CartDecomposition.hpp 41.1 KB
Newer Older
incardon's avatar
incardon committed
1 2 3
/*
 * CartDecomposition.hpp
 *
4
 *  Created on: Oct 07, 2015
5
 *      Author: Pietro Incardona, Antonio Leo
incardon's avatar
incardon committed
6 7 8 9 10 11
 */

#ifndef CARTDECOMPOSITION_HPP
#define CARTDECOMPOSITION_HPP

#include "config.h"
12
#include <cmath>
13 14
#include "VCluster.hpp"
#include "Graph/CartesianGraphFactory.hpp"
incardon's avatar
incardon committed
15
#include "Decomposition.hpp"
incardon's avatar
incardon committed
16
#include "Vector/map_vector.hpp"
incardon's avatar
incardon committed
17 18 19 20 21
#include <vector>
#include <initializer_list>
#include "SubdomainGraphNodes.hpp"
#include "dec_optimizer.hpp"
#include "Space/Shape/Box.hpp"
incardon's avatar
incardon committed
22
#include "Space/Shape/Point.hpp"
incardon's avatar
incardon committed
23
#include "NN/CellList/CellDecomposer.hpp"
incardon's avatar
incardon committed
24 25
#include <unordered_map>
#include "NN/CellList/CellList.hpp"
incardon's avatar
incardon committed
26
#include "Space/Ghost.hpp"
incardon's avatar
incardon committed
27 28
#include "common.hpp"
#include "ie_loc_ghost.hpp"
29 30
#include "ie_ghost.hpp"
#include "nn_processor.hpp"
31
#include "GraphMLWriter/GraphMLWriter.hpp"
32 33 34 35
#include "Distribution/ParMetisDistribution.hpp"
#include "Distribution/DistParMetisDistribution.hpp"
#include "Distribution/MetisDistribution.hpp"
#include "DLB/DLB.hpp"
36
#include "util/se_util.hpp"
37
#include "util/mathutil.hpp"
Pietro Incardona's avatar
Pietro Incardona committed
38
#include "CartDecomposition_ext.hpp"
incardon's avatar
incardon committed
39 40
#include "data_type/aggregate.hpp"
#include "Domain_NN_calculator_cart.hpp"
incardon's avatar
incardon committed
41

42 43
#define CARTDEC_ERROR 2000lu

incardon's avatar
incardon committed
44 45
#define COMPUTE_SKIN_SUB 1

incardon's avatar
incardon committed
46
/**
Pietro Incardona's avatar
Pietro Incardona committed
47
 * \brief This class decompose a space into sub-sub-domains and distribute them across processors
incardon's avatar
incardon committed
48 49 50 51
 *
 * \tparam dim is the dimensionality of the physical domain we are going to decompose.
 * \tparam T type of the space we decompose, Real, Integer, Complex ...
 * \tparam Memory Memory factory used to allocate memory
tonynsyde's avatar
tonynsyde committed
52
 * \tparam Distribution type of distribution, can be ParMetisDistribution or MetisDistribution
incardon's avatar
incardon committed
53
 *
54
 * Given an N-dimensional space, this class decompose the space into a Cartesian grid of small
incardon's avatar
incardon committed
55 56 57 58
 * sub-sub-domain. To each sub-sub-domain is assigned an id that identify at which processor is
 * assigned (in general the union of all the sub-sub-domain assigned to a processor is
 * simply connected space), a second step merge several sub-sub-domain with same id into bigger region
 *  sub-domain. Each sub-domain has an extended space called ghost part
59 60 61 62
 *
 * Assuming that VCluster.getProcessUnitID(), equivalent to the MPI processor rank, return the processor local
 * processor id, we define
 *
63 64
 * * local processor: processor rank
 * * local sub-domain: sub-domain given to the local processor
65 66 67 68 69 70 71 72 73 74 75 76
 * * external ghost box: (or ghost box) are the boxes that compose the ghost space of the processor, or the
 *   boxes produced expanding every local sub-domain by the ghost extension and intersecting with the sub-domain
 *   of the other processors
 * * Near processors are the processors adjacent to the local processor, where with adjacent we mean all the processor
 *   that has a non-zero intersection with the ghost part of the local processor, or all the processors that
 *   produce non-zero external boxes with the local processor, or all the processor that should communicate
 *   in case of ghost data synchronization
 * * internal ghost box: is the part of ghost of the near processor that intersect the space of the
 *       processor, or the boxes produced expanding the sub-domain of the near processors with the local sub-domain
 * * Near processor sub-domain: is a sub-domain that live in the a near (or contiguous) processor
 * * Near processor list: the list of all the near processor of the local processor (each processor has a list
 *                        of the near processor)
Pietro Incardona's avatar
Pietro Incardona committed
77
 * * Local ghosts internal or external are all the ghosts that does not involve inter-processor communications
78 79
 *
 * \see calculateGhostBoxes() for a visualization of internal and external ghost boxes
incardon's avatar
incardon committed
80
 *
81
 * ### Create a Cartesian decomposition object on a Box space, distribute, calculate internal and external ghost boxes
Pietro Incardona's avatar
Pietro Incardona committed
82
 *
83 84
 * \snippet CartDecomposition_unit_test.hpp Create CartDecomposition
 *
incardon's avatar
incardon committed
85 86
 */

Pietro Incardona's avatar
Pietro Incardona committed
87
template<unsigned int dim, typename T, typename Memory, typename Distribution>
incardon's avatar
incardon committed
88
class CartDecomposition: public ie_loc_ghost<dim, T>, public nn_prcs<dim, T>, public ie_ghost<dim, T>, public domain_nn_calculator_cart<dim>
incardon's avatar
incardon committed
89
{
incardon's avatar
incardon committed
90

incardon's avatar
incardon committed
91
public:
incardon's avatar
incardon committed
92

incardon's avatar
incardon committed
93 94 95 96
	//! Type of the domain we are going to decompose
	typedef T domain_type;

	//! It simplify to access the SpaceBox element
97
	typedef SpaceBox<dim, T> Box;
incardon's avatar
incardon committed
98

Pietro Incardona's avatar
Pietro Incardona committed
99 100 101 102 103 104 105
	//! This class is base of itself
	typedef CartDecomposition<dim,T,Memory,Distribution> base_type;

	//! This class admit a class defined on an extended domain
	typedef CartDecomposition_ext<dim,T,Memory,Distribution> extended_type;

protected:
incardon's avatar
incardon committed
106

incardon's avatar
incardon committed
107
	//! This is the key type to access  data_s, for example in the case of vector
incardon's avatar
incardon committed
108
	//! acc_key is size_t
Pietro Incardona's avatar
Pietro Incardona committed
109 110 111 112 113 114
	typedef typename openfpm::vector<SpaceBox<dim, T>,
			Memory,
			typename memory_traits_lin<SpaceBox<dim, T>>::type,
			memory_traits_lin,
			openfpm::vector_grow_policy_default,
			openfpm::vect_isel<SpaceBox<dim, T>>::value>::access_key acc_key;
incardon's avatar
incardon committed
115 116

	//! the set of all local sub-domain as vector
117
	openfpm::vector<SpaceBox<dim, T>> sub_domains;
incardon's avatar
incardon committed
118

incardon's avatar
incardon committed
119
	//! for each sub-domain, contain the list of the neighborhood processors
incardon's avatar
incardon committed
120 121
	openfpm::vector<openfpm::vector<long unsigned int> > box_nn_processor;

incardon's avatar
incardon committed
122
	//! Structure that contain for each sub-sub-domain box the processor id
incardon's avatar
Add ORB  
incardon committed
123
	//! exist for efficient global communication
incardon's avatar
incardon committed
124 125
	openfpm::vector<size_t> fine_s;

incardon's avatar
incardon committed
126
	//! Structure that store the cartesian grid information
127
	grid_sm<dim, void> gr;
incardon's avatar
incardon committed
128

incardon's avatar
incardon committed
129 130
	//! Structure that decompose your structure into cell without creating them
	//! useful to convert positions to CellId or sub-domain id in this case
131
	CellDecomposer_sm<dim, T, shift<dim,T>> cd;
incardon's avatar
incardon committed
132 133

	//! rectangular domain to decompose
Pietro Incardona's avatar
Pietro Incardona committed
134
	::Box<dim,T> domain;
incardon's avatar
incardon committed
135 136 137 138 139 140 141

	//! Box Spacing
	T spacing[dim];

	//! Runtime virtual cluster machine
	Vcluster & v_cl;

142
	//! Create distribution
143 144
	Distribution dist;

145
	//! Smallest subdivision on each direction
incardon's avatar
incardon committed
146 147
	::Box<dim,T> ss_box;

148
	//! Processor bounding box
incardon's avatar
incardon committed
149
	::Box<dim,T> bbox;
incardon's avatar
incardon committed
150

151
	//! reference counter of the object in case is shared between object
152 153
	long int ref_cnt;

154
	//! ghost info
155 156
	Ghost<dim,T> ghost;

157
	//! Boundary condition info
Pietro Incardona's avatar
Pietro Incardona committed
158
	size_t bc[dim];
incardon's avatar
incardon committed
159

incardon's avatar
incardon committed
160 161 162 163 164 165
	//! Processor domain bounding box
	::Box<dim,size_t> proc_box;

	//! set of Boxes produced by the decomposition optimizer
	openfpm::vector<::Box<dim, size_t>> loc_box;

Pietro Incardona's avatar
Pietro Incardona committed
166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207
	/*! \brief It convert the box from the domain decomposition into sub-domain
	 *
	 * The decomposition box from the domain-decomposition contain the box in integer
	 * coordinates
	 *
	 * \param loc_box local box
	 *
	 * \return the corresponding sib-domain
	 *
	 */
	SpaceBox<dim,T> convertDecBoxIntoSubDomain(const SpaceBox<dim,size_t> & loc_box)
	{
		// A point with all coordinate to one
		size_t one[dim];
		for (size_t i = 0 ; i < dim ; i++)	{one[i] = 1;}

		SpaceBox<dim, size_t> sub_dc = loc_box;
		SpaceBox<dim, size_t> sub_dce = sub_dc;
		sub_dce.expand(one);
		SpaceBox<dim, T> sub_d(sub_dce);
		sub_d.mul(spacing);
		sub_d += domain.getP1();

		// we add the

		// Fixing sub-domains to cover all the domain

		// Fixing sub_d
		// if (loc_box) is at the boundary we have to ensure that the box span the full
		// domain (avoiding rounding off error)
		for (size_t i = 0; i < dim; i++)
		{
			if (sub_dc.getHigh(i) == cd.getGrid().size(i) - 1)
				sub_d.setHigh(i, domain.getHigh(i));

			if (sub_dc.getLow(i) == 0)
				sub_d.setLow(i,domain.getLow(i));
		}

		return sub_d;
	}

Pietro Incardona's avatar
Pietro Incardona committed
208 209 210 211 212 213
protected:



public:

214
	/*! \brief Constructor, it decompose and distribute the sub-domains across the processors
incardon's avatar
incardon committed
215
	 *
216
	 * \param v_cl Virtual cluster, used internally for communications
Pietro Incardona's avatar
Pietro Incardona committed
217
	 * \param bc boundary conditions
incardon's avatar
incardon committed
218
	 * \param opt option (one option is to construct)
219
	 *
incardon's avatar
incardon committed
220
	 */
incardon's avatar
incardon committed
221
	void createSubdomains(Vcluster & v_cl, const size_t (& bc)[dim], size_t opt = 0)
incardon's avatar
incardon committed
222
	{
223 224 225 226 227 228 229
#ifdef SE_CLASS1
		if (&v_cl == NULL)
		{
			std::cerr << __FILE__ << ":" << __LINE__ << " error VCluster instance is null, check that you ever initialized it \n";
			ACTION_ON_ERROR()
		}
#endif
230 231 232

		int p_id = v_cl.getProcessUnitID();

incardon's avatar
incardon committed
233 234 235
		// Calculate the total number of box and and the spacing
		// on each direction
		// Get the box containing the domain
236
		SpaceBox<dim, T> bs = domain.getBox();
incardon's avatar
incardon committed
237

238
		for (unsigned int i = 0; i < dim; i++)
incardon's avatar
incardon committed
239 240
		{
			// Calculate the spacing
incardon's avatar
incardon committed
241
			spacing[i] = (bs.getHigh(i) - bs.getLow(i)) / gr.size(i);
incardon's avatar
incardon committed
242 243
		}

incardon's avatar
Add ORB  
incardon committed
244
		// fill the structure that store the processor id for each sub-domain
incardon's avatar
incardon committed
245
		fine_s.resize(gr.size());
incardon's avatar
Add ORB  
incardon committed
246

incardon's avatar
incardon committed
247 248
		// Optimize the decomposition creating bigger spaces
		// And reducing Ghost over-stress
249
		dec_optimizer<dim, Graph_CSR<nm_v, nm_e>> d_o(dist.getGraph(), gr.getSize());
incardon's avatar
incardon committed
250

251 252 253 254 255 256 257 258 259 260
		// Ghost
		Ghost<dim,long int> ghe;

		// Set the ghost
		for (size_t i = 0 ; i < dim ; i++)
		{
			ghe.setLow(i,static_cast<long int>(ghost.getLow(i)/spacing[i]) - 1);
			ghe.setHigh(i,static_cast<long int>(ghost.getHigh(i)/spacing[i]) + 1);
		}

incardon's avatar
incardon committed
261
		// optimize the decomposition
262
		d_o.template optimize<nm_v::sub_id, nm_v::proc_id>(dist.getGraph(), p_id, loc_box, box_nn_processor,ghe,bc);
incardon's avatar
incardon committed
263

Pietro Incardona's avatar
Pietro Incardona committed
264 265 266 267
		// reset ss_box
		ss_box = domain;
		ss_box -= ss_box.getP1();

incardon's avatar
incardon committed
268 269
		// Initialize ss_box and bbox
		if (loc_box.size() >= 0)
incardon's avatar
incardon committed
270
		{
Pietro Incardona's avatar
Pietro Incardona committed
271
			bbox = convertDecBoxIntoSubDomain(loc_box.get(0));
incardon's avatar
incardon committed
272 273
			proc_box = loc_box.get(0);
		}
Pietro Incardona's avatar
Pietro Incardona committed
274

incardon's avatar
incardon committed
275
		// convert into sub-domain
Pietro Incardona's avatar
Pietro Incardona committed
276
		for (size_t s = 0; s < loc_box.size(); s++)
incardon's avatar
incardon committed
277
		{
Pietro Incardona's avatar
Pietro Incardona committed
278
			SpaceBox<dim,T> sub_d = convertDecBoxIntoSubDomain(loc_box.get(s));
279

incardon's avatar
incardon committed
280 281
			// add the sub-domain
			sub_domains.add(sub_d);
incardon's avatar
incardon committed
282 283 284

			// Calculate the bound box
			bbox.enclose(sub_d);
incardon's avatar
incardon committed
285
			proc_box.enclose(loc_box.get(s));
incardon's avatar
incardon committed
286 287 288

			// Create the smallest box contained in all sub-domain
			ss_box.contained(sub_d);
incardon's avatar
incardon committed
289
		}
incardon's avatar
incardon committed
290

291
		nn_prcs<dim,T>::create(box_nn_processor, sub_domains);
incardon's avatar
incardon committed
292
		nn_prcs<dim,T>::refine_ss_box(ss_box);
Pietro Incardona's avatar
Pietro Incardona committed
293
		nn_prcs<dim,T>::applyBC(domain,ghost,bc);
294

incardon's avatar
incardon committed
295
		// fill fine_s structure
incardon's avatar
incardon committed
296 297 298
		// fine_s structure contain the processor id for each sub-sub-domain
		// with sub-sub-domain we mean the sub-domain decomposition before
		// running dec_optimizer (before merging sub-domains)
299
		auto it = dist.getGraph().getVertexIterator();
incardon's avatar
incardon committed
300 301 302 303 304 305

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

			// fill with the fine decomposition
306
			fine_s.get(key) = dist.getGraph().template vertex_p<nm_v::proc_id>(key);
incardon's avatar
incardon committed
307 308 309

			++it;
		}
310

incardon's avatar
incardon committed
311 312 313 314 315 316 317 318 319 320
		Initialize_geo_cell_lists();
	}

	/*! \brief Initialize geo_cell lists
	 *
	 *
	 *
	 */
	void Initialize_geo_cell_lists()
	{
321
		// Get the smallest sub-division on each direction
322
		::Box<dim, T> unit = getSmallestSubdivision();
323 324
		// Get the processor bounding Box
		::Box<dim,T> bound = getProcessorBounds();
Pietro Incardona's avatar
Pietro Incardona committed
325 326
		// Not necessary, but I prefer
		bound.enlarge(ghost);
327

incardon's avatar
incardon committed
328
		// calculate the sub-divisions
329
		size_t div[dim];
330 331
		for (size_t i = 0; i < dim; i++)
			div[i] = (size_t) ((bound.getHigh(i) - bound.getLow(i)) / unit.getHigh(i));
332 333

		// Initialize the geo_cell structure
334
		ie_ghost<dim,T>::Initialize_geo_cell(bound,div);
335

336 337
		// Initialize shift vectors
		ie_ghost<dim,T>::generateShiftVectors(domain);
incardon's avatar
incardon committed
338 339
	}

340 341 342 343 344 345
	/*! \brief Calculate communication and migration costs
	 *
	 * \param ts how many timesteps have passed since last calculation, used to approximate the cost
	 */
	void computeCommunicationAndMigrationCosts(size_t ts)
	{
tonynsyde's avatar
tonynsyde committed
346
		float migration = 0;
347 348

		SpaceBox<dim, T> cellBox = cd.getCellBox();
incardon's avatar
incardon committed
349 350
		float b_s = static_cast<float>(cellBox.getHigh(0));
		float gh_s = static_cast<float>(ghost.getHigh(0));
351 352 353 354 355

		// compute the gh_area for 2 dim case
		float gh_v = (gh_s * b_s);

		// multiply for sub-sub-domain side for each domain
356
		for (size_t i = 2; i < dim; i++)
357 358 359 360 361 362 363 364 365 366
			gh_v *= b_s;

		size_t norm = (size_t) (1.0 / gh_v);

		migration = pow(b_s, dim);

		size_t prev = 0;

		for (size_t i = 0; i < dist.getNSubSubDomains(); i++)
		{
367
			dist.setMigrationCost(i, norm * migration * dist.getSubSubDomainComputationCost(i));
368 369 370

			for (size_t s = 0; s < dist.getNSubSubDomainNeighbors(i); s++)
			{
371
				dist.setCommunicationCost(i, s, 1 * dist.getSubSubDomainComputationCost(i) * ts);
372 373 374 375
			}
			prev += dist.getNSubSubDomainNeighbors(i);
		}
	}
incardon's avatar
incardon committed
376

incardon's avatar
incardon committed
377
	/*! \brief Create the sub-domain that decompose your domain
incardon's avatar
incardon committed
378 379 380 381 382
	 *
	 */
	void CreateSubspaces()
	{
		// Create a grid where each point is a space
383
		grid_sm<dim, void> g(div);
incardon's avatar
incardon committed
384 385 386 387 388 389 390 391 392 393 394

		// create a grid_key_dx iterator
		grid_key_dx_iterator<dim> gk_it(g);

		// Divide the space into subspaces
		while (gk_it.isNext())
		{
			//! iterate through all subspaces
			grid_key_dx<dim> key = gk_it.get();

			//! Create a new subspace
395
			SpaceBox<dim, T> tmp;
incardon's avatar
incardon committed
396 397

			//! fill with the Margin of the box
398
			for (int i = 0; i < dim; i++)
incardon's avatar
incardon committed
399
			{
400 401
				tmp.setHigh(i, (key.get(i) + 1) * spacing[i]);
				tmp.setLow(i, key.get(i) * spacing[i]);
incardon's avatar
incardon committed
402 403 404 405 406
			}

			//! add the space box
			sub_domains.add(tmp);

incardon's avatar
incardon committed
407
			// Next sub-domain
incardon's avatar
incardon committed
408 409 410 411
			++gk_it;
		}
	}

412 413 414 415 416 417 418 419 420 421

	/*! It calculate the internal ghost boxes
	 *
	 * Example: Processor 10 calculate
	 * B8_0 B9_0 B9_1 and B5_0
	 *
	 *
	 *
	 \verbatim

Pietro Incardona's avatar
Pietro Incardona committed
422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445
	+----------------------------------------------------+
	|                                                    |
	|                 Processor 8                        |
	|                 Sub+domain 0                       +-----------------------------------+
	|                                                    |                                   |
	|                                                    |                                   |
	++--------------+---+---------------------------+----+        Processor 9                |
	 |              |   |     B8_0                  |    |        Subdomain 0                |
	 |              +------------------------------------+                                   |
	 |              |   |                           |    |                                   |
	 |              |   |                           |B9_0|                                   |
	 |              | B |    Local processor        |    |                                   |
	 | Processor 5  | 5 |    Subdomain 0            |    |                                   |
	 | Subdomain 0  | _ |                           +----------------------------------------+
	 |              | 0 |                           |    |                                   |
	 |              |   |                           |    |                                   |
	 |              |   |                           |    |        Processor 9                |
	 |              |   |                           |B9_1|        Subdomain 1                |
	 |              |   |                           |    |                                   |
	 |              |   |                           |    |                                   |
	 |              |   |                           |    |                                   |
	 +--------------+---+---------------------------+----+                                   |
														 |                                   |
														 +-----------------------------------+
446 447 448 449 450 451 452


 \endverbatim

       and also
       G8_0 G9_0 G9_1 G5_0 (External ghost boxes)

Pietro Incardona's avatar
Pietro Incardona committed
453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478
\verbatim

		  +----------------------------------------------------+
		  |                 Processor 8                        |
		  |                 Subdomain 0                        +-----------------------------------+
		  |                                                    |                                   |
		  |           +---------------------------------------------+                              |
		  |           |         G8_0                           |    |                              |
	+-----+---------------+------------------------------------+    |   Processor 9                |
	|                 |   |                                    |    |   Subdomain 0                |
	|                 |   |                                    |G9_0|                              |
	|                 |   |                                    |    |                              |
	|                 |   |                                    |    |                              |
	|                 |   |        Local processor             |    |                              |
	|  Processor 5    |   |        Sub+domain 0                |    |                              |
	|  Subdomain 0    |   |                                    +-----------------------------------+
	|                 |   |                                    |    |                              |
	|                 | G |                                    |    |                              |
	|                 | 5 |                                    |    |   Processor 9                |
	|                 | | |                                    |    |   Subdomain 1                |
	|                 | 0 |                                    |G9_1|                              |
	|                 |   |                                    |    |                              |
	|                 |   |                                    |    |                              |
	+---------------------+------------------------------------+    |                              |
					  |                                        |    |                              |
					  +----------------------------------------+----+------------------------------+
479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518

	 \endverbatim

	 *
	 *
	 *
	 * \param ghost margins for each dimensions (p1 negative part) (p2 positive part)
	 *
	 *
	 \verbatim

	 	 	 	 	 ^ p2[1]
	 	 	 	 	 |
	 	 	 	 	 |
	 	 	 	+----+----+
	 	 	 	|         |
	 	 	 	|         |
	 p1[0]<-----+         +----> p2[0]
	 	 	 	|         |
	 	 	 	|         |
	 	 	 	+----+----+
	 	 	 	 	 |
	 	 	 	 	 v  p1[1]

	 \endverbatim

	 *
	 *
	 */
	void calculateGhostBoxes()
	{
		// Intersect all the local sub-domains with the sub-domains of the contiguous processors

		// create the internal structures that store ghost information
		ie_ghost<dim, T>::create_box_nn_processor_ext(v_cl, ghost, sub_domains, box_nn_processor, *this);
		ie_ghost<dim, T>::create_box_nn_processor_int(v_cl, ghost, sub_domains, box_nn_processor, *this);

		ie_loc_ghost<dim,T>::create(sub_domains,domain,ghost,bc);
	}

incardon's avatar
incardon committed
519 520
public:

Pietro Incardona's avatar
Pietro Incardona committed
521
	//! Space dimensions
522 523
	static constexpr int dims = dim;

Pietro Incardona's avatar
Pietro Incardona committed
524
	//! Space type
525 526
	typedef T stype;

incardon's avatar
incardon committed
527 528 529 530 531 532 533 534 535 536 537 538 539 540
	//! Increment the reference counter
	void incRef()
	{ref_cnt++;}

	//! Decrement the reference counter
	void decRef()
	{ref_cnt--;}

	//! Return the reference counter
	long int ref()
	{
		return ref_cnt;
	}

incardon's avatar
incardon committed
541 542
	/*! \brief Cartesian decomposition constructor
	 *
543
	 * \param v_cl Virtual cluster, used internally to handle or pipeline communication
incardon's avatar
incardon committed
544 545
	 *
	 */
incardon's avatar
incardon committed
546 547
	CartDecomposition(Vcluster & v_cl)
	:nn_prcs<dim, T>(v_cl), v_cl(v_cl), dist(v_cl),ref_cnt(0)
incardon's avatar
incardon committed
548 549 550 551
	{
		// Reset the box to zero
		bbox.zero();
	}
incardon's avatar
incardon committed
552

553 554 555 556 557
	/*! \brief Cartesian decomposition copy constructor
	 *
     * \param cart object to copy
	 *
	 */
Pietro Incardona's avatar
Pietro Incardona committed
558
	CartDecomposition(const CartDecomposition<dim,T,Memory> & cart)
559
	:nn_prcs<dim,T>(cart.v_cl),v_cl(cart.v_cl),dist(v_cl),ref_cnt(0)
560 561 562 563 564 565 566 567 568
	{
		this->operator=(cart);
	}

	/*! \brief Cartesian decomposition copy constructor
	 *
     * \param cart object to copy
	 *
	 */
Pietro Incardona's avatar
Pietro Incardona committed
569
	CartDecomposition(CartDecomposition<dim,T,Memory> && cart)
570
	:nn_prcs<dim,T>(cart.v_cl),v_cl(cart.v_cl),dist(v_cl),ref_cnt(0)
571 572 573 574
	{
		this->operator=(cart);
	}

incardon's avatar
incardon committed
575 576
	//! Cartesian decomposition destructor
	~CartDecomposition()
577 578
	{
	}
incardon's avatar
incardon committed
579

580 581 582 583 584 585 586 587 588 589 590 591 592 593
	/*! \brief class to select the returned id by ghost_processorID
	 *
	 */
	class box_id
	{
	public:
		/*! \brief Return the box id
		 *
		 * \param p structure containing the id informations
		 * \param b_id box_id
		 *
		 * \return box id
		 *
		 */
594
		inline static size_t id(p_box<dim, T> & p, size_t b_id)
595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613
		{
			return b_id;
		}
	};

	/*! \brief class to select the returned id by ghost_processorID
	 *
	 */
	class processor_id
	{
	public:
		/*! \brief Return the processor id
		 *
		 * \param p structure containing the id informations
		 * \param b_id box_id
		 *
		 * \return processor id
		 *
		 */
614
		inline static size_t id(p_box<dim, T> & p, size_t b_id)
615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633
		{
			return p.proc;
		}
	};

	/*! \brief class to select the returned id by ghost_processorID
	 *
	 */
	class lc_processor_id
	{
	public:
		/*! \brief Return the near processor id
		 *
		 * \param p structure containing the id informations
		 * \param b_id box_id
		 *
		 * \return local processor id
		 *
		 */
634
		inline static size_t id(p_box<dim, T> & p, size_t b_id)
635 636 637 638 639
		{
			return p.lc_proc;
		}
	};

640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659
	/*! \brief class to select the returned id by ghost_processorID
	 *
	 */
	class shift_id
	{
	public:
		/*! \brief Return the shift id
		 *
		 * \param p structure containing the id informations
		 * \param b_id box_id
		 *
		 * \return shift_id id
		 *
		 */
		inline static size_t id(p_box<dim,T> & p, size_t b_id)
		{
			return p.shift_id;
		}
	};

660 661
	/*! \brief Apply boundary condition to the point
	 *
Pietro Incardona's avatar
Pietro Incardona committed
662 663 664 665 666
	 * If the particle go out to the right, bring back the particle on the left
	 * in case of periodic, nothing in case of non periodic
	 *
	 * \param pt Point to apply the boundary condition. (it's coordinated are changed according the
	 *        the explanation before)
667 668 669 670 671 672 673 674 675 676 677 678 679
	 *
	 */
	void applyPointBC(float (& pt)[dim]) const
	{
		for (size_t i = 0 ; i < dim ; i++)
		{
			if (bc[i] == PERIODIC)
				pt[i] = openfpm::math::periodic_l(pt[i],domain.getHigh(i),domain.getLow(i));
		}
	}

	/*! \brief Apply boundary condition to the point
	 *
Pietro Incardona's avatar
Pietro Incardona committed
680 681 682 683 684
	 * If the particle go out to the right, bring back the particle on the left
	 * in case of periodic, nothing in case of non periodic
	 *
	 * \param pt Point to apply the boundary conditions.(it's coordinated are changed according the
	 *        the explanation before)
685 686 687 688 689 690 691 692 693 694 695 696 697
	 *
	 */
	void applyPointBC(Point<dim,T> & pt) const
	{
		for (size_t i = 0 ; i < dim ; i++)
		{
			if (bc[i] == PERIODIC)
				pt.get(i) = openfpm::math::periodic_l(pt.get(i),domain.getHigh(i),domain.getLow(i));
		}
	}

	/*! \brief Apply boundary condition to the point
	 *
Pietro Incardona's avatar
Pietro Incardona committed
698 699 700 701 702
	 * If the particle go out to the right, bring back the particle on the left
	 * in case of periodic, nothing in case of non periodic
	 *
	 * \param pt encapsulated point object (it's coordinated are changed according the
	 *        the explanation before)
703 704 705 706 707 708 709 710 711 712 713
	 *
	 */
	template<typename Mem> void applyPointBC(encapc<1,Point<dim,T>,Mem> && pt) const
	{
		for (size_t i = 0 ; i < dim ; i++)
		{
			if (bc[i] == PERIODIC)
				pt.template get<0>()[i] = openfpm::math::periodic_l(pt.template get<0>()[i],domain.getHigh(i),domain.getLow(i));
		}
	}

incardon's avatar
incardon committed
714 715 716 717 718 719 720
	/*! \brief It create another object that contain the same decomposition information but with different ghost boxes
	 *
	 * \param g ghost
	 *
	 * \return a duplicated decomposition with different ghost boxes
	 *
	 */
Pietro Incardona's avatar
Pietro Incardona committed
721
	CartDecomposition<dim,T,Memory> duplicate(const Ghost<dim,T> & g) const
incardon's avatar
incardon committed
722
	{
Pietro Incardona's avatar
Pietro Incardona committed
723
		CartDecomposition<dim,T,Memory> cart(v_cl);
incardon's avatar
incardon committed
724 725 726 727 728 729 730 731 732 733 734 735 736 737

		cart.box_nn_processor = box_nn_processor;
		cart.sub_domains = sub_domains;
		cart.fine_s = fine_s;

		cart.gr = gr;
		cart.cd = cd;
		cart.domain = domain;
		std::copy(spacing,spacing+3,cart.spacing);

		cart.bbox = bbox;
		cart.ss_box = ss_box;
		cart.ghost = g;

738 739
		cart.dist = dist;

740 741 742
		for (size_t i = 0 ; i < dim ; i++)
			cart.bc[i] = bc[i];

743 744
		(static_cast<nn_prcs<dim,T> &>(cart)).create(box_nn_processor, sub_domains);
		(static_cast<nn_prcs<dim,T> &>(cart)).applyBC(domain,ghost,bc);
incardon's avatar
incardon committed
745

746 747
		cart.Initialize_geo_cell_lists();
		cart.calculateGhostBoxes();
incardon's avatar
incardon committed
748 749 750 751 752

		return cart;
	}

	/*! \brief It create another object that contain the same information and act in the same way
753
	 *
Pietro Incardona's avatar
Pietro Incardona committed
754
	 * \return a duplicated CartDecomposition object
755 756
	 *
	 */
Pietro Incardona's avatar
Pietro Incardona committed
757
	CartDecomposition<dim,T,Memory> duplicate() const
758
	{
Pietro Incardona's avatar
Pietro Incardona committed
759
		CartDecomposition<dim,T,Memory> cart(v_cl);
760 761 762 763 764 765 766 767 768 769 770 771 772 773 774

		(static_cast<ie_loc_ghost<dim,T>*>(&cart))->operator=(static_cast<ie_loc_ghost<dim,T>>(*this));
		(static_cast<nn_prcs<dim,T>*>(&cart))->operator=(static_cast<nn_prcs<dim,T>>(*this));
		(static_cast<ie_ghost<dim,T>*>(&cart))->operator=(static_cast<ie_ghost<dim,T>>(*this));

		cart.sub_domains = sub_domains;
		cart.box_nn_processor = box_nn_processor;
		cart.fine_s = fine_s;
		cart.gr = gr;
		cart.cd = cd;
		cart.domain = domain;
		std::copy(spacing,spacing+3,cart.spacing);

		cart.ghost = ghost;

incardon's avatar
incardon committed
775 776 777
		cart.bbox = bbox;
		cart.ss_box = ss_box;

778 779 780
		for (size_t i = 0 ; i < dim ; i++)
			cart.bc[i] = this->bc[i];

781 782 783 784 785 786 787
		return cart;
	}

	/*! \brief Copy the element
	 *
	 * \param cart element to copy
	 *
Pietro Incardona's avatar
Pietro Incardona committed
788 789
	 * \return itself
	 *
790
	 */
Pietro Incardona's avatar
Pietro Incardona committed
791
	CartDecomposition<dim,T,Memory> & operator=(const CartDecomposition & cart)
792 793 794 795 796 797 798 799 800 801 802 803 804 805 806
	{
		static_cast<ie_loc_ghost<dim,T>*>(this)->operator=(static_cast<ie_loc_ghost<dim,T>>(cart));
		static_cast<nn_prcs<dim,T>*>(this)->operator=(static_cast<nn_prcs<dim,T>>(cart));
		static_cast<ie_ghost<dim,T>*>(this)->operator=(static_cast<ie_ghost<dim,T>>(cart));

		sub_domains = cart.sub_domains;
		box_nn_processor = cart.box_nn_processor;
		fine_s = cart.fine_s;
		gr = cart.gr;
		cd = cart.cd;
		domain = cart.domain;
		std::copy(cart.spacing,cart.spacing+3,spacing);

		ghost = cart.ghost;

incardon's avatar
incardon committed
807 808 809
		bbox = cart.bbox;
		ss_box = cart.ss_box;

810 811 812
		for (size_t i = 0 ; i < dim ; i++)
			bc[i] = cart.bc[i];

813 814 815 816 817 818 819
		return *this;
	}

	/*! \brief Copy the element, move semantic
	 *
	 * \param cart element to copy
	 *
Pietro Incardona's avatar
Pietro Incardona committed
820 821
	 * \return itself
	 *
822
	 */
Pietro Incardona's avatar
Pietro Incardona committed
823
	CartDecomposition<dim,T,Memory> & operator=(CartDecomposition && cart)
824
	{
Pietro Incardona's avatar
Pietro Incardona committed
825 826 827
		static_cast<ie_loc_ghost<dim,T>*>(this)->operator=(static_cast<ie_loc_ghost<dim,T>>(cart));
		static_cast<nn_prcs<dim,T>*>(this)->operator=(static_cast<nn_prcs<dim,T>>(cart));
		static_cast<ie_ghost<dim,T>*>(this)->operator=(static_cast<ie_ghost<dim,T>>(cart));
828 829 830 831 832 833 834 835 836 837 838

		sub_domains.swap(cart.sub_domains);
		box_nn_processor.swap(cart.box_nn_processor);
		fine_s.swap(cart.fine_s);
		gr = cart.gr;
		cd = cart.cd;
		domain = cart.domain;
		std::copy(cart.spacing,cart.spacing+3,spacing);

		ghost = cart.ghost;

839 840
		bbox = cart.bbox;
		ss_box = cart.ss_box;
incardon's avatar
incardon committed
841

842
		for (size_t i = 0 ; i < dim ; i++)
843 844 845
			bc[i] = cart.bc[i];

		return *this;
846

847 848 849
		return *this;
	}

850 851 852 853 854 855
	/*! \brief The default grid size
	 *
	 *  The default grid is always an isotropic grid that adapt with the number of processors,
	 *  it define in how many cell it will be divided the space for a particular required minimum
	 *  number of sub-domain
	 *
Pietro Incardona's avatar
Pietro Incardona committed
856 857 858 859
	 * \param n_sub number of subdomains per processors
	 *
	 * \return grid dimension (it is one number because on the other dimensions is the same)
	 *
860 861 862 863 864
	 */
	static size_t getDefaultGrid(size_t n_sub)
	{
		// Calculate the number of sub-sub-domain on
		// each dimension
865
		return openfpm::math::round_big_2(pow(n_sub, 1.0 / dim));
866 867
	}

868
	/*! \brief Given a point return in which processor the particle should go
Pietro Incardona's avatar
Pietro Incardona committed
869 870
	 *
	 * \param p point
incardon's avatar
incardon committed
871 872 873 874
	 *
	 * \return processorID
	 *
	 */
Pietro Incardona's avatar
Pietro Incardona committed
875
	template<typename Mem, typename ofb> size_t inline processorID(encapc<1, Point<dim,T>, Mem> p)
incardon's avatar
incardon committed
876
	{
Pietro Incardona's avatar
Pietro Incardona committed
877
		return fine_s.get(cd.template getCell<ofb>(p));
incardon's avatar
incardon committed
878 879
	}

880
	/*! \brief Given a point return in which processor the particle should go
Pietro Incardona's avatar
Pietro Incardona committed
881 882
	 *
	 * \param p point
incardon's avatar
incardon committed
883
	 *
884
	 * \return processorID
incardon's avatar
incardon committed
885 886
	 *
	 */
887
	size_t inline processorID(const Point<dim,T> &p) const
incardon's avatar
incardon committed
888
	{
incardon's avatar
incardon committed
889
		return fine_s.get(cd.getCell(p));
incardon's avatar
incardon committed
890 891
	}

892
	/*! \brief Given a point return in which processor the particle should go
Pietro Incardona's avatar
Pietro Incardona committed
893 894
	 *
	 * \param p point
incardon's avatar
incardon committed
895 896 897 898
	 *
	 * \return processorID
	 *
	 */
899
	size_t inline processorID(const T (&p)[dim]) const
incardon's avatar
incardon committed
900
	{
incardon's avatar
incardon committed
901
		return fine_s.get(cd.getCell(p));
incardon's avatar
incardon committed
902
	}
incardon's avatar
incardon committed
903

Pietro Incardona's avatar
Pietro Incardona committed
904
	/*! \brief Given a point return in which processor the point/particle should go
incardon's avatar
incardon committed
905
	 *
906 907
	 * Boundary conditions are considered
	 *
Pietro Incardona's avatar
Pietro Incardona committed
908 909
	 * \param p point
	 *
910
	 * \return processorID
incardon's avatar
incardon committed
911 912
	 *
	 */
913
	template<typename Mem> size_t inline processorIDBC(encapc<1, Point<dim,T>, Mem> p)
incardon's avatar
incardon committed
914
	{
915 916 917 918
		Point<dim,T> pt = p;
		applyPointBC(pt);

		return fine_s.get(cd.getCell(pt));
incardon's avatar
incardon committed
919 920
	}

921
	/*! \brief Given a point return in which processor the particle should go
922 923
	 *
	 * Boundary conditions are considered
incardon's avatar
incardon committed
924
	 *
Pietro Incardona's avatar
Pietro Incardona committed
925 926
	 * \param p point
	 *
incardon's avatar
incardon committed
927 928 929
	 * \return processorID
	 *
	 */
Pietro Incardona's avatar
Pietro Incardona committed
930
	template<typename ofb> size_t inline processorIDBC(const Point<dim,T> &p) const
931 932 933
	{
		Point<dim,T> pt = p;
		applyPointBC(pt);
incardon's avatar
incardon committed
934

935 936 937 938 939 940 941
		return fine_s.get(cd.getCell(p));
	}

	/*! \brief Given a point return in which processor the particle should go
	 *
	 * Boundary consition are considered
	 *
Pietro Incardona's avatar
Pietro Incardona committed
942 943
	 * \param p point position
	 *
944 945 946
	 * \return processorID
	 *
	 */
Pietro Incardona's avatar
Pietro Incardona committed
947
	template<typename ofb> size_t inline processorIDBC(const T (&p)[dim]) const
incardon's avatar
incardon committed
948
	{
949 950 951
		Point<dim,T> pt = p;
		applyPointBC(pt);

incardon's avatar
incardon committed
952
		return fine_s.get(cd.getCell(p));
incardon's avatar
incardon committed
953 954
	}

955 956 957 958 959 960 961 962 963 964
	/*! \brief Get the smallest subdivision of the domain on each direction
	 *
	 * \return a box p1 is set to zero
	 *
	 */
	const ::Box<dim,T> & getSmallestSubdivision()
	{
		return ss_box;
	}

965 966 967 968 969 970 971
	/*! \brief Get the periodicity on i dimension
	 *
	 * \param i dimension
	 *
	 * \return the periodicity in direction i
	 *
	 */
972
	inline size_t periodicity(size_t i)
973 974 975 976
	{
		return bc[i];
	}

977 978 979 980 981 982 983 984 985 986 987
	/*! \brief Get the periodicity
	 *
	 *
	 * \return the periodicity
	 *
	 */
	inline const size_t (& periodicity() const) [dim]
	{
		return bc;
	}

incardon's avatar
incardon committed
988 989
	/*! \brief Set the parameter of the decomposition
	 *
990
	 * \param div_ storing into how many sub-sub-domains to decompose on each dimension
991
	 * \param domain_ domain to decompose
Pietro Incardona's avatar
Pietro Incardona committed
992
	 * \param bc boundary conditions
993
	 * \param ghost Ghost size
incardon's avatar
incardon committed
994 995
	 *
	 */
Pietro Incardona's avatar
Pietro Incardona committed
996
	void setParameters(const size_t (& div_)[dim], ::Box<dim,T> domain_, const size_t (& bc)[dim] ,const Ghost<dim,T> & ghost)
incardon's avatar
incardon committed
997
	{
Pietro Incardona's avatar
Pietro Incardona committed
998 999 1000 1001
		// set the boundary conditions
		for (size_t i = 0 ; i < dim ; i++)
			this->bc[i] = bc[i];

incardon's avatar
incardon committed
1002 1003
		// set the ghost
		this->ghost = ghost;
incardon's avatar
incardon committed
1004

1005
		// Set the decomposition parameters
incardon's avatar
incardon committed
1006
		gr.setDimensions(div_);
incardon's avatar
incardon committed
1007
		domain = domain_;
1008
		cd.setDimensions(domain, div_, 0);
incardon's avatar
incardon committed
1009

1010
		// init distribution
1011
		dist.createCartGraph(gr, domain);
1012 1013 1014

	}

Pietro Incardona's avatar
Pietro Incardona committed
1015 1016 1017 1018
	/*! \brief Delete the decomposition and reset the data-structure
	 *
	 *
	 */
1019 1020 1021 1022 1023 1024 1025 1026 1027 1028
	void reset()
	{
		sub_domains.clear();
		box_nn_processor.clear();
		fine_s.clear();
		nn_prcs<dim, T>::reset();
		ie_ghost<dim, T>::reset();
		ie_loc_ghost<dim, T>::reset();
	}

1029 1030 1031 1032 1033
	/*! \brief Start decomposition
	 *
	 */
	void decompose()
	{
1034 1035
		reset();

1036