vector_dist.hpp 43.9 KB
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/*
 * Vector.hpp
 *
 *  Created on: Mar 5, 2015
 *      Author: Pietro Incardona
 */

#ifndef VECTOR_HPP_
#define VECTOR_HPP_

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#include "HDF5_XdmfWriter/HDF5_XdmfWriter.hpp"
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#include "VCluster/VCluster.hpp"
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#include "Space/Shape/Point.hpp"
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#include "Vector/Iterators/vector_dist_iterator.hpp"
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#include "Space/Shape/Box.hpp"
#include "Vector/vector_dist_key.hpp"
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#include "memory/PtrMemory.hpp"
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#include "NN/CellList/CellList.hpp"
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#include "NN/CellList/CellListFast_hilb.hpp"
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#include "util/common.hpp"
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#include "util/object_util.hpp"
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#include "memory/ExtPreAlloc.hpp"
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#include "CSVWriter/CSVWriter.hpp"
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#include "VTKWriter/VTKWriter.hpp"
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#include "Decomposition/common.hpp"
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#include "Grid/Iterators/grid_dist_id_iterator_dec.hpp"
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#include "Grid/grid_key_dx_iterator_hilbert.hpp"
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#include "Vector/vector_dist_ofb.hpp"
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#include "Decomposition/CartDecomposition.hpp"
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#include "data_type/aggregate.hpp"
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#include "NN/VerletList/VerletList.hpp"
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#include "vector_dist_comm.hpp"
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#include "DLB/LB_Model.hpp"
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#define VECTOR_DIST_ERROR_OBJECT std::runtime_error("Runtime vector distributed error");

#ifdef SE_CLASS3
#include "se_class3_vector.hpp"
#endif

#ifdef SE_CLASS3
	#define SE_CLASS3_VDIST_CONSTRUCTOR ,se3(getDecomposition(),*this)
#else
	#define SE_CLASS3_VDIST_CONSTRUCTOR
#endif


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#define NO_ID false
#define ID true

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#define DEC_GRAN(gr) ((size_t)gr << 32)

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// Perform a ghost get or a ghost put
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#define GET	1
#define PUT 2

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// Write the particles with ghost
#define NO_GHOST 0
#define WITH_GHOST 2

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//! General function t get a cell-list
template<unsigned int dim, typename St, typename CellL, typename Vector>
struct gcl
{
	/*! \brief Get the Cell list based on the type
	 *
	 * \param vd Distributed vector
	 * \param r_cut Cut-off radius
	 * \param g Ghost
	 *
	 * \return the constructed cell-list
	 *
	 */
	static inline CellL get(Vector & vd, const St & r_cut, const Ghost<dim,St> & g)
	{
		return vd.getCellList(r_cut);
	}
};

//! General function t get a cell-list
template<unsigned int dim, typename St, typename Vector>
struct gcl<dim,St,CellList_hilb<dim, St, FAST, shift<dim, St> >,Vector>
{
	/*! \brief Get the Cell list based on the type
	 *
	 * \param vd Distributed vector
	 * \param r_cut Cut-off radius
	 * \param g Ghost
	 *
	 * \return the constructed cell-list
	 *
	 */
	static inline CellList_hilb<dim, St, FAST, shift<dim, St> > get(Vector & vd, const St & r_cut, const Ghost<dim,St> & g)
	{
		return vd.getCellList_hilb(r_cut,g);
	}
};

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/*! \brief Distributed vector
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 *
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 * This class reppresent a distributed vector, the distribution of the structure
 * is based on the positional information of the elements the vector store
 *
 * ## Create a vector of random elements on each processor 2D
 * \snippet vector_dist_unit_test.hpp Create a vector of random elements on each processor 2D
 *
 * ## Create a vector of random elements on each processor 3D
 * \snippet vector_dist_unit_test.hpp Create a vector of random elements on each processor 3D
 *
 * ## Create a vector of elements distributed on a grid like way
 * \snippet vector_dist_unit_test.hpp Create a vector of elements distributed on a grid like way
 *
 * ## Redistribute the particles and sync the ghost properties
 * \snippet vector_dist_unit_test.hpp Redistribute the particles and sync the ghost properties
 *
 * \tparam dim Dimensionality of the space where the elements lives
 * \tparam St type of space float, double ...
 * \tparam prop properties the vector element store in OpenFPM data structure format
 * \tparam Decomposition Decomposition strategy to use CartDecomposition ...
 * \tparam Memory Memory pool where store the information HeapMemory ...
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 *
 */

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template<unsigned int dim, typename St, typename prop, typename Decomposition = CartDecomposition<dim,St>, typename Memory = HeapMemory>
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class vector_dist : public vector_dist_comm<dim,St,prop,Decomposition,Memory>
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{
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public:

	//! Self type
	typedef vector_dist<dim,St,prop,Decomposition,Memory> self;

	//! property object
	typedef prop value_type;

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private:

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	//! Ghost marker, all the particle with id > g_m are ghost all with g_m < are real particle
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	size_t g_m = 0;

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	//! Particle position vector, (It has 2 elements) the first has real particles assigned to a processor
	//! the second element contain unassigned particles
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	openfpm::vector<Point<dim, St>> v_pos;
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	//! Particle properties vector, (It has 2 elements) the first has real particles assigned to a processor
	//! the second element contain unassigned particles
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	openfpm::vector<prop> v_prp;
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	//! Virtual cluster
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	Vcluster & v_cl;

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	//! option used to create this vector
	size_t opt = 0;

#ifdef SE_CLASS3

	se_class3_vector<prop::max_prop,dim,St,Decomposition,self> se3;

#endif
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	/*! \brief Initialize the structures
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	 *
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	 * \param np number of particles
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	 *
	 */
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	void init_structures(size_t np)
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	{
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		// convert to a local number of elements
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		size_t p_np = np / v_cl.getProcessingUnits();

		// Get non divisible part
		size_t r = np % v_cl.getProcessingUnits();

		// Distribute the remain particles
		if (v_cl.getProcessUnitID() < r)
			p_np++;
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		// resize the position vector
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		v_pos.resize(p_np);
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		// resize the properties vector
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		v_prp.resize(p_np);

		g_m = p_np;
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	}
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	/*! \brief Check if the parameters describe a valid vector. In case it does not report an error
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	 *
	 * \param box Box to check
	 *
	 */
	void check_parameters(Box<dim,St> & box)
	{
		// if the box is not valid return an error
		if (box.isValid() == false)
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		{
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			std::cerr << __FILE__ << ":" << __LINE__ << "  Error the domain is not valid " << box.toString() << std::endl;
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			ACTION_ON_ERROR(VECTOR_DIST_ERROR_OBJECT);
		}
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	}

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	/*! \brief It check that the r_cut is not bugger than the ghost
	 *
	 * \param r_cut cut-off radius
	 *
	 */
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	void check_ghost_compatible_rcut(St r_cut)
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	{
		for (size_t i = 0 ; i < dim ; i++)
		{
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			if (fabs(getDecomposition().getGhost().getLow(i)) < r_cut)
			{
				std::cerr << __FILE__ << ":" << __LINE__ << " Error the cut off radius " << r_cut << " is bigger that the ghost layer on the dimension " << i << " lower=" << getDecomposition().getGhost().getLow(i) << std::endl;
				ACTION_ON_ERROR(VECTOR_DIST_ERROR_OBJECT);
			}
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		}
	}

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public:

	//! space type
	typedef St stype;

	//! dimensions of space
	static const unsigned int dims = dim;

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	/*! \brief Operator= for distributed vector
	 *
	 * \param v vector to copy
	 *
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	 * \return itself
	 *
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	 */
	vector_dist<dim,St,prop,Decomposition,Memory> & operator=(const vector_dist<dim,St,prop,Decomposition,Memory> & v)
	{
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		static_cast<vector_dist_comm<dim,St,prop,Decomposition,Memory> *>(this)->operator=(static_cast<vector_dist_comm<dim,St,prop,Decomposition,Memory>>(v));
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		g_m = v.g_m;
		v_pos = v.v_pos;
		v_prp = v.v_prp;

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#ifdef SE_CLASS3
		se3 = v.se3;
#endif

		opt = v.opt;

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		return *this;
	}

	/*! \brief Operator= for distributed vector
	 *
	 * \param v vector to copy
	 *
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	 * \return itself
	 *
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	 */
	vector_dist<dim,St,prop,Decomposition,Memory> & operator=(vector_dist<dim,St,prop,Decomposition,Memory> && v)
	{
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		static_cast<vector_dist_comm<dim,St,prop,Decomposition,Memory> *>(this)->operator=(static_cast<vector_dist_comm<dim,St,prop,Decomposition,Memory> >(v));
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		g_m = v.g_m;
		v_pos.swap(v.v_pos);
		v_prp.swap(v.v_prp);

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#ifdef SE_CLASS3
		se3 = v.se3;
#endif

		opt = v.opt;

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		return *this;
	}

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	/*! \brief Copy Constructor
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	 *
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	 * \param v vector to copy
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	 *
	 */
	vector_dist(const vector_dist<dim,St,prop,Decomposition,Memory> & v)
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	:vector_dist_comm<dim,St,prop,Decomposition,Memory>(v.getDecomposition()),v_cl(v.v_cl) SE_CLASS3_VDIST_CONSTRUCTOR
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	{
#ifdef SE_CLASS2
		check_new(this,8,VECTOR_DIST_EVENT,4);
#endif

		this->operator=(v);
	}

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	/*! \brief Copy constructor
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	 *
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	 * \param v vector to copy
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	 *
	 */
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	vector_dist(vector_dist<dim,St,prop,Decomposition,Memory> && v) noexcept
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	:v_cl(v.v_cl) SE_CLASS3_VDIST_CONSTRUCTOR
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	{
#ifdef SE_CLASS2
		check_new(this,8,VECTOR_DIST_EVENT,4);
#endif

		this->operator=(v);
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#ifdef SE_CLASS3
		se3.Initialize();
#endif
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	}
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	/*! \brief Constructor with predefined decomposition
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	 *
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	 * \param dec is the decomposition
	 * \param np number of particles
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	 *
	 */
	vector_dist(const Decomposition & dec, size_t np) :
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	vector_dist_comm<dim,St,prop,Decomposition,Memory>(dec), v_cl(create_vcluster()) SE_CLASS3_VDIST_CONSTRUCTOR
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	{
#ifdef SE_CLASS2
		check_new(this,8,VECTOR_DIST_EVENT,4);
#endif

		init_structures(np);
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#ifdef SE_CLASS3
		se3.Initialize();
#endif
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	}


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	/*! \brief Constructor of a distributed vector
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	 *
	 * \param np number of elements
	 * \param box domain where the vector of elements live
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	 * \param bc boundary conditions
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	 * \param g Ghost margins
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	 * \param opt additional options. BIND_DEC_TO_GHOST Bind the decomposition to be multiple of the
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	 *          ghost size. This is required if we want to use symmetric to eliminate
	 *          ghost communications.
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	 *
	 */
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	vector_dist(size_t np, Box<dim, St> box, const size_t (&bc)[dim], const Ghost<dim, St> & g, size_t opt = 0)
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	:v_cl(create_vcluster()),opt(opt) SE_CLASS3_VDIST_CONSTRUCTOR
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	{
#ifdef SE_CLASS2
		check_new(this,8,VECTOR_DIST_EVENT,4);
#endif

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		if (opt >> 32 != 0)
			this->setDecompositionGranularity(opt >> 32);

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		check_parameters(box);

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		init_structures(np);
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		this->init_decomposition(box,bc,g,opt);
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#ifdef SE_CLASS3
		se3.Initialize();
#endif
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	}

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	~vector_dist()
	{
#ifdef SE_CLASS2
		check_delete(this);
#endif
	}

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	/*! \brief return the local size of the vector
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	 *
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	 * \return local size
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	 *
	 */
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	size_t size_local() const
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	{
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		return g_m;
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	}

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	/*! \brief return the local size of the vector
	 *
	 * \return local size
	 *
	 */
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	size_t size_local_with_ghost() const
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	{
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		return v_pos.size();
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	}

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#ifndef ONLY_READWRITE_GETTER

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	/*! \brief Get the position of an element
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	 *
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	 * see the vector_dist iterator usage to get an element key
	 *
	 * \param vec_key element
	 *
	 * \return the position of the element in space
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	 *
	 */
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	inline auto getPos(vect_dist_key_dx vec_key) -> decltype(v_pos.template get<0>(vec_key.getKey()))
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	{
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		return v_pos.template get<0>(vec_key.getKey());
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	}

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	/*! \brief Get the position of an element
	 *
	 * see the vector_dist iterator usage to get an element key
	 *
	 * \param vec_key element
	 *
	 * \return the position of the element in space
	 *
	 */
	inline auto getPos(vect_dist_key_dx vec_key) const -> decltype(v_pos.template get<0>(vec_key.getKey()))
	{
		return v_pos.template get<0>(vec_key.getKey());
	}

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	/*! \brief Get the property of an element
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	 *
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	 * see the vector_dist iterator usage to get an element key
	 *
	 * \tparam id property id
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	 * \param vec_key vector element
	 *
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	 * \return return the selected property of the vector element
	 *
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	 */
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	template<unsigned int id> inline auto getProp(vect_dist_key_dx vec_key) -> decltype(v_prp.template get<id>(vec_key.getKey()))
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	{
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		return v_prp.template get<id>(vec_key.getKey());
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	}

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	/*! \brief Get the property of an element
	 *
	 * see the vector_dist iterator usage to get an element key
	 *
	 * \tparam id property id
	 * \param vec_key vector element
	 *
	 * \return return the selected property of the vector element
	 *
	 */
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	template<unsigned int id> inline auto getProp(vect_dist_key_dx vec_key) const -> const decltype(v_prp.template get<id>(vec_key.getKey()))
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	{
		return v_prp.template get<id>(vec_key.getKey());
	}

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#endif

///////////////////// Read and Write function

	/*! \brief Get the position of an element
	 *
	 * see the vector_dist iterator usage to get an element key
	 *
	 * \param vec_key element
	 *
	 * \return the position of the element in space
	 *
	 */
	inline auto getPosWrite(vect_dist_key_dx vec_key) -> decltype(v_pos.template get<0>(vec_key.getKey()))
	{
#ifdef SE_CLASS3
		se3.template write<prop::max_prop_real>(*this,vec_key.getKey());
#endif

		return v_pos.template get<0>(vec_key.getKey());
	}

	/*! \brief Get the position of an element
	 *
	 * see the vector_dist iterator usage to get an element key
	 *
	 * \param vec_key element
	 *
	 * \return the position of the element in space
	 *
	 */
	inline auto getPosRead(vect_dist_key_dx vec_key) const -> decltype(v_pos.template get<0>(vec_key.getKey()))
	{
#ifdef SE_CLASS3
		se3.template read<prop::max_prop_real>(*this,vec_key.getKey());
#endif

		return v_pos.template get<0>(vec_key.getKey());
	}

	/*! \brief Get the property of an element
	 *
	 * see the vector_dist iterator usage to get an element key
	 *
	 * \tparam id property id
	 * \param vec_key vector element
	 *
	 * \return return the selected property of the vector element
	 *
	 */
	template<unsigned int id> inline auto getPropWrite(vect_dist_key_dx vec_key) -> decltype(v_prp.template get<id>(vec_key.getKey()))
	{
#ifdef SE_CLASS3
		se3.template write<id>(*this,vec_key.getKey());
#endif

		return v_prp.template get<id>(vec_key.getKey());
	}

	/*! \brief Get the property of an element
	 *
	 * see the vector_dist iterator usage to get an element key
	 *
	 * \tparam id property id
	 * \param vec_key vector element
	 *
	 * \return return the selected property of the vector element
	 *
	 */
	template<unsigned int id> inline auto getPropRead(vect_dist_key_dx vec_key) const -> const decltype(v_prp.template get<id>(vec_key.getKey()))
	{
#ifdef SE_CLASS3
		se3.template read<id>(*this,vec_key.getKey());
#endif

		return v_prp.template get<id>(vec_key.getKey());
	}

//////////////////////////////////////////////

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	/*! \brief Add local particle
	 *
	 * It add a local particle, with "local" we mean in this processor
	 * the particle can be also created out of the processor domain, in this
	 * case a call to map is required. Added particles are always created at the
	 * end and can be accessed with getLastPos and getLastProp
	 *
	 */
	void add()
	{
		v_prp.insert(g_m);
		v_pos.insert(g_m);

		g_m++;
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#ifdef SE_CLASS3
		for (size_t i = 0 ; i < prop::max_prop_real+1 ; i++)
			v_prp.template get<prop::max_prop_real>(g_m-1)[i] = UNINITIALIZED;
#endif
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	}

	/*! \brief Get the position of the last element
	 *
	 * \return the position of the element in space
	 *
	 */
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	inline auto getLastPos() -> decltype(v_pos.template get<0>(0))
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	{
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		return v_pos.template get<0>(g_m - 1);
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	}

	/*! \brief Get the property of the last element
	 *
	 * \tparam id property id
	 *
	 * \return return the selected property of the vector element
	 *
	 */
	template<unsigned int id> inline auto getLastProp() -> decltype(v_prp.template get<id>(0))
	{
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		return v_prp.template get<id>(g_m - 1);
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	}

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////////////////////////////// READ AND WRITE VERSION //////////

	/*! \brief Get the position of the last element
	 *
	 * \return the position of the element in space
	 *
	 */
	inline auto getLastPosRead() -> decltype(v_pos.template get<0>(0))
	{
#ifdef SE_CLASS3
		se3.read<prop::max_prop_real>(*this,g_m-1);
#endif

		return v_pos.template get<0>(g_m - 1);
	}

	/*! \brief Get the property of the last element
	 *
	 * \tparam id property id
	 *
	 * \return return the selected property of the vector element
	 *
	 */
	template<unsigned int id> inline auto getLastPropRead() -> decltype(v_prp.template get<id>(0))
	{
#ifdef SE_CLASS3
		se3.read<id>(*this,g_m-1);
#endif

		return v_prp.template get<id>(g_m - 1);
	}


	/*! \brief Get the position of the last element
	 *
	 * \return the position of the element in space
	 *
	 */
	inline auto getLastPosWrite() -> decltype(v_pos.template get<0>(0))
	{
#ifdef SE_CLASS3
		se3.write<prop::max_prop_real>(*this,g_m-1);
#endif

		return v_pos.template get<0>(g_m - 1);
	}

	/*! \brief Get the property of the last element
	 *
	 * \tparam id property id
	 *
	 * \return return the selected property of the vector element
	 *
	 */
	template<unsigned int id> inline auto getLastPropWrite() -> decltype(v_prp.template get<id>(0))
	{
#ifdef SE_CLASS3
		se3.write<id>(*this,g_m-1);
#endif

		return v_prp.template get<id>(g_m - 1);
	}

////////////////////////////////////////////////////////////////

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	/*! \brief Construct a cell list symmetric based on a cut of radius
	 *
	 * \tparam CellL CellList type to construct
	 *
	 * \param r_cut interation radius, or size of each cell
	 *
	 * \return the Cell list
	 *
	 */
	template<typename CellL = CellList<dim, St, FAST, shift<dim, St> > > CellL getCellListSym(St r_cut)
	{
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#ifdef SE_CLASS1
		if ((opt & BIND_DEC_TO_GHOST))
		{
			std::cerr << __FILE__ << ":" << __LINE__ << " error to get symmetric cell-list you must construct the vector with the option BIND_DEC_TO_GHOST " << std::endl;
			ACTION_ON_ERROR(VECTOR_DIST_ERROR_OBJECT);
		}
#endif

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		// Cell list
		CellL cell_list;

		size_t pad = 0;
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		CellDecomposer_sm<dim,St,shift<dim,St>> cd_sm;
		cl_param_calculateSym(getDecomposition().getDomain(),cd_sm,getDecomposition().getGhost(),r_cut,pad);
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		// Processor bounding box
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		Box<dim, St> pbox = getDecomposition().getProcessorBounds();

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		// Ghost padding extension
		Ghost<dim,size_t> g_ext(0);
		cell_list.Initialize(cd_sm,pbox,pad);
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		cell_list.set_ndec(getDecomposition().get_ndec());
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		updateCellListSym(cell_list);
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		return cell_list;
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	}

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	/*! \brief Construct a cell list starting from the stored particles
	 *
	 * \tparam CellL CellList type to construct
	 *
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	 * \param r_cut interation radius, or size of each cell
	 *
	 * \return the Cell list
	 *
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	 */
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	template<typename CellL = CellList<dim, St, FAST, shift<dim, St> > > CellL getCellList(St r_cut)
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	{
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#ifdef SE_CLASS3
		se3.getNN();
#endif
#ifdef SE_CLASS1
		check_ghost_compatible_rcut(r_cut);
#endif

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		// Get ghost and anlarge by 1%
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		Ghost<dim,St> g = getDecomposition().getGhost();
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		g.magnify(1.013);
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		return getCellList(r_cut, g);
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	}

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	/*! \brief Construct an hilbert cell list starting from the stored particles
	 *
	 * \tparam CellL CellList type to construct
	 *
	 * \param r_cut interation radius, or size of each cell
	 *
	 * \return the Cell list
	 *
	 */
	template<typename CellL = CellList_hilb<dim, St, FAST, shift<dim, St> > > CellL getCellList_hilb(St r_cut)
	{
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#ifdef SE_CLASS3
		se3.getNN();
#endif
#ifdef SE_CLASS1
		check_ghost_compatible_rcut(r_cut);
#endif

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		// Get ghost and anlarge by 1%
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		Ghost<dim,St> g = getDecomposition().getGhost();
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		g.magnify(1.013);
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		return getCellList_hilb(r_cut, g);
	}

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	/*! \brief Update a cell list using the stored particles
	 *
	 * \tparam CellL CellList type to construct
	 *
	 * \param cell_list Cell list to update
	 *
	 */
	template<typename CellL = CellList<dim, St, FAST, shift<dim, St> > > void updateCellList(CellL & cell_list)
	{
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#ifdef SE_CLASS3
		se3.getNN();
#endif

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		// This function assume equal spacing in all directions
		// but in the worst case we take the maximum
		St r_cut = 0;
		for (size_t i = 0 ; i < dim ; i++)
			r_cut = std::max(r_cut,cell_list.getCellBox().getHigh(i));

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		// Here we have to check that the Cell-list has been constructed
		// from the same decomposition
		bool to_reconstruct = cell_list.get_ndec() != getDecomposition().get_ndec();
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		if (to_reconstruct == false)
		{
			populate_cell_list(v_pos,cell_list,g_m,CL_NON_SYMMETRIC);

			cell_list.set_gm(g_m);
		}
		else
		{
			CellL cli_tmp = gcl<dim,St,CellL,self>::get(*this,r_cut,getDecomposition().getGhost());

			cell_list.swap(cli_tmp);
		}
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	}

	/*! \brief Update a cell list using the stored particles
	 *
	 * \tparam CellL CellList type to construct
	 *
	 * \param cell_list Cell list to update
	 *
	 */
	template<typename CellL = CellList<dim, St, FAST, shift<dim, St> > > void updateCellListSym(CellL & cell_list)
	{
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#ifdef SE_CLASS3
		se3.getNN();
#endif
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		// This function assume equal spacing in all directions
		// but in the worst case we take the maximum
		St r_cut = 0;
		for (size_t i = 0 ; i < dim ; i++)
			r_cut = std::max(r_cut,cell_list.getCellBox().getHigh(i));

		// Here we have to check that the Cell-list has been constructed
		// from the same decomposition
		bool to_reconstruct = cell_list.get_ndec() != getDecomposition().get_ndec();

		if (to_reconstruct == false)
		{
			populate_cell_list(v_pos,cell_list,g_m,CL_SYMMETRIC);

			cell_list.set_gm(g_m);
		}
		else
		{
			CellL cli_tmp = gcl<dim,St,CellL,self>::get(*this,r_cut,getDecomposition().getGhost());

			cell_list.swap(cli_tmp);
		}
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	}

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	/*! \brief Construct a cell list starting from the stored particles
	 *
	 * It differ from the get getCellList for an additional parameter, in case the
	 * domain + ghost is not big enough to contain additional padding particles, a Cell list
	 * with bigger space can be created
	 * (padding particles in general are particles added by the user out of the domains)
	 *
	 * \tparam CellL CellList type to construct
	 *
	 * \param r_cut interation radius, or size of each cell
	 * \param enlarge In case of padding particles the cell list must be enlarged, like a ghost this parameter say how much must be enlarged
	 *
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	 * \return the CellList
	 *
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	 */
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	template<typename CellL = CellList<dim, St, FAST, shift<dim, St> > > CellL getCellList(St r_cut, const Ghost<dim, St> & enlarge)
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	{
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#ifdef SE_CLASS3
		se3.getNN();
#endif

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		CellL cell_list;

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		// Division array
		size_t div[dim];
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		// get the processor bounding box
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		Box<dim, St> pbox = getDecomposition().getProcessorBounds();
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		// Processor bounding box
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		cl_param_calculate(pbox, div, r_cut, enlarge);
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		cell_list.Initialize(pbox, div);
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		cell_list.set_ndec(getDecomposition().get_ndec());
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		updateCellList(cell_list);

		return cell_list;
	}
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	/*! \brief Construct an hilbert cell list starting from the stored particles
	 *
	 * It differ from the get getCellList for an additional parameter, in case the
	 * domain + ghost is not big enough to contain additional padding particles, a Cell list
	 * with bigger space can be created
	 * (padding particles in general are particles added by the user out of the domains)
	 *
	 * \tparam CellL CellList type to construct
	 *
	 * \param r_cut interation radius, or size of each cell
	 * \param enlarge In case of padding particles the cell list must be enlarged, like a ghost this parameter say how much must be enlarged
	 *
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	 * \return The Cell-list
	 *
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	 */
	template<typename CellL = CellList_hilb<dim, St, FAST, shift<dim, St> > > CellL getCellList_hilb(St r_cut, const Ghost<dim, St> & enlarge)
	{
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#ifdef SE_CLASS3
		se3.getNN();
#endif

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		CellL cell_list;

		// Division array
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		size_t div[dim];

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		// get the processor bounding box
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		Box<dim, St> pbox = getDecomposition().getProcessorBounds();
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		// Processor bounding box
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		cl_param_calculate(pbox,div, r_cut, enlarge);
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		cell_list.Initialize(pbox, div, g_m);
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		cell_list.set_ndec(getDecomposition().get_ndec());
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		updateCellList(cell_list);
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		return cell_list;
	}
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	/*! \brief for each particle get the symmetric verlet list
	 *
	 * \param r_cut cut-off radius
	 *
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	 * \return the verlet list
	 *
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	 */
	VerletList<dim,St,FAST,shift<dim,St> > getVerletSym(St r_cut)
	{
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#ifdef SE_CLASS3
		se3.getNN();
#endif

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		VerletList<dim,St,FAST,shift<dim,St>> ver;
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		// Processor bounding box
		Box<dim, St> pbox = getDecomposition().getProcessorBounds();

		ver.InitializeSym(getDecomposition().getDomain(),pbox,getDecomposition().getGhost(),r_cut,v_pos,g_m);

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		ver.set_ndec(getDecomposition().get_ndec());

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		return ver;
	}
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	/*! \brief for each particle get the symmetric verlet list
	 *
	 * \param r_cut cut-off radius
	 *
	 * \return the verlet list
	 *
	 */
	VerletList<dim,St,FAST,shift<dim,St> > getVerletCrs(St r_cut)
	{
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#ifdef SE_CLASS3
		se3.getNN();
#endif

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		VerletList<dim,St,FAST,shift<dim,St>> ver;

		// Processor bounding box
		Box<dim, St> pbox = getDecomposition().getProcessorBounds();

		// Initialize the verlet list
		ver.InitializeCrs(getDecomposition().getDomain(),pbox,getDecomposition().getGhost(),r_cut,v_pos,g_m);

		// Get the internal cell list
		auto & NN = ver.getInternalCellList();

		// Shift
		grid_key_dx<dim> cell_shift = NN.getShift();

		// Shift
		grid_key_dx<dim> shift = NN.getShift();

		// Add padding
		for (size_t i = 0 ; i < dim ; i++)
			shift.set_d(i,shift.get(i) + NN.getPadding(i));

		grid_sm<dim,void> gs = NN.getInternalGrid();

		ver.createVerletCrs(r_cut,g_m,v_pos,getDecomposition().getDomainCells(shift,cell_shift,gs),getDecomposition().getAnomDomainCells(shift,cell_shift,gs));

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		ver.set_ndec(getDecomposition().get_ndec());

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		return ver;
	}

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	/*! \brief for each particle get the verlet list
	 *
	 * \param r_cut cut-off radius
	 *
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	 * \return a VerletList object
	 *
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	 */
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	VerletList<dim,St,FAST,shift<dim,St> > getVerlet(St r_cut)
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	{
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#ifdef SE_CLASS3
		se3.getNN();
#endif

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		VerletList<dim,St,FAST,shift<dim,St>> ver;

		// get the processor bounding box
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		Box<dim, St> bt = getDecomposition().getProcessorBounds();

		// Get the ghost
		Ghost<dim,St> g = getDecomposition().getGhost();
		g.magnify(1.013);
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		// enlarge the box where the Verlet is defined
		bt.enlarge(g);
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		ver.Initialize(bt,getDecomposition().getProcessorBounds(),r_cut,v_pos,g_m,VL_NON_SYMMETRIC);
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		ver.set_ndec(getDecomposition().get_ndec());

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		return ver;
	}

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	/*! \brief for each particle get the verlet list
	 *
	 * \param r_cut cut-off radius
	 * \param ver Verlet to update
	 * \param r_cut cutoff radius
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	 * \param opt option like VL_SYMMETRIC and VL_NON_SYMMETRIC or VL_CRS_SYMMETRIC
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	 *
	 */
	void updateVerlet(VerletList<dim,St,FAST,shift<dim,St> > & ver, St r_cut, size_t opt = VL_NON_SYMMETRIC)
	{
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#ifdef SE_CLASS3
		se3.getNN();
#endif

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		if (opt == VL_SYMMETRIC)
		{
			auto & NN = ver.getInternalCellList();

			// Here we have to check that the Box defined by the Cell-list is the same as the domain box of this
			// processor. if it is not like that we have to completely reconstruct from stratch
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			bool to_reconstruct = NN.get_ndec() != getDecomposition().get_ndec();
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			if (to_reconstruct == false)
				ver.update(getDecomposition().getDomain(),r_cut,v_pos,g_m, opt);
			else
			{
				VerletList<dim,St,FAST,shift<dim,St> > ver_tmp;

				ver_tmp = getVerlet(r_cut);
				ver.swap(ver);
			}
		}
		else if (opt == VL_CRS_SYMMETRIC)
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		{
			auto & NN = ver.getInternalCellList();

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			// Here we have to check that the Box defined by the Cell-list is the same as the domain box of this
			// processor. if it is not like that we have to completely reconstruct from stratch
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			bool to_reconstruct = NN.get_ndec() != getDecomposition().get_ndec();
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			if (to_reconstruct == false)
			{
				// Shift
				grid_key_dx<dim> cell_shift = NN.getShift();

				// Shift
				grid_key_dx<dim> shift = NN.getShift();

				// Add padding
				for (size_t i = 0 ; i < dim ; i++)
					shift.set_d(i,shift.get(i) + NN.getPadding(i));

				grid_sm<dim,void> gs = NN.getInternalGrid();

				ver.updateCrs(getDecomposition().getDomain(),r_cut,v_pos,g_m,getDecomposition().getDomainCells(shift,cell_shift,gs),getDecomposition().getAnomDomainCells(shift,cell_shift,gs));
			}
			else
			{
				VerletList<dim,St,FAST,shift<dim,St> > ver_tmp;

				ver_tmp = getVerletCrs(r_cut);
				ver.swap(ver_tmp);
			}
		}
		else
		{
			auto & NN = ver.getInternalCellList();

			// Here we have to check that the Box defined by the Cell-list is the same as the domain box of this
			// processor. if it is not like that we have to completely reconstruct from stratch
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			bool to_reconstruct = NN.get_ndec() != getDecomposition().get_ndec();
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			if (to_reconstruct == false)
				ver.update(getDecomposition().getDomain(),r_cut,v_pos,g_m, opt);
			else
			{
				VerletList<dim,St,FAST,shift<dim,St> > ver_tmp;
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				ver_tmp = getVerlet(r_cut);
				ver.swap(ver_tmp);
			}
		}
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	}

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#if 0

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/*	void getVerletDeprecated(openfpm::vector<openfpm::vector<size_t>> & verlet, St r_cut)
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	{
		// resize verlet to store the number of particles
		verlet.resize(size_local());

		// get the cell-list
		auto cl = getCellList(r_cut);

		// square of the cutting radius
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		St r_cut2 = r_cut * r_cut;
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		// iterate the particles
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		auto it_p = this->getDomainIterator();
		while (it_p.isNext())
		{
			// key
			vect_dist_key_dx key = it_p.get();

			// Get the position of the particles
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			Point<dim, St> p = this->getPos(key);
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			// Clear the neighborhood of the particle
			verlet.get(key.getKey()).clear();

			// Get the neighborhood of the particle
			auto NN = cl.template getNNIterator<NO_CHECK>(cl.getCell(p));
			while (NN.isNext())
			{
				auto nnp = NN.get();

				// p != q
				if (nnp == key.getKey())
				{
					++NN;
					continue;
				}

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				Point<dim, St> q = this->getPos(nnp);
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				if (p.distance2(q) < r_cut2)
					verlet.get(key.getKey()).add(nnp);

				// Next particle
				++NN;
			}

			// next particle
			++it_p;
		}
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	}*/
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#endif

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	/*! \brief Construct a cell list starting from the stored particles and reorder a vector according to the Hilberts curve
	 *
	 * \tparam CellL CellList type to construct
	 *
	 * \param m an order of a hilbert curve
	 *
	 */
	template<typename CellL=CellList<dim,St,FAST,shift<dim,St> > > void reorder (int32_t m)
	{
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		reorder(m,getDecomposition().getGhost());
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	}


	/*! \brief Construct a cell list starting from the stored particles and reorder a vector according to the Hilberts curve
	 *
	 *
	 *It differs from the reorder(m) for an additional parameter, in case the
	 * domain + ghost is not big enough to contain additional padding particles, a Cell list
	 * with bigger space can be created
	 * (padding particles in general are particles added by the user out of the domains)
	 *
	 * \param m order of a curve
	 * \param enlarge In case of padding particles the cell list must be enlarged, like a ghost this parameter say how much must be enlarged
	 *
	 */
	template<typename CellL=CellList<dim,St,FAST,shift<dim,St> > > void reorder(int32_t m, const Ghost<dim,St> & enlarge)
	{
		// reset the ghost part
		v_pos.resize(g_m);
		v_prp.resize(g_m);


		CellL cell_list;

		// calculate the parameters of the cell list

		// get the processor bounding box
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		Box<dim,St> pbox = getDecomposition().getProcessorBounds();
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		// extend by the ghost
		pbox.enlarge(enlarge);

		size_t div[dim];

		// Calculate the division array and the cell box
		for (size_t i = 0 ; i < dim ; i++)
		{
			div[i] = 1 << m;
		}

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		cell_list.Initialize(pbox,div);
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		// for each particle add the particle to the cell list

		auto it = getIterator();

		while (it.isNext())
		{
			auto key = it.get();

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			Point<dim,St> xp = this->getPos(key);

			cell_list.add(xp,key.getKey());
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			++it;
		}

		// Use cell_list to reorder v_pos

		//destination vector
		openfpm::vector<Point<dim,St>> v_pos_dest;
		openfpm::vector<prop> v_prp_dest;

		v_pos_dest.resize(v_pos.size());
		v_prp_dest.resize(v_prp.size());

		//hilberts curve iterator
		grid_key_dx_iterator_hilbert<dim> h_it(m);

		//Index for v_pos_dest
		size_t count = 0;

		grid_key_dx<dim> ksum;

		for (size_t i = 0; i < dim ; i++)
			ksum.set_d(i,cell_list.getPadding(i));

		while (h_it.isNext())
		{
		  auto key = h_it.get();
		  key += ksum;

		  size_t lin = cell_list.getGrid().LinId(key);

		  // for each particle in the Cell "lin"
		  for (size_t i = 0; i < cell_list.getNelements(lin); i++)
		  {
			  //reorder
			  auto v = cell_list.get(lin,i);
			  v_pos_dest.get(count) = v_pos.get(v);
			  v_prp_dest.get(count) = v_prp.get(v);

			  count++;
		  }
		  ++h_it;
		}

		v_pos.swap(v_pos_dest);
		v_prp.swap(v_prp_dest);
	}

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	/*! \brief It return the number of particles contained by the previous processors
	 *
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	 * \warning It only work with the initial decomposition
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	 *
	 * Given 1000 particles and 3 processors, you will get
	 *
	 * * Processor 0: 0
	 * * Processor 1: 334
	 * * Processor 2: 667
	 *
	 * \param np initial number of particles
	 *
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	 * \return number of particles contained by the previous processors
	 *
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	 */
	size_t init_size_accum(size_t np)
	{
		size_t accum = 0;

		// convert to a local number of elements
		size_t p_np = np / v_cl.getProcessingUnits();

		// Get non divisible part
		size_t r = np % v_cl.getProcessingUnits();

		accum = p_np * v_cl.getProcessUnitID();

		// Distribute the remain particles
		if (v_cl.getProcessUnitID() <= r)
			accum += v_cl.getProcessUnitID();
		else
			accum += r;

		return accum;
	}
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	/*! \brief Get an iterator that traverse domain and ghost particles
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	 *
	 * \return an iterator
	 *
	 */
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	vector_dist_iterator getIterator()
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	{
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#ifdef SE_CLASS3
		se3.getIterator();
#endif
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		return vector_dist_iterator(0, v_pos.size());
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	}

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	/*! /brief Get a grid Iterator
	 *
	 * Usefull function to place particles on a grid or grid-like (grid + noise)
	 *
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	 * \param sz size of the grid
	 *
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	 * \return a Grid iterator
	 *
	 */
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	inline grid_dist_id_iterator_dec<Decomposition> getGridIterator(const size_t (&sz)[dim])
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	{
		grid_key_dx<dim> start;
		grid_key_dx<dim> stop;
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		for (size_t i = 0; i < dim; i++)
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		{
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			start.set_d(i, 0);
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			stop.set_d(i, sz[i] - 1);
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		}

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		grid_dist_id_iterator_dec<Decomposition> it_dec(getDecomposition(), sz, start, stop);
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		return it_dec;
	}

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	/*! \brief Get the iterator across the position of the ghost particles
	 *
	 * \return an iterator
	 *
	 */
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	vector_dist_iterator getGhostIterator() const
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	{
#ifdef SE_CLASS3
		se3.getIterator();
#endif

		return vector_dist_iterator(g_m, v_pos.size());
	}

	/*! \brief Get the iterator across the position of the ghost particles
	 *
	 * \return an iterator
	 *
	 */
	vector_dist_iterator getGhostIterator_no_se3() const
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	{
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		return vector_dist_iterator(g_m, v_pos.size());
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	}

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	/*! \brief Get an iterator that traverse the particles in the domain
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	 *
	 * \return an iterator
	 *
	 */
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	vector_dist_iterator getDomainIterator() const
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	{
#ifdef SE_CLASS3
		se3.getIterator();
#endif

		return vector_dist_iterator(0, g_m);
	}

	/*! \brief Get an iterator that traverse the particles in the domain
	 *
	 * \return an iterator
	 *
	 */
	vector_dist_iterator getDomainIterator_no_se3() const
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	{
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		return vector_dist_iterator(0, g_m);
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	}

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	/*! \brief Get an iterator that traverse the particles in the domain
	 *
	 * \return an iterator
	 *
	 */
	vector_dist_iterator getDomainAndGhostIterator() const
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	{
#ifdef SE_CLASS3
		se3.getIterator();
#endif

		return vector_dist_iterator(0, v_pos.size());
	}

	/*! \brief Get an iterator that traverse the particles in the domain
	 *
	 * \return an iterator
	 *
	 */
	vector_dist_iterator getDomainAndGhostIterator_no_se3() const
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	{
		return vector_dist_iterator(0, v_pos.size());
	}

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	/*! \brief Get the decomposition
	 *
	 * \return
	 *
	 */
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	inline Decomposition & getDecomposition()
	{
		return vector_dist_comm<dim,St,prop,Decomposition,Memory>::getDecomposition();
	}

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