std::endl;
+ }
+ return false;
+}
+/**@brief Creates a directory if not already existent.
+ *
+ * @param path Std::string that contains path including name of the folder that should be created.
+ */
+static void create_directory_if_not_exist(std::string path)
+{
+ auto & v_cl = create_vcluster();
+ if (v_cl.rank() == 0)
+ {
+ if ( ! check_if_directory_exists(path))
+ {
+ boost::filesystem::create_directory(path);
+// BOOST_LOG_TRIVIAL(info) << "Created directory with name: " << path;
+ }
+ else std::cout << "Folder for current settings ( '" << path << "' ) already exists. New files will be saved to this folder." << std::endl;
+// BOOST_LOG_TRIVIAL(info) << "Folder for current settings ( '" << path << "' ) already exists. New files will be saved to this folder.";
+ }
+}
+
+
+
+
+
+#endif //FILES_READ_AND_WRITE_PATHSANDFILES_HPP
+
diff --git a/src/util/util.hpp b/src/util/util.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..70a8e48827f9e3c9ece093f9fbc1b2cded2b5777
--- /dev/null
+++ b/src/util/util.hpp
@@ -0,0 +1,390 @@
+/*
+ * util.hpp
+ *
+ * Created on: May 7, 2015
+ * Author: Pietro Incardona
+ */
+
+#include "config.h"
+
+#include "util/SimpleRNG.hpp"
+
+#ifndef UTIL_HPP_
+#define UTIL_HPP_
+
+#include <boost/iostreams/device/mapped_file.hpp>
+
+
+/*! \brief Compare two files, return true if they match
+ *
+ * \param file1 path1
+ * \param file2 path2
+ *
+ * \return true if they match
+ *
+ */
+static inline bool compare(std::string file1, std::string file2)
+{
+ boost::iostreams::mapped_file_source f1(file1);
+ boost::iostreams::mapped_file_source f2(file2);
+
+ if( f1.size() == f2.size() && std::equal(f1.data(), f1.data() + f1.size(), f2.data()) )
+ return true;
+ else
+ return false;
+}
+
+//! RGB color struct
+struct RGB
+{
+ //! Red
+ float R;
+
+ //! Green
+ float G;
+
+ //! Blue
+ float B;
+
+ //! Return the color as string
+ std::string toString()
+ {
+ return std::to_string(R) + " " + std::to_string(G) + " " + std::to_string(B);
+ }
+};
+
+/*! \brief Return the color sampled from one group
+ *
+ * groups:
+ *
+ * 0: Red
+ * 1: Green
+ * 2: Blue
+ * 3: Yellow
+ * 4: Cyan
+ * 5: Magenta
+ * 6: Orange
+ * 7: Chartreuse-Green
+ * 8: Spring Green
+ * 9: Azure
+ * 10: Violet
+ * 11: Rose
+ *
+ * \param group
+ *
+ */
+
+static inline struct RGB getColor(int group, SimpleRNG & d)
+{
+ struct RGB col;
+
+ float s = (float)d.GetUniform();
+
+ group = group % 12;
+
+#ifdef ON_IO_UNIT_TESTS
+ s = 0.5;
+#endif
+
+ if (group == 0)
+ {
+ col.R = s/2 + 0.5;
+ col.G = 0.0;
+ col.B = 0.0;
+ }
+ else if (group == 1)
+ {
+ col.R = 0.0;
+ col.G = s/2 + 0.5;
+ col.B = 0.0;
+ }
+ else if (group == 2)
+ {
+ col.R = 0.0;
+ col.G = 0.0;
+ col.B = s;
+ }
+ else if (group == 3)
+ {
+ col.R = s/2 + 0.5;
+ col.G = s/2 + 0.5;
+ col.B = 0.0;
+ }
+ else if (group == 4)
+ {
+ col.R = s/2 + 0.5;
+ col.G = 0.0;
+ col.B = s/2 + 0.5;
+ }
+ else if (group == 5)
+ {
+ col.R = 0.0;
+ col.G = s/2 + 0.5;
+ col.B = s/2 + 0.5;
+ }
+ else if (group == 6)
+ {
+ col.R = s/2 + 0.5;
+ col.G = s/4 + 0.5;
+ col.B = 0.0;
+ }
+ else if (group == 7)
+ {
+ col.R = s/4 + 0.5;
+ col.G = s/2 + 0.5;
+ col.B = 0.0;
+ }
+ else if (group == 8)
+ {
+ col.R = 0.0;
+ col.G = s/2 + 0.5;
+ col.B = s/4 + 0.5;
+ }
+ else if (group == 9)
+ {
+ col.R = 0.0;
+ col.G = s/4 + 0.5;
+ col.B = s/2 + 0.5;
+ }
+ else if (group == 10)
+ {
+ col.R = s/4 + 0.5;
+ col.G = 0.0;
+ col.B = s/2 + 0.5;
+ }
+ else
+ {
+ col.R = s/2 + 0.5;
+ col.G = 0.0;
+ col.B = s/4 + 0.5;
+ }
+
+ return col;
+}
+
+/*! \brief Check if one string end with a particular string
+ *
+ * \param fullString string to check
+ * \param ending ending string to check
+ *
+ */
+static inline bool hasEnding (std::string const &fullString, std::string const &ending)
+{
+ if (fullString.length() >= ending.length())
+ {return (0 == fullString.compare (fullString.length() - ending.length(), ending.length(), ending));}
+ else
+ {return false;}
+}
+
+static const std::string base64_chars =
+ "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
+ "abcdefghijklmnopqrstuvwxyz"
+ "0123456789+/";
+
+
+static inline bool is_base64(unsigned char c) {
+ return (isalnum(c) || (c == '+') || (c == '/'));
+}
+
+/*! \brief Encode to base64
+ *
+ * \param Byte String to encode
+ * \param Number of bytes to encode
+ *
+ */
+/*std::string base64_encode(unsigned char const* bytes_to_encode, unsigned int in_len) {
+ std::string ret;
+ int i = 0;
+ int j = 0;
+ unsigned char char_array_3[3];
+ unsigned char char_array_4[4];
+
+ while (in_len--) {
+ char_array_3[i++] = *(bytes_to_encode++);
+ if (i == 3) {
+ char_array_4[0] = (char_array_3[0] & 0xfc) >> 2;
+ char_array_4[1] = ((char_array_3[0] & 0x03) << 4) + ((char_array_3[1] & 0xf0) >> 4);
+ char_array_4[2] = ((char_array_3[1] & 0x0f) << 2) + ((char_array_3[2] & 0xc0) >> 6);
+ char_array_4[3] = char_array_3[2] & 0x3f;
+
+ for(i = 0; (i <4) ; i++)
+ ret += base64_chars[char_array_4[i]];
+ i = 0;
+ }
+ }
+
+ if (i)
+ {
+ for(j = i; j < 3; j++)
+ char_array_3[j] = '\0';
+
+ char_array_4[0] = (char_array_3[0] & 0xfc) >> 2;
+ char_array_4[1] = ((char_array_3[0] & 0x03) << 4) + ((char_array_3[1] & 0xf0) >> 4);
+ char_array_4[2] = ((char_array_3[1] & 0x0f) << 2) + ((char_array_3[2] & 0xc0) >> 6);
+ char_array_4[3] = char_array_3[2] & 0x3f;
+
+ for (j = 0; (j < i + 1); j++)
+ ret += base64_chars[char_array_4[j]];
+
+ while((i++ < 3))
+ ret += '=';
+
+ }
+
+ return ret;
+
+}
+
+*//*! \brief Decode base64
+ *
+ * \param Coded string
+ *
+ *//*
+std::string base64_decode(std::string const& encoded_string) {
+ int in_len = encoded_string.size();
+ int i = 0;
+ int j = 0;
+ int in_ = 0;
+ unsigned char char_array_4[4], char_array_3[3];
+ std::string ret;
+
+ while (in_len-- && ( encoded_string[in_] != '=') && is_base64(encoded_string[in_])) {
+ char_array_4[i++] = encoded_string[in_]; in_++;
+ if (i ==4) {
+ for (i = 0; i <4; i++)
+ char_array_4[i] = base64_chars.find(char_array_4[i]);
+
+ char_array_3[0] = (char_array_4[0] << 2) + ((char_array_4[1] & 0x30) >> 4);
+ char_array_3[1] = ((char_array_4[1] & 0xf) << 4) + ((char_array_4[2] & 0x3c) >> 2);
+ char_array_3[2] = ((char_array_4[2] & 0x3) << 6) + char_array_4[3];
+
+ for (i = 0; (i < 3); i++)
+ ret += char_array_3[i];
+ i = 0;
+ }
+ }
+
+ if (i) {
+ for (j = i; j <4; j++)
+ char_array_4[j] = 0;
+
+ for (j = 0; j <4; j++)
+ char_array_4[j] = base64_chars.find(char_array_4[j]);
+
+ char_array_3[0] = (char_array_4[0] << 2) + ((char_array_4[1] & 0x30) >> 4);
+ char_array_3[1] = ((char_array_4[1] & 0xf) << 4) + ((char_array_4[2] & 0x3c) >> 2);
+ char_array_3[2] = ((char_array_4[2] & 0x3) << 6) + char_array_4[3];
+
+ for (j = 0; (j < i - 1); j++) ret += char_array_3[j];
+ }
+
+ return ret;
+}*/
+
+
+static const unsigned char vtkBase64UtilitiesEncodeTable[65] =
+ "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
+ "abcdefghijklmnopqrstuvwxyz"
+ "0123456789+/";
+
+//----------------------------------------------------------------------------
+inline static unsigned char vtkBase64UtilitiesEncodeChar(unsigned char c)
+{
+ assert( c < 65 );
+ return vtkBase64UtilitiesEncodeTable[c];
+}
+
+//----------------------------------------------------------------------------
+static void EncodeTriplet(unsigned char i0,
+ unsigned char i1,
+ unsigned char i2,
+ unsigned char *o0,
+ unsigned char *o1,
+ unsigned char *o2,
+ unsigned char *o3)
+{
+ *o0 = vtkBase64UtilitiesEncodeChar((i0 >> 2) & 0x3F);
+ *o1 = vtkBase64UtilitiesEncodeChar(((i0 << 4) & 0x30)|((i1 >> 4) & 0x0F));
+ *o2 = vtkBase64UtilitiesEncodeChar(((i1 << 2) & 0x3C)|((i2 >> 6) & 0x03));
+ *o3 = vtkBase64UtilitiesEncodeChar(i2 & 0x3F);
+}
+
+//----------------------------------------------------------------------------
+static void EncodePair(unsigned char i0,
+ unsigned char i1,
+ unsigned char *o0,
+ unsigned char *o1,
+ unsigned char *o2,
+ unsigned char *o3)
+{
+ *o0 = vtkBase64UtilitiesEncodeChar((i0 >> 2) & 0x3F);
+ *o1 = vtkBase64UtilitiesEncodeChar(((i0 << 4) & 0x30)|((i1 >> 4) & 0x0F));
+ *o2 = vtkBase64UtilitiesEncodeChar(((i1 << 2) & 0x3C));
+ *o3 = '=';
+}
+
+//----------------------------------------------------------------------------
+static void EncodeSingle(unsigned char i0,
+ unsigned char *o0,
+ unsigned char *o1,
+ unsigned char *o2,
+ unsigned char *o3)
+{
+ *o0 = vtkBase64UtilitiesEncodeChar((i0 >> 2) & 0x3F);
+ *o1 = vtkBase64UtilitiesEncodeChar(((i0 << 4) & 0x30));
+ *o2 = '=';
+ *o3 = '=';
+}
+
+//----------------------------------------------------------------------------
+static unsigned long EncodeToBase64(const unsigned char *input,
+ unsigned long length,
+ unsigned char *output,
+ int mark_end)
+{
+
+ const unsigned char *ptr = input;
+ const unsigned char *end = input + length;
+ unsigned char *optr = output;
+
+ // Encode complete triplet
+
+ while ((end - ptr) >= 3)
+ {
+ EncodeTriplet(ptr[0], ptr[1], ptr[2],
+ &optr[0], &optr[1], &optr[2], &optr[3]);
+ ptr += 3;
+ optr += 4;
+ }
+
+ // Encodes a 2-byte ending into 3 bytes and 1 pad byte and writes.
+
+ if (end - ptr == 2)
+ {
+ EncodePair(ptr[0], ptr[1],
+ &optr[0], &optr[1], &optr[2], &optr[3]);
+ optr += 4;
+ }
+
+ // Encodes a 1-byte ending into 2 bytes and 2 pad bytes
+
+ else if (end - ptr == 1)
+ {
+ EncodeSingle(ptr[0],
+ &optr[0], &optr[1], &optr[2], &optr[3]);
+ optr += 4;
+ }
+
+ // Do we need to mark the end
+
+ else if (mark_end)
+ {
+ optr[0] = optr[1] = optr[2] = optr[3] = '=';
+ optr += 4;
+ }
+
+ return optr - output;
+}
+
+
+#endif /* UTIL_HPP_ */
diff --git a/test_data/char.csv b/test_data/char.csv
new file mode 100644
index 0000000000000000000000000000000000000000..91fcfcd53c9450c0816312df0860a464515d6049
--- /dev/null
+++ b/test_data/char.csv
@@ -0,0 +1,5 @@
+a,antilope
+b,ballena
+c,camel
+d,dackel
+e,elefant
\ No newline at end of file
diff --git a/test_data/csv_out_test.csv b/test_data/csv_out_test.csv
new file mode 100644
index 0000000000000000000000000000000000000000..a282d1bf36e8166650172be409bd953650989d0d
--- /dev/null
+++ b/test_data/csv_out_test.csv
@@ -0,0 +1,17 @@
+x[0],x[1],x[2],x,y,z,s,v_[0],v_[1],v_[2],t_[0][0],t_[0][1],t_[0][2],t_[1][0],t_[1][1],t_[1][2],t_[2][0],t_[2][1],t_[2][2]
+1,2,3,1,2,3,4,1,2,7,10,13,8,19,23,5,4,3,11
+1,2,3,1,2,3,4,2,3,8,11,14,9,20,24,6,5,4,12
+1,2,3,1,2,3,4,3,4,9,12,15,10,21,25,7,6,5,13
+1,2,3,1,2,3,4,4,5,10,13,16,11,22,26,8,7,6,14
+1,2,3,1,2,3,4,5,6,11,14,17,12,23,27,9,8,7,15
+1,2,3,1,2,3,4,6,7,12,15,18,13,24,28,10,9,8,16
+1,2,3,1,2,3,4,7,8,13,16,19,14,25,29,11,10,9,17
+1,2,3,1,2,3,4,8,9,14,17,20,15,26,30,12,11,10,18
+1,2,3,0,0,0,0,9,10,15,18,21,16,27,31,13,12,11,19
+1,2,3,0,0,0,0,10,11,16,19,22,17,28,32,14,13,12,20
+1,2,3,0,0,0,0,11,12,17,20,23,18,29,33,15,14,13,21
+1,2,3,0,0,0,0,12,13,18,21,24,19,30,34,16,15,14,22
+1,2,3,0,0,0,0,13,14,19,22,25,20,31,35,17,16,15,23
+1,2,3,0,0,0,0,14,15,20,23,26,21,32,36,18,17,16,24
+1,2,3,0,0,0,0,15,16,21,24,27,22,33,37,19,18,17,25
+1,2,3,0,0,0,0,16,17,22,25,28,23,34,38,20,19,18,26
diff --git a/test_data/csv_out_unk_test.csv b/test_data/csv_out_unk_test.csv
new file mode 100644
index 0000000000000000000000000000000000000000..76fe7f51015868b919e8bbb9b4e2fa13c3c50bf7
--- /dev/null
+++ b/test_data/csv_out_unk_test.csv
@@ -0,0 +1,17 @@
+x[0],x[1],x[2],column_0,column_1,column_2,column_3,column_4_[0],column_4_[1],column_4_[2],column_5_[0][0],column_5_[0][1],column_5_[0][2],column_5_[1][0],column_5_[1][1],column_5_[1][2],column_5_[2][0],column_5_[2][1],column_5_[2][2],column_6
+1,2,3,100,102,107,109,1,2,7,10,13,8,19,23,5,4,3,11,0
+1,2,3,101,103,108,110,2,3,8,11,14,9,20,24,6,5,4,12,0
+1,2,3,102,104,109,111,3,4,9,12,15,10,21,25,7,6,5,13,0
+1,2,3,103,105,110,112,4,5,10,13,16,11,22,26,8,7,6,14,0
+1,2,3,104,106,111,113,5,6,11,14,17,12,23,27,9,8,7,15,0
+1,2,3,105,107,112,114,6,7,12,15,18,13,24,28,10,9,8,16,0
+1,2,3,106,108,113,115,7,8,13,16,19,14,25,29,11,10,9,17,0
+1,2,3,107,109,114,116,8,9,14,17,20,15,26,30,12,11,10,18,0
+1,2,3,108,110,115,117,9,10,15,18,21,16,27,31,13,12,11,19,0
+1,2,3,109,111,116,118,10,11,16,19,22,17,28,32,14,13,12,20,0
+1,2,3,110,112,117,119,11,12,17,20,23,18,29,33,15,14,13,21,0
+1,2,3,111,113,118,120,12,13,18,21,24,19,30,34,16,15,14,22,0
+1,2,3,112,114,119,121,13,14,19,22,25,20,31,35,17,16,15,23,0
+1,2,3,113,115,120,122,14,15,20,23,26,21,32,36,18,17,16,24,0
+1,2,3,114,116,121,123,15,16,21,24,27,22,33,37,19,18,17,25,0
+1,2,3,115,117,122,124,16,17,22,25,28,23,34,38,20,19,18,26,0
diff --git a/test_data/gc_num_plot_test.html b/test_data/gc_num_plot_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..455f7c46e1ee67ad0c4a5a38faad543bd4917c38
--- /dev/null
+++ b/test_data/gc_num_plot_test.html
@@ -0,0 +1,50 @@
+<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('number','X Axis');
+data0.addColumn('number','dataset1');
+data0.addColumn('number','dataset2');
+data0.addColumn('number','dataset3');
+data0.addColumn('number','dataset4');
+data0.addRows([
+[0.1,2,3,5,6],
+[0.2,5,6,1,6],
+[0.3,2,1,6,9],
+[0.4,1,6,3,2],
+[0.5,3,3,0,6],
+[0.6,2,1,4,6],
+]);
+var options0= {
+title : 'Example',
+vAxis: {title: 'Y Axis'},
+hAxis: {title: 'X Axis'},
+curveType: 'function',
+lineWidth: 4,
+intervals: { 'style':'area' }};
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/test_data/gc_num_ydif_plot_test.html b/test_data/gc_num_ydif_plot_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..0a54032227398f1544586ea733e28cf5c22cd276
--- /dev/null
+++ b/test_data/gc_num_ydif_plot_test.html
@@ -0,0 +1,59 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(this).attr({'href': svgData,'target': '_blank'});
+}
+
+ function drawVisualization() {
+var data0 = new google.visualization.DataTable();
+data0.addColumn('number','X Axis');
+data0.addColumn('number','dataset1');
+data0.addColumn('number','dataset2');
+data0.addColumn('number','dataset3');
+data0.addRows([
+[0.1,4.5,null,3.5],
+[0.15,null,1.5,null],
+[0.2,3,4.5,6.5],
+[0.3,5.5,null,null],
+[0.35,null,2.5,null],
+[0.37,null,null,1.5],
+[0.4,3.3,null,2.5],
+[0.45,null,6.5,null],
+[0.5,1,null,7.5],
+[0.6,7,null,null],
+[0.63,null,null,1.5],
+[0.7,null,null,3.5],
+[0.82,null,null,2.5],
+[0.91,null,null,5.5],
+[1,null,null,1.5],
+]);
+var options0= {
+interpolateNulls : true,
+title : 'Example',
+vAxis: {title: 'Y Axis'},
+hAxis: {title: 'X Axis'},
+curveType: 'function',
+lineWidth: 4,
+intervals: { 'style':'area' }};
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/test_data/gc_out2_test.html b/test_data/gc_out2_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..16f6147e1cae865ac05b60a01a8385b70007554f
--- /dev/null
+++ b/test_data/gc_out2_test.html
@@ -0,0 +1,48 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(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',2.2,1.3,4.5,0.6],
+['colum2',5,6.1,1.3,2.6],
+['colum3',2.1,1,6.1,9.3],
+['colum4',1.1,6.1,3,2],
+['colum5',3.3,0.3,0,6.2],
+['colum6',2,1.1,4,6.1],
+]);
+var options0= {
+title : 'Example',
+vAxis: {title: 'Y Axis'},
+hAxis: {title: 'X Axis'},
+seriesType: 'bars'};
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/test_data/gc_out3_test.html b/test_data/gc_out3_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..3eaf8466eb869c19006628900982ec5dd46783ac
--- /dev/null
+++ b/test_data/gc_out3_test.html
@@ -0,0 +1,48 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(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',2.2,1.3,4.5,0.6],
+['colum2',5,6.1,1.3,2.6],
+['colum3',2.1,1,6.1,9.3],
+['colum4',1.1,6.1,3,2],
+['colum5',3.3,0.3,0,6.2],
+['colum6',2,1.1,4,6.1],
+]);
+var options0= {
+title : 'Example',
+vAxis: {title: 'Y Axis'},
+hAxis: {title: 'X Axis'},
+seriesType: ''};
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/test_data/gc_out4_test.html b/test_data/gc_out4_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..f851830c498ab3315b7e8585f9d0cb6ac2e27b47
--- /dev/null
+++ b/test_data/gc_out4_test.html
@@ -0,0 +1,48 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(this).attr({'href': svgData,'target': '_blank'});
+}
+
+ function drawVisualization() {
+var data0 = new google.visualization.DataTable();
+data0.addColumn('string','');
+data0.addColumn('number','dataset1');
+data0.addColumn('number','dataset2');
+data0.addColumn('number','dataset3');
+data0.addColumn('number','dataset4');
+data0.addRows([
+['colum1',2.2,1.3,4.5,0.6],
+['colum2',5,6.1,1.3,2.6],
+['colum3',2.1,1,6.1,9.3],
+['colum4',1.1,6.1,3,2],
+['colum5',3.3,0.3,0,6.2],
+['colum6',2,1.1,4,6.1],
+]);
+var options0= {
+title : '',
+vAxis: {title: ''},
+hAxis: {title: ''},
+seriesType: ''};
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/test_data/gc_out5_test.html b/test_data/gc_out5_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..4ef5259fdec336339185223f522efd6d0e93930d
--- /dev/null
+++ b/test_data/gc_out5_test.html
@@ -0,0 +1,48 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(this).attr({'href': svgData,'target': '_blank'});
+}
+
+ function drawVisualization() {
+var data0 = new google.visualization.DataTable();
+data0.addColumn('string','');
+data0.addColumn('number','');
+data0.addColumn('number','');
+data0.addColumn('number','');
+data0.addColumn('number','');
+data0.addRows([
+['colum1',2.2,1.3,4.5,0.6],
+['colum2',5,6.1,1.3,2.6],
+['colum3',2.1,1,6.1,9.3],
+['colum4',1.1,6.1,3,2],
+['colum5',3.3,0.3,0,6.2],
+['colum6',2,1.1,4,6.1],
+]);
+var options0= {
+title : '',
+vAxis: {title: ''},
+hAxis: {title: ''},
+seriesType: ''};
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/test_data/gc_out6_test.html b/test_data/gc_out6_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..8b1afbb0f181a8cab8efceb11bc61e786a851d64
--- /dev/null
+++ b/test_data/gc_out6_test.html
@@ -0,0 +1,48 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(this).attr({'href': svgData,'target': '_blank'});
+}
+
+ function drawVisualization() {
+var data0 = new google.visualization.DataTable();
+data0.addColumn('string','');
+data0.addColumn('number','');
+data0.addColumn('number','');
+data0.addColumn('number','');
+data0.addColumn('number','');
+data0.addRows([
+['',2.2,1.3,4.5,0.6],
+['',5,6.1,1.3,2.6],
+['',2.1,1,6.1,9.3],
+['',1.1,6.1,3,2],
+['',3.3,0.3,0,6.2],
+['',2,1.1,4,6.1],
+]);
+var options0= {
+title : '',
+vAxis: {title: ''},
+hAxis: {title: ''},
+seriesType: ''};
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/test_data/gc_out7_test.html b/test_data/gc_out7_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..b157cd50033ee4c2af1833d719f7d38d4996ea54
--- /dev/null
+++ b/test_data/gc_out7_test.html
@@ -0,0 +1,97 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(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 data1 = new google.visualization.DataTable();
+data1.addColumn('string','X Axis');
+data1.addColumn('number','dataset1');
+data1.addColumn('number','dataset2');
+data1.addColumn('number','dataset3');
+data1.addColumn('number','dataset4');
+data1.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 data2 = new google.visualization.DataTable();
+data2.addColumn('string','X Axis');
+data2.addColumn('number','dataset1');
+data2.addColumn('number','dataset2');
+data2.addColumn('number','dataset3');
+data2.addColumn('number','dataset4');
+data2.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 options1= {
+title : 'Example',
+vAxis: {title: 'Y Axis'},
+hAxis: {title: 'X Axis'},
+seriesType: 'bars',
+series: {3: {type: 'line'}}};
+var options2= {
+title : 'Example',
+vAxis: {title: 'Y Axis'},
+hAxis: {title: 'X Axis'},
+seriesType: 'bars',
+series: {3: {type: 'line'}}};
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
+$("#export_svg1").on("click", function (event) {exportToSVG.apply(this,[1]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div1'));
+chart.draw(data1, options1);
+$("#export_svg2").on("click", function (event) {exportToSVG.apply(this,[2]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div2'));
+chart.draw(data2, options2);
+}</script>
+</head>
+<body>
+<h2>Before first graph</h2><a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+<h2>Before second graph</h2><a href="#" download="graph1.svg" id="export_svg1"><button>Export data into svg</button></a><div id="chart_div1" style="width: 900px; height: 500px;"></div>
+<h2>Before third graph</h2><a href="#" download="graph1.svg" id="export_svg2"><button>Export data into svg</button></a><div id="chart_div2" style="width: 900px; height: 500px;"></div>
+<h2>At the end</h2></body>
+</html>
diff --git a/test_data/gc_out_sc_test.html b/test_data/gc_out_sc_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..c704abb8a4653bbb95e732b3eed2d6ba78eb67ba
--- /dev/null
+++ b/test_data/gc_out_sc_test.html
@@ -0,0 +1,65 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(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" }
+]
+);
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(view0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/test_data/gc_out_test.html b/test_data/gc_out_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..b65719ef3b2d79be7ccad9ed89d3b0fe9ce04126
--- /dev/null
+++ b/test_data/gc_out_test.html
@@ -0,0 +1,49 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(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'}}};
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/test_data/gc_plot2_out_test.html b/test_data/gc_plot2_out_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..f48dbf2078e27c13cdce1be8f88222b2029c8627
--- /dev/null
+++ b/test_data/gc_plot2_out_test.html
@@ -0,0 +1,55 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(this).attr({'href': svgData,'target': '_blank'});
+}
+
+ function drawVisualization() {
+var data0 = new google.visualization.DataTable();
+data0.addColumn('string','X Axis');
+data0.addColumn('number','line0');
+data0.addColumn('number','line1');
+data0.addColumn('number','line2');
+data0.addColumn('number','line3');
+data0.addColumn('number','line4');
+data0.addColumn('number','line5');
+data0.addColumn('number','line6');
+data0.addColumn('number','line7');
+data0.addColumn('number','line8');
+data0.addRows([
+['colum1',0.1,0.2,0.19,0.22,0.195,0.215,0.35,0.34,0.36],
+['colum2',0.11,0.21,0.18,0.22,0.19,0.215,0.36,0.35,0.37],
+['colum3',0.12,0.22,0.21,0.23,0.215,0.225,0.35,0.34,0.36],
+['colum4',0.15,0.25,0.2,0.26,0.22,0.255,0.36,0.35,0.37],
+['colum5',0.09,0.29,0.25,0.3,0.26,0.295,0.35,0.34,0.36],
+['colum6',0.08,0.28,0.27,0.29,0.275,0.285,0.36,0.35,0.37],
+]);
+var options0= {
+title : 'Example',
+vAxis: {title: 'Y Axis'},
+hAxis: {title: 'X Axis'},
+curveType: 'function',
+lineWidth: 1,
+intervals: { 'style':'area' }};
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/test_data/gc_plot_out_test.html b/test_data/gc_plot_out_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..a52ce00093bec66089e37e2099e7899cc5492169
--- /dev/null
+++ b/test_data/gc_plot_out_test.html
@@ -0,0 +1,57 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(this).attr({'href': svgData,'target': '_blank'});
+}
+
+ function drawVisualization() {
+var data0 = new google.visualization.DataTable();
+data0.addColumn('string','X Axis');
+data0.addColumn('number','line1');
+data0.addColumn('number','line2');
+data0.addColumn({id:'i0', type:'number', role:'interval'});
+data0.addColumn({id:'i0', type:'number', role:'interval'});
+data0.addColumn({id:'i1', type:'number', role:'interval'});
+data0.addColumn({id:'i1', type:'number', role:'interval'});
+data0.addColumn('number','line3');
+data0.addColumn({id:'i2', type:'number', role:'interval'});
+data0.addColumn({id:'i2', type:'number', role:'interval'});
+data0.addRows([
+['colum1',0.1,0.2,0.19,0.22,0.195,0.215,0.35,0.34,0.36],
+['colum2',0.11,0.21,0.18,0.22,0.19,0.215,0.36,0.35,0.37],
+['colum3',0.12,0.22,0.21,0.23,0.215,0.225,0.35,0.34,0.36],
+['colum4',0.15,0.25,0.2,0.26,0.22,0.255,0.36,0.35,0.37],
+['colum5',0.09,0.29,0.25,0.3,0.26,0.295,0.35,0.34,0.36],
+['colum6',0.08,0.28,0.27,0.29,0.275,0.285,0.36,0.35,0.37],
+]);
+var options0= {
+title : 'Example',
+vAxis: {title: 'Y Axis'},
+hAxis: {title: 'X Axis'},
+curveType: 'function',
+lineWidth: 1,
+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);
+}</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/integer.csv b/test_data/integer.csv
new file mode 100644
index 0000000000000000000000000000000000000000..26f59ab685209150603a0b8f06eba7a4eb0d03b5
--- /dev/null
+++ b/test_data/integer.csv
@@ -0,0 +1,4 @@
+1,2,2
+2,4,8
+3,6,18
+4,8,32
\ No newline at end of file
diff --git a/test_data/pvtp_points_test.pvtp b/test_data/pvtp_points_test.pvtp
new file mode 100644
index 0000000000000000000000000000000000000000..62f5f01d003d720e127fb1e4123ed9de3c5c357c
--- /dev/null
+++ b/test_data/pvtp_points_test.pvtp
@@ -0,0 +1,14 @@
+<VTKFile type="PPolyData" version="1.0" byte_order="LittleEndian" header_type="UInt64">
+ <PPolyData>
+ <PPointData>
+ <PDataArray type="Float32" Name="attr0"/>
+ <PDataArray type="Float32" Name="attr1" NumberOfComponents="3"/>
+ <PDataArray type="Float32" Name="domain"/>
+ </PPointData>
+ <PPoints>
+ <PDataArray type="Float64" Name="Points" NumberOfComponents="3"/>
+ </PPoints>
+ <Piece Source="vtk_points_0.vtp"/>
+ <Piece Source="vtk_points_1.vtp"/>
+ </PPolyData>
+</VTKFile>
\ No newline at end of file
diff --git a/test_data/raw_read_sv_test.bin b/test_data/raw_read_sv_test.bin
new file mode 100644
index 0000000000000000000000000000000000000000..72ebe08fa554496f4257363ad24236f3b7237b2c
Binary files /dev/null and b/test_data/raw_read_sv_test.bin differ
diff --git a/test_data/test_graph2_test.graphml b/test_data/test_graph2_test.graphml
new file mode 100644
index 0000000000000000000000000000000000000000..da443afbd0fe26b6a72dea6329f9b8ea8b80c29f
--- /dev/null
+++ b/test_data/test_graph2_test.graphml
@@ -0,0 +1,100 @@
+<?xml version="1.0" encoding="UTF-8"?>
+ <graphml xmlns="http://graphml.graphdrawing.org/xmlns"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
+ http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
+<graph id="Graph" edgedefault="undirected">
+<key id="vk3" for="node" attr.name="double_num" attr.type="double"/>
+<key id="vk4" for="node" attr.name="long_num" attr.type="long"/>
+<key id="vk5" for="node" attr.name="integer" attr.type="int"/>
+<key id="vk6" for="node" attr.name="string" attr.type="string"/>
+<key id="ek0" for="edge" attr.name="x" attr.type="float"/>
+<key id="ek1" for="edge" attr.name="y" attr.type="float"/>
+<key id="ek2" for="edge" attr.name="z" attr.type="float"/>
+<key id="ek3" for="edge" attr.name="double_num" attr.type="double"/>
+<key id="ek4" for="edge" attr.name="long_num" attr.type="long"/>
+<key id="ek5" for="edge" attr.name="integer" attr.type="int"/>
+<key id="ek6" for="edge" attr.name="string" attr.type="string"/>
+<node id="n0">
+ <data key="vk0">1.000000</data>
+ <data key="vk1">2.000000</data>
+ <data key="vk2">3.000000</data>
+ <data key="vk3">4.000000</data>
+ <data key="vk4">5</data>
+ <data key="vk5">6</data>
+ <data key="vk6">test</data>
+</node>
+<node id="n1">
+ <data key="vk0">1.000000</data>
+ <data key="vk1">2.000000</data>
+ <data key="vk2">3.000000</data>
+ <data key="vk3">4.000000</data>
+ <data key="vk4">5</data>
+ <data key="vk5">6</data>
+ <data key="vk6">tes2</data>
+</node>
+<node id="n2">
+ <data key="vk0">1.000000</data>
+ <data key="vk1">2.000000</data>
+ <data key="vk2">3.000000</data>
+ <data key="vk3">4.000000</data>
+ <data key="vk4">5</data>
+ <data key="vk5">6</data>
+ <data key="vk6">test3</data>
+</node>
+<node id="n3">
+ <data key="vk0">1.000000</data>
+ <data key="vk1">2.000000</data>
+ <data key="vk2">3.000000</data>
+ <data key="vk3">4.000000</data>
+ <data key="vk4">5</data>
+ <data key="vk5">6</data>
+ <data key="vk6">test4</data>
+</node>
+<edge id="e0" source="n0" target="n1">
+ <data key="ek0">1.000000</data>
+ <data key="ek1">2.000000</data>
+ <data key="ek2">3.000000</data>
+ <data key="ek3">4.000000</data>
+ <data key="ek4">5</data>
+ <data key="ek5">6</data>
+ <data key="ek6">test5</data>
+</edge>
+<edge id="e1" source="n2" target="n1">
+ <data key="ek0">1.000000</data>
+ <data key="ek1">2.000000</data>
+ <data key="ek2">3.000000</data>
+ <data key="ek3">4.000000</data>
+ <data key="ek4">5</data>
+ <data key="ek5">6</data>
+ <data key="ek6">test6</data>
+</edge>
+<edge id="e2" source="n2" target="n0">
+ <data key="ek0">1.000000</data>
+ <data key="ek1">2.000000</data>
+ <data key="ek2">3.000000</data>
+ <data key="ek3">4.000000</data>
+ <data key="ek4">5</data>
+ <data key="ek5">6</data>
+ <data key="ek6">test8</data>
+</edge>
+<edge id="e3" source="n3" target="n1">
+ <data key="ek0">1.000000</data>
+ <data key="ek1">2.000000</data>
+ <data key="ek2">3.000000</data>
+ <data key="ek3">4.000000</data>
+ <data key="ek4">5</data>
+ <data key="ek5">6</data>
+ <data key="ek6">test7</data>
+</edge>
+<edge id="e4" source="n3" target="n2">
+ <data key="ek0">1.000000</data>
+ <data key="ek1">2.000000</data>
+ <data key="ek2">3.000000</data>
+ <data key="ek3">4.000000</data>
+ <data key="ek4">5</data>
+ <data key="ek5">6</data>
+ <data key="ek6">test9</data>
+</edge>
+</graph>
+</graphml>
\ No newline at end of file
diff --git a/test_data/test_graph_test.graphml b/test_data/test_graph_test.graphml
new file mode 100644
index 0000000000000000000000000000000000000000..df8e14858909042ab0960a8557e54eb5ce8ddbf1
--- /dev/null
+++ b/test_data/test_graph_test.graphml
@@ -0,0 +1,28819 @@
+<?xml version="1.0" encoding="UTF-8"?>
+ <graphml xmlns="http://graphml.graphdrawing.org/xmlns"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
+ http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
+<graph id="Graph" edgedefault="undirected">
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+<key id="vk4" for="node" attr.name="long_num" attr.type="long"/>
+<key id="vk5" for="node" attr.name="integer" attr.type="int"/>
+<key id="vk6" for="node" attr.name="string" attr.type="string"/>
+<key id="ek0" for="edge" attr.name="x" attr.type="float"/>
+<key id="ek1" for="edge" attr.name="y" attr.type="float"/>
+<key id="ek2" for="edge" attr.name="z" attr.type="float"/>
+<key id="ek3" for="edge" attr.name="double_num" attr.type="double"/>
+<key id="ek4" for="edge" attr.name="long_num" attr.type="long"/>
+<key id="ek5" for="edge" attr.name="integer" attr.type="int"/>
+<key id="ek6" for="edge" attr.name="string" attr.type="string"/>
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+
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+
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diff --git a/test_data/vtk_box_3D_test.vtk b/test_data/vtk_box_3D_test.vtk
new file mode 100644
index 0000000000000000000000000000000000000000..980304a73f66719820158482eb6a351a82227816
--- /dev/null
+++ b/test_data/vtk_box_3D_test.vtk
@@ -0,0 +1,77 @@
+# vtk DataFile Version 3.0
+Graph
+ASCII
+DATASET UNSTRUCTURED_GRID
+POINTS 48 float
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+CELL_TYPES 6
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diff --git a/test_data/vtk_box_test.vtk b/test_data/vtk_box_test.vtk
new file mode 100644
index 0000000000000000000000000000000000000000..e8a1a70e32941cded7b1e5e4c7d964b77d8e27cf
--- /dev/null
+++ b/test_data/vtk_box_test.vtk
@@ -0,0 +1,53 @@
+# vtk DataFile Version 3.0
+Graph
+ASCII
+DATASET UNSTRUCTURED_GRID
+POINTS 24 float
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+CELL_TYPES 6
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diff --git a/test_data/vtk_graph_test.vtk b/test_data/vtk_graph_test.vtk
new file mode 100644
index 0000000000000000000000000000000000000000..70381888e9790b51068989b436beae7d47697c61
--- /dev/null
+++ b/test_data/vtk_graph_test.vtk
@@ -0,0 +1,509 @@
+# vtk DataFile Version 3.0
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+ASCII
+DATASET POLYDATA
+POINTS 8 float
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diff --git a/test_data/vtk_graph_v2_test.vtk b/test_data/vtk_graph_v2_test.vtk
new file mode 100644
index 0000000000000000000000000000000000000000..1aad699e246786556103a19bd63af7cc61123524
--- /dev/null
+++ b/test_data/vtk_graph_v2_test.vtk
@@ -0,0 +1,458 @@
+# vtk DataFile Version 3.0
+Graph
+ASCII
+DATASET POLYDATA
+POINTS 8 float
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+VERTICES 8 16
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+LINES 36 108
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diff --git a/test_data/vtk_graph_v3_test.vtk b/test_data/vtk_graph_v3_test.vtk
new file mode 100644
index 0000000000000000000000000000000000000000..e39bf864844b4439361778a94c5508b6d4587afb
--- /dev/null
+++ b/test_data/vtk_graph_v3_test.vtk
@@ -0,0 +1,118 @@
+# vtk DataFile Version 3.0
+Graph
+ASCII
+DATASET POLYDATA
+POINTS 4 float
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+0.000000 1.000000 0.000000
+1.000000 0.000000 0.000000
+1.000000 1.000000 0.000000
+VERTICES 4 8
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+1 3
+LINES 4 12
+2 0 1
+2 1 3
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diff --git a/test_data/vtk_graph_v4_test.vtk b/test_data/vtk_graph_v4_test.vtk
new file mode 100644
index 0000000000000000000000000000000000000000..f65cfa2932cbeed275fd9645a01c02ae7189b377
--- /dev/null
+++ b/test_data/vtk_graph_v4_test.vtk
@@ -0,0 +1,227 @@
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diff --git a/test_data/vtk_grids_prp_test.vtk b/test_data/vtk_grids_prp_test.vtk
new file mode 100644
index 0000000000000000000000000000000000000000..4bb0f0447ab7d3c80c4a03275327bd73216b95c3
--- /dev/null
+++ b/test_data/vtk_grids_prp_test.vtk
@@ -0,0 +1,7185 @@
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diff --git a/test_data/vtk_grids_st_test.vtk b/test_data/vtk_grids_st_test.vtk
new file mode 100644
index 0000000000000000000000000000000000000000..d6ab6ae2eda711e12e45df3219e8975028328b7f
--- /dev/null
+++ b/test_data/vtk_grids_st_test.vtk
@@ -0,0 +1,3083 @@
+# vtk DataFile Version 3.0
+grids
+ASCII
+DATASET POLYDATA
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diff --git a/test_data/vtk_grids_test.vtk b/test_data/vtk_grids_test.vtk
new file mode 100644
index 0000000000000000000000000000000000000000..681ef860b4a6b27581aa8a14337cebc520fd4aed
--- /dev/null
+++ b/test_data/vtk_grids_test.vtk
@@ -0,0 +1,17444 @@
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diff --git a/test_data/vtk_grids_test_1d.vtk b/test_data/vtk_grids_test_1d.vtk
new file mode 100644
index 0000000000000000000000000000000000000000..0ad208b3e2500e16120ec72b918a80ab8ef04c44
--- /dev/null
+++ b/test_data/vtk_grids_test_1d.vtk
@@ -0,0 +1,1124 @@
+# vtk DataFile Version 3.0
+grids
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diff --git a/test_data/vtk_points_2d_bin_test.vtp b/test_data/vtk_points_2d_bin_test.vtp
new file mode 100644
index 0000000000000000000000000000000000000000..afb88be758be47eae33d0842bf456a8a5bcd53d7
--- /dev/null
+++ b/test_data/vtk_points_2d_bin_test.vtp
@@ -0,0 +1,54 @@
+<VTKFile type="PolyData" version="1.0" byte_order="LittleEndian" header_type="UInt64">
+ <PolyData>
+ <Piece NumberOfPoints="300" NumberOfVerts="300">
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diff --git a/test_data/vtk_points_2d_pp_bin_test.vtp b/test_data/vtk_points_2d_pp_bin_test.vtp
new file mode 100644
index 0000000000000000000000000000000000000000..0ae065fff49829bc8176966e73ab9ed962597d92
--- /dev/null
+++ b/test_data/vtk_points_2d_pp_bin_test.vtp
@@ -0,0 +1,30 @@
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diff --git a/test_data/vtk_points_bin_test.vtp b/test_data/vtk_points_bin_test.vtp
new file mode 100644
index 0000000000000000000000000000000000000000..be9a64ab51241e74464a12178506be850ad99d3d
--- /dev/null
+++ b/test_data/vtk_points_bin_test.vtp
@@ -0,0 +1,30 @@
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diff --git a/test_data/vtk_points_pp_bin_test.vtp b/test_data/vtk_points_pp_bin_test.vtp
new file mode 100644
index 0000000000000000000000000000000000000000..1638c7d9a23415626f0f74fce79cf54e2f094eb7
--- /dev/null
+++ b/test_data/vtk_points_pp_bin_test.vtp
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diff --git a/test_data/vtk_points_pp_header_bin_test.vtp b/test_data/vtk_points_pp_header_bin_test.vtp
new file mode 100644
index 0000000000000000000000000000000000000000..da6d2e69126c8f0918f245d41df7c00c946e4a2c
--- /dev/null
+++ b/test_data/vtk_points_pp_header_bin_test.vtp
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diff --git a/test_data/vtk_points_pp_header_test.vtp b/test_data/vtk_points_pp_header_test.vtp
new file mode 100644
index 0000000000000000000000000000000000000000..79f2228ac371b9f414e1922000ef7278d6c9a5dc
--- /dev/null
+++ b/test_data/vtk_points_pp_header_test.vtp
@@ -0,0 +1,629 @@
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diff --git a/test_data/vtk_points_pp_test.vtp b/test_data/vtk_points_pp_test.vtp
new file mode 100644
index 0000000000000000000000000000000000000000..cef332caf4341d6a98ddea79f5e38b216e28153d
--- /dev/null
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diff --git a/test_data/vtk_points_test.vtp b/test_data/vtk_points_test.vtp
new file mode 100644
index 0000000000000000000000000000000000000000..9cea49ec937c8dc8c070253b64176a8cb773d7b5
--- /dev/null
+++ b/test_data/vtk_points_test.vtp
@@ -0,0 +1,1824 @@
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\ No newline at end of file
diff --git a/test_data/vtk_points_with_prp_names_prec_check_test.vtk b/test_data/vtk_points_with_prp_names_prec_check_test.vtk
new file mode 100644
index 0000000000000000000000000000000000000000..db8cdb097c78efc3b835a67f09011d74c5139a2f
--- /dev/null
+++ b/test_data/vtk_points_with_prp_names_prec_check_test.vtk
@@ -0,0 +1,512 @@
+# vtk DataFile Version 3.0
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diff --git a/test_data/vtk_points_with_prp_names_prec_check_test.vtp b/test_data/vtk_points_with_prp_names_prec_check_test.vtp
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index 0000000000000000000000000000000000000000..34790ee338d297ee59864e5e87a04766da41e35e
--- /dev/null
+++ b/test_data/vtk_points_with_prp_names_prec_check_test.vtp
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diff --git a/test_data/vtk_points_with_prp_names_test.vtp b/test_data/vtk_points_with_prp_names_test.vtp
new file mode 100644
index 0000000000000000000000000000000000000000..4393c1b3d51591d2e339e4c73b6e551ef8ec8eef
--- /dev/null
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