Grid iterator from decomposition

src/Decomposition/CartDecomposition.hpp

@@ -352,6 +352,10 @@ private:
 
 public:
 
+	static constexpr int dims = dim;
+
+	typedef T stype;
+
 	//! Increment the reference counter
 	void incRef()
 	{ref_cnt++;}

src/Grid/grid_dist_id.hpp

@@ -7,6 +7,7 @@
 #include "VCluster.hpp"
 #include "Space/SpaceBox.hpp"
 #include "util/mathutil.hpp"
+#include "grid_dist_id_iterator_dec.hpp"
 #include "grid_dist_id_iterator.hpp"
 #include "grid_dist_id_iterator_sub.hpp"
 #include "grid_dist_key.hpp"
@@ -56,7 +57,7 @@ class grid_dist_id
 	Ghost<dim,St> ghost;
 
 	//! Local grids
-	Vcluster_object_array<device_grid> loc_grid;
+	openfpm::vector<device_grid> loc_grid;
 
 	//! Space Decomposition
 	Decomposition & dec;
@@ -369,8 +370,11 @@ class grid_dist_id
 		// Get the number of local grid needed
 		size_t n_grid = dec.getNLocalHyperCube();
 
+		// create gdb
+		create_gdb_ext<dim,Decomposition>(gdb_ext,dec,cd_sm);
+
 		// create local grids for each hyper-cube
-		loc_grid = v_cl.allocate<device_grid>(n_grid);
+		loc_grid.resize(n_grid);
 
 		// Size of the grid on each dimension
 		size_t l_res[dim];
@@ -378,32 +382,16 @@ class grid_dist_id
 		// Allocate the grids
 		for (size_t i = 0 ; i < n_grid ; i++)
 		{
-			gdb_ext.add();
-
-			// Get the local hyper-cube
-			SpaceBox<dim,St> sp = dec.getLocalHyperCube(i);
-			SpaceBox<dim,St> sp_g = dec.getSubDomainWithGhost(i);
-
-			// Convert from SpaceBox<dim,St> to SpaceBox<dim,long int>
-			SpaceBox<dim,long int> sp_t = cd_sm.convertDomainSpaceIntoGridUnits(sp);
-			SpaceBox<dim,long int> sp_tg = cd_sm.convertDomainSpaceIntoGridUnits(sp_g);
-
-			//! Save the origin of the sub-domain of the local grid
-			gdb_ext.last().origin = sp_tg.getP1();
 
-			// save information about the local grid: domain box seen inside the domain + ghost box (see GDBoxes for a visual meaning)
-			// and where the GDBox start, or the origin of the local grid (+ghost) in global coordinate
-			gdb_ext.last().Dbox = sp_t;
-			gdb_ext.last().Dbox -= sp_tg.getP1();
-
-			gdb_ext.last().GDbox = sp_tg;
-			gdb_ext.last().GDbox -= sp_tg.getP1();
-
-			// center to zero
-			sp_tg -= sp_tg.getP1();
+			SpaceBox<dim,long int> sp_tg = gdb_ext.get(i).GDbox;
 
 			// Get the size of the local grid
-			for (size_t i = 0 ; i < dim ; i++) {l_res[i] = (sp_tg.getHigh(i) >= 0)?(sp_tg.getHigh(i)+1):0;}
+			// The boxes indicate the extension of the index the size
+			// is this extension +1
+			// for example a 1D box (interval) from 0 to 3 in one dimension have
+			// the points 0,1,2,3 = so a total of 4 points
+			for (size_t i = 0 ; i < dim ; i++)
+				l_res[i] = (sp_tg.getHigh(i) >= 0)?(sp_tg.getHigh(i)+1):0;
 
 			// Set the dimensions of the local grid
 			loc_grid.get(i).resize(l_res);
@@ -591,6 +579,7 @@ public:
 		InitializeStructures(g_sz);
 	}
 
+
 	/*! \brief Get an object containing the grid informations
 	 *
 	 * \return an information object about this grid

src/Grid/grid_dist_id_iterator.hpp

@@ -85,7 +85,7 @@ class grid_dist_iterator<dim,device_grid,FREE>
 	size_t g_c;
 
 	//! List of the grids we are going to iterate
-	Vcluster_object_array<device_grid> & gList;
+	openfpm::vector<device_grid> & gList;
 
 	//! Extension of each grid: domain and ghost + domain
 	openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext;
@@ -102,12 +102,12 @@ class grid_dist_iterator<dim,device_grid,FREE>
 	void selectValidGrid()
 	{
 		// When the grid has size 0 potentially all the other informations are garbage
-		while (g_c < gList.size() && (gList[g_c].size() == 0 || gdb_ext.get(g_c).Dbox.isValid() == false ) ) g_c++;
+		while (g_c < gList.size() && (gList.get(g_c).size() == 0 || gdb_ext.get(g_c).Dbox.isValid() == false ) ) g_c++;
 
 		// get the next grid iterator
 		if (g_c < gList.size())
 		{
-			a_it.reinitialize(gList[g_c].getIterator(gdb_ext.get(g_c).Dbox.getKP1(),gdb_ext.get(g_c).Dbox.getKP2()));
+			a_it.reinitialize(gList.get(g_c).getIterator(gdb_ext.get(g_c).Dbox.getKP1(),gdb_ext.get(g_c).Dbox.getKP2()));
 		}
 	}
 
@@ -134,7 +134,7 @@ class grid_dist_iterator<dim,device_grid,FREE>
 	 * \param gk std::vector of the local grid
 	 *
 	 */
-	grid_dist_iterator(Vcluster_object_array<device_grid> & gk, openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext)
+	grid_dist_iterator(openfpm::vector<device_grid> & gk, openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext)
 	:g_c(0),gList(gk),gdb_ext(gdb_ext),m(0)
 	{
 		// Initialize the current iterator
@@ -215,7 +215,7 @@ class grid_dist_iterator<dim,device_grid,FIXED>
 	size_t g_c;
 
 	//! List of the grids we are going to iterate
-	Vcluster_object_array<device_grid> & gList;
+	openfpm::vector<device_grid> & gList;
 
 	//! Extension of each grid: domain and ghost + domain
 	const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext;
@@ -229,12 +229,12 @@ class grid_dist_iterator<dim,device_grid,FIXED>
 	void selectValidGrid()
 	{
 		// When the grid has size 0 potentially all the other informations are garbage
-		while (g_c < gList.size() && (gList[g_c].size() == 0 || gdb_ext.get(g_c).Dbox.isValid() == false ) ) g_c++;
+		while (g_c < gList.size() && (gList.get(g_c).size() == 0 || gdb_ext.get(g_c).Dbox.isValid() == false ) ) g_c++;
 
 		// get the next grid iterator
 		if (g_c < gList.size())
 		{
-			a_it.reinitialize(gList[g_c].getIterator(gdb_ext.get(g_c).Dbox.getKP1(),gdb_ext.get(g_c).Dbox.getKP2()));
+			a_it.reinitialize(gList.get(g_c).getIterator(gdb_ext.get(g_c).Dbox.getKP1(),gdb_ext.get(g_c).Dbox.getKP2()));
 		}
 	}
 
@@ -260,7 +260,7 @@ class grid_dist_iterator<dim,device_grid,FIXED>
 	 * \param gk std::vector of the local grid
 	 *
 	 */
-	grid_dist_iterator(Vcluster_object_array<device_grid> & gk, const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext)
+	grid_dist_iterator(openfpm::vector<device_grid> & gk, const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext)
 	:g_c(0),gList(gk),gdb_ext(gdb_ext)
 	{
 		// Initialize the current iterator

src/Grid/grid_dist_id_iterator_sub.hpp

@@ -34,7 +34,7 @@ class grid_dist_iterator_sub
 	size_t g_c;
 
 	//! List of the grids we are going to iterate
-	Vcluster_object_array<device_grid> & gList;
+	openfpm::vector<device_grid> & gList;
 
 	//! Extension of each grid: domain and ghost + domain
 	openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext;
@@ -97,13 +97,13 @@ class grid_dist_iterator_sub
 
 		// When the grid has size 0 potentially all the other informations are garbage
 		while (g_c < gList.size() &&
-			   (gList[g_c].size() == 0 || gdb_ext.get(g_c).Dbox.isValid() == false || compute_subset(g_c,start_c,stop_c) == false ))
+			   (gList.get(g_c).size() == 0 || gdb_ext.get(g_c).Dbox.isValid() == false || compute_subset(g_c,start_c,stop_c) == false ))
 		{g_c++;}
 
 		// get the next grid iterator
 		if (g_c < gList.size())
 		{
-			a_it.reinitialize(gList[g_c].getIterator(start_c,stop_c));
+			a_it.reinitialize(gList.get(g_c).getIterator(start_c,stop_c));
 		}
 	}
 
@@ -144,7 +144,7 @@ class grid_dist_iterator_sub
 	 * \param gdb_ext information about the local grids
 	 *
 	 */
-	grid_dist_iterator_sub(const grid_key_dx<dim> & start, const grid_key_dx<dim> & stop ,Vcluster_object_array<device_grid> & gk, openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext)
+	grid_dist_iterator_sub(const grid_key_dx<dim> & start, const grid_key_dx<dim> & stop ,openfpm::vector<device_grid> & gk, openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext)
 	:g_c(0),gList(gk),gdb_ext(gdb_ext),start(start),stop(stop),m(0)
 	{
 		// Initialize the current iterator
@@ -229,8 +229,4 @@ class grid_dist_iterator_sub
 	}
 };
 
-
-
-
-
 #endif /* SRC_GRID_GRID_DIST_ID_ITERATOR_SUB_HPP_ */

src/Grid/grid_dist_id_unit_test.hpp

@@ -1007,6 +1007,83 @@ void Test3D_dup(const Box<3,float> & domain, long int k)
 	}
 }
 
+// Test decomposition grid iterator
+
+void Test3D_decit(const Box<3,float> & domain, long int k)
+{
+	typedef Point_test<float> p;
+
+	Vcluster & v_cl = *global_v_cluster;
+
+	if ( v_cl.getProcessingUnits() > 32 )
+		return;
+
+	long int big_step = k / 30;
+	big_step = (big_step == 0)?1:big_step;
+	long int small_step = 21;
+
+	print_test( "Testing grid iterator from decomposition k<=",k);
+
+	// 3D test
+	for ( ; k >= 2 ; k-= (k > 2*big_step)?big_step:small_step )
+	{
+		BOOST_TEST_CHECKPOINT( "Testing grid iterator from decomposition k<=" << k );
+
+		// grid size
+		size_t sz[3];
+		sz[0] = k;
+		sz[1] = k;
+		sz[2] = k;
+
+		// factor
+		float factor = pow(global_v_cluster->getProcessingUnits()/2.0f,1.0f/3.0f);
+
+		// Ghost
+		Ghost<3,float> g(0.01 / factor);
+
+		// Distributed grid with id decomposition
+		grid_dist_id<3, float, Point_test<float>, CartDecomposition<3,float>> g_dist(sz,domain,g);
+
+		// check the consistency of the decomposition
+		bool val = g_dist.getDecomposition().check_consistency();
+		BOOST_REQUIRE_EQUAL(val,true);
+
+		// Grid sm
+		grid_sm<3,void> info(sz);
+
+		auto dom = g_dist.getSubDomainIterator({0,0,0},{sz[0]-1,sz[1]-1,sz[2]-1});
+
+		bool match = true;
+
+		// create a grid iterator from the decomposition
+
+		grid_dist_id_iterator_dec<CartDecomposition<3,float>> it_dec(g_dist.getDecomposition(),g_dist.getGridInfoVoid().getSize());
+
+		while (dom.isNext())
+		{
+			auto key = dom.get();
+			auto key_g = g_dist.getGKey(key);
+
+			auto key_dec = it_dec.get();
+
+			// Check if the two keys match
+			match &= key_dec == key_g;
+
+
+			if (match == false)
+			{
+				int debug = 0;
+				debug++;
+			}
+
+			++dom;
+			++it_dec;
+		}
+
+		BOOST_REQUIRE_EQUAL(match,true);
+	}
+}
+
 BOOST_AUTO_TEST_CASE( grid_dist_id_iterator_test_use)
 {
 	// Domain
@@ -1074,7 +1151,6 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_with_grid_unit_ghost )
 	long int k = 1024*1024*global_v_cluster->getProcessingUnits();
 	k = std::pow(k, 1/2.);
 
-//	Test2D_gg(domain,k);
 	// Domain
 	Box<3,float> domain3({0.0,0.0,0.0},{1.0,1.0,1.0});
 
@@ -1083,6 +1159,25 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_with_grid_unit_ghost )
 	Test3D_gg(domain3,k,1);
 }
 
+BOOST_AUTO_TEST_CASE( grid_dist_id_decomposition )
+{
+	// Domain
+	Box<2,float> domain({0.0,0.0},{1.0,1.0});
+
+	// Initialize the global VCluster
+	init_global_v_cluster(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv);
+
+	long int k = 1024*1024*global_v_cluster->getProcessingUnits();
+	k = std::pow(k, 1/2.);
+
+	// Domain
+	Box<3,float> domain3({0.0,0.0,0.0},{1.0,1.0,1.0});
+
+	k = 128*128*128*global_v_cluster->getProcessingUnits();
+	k = std::pow(k, 1/3.);
+	Test3D_decit(domain3,k);
+}
+
 BOOST_AUTO_TEST_SUITE_END()
 
 #endif

src/Grid/grid_dist_util.hpp

+/*
+ * grid_dist_util.hpp
+ *
+ *  Created on: Jan 28, 2016
+ *      Author: i-bird
+ */
+
+#ifndef SRC_GRID_GRID_DIST_UTIL_HPP_
+#define SRC_GRID_GRID_DIST_UTIL_HPP_
+
+#include "NN/CellList/CellDecomposer.hpp"
+
+/*! \brief Create the gdb_ext
+ *
+ * \param gdb_ext Vector of Boxes that define the local grids extension
+ * \param dec Decomposition
+ * \param cd_sm CellDecomposer the size of cell is equal to the distance between grid points
+ *
+ */
+template<int dim, typename Decomposition> inline void create_gdb_ext(openfpm::vector<GBoxes<Decomposition::dims>> & gdb_ext, Decomposition & dec, CellDecomposer_sm<Decomposition::dims,typename Decomposition::stype> & cd_sm)
+{
+	Box<Decomposition::dims, typename Decomposition::stype> g_rnd_box;
+	for (size_t i = 0 ; i < Decomposition::dims ; i++)	{g_rnd_box.setHigh(i,0.5); g_rnd_box.setLow(i,-0.5);}
+
+	// Get the number of local grid needed
+	size_t n_grid = dec.getNLocalHyperCube();
+
+	// Allocate the grids
+	for (size_t i = 0 ; i < n_grid ; i++)
+	{
+		gdb_ext.add();
+
+		// Get the local hyper-cube
+		SpaceBox<Decomposition::dims, typename Decomposition::stype> sp = dec.getLocalHyperCube(i);
+		SpaceBox<Decomposition::dims, typename Decomposition::stype> sp_g = dec.getSubDomainWithGhost(i);
+
+		// Convert from SpaceBox<dim,St> to SpaceBox<dim,long int>
+		SpaceBox<Decomposition::dims,long int> sp_t = cd_sm.convertDomainSpaceIntoGridUnits(sp);
+		SpaceBox<Decomposition::dims,long int> sp_tg = cd_sm.convertDomainSpaceIntoGridUnits(sp_g);
+
+		//! Save the origin of the sub-domain of the local grid
+		gdb_ext.last().origin = sp_tg.getP1();
+
+		// save information about the local grid: domain box seen inside the domain + ghost box (see GDBoxes for a visual meaning)
+		// and where the GDBox start, or the origin of the local grid (+ghost) in global coordinate
+		gdb_ext.last().Dbox = sp_t;
+		gdb_ext.last().Dbox -= sp_tg.getP1();
+
+		gdb_ext.last().GDbox = sp_tg;
+		gdb_ext.last().GDbox -= sp_tg.getP1();
+	}
+}
+
+/*! \brief Create the gdb_ext
+ *
+ * \param gdb_ext Vector of Boxes that define the local grids extension
+ * \param dec Decomposition
+ * \param Global grid grid size
+ *
+ */
+template<int dim, typename Decomposition> inline void create_gdb_ext(openfpm::vector<GBoxes<dim>> & gdb_ext, Decomposition & dec, const size_t (& sz)[dim], const Box<Decomposition::dims,typename Decomposition::stype> & domain)
+{
+	// Create the cell decomposer
+
+	CellDecomposer_sm<Decomposition::dims,typename Decomposition::stype> cd_sm;
+	cd_sm.setDimensions(domain,sz,0);
+
+	create_gdb_ext<dim,Decomposition>(gdb_ext,dec,cd_sm);
+}
+
+#endif /* SRC_GRID_GRID_DIST_UTIL_HPP_ */

src/Vector/vector_dist_unit_test.hpp

@@ -822,6 +822,43 @@ BOOST_AUTO_TEST_CASE( vector_dist_not_periodic_map )
 	}
 }
 
+
+BOOST_AUTO_TEST_CASE( vector_dist_cell_verlet_test )
+{
+/*	typedef Point<3,float> s;
+
+	Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});
+
+	// Boundary conditions
+	size_t bc[3]={PERIODIC,PERIODIC,PERIODIC};
+
+	// factor
+	float factor = pow(global_v_cluster->getProcessingUnits()/2.0f,1.0f/3.0f);
+
+	// ghost
+	Ghost<3,float> ghost(0.05 / factor);
+
+	// Distributed vector
+	vector_dist<3,float, Point_test<float>, CartDecomposition<3,float> > vd(1,box,bc,ghost);
+
+	// Put particles on a grid creating a Grid iterator
+	auto it = vd.getGridIterator(sz);
+
+	while (it.isNext())
+	{
+		auto key = it.get();
+
+		vd.template getPos<s::x>(key)[0] = key.get(0);
+		vd.template getPos<s::x>(key)[1] = key.get(1);
+		vd.template getPos<s::x>(key)[2] = key.get(2);
+
+		++it;
+	}
+
+	vd.map();*/
+
+}
+
 BOOST_AUTO_TEST_SUITE_END()
 
 #endif /* VECTOR_DIST_UNIT_TEST_HPP_ */

src/gargabe.hpp

@@ -389,4 +389,236 @@
 
 
 >>>>>>> Jenkin script for taurus
+
+
+/*! \brief Allocate a set of objects
+ *
+ * \tparam obj
+ * \param n number of object
+ *
+ * \return an object representing an array of objects
+ *
+ */
+/*	template <typename obj> Vcluster_object_array<obj> allocate(size_t n)
+{
+	// Vcluster object array
+	Vcluster_object_array<obj> vo;
+
+	// resize the array
+	vo.resize(n);
+
+	// Create the object on memory and return a Vcluster_object_array
+	return vo;
+}*/
+
+
+/*template<typename T>
+class Vcluster_object_array : public VObject
+{
+	std::vector<T> objects;
+
+public:*/
+
+	/*! \brief Constructor of object array
+	 *
+	 */
+/*	Vcluster_object_array()
+	{
+
+	}*/
+
+	/*! \brief Return the size of the objects array
+	 *
+	 * \return the size of the array
+	 *
+	 */
+/*	size_t size() const
+	{
+		return objects.size();
+	}*/
+
+	/*! \brief Return the element i
+	 *
+	 * \return a reference to the object i
+	 *
+	 */
+
+/*	T & get(unsigned int i)
+	{
+		return objects[i];
+	}*/
+
+	/*! \brief Return the element i
+	 *
+	 * \return a reference to the object i
+	 *
+	 */
+/*	const T & get(unsigned int i) const
+	{
+		return objects[i];
+	}*/
+
+	/*! \brief Check if this Object is an array
+	 *
+	 * \return true, it is an array
+	 *
+	 */
+/*	bool isArray()
+	{
+		return true;
+	}*/
+
+	/*! \brief Destroy the object
+	 *
+	 */
+/*	virtual void destroy()
+	{
+		// Destroy the objects
+		objects.clear();
+	}*/
+
+	/*! \brief Get the size of the memory needed to pack the object
+	 *
+	 * \return the size of the message to pack the object
+	 *
+	 */
+/*	size_t packObjectSize()
+	{
+		size_t message = 0;
+
+		// Destroy each objects
+		for (size_t i = 0 ; i < objects.size() ; i++)
+		{
+			message += objects[i].packObjectSize();
+		}
+
+		return message;
+	}*/
+
+
+	/*! \brief Get the size of the memory needed to pack the object
+	 *
+	 * \param Memory where to write the packed object
+	 *
+	 * \return the size of the message to pack the object
+	 *
+	 */
+/*	size_t packObject(void * mem)
+	{
+		// Pointer is zero
+		size_t ptr = 0;
+		unsigned char * m = (unsigned char *)mem;
+
+		// pack each object
+		for (size_t i = 0 ; i < objects.size() ; i++)
+		{
+			ptr += objects[i].packObject(&m[ptr]);
+		}
+
+#ifdef DEBUG
+		if (ptr != packObjectSize())
+		{
+			std::cerr << "Error " << __FILE__ << " " << __LINE__ << " the pack object size does not match the message" << "\n";
+		}
+#endif
+
+		return ptr;
+	}*/
+
+	/*! \brief Calculate the size to pack an object in the array
+	 *
+	 * \param array object index
+	 *
+	 */
+/*	size_t packObjectInArraySize(size_t i)
+	{
+		return objects[i].packObjectSize();
+	}*/
+
+	/*! \brief pack the object in the array (the message produced can be used to move one)
+	 * object from one processor to another
+	 *
+	 * \param i index of the object to pack
+	 * \param p Memory of the packed object message
+	 *
+	 */
+/*	size_t packObjectInArray(size_t i, void * p)
+	{
+		return objects[i].packObject(p);
+	}*/
+
+	/*! \brief Destroy an object from the array
+	 *
+	 * \param i object to destroy
+	 *
+	 */
+/*	void destroy(size_t i)
+	{
+		objects.erase(objects.begin() + i);
+	}*/
+
+	/*! \brief Return the object j in the array
+	 *
+	 * \param j element j
+	 *
+	 */
+/*	T & operator[](size_t j)
+	{
+		return objects[j];
+	}*/
+
+	/*! \brief Return the object j in the array
+	 *
+	 * \param j element j