examples SPH update

example/Vector/0_simple/main.cpp

@@ -11,6 +11,7 @@
  * \subpage Vector_5_md_vl_sym
  * \subpage Vector_5_md_vl_sym_crs
  * \subpage Vector_6_complex_usage
+ * \subpage Vector_7_sph_dlb
  *
  */
 

example/Vector/4_multiphase_celllist_verlet/main.cpp

@@ -317,7 +317,7 @@ int main(int argc, char* argv[])
 	CL_phase1 = phases.get(1).getCellListSym(r_cut);
 
 	// This function create a Verlet-list between phases 0 and 1
-	NN_ver01 = createVerletSym(phases.get(0),CL_phase1,r_cut);
+	NN_ver01 = createVerletSym(phases.get(0),phases.get(1),CL_phase1,r_cut);
 
 	// Get an iterator over the real and ghost particles
 	it = phases.get(0).getDomainAndGhostIterator();
@@ -419,7 +419,7 @@ int main(int argc, char* argv[])
 	CL_all = createCellListSymM<2>(phases,r_cut);
 
 	// Type of the multiphase Verlet-list
-	typedef decltype(createVerletSymM<2>(phases.get(0),CL_all,r_cut)) verlet_type;
+	typedef decltype(createVerletSymM<2>(phases.get(0),phases,CL_all,r_cut)) verlet_type;
 
 	// for each phase we create one Verlet-list that contain the neighborhood
 	// from all the phases

openfpm_numerics @ 9e49bd95

-Subproject commit 2a805e31cd0bc1e5fe89c8f6a03ba22b1691ad2d
+Subproject commit 9e49bd9594b1b1c0d9cdd19e609aaba7a163d907

openfpm_pdata.doc

@@ -38,7 +38,7 @@ PROJECT_NAME           = "OpenFPM_pdata"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 0.7.0
+PROJECT_NUMBER         = 0.8.0
 
 # 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

src/Decomposition/CartDecomposition.hpp

@@ -351,11 +351,11 @@ public:
 
 		for (size_t i = 0; i < dist.getNSubSubDomains(); i++)
 		{
-			dist.setMigrationCost(i, norm * migration * dist.getSubSubDomainComputationCost(i));
+			dist.setMigrationCost(i, norm * migration /* * dist.getSubSubDomainComputationCost(i) */);
 
 			for (size_t s = 0; s < dist.getNSubSubDomainNeighbors(i); s++)
 			{
-				dist.setCommunicationCost(i, s, 1 * dist.getSubSubDomainComputationCost(i) * ts);
+				dist.setCommunicationCost(i, s, 1 * /* dist.getSubSubDomainComputationCost(i)  * */ ts);
 			}
 			prev += dist.getNSubSubDomainNeighbors(i);
 		}
@@ -994,6 +994,7 @@ public:
 		sub_domains.clear();
 		box_nn_processor.clear();
 		fine_s.clear();
+		loc_box.clear();
 		nn_prcs<dim, T>::reset();
 		ie_ghost<dim, T>::reset();
 		ie_loc_ghost<dim, T>::reset();
@@ -1122,7 +1123,7 @@ public:
 	 */
 	inline size_t getSubSubDomainComputationCost(size_t id)
 	{
-		return dist.getComputationCost(id);
+		return dist.getSubSubDomainComputationCost(id);
 	}
 
 	/*! \brief Operator to access the size of the sub-graph

src/Decomposition/Distribution/ParMetisDistribution.hpp

@@ -118,28 +118,33 @@ class ParMetisDistribution
 		for (size_t i = 0; i <= Np; i++)
 			vtxdist.get(i) = n_vtxdist.get(i);
 
+		openfpm::vector<size_t> cnt;
+		cnt.resize(Np);
+
 		// Renumber the main graph and re-create the map
-		for (size_t p = 0; p < (size_t)Np; p++)
+/*		for (size_t p = 0; p < (size_t)Np; p++)
 		{
 			size_t i = 0;
 			for (rid j = vtxdist.get(p); j < vtxdist.get(p + 1); ++j, i++)
 			{
 				setMapId(j, v_per_proc.get(p).get(i));
-				gp.vertex(v_per_proc.get(p).get(i).id).template get<nm_v::id>() = j.id;
+				gp.vertex(v_per_proc.get(p).get(i).id).template get<nm_v::id>() = cnt.get(p) + vtxdist.get(p).id;
+				cnt.get(p)++;
 			}
-		}
-	}
-
-	void createMapsFromGlobalGraph(openfpm::vector<size_t> & vtxdist)
-	{
-/*		openfpm::vector<size_t> cnt_np;
+		}*/
 
-		for (size_t i = 0 ; i < gp.getNVertex() ; i++)
+		for (size_t i = 0 ; i < gp.getNVertex(); ++i)
 		{
-			cnt_np(gp.template vertex<nm_v::proc_id>)++;
+			size_t pid = gp.template vertex_p<nm_v::proc_id>(i);
 
-			gp.setMapId()
-		}*/
+			rid j = rid(vtxdist.get(pid).id + cnt.get(pid));
+			gid gi = gid(i);
+
+			gp.template vertex_p<nm_v::id>(i) = j.id;
+			cnt.get(pid)++;
+
+			setMapId(j,gi);
+		}
 	}
 
 	/*! \brief operator to access the vertex by mapped position

src/Graph/CartesianGraphFactory.hpp

@@ -76,6 +76,9 @@ struct fill_id<dim, G_v, NO_VERTEX_ID>
 template<unsigned int dim, int lin_id, typename dT, typename G_v, typename v, int impl>
 class fill_prop
 {
+	//! Domain
+	const Box<dim,dT> & domain;
+
 	//! Reference to an array containing the spacing
 	const dT (&szd)[dim];
 
@@ -91,8 +94,8 @@ class fill_prop
 public:
 
 	//! Fill the object from where to take the properties
-	fill_prop(G_v & g_v, const dT (&szd)[dim], grid_key_dx<dim> & gk, const grid_sm<dim, void> & gs) :
-			szd(szd), gk(gk), g_v(g_v), gs(gs)
+	fill_prop(G_v & g_v, const dT (&szd)[dim], grid_key_dx<dim> & gk, const grid_sm<dim, void> & gs, const Box<dim,dT> & domain)
+	:domain(domain), szd(szd), gk(gk), g_v(g_v), gs(gs)
 	{
 	}
 
@@ -102,7 +105,7 @@ public:
 	{
 		typedef typename boost::fusion::result_of::at<v, boost::mpl::int_<T::value>>::type t_val;
 
-		g_v.template get<t_val::value>() = gk.get(T::value) * szd[T::value];
+		g_v.template get<t_val::value>() = gk.get(T::value) * szd[T::value] + domain.getLow(T::value);
 		fill_id<dim, G_v, lin_id>::fill(g_v, gk, gs);
 	}
 };
@@ -140,7 +143,7 @@ class fill_prop<dim, lin_id, dT, G_v, v, 0>
 public:
 
 	//! Fill the object from where to take the properties
-	fill_prop(G_v & g_v, const dT (&szd)[dim], grid_key_dx<dim> & gk, const grid_sm<dim, void> & gs)
+	fill_prop(G_v & g_v, const dT (&szd)[dim], grid_key_dx<dim> & gk, const grid_sm<dim, void> & gs, const Box<dim,dT> & domain)
 	{
 	}
 
@@ -180,6 +183,8 @@ public:
 template<unsigned int dim, int lin_id, typename dT, typename G_v, typename v>
 class fill_prop<dim, lin_id, dT, G_v, v, 2>
 {
+	//! Domain
+	const Box<dim,dT> & domain;
 
 	//! Reference to an array containing the spacing
 	const dT (&szd)[dim];
@@ -196,8 +201,8 @@ class fill_prop<dim, lin_id, dT, G_v, v, 2>
 public:
 
 	//! Fill the object from where to take the properties
-	fill_prop(G_v & g_v, const dT (&szd)[dim], grid_key_dx<dim> & gk, const grid_sm<dim, void> & gs) :
-			szd(szd), gk(gk), g_v(g_v), gs(gs)
+	fill_prop(G_v & g_v, const dT (&szd)[dim], grid_key_dx<dim> & gk, const grid_sm<dim, void> & gs, const Box<dim,dT> & domain)
+	:domain(domain), szd(szd), gk(gk), g_v(g_v), gs(gs)
 	{
 	}
 
@@ -212,7 +217,7 @@ public:
 			g_v.template get<t_val::value>()[i] = 0.0;
 
 		for (size_t i = 0 ; i < dim ; i++)
-			g_v.template get<t_val::value>()[i] = gk.get(i) * static_cast<float>(szd[i]);
+			g_v.template get<t_val::value>()[i] = gk.get(i) * static_cast<float>(szd[i]) + domain.getLow(i);
 
 		fill_id<dim, G_v, lin_id>::fill(g_v, gk, gs);
 	}
@@ -330,7 +335,7 @@ public:
 
 			// vertex spatial properties functor
 
-			fill_prop<dim, lin_id, T, decltype(gp.vertex(g.LinId(key))), typename to_boost_vmpl<pos...>::type, fill_prop_by_type<sizeof...(pos), p, Graph, pos...>::value> flp(obj, szd, key, g);
+			fill_prop<dim, lin_id, T, decltype(gp.vertex(g.LinId(key))), typename to_boost_vmpl<pos...>::type, fill_prop_by_type<sizeof...(pos), p, Graph, pos...>::value> flp(obj, szd, key, g, dom);
 
 			// fill properties
 
@@ -451,7 +456,7 @@ public:
 
 			// vertex spatial properties functor
 
-			fill_prop<dim, lin_id, T, decltype(gp.vertex(g.LinId(key))), typename to_boost_vmpl<pos...>::type, fill_prop_by_type<sizeof...(pos), p, Graph, pos...>::value> flp(obj, szd, key, g);
+			fill_prop<dim, lin_id, T, decltype(gp.vertex(g.LinId(key))), typename to_boost_vmpl<pos...>::type, fill_prop_by_type<sizeof...(pos), p, Graph, pos...>::value> flp(obj, szd, key, g, dom);
 
 			// fill properties
 

src/Graph/ids.hpp

@@ -17,8 +17,17 @@
  */
 struct rid
 {
+	//! id
 	idx_t id;
 
+	//! Cosntructor
+	rid(size_t id)
+	:id(id)
+	{}
+
+	//! Constructor
+	rid()	{}
+
 	inline bool operator<=(const rid & r) const
 	{
 		return id <= r.id;
@@ -79,6 +88,14 @@ struct rid
 struct gid
 {
 	size_t id;
+
+	//! Constructor
+	gid(){};
+
+	//! Constructor
+	gid(size_t id)
+	:id(id)
+	{}
 };
 
 /*! Here we define different the remapped-id

src/Makefile.am

@@ -14,7 +14,7 @@ nobase_include_HEADERS = Decomposition/CartDecomposition.hpp Decomposition/CartD
          example.mk \
          Decomposition/Distribution/metis_util.hpp Decomposition/Distribution/SpaceDistribution.hpp Decomposition/Distribution/parmetis_dist_util.hpp  Decomposition/Distribution/parmetis_util.hpp Decomposition/Distribution/MetisDistribution.hpp Decomposition/Distribution/ParMetisDistribution.hpp Decomposition/Distribution/DistParMetisDistribution.hpp  dec_optimizer.hpp SubdomainGraphNodes.hpp \
          Graph/ids.hpp Graph/dist_map_graph.hpp Graph/DistGraphFactory.hpp \
-         DLB/DLB.hpp
+         DLB/DLB.hpp DLB/LB_Model.hpp
 
 lib_LIBRARIES = libofpm_pdata.a
 libofpm_pdata_a_SOURCES = lib/pdata.cpp

src/Vector/vector_dist.hpp

@@ -30,10 +30,13 @@
 #include "data_type/aggregate.hpp"
 #include "NN/VerletList/VerletList.hpp"
 #include "vector_dist_comm.hpp"
+#include "DLB/LB_Model.hpp"
 
 #define NO_ID false
 #define ID true
 
+#define DEC_GRAN(gr) ((size_t)gr << 32)
+
 // Perform a ghost get or a ghost put
 #define GET	1
 #define PUT 2
@@ -236,6 +239,9 @@ public:
 		check_new(this,8,VECTOR_DIST_EVENT,4);
 #endif
 
+		if (opt >> 32 != 0)
+			this->setDecompositionGranularity(opt >> 32);
+
 		check_parameters(box);
 
 		init_structures(np);
@@ -1022,21 +1028,19 @@ public:
 		g_m--;
 	}
 
-	/*! \brief Add the computation cost on the decomposition comming from the particles
+	/*! \brief Add the computation cost on the decomposition coming from the particles
 	 *
 	 */
-	inline void addComputationCosts()
+	template <typename Model=ModelLin>inline void addComputationCosts(Model md=Model())
 	{
-		CellDecomposer_sm<dim, St> cdsm;
+		CellDecomposer_sm<dim, St, shift<dim,St>> cdsm;
 
 		Decomposition & dec = getDecomposition();
 
 		cdsm.setDimensions(dec.getDomain(), dec.getGrid().getSize(), 0);
 
 		for (size_t i = 0; i < getDecomposition().getNSubSubDomains(); i++)
-		{
 			dec.setSubSubDomainComputationCost(i, 1);
-		}
 
 		auto it = getDomainIterator();
 
@@ -1044,11 +1048,15 @@ public:
 		{
 			size_t v = cdsm.getCell(this->getPos(it.get()));
 
-			dec.addComputationCost(v, 1);
+			md.addComputation(dec,*this,v,it.get().getKey());
 
 			++it;
 		}
 
+		// Go throught all the sub-sub-domains and apply the model
+
+		for (size_t i = 0 ; i < dec.getDistribution().getNSubSubDomains(); i++)
+			md.applyModel(dec,i);
 	}
 
 	/*! \brief Output particle position and properties

src/Vector/vector_dist_MP_unit_tests.hpp

@@ -85,7 +85,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_multiphase_cell_list_test )
 	auto CL_phase1 = phases.get(1).getCellList(r_cut);
 
 	// This function create a Verlet-list between phases 0 and 1
-	auto NN_ver01 = createVerlet(phases.get(0),CL_phase1,r_cut);
+	auto NN_ver01 = createVerlet(phases.get(0),phases.get(1),CL_phase1,r_cut);
 
 	// Check NNver0_1
 
@@ -128,7 +128,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_multiphase_cell_list_test )
 	auto CL_all = createCellListM<2>(phases,r_cut);
 
 	// This create a Verlet-list between phase 0 and all the other phases
-	auto NNver0_all = createVerletM<2>(phases.get(0),CL_all,r_cut);
+	auto NNver0_all = createVerletM<2>(phases.get(0),phases,CL_all,r_cut);
 
 	it = phases.get(0).getDomainIterator();
 
@@ -235,7 +235,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_multiphase_cell_list_sym_test )
 	auto CL_phase1 = phases.get(1).getCellListSym(r_cut);
 
 	// This function create a Verlet-list between phases 0 and 1
-	auto NN_ver01 = createVerletSym(phases.get(0),CL_phase1,r_cut);
+	auto NN_ver01 = createVerletSym(phases.get(0),phases.get(1),CL_phase1,r_cut);
 
 	// Check NNver0_1
 
@@ -305,15 +305,15 @@ BOOST_AUTO_TEST_CASE( vector_dist_multiphase_cell_list_sym_test )
 	// This function create an "Empty" Multiphase Cell List
 	auto CL_all = createCellListSymM<2>(phases,r_cut);
 
-	typedef decltype(createVerletSymM<2>(phases.get(0),CL_all,r_cut)) verlet_type;
+	typedef decltype(createVerletSymM<2>(phases.get(0),phases,CL_all,r_cut)) verlet_type;
 
 	verlet_type NNver_all[4];
 
 	// This create a Verlet-list between phase all phases to all the other phases
-	NNver_all[0] = createVerletSymM<2>(phases.get(0),CL_all,r_cut);
-	NNver_all[1] = createVerletSymM<2>(phases.get(1),CL_all,r_cut);
-	NNver_all[2] = createVerletSymM<2>(phases.get(2),CL_all,r_cut);
-	NNver_all[3] = createVerletSymM<2>(phases.get(3),CL_all,r_cut);
+	NNver_all[0] = createVerletSymM<2>(phases.get(0),phases,CL_all,r_cut);
+	NNver_all[1] = createVerletSymM<2>(phases.get(1),phases,CL_all,r_cut);
+	NNver_all[2] = createVerletSymM<2>(phases.get(2),phases,CL_all,r_cut);
+	NNver_all[3] = createVerletSymM<2>(phases.get(3),phases,CL_all,r_cut);
 
 	// all phases to all phases
 

src/Vector/vector_dist_comm.hpp

@@ -8,8 +8,6 @@
 #ifndef SRC_VECTOR_VECTOR_DIST_COMM_HPP_
 #define SRC_VECTOR_VECTOR_DIST_COMM_HPP_
 
-#define V_SUB_UNIT_FACTOR 64
-
 #define SKIP_LABELLING 512
 #define KEEP_PROPERTIES 512
 
@@ -47,6 +45,9 @@ inline static size_t compute_options(size_t opt)
 template<unsigned int dim, typename St, typename prop, typename Decomposition = CartDecomposition<dim,St>, typename Memory = HeapMemory>
 class vector_dist_comm
 {
+	//! Number of units for each sub-domain
+	size_t v_sub_unit_factor = 64;
+
 	//! definition of the send vector for position
 	typedef openfpm::vector<Point<dim, St>, Memory> send_pos_vector;
 
@@ -784,14 +785,24 @@ public:
 	{
 	}
 
-	/*! \brief Get the number of minimum sub-domain
+	/*! \brief Get the number of minimum sub-domain per processor
 	 *
 	 * \return minimum number
 	 *
 	 */
-	static size_t getDefaultNsubsub()
+	size_t getDecompositionGranularity()
+	{
+		return v_sub_unit_factor;
+	}
+
+	/*! \brief Set the minimum number of sub-domain per processor
+	 *
+	 * \param n_sub
+	 *
+	 */
+	void setDecompositionGranularity(size_t n_sub)
 	{
-		return V_SUB_UNIT_FACTOR;
+		this->v_sub_unit_factor = n_sub;
 	}
 
 	/*! \brief Initialize the decomposition
@@ -826,7 +837,7 @@ public:
 			// Get the number of processor and calculate the number of sub-domain
 			// for decomposition
 			size_t n_proc = v_cl.getProcessingUnits();
-			size_t n_sub = n_proc * getDefaultNsubsub();
+			size_t n_sub = n_proc * getDecompositionGranularity();
 
 			// Calculate the maximum number (before merging) of sub-domain on
 			// each dimension

src/Vector/vector_dist_multiphase_functions.hpp

@@ -11,20 +11,25 @@
 #include "NN/CellList/CellListM.hpp"
 #include "NN/VerletList/VerletListM.hpp"
 
-template<typename Vector,typename CL, typename T> VerletList<Vector::dims,typename Vector::stype,FAST,shift<Vector::dims,typename Vector::stype>> createVerlet(Vector & v, CL & cl, T r_cut)
+template<typename Vector, typename CL, typename T> VerletList<Vector::dims,typename Vector::stype,FAST,shift<Vector::dims,typename Vector::stype>> createVerlet(Vector & v, Vector & v1, CL & cl, T r_cut)
 {
 	VerletList<Vector::dims,typename Vector::stype,FAST,shift<Vector::dims,typename Vector::stype>> ver;
 
-	ver.Initialize(cl,r_cut,v.getPosVector(),v.size_local());
+	ver.Initialize(cl,r_cut,v.getPosVector(),v1.getPosVector(),v.size_local());
 
 	return ver;
 }
 
-template<unsigned int sh_byte, typename Vector,typename CL, typename T> VerletListM<Vector::dims,typename Vector::stype,sh_byte,shift<Vector::dims,typename Vector::stype>> createVerletM(Vector & v, CL & cl, T r_cut)
+template<unsigned int sh_byte, typename Vector , typename Vector1,typename CL, typename T> VerletListM<Vector::dims,typename Vector::stype,sh_byte,CL,shift<Vector::dims,typename Vector::stype>> createVerletM(Vector & v, Vector1 & phases, CL & cl, T r_cut)
 {
-	VerletListM<Vector::dims,typename Vector::stype,sh_byte,shift<Vector::dims,typename Vector::stype>> ver;
+	VerletListM<Vector::dims,typename Vector::stype,sh_byte,CL,shift<Vector::dims,typename Vector::stype>> ver;
 
-	ver.Initialize(cl,r_cut,v.getPosVector(),v.size_local());
+	openfpm::vector<pos_v<Vector::dims,typename Vector::stype>> v_phases;
+
+	for (size_t i = 0 ; i < phases.size() ; i++)
+		v_phases.add(pos_v<Vector::dims,typename Vector::stype>(phases.get(i).getPosVector()));
+
+	ver.Initialize(cl,r_cut,v.getPosVector(),v_phases,v.size_local());
 
 	return ver;
 }
@@ -65,20 +70,25 @@ template<unsigned int nbit, typename Vector, typename T> CellListM<Vector::dims,
 
 /////// Symmetric version
 
-template<typename Vector,typename CL, typename T> VerletList<Vector::dims,typename Vector::stype,FAST,shift<Vector::dims,typename Vector::stype>> createVerletSym(Vector & v, CL & cl, T r_cut)
+template<typename Vector,typename CL, typename T> VerletList<Vector::dims,typename Vector::stype,FAST,shift<Vector::dims,typename Vector::stype>> createVerletSym(Vector & v, Vector & v1, CL & cl, T r_cut)
 {
 	VerletList<Vector::dims,typename Vector::stype,FAST,shift<Vector::dims,typename Vector::stype>> ver;
 
-	ver.Initialize(cl,r_cut,v.getPosVector(),v.size_local());
+	ver.Initialize(cl,r_cut,v.getPosVector(),v1.getPosVector(),v.size_local());
 
 	return ver;
 }
 
-template<unsigned int sh_byte, typename Vector,typename CL, typename T> VerletListM<Vector::dims,typename Vector::stype,sh_byte,shift<Vector::dims,typename Vector::stype>> createVerletSymM(Vector & v, CL & cl, T r_cut)
+template<unsigned int sh_byte, typename Vector, typename Vector1 ,typename CL, typename T> VerletListM<Vector::dims,typename Vector::stype,sh_byte,CL,shift<Vector::dims,typename Vector::stype>> createVerletSymM(Vector & v, Vector1 & phases, CL & cl, T r_cut)
 {
-	VerletListM<Vector::dims,typename Vector::stype,sh_byte,shift<Vector::dims,typename Vector::stype>> ver;
+	VerletListM<Vector::dims,typename Vector::stype,sh_byte,CL,shift<Vector::dims,typename Vector::stype>> ver;
+
+	openfpm::vector<pos_v<Vector::dims,typename Vector::stype>> v_phases;
+
+	for (size_t i = 0 ; i < phases.size() ; i++)
+		v_phases.add(pos_v<Vector::dims,typename Vector::stype>(phases.get(i).getPosVector()));
 
-	ver.Initialize(cl,r_cut,v.getPosVector(),v.size_local(),VL_SYMMETRIC);
+	ver.Initialize(cl,r_cut,v.getPosVector(),v_phases,v.size_local(),VL_SYMMETRIC);
 
 	return ver;
 }

src/Vector/vector_dist_unit_test.hpp

@@ -105,7 +105,7 @@ void Test2D_ghost(Box<2,float> & box)
 	typedef Point_test<float> p;
 
 	// Get the default minimum number of sub-sub-domain per processor (granularity of the decomposition)
-	size_t n_sub = vector_dist<2,float, Point_test<float>, CartDecomposition<2,float> >::getDefaultNsubsub() * v_cl.getProcessingUnits();
+	size_t n_sub = 64 * v_cl.getProcessingUnits();
 	// Convert the request of having a minimum n_sub number of sub-sub domain into grid decompsition of the space
 	size_t sz = CartDecomposition<2,float>::getDefaultGrid(n_sub);