/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn

Bug Summary

File:	gromacs/mdlib/nbnxn_search.c
Location:	line 2826, column 5
Description:	Value stored to 'work' is never read

Annotated Source Code

1	/*
2	* This file is part of the GROMACS molecular simulation package.
3	*
4	* Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
5	* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6	* and including many others, as listed in the AUTHORS file in the
7	* top-level source directory and at http://www.gromacs.org.
8	*
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34	*/
35
36	#ifdef HAVE_CONFIG_H1
37	#include <config.h>
38	#endif
39
40	#include <math.h>
41	#include <string.h>
42	#include <assert.h>
43
44	#include "gromacs/utility/smalloc.h"
45	#include "types/commrec.h"
46	#include "macros.h"
47	#include "gromacs/math/utilities.h"
48	#include "gromacs/math/vec.h"
49	#include "pbc.h"
50	#include "nbnxn_consts.h"
51	/* nbnxn_internal.h included gromacs/simd/macros.h */
52	#include "nbnxn_internal.h"
53	#ifdef GMX_NBNXN_SIMD
54	#include "gromacs/simd/vector_operations.h"
55	#endif
56	#include "nbnxn_atomdata.h"
57	#include "nbnxn_search.h"
58	#include "gmx_omp_nthreads.h"
59	#include "nrnb.h"
60	#include "ns.h"
61
62	#include "gromacs/fileio/gmxfio.h"
63
64	#ifdef NBNXN_SEARCH_BB_SIMD4
65	/* Always use 4-wide SIMD for bounding box calculations */
66
67	# ifndef GMX_DOUBLE
68	/* Single precision BBs + coordinates, we can also load coordinates with SIMD */
69	# define NBNXN_SEARCH_SIMD4_FLOAT_X_BB
70	# endif
71
72	# if defined NBNXN_SEARCH_SIMD4_FLOAT_X_BB && (GPU_NSUBCELL(222) == 4 \|\| GPU_NSUBCELL(222) == 8)
73	/* Store bounding boxes with x, y and z coordinates in packs of 4 */
74	# define NBNXN_PBB_SIMD4
75	# endif
76
77	/* The packed bounding box coordinate stride is always set to 4.
78	* With AVX we could use 8, but that turns out not to be faster.
79	*/
80	# define STRIDE_PBB4 4
81	# define STRIDE_PBB_2LOG2 2
82
83	#endif /* NBNXN_SEARCH_BB_SIMD4 */
84
85	#ifdef GMX_NBNXN_SIMD
86
87	/* The functions below are macros as they are performance sensitive */
88
89	/* 4x4 list, pack=4: no complex conversion required */
90	/* i-cluster to j-cluster conversion */
91	#define CI_TO_CJ_J4(ci)(ci) (ci)
92	/* cluster index to coordinate array index conversion */
93	#define X_IND_CI_J4(ci)((ci)(34)) ((ci)STRIDE_P4(34))
94	#define X_IND_CJ_J4(cj)((cj)(34)) ((cj)STRIDE_P4(34))
95
96	/* 4x2 list, pack=4: j-cluster size is half the packing width */
97	/* i-cluster to j-cluster conversion */
98	#define CI_TO_CJ_J2(ci)((ci)<<1) ((ci)<<1)
99	/* cluster index to coordinate array index conversion */
100	#define X_IND_CI_J2(ci)((ci)(34)) ((ci)STRIDE_P4(34))
101	#define X_IND_CJ_J2(cj)(((cj)>>1)(34) + ((cj) & 1)(4>>1)) (((cj)>>1)STRIDE_P4(34) + ((cj) & 1)(PACK_X44>>1))
102
103	/* 4x8 list, pack=8: i-cluster size is half the packing width */
104	/* i-cluster to j-cluster conversion */
105	#define CI_TO_CJ_J8(ci)((ci)>>1) ((ci)>>1)
106	/* cluster index to coordinate array index conversion */
107	#define X_IND_CI_J8(ci)(((ci)>>1)(38) + ((ci) & 1)(8>>1)) (((ci)>>1)STRIDE_P8(38) + ((ci) & 1)(PACK_X88>>1))
108	#define X_IND_CJ_J8(cj)((cj)(38)) ((cj)STRIDE_P8(38))
109
110	/* The j-cluster size is matched to the SIMD width */
111	#if GMX_SIMD_REAL_WIDTH4 == 2
112	#define CI_TO_CJ_SIMD_4XN(ci)(ci) CI_TO_CJ_J2(ci)((ci)<<1)
113	#define X_IND_CI_SIMD_4XN(ci)((ci)(34)) X_IND_CI_J2(ci)((ci)(34))
114	#define X_IND_CJ_SIMD_4XN(cj)((cj)(34)) X_IND_CJ_J2(cj)(((cj)>>1)(34) + ((cj) & 1)*(4>>1))
115	#else
116	#if GMX_SIMD_REAL_WIDTH4 == 4
117	#define CI_TO_CJ_SIMD_4XN(ci)(ci) CI_TO_CJ_J4(ci)(ci)
118	#define X_IND_CI_SIMD_4XN(ci)((ci)(34)) X_IND_CI_J4(ci)((ci)(34))
119	#define X_IND_CJ_SIMD_4XN(cj)((cj)(34)) X_IND_CJ_J4(cj)((cj)(34))
120	#else
121	#if GMX_SIMD_REAL_WIDTH4 == 8
122	#define CI_TO_CJ_SIMD_4XN(ci)(ci) CI_TO_CJ_J8(ci)((ci)>>1)
123	#define X_IND_CI_SIMD_4XN(ci)((ci)(34)) X_IND_CI_J8(ci)(((ci)>>1)(38) + ((ci) & 1)*(8>>1))
124	#define X_IND_CJ_SIMD_4XN(cj)((cj)(34)) X_IND_CJ_J8(cj)((cj)(38))
125	/* Half SIMD with j-cluster size */
126	#define CI_TO_CJ_SIMD_2XNN(ci) CI_TO_CJ_J4(ci)(ci)
127	#define X_IND_CI_SIMD_2XNN(ci) X_IND_CI_J4(ci)((ci)(34))
128	#define X_IND_CJ_SIMD_2XNN(cj) X_IND_CJ_J4(cj)((cj)(34))
129	#else
130	#if GMX_SIMD_REAL_WIDTH4 == 16
131	#define CI_TO_CJ_SIMD_2XNN(ci) CI_TO_CJ_J8(ci)((ci)>>1)
132	#define X_IND_CI_SIMD_2XNN(ci) X_IND_CI_J8(ci)(((ci)>>1)(38) + ((ci) & 1)*(8>>1))
133	#define X_IND_CJ_SIMD_2XNN(cj) X_IND_CJ_J8(cj)((cj)(38))
134	#else
135	#error "unsupported GMX_SIMD_REAL_WIDTH"
136	#endif
137	#endif
138	#endif
139	#endif
140
141	#endif /* GMX_NBNXN_SIMD */
142
143
144	#ifdef NBNXN_SEARCH_BB_SIMD4
145	/* Store bounding boxes corners as quadruplets: xxxxyyyyzzzz */
146	#define NBNXN_BBXXXX
147	/* Size of bounding box corners quadruplet */
148	#define NNBSBB_XXXX(234) (NNBSBB_D2DIM3STRIDE_PBB4)
149	#endif
150
151	/* We shift the i-particles backward for PBC.
152	* This leads to more conditionals than shifting forward.
153	* We do this to get more balanced pair lists.
154	*/
155	#define NBNXN_SHIFT_BACKWARD
156
157
158	/* This define is a lazy way to avoid interdependence of the grid
159	* and searching data structures.
160	*/
161	#define NBNXN_NA_SC_MAX((222)8) (GPU_NSUBCELL(222)NBNXN_GPU_CLUSTER_SIZE8)
162
163
164	static void nbs_cycle_clear(nbnxn_cycle_t *cc)
165	{
166	int i;
167
168	for (i = 0; i < enbsCCnr; i++)
169	{
170	cc[i].count = 0;
171	cc[i].c = 0;
172	}
173	}
174
175	static double Mcyc_av(const nbnxn_cycle_t *cc)
176	{
177	return (double)cc->c*1e-6/cc->count;
178	}
179
180	static void nbs_cycle_print(FILE *fp, const nbnxn_search_t nbs)
181	{
182	int n;
183	int t;
184
185	fprintf(fp, "\n");
186	fprintf(fp, "ns %4d grid %4.1f search %4.1f red.f %5.3f",
187	nbs->cc[enbsCCgrid].count,
188	Mcyc_av(&nbs->cc[enbsCCgrid]),
189	Mcyc_av(&nbs->cc[enbsCCsearch]),
190	Mcyc_av(&nbs->cc[enbsCCreducef]));
191
192	if (nbs->nthread_max > 1)
193	{
194	if (nbs->cc[enbsCCcombine].count > 0)
195	{
196	fprintf(fp, " comb %5.2f",
197	Mcyc_av(&nbs->cc[enbsCCcombine]));
198	}
199	fprintf(fp, " s. th");
200	for (t = 0; t < nbs->nthread_max; t++)
201	{
202	fprintf(fp, " %4.1f",
203	Mcyc_av(&nbs->work[t].cc[enbsCCsearch]));
204	}
205	}
206	fprintf(fp, "\n");
207	}
208
209	static void nbnxn_grid_init(nbnxn_grid_t * grid)
210	{
211	grid->cxy_na = NULL((void*)0);
212	grid->cxy_ind = NULL((void*)0);
213	grid->cxy_nalloc = 0;
214	grid->bb = NULL((void*)0);
215	grid->bbj = NULL((void*)0);
216	grid->nc_nalloc = 0;
217	}
218
219	static int get_2log(int n)
220	{
221	int log2;
222
223	log2 = 0;
224	while ((1<<log2) < n)
225	{
226	log2++;
227	}
228	if ((1<<log2) != n)
229	{
230	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 230, "nbnxn na_c (%d) is not a power of 2", n);
231	}
232
233	return log2;
234	}
235
236	static int nbnxn_kernel_to_ci_size(int nb_kernel_type)
237	{
238	switch (nb_kernel_type)
239	{
240	case nbnxnk4x4_PlainC:
241	case nbnxnk4xN_SIMD_4xN:
242	case nbnxnk4xN_SIMD_2xNN:
243	return NBNXN_CPU_CLUSTER_I_SIZE4;
244	case nbnxnk8x8x8_CUDA:
245	case nbnxnk8x8x8_PlainC:
246	/* The cluster size for super/sub lists is only set here.
247	* Any value should work for the pair-search and atomdata code.
248	* The kernels, of course, might require a particular value.
249	*/
250	return NBNXN_GPU_CLUSTER_SIZE8;
251	default:
252	gmx_incons("unknown kernel type")_gmx_error("incons", "unknown kernel type", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 252);
253	}
254
255	return 0;
256	}
257
258	int nbnxn_kernel_to_cj_size(int nb_kernel_type)
259	{
260	int nbnxn_simd_width = 0;
261	int cj_size = 0;
262
263	#ifdef GMX_NBNXN_SIMD
264	nbnxn_simd_width = GMX_SIMD_REAL_WIDTH4;
265	#endif
266
267	switch (nb_kernel_type)
268	{
269	case nbnxnk4x4_PlainC:
270	cj_size = NBNXN_CPU_CLUSTER_I_SIZE4;
271	break;
272	case nbnxnk4xN_SIMD_4xN:
273	cj_size = nbnxn_simd_width;
274	break;
275	case nbnxnk4xN_SIMD_2xNN:
276	cj_size = nbnxn_simd_width/2;
277	break;
278	case nbnxnk8x8x8_CUDA:
279	case nbnxnk8x8x8_PlainC:
280	cj_size = nbnxn_kernel_to_ci_size(nb_kernel_type);
281	break;
282	default:
283	gmx_incons("unknown kernel type")_gmx_error("incons", "unknown kernel type", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 283);
284	}
285
286	return cj_size;
287	}
288
289	static int ci_to_cj(int na_cj_2log, int ci)
290	{
291	switch (na_cj_2log)
292	{
293	case 2: return ci; break;
294	case 1: return (ci<<1); break;
295	case 3: return (ci>>1); break;
296	}
297
298	return 0;
299	}
300
301	gmx_bool nbnxn_kernel_pairlist_simple(int nb_kernel_type)
302	{
303	if (nb_kernel_type == nbnxnkNotSet)
304	{
305	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 305, "Non-bonded kernel type not set for Verlet-style pair-list.");
306	}
307
308	switch (nb_kernel_type)
309	{
310	case nbnxnk8x8x8_CUDA:
311	case nbnxnk8x8x8_PlainC:
312	return FALSE0;
313
314	case nbnxnk4x4_PlainC:
315	case nbnxnk4xN_SIMD_4xN:
316	case nbnxnk4xN_SIMD_2xNN:
317	return TRUE1;
318
319	default:
320	gmx_incons("Invalid nonbonded kernel type passed!")_gmx_error("incons", "Invalid nonbonded kernel type passed!", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 320);
321	return FALSE0;
322	}
323	}
324
325	/* Initializes a single nbnxn_pairlist_t data structure */
326	static void nbnxn_init_pairlist_fep(t_nblist *nl)
327	{
328	nl->type = GMX_NBLIST_INTERACTION_FREE_ENERGY;
329	nl->igeometry = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
330	/* The interaction functions are set in the free energy kernel fuction */
331	nl->ivdw = -1;
332	nl->ivdwmod = -1;
333	nl->ielec = -1;
334	nl->ielecmod = -1;
335
336	nl->maxnri = 0;
337	nl->maxnrj = 0;
338	nl->nri = 0;
339	nl->nrj = 0;
340	nl->iinr = NULL((void*)0);
341	nl->gid = NULL((void*)0);
342	nl->shift = NULL((void*)0);
343	nl->jindex = NULL((void*)0);
344	nl->jjnr = NULL((void*)0);
345	nl->excl_fep = NULL((void*)0);
346
347	}
348
349	void nbnxn_init_search(nbnxn_search_t * nbs_ptr,
350	ivec *n_dd_cells,
351	gmx_domdec_zones_t *zones,
352	gmx_bool bFEP,
353	int nthread_max)
354	{
355	nbnxn_search_t nbs;
356	int d, g, t;
357
358	snew(nbs, 1)(nbs) = save_calloc("nbs", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 358, (1), sizeof(*(nbs)));
359	*nbs_ptr = nbs;
360
361	nbs->bFEP = bFEP;
362
363	nbs->DomDec = (n_dd_cells != NULL((void*)0));
364
365	clear_ivec(nbs->dd_dim);
366	nbs->ngrid = 1;
367	if (nbs->DomDec)
368	{
369	nbs->zones = zones;
370
371	for (d = 0; d < DIM3; d++)
372	{
373	if ((*n_dd_cells)[d] > 1)
374	{
375	nbs->dd_dim[d] = 1;
376	/* Each grid matches a DD zone */
377	nbs->ngrid *= 2;
378	}
379	}
380	}
381
382	snew(nbs->grid, nbs->ngrid)(nbs->grid) = save_calloc("nbs->grid", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 382, (nbs->ngrid), sizeof(*(nbs->grid)));
383	for (g = 0; g < nbs->ngrid; g++)
384	{
385	nbnxn_grid_init(&nbs->grid[g]);
386	}
387	nbs->cell = NULL((void*)0);
388	nbs->cell_nalloc = 0;
389	nbs->a = NULL((void*)0);
390	nbs->a_nalloc = 0;
391
392	nbs->nthread_max = nthread_max;
393
394	/* Initialize the work data structures for each thread */
395	snew(nbs->work, nbs->nthread_max)(nbs->work) = save_calloc("nbs->work", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 395, (nbs->nthread_max), sizeof(*(nbs->work)));
396	for (t = 0; t < nbs->nthread_max; t++)
397	{
398	nbs->work[t].cxy_na = NULL((void*)0);
399	nbs->work[t].cxy_na_nalloc = 0;
400	nbs->work[t].sort_work = NULL((void*)0);
401	nbs->work[t].sort_work_nalloc = 0;
402
403	snew(nbs->work[t].nbl_fep, 1)(nbs->work[t].nbl_fep) = save_calloc("nbs->work[t].nbl_fep" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 403, (1), sizeof(*(nbs->work[t].nbl_fep)));
404	nbnxn_init_pairlist_fep(nbs->work[t].nbl_fep);
405	}
406
407	/* Initialize detailed nbsearch cycle counting */
408	nbs->print_cycles = (getenv("GMX_NBNXN_CYCLE") != 0);
409	nbs->search_count = 0;
410	nbs_cycle_clear(nbs->cc);
411	for (t = 0; t < nbs->nthread_max; t++)
412	{
413	nbs_cycle_clear(nbs->work[t].cc);
414	}
415	}
416
417	static real grid_atom_density(int n, rvec corner0, rvec corner1)
418	{
419	rvec size;
420
421	rvec_sub(corner1, corner0, size);
422
423	return n/(size[XX0]size[YY1]size[ZZ2]);
424	}
425
426	static int set_grid_size_xy(const nbnxn_search_t nbs,
427	nbnxn_grid_t *grid,
428	int dd_zone,
429	int n, rvec corner0, rvec corner1,
430	real atom_density)
431	{
432	rvec size;
433	int na_c;
434	real adens, tlen, tlen_x, tlen_y, nc_max;
435	int t;
436
437	rvec_sub(corner1, corner0, size);
438
439	if (n > grid->na_sc)
440	{
441	/* target cell length */
442	if (grid->bSimple)
443	{
444	/* To minimize the zero interactions, we should make
445	* the largest of the i/j cell cubic.
446	*/
447	na_c = max(grid->na_c, grid->na_cj)(((grid->na_c) > (grid->na_cj)) ? (grid->na_c) : ( grid->na_cj) );
448
449	/* Approximately cubic cells */
450	tlen = pow(na_c/atom_density, 1.0/3.0);
451	tlen_x = tlen;
452	tlen_y = tlen;
453	}
454	else
455	{
456	/* Approximately cubic sub cells */
457	tlen = pow(grid->na_c/atom_density, 1.0/3.0);
458	tlen_x = tlen*GPU_NSUBCELL_X2;
459	tlen_y = tlen*GPU_NSUBCELL_Y2;
460	}
461	/* We round ncx and ncy down, because we get less cell pairs
462	* in the nbsist when the fixed cell dimensions (x,y) are
463	* larger than the variable one (z) than the other way around.
464	*/
465	grid->ncx = max(1, (int)(size[XX]/tlen_x))(((1) > ((int)(size[0]/tlen_x))) ? (1) : ((int)(size[0]/tlen_x )) );
466	grid->ncy = max(1, (int)(size[YY]/tlen_y))(((1) > ((int)(size[1]/tlen_y))) ? (1) : ((int)(size[1]/tlen_y )) );
467	}
468	else
469	{
470	grid->ncx = 1;
471	grid->ncy = 1;
472	}
473
474	grid->sx = size[XX0]/grid->ncx;
475	grid->sy = size[YY1]/grid->ncy;
476	grid->inv_sx = 1/grid->sx;
477	grid->inv_sy = 1/grid->sy;
478
479	if (dd_zone > 0)
480	{
481	/* This is a non-home zone, add an extra row of cells
482	* for particles communicated for bonded interactions.
483	* These can be beyond the cut-off. It doesn't matter where
484	* they end up on the grid, but for performance it's better
485	* if they don't end up in cells that can be within cut-off range.
486	*/
487	grid->ncx++;
488	grid->ncy++;
489	}
490
491	/* We need one additional cell entry for particles moved by DD */
492	if (grid->ncx*grid->ncy+1 > grid->cxy_nalloc)
493	{
494	grid->cxy_nalloc = over_alloc_large(grid->ncxgrid->ncy+1)(int)(1.19(grid->ncx*grid->ncy+1) + 1000);
495	srenew(grid->cxy_na, grid->cxy_nalloc)(grid->cxy_na) = save_realloc("grid->cxy_na", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 495, (grid->cxy_na), (grid->cxy_nalloc), sizeof(*(grid ->cxy_na)));
496	srenew(grid->cxy_ind, grid->cxy_nalloc+1)(grid->cxy_ind) = save_realloc("grid->cxy_ind", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 496, (grid->cxy_ind), (grid->cxy_nalloc+1), sizeof(*( grid->cxy_ind)));
497	}
498	for (t = 0; t < nbs->nthread_max; t++)
499	{
500	if (grid->ncx*grid->ncy+1 > nbs->work[t].cxy_na_nalloc)
501	{
502	nbs->work[t].cxy_na_nalloc = over_alloc_large(grid->ncxgrid->ncy+1)(int)(1.19(grid->ncx*grid->ncy+1) + 1000);
503	srenew(nbs->work[t].cxy_na, nbs->work[t].cxy_na_nalloc)(nbs->work[t].cxy_na) = save_realloc("nbs->work[t].cxy_na" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 503, (nbs->work[t].cxy_na), (nbs->work[t].cxy_na_nalloc ), sizeof(*(nbs->work[t].cxy_na)));
504	}
505	}
506
507	/* Worst case scenario of 1 atom in each last cell */
508	if (grid->na_cj <= grid->na_c)
509	{
510	nc_max = n/grid->na_sc + grid->ncx*grid->ncy;
511	}
512	else
513	{
514	nc_max = n/grid->na_sc + grid->ncxgrid->ncygrid->na_cj/grid->na_c;
515	}
516
517	if (nc_max > grid->nc_nalloc)
518	{
519	grid->nc_nalloc = over_alloc_large(nc_max)(int)(1.19*(nc_max) + 1000);
520	srenew(grid->nsubc, grid->nc_nalloc)(grid->nsubc) = save_realloc("grid->nsubc", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 520, (grid->nsubc), (grid->nc_nalloc), sizeof(*(grid-> nsubc)));
521	srenew(grid->bbcz, grid->nc_nallocNNBSBB_D)(grid->bbcz) = save_realloc("grid->bbcz", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 521, (grid->bbcz), (grid->nc_nalloc2), sizeof(*(grid ->bbcz)));
522
523	sfree_aligned(grid->bb)save_free_aligned("grid->bb", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 523, (grid->bb));
524	/* This snew also zeros the contents, this avoid possible
525	* floating exceptions in SIMD with the unused bb elements.
526	*/
527	if (grid->bSimple)
528	{
529	snew_aligned(grid->bb, grid->nc_nalloc, 16)(grid->bb) = save_calloc_aligned("grid->bb", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 529, (grid->nc_nalloc), sizeof(*(grid->bb)), 16);
530	}
531	else
532	{
533	#ifdef NBNXN_BBXXXX
534	int pbb_nalloc;
535
536	pbb_nalloc = grid->nc_nallocGPU_NSUBCELL(222)/STRIDE_PBB4NNBSBB_XXXX(234);
537	snew_aligned(grid->pbb, pbb_nalloc, 16)(grid->pbb) = save_calloc_aligned("grid->pbb", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 537, (pbb_nalloc), sizeof(*(grid->pbb)), 16);
538	#else
539	snew_aligned(grid->bb, grid->nc_nallocGPU_NSUBCELL, 16)(grid->bb) = save_calloc_aligned("grid->bb", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 539, (grid->nc_nalloc(222)), sizeof(*(grid->bb)), 16 );
540	#endif
541	}
542
543	if (grid->bSimple)
544	{
545	if (grid->na_cj == grid->na_c)
546	{
547	grid->bbj = grid->bb;
548	}
549	else
550	{
551	sfree_aligned(grid->bbj)save_free_aligned("grid->bbj", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 551, (grid->bbj));
552	snew_aligned(grid->bbj, grid->nc_nallocgrid->na_c/grid->na_cj, 16)(grid->bbj) = save_calloc_aligned("grid->bbj", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 552, (grid->nc_nallocgrid->na_c/grid->na_cj), sizeof (*(grid->bbj)), 16);
553	}
554	}
555
556	srenew(grid->flags, grid->nc_nalloc)(grid->flags) = save_realloc("grid->flags", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 556, (grid->flags), (grid->nc_nalloc), sizeof(*(grid-> flags)));
557	if (nbs->bFEP)
558	{
559	srenew(grid->fep, grid->nc_nallocgrid->na_sc/grid->na_c)(grid->fep) = save_realloc("grid->fep", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 559, (grid->fep), (grid->nc_nallocgrid->na_sc/grid ->na_c), sizeof(*(grid->fep)));
560	}
561	}
562
563	copy_rvec(corner0, grid->c0);
564	copy_rvec(corner1, grid->c1);
565
566	return nc_max;
567	}
568
569	/* We need to sort paricles in grid columns on z-coordinate.
570	* As particle are very often distributed homogeneously, we a sorting
571	* algorithm similar to pigeonhole sort. We multiply the z-coordinate
572	* by a factor, cast to an int and try to store in that hole. If the hole
573	* is full, we move this or another particle. A second pass is needed to make
574	* contiguous elements. SORT_GRID_OVERSIZE is the ratio of holes to particles.
575	* 4 is the optimal value for homogeneous particle distribution and allows
576	* for an O(#particles) sort up till distributions were all particles are
577	* concentrated in 1/4 of the space. No NlogN fallback is implemented,
578	* as it can be expensive to detect imhomogeneous particle distributions.
579	* SGSF is the maximum ratio of holes used, in the worst case all particles
580	* end up in the last hole and we need #particles extra holes at the end.
581	*/
582	#define SORT_GRID_OVERSIZE4 4
583	#define SGSF(4 + 1) (SORT_GRID_OVERSIZE4 + 1)
584
585	/* Sort particle index a on coordinates x along dim.
586	* Backwards tells if we want decreasing iso increasing coordinates.
587	* h0 is the minimum of the coordinate range.
588	* invh is the 1/length of the sorting range.
589	* n_per_h (>=n) is the expected average number of particles per 1/invh
590	* sort is the sorting work array.
591	* sort should have a size of at least n_per_h*SORT_GRID_OVERSIZE + n,
592	* or easier, allocate at least n*SGSF elements.
593	*/
594	static void sort_atoms(int dim, gmx_bool Backwards,
595	int gmx_unused__attribute__ ((unused)) dd_zone,
596	int a, int n, rvec x,
597	real h0, real invh, int n_per_h,
598	int *sort)
599	{
600	int nsort, i, c;
601	int zi, zim, zi_min, zi_max;
602	int cp, tmp;
603
604	if (n <= 1)
605	{
606	/* Nothing to do */
607	return;
608	}
609
610	#ifndef NDEBUG1
611	if (n > n_per_h)
612	{
613	gmx_incons("n > n_per_h")_gmx_error("incons", "n > n_per_h", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 613);
614	}
615	#endif
616
617	/* Transform the inverse range height into the inverse hole height */
618	invh = n_per_hSORT_GRID_OVERSIZE4;
619
620	/* Set nsort to the maximum possible number of holes used.
621	* In worst case all n elements end up in the last bin.
622	*/
623	nsort = n_per_h*SORT_GRID_OVERSIZE4 + n;
624
625	/* Determine the index range used, so we can limit it for the second pass */
626	zi_min = INT_MAX2147483647;
627	zi_max = -1;
628
629	/* Sort the particles using a simple index sort */
630	for (i = 0; i < n; i++)
631	{
632	/* The cast takes care of float-point rounding effects below zero.
633	* This code assumes particles are less than 1/SORT_GRID_OVERSIZE
634	* times the box height out of the box.
635	*/
636	zi = (int)((x[a[i]][dim] - h0)*invh);
637
638	#ifndef NDEBUG1
639	/* As we can have rounding effect, we use > iso >= here */
640	if (zi < 0 \|\| (dd_zone == 0 && zi > n_per_h*SORT_GRID_OVERSIZE4))
641	{
642	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 642, "(int)((x[%d][%c]=%f - %f)%f) = %d, not in 0 - %d%d\n",
643	a[i], 'x'+dim, x[a[i]][dim], h0, invh, zi,
644	n_per_h, SORT_GRID_OVERSIZE4);
645	}
646	#endif
647
648	/* In a non-local domain, particles communcated for bonded interactions
649	* can be far beyond the grid size, which is set by the non-bonded
650	* cut-off distance. We sort such particles into the last cell.
651	*/
652	if (zi > n_per_h*SORT_GRID_OVERSIZE4)
653	{
654	zi = n_per_h*SORT_GRID_OVERSIZE4;
655	}
656
657	/* Ideally this particle should go in sort cell zi,
658	* but that might already be in use,
659	* in that case find the first empty cell higher up
660	*/
661	if (sort[zi] < 0)
662	{
663	sort[zi] = a[i];
664	zi_min = min(zi_min, zi)(((zi_min) < (zi)) ? (zi_min) : (zi) );
665	zi_max = max(zi_max, zi)(((zi_max) > (zi)) ? (zi_max) : (zi) );
666	}
667	else
668	{
669	/* We have multiple atoms in the same sorting slot.
670	* Sort on real z for minimal bounding box size.
671	* There is an extra check for identical z to ensure
672	* well-defined output order, independent of input order
673	* to ensure binary reproducibility after restarts.
674	*/
675	while (sort[zi] >= 0 && ( x[a[i]][dim] > x[sort[zi]][dim] \|\|
676	(x[a[i]][dim] == x[sort[zi]][dim] &&
677	a[i] > sort[zi])))
678	{
679	zi++;
680	}
681
682	if (sort[zi] >= 0)
683	{
684	/* Shift all elements by one slot until we find an empty slot */
685	cp = sort[zi];
686	zim = zi + 1;
687	while (sort[zim] >= 0)
688	{
689	tmp = sort[zim];
690	sort[zim] = cp;
691	cp = tmp;
692	zim++;
693	}
694	sort[zim] = cp;
695	zi_max = max(zi_max, zim)(((zi_max) > (zim)) ? (zi_max) : (zim) );
696	}
697	sort[zi] = a[i];
698	zi_max = max(zi_max, zi)(((zi_max) > (zi)) ? (zi_max) : (zi) );
699	}
700	}
701
702	c = 0;
703	if (!Backwards)
704	{
705	for (zi = 0; zi < nsort; zi++)
706	{
707	if (sort[zi] >= 0)
708	{
709	a[c++] = sort[zi];
710	sort[zi] = -1;
711	}
712	}
713	}
714	else
715	{
716	for (zi = zi_max; zi >= zi_min; zi--)
717	{
718	if (sort[zi] >= 0)
719	{
720	a[c++] = sort[zi];
721	sort[zi] = -1;
722	}
723	}
724	}
725	if (c < n)
726	{
727	gmx_incons("Lost particles while sorting")_gmx_error("incons", "Lost particles while sorting", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 727);
728	}
729	}
730
731	#ifdef GMX_DOUBLE
732	#define R2F_D(x)(x) ((float)((x) >= 0 ? ((1-GMX_FLOAT_EPS5.96046448E-08)(x)) : ((1+GMX_FLOAT_EPS5.96046448E-08)(x))))
733	#define R2F_U(x)(x) ((float)((x) >= 0 ? ((1+GMX_FLOAT_EPS5.96046448E-08)(x)) : ((1-GMX_FLOAT_EPS5.96046448E-08)(x))))
734	#else
735	#define R2F_D(x)(x) (x)
736	#define R2F_U(x)(x) (x)
737	#endif
738
739	/* Coordinate order x,y,z, bb order xyz0 */
740	static void calc_bounding_box(int na, int stride, const real x, nbnxn_bb_t bb)
741	{
742	int i, j;
743	real xl, xh, yl, yh, zl, zh;
744
745	i = 0;
746	xl = x[i+XX0];
747	xh = x[i+XX0];
748	yl = x[i+YY1];
749	yh = x[i+YY1];
750	zl = x[i+ZZ2];
751	zh = x[i+ZZ2];
752	i += stride;
753	for (j = 1; j < na; j++)
754	{
755	xl = min(xl, x[i+XX])(((xl) < (x[i+0])) ? (xl) : (x[i+0]) );
756	xh = max(xh, x[i+XX])(((xh) > (x[i+0])) ? (xh) : (x[i+0]) );
757	yl = min(yl, x[i+YY])(((yl) < (x[i+1])) ? (yl) : (x[i+1]) );
758	yh = max(yh, x[i+YY])(((yh) > (x[i+1])) ? (yh) : (x[i+1]) );
759	zl = min(zl, x[i+ZZ])(((zl) < (x[i+2])) ? (zl) : (x[i+2]) );
760	zh = max(zh, x[i+ZZ])(((zh) > (x[i+2])) ? (zh) : (x[i+2]) );
761	i += stride;
762	}
763	/* Note: possible double to float conversion here */
764	bb->lower[BB_X0] = R2F_D(xl)(xl);
765	bb->lower[BB_Y1] = R2F_D(yl)(yl);
766	bb->lower[BB_Z2] = R2F_D(zl)(zl);
767	bb->upper[BB_X0] = R2F_U(xh)(xh);
768	bb->upper[BB_Y1] = R2F_U(yh)(yh);
769	bb->upper[BB_Z2] = R2F_U(zh)(zh);
770	}
771
772	/* Packed coordinates, bb order xyz0 */
773	static void calc_bounding_box_x_x4(int na, const real x, nbnxn_bb_t bb)
774	{
775	int j;
776	real xl, xh, yl, yh, zl, zh;
777
778	xl = x[XX0*PACK_X44];
779	xh = x[XX0*PACK_X44];
780	yl = x[YY1*PACK_X44];
781	yh = x[YY1*PACK_X44];
782	zl = x[ZZ2*PACK_X44];
783	zh = x[ZZ2*PACK_X44];
784	for (j = 1; j < na; j++)
785	{
786	xl = min(xl, x[j+XXPACK_X4])(((xl) < (x[j+04])) ? (xl) : (x[j+0*4]) );
787	xh = max(xh, x[j+XXPACK_X4])(((xh) > (x[j+04])) ? (xh) : (x[j+0*4]) );
788	yl = min(yl, x[j+YYPACK_X4])(((yl) < (x[j+14])) ? (yl) : (x[j+1*4]) );
789	yh = max(yh, x[j+YYPACK_X4])(((yh) > (x[j+14])) ? (yh) : (x[j+1*4]) );
790	zl = min(zl, x[j+ZZPACK_X4])(((zl) < (x[j+24])) ? (zl) : (x[j+2*4]) );
791	zh = max(zh, x[j+ZZPACK_X4])(((zh) > (x[j+24])) ? (zh) : (x[j+2*4]) );
792	}
793	/* Note: possible double to float conversion here */
794	bb->lower[BB_X0] = R2F_D(xl)(xl);
795	bb->lower[BB_Y1] = R2F_D(yl)(yl);
796	bb->lower[BB_Z2] = R2F_D(zl)(zl);
797	bb->upper[BB_X0] = R2F_U(xh)(xh);
798	bb->upper[BB_Y1] = R2F_U(yh)(yh);
799	bb->upper[BB_Z2] = R2F_U(zh)(zh);
800	}
801
802	/* Packed coordinates, bb order xyz0 */
803	static void calc_bounding_box_x_x8(int na, const real x, nbnxn_bb_t bb)
804	{
805	int j;
806	real xl, xh, yl, yh, zl, zh;
807
808	xl = x[XX0*PACK_X88];
809	xh = x[XX0*PACK_X88];
810	yl = x[YY1*PACK_X88];
811	yh = x[YY1*PACK_X88];
812	zl = x[ZZ2*PACK_X88];
813	zh = x[ZZ2*PACK_X88];
814	for (j = 1; j < na; j++)
815	{
816	xl = min(xl, x[j+XXPACK_X8])(((xl) < (x[j+08])) ? (xl) : (x[j+0*8]) );
817	xh = max(xh, x[j+XXPACK_X8])(((xh) > (x[j+08])) ? (xh) : (x[j+0*8]) );
818	yl = min(yl, x[j+YYPACK_X8])(((yl) < (x[j+18])) ? (yl) : (x[j+1*8]) );
819	yh = max(yh, x[j+YYPACK_X8])(((yh) > (x[j+18])) ? (yh) : (x[j+1*8]) );
820	zl = min(zl, x[j+ZZPACK_X8])(((zl) < (x[j+28])) ? (zl) : (x[j+2*8]) );
821	zh = max(zh, x[j+ZZPACK_X8])(((zh) > (x[j+28])) ? (zh) : (x[j+2*8]) );
822	}
823	/* Note: possible double to float conversion here */
824	bb->lower[BB_X0] = R2F_D(xl)(xl);
825	bb->lower[BB_Y1] = R2F_D(yl)(yl);
826	bb->lower[BB_Z2] = R2F_D(zl)(zl);
827	bb->upper[BB_X0] = R2F_U(xh)(xh);
828	bb->upper[BB_Y1] = R2F_U(yh)(yh);
829	bb->upper[BB_Z2] = R2F_U(zh)(zh);
830	}
831
832	/* Packed coordinates, bb order xyz0 */
833	static void calc_bounding_box_x_x4_halves(int na, const real *x,
834	nbnxn_bb_t bb, nbnxn_bb_t bbj)
835	{
836	calc_bounding_box_x_x4(min(na, 2)(((na) < (2)) ? (na) : (2) ), x, bbj);
837
838	if (na > 2)
839	{
840	calc_bounding_box_x_x4(min(na-2, 2)(((na-2) < (2)) ? (na-2) : (2) ), x+(PACK_X44>>1), bbj+1);
841	}
842	else
843	{
844	/* Set the "empty" bounding box to the same as the first one,
845	* so we don't need to treat special cases in the rest of the code.
846	*/
847	#ifdef NBNXN_SEARCH_BB_SIMD4
848	gmx_simd4_store_f_mm_store_ps(&bbj[1].lower[0], gmx_simd4_load_f_mm_load_ps(&bbj[0].lower[0]));
849	gmx_simd4_store_f_mm_store_ps(&bbj[1].upper[0], gmx_simd4_load_f_mm_load_ps(&bbj[0].upper[0]));
850	#else
851	bbj[1] = bbj[0];
852	#endif
853	}
854
855	#ifdef NBNXN_SEARCH_BB_SIMD4
856	gmx_simd4_store_f_mm_store_ps(&bb->lower[0],
857	gmx_simd4_min_f_mm_min_ps(gmx_simd4_load_f_mm_load_ps(&bbj[0].lower[0]),
858	gmx_simd4_load_f_mm_load_ps(&bbj[1].lower[0])));
859	gmx_simd4_store_f_mm_store_ps(&bb->upper[0],
860	gmx_simd4_max_f_mm_max_ps(gmx_simd4_load_f_mm_load_ps(&bbj[0].upper[0]),
861	gmx_simd4_load_f_mm_load_ps(&bbj[1].upper[0])));
862	#else
863	{
864	int i;
865
866	for (i = 0; i < NNBSBB_C4; i++)
867	{
868	bb->lower[i] = min(bbj[0].lower[i], bbj[1].lower[i])(((bbj[0].lower[i]) < (bbj[1].lower[i])) ? (bbj[0].lower[i ]) : (bbj[1].lower[i]) );
869	bb->upper[i] = max(bbj[0].upper[i], bbj[1].upper[i])(((bbj[0].upper[i]) > (bbj[1].upper[i])) ? (bbj[0].upper[i ]) : (bbj[1].upper[i]) );
870	}
871	}
872	#endif
873	}
874
875	#ifdef NBNXN_SEARCH_BB_SIMD4
876
877	/* Coordinate order xyz, bb order xxxxyyyyzzzz */
878	static void calc_bounding_box_xxxx(int na, int stride, const real x, float bb)
879	{
880	int i, j;
881	real xl, xh, yl, yh, zl, zh;
882
883	i = 0;
884	xl = x[i+XX0];
885	xh = x[i+XX0];
886	yl = x[i+YY1];
887	yh = x[i+YY1];
888	zl = x[i+ZZ2];
889	zh = x[i+ZZ2];
890	i += stride;
891	for (j = 1; j < na; j++)
892	{
893	xl = min(xl, x[i+XX])(((xl) < (x[i+0])) ? (xl) : (x[i+0]) );
894	xh = max(xh, x[i+XX])(((xh) > (x[i+0])) ? (xh) : (x[i+0]) );
895	yl = min(yl, x[i+YY])(((yl) < (x[i+1])) ? (yl) : (x[i+1]) );
896	yh = max(yh, x[i+YY])(((yh) > (x[i+1])) ? (yh) : (x[i+1]) );
897	zl = min(zl, x[i+ZZ])(((zl) < (x[i+2])) ? (zl) : (x[i+2]) );
898	zh = max(zh, x[i+ZZ])(((zh) > (x[i+2])) ? (zh) : (x[i+2]) );
899	i += stride;
900	}
901	/* Note: possible double to float conversion here */
902	bb[0*STRIDE_PBB4] = R2F_D(xl)(xl);
903	bb[1*STRIDE_PBB4] = R2F_D(yl)(yl);
904	bb[2*STRIDE_PBB4] = R2F_D(zl)(zl);
905	bb[3*STRIDE_PBB4] = R2F_U(xh)(xh);
906	bb[4*STRIDE_PBB4] = R2F_U(yh)(yh);
907	bb[5*STRIDE_PBB4] = R2F_U(zh)(zh);
908	}
909
910	#endif /* NBNXN_SEARCH_BB_SIMD4 */
911
912	#ifdef NBNXN_SEARCH_SIMD4_FLOAT_X_BB
913
914	/* Coordinate order xyz?, bb order xyz0 */
915	static void calc_bounding_box_simd4(int na, const float x, nbnxn_bb_t bb)
916	{
917	gmx_simd4_float_t__m128 bb_0_S, bb_1_S;
918	gmx_simd4_float_t__m128 x_S;
919
920	int i;
921
922	bb_0_S = gmx_simd4_load_f_mm_load_ps(x);
923	bb_1_S = bb_0_S;
924
925	for (i = 1; i < na; i++)
926	{
927	x_S = gmx_simd4_load_f_mm_load_ps(x+i*NNBSBB_C4);
928	bb_0_S = gmx_simd4_min_f_mm_min_ps(bb_0_S, x_S);
929	bb_1_S = gmx_simd4_max_f_mm_max_ps(bb_1_S, x_S);
930	}
931
932	gmx_simd4_store_f_mm_store_ps(&bb->lower[0], bb_0_S);
933	gmx_simd4_store_f_mm_store_ps(&bb->upper[0], bb_1_S);
934	}
935
936	/* Coordinate order xyz?, bb order xxxxyyyyzzzz */
937	static void calc_bounding_box_xxxx_simd4(int na, const float *x,
938	nbnxn_bb_t *bb_work_aligned,
939	real *bb)
940	{
941	calc_bounding_box_simd4(na, x, bb_work_aligned);
942
943	bb[0*STRIDE_PBB4] = bb_work_aligned->lower[BB_X0];
944	bb[1*STRIDE_PBB4] = bb_work_aligned->lower[BB_Y1];
945	bb[2*STRIDE_PBB4] = bb_work_aligned->lower[BB_Z2];
946	bb[3*STRIDE_PBB4] = bb_work_aligned->upper[BB_X0];
947	bb[4*STRIDE_PBB4] = bb_work_aligned->upper[BB_Y1];
948	bb[5*STRIDE_PBB4] = bb_work_aligned->upper[BB_Z2];
949	}
950
951	#endif /* NBNXN_SEARCH_SIMD4_FLOAT_X_BB */
952
953
954	/* Combines pairs of consecutive bounding boxes */
955	static void combine_bounding_box_pairs(nbnxn_grid_t grid, const nbnxn_bb_t bb)
956	{
957	int i, j, sc2, nc2, c2;
958
959	for (i = 0; i < grid->ncx*grid->ncy; i++)
960	{
961	/* Starting bb in a column is expected to be 2-aligned */
962	sc2 = grid->cxy_ind[i]>>1;
963	/* For odd numbers skip the last bb here */
964	nc2 = (grid->cxy_na[i]+3)>>(2+1);
965	for (c2 = sc2; c2 < sc2+nc2; c2++)
966	{
967	#ifdef NBNXN_SEARCH_BB_SIMD4
968	gmx_simd4_float_t__m128 min_S, max_S;
969
970	min_S = gmx_simd4_min_f_mm_min_ps(gmx_simd4_load_f_mm_load_ps(&bb[c2*2+0].lower[0]),
971	gmx_simd4_load_f_mm_load_ps(&bb[c2*2+1].lower[0]));
972	max_S = gmx_simd4_max_f_mm_max_ps(gmx_simd4_load_f_mm_load_ps(&bb[c2*2+0].upper[0]),
973	gmx_simd4_load_f_mm_load_ps(&bb[c2*2+1].upper[0]));
974	gmx_simd4_store_f_mm_store_ps(&grid->bbj[c2].lower[0], min_S);
975	gmx_simd4_store_f_mm_store_ps(&grid->bbj[c2].upper[0], max_S);
976	#else
977	for (j = 0; j < NNBSBB_C4; j++)
978	{
979	grid->bbj[c2].lower[j] = min(bb[c22+0].lower[j],(((bb[c22+0].lower[j]) < (bb[c22+1].lower[j])) ? (bb[c2 2+0].lower[j]) : (bb[c2*2+1].lower[j]) )
980	bb[c22+1].lower[j])(((bb[c22+0].lower[j]) < (bb[c22+1].lower[j])) ? (bb[c2 2+0].lower[j]) : (bb[c2*2+1].lower[j]) );
981	grid->bbj[c2].upper[j] = max(bb[c22+0].upper[j],(((bb[c22+0].upper[j]) > (bb[c22+1].upper[j])) ? (bb[c2 2+0].upper[j]) : (bb[c2*2+1].upper[j]) )
982	bb[c22+1].upper[j])(((bb[c22+0].upper[j]) > (bb[c22+1].upper[j])) ? (bb[c2 2+0].upper[j]) : (bb[c2*2+1].upper[j]) );
983	}
984	#endif
985	}
986	if (((grid->cxy_na[i]+3)>>2) & 1)
987	{
988	/* The bb count in this column is odd: duplicate the last bb */
989	for (j = 0; j < NNBSBB_C4; j++)
990	{
991	grid->bbj[c2].lower[j] = bb[c2*2].lower[j];
992	grid->bbj[c2].upper[j] = bb[c2*2].upper[j];
993	}
994	}
995	}
996	}
997
998
999	/* Prints the average bb size, used for debug output */
1000	static void print_bbsizes_simple(FILE *fp,
1001	const nbnxn_search_t nbs,
1002	const nbnxn_grid_t *grid)
1003	{
1004	int c, d;
1005	dvec ba;
1006
1007	clear_dvec(ba);
1008	for (c = 0; c < grid->nc; c++)
1009	{
1010	for (d = 0; d < DIM3; d++)
1011	{
1012	ba[d] += grid->bb[c].upper[d] - grid->bb[c].lower[d];
1013	}
1014	}
1015	dsvmul(1.0/grid->nc, ba, ba);
1016
1017	fprintf(fp, "ns bb: %4.2f %4.2f %4.2f %4.2f %4.2f %4.2f rel %4.2f %4.2f %4.2f\n",
1018	nbs->box[XX0][XX0]/grid->ncx,
1019	nbs->box[YY1][YY1]/grid->ncy,
1020	nbs->box[ZZ2][ZZ2]grid->ncxgrid->ncy/grid->nc,
1021	ba[XX0], ba[YY1], ba[ZZ2],
1022	ba[XX0]*grid->ncx/nbs->box[XX0][XX0],
1023	ba[YY1]*grid->ncy/nbs->box[YY1][YY1],
1024	ba[ZZ2]grid->nc/(grid->ncxgrid->ncy*nbs->box[ZZ2][ZZ2]));
1025	}
1026
1027	/* Prints the average bb size, used for debug output */
1028	static void print_bbsizes_supersub(FILE *fp,
1029	const nbnxn_search_t nbs,
1030	const nbnxn_grid_t *grid)
1031	{
1032	int ns, c, s;
1033	dvec ba;
1034
1035	clear_dvec(ba);
1036	ns = 0;
1037	for (c = 0; c < grid->nc; c++)
1038	{
1039	#ifdef NBNXN_BBXXXX
1040	for (s = 0; s < grid->nsubc[c]; s += STRIDE_PBB4)
1041	{
1042	int cs_w, i, d;
1043
1044	cs_w = (cGPU_NSUBCELL(22*2) + s)/STRIDE_PBB4;
1045	for (i = 0; i < STRIDE_PBB4; i++)
1046	{
1047	for (d = 0; d < DIM3; d++)
1048	{
1049	ba[d] +=
1050	grid->pbb[cs_wNNBSBB_XXXX(234)+(DIM3+d)STRIDE_PBB4+i] -
1051	grid->pbb[cs_wNNBSBB_XXXX(234)+ d STRIDE_PBB4+i];
1052	}
1053	}
1054	}
1055	#else
1056	for (s = 0; s < grid->nsubc[c]; s++)
1057	{
1058	int cs, d;
1059
1060	cs = cGPU_NSUBCELL(22*2) + s;
1061	for (d = 0; d < DIM3; d++)
1062	{
1063	ba[d] += grid->bb[cs].upper[d] - grid->bb[cs].lower[d];
1064	}
1065	}
1066	#endif
1067	ns += grid->nsubc[c];
1068	}
1069	dsvmul(1.0/ns, ba, ba);
1070
1071	fprintf(fp, "ns bb: %4.2f %4.2f %4.2f %4.2f %4.2f %4.2f rel %4.2f %4.2f %4.2f\n",
1072	nbs->box[XX0][XX0]/(grid->ncx*GPU_NSUBCELL_X2),
1073	nbs->box[YY1][YY1]/(grid->ncy*GPU_NSUBCELL_Y2),
1074	nbs->box[ZZ2][ZZ2]grid->ncxgrid->ncy/(grid->nc*GPU_NSUBCELL_Z2),
1075	ba[XX0], ba[YY1], ba[ZZ2],
1076	ba[XX0]grid->ncxGPU_NSUBCELL_X2/nbs->box[XX0][XX0],
1077	ba[YY1]grid->ncyGPU_NSUBCELL_Y2/nbs->box[YY1][YY1],
1078	ba[ZZ2]grid->ncGPU_NSUBCELL_Z2/(grid->ncxgrid->ncynbs->box[ZZ2][ZZ2]));
1079	}
1080
1081	/* Potentially sorts atoms on LJ coefficients !=0 and ==0.
1082	* Also sets interaction flags.
1083	*/
1084	void sort_on_lj(int na_c,
1085	int a0, int a1, const int *atinfo,
1086	int *order,
1087	int *flags)
1088	{
1089	int subc, s, a, n1, n2, a_lj_max, i, j;
1090	int sort1[NBNXN_NA_SC_MAX((222)8)/GPU_NSUBCELL(22*2)];
1091	int sort2[NBNXN_NA_SC_MAX((222)8)/GPU_NSUBCELL(22*2)];
1092	gmx_bool haveQ, bFEP;
1093
1094	*flags = 0;
1095
1096	subc = 0;
1097	for (s = a0; s < a1; s += na_c)
1098	{
1099	/* Make lists for this (sub-)cell on atoms with and without LJ */
1100	n1 = 0;
1101	n2 = 0;
1102	haveQ = FALSE0;
1103	a_lj_max = -1;
1104	for (a = s; a < min(s+na_c, a1)(((s+na_c) < (a1)) ? (s+na_c) : (a1) ); a++)
1105	{
1106	haveQ = haveQ \|\| GET_CGINFO_HAS_Q(atinfo[order[a]])( (atinfo[order[a]]) & (1<<24));
1107
1108	if (GET_CGINFO_HAS_VDW(atinfo[order[a]])( (atinfo[order[a]]) & (1<<23)))
1109	{
1110	sort1[n1++] = order[a];
1111	a_lj_max = a;
1112	}
1113	else
1114	{
1115	sort2[n2++] = order[a];
1116	}
1117	}
1118
1119	/* If we don't have atoms with LJ, there's nothing to sort */
1120	if (n1 > 0)
1121	{
1122	flags \|= NBNXN_CI_DO_LJ(subc)(1<<(7+3(subc)));
1123
1124	if (2*n1 <= na_c)
1125	{
1126	/* Only sort when strictly necessary. Ordering particles
1127	* Ordering particles can lead to less accurate summation
1128	* due to rounding, both for LJ and Coulomb interactions.
1129	*/
1130	if (2*(a_lj_max - s) >= na_c)
1131	{
1132	for (i = 0; i < n1; i++)
1133	{
1134	order[a0+i] = sort1[i];
1135	}
1136	for (j = 0; j < n2; j++)
1137	{
1138	order[a0+n1+j] = sort2[j];
1139	}
1140	}
1141
1142	flags \|= NBNXN_CI_HALF_LJ(subc)(1<<(8+3(subc)));
1143	}
1144	}
1145	if (haveQ)
1146	{
1147	flags \|= NBNXN_CI_DO_COUL(subc)(1<<(9+3(subc)));
1148	}
1149	subc++;
1150	}
1151	}
1152
1153	/* Fill a pair search cell with atoms.
1154	* Potentially sorts atoms and sets the interaction flags.
1155	*/
1156	void fill_cell(const nbnxn_search_t nbs,
1157	nbnxn_grid_t *grid,
1158	nbnxn_atomdata_t *nbat,
1159	int a0, int a1,
1160	const int *atinfo,
1161	rvec *x,
1162	int sx, int sy, int sz,
1163	nbnxn_bb_t gmx_unused__attribute__ ((unused)) *bb_work_aligned)
1164	{
1165	int na, a;
1166	size_t offset;
1167	nbnxn_bb_t *bb_ptr;
1168	#ifdef NBNXN_BBXXXX
1169	float *pbb_ptr;
1170	#endif
1171
1172	na = a1 - a0;
1173
1174	if (grid->bSimple)
1175	{
1176	sort_on_lj(grid->na_c, a0, a1, atinfo, nbs->a,
1177	grid->flags+(a0>>grid->na_c_2log)-grid->cell0);
1178	}
1179
1180	if (nbs->bFEP)
1181	{
1182	/* Set the fep flag for perturbed atoms in this (sub-)cell */
1183	int c, at;
1184
1185	/* The grid-local cluster/(sub-)cell index */
1186	c = (a0 >> grid->na_c_2log) - grid->cell0(grid->bSimple ? 1 : GPU_NSUBCELL(22*2));
1187	grid->fep[c] = 0;
1188	for (at = a0; at < a1; at++)
1189	{
1190	if (nbs->a[at] >= 0 && GET_CGINFO_FEP(atinfo[nbs->a[at]])( (atinfo[nbs->a[at]]) & (1<<15)))
1191	{
1192	grid->fep[c] \|= (1 << (at - a0));
1193	}
1194	}
1195	}
1196
1197	/* Now we have sorted the atoms, set the cell indices */
1198	for (a = a0; a < a1; a++)
1199	{
1200	nbs->cell[nbs->a[a]] = a;
1201	}
1202
1203	copy_rvec_to_nbat_real(nbs->a+a0, a1-a0, grid->na_c, x,
1204	nbat->XFormat, nbat->x, a0,
1205	sx, sy, sz);
1206
1207	if (nbat->XFormat == nbatX4)
1208	{
1209	/* Store the bounding boxes as xyz.xyz. */
1210	offset = (a0 - grid->cell0*grid->na_sc) >> grid->na_c_2log;
1211	bb_ptr = grid->bb + offset;
1212
1213	#if defined GMX_NBNXN_SIMD && GMX_SIMD_REAL_WIDTH4 == 2
1214	if (2*grid->na_cj == grid->na_c)
1215	{
1216	calc_bounding_box_x_x4_halves(na, nbat->x+X4_IND_A(a0)((34)((a0) >> 2) + ((a0) & (4 - 1))), bb_ptr,
1217	grid->bbj+offset*2);
1218	}
1219	else
1220	#endif
1221	{
1222	calc_bounding_box_x_x4(na, nbat->x+X4_IND_A(a0)((34)((a0) >> 2) + ((a0) & (4 - 1))), bb_ptr);
1223	}
1224	}
1225	else if (nbat->XFormat == nbatX8)
1226	{
1227	/* Store the bounding boxes as xyz.xyz. */
1228	offset = (a0 - grid->cell0*grid->na_sc) >> grid->na_c_2log;
1229	bb_ptr = grid->bb + offset;
1230
1231	calc_bounding_box_x_x8(na, nbat->x+X8_IND_A(a0)((38)((a0) >> 3) + ((a0) & (8 - 1))), bb_ptr);
1232	}
1233	#ifdef NBNXN_BBXXXX
1234	else if (!grid->bSimple)
1235	{
1236	/* Store the bounding boxes in a format convenient
1237	* for SIMD4 calculations: xxxxyyyyzzzz...
1238	*/
1239	pbb_ptr =
1240	grid->pbb +
1241	((a0-grid->cell0grid->na_sc)>>(grid->na_c_2log+STRIDE_PBB_2LOG2))NNBSBB_XXXX(234) +
1242	(((a0-grid->cell0*grid->na_sc)>>grid->na_c_2log) & (STRIDE_PBB4-1));
1243
1244	#ifdef NBNXN_SEARCH_SIMD4_FLOAT_X_BB
1245	if (nbat->XFormat == nbatXYZQ)
1246	{
1247	calc_bounding_box_xxxx_simd4(na, nbat->x+a0*nbat->xstride,
1248	bb_work_aligned, pbb_ptr);
1249	}
1250	else
1251	#endif
1252	{
1253	calc_bounding_box_xxxx(na, nbat->xstride, nbat->x+a0*nbat->xstride,
1254	pbb_ptr);
1255	}
1256	if (gmx_debug_at)
1257	{
1258	fprintf(debug, "%2d %2d %2d bb %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f\n",
1259	sx, sy, sz,
1260	pbb_ptr[0STRIDE_PBB4], pbb_ptr[3STRIDE_PBB4],
1261	pbb_ptr[1STRIDE_PBB4], pbb_ptr[4STRIDE_PBB4],
1262	pbb_ptr[2STRIDE_PBB4], pbb_ptr[5STRIDE_PBB4]);
1263	}
1264	}
1265	#endif
1266	else
1267	{
1268	/* Store the bounding boxes as xyz.xyz. */
1269	bb_ptr = grid->bb+((a0-grid->cell0*grid->na_sc)>>grid->na_c_2log);
1270
1271	calc_bounding_box(na, nbat->xstride, nbat->x+a0*nbat->xstride,
1272	bb_ptr);
1273
1274	if (gmx_debug_at)
1275	{
1276	int bbo;
1277	bbo = (a0 - grid->cell0*grid->na_sc)/grid->na_c;
1278	fprintf(debug, "%2d %2d %2d bb %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f\n",
1279	sx, sy, sz,
1280	grid->bb[bbo].lower[BB_X0],
1281	grid->bb[bbo].lower[BB_Y1],
1282	grid->bb[bbo].lower[BB_Z2],
1283	grid->bb[bbo].upper[BB_X0],
1284	grid->bb[bbo].upper[BB_Y1],
1285	grid->bb[bbo].upper[BB_Z2]);
1286	}
1287	}
1288	}
1289
1290	/* Spatially sort the atoms within one grid column */
1291	static void sort_columns_simple(const nbnxn_search_t nbs,
1292	int dd_zone,
1293	nbnxn_grid_t *grid,
1294	int a0, int a1,
1295	const int *atinfo,
1296	rvec *x,
1297	nbnxn_atomdata_t *nbat,
1298	int cxy_start, int cxy_end,
1299	int *sort_work)
1300	{
1301	int cxy;
1302	int cx, cy, cz, ncz, cfilled, c;
1303	int na, ash, ind, a;
1304	int na_c, ash_c;
1305
1306	if (debug)
1307	{
1308	fprintf(debug, "cell0 %d sorting columns %d - %d, atoms %d - %d\n",
1309	grid->cell0, cxy_start, cxy_end, a0, a1);
1310	}
1311
1312	/* Sort the atoms within each x,y column in 3 dimensions */
1313	for (cxy = cxy_start; cxy < cxy_end; cxy++)
1314	{
1315	cx = cxy/grid->ncy;
1316	cy = cxy - cx*grid->ncy;
1317
1318	na = grid->cxy_na[cxy];
1319	ncz = grid->cxy_ind[cxy+1] - grid->cxy_ind[cxy];
1320	ash = (grid->cell0 + grid->cxy_ind[cxy])*grid->na_sc;
1321
1322	/* Sort the atoms within each x,y column on z coordinate */
1323	sort_atoms(ZZ2, FALSE0, dd_zone,
1324	nbs->a+ash, na, x,
1325	grid->c0[ZZ2],
1326	1.0/nbs->box[ZZ2][ZZ2], ncz*grid->na_sc,
1327	sort_work);
1328
1329	/* Fill the ncz cells in this column */
1330	cfilled = grid->cxy_ind[cxy];
1331	for (cz = 0; cz < ncz; cz++)
1332	{
1333	c = grid->cxy_ind[cxy] + cz;
1334
1335	ash_c = ash + cz*grid->na_sc;
1336	na_c = min(grid->na_sc, na-(ash_c-ash))(((grid->na_sc) < (na-(ash_c-ash))) ? (grid->na_sc) : (na-(ash_c-ash)) );
1337
1338	fill_cell(nbs, grid, nbat,
1339	ash_c, ash_c+na_c, atinfo, x,
1340	grid->na_sc*cx + (dd_zone >> 2),
1341	grid->na_sc*cy + (dd_zone & 3),
1342	grid->na_sc*cz,
1343	NULL((void*)0));
1344
1345	/* This copy to bbcz is not really necessary.
1346	* But it allows to use the same grid search code
1347	* for the simple and supersub cell setups.
1348	*/
1349	if (na_c > 0)
1350	{
1351	cfilled = c;
1352	}
1353	grid->bbcz[c*NNBSBB_D2 ] = grid->bb[cfilled].lower[BB_Z2];
1354	grid->bbcz[c*NNBSBB_D2+1] = grid->bb[cfilled].upper[BB_Z2];
1355	}
1356
1357	/* Set the unused atom indices to -1 */
1358	for (ind = na; ind < ncz*grid->na_sc; ind++)
1359	{
1360	nbs->a[ash+ind] = -1;
1361	}
1362	}
1363	}
1364
1365	/* Spatially sort the atoms within one grid column */
1366	static void sort_columns_supersub(const nbnxn_search_t nbs,
1367	int dd_zone,
1368	nbnxn_grid_t *grid,
1369	int a0, int a1,
1370	const int *atinfo,
1371	rvec *x,
1372	nbnxn_atomdata_t *nbat,
1373	int cxy_start, int cxy_end,
1374	int *sort_work)
1375	{
1376	int cxy;
1377	int cx, cy, cz = -1, c = -1, ncz;
1378	int na, ash, na_c, ind, a;
1379	int subdiv_z, sub_z, na_z, ash_z;
1380	int subdiv_y, sub_y, na_y, ash_y;
1381	int subdiv_x, sub_x, na_x, ash_x;
1382
1383	/* cppcheck-suppress unassignedVariable */
1384	nbnxn_bb_t bb_work_array[2], *bb_work_aligned;
1385
1386	bb_work_aligned = (nbnxn_bb_t *)(((size_t)(bb_work_array+1)) & (~((size_t)15)));
1387
1388	if (debug)
1389	{
1390	fprintf(debug, "cell0 %d sorting columns %d - %d, atoms %d - %d\n",
1391	grid->cell0, cxy_start, cxy_end, a0, a1);
1392	}
1393
1394	subdiv_x = grid->na_c;
1395	subdiv_y = GPU_NSUBCELL_X2*subdiv_x;
1396	subdiv_z = GPU_NSUBCELL_Y2*subdiv_y;
1397
1398	/* Sort the atoms within each x,y column in 3 dimensions */
1399	for (cxy = cxy_start; cxy < cxy_end; cxy++)
1400	{
1401	cx = cxy/grid->ncy;
1402	cy = cxy - cx*grid->ncy;
1403
1404	na = grid->cxy_na[cxy];
1405	ncz = grid->cxy_ind[cxy+1] - grid->cxy_ind[cxy];
1406	ash = (grid->cell0 + grid->cxy_ind[cxy])*grid->na_sc;
1407
1408	/* Sort the atoms within each x,y column on z coordinate */
1409	sort_atoms(ZZ2, FALSE0, dd_zone,
1410	nbs->a+ash, na, x,
1411	grid->c0[ZZ2],
1412	1.0/nbs->box[ZZ2][ZZ2], ncz*grid->na_sc,
1413	sort_work);
1414
1415	/* This loop goes over the supercells and subcells along z at once */
1416	for (sub_z = 0; sub_z < ncz*GPU_NSUBCELL_Z2; sub_z++)
1417	{
1418	ash_z = ash + sub_z*subdiv_z;
1419	na_z = min(subdiv_z, na-(ash_z-ash))(((subdiv_z) < (na-(ash_z-ash))) ? (subdiv_z) : (na-(ash_z -ash)) );
1420
1421	/* We have already sorted on z */
1422
1423	if (sub_z % GPU_NSUBCELL_Z2 == 0)
1424	{
1425	cz = sub_z/GPU_NSUBCELL_Z2;
1426	c = grid->cxy_ind[cxy] + cz;
1427
1428	/* The number of atoms in this supercell */
1429	na_c = min(grid->na_sc, na-(ash_z-ash))(((grid->na_sc) < (na-(ash_z-ash))) ? (grid->na_sc) : (na-(ash_z-ash)) );
1430
1431	grid->nsubc[c] = min(GPU_NSUBCELL, (na_c+grid->na_c-1)/grid->na_c)((((222)) < ((na_c+grid->na_c-1)/grid->na_c)) ? (( 222)) : ((na_c+grid->na_c-1)/grid->na_c) );
1432
1433	/* Store the z-boundaries of the super cell */
1434	grid->bbcz[c*NNBSBB_D2 ] = x[nbs->a[ash_z]][ZZ2];
1435	grid->bbcz[c*NNBSBB_D2+1] = x[nbs->a[ash_z+na_c-1]][ZZ2];
1436	}
1437
1438	#if GPU_NSUBCELL_Y2 > 1
1439	/* Sort the atoms along y */
1440	sort_atoms(YY1, (sub_z & 1), dd_zone,
1441	nbs->a+ash_z, na_z, x,
1442	grid->c0[YY1]+cy*grid->sy,
1443	grid->inv_sy, subdiv_z,
1444	sort_work);
1445	#endif
1446
1447	for (sub_y = 0; sub_y < GPU_NSUBCELL_Y2; sub_y++)
1448	{
1449	ash_y = ash_z + sub_y*subdiv_y;
1450	na_y = min(subdiv_y, na-(ash_y-ash))(((subdiv_y) < (na-(ash_y-ash))) ? (subdiv_y) : (na-(ash_y -ash)) );
1451
1452	#if GPU_NSUBCELL_X2 > 1
1453	/* Sort the atoms along x */
1454	sort_atoms(XX0, ((cz*GPU_NSUBCELL_Y2 + sub_y) & 1), dd_zone,
1455	nbs->a+ash_y, na_y, x,
1456	grid->c0[XX0]+cx*grid->sx,
1457	grid->inv_sx, subdiv_y,
1458	sort_work);
1459	#endif
1460
1461	for (sub_x = 0; sub_x < GPU_NSUBCELL_X2; sub_x++)
1462	{
1463	ash_x = ash_y + sub_x*subdiv_x;
1464	na_x = min(subdiv_x, na-(ash_x-ash))(((subdiv_x) < (na-(ash_x-ash))) ? (subdiv_x) : (na-(ash_x -ash)) );
1465
1466	fill_cell(nbs, grid, nbat,
1467	ash_x, ash_x+na_x, atinfo, x,
1468	grid->na_c(cxGPU_NSUBCELL_X2+sub_x) + (dd_zone >> 2),
1469	grid->na_c(cyGPU_NSUBCELL_Y2+sub_y) + (dd_zone & 3),
1470	grid->na_c*sub_z,
1471	bb_work_aligned);
1472	}
1473	}
1474	}
1475
1476	/* Set the unused atom indices to -1 */
1477	for (ind = na; ind < ncz*grid->na_sc; ind++)
1478	{
1479	nbs->a[ash+ind] = -1;
1480	}
1481	}
1482	}
1483
1484	/* Determine in which grid column atoms should go */
1485	static void calc_column_indices(nbnxn_grid_t *grid,
1486	int a0, int a1,
1487	rvec *x,
1488	int dd_zone, const int *move,
1489	int thread, int nthread,
1490	int *cell,
1491	int *cxy_na)
1492	{
1493	int n0, n1, i;
1494	int cx, cy;
1495
1496	/* We add one extra cell for particles which moved during DD */
1497	for (i = 0; i < grid->ncx*grid->ncy+1; i++)
1498	{
1499	cxy_na[i] = 0;
1500	}
1501
1502	n0 = a0 + (int)((thread+0)*(a1 - a0))/nthread;
1503	n1 = a0 + (int)((thread+1)*(a1 - a0))/nthread;
1504	if (dd_zone == 0)
1505	{
1506	/* Home zone */
1507	for (i = n0; i < n1; i++)
1508	{
1509	if (move == NULL((void*)0) \|\| move[i] >= 0)
1510	{
1511	/* We need to be careful with rounding,
1512	* particles might be a few bits outside the local zone.
1513	* The int cast takes care of the lower bound,
1514	* we will explicitly take care of the upper bound.
1515	*/
1516	cx = (int)((x[i][XX0] - grid->c0[XX0])*grid->inv_sx);
1517	cy = (int)((x[i][YY1] - grid->c0[YY1])*grid->inv_sy);
1518
1519	#ifndef NDEBUG1
1520	if (cx < 0 \|\| cx > grid->ncx \|\|
1521	cy < 0 \|\| cy > grid->ncy)
1522	{
1523	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 1523,
1524	"grid cell cx %d cy %d out of range (max %d %d)\n"
1525	"atom %f %f %f, grid->c0 %f %f",
1526	cx, cy, grid->ncx, grid->ncy,
1527	x[i][XX0], x[i][YY1], x[i][ZZ2], grid->c0[XX0], grid->c0[YY1]);
1528	}
1529	#endif
1530	/* Take care of potential rouding issues */
1531	cx = min(cx, grid->ncx - 1)(((cx) < (grid->ncx - 1)) ? (cx) : (grid->ncx - 1) );
1532	cy = min(cy, grid->ncy - 1)(((cy) < (grid->ncy - 1)) ? (cy) : (grid->ncy - 1) );
1533
1534	/* For the moment cell will contain only the, grid local,
1535	* x and y indices, not z.
1536	*/
1537	cell[i] = cx*grid->ncy + cy;
1538	}
1539	else
1540	{
1541	/* Put this moved particle after the end of the grid,
1542	* so we can process it later without using conditionals.
1543	*/
1544	cell[i] = grid->ncx*grid->ncy;
1545	}
1546
1547	cxy_na[cell[i]]++;
1548	}
1549	}
1550	else
1551	{
1552	/* Non-home zone */
1553	for (i = n0; i < n1; i++)
1554	{
1555	cx = (int)((x[i][XX0] - grid->c0[XX0])*grid->inv_sx);
1556	cy = (int)((x[i][YY1] - grid->c0[YY1])*grid->inv_sy);
1557
1558	/* For non-home zones there could be particles outside
1559	* the non-bonded cut-off range, which have been communicated
1560	* for bonded interactions only. For the result it doesn't
1561	* matter where these end up on the grid. For performance
1562	* we put them in an extra row at the border.
1563	*/
1564	cx = max(cx, 0)(((cx) > (0)) ? (cx) : (0) );
1565	cx = min(cx, grid->ncx - 1)(((cx) < (grid->ncx - 1)) ? (cx) : (grid->ncx - 1) );
1566	cy = max(cy, 0)(((cy) > (0)) ? (cy) : (0) );
1567	cy = min(cy, grid->ncy - 1)(((cy) < (grid->ncy - 1)) ? (cy) : (grid->ncy - 1) );
1568
1569	/* For the moment cell will contain only the, grid local,
1570	* x and y indices, not z.
1571	*/
1572	cell[i] = cx*grid->ncy + cy;
1573
1574	cxy_na[cell[i]]++;
1575	}
1576	}
1577	}
1578
1579	/* Determine in which grid cells the atoms should go */
1580	static void calc_cell_indices(const nbnxn_search_t nbs,
1581	int dd_zone,
1582	nbnxn_grid_t *grid,
1583	int a0, int a1,
1584	const int *atinfo,
1585	rvec *x,
1586	const int *move,
1587	nbnxn_atomdata_t *nbat)
1588	{
1589	int n0, n1, i;
1590	int cx, cy, cxy, ncz_max, ncz;
1591	int nthread, thread;
1592	int *cxy_na, cxy_na_i;
1593
1594	nthread = gmx_omp_nthreads_get(emntPairsearch);
1595
1596	#pragma omp parallel for num_threads(nthread) schedule(static)
1597	for (thread = 0; thread < nthread; thread++)
1598	{
1599	calc_column_indices(grid, a0, a1, x, dd_zone, move, thread, nthread,
1600	nbs->cell, nbs->work[thread].cxy_na);
1601	}
1602
1603	/* Make the cell index as a function of x and y */
1604	ncz_max = 0;
1605	ncz = 0;
1606	grid->cxy_ind[0] = 0;
1607	for (i = 0; i < grid->ncx*grid->ncy+1; i++)
1608	{
1609	/* We set ncz_max at the beginning of the loop iso at the end
1610	* to skip i=grid->ncx*grid->ncy which are moved particles
1611	* that do not need to be ordered on the grid.
1612	*/
1613	if (ncz > ncz_max)
1614	{
1615	ncz_max = ncz;
1616	}
1617	cxy_na_i = nbs->work[0].cxy_na[i];
1618	for (thread = 1; thread < nthread; thread++)
1619	{
1620	cxy_na_i += nbs->work[thread].cxy_na[i];
1621	}
1622	ncz = (cxy_na_i + grid->na_sc - 1)/grid->na_sc;
1623	if (nbat->XFormat == nbatX8)
1624	{
1625	/* Make the number of cell a multiple of 2 */
1626	ncz = (ncz + 1) & ~1;
1627	}
1628	grid->cxy_ind[i+1] = grid->cxy_ind[i] + ncz;
1629	/* Clear cxy_na, so we can reuse the array below */
1630	grid->cxy_na[i] = 0;
1631	}
1632	grid->nc = grid->cxy_ind[grid->ncx*grid->ncy] - grid->cxy_ind[0];
1633
1634	nbat->natoms = (grid->cell0 + grid->nc)*grid->na_sc;
1635
1636	if (debug)
1637	{
1638	fprintf(debug, "ns na_sc %d na_c %d super-cells: %d x %d y %d z %.1f maxz %d\n",
1639	grid->na_sc, grid->na_c, grid->nc,
1640	grid->ncx, grid->ncy, grid->nc/((double)(grid->ncx*grid->ncy)),
1641	ncz_max);
1642	if (gmx_debug_at)
1643	{
1644	i = 0;
1645	for (cy = 0; cy < grid->ncy; cy++)
1646	{
1647	for (cx = 0; cx < grid->ncx; cx++)
1648	{
1649	fprintf(debug, " %2d", grid->cxy_ind[i+1]-grid->cxy_ind[i]);
1650	i++;
1651	}
1652	fprintf(debug, "\n");
1653	}
1654	}
1655	}
1656
1657	/* Make sure the work array for sorting is large enough */
1658	if (ncz_maxgrid->na_scSGSF(4 + 1) > nbs->work[0].sort_work_nalloc)
1659	{
1660	for (thread = 0; thread < nbs->nthread_max; thread++)
1661	{
1662	nbs->work[thread].sort_work_nalloc =
1663	over_alloc_large(ncz_maxgrid->na_scSGSF)(int)(1.19(ncz_maxgrid->na_sc*(4 + 1)) + 1000);
1664	srenew(nbs->work[thread].sort_work,(nbs->work[thread].sort_work) = save_realloc("nbs->work[thread].sort_work" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 1665, (nbs->work[thread].sort_work), (nbs->work[thread ].sort_work_nalloc), sizeof(*(nbs->work[thread].sort_work) ))
1665	nbs->work[thread].sort_work_nalloc)(nbs->work[thread].sort_work) = save_realloc("nbs->work[thread].sort_work" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 1665, (nbs->work[thread].sort_work), (nbs->work[thread ].sort_work_nalloc), sizeof(*(nbs->work[thread].sort_work) ));
1666	/* When not in use, all elements should be -1 */
1667	for (i = 0; i < nbs->work[thread].sort_work_nalloc; i++)
1668	{
1669	nbs->work[thread].sort_work[i] = -1;
1670	}
1671	}
1672	}
1673
1674	/* Now we know the dimensions we can fill the grid.
1675	* This is the first, unsorted fill. We sort the columns after this.
1676	*/
1677	for (i = a0; i < a1; i++)
1678	{
1679	/* At this point nbs->cell contains the local grid x,y indices */
1680	cxy = nbs->cell[i];
1681	nbs->a[(grid->cell0 + grid->cxy_ind[cxy])*grid->na_sc + grid->cxy_na[cxy]++] = i;
1682	}
1683
1684	if (dd_zone == 0)
1685	{
1686	/* Set the cell indices for the moved particles */
1687	n0 = grid->nc*grid->na_sc;
1688	n1 = grid->ncgrid->na_sc+grid->cxy_na[grid->ncxgrid->ncy];
1689	if (dd_zone == 0)
1690	{
1691	for (i = n0; i < n1; i++)
1692	{
1693	nbs->cell[nbs->a[i]] = i;
1694	}
1695	}
1696	}
1697
1698	/* Sort the super-cell columns along z into the sub-cells. */
1699	#pragma omp parallel for num_threads(nbs->nthread_max) schedule(static)
1700	for (thread = 0; thread < nbs->nthread_max; thread++)
1701	{
1702	if (grid->bSimple)
1703	{
1704	sort_columns_simple(nbs, dd_zone, grid, a0, a1, atinfo, x, nbat,
1705	((thread+0)grid->ncxgrid->ncy)/nthread,
1706	((thread+1)grid->ncxgrid->ncy)/nthread,
1707	nbs->work[thread].sort_work);
1708	}
1709	else
1710	{
1711	sort_columns_supersub(nbs, dd_zone, grid, a0, a1, atinfo, x, nbat,
1712	((thread+0)grid->ncxgrid->ncy)/nthread,
1713	((thread+1)grid->ncxgrid->ncy)/nthread,
1714	nbs->work[thread].sort_work);
1715	}
1716	}
1717
1718	if (grid->bSimple && nbat->XFormat == nbatX8)
1719	{
1720	combine_bounding_box_pairs(grid, grid->bb);
1721	}
1722
1723	if (!grid->bSimple)
1724	{
1725	grid->nsubc_tot = 0;
1726	for (i = 0; i < grid->nc; i++)
1727	{
1728	grid->nsubc_tot += grid->nsubc[i];
1729	}
1730	}
1731
1732	if (debug)
1733	{
1734	if (grid->bSimple)
1735	{
1736	print_bbsizes_simple(debug, nbs, grid);
1737	}
1738	else
1739	{
1740	fprintf(debug, "ns non-zero sub-cells: %d average atoms %.2f\n",
1741	grid->nsubc_tot, (a1-a0)/(double)grid->nsubc_tot);
1742
1743	print_bbsizes_supersub(debug, nbs, grid);
1744	}
1745	}
1746	}
1747
1748	static void init_buffer_flags(nbnxn_buffer_flags_t *flags,
1749	int natoms)
1750	{
1751	int b;
1752
1753	flags->nflag = (natoms + NBNXN_BUFFERFLAG_SIZE16 - 1)/NBNXN_BUFFERFLAG_SIZE16;
1754	if (flags->nflag > flags->flag_nalloc)
1755	{
1756	flags->flag_nalloc = over_alloc_large(flags->nflag)(int)(1.19*(flags->nflag) + 1000);
1757	srenew(flags->flag, flags->flag_nalloc)(flags->flag) = save_realloc("flags->flag", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 1757, (flags->flag), (flags->flag_nalloc), sizeof(*(flags ->flag)));
1758	}
1759	for (b = 0; b < flags->nflag; b++)
1760	{
1761	flags->flag[b] = 0;
1762	}
1763	}
1764
1765	/* Sets up a grid and puts the atoms on the grid.
1766	* This function only operates on one domain of the domain decompostion.
1767	* Note that without domain decomposition there is only one domain.
1768	*/
1769	void nbnxn_put_on_grid(nbnxn_search_t nbs,
1770	int ePBC, matrix box,
1771	int dd_zone,
1772	rvec corner0, rvec corner1,
1773	int a0, int a1,
1774	real atom_density,
1775	const int *atinfo,
1776	rvec *x,
1777	int nmoved, int *move,
1778	int nb_kernel_type,
1779	nbnxn_atomdata_t *nbat)
1780	{
1781	nbnxn_grid_t *grid;
1782	int n;
1783	int nc_max_grid, nc_max;
1784
1785	grid = &nbs->grid[dd_zone];
1786
1787	nbs_cycle_start(&nbs->cc[enbsCCgrid]);
1788
1789	grid->bSimple = nbnxn_kernel_pairlist_simple(nb_kernel_type);
1790
1791	grid->na_c = nbnxn_kernel_to_ci_size(nb_kernel_type);
1792	grid->na_cj = nbnxn_kernel_to_cj_size(nb_kernel_type);
1793	grid->na_sc = (grid->bSimple ? 1 : GPU_NSUBCELL(222))*grid->na_c;
1794	grid->na_c_2log = get_2log(grid->na_c);
1795
1796	nbat->na_c = grid->na_c;
1797
1798	if (dd_zone == 0)
1799	{
1800	grid->cell0 = 0;
1801	}
1802	else
1803	{
1804	grid->cell0 =
1805	(nbs->grid[dd_zone-1].cell0 + nbs->grid[dd_zone-1].nc)*
1806	nbs->grid[dd_zone-1].na_sc/grid->na_sc;
1807	}
1808
1809	n = a1 - a0;
1810
1811	if (dd_zone == 0)
1812	{
1813	nbs->ePBC = ePBC;
1814	copy_mat(box, nbs->box);
1815
1816	if (atom_density >= 0)
1817	{
1818	grid->atom_density = atom_density;
1819	}
1820	else
1821	{
1822	grid->atom_density = grid_atom_density(n-nmoved, corner0, corner1);
1823	}
1824
1825	grid->cell0 = 0;
1826
1827	nbs->natoms_local = a1 - nmoved;
1828	/* We assume that nbnxn_put_on_grid is called first
1829	* for the local atoms (dd_zone=0).
1830	*/
1831	nbs->natoms_nonlocal = a1 - nmoved;
1832	}
1833	else
1834	{
1835	nbs->natoms_nonlocal = max(nbs->natoms_nonlocal, a1)(((nbs->natoms_nonlocal) > (a1)) ? (nbs->natoms_nonlocal ) : (a1) );
1836	}
1837
1838	nc_max_grid = set_grid_size_xy(nbs, grid,
1839	dd_zone, n-nmoved, corner0, corner1,
1840	nbs->grid[0].atom_density);
1841
1842	nc_max = grid->cell0 + nc_max_grid;
1843
1844	if (a1 > nbs->cell_nalloc)
1845	{
1846	nbs->cell_nalloc = over_alloc_large(a1)(int)(1.19*(a1) + 1000);
1847	srenew(nbs->cell, nbs->cell_nalloc)(nbs->cell) = save_realloc("nbs->cell", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 1847, (nbs->cell), (nbs->cell_nalloc), sizeof(*(nbs-> cell)));
1848	}
1849
1850	/* To avoid conditionals we store the moved particles at the end of a,
1851	* make sure we have enough space.
1852	*/
1853	if (nc_max*grid->na_sc + nmoved > nbs->a_nalloc)
1854	{
1855	nbs->a_nalloc = over_alloc_large(nc_maxgrid->na_sc + nmoved)(int)(1.19(nc_max*grid->na_sc + nmoved) + 1000);
1856	srenew(nbs->a, nbs->a_nalloc)(nbs->a) = save_realloc("nbs->a", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 1856, (nbs->a), (nbs->a_nalloc), sizeof(*(nbs->a)) );
1857	}
1858
1859	/* We need padding up to a multiple of the buffer flag size: simply add */
1860	if (nc_max*grid->na_sc + NBNXN_BUFFERFLAG_SIZE16 > nbat->nalloc)
1861	{
1862	nbnxn_atomdata_realloc(nbat, nc_max*grid->na_sc+NBNXN_BUFFERFLAG_SIZE16);
1863	}
1864
1865	calc_cell_indices(nbs, dd_zone, grid, a0, a1, atinfo, x, move, nbat);
1866
1867	if (dd_zone == 0)
1868	{
1869	nbat->natoms_local = nbat->natoms;
1870	}
1871
1872	nbs_cycle_stop(&nbs->cc[enbsCCgrid]);
1873	}
1874
1875	/* Calls nbnxn_put_on_grid for all non-local domains */
1876	void nbnxn_put_on_grid_nonlocal(nbnxn_search_t nbs,
1877	const gmx_domdec_zones_t *zones,
1878	const int *atinfo,
1879	rvec *x,
1880	int nb_kernel_type,
1881	nbnxn_atomdata_t *nbat)
1882	{
1883	int zone, d;
1884	rvec c0, c1;
1885
1886	for (zone = 1; zone < zones->n; zone++)
1887	{
1888	for (d = 0; d < DIM3; d++)
1889	{
1890	c0[d] = zones->size[zone].bb_x0[d];
1891	c1[d] = zones->size[zone].bb_x1[d];
1892	}
1893
1894	nbnxn_put_on_grid(nbs, nbs->ePBC, NULL((void*)0),
1895	zone, c0, c1,
1896	zones->cg_range[zone],
1897	zones->cg_range[zone+1],
1898	-1,
1899	atinfo,
1900	x,
1901	0, NULL((void*)0),
1902	nb_kernel_type,
1903	nbat);
1904	}
1905	}
1906
1907	/* Add simple grid type information to the local super/sub grid */
1908	void nbnxn_grid_add_simple(nbnxn_search_t nbs,
1909	nbnxn_atomdata_t *nbat)
1910	{
1911	nbnxn_grid_t *grid;
1912	float *bbcz;
1913	nbnxn_bb_t *bb;
1914	int ncd, sc;
1915
1916	grid = &nbs->grid[0];
1917
1918	if (grid->bSimple)
1919	{
1920	gmx_incons("nbnxn_grid_simple called with a simple grid")_gmx_error("incons", "nbnxn_grid_simple called with a simple grid" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 1920);
1921	}
1922
1923	ncd = grid->na_sc/NBNXN_CPU_CLUSTER_I_SIZE4;
1924
1925	if (grid->nc*ncd > grid->nc_nalloc_simple)
1926	{
1927	grid->nc_nalloc_simple = over_alloc_large(grid->ncncd)(int)(1.19(grid->nc*ncd) + 1000);
1928	srenew(grid->bbcz_simple, grid->nc_nalloc_simpleNNBSBB_D)(grid->bbcz_simple) = save_realloc("grid->bbcz_simple", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 1928, (grid->bbcz_simple), (grid->nc_nalloc_simple2) , sizeof(*(grid->bbcz_simple)));
1929	srenew(grid->bb_simple, grid->nc_nalloc_simple)(grid->bb_simple) = save_realloc("grid->bb_simple", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 1929, (grid->bb_simple), (grid->nc_nalloc_simple), sizeof (*(grid->bb_simple)));
1930	srenew(grid->flags_simple, grid->nc_nalloc_simple)(grid->flags_simple) = save_realloc("grid->flags_simple" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 1930, (grid->flags_simple), (grid->nc_nalloc_simple), sizeof(*(grid->flags_simple)));
1931	if (nbat->XFormat)
1932	{
1933	sfree_aligned(grid->bbj)save_free_aligned("grid->bbj", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 1933, (grid->bbj));
1934	snew_aligned(grid->bbj, grid->nc_nalloc_simple/2, 16)(grid->bbj) = save_calloc_aligned("grid->bbj", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 1934, (grid->nc_nalloc_simple/2), sizeof(*(grid->bbj) ), 16);
1935	}
1936	}
1937
1938	bbcz = grid->bbcz_simple;
1939	bb = grid->bb_simple;
1940
1941	#pragma omp parallel for num_threads(gmx_omp_nthreads_get(emntPairsearch)) schedule(static)
1942	for (sc = 0; sc < grid->nc; sc++)
1943	{
1944	int c, tx, na;
1945
1946	for (c = 0; c < ncd; c++)
1947	{
1948	tx = sc*ncd + c;
1949
1950	na = NBNXN_CPU_CLUSTER_I_SIZE4;
1951	while (na > 0 &&
1952	nbat->type[tx*NBNXN_CPU_CLUSTER_I_SIZE4+na-1] == nbat->ntype-1)
1953	{
1954	na--;
1955	}
1956
1957	if (na > 0)
1958	{
1959	switch (nbat->XFormat)
1960	{
1961	case nbatX4:
1962	/* PACK_X4==NBNXN_CPU_CLUSTER_I_SIZE, so this is simple */
1963	calc_bounding_box_x_x4(na, nbat->x+txSTRIDE_P4(34),
1964	bb+tx);
1965	break;
1966	case nbatX8:
1967	/* PACK_X8>NBNXN_CPU_CLUSTER_I_SIZE, more complicated */
1968	calc_bounding_box_x_x8(na, nbat->x+X8_IND_A(txNBNXN_CPU_CLUSTER_I_SIZE)((38)((tx4) >> 3) + ((tx*4) & (8 - 1))),
1969	bb+tx);
1970	break;
1971	default:
1972	calc_bounding_box(na, nbat->xstride,
1973	nbat->x+txNBNXN_CPU_CLUSTER_I_SIZE4nbat->xstride,
1974	bb+tx);
1975	break;
1976	}
1977	bbcz[tx*NNBSBB_D2+0] = bb[tx].lower[BB_Z2];
1978	bbcz[tx*NNBSBB_D2+1] = bb[tx].upper[BB_Z2];
1979
1980	/* No interaction optimization yet here */
1981	grid->flags_simple[tx] = NBNXN_CI_DO_LJ(0)(1<<(7+3(0))) \| NBNXN_CI_DO_COUL(0)(1<<(9+3(0)));
1982	}
1983	else
1984	{
1985	grid->flags_simple[tx] = 0;
1986	}
1987	}
1988	}
1989
1990	if (grid->bSimple && nbat->XFormat == nbatX8)
1991	{
1992	combine_bounding_box_pairs(grid, grid->bb_simple);
1993	}
1994	}
1995
1996	void nbnxn_get_ncells(nbnxn_search_t nbs, int ncx, int ncy)
1997	{
1998	*ncx = nbs->grid[0].ncx;
1999	*ncy = nbs->grid[0].ncy;
2000	}
2001
2002	void nbnxn_get_atomorder(nbnxn_search_t nbs, int *a, int n)
2003	{
2004	const nbnxn_grid_t *grid;
2005
2006	grid = &nbs->grid[0];
2007
2008	/* Return the atom order for the home cell (index 0) */
2009	*a = nbs->a;
2010
2011	n = grid->cxy_ind[grid->ncxgrid->ncy]*grid->na_sc;
2012	}
2013
2014	void nbnxn_set_atomorder(nbnxn_search_t nbs)
2015	{
2016	nbnxn_grid_t *grid;
2017	int ao, cx, cy, cxy, cz, j;
2018
2019	/* Set the atom order for the home cell (index 0) */
2020	grid = &nbs->grid[0];
2021
2022	ao = 0;
2023	for (cx = 0; cx < grid->ncx; cx++)
2024	{
2025	for (cy = 0; cy < grid->ncy; cy++)
2026	{
2027	cxy = cx*grid->ncy + cy;
2028	j = grid->cxy_ind[cxy]*grid->na_sc;
2029	for (cz = 0; cz < grid->cxy_na[cxy]; cz++)
2030	{
2031	nbs->a[j] = ao;
2032	nbs->cell[ao] = j;
2033	ao++;
2034	j++;
2035	}
2036	}
2037	}
2038	}
2039
2040	/* Determines the cell range along one dimension that
2041	* the bounding box b0 - b1 sees.
2042	*/
2043	static void get_cell_range(real b0, real b1,
2044	int nc, real c0, real s, real invs,
2045	real d2, real r2, int cf, int cl)
2046	{
2047	cf = max((int)((b0 - c0)invs), 0)((((int)((b0 - c0)invs)) > (0)) ? ((int)((b0 - c0)invs)) : (0) );
2048
2049	while (cf > 0 && d2 + sqr((b0 - c0) - (cf-1+1)*s) < r2)
2050	{
2051	(*cf)--;
2052	}
2053
2054	cl = min((int)((b1 - c0)invs), nc-1)((((int)((b1 - c0)invs)) < (nc-1)) ? ((int)((b1 - c0)invs )) : (nc-1) );
2055	while (cl < nc-1 && d2 + sqr((cl+1)*s - (b1 - c0)) < r2)
2056	{
2057	(*cl)++;
2058	}
2059	}
2060
2061	/* Reference code calculating the distance^2 between two bounding boxes */
2062	static float box_dist2(float bx0, float bx1, float by0,
2063	float by1, float bz0, float bz1,
2064	const nbnxn_bb_t *bb)
2065	{
2066	float d2;
2067	float dl, dh, dm, dm0;
2068
2069	d2 = 0;
2070
2071	dl = bx0 - bb->upper[BB_X0];
2072	dh = bb->lower[BB_X0] - bx1;
2073	dm = max(dl, dh)(((dl) > (dh)) ? (dl) : (dh) );
2074	dm0 = max(dm, 0)(((dm) > (0)) ? (dm) : (0) );
2075	d2 += dm0*dm0;
2076
2077	dl = by0 - bb->upper[BB_Y1];
2078	dh = bb->lower[BB_Y1] - by1;
2079	dm = max(dl, dh)(((dl) > (dh)) ? (dl) : (dh) );
2080	dm0 = max(dm, 0)(((dm) > (0)) ? (dm) : (0) );
2081	d2 += dm0*dm0;
2082
2083	dl = bz0 - bb->upper[BB_Z2];
2084	dh = bb->lower[BB_Z2] - bz1;
2085	dm = max(dl, dh)(((dl) > (dh)) ? (dl) : (dh) );
2086	dm0 = max(dm, 0)(((dm) > (0)) ? (dm) : (0) );
2087	d2 += dm0*dm0;
2088
2089	return d2;
2090	}
2091
2092	/* Plain C code calculating the distance^2 between two bounding boxes */
2093	static float subc_bb_dist2(int si, const nbnxn_bb_t *bb_i_ci,
2094	int csj, const nbnxn_bb_t *bb_j_all)
2095	{
2096	const nbnxn_bb_t bb_i, bb_j;
2097	float d2;
2098	float dl, dh, dm, dm0;
2099
2100	bb_i = bb_i_ci + si;
2101	bb_j = bb_j_all + csj;
2102
2103	d2 = 0;
2104
2105	dl = bb_i->lower[BB_X0] - bb_j->upper[BB_X0];
2106	dh = bb_j->lower[BB_X0] - bb_i->upper[BB_X0];
2107	dm = max(dl, dh)(((dl) > (dh)) ? (dl) : (dh) );
2108	dm0 = max(dm, 0)(((dm) > (0)) ? (dm) : (0) );
2109	d2 += dm0*dm0;
2110
2111	dl = bb_i->lower[BB_Y1] - bb_j->upper[BB_Y1];
2112	dh = bb_j->lower[BB_Y1] - bb_i->upper[BB_Y1];
2113	dm = max(dl, dh)(((dl) > (dh)) ? (dl) : (dh) );
2114	dm0 = max(dm, 0)(((dm) > (0)) ? (dm) : (0) );
2115	d2 += dm0*dm0;
2116
2117	dl = bb_i->lower[BB_Z2] - bb_j->upper[BB_Z2];
2118	dh = bb_j->lower[BB_Z2] - bb_i->upper[BB_Z2];
2119	dm = max(dl, dh)(((dl) > (dh)) ? (dl) : (dh) );
2120	dm0 = max(dm, 0)(((dm) > (0)) ? (dm) : (0) );
2121	d2 += dm0*dm0;
2122
2123	return d2;
2124	}
2125
2126	#ifdef NBNXN_SEARCH_BB_SIMD4
2127
2128	/* 4-wide SIMD code for bb distance for bb format xyz0 */
2129	static float subc_bb_dist2_simd4(int si, const nbnxn_bb_t *bb_i_ci,
2130	int csj, const nbnxn_bb_t *bb_j_all)
2131	{
2132	gmx_simd4_float_t__m128 bb_i_S0, bb_i_S1;
2133	gmx_simd4_float_t__m128 bb_j_S0, bb_j_S1;
2134	gmx_simd4_float_t__m128 dl_S;
2135	gmx_simd4_float_t__m128 dh_S;
2136	gmx_simd4_float_t__m128 dm_S;
2137	gmx_simd4_float_t__m128 dm0_S;
2138
2139	bb_i_S0 = gmx_simd4_load_f_mm_load_ps(&bb_i_ci[si].lower[0]);
2140	bb_i_S1 = gmx_simd4_load_f_mm_load_ps(&bb_i_ci[si].upper[0]);
2141	bb_j_S0 = gmx_simd4_load_f_mm_load_ps(&bb_j_all[csj].lower[0]);
2142	bb_j_S1 = gmx_simd4_load_f_mm_load_ps(&bb_j_all[csj].upper[0]);
2143
2144	dl_S = gmx_simd4_sub_f_mm_sub_ps(bb_i_S0, bb_j_S1);
2145	dh_S = gmx_simd4_sub_f_mm_sub_ps(bb_j_S0, bb_i_S1);
2146
2147	dm_S = gmx_simd4_max_f_mm_max_ps(dl_S, dh_S);
2148	dm0_S = gmx_simd4_max_f_mm_max_ps(dm_S, gmx_simd4_setzero_f_mm_setzero_ps());
2149
2150	return gmx_simd4_dotproduct3_fgmx_simd4_dotproduct3_f_sse4_1(dm0_S, dm0_S);
2151	}
2152
2153	/* Calculate bb bounding distances of bb_i[si,...,si+3] and store them in d2 */
2154	#define SUBC_BB_DIST2_SIMD4_XXXX_INNER(si, bb_i, d2){ int shi; __m128 dx_0, dy_0, dz_0; __m128 dx_1, dy_1, dz_1; __m128 mx, my, mz; __m128 m0x, m0y, m0z; __m128 d2x, d2y, d2z; __m128 d2s, d2t; shi = si23; xi_l = _mm_load_ps(bb_i+shi+04); yi_l = _mm_load_ps(bb_i+shi+14); zi_l = _mm_load_ps(bb_i+shi+24 ); xi_h = _mm_load_ps(bb_i+shi+34); yi_h = _mm_load_ps(bb_i+ shi+44); zi_h = _mm_load_ps(bb_i+shi+54); dx_0 = _mm_sub_ps (xi_l, xj_h); dy_0 = _mm_sub_ps(yi_l, yj_h); dz_0 = _mm_sub_ps (zi_l, zj_h); dx_1 = _mm_sub_ps(xj_l, xi_h); dy_1 = _mm_sub_ps (yj_l, yi_h); dz_1 = _mm_sub_ps(zj_l, zi_h); mx = _mm_max_ps( dx_0, dx_1); my = _mm_max_ps(dy_0, dy_1); mz = _mm_max_ps(dz_0 , dz_1); m0x = _mm_max_ps(mx, zero); m0y = _mm_max_ps(my, zero ); m0z = _mm_max_ps(mz, zero); d2x = _mm_mul_ps(m0x, m0x); d2y = _mm_mul_ps(m0y, m0y); d2z = _mm_mul_ps(m0z, m0z); d2s = _mm_add_ps (d2x, d2y); d2t = _mm_add_ps(d2s, d2z); _mm_store_ps(d2+si, d2t ); } \
2155	{ \
2156	int shi; \
2157	\
2158	gmx_simd4_float_t__m128 dx_0, dy_0, dz_0; \
2159	gmx_simd4_float_t__m128 dx_1, dy_1, dz_1; \
2160	\
2161	gmx_simd4_float_t__m128 mx, my, mz; \
2162	gmx_simd4_float_t__m128 m0x, m0y, m0z; \
2163	\
2164	gmx_simd4_float_t__m128 d2x, d2y, d2z; \
2165	gmx_simd4_float_t__m128 d2s, d2t; \
2166	\
2167	shi = siNNBSBB_D2DIM3; \
2168	\
2169	xi_l = gmx_simd4_load_f_mm_load_ps(bb_i+shi+0*STRIDE_PBB4); \
2170	yi_l = gmx_simd4_load_f_mm_load_ps(bb_i+shi+1*STRIDE_PBB4); \
2171	zi_l = gmx_simd4_load_f_mm_load_ps(bb_i+shi+2*STRIDE_PBB4); \
2172	xi_h = gmx_simd4_load_f_mm_load_ps(bb_i+shi+3*STRIDE_PBB4); \
2173	yi_h = gmx_simd4_load_f_mm_load_ps(bb_i+shi+4*STRIDE_PBB4); \
2174	zi_h = gmx_simd4_load_f_mm_load_ps(bb_i+shi+5*STRIDE_PBB4); \
2175	\
2176	dx_0 = gmx_simd4_sub_f_mm_sub_ps(xi_l, xj_h); \
2177	dy_0 = gmx_simd4_sub_f_mm_sub_ps(yi_l, yj_h); \
2178	dz_0 = gmx_simd4_sub_f_mm_sub_ps(zi_l, zj_h); \
2179	\
2180	dx_1 = gmx_simd4_sub_f_mm_sub_ps(xj_l, xi_h); \
2181	dy_1 = gmx_simd4_sub_f_mm_sub_ps(yj_l, yi_h); \
2182	dz_1 = gmx_simd4_sub_f_mm_sub_ps(zj_l, zi_h); \
2183	\
2184	mx = gmx_simd4_max_f_mm_max_ps(dx_0, dx_1); \
2185	my = gmx_simd4_max_f_mm_max_ps(dy_0, dy_1); \
2186	mz = gmx_simd4_max_f_mm_max_ps(dz_0, dz_1); \
2187	\
2188	m0x = gmx_simd4_max_f_mm_max_ps(mx, zero); \
2189	m0y = gmx_simd4_max_f_mm_max_ps(my, zero); \
2190	m0z = gmx_simd4_max_f_mm_max_ps(mz, zero); \
2191	\
2192	d2x = gmx_simd4_mul_f_mm_mul_ps(m0x, m0x); \
2193	d2y = gmx_simd4_mul_f_mm_mul_ps(m0y, m0y); \
2194	d2z = gmx_simd4_mul_f_mm_mul_ps(m0z, m0z); \
2195	\
2196	d2s = gmx_simd4_add_f_mm_add_ps(d2x, d2y); \
2197	d2t = gmx_simd4_add_f_mm_add_ps(d2s, d2z); \
2198	\
2199	gmx_simd4_store_f_mm_store_ps(d2+si, d2t); \
2200	}
2201
2202	/* 4-wide SIMD code for nsi bb distances for bb format xxxxyyyyzzzz */
2203	static void subc_bb_dist2_simd4_xxxx(const float *bb_j,
2204	int nsi, const float *bb_i,
2205	float *d2)
2206	{
2207	gmx_simd4_float_t__m128 xj_l, yj_l, zj_l;
2208	gmx_simd4_float_t__m128 xj_h, yj_h, zj_h;
2209	gmx_simd4_float_t__m128 xi_l, yi_l, zi_l;
2210	gmx_simd4_float_t__m128 xi_h, yi_h, zi_h;
2211
2212	gmx_simd4_float_t__m128 zero;
2213
2214	zero = gmx_simd4_setzero_f_mm_setzero_ps();
2215
2216	xj_l = gmx_simd4_set1_f_mm_set1_ps(bb_j[0*STRIDE_PBB4]);
2217	yj_l = gmx_simd4_set1_f_mm_set1_ps(bb_j[1*STRIDE_PBB4]);
2218	zj_l = gmx_simd4_set1_f_mm_set1_ps(bb_j[2*STRIDE_PBB4]);
2219	xj_h = gmx_simd4_set1_f_mm_set1_ps(bb_j[3*STRIDE_PBB4]);
2220	yj_h = gmx_simd4_set1_f_mm_set1_ps(bb_j[4*STRIDE_PBB4]);
2221	zj_h = gmx_simd4_set1_f_mm_set1_ps(bb_j[5*STRIDE_PBB4]);
2222
2223	/* Here we "loop" over si (0,STRIDE_PBB) from 0 to nsi with step STRIDE_PBB.
2224	* But as we know the number of iterations is 1 or 2, we unroll manually.
2225	*/
2226	SUBC_BB_DIST2_SIMD4_XXXX_INNER(0, bb_i, d2){ int shi; __m128 dx_0, dy_0, dz_0; __m128 dx_1, dy_1, dz_1; __m128 mx, my, mz; __m128 m0x, m0y, m0z; __m128 d2x, d2y, d2z; __m128 d2s, d2t; shi = 023; xi_l = _mm_load_ps(bb_i+shi+04); yi_l = _mm_load_ps(bb_i+shi+14); zi_l = _mm_load_ps(bb_i+shi+24 ); xi_h = _mm_load_ps(bb_i+shi+34); yi_h = _mm_load_ps(bb_i+ shi+44); zi_h = _mm_load_ps(bb_i+shi+54); dx_0 = _mm_sub_ps (xi_l, xj_h); dy_0 = _mm_sub_ps(yi_l, yj_h); dz_0 = _mm_sub_ps (zi_l, zj_h); dx_1 = _mm_sub_ps(xj_l, xi_h); dy_1 = _mm_sub_ps (yj_l, yi_h); dz_1 = _mm_sub_ps(zj_l, zi_h); mx = _mm_max_ps( dx_0, dx_1); my = _mm_max_ps(dy_0, dy_1); mz = _mm_max_ps(dz_0 , dz_1); m0x = _mm_max_ps(mx, zero); m0y = _mm_max_ps(my, zero ); m0z = _mm_max_ps(mz, zero); d2x = _mm_mul_ps(m0x, m0x); d2y = _mm_mul_ps(m0y, m0y); d2z = _mm_mul_ps(m0z, m0z); d2s = _mm_add_ps (d2x, d2y); d2t = _mm_add_ps(d2s, d2z); _mm_store_ps(d2+0, d2t ); };
2227	if (STRIDE_PBB4 < nsi)
2228	{
2229	SUBC_BB_DIST2_SIMD4_XXXX_INNER(STRIDE_PBB, bb_i, d2){ int shi; __m128 dx_0, dy_0, dz_0; __m128 dx_1, dy_1, dz_1; __m128 mx, my, mz; __m128 m0x, m0y, m0z; __m128 d2x, d2y, d2z; __m128 d2s, d2t; shi = 423; xi_l = _mm_load_ps(bb_i+shi+04); yi_l = _mm_load_ps(bb_i+shi+14); zi_l = _mm_load_ps(bb_i+shi+24 ); xi_h = _mm_load_ps(bb_i+shi+34); yi_h = _mm_load_ps(bb_i+ shi+44); zi_h = _mm_load_ps(bb_i+shi+54); dx_0 = _mm_sub_ps (xi_l, xj_h); dy_0 = _mm_sub_ps(yi_l, yj_h); dz_0 = _mm_sub_ps (zi_l, zj_h); dx_1 = _mm_sub_ps(xj_l, xi_h); dy_1 = _mm_sub_ps (yj_l, yi_h); dz_1 = _mm_sub_ps(zj_l, zi_h); mx = _mm_max_ps( dx_0, dx_1); my = _mm_max_ps(dy_0, dy_1); mz = _mm_max_ps(dz_0 , dz_1); m0x = _mm_max_ps(mx, zero); m0y = _mm_max_ps(my, zero ); m0z = _mm_max_ps(mz, zero); d2x = _mm_mul_ps(m0x, m0x); d2y = _mm_mul_ps(m0y, m0y); d2z = _mm_mul_ps(m0z, m0z); d2s = _mm_add_ps (d2x, d2y); d2t = _mm_add_ps(d2s, d2z); _mm_store_ps(d2+4, d2t ); };
2230	}
2231	}
2232
2233	#endif /* NBNXN_SEARCH_BB_SIMD4 */
2234
2235	/* Plain C function which determines if any atom pair between two cells
2236	* is within distance sqrt(rl2).
2237	*/
2238	static gmx_bool subc_in_range_x(int na_c,
2239	int si, const real *x_i,
2240	int csj, int stride, const real *x_j,
2241	real rl2)
2242	{
2243	int i, j, i0, j0;
2244	real d2;
2245
2246	for (i = 0; i < na_c; i++)
2247	{
2248	i0 = (sina_c + i)DIM3;
2249	for (j = 0; j < na_c; j++)
2250	{
2251	j0 = (csjna_c + j)stride;
2252
2253	d2 = sqr(x_i[i0 ] - x_j[j0 ]) +
2254	sqr(x_i[i0+1] - x_j[j0+1]) +
2255	sqr(x_i[i0+2] - x_j[j0+2]);
2256
2257	if (d2 < rl2)
2258	{
2259	return TRUE1;
2260	}
2261	}
2262	}
2263
2264	return FALSE0;
2265	}
2266
2267	#ifdef NBNXN_SEARCH_SIMD4_FLOAT_X_BB
2268
2269	/* 4-wide SIMD function which determines if any atom pair between two cells,
2270	* both with 8 atoms, is within distance sqrt(rl2).
2271	* Using 8-wide AVX is not faster on Intel Sandy Bridge.
2272	*/
2273	static gmx_bool subc_in_range_simd4(int na_c,
2274	int si, const real *x_i,
2275	int csj, int stride, const real *x_j,
2276	real rl2)
2277	{
2278	gmx_simd4_real_t__m128 ix_S0, iy_S0, iz_S0;
2279	gmx_simd4_real_t__m128 ix_S1, iy_S1, iz_S1;
2280
2281	gmx_simd4_real_t__m128 rc2_S;
2282
2283	int dim_stride;
2284	int j0, j1;
2285
2286	rc2_S = gmx_simd4_set1_r_mm_set1_ps(rl2);
2287
2288	dim_stride = NBNXN_GPU_CLUSTER_SIZE8/STRIDE_PBB4*DIM3;
2289	ix_S0 = gmx_simd4_load_r_mm_load_ps(x_i+(sidim_stride+0)STRIDE_PBB4);
2290	iy_S0 = gmx_simd4_load_r_mm_load_ps(x_i+(sidim_stride+1)STRIDE_PBB4);
2291	iz_S0 = gmx_simd4_load_r_mm_load_ps(x_i+(sidim_stride+2)STRIDE_PBB4);
2292	ix_S1 = gmx_simd4_load_r_mm_load_ps(x_i+(sidim_stride+3)STRIDE_PBB4);
2293	iy_S1 = gmx_simd4_load_r_mm_load_ps(x_i+(sidim_stride+4)STRIDE_PBB4);
2294	iz_S1 = gmx_simd4_load_r_mm_load_ps(x_i+(sidim_stride+5)STRIDE_PBB4);
2295
2296	/* We loop from the outer to the inner particles to maximize
2297	* the chance that we find a pair in range quickly and return.
2298	*/
2299	j0 = csj*na_c;
2300	j1 = j0 + na_c - 1;
2301	while (j0 < j1)
2302	{
2303	gmx_simd4_real_t__m128 jx0_S, jy0_S, jz0_S;
2304	gmx_simd4_real_t__m128 jx1_S, jy1_S, jz1_S;
2305
2306	gmx_simd4_real_t__m128 dx_S0, dy_S0, dz_S0;
2307	gmx_simd4_real_t__m128 dx_S1, dy_S1, dz_S1;
2308	gmx_simd4_real_t__m128 dx_S2, dy_S2, dz_S2;
2309	gmx_simd4_real_t__m128 dx_S3, dy_S3, dz_S3;
2310
2311	gmx_simd4_real_t__m128 rsq_S0;
2312	gmx_simd4_real_t__m128 rsq_S1;
2313	gmx_simd4_real_t__m128 rsq_S2;
2314	gmx_simd4_real_t__m128 rsq_S3;
2315
2316	gmx_simd4_bool_t__m128 wco_S0;
2317	gmx_simd4_bool_t__m128 wco_S1;
2318	gmx_simd4_bool_t__m128 wco_S2;
2319	gmx_simd4_bool_t__m128 wco_S3;
2320	gmx_simd4_bool_t__m128 wco_any_S01, wco_any_S23, wco_any_S;
2321
2322	jx0_S = gmx_simd4_set1_r_mm_set1_ps(x_j[j0*stride+0]);
2323	jy0_S = gmx_simd4_set1_r_mm_set1_ps(x_j[j0*stride+1]);
2324	jz0_S = gmx_simd4_set1_r_mm_set1_ps(x_j[j0*stride+2]);
2325
2326	jx1_S = gmx_simd4_set1_r_mm_set1_ps(x_j[j1*stride+0]);
2327	jy1_S = gmx_simd4_set1_r_mm_set1_ps(x_j[j1*stride+1]);
2328	jz1_S = gmx_simd4_set1_r_mm_set1_ps(x_j[j1*stride+2]);
2329
2330	/* Calculate distance */
2331	dx_S0 = gmx_simd4_sub_r_mm_sub_ps(ix_S0, jx0_S);
2332	dy_S0 = gmx_simd4_sub_r_mm_sub_ps(iy_S0, jy0_S);
2333	dz_S0 = gmx_simd4_sub_r_mm_sub_ps(iz_S0, jz0_S);
2334	dx_S1 = gmx_simd4_sub_r_mm_sub_ps(ix_S1, jx0_S);
2335	dy_S1 = gmx_simd4_sub_r_mm_sub_ps(iy_S1, jy0_S);
2336	dz_S1 = gmx_simd4_sub_r_mm_sub_ps(iz_S1, jz0_S);
2337	dx_S2 = gmx_simd4_sub_r_mm_sub_ps(ix_S0, jx1_S);
2338	dy_S2 = gmx_simd4_sub_r_mm_sub_ps(iy_S0, jy1_S);
2339	dz_S2 = gmx_simd4_sub_r_mm_sub_ps(iz_S0, jz1_S);
2340	dx_S3 = gmx_simd4_sub_r_mm_sub_ps(ix_S1, jx1_S);
2341	dy_S3 = gmx_simd4_sub_r_mm_sub_ps(iy_S1, jy1_S);
2342	dz_S3 = gmx_simd4_sub_r_mm_sub_ps(iz_S1, jz1_S);
2343
2344	/* rsq = dxdx+dydy+dzdz /
2345	rsq_S0 = gmx_simd4_calc_rsq_rgmx_simd4_norm2_f(dx_S0, dy_S0, dz_S0);
2346	rsq_S1 = gmx_simd4_calc_rsq_rgmx_simd4_norm2_f(dx_S1, dy_S1, dz_S1);
2347	rsq_S2 = gmx_simd4_calc_rsq_rgmx_simd4_norm2_f(dx_S2, dy_S2, dz_S2);
2348	rsq_S3 = gmx_simd4_calc_rsq_rgmx_simd4_norm2_f(dx_S3, dy_S3, dz_S3);
2349
2350	wco_S0 = gmx_simd4_cmplt_r_mm_cmplt_ps(rsq_S0, rc2_S);
2351	wco_S1 = gmx_simd4_cmplt_r_mm_cmplt_ps(rsq_S1, rc2_S);
2352	wco_S2 = gmx_simd4_cmplt_r_mm_cmplt_ps(rsq_S2, rc2_S);
2353	wco_S3 = gmx_simd4_cmplt_r_mm_cmplt_ps(rsq_S3, rc2_S);
2354
2355	wco_any_S01 = gmx_simd4_or_b_mm_or_ps(wco_S0, wco_S1);
2356	wco_any_S23 = gmx_simd4_or_b_mm_or_ps(wco_S2, wco_S3);
2357	wco_any_S = gmx_simd4_or_b_mm_or_ps(wco_any_S01, wco_any_S23);
2358
2359	if (gmx_simd4_anytrue_b_mm_movemask_ps(wco_any_S))
2360	{
2361	return TRUE1;
2362	}
2363
2364	j0++;
2365	j1--;
2366	}
2367	return FALSE0;
2368
2369	}
2370	#endif
2371
2372
2373	/* Returns the j sub-cell for index cj_ind */
2374	static int nbl_cj(const nbnxn_pairlist_t *nbl, int cj_ind)
2375	{
2376	return nbl->cj4[cj_ind >> NBNXN_GPU_JGROUP_SIZE_2LOG2].cj[cj_ind & (NBNXN_GPU_JGROUP_SIZE4 - 1)];
2377	}
2378
2379	/* Returns the i-interaction mask of the j sub-cell for index cj_ind */
2380	static unsigned int nbl_imask0(const nbnxn_pairlist_t *nbl, int cj_ind)
2381	{
2382	return nbl->cj4[cj_ind >> NBNXN_GPU_JGROUP_SIZE_2LOG2].imei[0].imask;
2383	}
2384
2385	/* Ensures there is enough space for extra extra exclusion masks */
2386	static void check_excl_space(nbnxn_pairlist_t *nbl, int extra)
2387	{
2388	if (nbl->nexcl+extra > nbl->excl_nalloc)
2389	{
2390	nbl->excl_nalloc = over_alloc_small(nbl->nexcl+extra)(int)(1.19*(nbl->nexcl+extra) + 8000);
2391	nbnxn_realloc_void((void **)&nbl->excl,
2392	nbl->nexclsizeof(nbl->excl),
2393	nbl->excl_nallocsizeof(nbl->excl),
2394	nbl->alloc, nbl->free);
2395	}
2396	}
2397
2398	/* Ensures there is enough space for ncell extra j-cells in the list */
2399	static void check_subcell_list_space_simple(nbnxn_pairlist_t *nbl,
2400	int ncell)
2401	{
2402	int cj_max;
2403
2404	cj_max = nbl->ncj + ncell;
2405
2406	if (cj_max > nbl->cj_nalloc)
2407	{
2408	nbl->cj_nalloc = over_alloc_small(cj_max)(int)(1.19*(cj_max) + 8000);
2409	nbnxn_realloc_void((void **)&nbl->cj,
2410	nbl->ncjsizeof(nbl->cj),
2411	nbl->cj_nallocsizeof(nbl->cj),
2412	nbl->alloc, nbl->free);
2413	}
2414	}
2415
2416	/* Ensures there is enough space for ncell extra j-subcells in the list */
2417	static void check_subcell_list_space_supersub(nbnxn_pairlist_t *nbl,
2418	int nsupercell)
2419	{
2420	int ncj4_max, j4, j, w, t;
2421
2422	#define NWARP2 2
2423	#define WARP_SIZE32 32
2424
2425	/* We can have maximally nsupercellGPU_NSUBCELL sj lists /
2426	/* We can store 4 j-subcell - i-supercell pairs in one struct.
2427	* since we round down, we need one extra entry.
2428	*/
2429	ncj4_max = ((nbl->work->cj_ind + nsupercellGPU_NSUBCELL(22*2) + NBNXN_GPU_JGROUP_SIZE4 - 1) >> NBNXN_GPU_JGROUP_SIZE_2LOG2);
2430
2431	if (ncj4_max > nbl->cj4_nalloc)
2432	{
2433	nbl->cj4_nalloc = over_alloc_small(ncj4_max)(int)(1.19*(ncj4_max) + 8000);
2434	nbnxn_realloc_void((void **)&nbl->cj4,
2435	nbl->work->cj4_initsizeof(nbl->cj4),
2436	nbl->cj4_nallocsizeof(nbl->cj4),
2437	nbl->alloc, nbl->free);
2438	}
2439
2440	if (ncj4_max > nbl->work->cj4_init)
2441	{
2442	for (j4 = nbl->work->cj4_init; j4 < ncj4_max; j4++)
2443	{
2444	/* No i-subcells and no excl's in the list initially */
2445	for (w = 0; w < NWARP2; w++)
2446	{
2447	nbl->cj4[j4].imei[w].imask = 0U;
2448	nbl->cj4[j4].imei[w].excl_ind = 0;
2449
2450	}
2451	}
2452	nbl->work->cj4_init = ncj4_max;
2453	}
2454	}
2455
2456	/* Set all excl masks for one GPU warp no exclusions */
2457	static void set_no_excls(nbnxn_excl_t *excl)
2458	{
2459	int t;
2460
2461	for (t = 0; t < WARP_SIZE32; t++)
2462	{
2463	/* Turn all interaction bits on */
2464	excl->pair[t] = NBNXN_INTERACTION_MASK_ALL;
2465	}
2466	}
2467
2468	/* Initializes a single nbnxn_pairlist_t data structure */
2469	static void nbnxn_init_pairlist(nbnxn_pairlist_t *nbl,
2470	gmx_bool bSimple,
2471	nbnxn_alloc_t *alloc,
2472	nbnxn_free_t *free)
2473	{
2474	if (alloc == NULL((void*)0))
2475	{
2476	nbl->alloc = nbnxn_alloc_aligned;
2477	}
2478	else
2479	{
2480	nbl->alloc = alloc;
2481	}
2482	if (free == NULL((void*)0))
2483	{
2484	nbl->free = nbnxn_free_aligned;
2485	}
2486	else
2487	{
2488	nbl->free = free;
2489	}
2490
2491	nbl->bSimple = bSimple;
2492	nbl->na_sc = 0;
2493	nbl->na_ci = 0;
2494	nbl->na_cj = 0;
2495	nbl->nci = 0;
2496	nbl->ci = NULL((void*)0);
2497	nbl->ci_nalloc = 0;
2498	nbl->ncj = 0;
2499	nbl->cj = NULL((void*)0);
2500	nbl->cj_nalloc = 0;
2501	nbl->ncj4 = 0;
2502	/* We need one element extra in sj, so alloc initially with 1 */
2503	nbl->cj4_nalloc = 0;
2504	nbl->cj4 = NULL((void*)0);
2505	nbl->nci_tot = 0;
2506
2507	if (!nbl->bSimple)
2508	{
2509	nbl->excl = NULL((void*)0);
2510	nbl->excl_nalloc = 0;
2511	nbl->nexcl = 0;
2512	check_excl_space(nbl, 1);
2513	nbl->nexcl = 1;
2514	set_no_excls(&nbl->excl[0]);
2515	}
2516
2517	snew(nbl->work, 1)(nbl->work) = save_calloc("nbl->work", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2517, (1), sizeof(*(nbl->work)));
2518	if (nbl->bSimple)
2519	{
2520	snew_aligned(nbl->work->bb_ci, 1, NBNXN_SEARCH_BB_MEM_ALIGN)(nbl->work->bb_ci) = save_calloc_aligned("nbl->work->bb_ci" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2520, (1), sizeof((nbl->work->bb_ci)), (4sizeof(float )));
2521	}
2522	else
2523	{
2524	#ifdef NBNXN_BBXXXX
2525	snew_aligned(nbl->work->pbb_ci, GPU_NSUBCELL/STRIDE_PBBNNBSBB_XXXX, NBNXN_SEARCH_BB_MEM_ALIGN)(nbl->work->pbb_ci) = save_calloc_aligned("nbl->work->pbb_ci" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2525, ((222)/4(234)), sizeof((nbl->work->pbb_ci )), (4sizeof(float)));
2526	#else
2527	snew_aligned(nbl->work->bb_ci, GPU_NSUBCELL, NBNXN_SEARCH_BB_MEM_ALIGN)(nbl->work->bb_ci) = save_calloc_aligned("nbl->work->bb_ci" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2527, ((222)), sizeof((nbl->work->bb_ci)), (4sizeof (float)));
2528	#endif
2529	}
2530	snew_aligned(nbl->work->x_ci, NBNXN_NA_SC_MAXDIM, NBNXN_SEARCH_BB_MEM_ALIGN)(nbl->work->x_ci) = save_calloc_aligned("nbl->work->x_ci" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2530, (((222)8)3), sizeof((nbl->work->x_ci)), (4 *sizeof(float)));
2531	#ifdef GMX_NBNXN_SIMD
2532	snew_aligned(nbl->work->x_ci_simd_4xn, 1, NBNXN_MEM_ALIGN)(nbl->work->x_ci_simd_4xn) = save_calloc_aligned("nbl->work->x_ci_simd_4xn" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2532, (1), sizeof((nbl->work->x_ci_simd_4xn)), (4sizeof (real)));
2533	snew_aligned(nbl->work->x_ci_simd_2xnn, 1, NBNXN_MEM_ALIGN)(nbl->work->x_ci_simd_2xnn) = save_calloc_aligned("nbl->work->x_ci_simd_2xnn" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2533, (1), sizeof((nbl->work->x_ci_simd_2xnn)), (4sizeof (real)));
2534	#endif
2535	snew_aligned(nbl->work->d2, GPU_NSUBCELL, NBNXN_SEARCH_BB_MEM_ALIGN)(nbl->work->d2) = save_calloc_aligned("nbl->work->d2" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2535, ((222)), sizeof((nbl->work->d2)), (4sizeof( float)));
2536
2537	nbl->work->sort = NULL((void*)0);
2538	nbl->work->sort_nalloc = 0;
2539	nbl->work->sci_sort = NULL((void*)0);
2540	nbl->work->sci_sort_nalloc = 0;
2541	}
2542
2543	void nbnxn_init_pairlist_set(nbnxn_pairlist_set_t *nbl_list,
2544	gmx_bool bSimple, gmx_bool bCombined,
2545	nbnxn_alloc_t *alloc,
2546	nbnxn_free_t *free)
2547	{
2548	int i;
2549
2550	nbl_list->bSimple = bSimple;
2551	nbl_list->bCombined = bCombined;
2552
2553	nbl_list->nnbl = gmx_omp_nthreads_get(emntNonbonded);
2554
2555	if (!nbl_list->bCombined &&
2556	nbl_list->nnbl > NBNXN_BUFFERFLAG_MAX_THREADS32)
2557	{
2558	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2558, "%d OpenMP threads were requested. Since the non-bonded force buffer reduction is prohibitively slow with more than %d threads, we do not allow this. Use %d or less OpenMP threads.",
2559	nbl_list->nnbl, NBNXN_BUFFERFLAG_MAX_THREADS32, NBNXN_BUFFERFLAG_MAX_THREADS32);
2560	}
2561
2562	snew(nbl_list->nbl, nbl_list->nnbl)(nbl_list->nbl) = save_calloc("nbl_list->nbl", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2562, (nbl_list->nnbl), sizeof(*(nbl_list->nbl)));
2563	snew(nbl_list->nbl_fep, nbl_list->nnbl)(nbl_list->nbl_fep) = save_calloc("nbl_list->nbl_fep", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2563, (nbl_list->nnbl), sizeof(*(nbl_list->nbl_fep)));
2564	/* Execute in order to avoid memory interleaving between threads */
2565	#pragma omp parallel for num_threads(nbl_list->nnbl) schedule(static)
2566	for (i = 0; i < nbl_list->nnbl; i++)
2567	{
2568	/* Allocate the nblist data structure locally on each thread
2569	* to optimize memory access for NUMA architectures.
2570	*/
2571	snew(nbl_list->nbl[i], 1)(nbl_list->nbl[i]) = save_calloc("nbl_list->nbl[i]", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2571, (1), sizeof(*(nbl_list->nbl[i])));
2572
2573	/* Only list 0 is used on the GPU, use normal allocation for i>0 */
2574	if (i == 0)
2575	{
2576	nbnxn_init_pairlist(nbl_list->nbl[i], nbl_list->bSimple, alloc, free);
2577	}
2578	else
2579	{
2580	nbnxn_init_pairlist(nbl_list->nbl[i], nbl_list->bSimple, NULL((void)0), NULL((void)0));
2581	}
2582
2583	snew(nbl_list->nbl_fep[i], 1)(nbl_list->nbl_fep[i]) = save_calloc("nbl_list->nbl_fep[i]" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 2583, (1), sizeof(*(nbl_list->nbl_fep[i])));
2584	nbnxn_init_pairlist_fep(nbl_list->nbl_fep[i]);
2585	}
2586	}
2587
2588	/* Print statistics of a pair list, used for debug output */
2589	static void print_nblist_statistics_simple(FILE fp, const nbnxn_pairlist_t nbl,
2590	const nbnxn_search_t nbs, real rl)
2591	{
2592	const nbnxn_grid_t *grid;
2593	int cs[SHIFTS((21 +1)(21 +1)(2*2 +1))];
2594	int s, i, j;
2595	int npexcl;
2596
2597	/* This code only produces correct statistics with domain decomposition */
2598	grid = &nbs->grid[0];
2599
2600	fprintf(fp, "nbl nci %d ncj %d\n",
2601	nbl->nci, nbl->ncj);
2602	fprintf(fp, "nbl na_sc %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
2603	nbl->na_sc, rl, nbl->ncj, nbl->ncj/(double)grid->nc,
2604	nbl->ncj/(double)grid->nc*grid->na_sc,
2605	nbl->ncj/(double)grid->ncgrid->na_sc/(0.54.0/3.0M_PI3.14159265358979323846rlrlrlgrid->ncgrid->na_sc/det(nbs->box)));
2606
2607	fprintf(fp, "nbl average j cell list length %.1f\n",
2608	0.25*nbl->ncj/(double)nbl->nci);
2609
2610	for (s = 0; s < SHIFTS((21 +1)(21 +1)(2*2 +1)); s++)
2611	{
2612	cs[s] = 0;
2613	}
2614	npexcl = 0;
2615	for (i = 0; i < nbl->nci; i++)
2616	{
2617	cs[nbl->ci[i].shift & NBNXN_CI_SHIFT127] +=
2618	nbl->ci[i].cj_ind_end - nbl->ci[i].cj_ind_start;
2619
2620	j = nbl->ci[i].cj_ind_start;
2621	while (j < nbl->ci[i].cj_ind_end &&
2622	nbl->cj[j].excl != NBNXN_INTERACTION_MASK_ALL)
2623	{
2624	npexcl++;
2625	j++;
2626	}
2627	}
2628	fprintf(fp, "nbl cell pairs, total: %d excl: %d %.1f%%\n",
2629	nbl->ncj, npexcl, 100*npexcl/(double)nbl->ncj);
2630	for (s = 0; s < SHIFTS((21 +1)(21 +1)(2*2 +1)); s++)
2631	{
2632	if (cs[s] > 0)
2633	{
2634	fprintf(fp, "nbl shift %2d ncj %3d\n", s, cs[s]);
2635	}
2636	}
2637	}
2638
2639	/* Print statistics of a pair lists, used for debug output */
2640	static void print_nblist_statistics_supersub(FILE fp, const nbnxn_pairlist_t nbl,
2641	const nbnxn_search_t nbs, real rl)
2642	{
2643	const nbnxn_grid_t *grid;
2644	int i, j4, j, si, b;
2645	int c[GPU_NSUBCELL(222)+1];
2646
2647	/* This code only produces correct statistics with domain decomposition */
2648	grid = &nbs->grid[0];
2649
2650	fprintf(fp, "nbl nsci %d ncj4 %d nsi %d excl4 %d\n",
2651	nbl->nsci, nbl->ncj4, nbl->nci_tot, nbl->nexcl);
2652	fprintf(fp, "nbl na_c %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
2653	nbl->na_ci, rl, nbl->nci_tot, nbl->nci_tot/(double)grid->nsubc_tot,
2654	nbl->nci_tot/(double)grid->nsubc_tot*grid->na_c,
2655	nbl->nci_tot/(double)grid->nsubc_totgrid->na_c/(0.54.0/3.0M_PI3.14159265358979323846rlrlrlgrid->nsubc_totgrid->na_c/det(nbs->box)));
2656
2657	fprintf(fp, "nbl average j super cell list length %.1f\n",
2658	0.25*nbl->ncj4/(double)nbl->nsci);
2659	fprintf(fp, "nbl average i sub cell list length %.1f\n",
2660	nbl->nci_tot/((double)nbl->ncj4));
2661
2662	for (si = 0; si <= GPU_NSUBCELL(222); si++)
2663	{
2664	c[si] = 0;
2665	}
2666	for (i = 0; i < nbl->nsci; i++)
2667	{
2668	for (j4 = nbl->sci[i].cj4_ind_start; j4 < nbl->sci[i].cj4_ind_end; j4++)
2669	{
2670	for (j = 0; j < NBNXN_GPU_JGROUP_SIZE4; j++)
2671	{
2672	b = 0;
2673	for (si = 0; si < GPU_NSUBCELL(222); si++)
2674	{
2675	if (nbl->cj4[j4].imei[0].imask & (1U << (jGPU_NSUBCELL(22*2) + si)))
2676	{
2677	b++;
2678	}
2679	}
2680	c[b]++;
2681	}
2682	}
2683	}
2684	for (b = 0; b <= GPU_NSUBCELL(222); b++)
2685	{
2686	fprintf(fp, "nbl j-list #i-subcell %d %7d %4.1f\n",
2687	b, c[b], 100.0c[b]/(double)(nbl->ncj4NBNXN_GPU_JGROUP_SIZE4));
2688	}
2689	}
2690
2691	/* Returns a pointer to the exclusion mask for cj4-unit cj4, warp warp */
2692	static void low_get_nbl_exclusions(nbnxn_pairlist_t *nbl, int cj4,
2693	int warp, nbnxn_excl_t **excl)
2694	{
2695	if (nbl->cj4[cj4].imei[warp].excl_ind == 0)
2696	{
2697	/* No exclusions set, make a new list entry */
2698	nbl->cj4[cj4].imei[warp].excl_ind = nbl->nexcl;
2699	nbl->nexcl++;
2700	*excl = &nbl->excl[nbl->cj4[cj4].imei[warp].excl_ind];
2701	set_no_excls(*excl);
2702	}
2703	else
2704	{
2705	/* We already have some exclusions, new ones can be added to the list */
2706	*excl = &nbl->excl[nbl->cj4[cj4].imei[warp].excl_ind];
2707	}
2708	}
2709
2710	/* Returns a pointer to the exclusion mask for cj4-unit cj4, warp warp,
2711	* generates a new element and allocates extra memory, if necessary.
2712	*/
2713	static void get_nbl_exclusions_1(nbnxn_pairlist_t *nbl, int cj4,
2714	int warp, nbnxn_excl_t **excl)
2715	{
2716	if (nbl->cj4[cj4].imei[warp].excl_ind == 0)
2717	{
2718	/* We need to make a new list entry, check if we have space */
2719	check_excl_space(nbl, 1);
2720	}
2721	low_get_nbl_exclusions(nbl, cj4, warp, excl);
2722	}
2723
2724	/* Returns pointers to the exclusion mask for cj4-unit cj4 for both warps,
2725	* generates a new element and allocates extra memory, if necessary.
2726	*/
2727	static void get_nbl_exclusions_2(nbnxn_pairlist_t *nbl, int cj4,
2728	nbnxn_excl_t **excl_w0,
2729	nbnxn_excl_t **excl_w1)
2730	{
2731	/* Check for space we might need */
2732	check_excl_space(nbl, 2);
2733
2734	low_get_nbl_exclusions(nbl, cj4, 0, excl_w0);
2735	low_get_nbl_exclusions(nbl, cj4, 1, excl_w1);
2736	}
2737
2738	/* Sets the self exclusions i=j and pair exclusions i>j */
2739	static void set_self_and_newton_excls_supersub(nbnxn_pairlist_t *nbl,
2740	int cj4_ind, int sj_offset,
2741	int si)
2742	{
2743	nbnxn_excl_t *excl[2];
2744	int ei, ej, w;
2745
2746	/* Here we only set the set self and double pair exclusions */
2747
2748	get_nbl_exclusions_2(nbl, cj4_ind, &excl[0], &excl[1]);
2749
2750	/* Only minor < major bits set */
2751	for (ej = 0; ej < nbl->na_ci; ej++)
2752	{
2753	w = (ej>>2);
2754	for (ei = ej; ei < nbl->na_ci; ei++)
2755	{
2756	excl[w]->pair[(ej & (NBNXN_GPU_JGROUP_SIZE4-1))*nbl->na_ci + ei] &=
2757	~(1U << (sj_offsetGPU_NSUBCELL(22*2) + si));
2758	}
2759	}
2760	}
2761
2762	/* Returns a diagonal or off-diagonal interaction mask for plain C lists */
2763	static unsigned int get_imask(gmx_bool rdiag, int ci, int cj)
2764	{
2765	return (rdiag && ci == cj ? NBNXN_INTERACTION_MASK_DIAG : NBNXN_INTERACTION_MASK_ALL);
2766	}
2767
2768	/* Returns a diagonal or off-diagonal interaction mask for cj-size=2 */
2769	static unsigned int get_imask_simd_j2(gmx_bool rdiag, int ci, int cj)
2770	{
2771	return (rdiag && ci*2 == cj ? NBNXN_INTERACTION_MASK_DIAG_J2_0 :
2772	(rdiag && ci*2+1 == cj ? NBNXN_INTERACTION_MASK_DIAG_J2_1 :
2773	NBNXN_INTERACTION_MASK_ALL));
2774	}
2775
2776	/* Returns a diagonal or off-diagonal interaction mask for cj-size=4 */
2777	static unsigned int get_imask_simd_j4(gmx_bool rdiag, int ci, int cj)
2778	{
2779	return (rdiag && ci == cj ? NBNXN_INTERACTION_MASK_DIAG : NBNXN_INTERACTION_MASK_ALL);
2780	}
2781
2782	/* Returns a diagonal or off-diagonal interaction mask for cj-size=8 */
2783	static unsigned int get_imask_simd_j8(gmx_bool rdiag, int ci, int cj)
2784	{
2785	return (rdiag && ci == cj*2 ? NBNXN_INTERACTION_MASK_DIAG_J8_0 :
2786	(rdiag && ci == cj*2+1 ? NBNXN_INTERACTION_MASK_DIAG_J8_1 :
2787	NBNXN_INTERACTION_MASK_ALL));
2788	}
2789
2790	#ifdef GMX_NBNXN_SIMD
2791	#if GMX_SIMD_REAL_WIDTH4 == 2
2792	#define get_imask_simd_4xnget_imask_simd_j4 get_imask_simd_j2
2793	#endif
2794	#if GMX_SIMD_REAL_WIDTH4 == 4
2795	#define get_imask_simd_4xnget_imask_simd_j4 get_imask_simd_j4
2796	#endif
2797	#if GMX_SIMD_REAL_WIDTH4 == 8
2798	#define get_imask_simd_4xnget_imask_simd_j4 get_imask_simd_j8
2799	#define get_imask_simd_2xnn get_imask_simd_j4
2800	#endif
2801	#if GMX_SIMD_REAL_WIDTH4 == 16
2802	#define get_imask_simd_2xnn get_imask_simd_j8
2803	#endif
2804	#endif
2805
2806	/* Plain C code for making a pair list of cell ci vs cell cjf-cjl.
2807	* Checks bounding box distances and possibly atom pair distances.
2808	*/
2809	static void make_cluster_list_simple(const nbnxn_grid_t *gridj,
2810	nbnxn_pairlist_t *nbl,
2811	int ci, int cjf, int cjl,
2812	gmx_bool remove_sub_diag,
2813	const real *x_j,
2814	real rl2, float rbb2,
2815	int *ndistc)
2816	{
2817	const nbnxn_list_work_t *work;
2818
2819	const nbnxn_bb_t *bb_ci;
2820	const real *x_ci;
2821
2822	gmx_bool InRange;
2823	real d2;
2824	int cjf_gl, cjl_gl, cj;
2825
2826	work = nbl->work;
	Value stored to 'work' is never read
2827
2828	bb_ci = nbl->work->bb_ci;
2829	x_ci = nbl->work->x_ci;
2830
2831	InRange = FALSE0;
2832	while (!InRange && cjf <= cjl)
2833	{
2834	d2 = subc_bb_dist2(0, bb_ci, cjf, gridj->bb);
2835	*ndistc += 2;
2836
2837	/* Check if the distance is within the distance where
2838	* we use only the bounding box distance rbb,
2839	* or within the cut-off and there is at least one atom pair
2840	* within the cut-off.
2841	*/
2842	if (d2 < rbb2)
2843	{
2844	InRange = TRUE1;
2845	}
2846	else if (d2 < rl2)
2847	{
2848	int i, j;
2849
2850	cjf_gl = gridj->cell0 + cjf;
2851	for (i = 0; i < NBNXN_CPU_CLUSTER_I_SIZE4 && !InRange; i++)
2852	{
2853	for (j = 0; j < NBNXN_CPU_CLUSTER_I_SIZE4; j++)
2854	{
2855	InRange = InRange \|\|
2856	(sqr(x_ci[iSTRIDE_XYZ3+XX0] - x_j[(cjf_glNBNXN_CPU_CLUSTER_I_SIZE4+j)*STRIDE_XYZ3+XX0]) +
2857	sqr(x_ci[iSTRIDE_XYZ3+YY1] - x_j[(cjf_glNBNXN_CPU_CLUSTER_I_SIZE4+j)*STRIDE_XYZ3+YY1]) +
2858	sqr(x_ci[iSTRIDE_XYZ3+ZZ2] - x_j[(cjf_glNBNXN_CPU_CLUSTER_I_SIZE4+j)*STRIDE_XYZ3+ZZ2]) < rl2);
2859	}
2860	}
2861	ndistc += NBNXN_CPU_CLUSTER_I_SIZE4NBNXN_CPU_CLUSTER_I_SIZE4;
2862	}
2863	if (!InRange)
2864	{
2865	cjf++;
2866	}
2867	}
2868	if (!InRange)
2869	{
2870	return;
2871	}
2872
2873	InRange = FALSE0;
2874	while (!InRange && cjl > cjf)
2875	{
2876	d2 = subc_bb_dist2(0, bb_ci, cjl, gridj->bb);
2877	*ndistc += 2;
2878
2879	/* Check if the distance is within the distance where
2880	* we use only the bounding box distance rbb,
2881	* or within the cut-off and there is at least one atom pair
2882	* within the cut-off.
2883	*/
2884	if (d2 < rbb2)
2885	{
2886	InRange = TRUE1;
2887	}
2888	else if (d2 < rl2)
2889	{
2890	int i, j;
2891
2892	cjl_gl = gridj->cell0 + cjl;
2893	for (i = 0; i < NBNXN_CPU_CLUSTER_I_SIZE4 && !InRange; i++)
2894	{
2895	for (j = 0; j < NBNXN_CPU_CLUSTER_I_SIZE4; j++)
2896	{
2897	InRange = InRange \|\|
2898	(sqr(x_ci[iSTRIDE_XYZ3+XX0] - x_j[(cjl_glNBNXN_CPU_CLUSTER_I_SIZE4+j)*STRIDE_XYZ3+XX0]) +
2899	sqr(x_ci[iSTRIDE_XYZ3+YY1] - x_j[(cjl_glNBNXN_CPU_CLUSTER_I_SIZE4+j)*STRIDE_XYZ3+YY1]) +
2900	sqr(x_ci[iSTRIDE_XYZ3+ZZ2] - x_j[(cjl_glNBNXN_CPU_CLUSTER_I_SIZE4+j)*STRIDE_XYZ3+ZZ2]) < rl2);
2901	}
2902	}
2903	ndistc += NBNXN_CPU_CLUSTER_I_SIZE4NBNXN_CPU_CLUSTER_I_SIZE4;
2904	}
2905	if (!InRange)
2906	{
2907	cjl--;
2908	}
2909	}
2910
2911	if (cjf <= cjl)
2912	{
2913	for (cj = cjf; cj <= cjl; cj++)
2914	{
2915	/* Store cj and the interaction mask */
2916	nbl->cj[nbl->ncj].cj = gridj->cell0 + cj;
2917	nbl->cj[nbl->ncj].excl = get_imask(remove_sub_diag, ci, cj);
2918	nbl->ncj++;
2919	}
2920	/* Increase the closing index in i super-cell list */
2921	nbl->ci[nbl->nci].cj_ind_end = nbl->ncj;
2922	}
2923	}
2924
2925	#ifdef GMX_NBNXN_SIMD_4XN
2926	#include "nbnxn_search_simd_4xn.h"
2927	#endif
2928	#ifdef GMX_NBNXN_SIMD_2XNN
2929	#include "nbnxn_search_simd_2xnn.h"
2930	#endif
2931
2932	/* Plain C or SIMD4 code for making a pair list of super-cell sci vs scj.
2933	* Checks bounding box distances and possibly atom pair distances.
2934	*/
2935	static void make_cluster_list_supersub(const nbnxn_grid_t *gridi,
2936	const nbnxn_grid_t *gridj,
2937	nbnxn_pairlist_t *nbl,
2938	int sci, int scj,
2939	gmx_bool sci_equals_scj,
2940	int stride, const real *x,
2941	real rl2, float rbb2,
2942	int *ndistc)
2943	{
2944	int na_c;
2945	int npair;
2946	int cjo, ci1, ci, cj, cj_gl;
2947	int cj4_ind, cj_offset;
2948	unsigned int imask;
2949	nbnxn_cj4_t *cj4;
2950	#ifdef NBNXN_BBXXXX
2951	const float *pbb_ci;
2952	#else
2953	const nbnxn_bb_t *bb_ci;
2954	#endif
2955	const real *x_ci;
2956	float *d2l, d2;
2957	int w;
2958	#define PRUNE_LIST_CPU_ONE
2959	#ifdef PRUNE_LIST_CPU_ONE
2960	int ci_last = -1;
2961	#endif
2962
2963	d2l = nbl->work->d2;
2964
2965	#ifdef NBNXN_BBXXXX
2966	pbb_ci = nbl->work->pbb_ci;
2967	#else
2968	bb_ci = nbl->work->bb_ci;
2969	#endif
2970	x_ci = nbl->work->x_ci;
2971
2972	na_c = gridj->na_c;
2973
2974	for (cjo = 0; cjo < gridj->nsubc[scj]; cjo++)
2975	{
2976	cj4_ind = (nbl->work->cj_ind >> NBNXN_GPU_JGROUP_SIZE_2LOG2);
2977	cj_offset = nbl->work->cj_ind - cj4_ind*NBNXN_GPU_JGROUP_SIZE4;
2978	cj4 = &nbl->cj4[cj4_ind];
2979
2980	cj = scjGPU_NSUBCELL(22*2) + cjo;
2981
2982	cj_gl = gridj->cell0GPU_NSUBCELL(22*2) + cj;
2983
2984	/* Initialize this j-subcell i-subcell list */
2985	cj4->cj[cj_offset] = cj_gl;
2986	imask = 0;
2987
2988	if (sci_equals_scj)
2989	{
2990	ci1 = cjo + 1;
2991	}
2992	else
2993	{
2994	ci1 = gridi->nsubc[sci];
2995	}
2996
2997	#ifdef NBNXN_BBXXXX
2998	/* Determine all ci1 bb distances in one call with SIMD4 */
2999	subc_bb_dist2_simd4_xxxx(gridj->pbb+(cj>>STRIDE_PBB_2LOG2)NNBSBB_XXXX(23*4)+(cj & (STRIDE_PBB4-1)),
3000	ci1, pbb_ci, d2l);
3001	ndistc += na_c2;
3002	#endif
3003
3004	npair = 0;
3005	/* We use a fixed upper-bound instead of ci1 to help optimization */
3006	for (ci = 0; ci < GPU_NSUBCELL(222); ci++)
3007	{
3008	if (ci == ci1)
3009	{
3010	break;
3011	}
3012
3013	#ifndef NBNXN_BBXXXX
3014	/* Determine the bb distance between ci and cj */
3015	d2l[ci] = subc_bb_dist2(ci, bb_ci, cj, gridj->bb);
3016	*ndistc += 2;
3017	#endif
3018	d2 = d2l[ci];
3019
3020	#ifdef PRUNE_LIST_CPU_ALL
3021	/* Check if the distance is within the distance where
3022	* we use only the bounding box distance rbb,
3023	* or within the cut-off and there is at least one atom pair
3024	* within the cut-off. This check is very costly.
3025	*/
3026	ndistc += na_cna_c;
3027	if (d2 < rbb2 \|\|
3028	(d2 < rl2 &&
3029	#ifdef NBNXN_PBB_SIMD4
3030	subc_in_range_simd4
3031	#else
3032	subc_in_range_x
3033	#endif
3034	(na_c, ci, x_ci, cj_gl, stride, x, rl2)))
3035	#else
3036	/* Check if the distance between the two bounding boxes
3037	* in within the pair-list cut-off.
3038	*/
3039	if (d2 < rl2)
3040	#endif
3041	{
3042	/* Flag this i-subcell to be taken into account */
3043	imask \|= (1U << (cj_offsetGPU_NSUBCELL(22*2)+ci));
3044
3045	#ifdef PRUNE_LIST_CPU_ONE
3046	ci_last = ci;
3047	#endif
3048
3049	npair++;
3050	}
3051	}
3052
3053	#ifdef PRUNE_LIST_CPU_ONE
3054	/* If we only found 1 pair, check if any atoms are actually
3055	* within the cut-off, so we could get rid of it.
3056	*/
3057	if (npair == 1 && d2l[ci_last] >= rbb2)
3058	{
3059	/* Avoid using function pointers here, as it's slower */
3060	if (
3061	#ifdef NBNXN_PBB_SIMD4
3062	!subc_in_range_simd4
3063	#else
3064	!subc_in_range_x
3065	#endif
3066	(na_c, ci_last, x_ci, cj_gl, stride, x, rl2))
3067	{
3068	imask &= ~(1U << (cj_offsetGPU_NSUBCELL(22*2)+ci_last));
3069	npair--;
3070	}
3071	}
3072	#endif
3073
3074	if (npair > 0)
3075	{
3076	/* We have a useful sj entry, close it now */
3077
3078	/* Set the exclucions for the ci== sj entry.
3079	* Here we don't bother to check if this entry is actually flagged,
3080	* as it will nearly always be in the list.
3081	*/
3082	if (sci_equals_scj)
3083	{
3084	set_self_and_newton_excls_supersub(nbl, cj4_ind, cj_offset, cjo);
3085	}
3086
3087	/* Copy the cluster interaction mask to the list */
3088	for (w = 0; w < NWARP2; w++)
3089	{
3090	cj4->imei[w].imask \|= imask;
3091	}
3092
3093	nbl->work->cj_ind++;
3094
3095	/* Keep the count */
3096	nbl->nci_tot += npair;
3097
3098	/* Increase the closing index in i super-cell list */
3099	nbl->sci[nbl->nsci].cj4_ind_end =
3100	((nbl->work->cj_ind+NBNXN_GPU_JGROUP_SIZE4-1) >> NBNXN_GPU_JGROUP_SIZE_2LOG2);
3101	}
3102	}
3103	}
3104
3105	/* Set all atom-pair exclusions from the topology stored in excl
3106	* as masks in the pair-list for simple list i-entry nbl_ci
3107	*/
3108	static void set_ci_top_excls(const nbnxn_search_t nbs,
3109	nbnxn_pairlist_t *nbl,
3110	gmx_bool diagRemoved,
3111	int na_ci_2log,
3112	int na_cj_2log,
3113	const nbnxn_ci_t *nbl_ci,
3114	const t_blocka *excl)
3115	{
3116	const int *cell;
3117	int ci;
3118	int cj_ind_first, cj_ind_last;
3119	int cj_first, cj_last;
3120	int ndirect;
3121	int i, ai, aj, si, eind, ge, se;
3122	int found, cj_ind_0, cj_ind_1, cj_ind_m;
3123	int cj_m;
3124	gmx_bool Found_si;
3125	int si_ind;
3126	nbnxn_excl_t *nbl_excl;
3127	int inner_i, inner_e;
3128
3129	cell = nbs->cell;
3130
3131	if (nbl_ci->cj_ind_end == nbl_ci->cj_ind_start)
3132	{
3133	/* Empty list */
3134	return;
3135	}
3136
3137	ci = nbl_ci->ci;
3138
3139	cj_ind_first = nbl_ci->cj_ind_start;
3140	cj_ind_last = nbl->ncj - 1;
3141
3142	cj_first = nbl->cj[cj_ind_first].cj;
3143	cj_last = nbl->cj[cj_ind_last].cj;
3144
3145	/* Determine how many contiguous j-cells we have starting
3146	* from the first i-cell. This number can be used to directly
3147	* calculate j-cell indices for excluded atoms.
3148	*/
3149	ndirect = 0;
3150	if (na_ci_2log == na_cj_2log)
3151	{
3152	while (cj_ind_first + ndirect <= cj_ind_last &&
3153	nbl->cj[cj_ind_first+ndirect].cj == ci + ndirect)
3154	{
3155	ndirect++;
3156	}
3157	}
3158	#ifdef NBNXN_SEARCH_BB_SIMD4
3159	else
3160	{
3161	while (cj_ind_first + ndirect <= cj_ind_last &&
3162	nbl->cj[cj_ind_first+ndirect].cj == ci_to_cj(na_cj_2log, ci) + ndirect)
3163	{
3164	ndirect++;
3165	}
3166	}
3167	#endif
3168
3169	/* Loop over the atoms in the i super-cell */
3170	for (i = 0; i < nbl->na_sc; i++)
3171	{
3172	ai = nbs->a[ci*nbl->na_sc+i];
3173	if (ai >= 0)
3174	{
3175	si = (i>>na_ci_2log);
3176
3177	/* Loop over the topology-based exclusions for this i-atom */
3178	for (eind = excl->index[ai]; eind < excl->index[ai+1]; eind++)
3179	{
3180	aj = excl->a[eind];
3181
3182	if (aj == ai)
3183	{
3184	/* The self exclusion are already set, save some time */
3185	continue;
3186	}
3187
3188	ge = cell[aj];
3189
3190	/* Without shifts we only calculate interactions j>i
3191	* for one-way pair-lists.
3192	*/
3193	if (diagRemoved && ge <= ci*nbl->na_sc + i)
3194	{
3195	continue;
3196	}
3197
3198	se = (ge >> na_cj_2log);
3199
3200	/* Could the cluster se be in our list? */
3201	if (se >= cj_first && se <= cj_last)
3202	{
3203	if (se < cj_first + ndirect)
3204	{
3205	/* We can calculate cj_ind directly from se */
3206	found = cj_ind_first + se - cj_first;
3207	}
3208	else
3209	{
3210	/* Search for se using bisection */
3211	found = -1;
3212	cj_ind_0 = cj_ind_first + ndirect;
3213	cj_ind_1 = cj_ind_last + 1;
3214	while (found == -1 && cj_ind_0 < cj_ind_1)
3215	{
3216	cj_ind_m = (cj_ind_0 + cj_ind_1)>>1;
3217
3218	cj_m = nbl->cj[cj_ind_m].cj;
3219
3220	if (se == cj_m)
3221	{
3222	found = cj_ind_m;
3223	}
3224	else if (se < cj_m)
3225	{
3226	cj_ind_1 = cj_ind_m;
3227	}
3228	else
3229	{
3230	cj_ind_0 = cj_ind_m + 1;
3231	}
3232	}
3233	}
3234
3235	if (found >= 0)
3236	{
3237	inner_i = i - (si << na_ci_2log);
3238	inner_e = ge - (se << na_cj_2log);
3239
3240	nbl->cj[found].excl &= ~(1U<<((inner_i<<na_cj_2log) + inner_e));
3241	/* The next code line is usually not needed. We do not want to version
3242	* away the above line, because there is logic that relies on being
3243	* able to detect easily whether any exclusions exist. */
3244	#if (defined GMX_SIMD_IBM_QPX)
3245	nbl->cj[found].interaction_mask_indices[inner_i] &= ~(1U << inner_e);
3246	#endif
3247	}
3248	}
3249	}
3250	}
3251	}
3252	}
3253
3254	/* Add a new i-entry to the FEP list and copy the i-properties */
3255	static gmx_inlineinline void fep_list_new_nri_copy(t_nblist *nlist)
3256	{
3257	/* Add a new i-entry */
3258	nlist->nri++;
3259
3260	assert(nlist->nri < nlist->maxnri)((void) (0));
3261
3262	/* Duplicate the last i-entry, except for jindex, which continues */
3263	nlist->iinr[nlist->nri] = nlist->iinr[nlist->nri-1];
3264	nlist->shift[nlist->nri] = nlist->shift[nlist->nri-1];
3265	nlist->gid[nlist->nri] = nlist->gid[nlist->nri-1];
3266	nlist->jindex[nlist->nri] = nlist->nrj;
3267	}
3268
3269	/* For load balancing of the free-energy lists over threads, we set
3270	* the maximum nrj size of an i-entry to 40. This leads to good
3271	* load balancing in the worst case scenario of a single perturbed
3272	* particle on 16 threads, while not introducing significant overhead.
3273	* Note that half of the perturbed pairs will anyhow end up in very small lists,
3274	* since non perturbed i-particles will see few perturbed j-particles).
3275	*/
3276	const int max_nrj_fep = 40;
3277
3278	/* Exclude the perturbed pairs from the Verlet list. This is only done to avoid
3279	* singularities for overlapping particles (0/0), since the charges and
3280	* LJ parameters have been zeroed in the nbnxn data structure.
3281	* Simultaneously make a group pair list for the perturbed pairs.
3282	*/
3283	static void make_fep_list(const nbnxn_search_t nbs,
3284	const nbnxn_atomdata_t *nbat,
3285	nbnxn_pairlist_t *nbl,
3286	gmx_bool bDiagRemoved,
3287	nbnxn_ci_t *nbl_ci,
3288	const nbnxn_grid_t *gridi,
3289	const nbnxn_grid_t *gridj,
3290	t_nblist *nlist)
3291	{
3292	int ci, cj_ind_start, cj_ind_end, cj_ind, cja, cjr;
3293	int nri_max;
3294	int ngid, gid_i = 0, gid_j, gid;
3295	int egp_shift, egp_mask;
3296	int gid_cj = 0;
3297	int i, j, ind_i, ind_j, ai, aj;
3298	int nri;
3299	gmx_bool bFEP_i, bFEP_i_all;
3300
3301	if (nbl_ci->cj_ind_end == nbl_ci->cj_ind_start)
3302	{
3303	/* Empty list */
3304	return;
3305	}
3306
3307	ci = nbl_ci->ci;
3308
3309	cj_ind_start = nbl_ci->cj_ind_start;
3310	cj_ind_end = nbl_ci->cj_ind_end;
3311
3312	/* In worst case we have alternating energy groups and create npair lists */
3313	nri_max = nbl->na_ci*(cj_ind_end - cj_ind_start);
3314	if (nlist->nri + nri_max > nlist->maxnri)
3315	{
3316	nlist->maxnri = over_alloc_large(nlist->nri + nri_max)(int)(1.19*(nlist->nri + nri_max) + 1000);
3317	reallocate_nblist(nlist);
3318	}
3319
3320	ngid = nbat->nenergrp;
3321
3322	if (ngidgridj->na_cj > sizeof(gid_cj)8)
3323	{
3324	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 3324, "The Verlet scheme with %dx%d kernels and free-energy only supports up to %d energy groups",
3325	gridi->na_c, gridj->na_cj, (sizeof(gid_cj)*8)/gridj->na_cj);
3326	}
3327
3328	egp_shift = nbat->neg_2log;
3329	egp_mask = (1<<nbat->neg_2log) - 1;
3330
3331	/* Loop over the atoms in the i sub-cell */
3332	bFEP_i_all = TRUE1;
3333	for (i = 0; i < nbl->na_ci; i++)
3334	{
3335	ind_i = ci*nbl->na_ci + i;
3336	ai = nbs->a[ind_i];
3337	if (ai >= 0)
3338	{
3339	nri = nlist->nri;
3340	nlist->jindex[nri+1] = nlist->jindex[nri];
3341	nlist->iinr[nri] = ai;
3342	/* The actual energy group pair index is set later */
3343	nlist->gid[nri] = 0;
3344	nlist->shift[nri] = nbl_ci->shift & NBNXN_CI_SHIFT127;
3345
3346	bFEP_i = gridi->fep[ci - gridi->cell0] & (1 << i);
3347
3348	bFEP_i_all = bFEP_i_all && bFEP_i;
3349
3350	if ((nlist->nrj + cj_ind_end - cj_ind_start)*nbl->na_cj > nlist->maxnrj)
3351	{
3352	nlist->maxnrj = over_alloc_small((nlist->nrj + cj_ind_end - cj_ind_start)nbl->na_cj)(int)(1.19((nlist->nrj + cj_ind_end - cj_ind_start)*nbl-> na_cj) + 8000);
3353	srenew(nlist->jjnr, nlist->maxnrj)(nlist->jjnr) = save_realloc("nlist->jjnr", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 3353, (nlist->jjnr), (nlist->maxnrj), sizeof(*(nlist-> jjnr)));
3354	srenew(nlist->excl_fep, nlist->maxnrj)(nlist->excl_fep) = save_realloc("nlist->excl_fep", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 3354, (nlist->excl_fep), (nlist->maxnrj), sizeof(*(nlist ->excl_fep)));
3355	}
3356
3357	if (ngid > 1)
3358	{
3359	gid_i = (nbat->energrp[ci] >> (egp_shift*i)) & egp_mask;
3360	}
3361
3362	for (cj_ind = cj_ind_start; cj_ind < cj_ind_end; cj_ind++)
3363	{
3364	unsigned int fep_cj;
3365
3366	cja = nbl->cj[cj_ind].cj;
3367
3368	if (gridj->na_cj == gridj->na_c)
3369	{
3370	cjr = cja - gridj->cell0;
3371	fep_cj = gridj->fep[cjr];
3372	if (ngid > 1)
3373	{
3374	gid_cj = nbat->energrp[cja];
3375	}
3376	}
3377	else if (2*gridj->na_cj == gridj->na_c)
3378	{
3379	cjr = cja - gridj->cell0*2;
3380	/* Extract half of the ci fep/energrp mask */
3381	fep_cj = (gridj->fep[cjr>>1] >> ((cjr&1)*gridj->na_cj)) & ((1<<gridj->na_cj) - 1);
3382	if (ngid > 1)
3383	{
3384	gid_cj = nbat->energrp[cja>>1] >> ((cja&1)gridj->na_cjegp_shift) & ((1<<(gridj->na_cj*egp_shift)) - 1);
3385	}
3386	}
3387	else
3388	{
3389	cjr = cja - (gridj->cell0>>1);
3390	/* Combine two ci fep masks/energrp */
3391	fep_cj = gridj->fep[cjr2] + (gridj->fep[cjr2+1] << gridj->na_c);
3392	if (ngid > 1)
3393	{
3394	gid_cj = nbat->energrp[cja2] + (nbat->energrp[cja2+1] << (gridj->na_c*egp_shift));
3395	}
3396	}
3397
3398	if (bFEP_i \|\| fep_cj != 0)
3399	{
3400	for (j = 0; j < nbl->na_cj; j++)
3401	{
3402	/* Is this interaction perturbed and not excluded? */
3403	ind_j = cja*nbl->na_cj + j;
3404	aj = nbs->a[ind_j];
3405	if (aj >= 0 &&
3406	(bFEP_i \|\| (fep_cj & (1 << j))) &&
3407	(!bDiagRemoved \|\| ind_j >= ind_i))
3408	{
3409	if (ngid > 1)
3410	{
3411	gid_j = (gid_cj >> (j*egp_shift)) & egp_mask;
3412	gid = GID(gid_i, gid_j, ngid)((gid_i < gid_j) ? (gid_ingid+gid_j) : (gid_jngid+gid_i) );
3413
3414	if (nlist->nrj > nlist->jindex[nri] &&
3415	nlist->gid[nri] != gid)
3416	{
3417	/* Energy group pair changed: new list */
3418	fep_list_new_nri_copy(nlist);
3419	nri = nlist->nri;
3420	}
3421	nlist->gid[nri] = gid;
3422	}
3423
3424	if (nlist->nrj - nlist->jindex[nri] >= max_nrj_fep)
3425	{
3426	fep_list_new_nri_copy(nlist);
3427	nri = nlist->nri;
3428	}
3429
3430	/* Add it to the FEP list */
3431	nlist->jjnr[nlist->nrj] = aj;
3432	nlist->excl_fep[nlist->nrj] = (nbl->cj[cj_ind].excl >> (i*nbl->na_cj + j)) & 1;
3433	nlist->nrj++;
3434
3435	/* Exclude it from the normal list.
3436	* Note that the charge has been set to zero,
3437	* but we need to avoid 0/0, as perturbed atoms
3438	* can be on top of each other.
3439	* (and the LJ parameters have not been zeroed)
3440	*/
3441	nbl->cj[cj_ind].excl &= ~(1U << (i*nbl->na_cj + j));
3442	}
3443	}
3444	}
3445	}
3446
3447	if (nlist->nrj > nlist->jindex[nri])
3448	{
3449	nlist->nri++;
3450	nlist->jindex[nlist->nri] = nlist->nrj;
3451	}
3452	}
3453	}
3454
3455	if (bFEP_i_all)
3456	{
3457	/* All interactions are perturbed, we can skip this entry */
3458	nbl_ci->cj_ind_end = cj_ind_start;
3459	}
3460	}
3461
3462	/* Return the index of atom a within a cluster */
3463	static gmx_inlineinline int cj_mod_cj4(int cj)
3464	{
3465	return cj & (NBNXN_GPU_JGROUP_SIZE4 - 1);
3466	}
3467
3468	/* Convert a j-cluster to a cj4 group */
3469	static gmx_inlineinline int cj_to_cj4(int cj)
3470	{
3471	return cj >> NBNXN_GPU_JGROUP_SIZE_2LOG2;
3472	}
3473
3474	/* Return the index of an j-atom within a warp */
3475	static gmx_inlineinline int a_mod_wj(int a)
3476	{
3477	return a & (NBNXN_GPU_CLUSTER_SIZE8/2 - 1);
3478	}
3479
3480	/* As make_fep_list above, but for super/sub lists. */
3481	static void make_fep_list_supersub(const nbnxn_search_t nbs,
3482	const nbnxn_atomdata_t *nbat,
3483	nbnxn_pairlist_t *nbl,
3484	gmx_bool bDiagRemoved,
3485	const nbnxn_sci_t *nbl_sci,
3486	real shx,
3487	real shy,
3488	real shz,
3489	real rlist_fep2,
3490	const nbnxn_grid_t *gridi,
3491	const nbnxn_grid_t *gridj,
3492	t_nblist *nlist)
3493	{
3494	int sci, cj4_ind_start, cj4_ind_end, cj4_ind, gcj, cjr;
3495	int nri_max;
3496	int c, c_abs;
3497	int i, j, ind_i, ind_j, ai, aj;
3498	int nri;
3499	gmx_bool bFEP_i;
3500	real xi, yi, zi;
3501	const nbnxn_cj4_t *cj4;
3502
3503	if (nbl_sci->cj4_ind_end == nbl_sci->cj4_ind_start)
3504	{
3505	/* Empty list */
3506	return;
3507	}
3508
3509	sci = nbl_sci->sci;
3510
3511	cj4_ind_start = nbl_sci->cj4_ind_start;
3512	cj4_ind_end = nbl_sci->cj4_ind_end;
3513
3514	/* No energy groups (yet), so we split lists in max_nrj_fep pairs */
3515	nri_max = nbl->na_sc(1 + ((cj4_ind_end - cj4_ind_start)NBNXN_GPU_JGROUP_SIZE4)/max_nrj_fep);
3516	if (nlist->nri + nri_max > nlist->maxnri)
3517	{
3518	nlist->maxnri = over_alloc_large(nlist->nri + nri_max)(int)(1.19*(nlist->nri + nri_max) + 1000);
3519	reallocate_nblist(nlist);
3520	}
3521
3522	/* Loop over the atoms in the i super-cluster */
3523	for (c = 0; c < GPU_NSUBCELL(222); c++)
3524	{
3525	c_abs = sciGPU_NSUBCELL(22*2) + c;
3526
3527	for (i = 0; i < nbl->na_ci; i++)
3528	{
3529	ind_i = c_abs*nbl->na_ci + i;
3530	ai = nbs->a[ind_i];
3531	if (ai >= 0)
3532	{
3533	nri = nlist->nri;
3534	nlist->jindex[nri+1] = nlist->jindex[nri];
3535	nlist->iinr[nri] = ai;
3536	/* With GPUs, energy groups are not supported */
3537	nlist->gid[nri] = 0;
3538	nlist->shift[nri] = nbl_sci->shift & NBNXN_CI_SHIFT127;
3539
3540	bFEP_i = (gridi->fep[c_abs - gridi->cell0] & (1 << i));
3541
3542	xi = nbat->x[ind_i*nbat->xstride+XX0] + shx;
3543	yi = nbat->x[ind_i*nbat->xstride+YY1] + shy;
3544	zi = nbat->x[ind_i*nbat->xstride+ZZ2] + shz;
3545
3546	if ((nlist->nrj + cj4_ind_end - cj4_ind_start)NBNXN_GPU_JGROUP_SIZE4nbl->na_cj > nlist->maxnrj)
3547	{
3548	nlist->maxnrj = over_alloc_small((nlist->nrj + cj4_ind_end - cj4_ind_start)NBNXN_GPU_JGROUP_SIZEnbl->na_cj)(int)(1.19((nlist->nrj + cj4_ind_end - cj4_ind_start)4*nbl ->na_cj) + 8000);
3549	srenew(nlist->jjnr, nlist->maxnrj)(nlist->jjnr) = save_realloc("nlist->jjnr", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 3549, (nlist->jjnr), (nlist->maxnrj), sizeof(*(nlist-> jjnr)));
3550	srenew(nlist->excl_fep, nlist->maxnrj)(nlist->excl_fep) = save_realloc("nlist->excl_fep", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 3550, (nlist->excl_fep), (nlist->maxnrj), sizeof(*(nlist ->excl_fep)));
3551	}
3552
3553	for (cj4_ind = cj4_ind_start; cj4_ind < cj4_ind_end; cj4_ind++)
3554	{
3555	cj4 = &nbl->cj4[cj4_ind];
3556
3557	for (gcj = 0; gcj < NBNXN_GPU_JGROUP_SIZE4; gcj++)
3558	{
3559	unsigned int fep_cj;
3560
3561	if ((cj4->imei[0].imask & (1U << (gcjGPU_NSUBCELL(22*2) + c))) == 0)
3562	{
3563	/* Skip this ci for this cj */
3564	continue;
3565	}
3566
3567	cjr = cj4->cj[gcj] - gridj->cell0GPU_NSUBCELL(22*2);
3568
3569	fep_cj = gridj->fep[cjr];
3570
3571	if (bFEP_i \|\| fep_cj != 0)
3572	{
3573	for (j = 0; j < nbl->na_cj; j++)
3574	{
3575	/* Is this interaction perturbed and not excluded? */
3576	ind_j = (gridj->cell0GPU_NSUBCELL(222) + cjr)nbl->na_cj + j;
3577	aj = nbs->a[ind_j];
3578	if (aj >= 0 &&
3579	(bFEP_i \|\| (fep_cj & (1 << j))) &&
3580	(!bDiagRemoved \|\| ind_j >= ind_i))
3581	{
3582	nbnxn_excl_t *excl;
3583	int excl_pair;
3584	unsigned int excl_bit;
3585	real dx, dy, dz;
3586
3587	get_nbl_exclusions_1(nbl, cj4_ind, j>>2, &excl);
3588
3589	excl_pair = a_mod_wj(j)*nbl->na_ci + i;
3590	excl_bit = (1U << (gcjGPU_NSUBCELL(22*2) + c));
3591
3592	dx = nbat->x[ind_j*nbat->xstride+XX0] - xi;
3593	dy = nbat->x[ind_j*nbat->xstride+YY1] - yi;
3594	dz = nbat->x[ind_j*nbat->xstride+ZZ2] - zi;
3595
3596	/* The unpruned GPU list has more than 2/3
3597	* of the atom pairs beyond rlist. Using
3598	* this list will cause a lot of overhead
3599	* in the CPU FEP kernels, especially
3600	* relative to the fast GPU kernels.
3601	* So we prune the FEP list here.
3602	*/
3603	if (dxdx + dydy + dz*dz < rlist_fep2)
3604	{
3605	if (nlist->nrj - nlist->jindex[nri] >= max_nrj_fep)
3606	{
3607	fep_list_new_nri_copy(nlist);
3608	nri = nlist->nri;
3609	}
3610
3611	/* Add it to the FEP list */
3612	nlist->jjnr[nlist->nrj] = aj;
3613	nlist->excl_fep[nlist->nrj] = (excl->pair[excl_pair] & excl_bit) ? 1 : 0;
3614	nlist->nrj++;
3615	}
3616
3617	/* Exclude it from the normal list.
3618	* Note that the charge and LJ parameters have
3619	* been set to zero, but we need to avoid 0/0,
3620	* as perturbed atoms can be on top of each other.
3621	*/
3622	excl->pair[excl_pair] &= ~excl_bit;
3623	}
3624	}
3625
3626	/* Note that we could mask out this pair in imask
3627	* if all i- and/or all j-particles are perturbed.
3628	* But since the perturbed pairs on the CPU will
3629	* take an order of magnitude more time, the GPU
3630	* will finish before the CPU and there is no gain.
3631	*/
3632	}
3633	}
3634	}
3635
3636	if (nlist->nrj > nlist->jindex[nri])
3637	{
3638	nlist->nri++;
3639	nlist->jindex[nlist->nri] = nlist->nrj;
3640	}
3641	}
3642	}
3643	}
3644	}
3645
3646	/* Set all atom-pair exclusions from the topology stored in excl
3647	* as masks in the pair-list for i-super-cell entry nbl_sci
3648	*/
3649	static void set_sci_top_excls(const nbnxn_search_t nbs,
3650	nbnxn_pairlist_t *nbl,
3651	gmx_bool diagRemoved,
3652	int na_c_2log,
3653	const nbnxn_sci_t *nbl_sci,
3654	const t_blocka *excl)
3655	{
3656	const int *cell;
3657	int na_c;
3658	int sci;
3659	int cj_ind_first, cj_ind_last;
3660	int cj_first, cj_last;
3661	int ndirect;
3662	int i, ai, aj, si, eind, ge, se;
3663	int found, cj_ind_0, cj_ind_1, cj_ind_m;
3664	int cj_m;
3665	gmx_bool Found_si;
3666	int si_ind;
3667	nbnxn_excl_t *nbl_excl;
3668	int inner_i, inner_e, w;
3669
3670	cell = nbs->cell;
3671
3672	na_c = nbl->na_ci;
3673
3674	if (nbl_sci->cj4_ind_end == nbl_sci->cj4_ind_start)
3675	{
3676	/* Empty list */
3677	return;
3678	}
3679
3680	sci = nbl_sci->sci;
3681
3682	cj_ind_first = nbl_sci->cj4_ind_start*NBNXN_GPU_JGROUP_SIZE4;
3683	cj_ind_last = nbl->work->cj_ind - 1;
3684
3685	cj_first = nbl->cj4[nbl_sci->cj4_ind_start].cj[0];
3686	cj_last = nbl_cj(nbl, cj_ind_last);
3687
3688	/* Determine how many contiguous j-clusters we have starting
3689	* from the first i-cluster. This number can be used to directly
3690	* calculate j-cluster indices for excluded atoms.
3691	*/
3692	ndirect = 0;
3693	while (cj_ind_first + ndirect <= cj_ind_last &&
3694	nbl_cj(nbl, cj_ind_first+ndirect) == sciGPU_NSUBCELL(22*2) + ndirect)
3695	{
3696	ndirect++;
3697	}
3698
3699	/* Loop over the atoms in the i super-cell */
3700	for (i = 0; i < nbl->na_sc; i++)
3701	{
3702	ai = nbs->a[sci*nbl->na_sc+i];
3703	if (ai >= 0)
3704	{
3705	si = (i>>na_c_2log);
3706
3707	/* Loop over the topology-based exclusions for this i-atom */
3708	for (eind = excl->index[ai]; eind < excl->index[ai+1]; eind++)
3709	{
3710	aj = excl->a[eind];
3711
3712	if (aj == ai)
3713	{
3714	/* The self exclusion are already set, save some time */
3715	continue;
3716	}
3717
3718	ge = cell[aj];
3719
3720	/* Without shifts we only calculate interactions j>i
3721	* for one-way pair-lists.
3722	*/
3723	if (diagRemoved && ge <= sci*nbl->na_sc + i)
3724	{
3725	continue;
3726	}
3727
3728	se = ge>>na_c_2log;
3729	/* Could the cluster se be in our list? */
3730	if (se >= cj_first && se <= cj_last)
3731	{
3732	if (se < cj_first + ndirect)
3733	{
3734	/* We can calculate cj_ind directly from se */
3735	found = cj_ind_first + se - cj_first;
3736	}
3737	else
3738	{
3739	/* Search for se using bisection */
3740	found = -1;
3741	cj_ind_0 = cj_ind_first + ndirect;
3742	cj_ind_1 = cj_ind_last + 1;
3743	while (found == -1 && cj_ind_0 < cj_ind_1)
3744	{
3745	cj_ind_m = (cj_ind_0 + cj_ind_1)>>1;
3746
3747	cj_m = nbl_cj(nbl, cj_ind_m);
3748
3749	if (se == cj_m)
3750	{
3751	found = cj_ind_m;
3752	}
3753	else if (se < cj_m)
3754	{
3755	cj_ind_1 = cj_ind_m;
3756	}
3757	else
3758	{
3759	cj_ind_0 = cj_ind_m + 1;
3760	}
3761	}
3762	}
3763
3764	if (found >= 0)
3765	{
3766	inner_i = i - si*na_c;
3767	inner_e = ge - se*na_c;
3768
3769	if (nbl_imask0(nbl, found) & (1U << (cj_mod_cj4(found)GPU_NSUBCELL(22*2) + si)))
3770	{
3771	w = (inner_e >> 2);
3772
3773	get_nbl_exclusions_1(nbl, cj_to_cj4(found), w, &nbl_excl);
3774
3775	nbl_excl->pair[a_mod_wj(inner_e)*nbl->na_ci+inner_i] &=
3776	~(1U << (cj_mod_cj4(found)GPU_NSUBCELL(22*2) + si));
3777	}
3778	}
3779	}
3780	}
3781	}
3782	}
3783	}
3784
3785	/* Reallocate the simple ci list for at least n entries */
3786	static void nb_realloc_ci(nbnxn_pairlist_t *nbl, int n)
3787	{
3788	nbl->ci_nalloc = over_alloc_small(n)(int)(1.19*(n) + 8000);
3789	nbnxn_realloc_void((void **)&nbl->ci,
3790	nbl->ncisizeof(nbl->ci),
3791	nbl->ci_nallocsizeof(nbl->ci),
3792	nbl->alloc, nbl->free);
3793	}
3794
3795	/* Reallocate the super-cell sci list for at least n entries */
3796	static void nb_realloc_sci(nbnxn_pairlist_t *nbl, int n)
3797	{
3798	nbl->sci_nalloc = over_alloc_small(n)(int)(1.19*(n) + 8000);
3799	nbnxn_realloc_void((void **)&nbl->sci,
3800	nbl->nscisizeof(nbl->sci),
3801	nbl->sci_nallocsizeof(nbl->sci),
3802	nbl->alloc, nbl->free);
3803	}
3804
3805	/* Make a new ci entry at index nbl->nci */
3806	static void new_ci_entry(nbnxn_pairlist_t *nbl, int ci, int shift, int flags)
3807	{
3808	if (nbl->nci + 1 > nbl->ci_nalloc)
3809	{
3810	nb_realloc_ci(nbl, nbl->nci+1);
3811	}
3812	nbl->ci[nbl->nci].ci = ci;
3813	nbl->ci[nbl->nci].shift = shift;
3814	/* Store the interaction flags along with the shift */
3815	nbl->ci[nbl->nci].shift \|= flags;
3816	nbl->ci[nbl->nci].cj_ind_start = nbl->ncj;
3817	nbl->ci[nbl->nci].cj_ind_end = nbl->ncj;
3818	}
3819
3820	/* Make a new sci entry at index nbl->nsci */
3821	static void new_sci_entry(nbnxn_pairlist_t *nbl, int sci, int shift)
3822	{
3823	if (nbl->nsci + 1 > nbl->sci_nalloc)
3824	{
3825	nb_realloc_sci(nbl, nbl->nsci+1);
3826	}
3827	nbl->sci[nbl->nsci].sci = sci;
3828	nbl->sci[nbl->nsci].shift = shift;
3829	nbl->sci[nbl->nsci].cj4_ind_start = nbl->ncj4;
3830	nbl->sci[nbl->nsci].cj4_ind_end = nbl->ncj4;
3831	}
3832
3833	/* Sort the simple j-list cj on exclusions.
3834	* Entries with exclusions will all be sorted to the beginning of the list.
3835	*/
3836	static void sort_cj_excl(nbnxn_cj_t *cj, int ncj,
3837	nbnxn_list_work_t *work)
3838	{
3839	int jnew, j;
3840
3841	if (ncj > work->cj_nalloc)
3842	{
3843	work->cj_nalloc = over_alloc_large(ncj)(int)(1.19*(ncj) + 1000);
3844	srenew(work->cj, work->cj_nalloc)(work->cj) = save_realloc("work->cj", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 3844, (work->cj), (work->cj_nalloc), sizeof(*(work-> cj)));
3845	}
3846
3847	/* Make a list of the j-cells involving exclusions */
3848	jnew = 0;
3849	for (j = 0; j < ncj; j++)
3850	{
3851	if (cj[j].excl != NBNXN_INTERACTION_MASK_ALL)
3852	{
3853	work->cj[jnew++] = cj[j];
3854	}
3855	}
3856	/* Check if there are exclusions at all or not just the first entry */
3857	if (!((jnew == 0) \|\|
3858	(jnew == 1 && cj[0].excl != NBNXN_INTERACTION_MASK_ALL)))
3859	{
3860	for (j = 0; j < ncj; j++)
3861	{
3862	if (cj[j].excl == NBNXN_INTERACTION_MASK_ALL)
3863	{
3864	work->cj[jnew++] = cj[j];
3865	}
3866	}
3867	for (j = 0; j < ncj; j++)
3868	{
3869	cj[j] = work->cj[j];
3870	}
3871	}
3872	}
3873
3874	/* Close this simple list i entry */
3875	static void close_ci_entry_simple(nbnxn_pairlist_t *nbl)
3876	{
3877	int jlen;
3878
3879	/* All content of the new ci entry have already been filled correctly,
3880	* we only need to increase the count here (for non empty lists).
3881	*/
3882	jlen = nbl->ci[nbl->nci].cj_ind_end - nbl->ci[nbl->nci].cj_ind_start;
3883	if (jlen > 0)
3884	{
3885	sort_cj_excl(nbl->cj+nbl->ci[nbl->nci].cj_ind_start, jlen, nbl->work);
3886
3887	/* The counts below are used for non-bonded pair/flop counts
3888	* and should therefore match the available kernel setups.
3889	*/
3890	if (!(nbl->ci[nbl->nci].shift & NBNXN_CI_DO_COUL(0)(1<<(9+3*(0)))))
3891	{
3892	nbl->work->ncj_noq += jlen;
3893	}
3894	else if ((nbl->ci[nbl->nci].shift & NBNXN_CI_HALF_LJ(0)(1<<(8+3*(0)))) \|\|
3895	!(nbl->ci[nbl->nci].shift & NBNXN_CI_DO_LJ(0)(1<<(7+3*(0)))))
3896	{
3897	nbl->work->ncj_hlj += jlen;
3898	}
3899
3900	nbl->nci++;
3901	}
3902	}
3903
3904	/* Split sci entry for load balancing on the GPU.
3905	* Splitting ensures we have enough lists to fully utilize the whole GPU.
3906	* With progBal we generate progressively smaller lists, which improves
3907	* load balancing. As we only know the current count on our own thread,
3908	* we will need to estimate the current total amount of i-entries.
3909	* As the lists get concatenated later, this estimate depends
3910	* both on nthread and our own thread index.
3911	*/
3912	static void split_sci_entry(nbnxn_pairlist_t *nbl,
3913	int nsp_max_av, gmx_bool progBal, int nc_bal,
3914	int thread, int nthread)
3915	{
3916	int nsci_est;
3917	int nsp_max;
3918	int cj4_start, cj4_end, j4len, cj4;
3919	int sci;
3920	int nsp, nsp_sci, nsp_cj4, nsp_cj4_e, nsp_cj4_p;
3921	int p;
3922
3923	if (progBal)
3924	{
3925	/* Estimate the total numbers of ci's of the nblist combined
3926	* over all threads using the target number of ci's.
3927	*/
3928	nsci_est = nc_bal*thread/nthread + nbl->nsci;
3929
3930	/* The first ci blocks should be larger, to avoid overhead.
3931	* The last ci blocks should be smaller, to improve load balancing.
3932	*/
3933	nsp_max = max(1,(((1) > (nsp_max_avnc_bal3/(2(nsci_est - 1 + nc_bal)))) ? (1) : (nsp_max_avnc_bal3/(2(nsci_est - 1 + nc_bal))) )
3934	nsp_max_avnc_bal3/(2(nsci_est - 1 + nc_bal)))(((1) > (nsp_max_avnc_bal3/(2(nsci_est - 1 + nc_bal)))) ? (1) : (nsp_max_avnc_bal3/(2*(nsci_est - 1 + nc_bal))) );
3935	}
3936	else
3937	{
3938	nsp_max = nsp_max_av;
3939	}
3940
3941	cj4_start = nbl->sci[nbl->nsci-1].cj4_ind_start;
3942	cj4_end = nbl->sci[nbl->nsci-1].cj4_ind_end;
3943	j4len = cj4_end - cj4_start;
3944
3945	if (j4len > 1 && j4lenGPU_NSUBCELL(222)NBNXN_GPU_JGROUP_SIZE4 > nsp_max)
3946	{
3947	/* Remove the last ci entry and process the cj4's again */
3948	nbl->nsci -= 1;
3949
3950	sci = nbl->nsci;
3951	nsp = 0;
3952	nsp_sci = 0;
3953	nsp_cj4_e = 0;
3954	nsp_cj4 = 0;
3955	for (cj4 = cj4_start; cj4 < cj4_end; cj4++)
3956	{
3957	nsp_cj4_p = nsp_cj4;
3958	/* Count the number of cluster pairs in this cj4 group */
3959	nsp_cj4 = 0;
3960	for (p = 0; p < GPU_NSUBCELL(222)*NBNXN_GPU_JGROUP_SIZE4; p++)
3961	{
3962	nsp_cj4 += (nbl->cj4[cj4].imei[0].imask >> p) & 1;
3963	}
3964
3965	if (nsp_cj4 > 0 && nsp + nsp_cj4 > nsp_max)
3966	{
3967	/* Split the list at cj4 */
3968	nbl->sci[sci].cj4_ind_end = cj4;
3969	/* Create a new sci entry */
3970	sci++;
3971	nbl->nsci++;
3972	if (nbl->nsci+1 > nbl->sci_nalloc)
3973	{
3974	nb_realloc_sci(nbl, nbl->nsci+1);
3975	}
3976	nbl->sci[sci].sci = nbl->sci[nbl->nsci-1].sci;
3977	nbl->sci[sci].shift = nbl->sci[nbl->nsci-1].shift;
3978	nbl->sci[sci].cj4_ind_start = cj4;
3979	nsp_sci = nsp;
3980	nsp_cj4_e = nsp_cj4_p;
3981	nsp = 0;
3982	}
3983	nsp += nsp_cj4;
3984	}
3985
3986	/* Put the remaining cj4's in the last sci entry */
3987	nbl->sci[sci].cj4_ind_end = cj4_end;
3988
3989	/* Possibly balance out the last two sci's
3990	* by moving the last cj4 of the second last sci.
3991	*/
3992	if (nsp_sci - nsp_cj4_e >= nsp + nsp_cj4_e)
3993	{
3994	nbl->sci[sci-1].cj4_ind_end--;
3995	nbl->sci[sci].cj4_ind_start--;
3996	}
3997
3998	nbl->nsci++;
3999	}
4000	}
4001
4002	/* Clost this super/sub list i entry */
4003	static void close_ci_entry_supersub(nbnxn_pairlist_t *nbl,
4004	int nsp_max_av,
4005	gmx_bool progBal, int nc_bal,
4006	int thread, int nthread)
4007	{
4008	int j4len, tlen;
4009	int nb, b;
4010
4011	/* All content of the new ci entry have already been filled correctly,
4012	* we only need to increase the count here (for non empty lists).
4013	*/
4014	j4len = nbl->sci[nbl->nsci].cj4_ind_end - nbl->sci[nbl->nsci].cj4_ind_start;
4015	if (j4len > 0)
4016	{
4017	/* We can only have complete blocks of 4 j-entries in a list,
4018	* so round the count up before closing.
4019	*/
4020	nbl->ncj4 = ((nbl->work->cj_ind + NBNXN_GPU_JGROUP_SIZE4 - 1) >> NBNXN_GPU_JGROUP_SIZE_2LOG2);
4021	nbl->work->cj_ind = nbl->ncj4*NBNXN_GPU_JGROUP_SIZE4;
4022
4023	nbl->nsci++;
4024
4025	if (nsp_max_av > 0)
4026	{
4027	/* Measure the size of the new entry and potentially split it */
4028	split_sci_entry(nbl, nsp_max_av, progBal, nc_bal, thread, nthread);
4029	}
4030	}
4031	}
4032
4033	/* Syncs the working array before adding another grid pair to the list */
4034	static void sync_work(nbnxn_pairlist_t *nbl)
4035	{
4036	if (!nbl->bSimple)
4037	{
4038	nbl->work->cj_ind = nbl->ncj4*NBNXN_GPU_JGROUP_SIZE4;
4039	nbl->work->cj4_init = nbl->ncj4;
4040	}
4041	}
4042
4043	/* Clears an nbnxn_pairlist_t data structure */
4044	static void clear_pairlist(nbnxn_pairlist_t *nbl)
4045	{
4046	nbl->nci = 0;
4047	nbl->nsci = 0;
4048	nbl->ncj = 0;
4049	nbl->ncj4 = 0;
4050	nbl->nci_tot = 0;
4051	nbl->nexcl = 1;
4052
4053	nbl->work->ncj_noq = 0;
4054	nbl->work->ncj_hlj = 0;
4055	}
4056
4057	/* Clears a group scheme pair list */
4058	static void clear_pairlist_fep(t_nblist *nl)
4059	{
4060	nl->nri = 0;
4061	nl->nrj = 0;
4062	if (nl->jindex == NULL((void*)0))
4063	{
4064	snew(nl->jindex, 1)(nl->jindex) = save_calloc("nl->jindex", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 4064, (1), sizeof(*(nl->jindex)));
4065	}
4066	nl->jindex[0] = 0;
4067	}
4068
4069	/* Sets a simple list i-cell bounding box, including PBC shift */
4070	static gmx_inlineinline void set_icell_bb_simple(const nbnxn_bb_t *bb, int ci,
4071	real shx, real shy, real shz,
4072	nbnxn_bb_t *bb_ci)
4073	{
4074	bb_ci->lower[BB_X0] = bb[ci].lower[BB_X0] + shx;
4075	bb_ci->lower[BB_Y1] = bb[ci].lower[BB_Y1] + shy;
4076	bb_ci->lower[BB_Z2] = bb[ci].lower[BB_Z2] + shz;
4077	bb_ci->upper[BB_X0] = bb[ci].upper[BB_X0] + shx;
4078	bb_ci->upper[BB_Y1] = bb[ci].upper[BB_Y1] + shy;
4079	bb_ci->upper[BB_Z2] = bb[ci].upper[BB_Z2] + shz;
4080	}
4081
4082	#ifdef NBNXN_BBXXXX
4083	/* Sets a super-cell and sub cell bounding boxes, including PBC shift */
4084	static void set_icell_bbxxxx_supersub(const float *bb, int ci,
4085	real shx, real shy, real shz,
4086	float *bb_ci)
4087	{
4088	int ia, m, i;
4089
4090	ia = ci(GPU_NSUBCELL(222)>>STRIDE_PBB_2LOG2)NNBSBB_XXXX(234);
4091	for (m = 0; m < (GPU_NSUBCELL(222)>>STRIDE_PBB_2LOG2)NNBSBB_XXXX(234); m += NNBSBB_XXXX(23*4))
4092	{
4093	for (i = 0; i < STRIDE_PBB4; i++)
4094	{
4095	bb_ci[m+0STRIDE_PBB4+i] = bb[ia+m+0STRIDE_PBB4+i] + shx;
4096	bb_ci[m+1STRIDE_PBB4+i] = bb[ia+m+1STRIDE_PBB4+i] + shy;
4097	bb_ci[m+2STRIDE_PBB4+i] = bb[ia+m+2STRIDE_PBB4+i] + shz;
4098	bb_ci[m+3STRIDE_PBB4+i] = bb[ia+m+3STRIDE_PBB4+i] + shx;
4099	bb_ci[m+4STRIDE_PBB4+i] = bb[ia+m+4STRIDE_PBB4+i] + shy;
4100	bb_ci[m+5STRIDE_PBB4+i] = bb[ia+m+5STRIDE_PBB4+i] + shz;
4101	}
4102	}
4103	}
4104	#endif
4105
4106	/* Sets a super-cell and sub cell bounding boxes, including PBC shift */
4107	static void set_icell_bb_supersub(const nbnxn_bb_t *bb, int ci,
4108	real shx, real shy, real shz,
4109	nbnxn_bb_t *bb_ci)
4110	{
4111	int i;
4112
4113	for (i = 0; i < GPU_NSUBCELL(222); i++)
4114	{
4115	set_icell_bb_simple(bb, ciGPU_NSUBCELL(22*2)+i,
4116	shx, shy, shz,
4117	&bb_ci[i]);
4118	}
4119	}
4120
4121	/* Copies PBC shifted i-cell atom coordinates x,y,z to working array */
4122	static void icell_set_x_simple(int ci,
4123	real shx, real shy, real shz,
4124	int gmx_unused__attribute__ ((unused)) na_c,
4125	int stride, const real *x,
4126	nbnxn_list_work_t *work)
4127	{
4128	int ia, i;
4129
4130	ia = ci*NBNXN_CPU_CLUSTER_I_SIZE4;
4131
4132	for (i = 0; i < NBNXN_CPU_CLUSTER_I_SIZE4; i++)
4133	{
4134	work->x_ci[iSTRIDE_XYZ3+XX0] = x[(ia+i)stride+XX0] + shx;
4135	work->x_ci[iSTRIDE_XYZ3+YY1] = x[(ia+i)stride+YY1] + shy;
4136	work->x_ci[iSTRIDE_XYZ3+ZZ2] = x[(ia+i)stride+ZZ2] + shz;
4137	}
4138	}
4139
4140	/* Copies PBC shifted super-cell atom coordinates x,y,z to working array */
4141	static void icell_set_x_supersub(int ci,
4142	real shx, real shy, real shz,
4143	int na_c,
4144	int stride, const real *x,
4145	nbnxn_list_work_t *work)
4146	{
4147	int ia, i;
4148	real *x_ci;
4149
4150	x_ci = work->x_ci;
4151
4152	ia = ciGPU_NSUBCELL(222)na_c;
4153	for (i = 0; i < GPU_NSUBCELL(222)*na_c; i++)
4154	{
4155	x_ci[iDIM3 + XX0] = x[(ia+i)stride + XX0] + shx;
4156	x_ci[iDIM3 + YY1] = x[(ia+i)stride + YY1] + shy;
4157	x_ci[iDIM3 + ZZ2] = x[(ia+i)stride + ZZ2] + shz;
4158	}
4159	}
4160
4161	#ifdef NBNXN_SEARCH_BB_SIMD4
4162	/* Copies PBC shifted super-cell packed atom coordinates to working array */
4163	static void icell_set_x_supersub_simd4(int ci,
4164	real shx, real shy, real shz,
4165	int na_c,
4166	int stride, const real *x,
4167	nbnxn_list_work_t *work)
4168	{
4169	int si, io, ia, i, j;
4170	real *x_ci;
4171
4172	x_ci = work->x_ci;
4173
4174	for (si = 0; si < GPU_NSUBCELL(222); si++)
4175	{
4176	for (i = 0; i < na_c; i += STRIDE_PBB4)
4177	{
4178	io = si*na_c + i;
4179	ia = ciGPU_NSUBCELL(222)na_c + io;
4180	for (j = 0; j < STRIDE_PBB4; j++)
4181	{
4182	x_ci[ioDIM3 + j + XX0STRIDE_PBB4] = x[(ia+j)*stride+XX0] + shx;
4183	x_ci[ioDIM3 + j + YY1STRIDE_PBB4] = x[(ia+j)*stride+YY1] + shy;
4184	x_ci[ioDIM3 + j + ZZ2STRIDE_PBB4] = x[(ia+j)*stride+ZZ2] + shz;
4185	}
4186	}
4187	}
4188	}
4189	#endif
4190
4191	static real minimum_subgrid_size_xy(const nbnxn_grid_t *grid)
4192	{
4193	if (grid->bSimple)
4194	{
4195	return min(grid->sx, grid->sy)(((grid->sx) < (grid->sy)) ? (grid->sx) : (grid-> sy) );
4196	}
4197	else
4198	{
4199	return min(grid->sx/GPU_NSUBCELL_X, grid->sy/GPU_NSUBCELL_Y)(((grid->sx/2) < (grid->sy/2)) ? (grid->sx/2) : ( grid->sy/2) );
4200	}
4201	}
4202
4203	static real effective_buffer_1x1_vs_MxN(const nbnxn_grid_t *gridi,
4204	const nbnxn_grid_t *gridj)
4205	{
4206	const real eff_1x1_buffer_fac_overest = 0.1;
4207
4208	/* Determine an atom-pair list cut-off buffer size for atom pairs,
4209	* to be added to rlist (including buffer) used for MxN.
4210	* This is for converting an MxN list to a 1x1 list. This means we can't
4211	* use the normal buffer estimate, as we have an MxN list in which
4212	* some atom pairs beyond rlist are missing. We want to capture
4213	* the beneficial effect of buffering by extra pairs just outside rlist,
4214	* while removing the useless pairs that are further away from rlist.
4215	* (Also the buffer could have been set manually not using the estimate.)
4216	* This buffer size is an overestimate.
4217	* We add 10% of the smallest grid sub-cell dimensions.
4218	* Note that the z-size differs per cell and we don't use this,
4219	* so we overestimate.
4220	* With PME, the 10% value gives a buffer that is somewhat larger
4221	* than the effective buffer with a tolerance of 0.005 kJ/mol/ps.
4222	* Smaller tolerances or using RF lead to a smaller effective buffer,
4223	* so 10% gives a safe overestimate.
4224	*/
4225	return eff_1x1_buffer_fac_overest*(minimum_subgrid_size_xy(gridi) +
4226	minimum_subgrid_size_xy(gridj));
4227	}
4228
4229	/* Clusters at the cut-off only increase rlist by 60% of their size */
4230	static real nbnxn_rlist_inc_outside_fac = 0.6;
4231
4232	/* Due to the cluster size the effective pair-list is longer than
4233	* that of a simple atom pair-list. This function gives the extra distance.
4234	*/
4235	real nbnxn_get_rlist_effective_inc(int cluster_size_j, real atom_density)
4236	{
4237	int cluster_size_i;
4238	real vol_inc_i, vol_inc_j;
4239
4240	/* We should get this from the setup, but currently it's the same for
4241	* all setups, including GPUs.
4242	*/
4243	cluster_size_i = NBNXN_CPU_CLUSTER_I_SIZE4;
4244
4245	vol_inc_i = (cluster_size_i - 1)/atom_density;
4246	vol_inc_j = (cluster_size_j - 1)/atom_density;
4247
4248	return nbnxn_rlist_inc_outside_fac*pow(vol_inc_i + vol_inc_j, 1.0/3.0);
4249	}
4250
4251	/* Estimates the interaction volume^2 for non-local interactions */
4252	static real nonlocal_vol2(const gmx_domdec_zones_t *zones, rvec ls, real r)
4253	{
4254	int z, d;
4255	real cl, ca, za;
4256	real vold_est;
4257	real vol2_est_tot;
4258
4259	vol2_est_tot = 0;
4260
4261	/* Here we simply add up the volumes of 1, 2 or 3 1D decomposition
4262	* not home interaction volume^2. As these volumes are not additive,
4263	* this is an overestimate, but it would only be significant in the limit
4264	* of small cells, where we anyhow need to split the lists into
4265	* as small parts as possible.
4266	*/
4267
4268	for (z = 0; z < zones->n; z++)
4269	{
4270	if (zones->shift[z][XX0] + zones->shift[z][YY1] + zones->shift[z][ZZ2] == 1)
4271	{
4272	cl = 0;
4273	ca = 1;
4274	za = 1;
4275	for (d = 0; d < DIM3; d++)
4276	{
4277	if (zones->shift[z][d] == 0)
4278	{
4279	cl += 0.5*ls[d];
4280	ca *= ls[d];
4281	za *= zones->size[z].x1[d] - zones->size[z].x0[d];
4282	}
4283	}
4284
4285	/* 4 octants of a sphere */
4286	vold_est = 0.25M_PI3.14159265358979323846rrr*r;
4287	/* 4 quarter pie slices on the edges */
4288	vold_est += 4clM_PI3.14159265358979323846/6.0rr*r;
4289	/* One rectangular volume on a face */
4290	vold_est += ca0.5r*r;
4291
4292	vol2_est_tot += vold_est*za;
4293	}
4294	}
4295
4296	return vol2_est_tot;
4297	}
4298
4299	/* Estimates the average size of a full j-list for super/sub setup */
4300	static int get_nsubpair_max(const nbnxn_search_t nbs,
4301	int iloc,
4302	real rlist,
4303	int min_ci_balanced)
4304	{
4305	const nbnxn_grid_t *grid;
4306	rvec ls;
4307	real xy_diag2, r_eff_sup, vol_est, nsp_est, nsp_est_nl;
4308	int nsubpair_max;
4309
4310	grid = &nbs->grid[0];
4311
4312	ls[XX0] = (grid->c1[XX0] - grid->c0[XX0])/(grid->ncx*GPU_NSUBCELL_X2);
4313	ls[YY1] = (grid->c1[YY1] - grid->c0[YY1])/(grid->ncy*GPU_NSUBCELL_Y2);
4314	ls[ZZ2] = (grid->c1[ZZ2] - grid->c0[ZZ2])grid->ncxgrid->ncy/(grid->nc*GPU_NSUBCELL_Z2);
4315
4316	/* The average squared length of the diagonal of a sub cell */
4317	xy_diag2 = ls[XX0]ls[XX0] + ls[YY1]ls[YY1] + ls[ZZ2]*ls[ZZ2];
4318
4319	/* The formulas below are a heuristic estimate of the average nsj per si*/
4320	r_eff_sup = rlist + nbnxn_rlist_inc_outside_facsqr((grid->na_c - 1.0)/grid->na_c)sqrt(xy_diag2/3);
4321
4322	if (!nbs->DomDec \|\| nbs->zones->n == 1)
4323	{
4324	nsp_est_nl = 0;
4325	}
4326	else
4327	{
4328	nsp_est_nl =
4329	sqr(grid->atom_density/grid->na_c)*
4330	nonlocal_vol2(nbs->zones, ls, r_eff_sup);
4331	}
4332
4333	if (LOCAL_I(iloc)((iloc) == eintLocal))
4334	{
4335	/* Sub-cell interacts with itself */
4336	vol_est = ls[XX0]ls[YY1]ls[ZZ2];
4337	/* 6/2 rectangular volume on the faces */
4338	vol_est += (ls[XX0]ls[YY1] + ls[XX0]ls[ZZ2] + ls[YY1]ls[ZZ2])r_eff_sup;
4339	/* 12/2 quarter pie slices on the edges */
4340	vol_est += 2(ls[XX0] + ls[YY1] + ls[ZZ2])0.25M_PI3.14159265358979323846sqr(r_eff_sup);
4341	/* 4 octants of a sphere */
4342	vol_est += 0.54.0/3.0M_PI3.14159265358979323846*pow(r_eff_sup, 3);
4343
4344	nsp_est = grid->nsubc_totvol_estgrid->atom_density/grid->na_c;
4345
4346	/* Subtract the non-local pair count */
4347	nsp_est -= nsp_est_nl;
4348
4349	if (debug)
4350	{
4351	fprintf(debug, "nsp_est local %5.1f non-local %5.1f\n",
4352	nsp_est, nsp_est_nl);
4353	}
4354	}
4355	else
4356	{
4357	nsp_est = nsp_est_nl;
4358	}
4359
4360	if (min_ci_balanced <= 0 \|\| grid->nc >= min_ci_balanced \|\| grid->nc == 0)
4361	{
4362	/* We don't need to worry */
4363	nsubpair_max = -1;
4364	}
4365	else
4366	{
4367	/* Thus the (average) maximum j-list size should be as follows */
4368	nsubpair_max = max(1, (int)(nsp_est/min_ci_balanced+0.5))(((1) > ((int)(nsp_est/min_ci_balanced+0.5))) ? (1) : ((int )(nsp_est/min_ci_balanced+0.5)) );
4369
4370	/* Since the target value is a maximum (this avoids high outliers,
4371	* which lead to load imbalance), not average, we add half the
4372	* number of pairs in a cj4 block to get the average about right.
4373	*/
4374	nsubpair_max += GPU_NSUBCELL(222)*NBNXN_GPU_JGROUP_SIZE4/2;
4375	}
4376
4377	if (debug)
4378	{
4379	fprintf(debug, "nbl nsp estimate %.1f, nsubpair_max %d\n",
4380	nsp_est, nsubpair_max);
4381	}
4382
4383	return nsubpair_max;
4384	}
4385
4386	/* Debug list print function */
4387	static void print_nblist_ci_cj(FILE fp, const nbnxn_pairlist_t nbl)
4388	{
4389	int i, j;
4390
4391	for (i = 0; i < nbl->nci; i++)
4392	{
4393	fprintf(fp, "ci %4d shift %2d ncj %3d\n",
4394	nbl->ci[i].ci, nbl->ci[i].shift,
4395	nbl->ci[i].cj_ind_end - nbl->ci[i].cj_ind_start);
4396
4397	for (j = nbl->ci[i].cj_ind_start; j < nbl->ci[i].cj_ind_end; j++)
4398	{
4399	fprintf(fp, " cj %5d imask %x\n",
4400	nbl->cj[j].cj,
4401	nbl->cj[j].excl);
4402	}
4403	}
4404	}
4405
4406	/* Debug list print function */
4407	static void print_nblist_sci_cj(FILE fp, const nbnxn_pairlist_t nbl)
4408	{
4409	int i, j4, j, ncp, si;
4410
4411	for (i = 0; i < nbl->nsci; i++)
4412	{
4413	fprintf(fp, "ci %4d shift %2d ncj4 %2d\n",
4414	nbl->sci[i].sci, nbl->sci[i].shift,
4415	nbl->sci[i].cj4_ind_end - nbl->sci[i].cj4_ind_start);
4416
4417	ncp = 0;
4418	for (j4 = nbl->sci[i].cj4_ind_start; j4 < nbl->sci[i].cj4_ind_end; j4++)
4419	{
4420	for (j = 0; j < NBNXN_GPU_JGROUP_SIZE4; j++)
4421	{
4422	fprintf(fp, " sj %5d imask %x\n",
4423	nbl->cj4[j4].cj[j],
4424	nbl->cj4[j4].imei[0].imask);
4425	for (si = 0; si < GPU_NSUBCELL(222); si++)
4426	{
4427	if (nbl->cj4[j4].imei[0].imask & (1U << (jGPU_NSUBCELL(22*2) + si)))
4428	{
4429	ncp++;
4430	}
4431	}
4432	}
4433	}
4434	fprintf(fp, "ci %4d shift %2d ncj4 %2d ncp %3d\n",
4435	nbl->sci[i].sci, nbl->sci[i].shift,
4436	nbl->sci[i].cj4_ind_end - nbl->sci[i].cj4_ind_start,
4437	ncp);
4438	}
4439	}
4440
4441	/* Combine pair lists nbl generated on multiple threads nblc /
4442	static void combine_nblists(int nnbl, nbnxn_pairlist_t **nbl,
4443	nbnxn_pairlist_t *nblc)
4444	{
4445	int nsci, ncj4, nexcl;
4446	int n, i;
4447
4448	if (nblc->bSimple)
4449	{
4450	gmx_incons("combine_nblists does not support simple lists")_gmx_error("incons", "combine_nblists does not support simple lists" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 4450);
4451	}
4452
4453	nsci = nblc->nsci;
4454	ncj4 = nblc->ncj4;
4455	nexcl = nblc->nexcl;
4456	for (i = 0; i < nnbl; i++)
4457	{
4458	nsci += nbl[i]->nsci;
4459	ncj4 += nbl[i]->ncj4;
4460	nexcl += nbl[i]->nexcl;
4461	}
4462
4463	if (nsci > nblc->sci_nalloc)
4464	{
4465	nb_realloc_sci(nblc, nsci);
4466	}
4467	if (ncj4 > nblc->cj4_nalloc)
4468	{
4469	nblc->cj4_nalloc = over_alloc_small(ncj4)(int)(1.19*(ncj4) + 8000);
4470	nbnxn_realloc_void((void **)&nblc->cj4,
4471	nblc->ncj4sizeof(nblc->cj4),
4472	nblc->cj4_nallocsizeof(nblc->cj4),
4473	nblc->alloc, nblc->free);
4474	}
4475	if (nexcl > nblc->excl_nalloc)
4476	{
4477	nblc->excl_nalloc = over_alloc_small(nexcl)(int)(1.19*(nexcl) + 8000);
4478	nbnxn_realloc_void((void **)&nblc->excl,
4479	nblc->nexclsizeof(nblc->excl),
4480	nblc->excl_nallocsizeof(nblc->excl),
4481	nblc->alloc, nblc->free);
4482	}
4483
4484	/* Each thread should copy its own data to the combined arrays,
4485	* as otherwise data will go back and forth between different caches.
4486	*/
4487	#pragma omp parallel for num_threads(gmx_omp_nthreads_get(emntPairsearch)) schedule(static)
4488	for (n = 0; n < nnbl; n++)
4489	{
4490	int sci_offset;
4491	int cj4_offset;
4492	int ci_offset;
4493	int excl_offset;
4494	int i, j4;
4495	const nbnxn_pairlist_t *nbli;
4496
4497	/* Determine the offset in the combined data for our thread */
4498	sci_offset = nblc->nsci;
4499	cj4_offset = nblc->ncj4;
4500	ci_offset = nblc->nci_tot;
4501	excl_offset = nblc->nexcl;
4502
4503	for (i = 0; i < n; i++)
4504	{
4505	sci_offset += nbl[i]->nsci;
4506	cj4_offset += nbl[i]->ncj4;
4507	ci_offset += nbl[i]->nci_tot;
4508	excl_offset += nbl[i]->nexcl;
4509	}
4510
4511	nbli = nbl[n];
4512
4513	for (i = 0; i < nbli->nsci; i++)
4514	{
4515	nblc->sci[sci_offset+i] = nbli->sci[i];
4516	nblc->sci[sci_offset+i].cj4_ind_start += cj4_offset;
4517	nblc->sci[sci_offset+i].cj4_ind_end += cj4_offset;
4518	}
4519
4520	for (j4 = 0; j4 < nbli->ncj4; j4++)
4521	{
4522	nblc->cj4[cj4_offset+j4] = nbli->cj4[j4];
4523	nblc->cj4[cj4_offset+j4].imei[0].excl_ind += excl_offset;
4524	nblc->cj4[cj4_offset+j4].imei[1].excl_ind += excl_offset;
4525	}
4526
4527	for (j4 = 0; j4 < nbli->nexcl; j4++)
4528	{
4529	nblc->excl[excl_offset+j4] = nbli->excl[j4];
4530	}
4531	}
4532
4533	for (n = 0; n < nnbl; n++)
4534	{
4535	nblc->nsci += nbl[n]->nsci;
4536	nblc->ncj4 += nbl[n]->ncj4;
4537	nblc->nci_tot += nbl[n]->nci_tot;
4538	nblc->nexcl += nbl[n]->nexcl;
4539	}
4540	}
4541
4542	static void balance_fep_lists(const nbnxn_search_t nbs,
4543	nbnxn_pairlist_set_t *nbl_lists)
4544	{
4545	int nnbl, th;
4546	int nri_tot, nrj_tot, nrj_target;
4547	int th_dest;
4548	t_nblist *nbld;
4549
4550	nnbl = nbl_lists->nnbl;
4551
4552	if (nnbl == 1)
4553	{
4554	/* Nothing to balance */
4555	return;
4556	}
4557
4558	/* Count the total i-lists and pairs */
4559	nri_tot = 0;
4560	nrj_tot = 0;
4561	for (th = 0; th < nnbl; th++)
4562	{
4563	nri_tot += nbl_lists->nbl_fep[th]->nri;
4564	nrj_tot += nbl_lists->nbl_fep[th]->nrj;
4565	}
4566
4567	nrj_target = (nrj_tot + nnbl - 1)/nnbl;
4568
4569	assert(gmx_omp_nthreads_get(emntNonbonded) == nnbl)((void) (0));
4570
4571	#pragma omp parallel for schedule(static) num_threads(nnbl)
4572	for (th = 0; th < nnbl; th++)
4573	{
4574	t_nblist *nbl;
4575
4576	nbl = nbs->work[th].nbl_fep;
4577
4578	/* Note that here we allocate for the total size, instead of
4579	* a per-thread esimate (which is hard to obtain).
4580	*/
4581	if (nri_tot > nbl->maxnri)
4582	{
4583	nbl->maxnri = over_alloc_large(nri_tot)(int)(1.19*(nri_tot) + 1000);
4584	reallocate_nblist(nbl);
4585	}
4586	if (nri_tot > nbl->maxnri \|\| nrj_tot > nbl->maxnrj)
4587	{
4588	nbl->maxnrj = over_alloc_small(nrj_tot)(int)(1.19*(nrj_tot) + 8000);
4589	srenew(nbl->jjnr, nbl->maxnrj)(nbl->jjnr) = save_realloc("nbl->jjnr", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 4589, (nbl->jjnr), (nbl->maxnrj), sizeof(*(nbl->jjnr )));
4590	srenew(nbl->excl_fep, nbl->maxnrj)(nbl->excl_fep) = save_realloc("nbl->excl_fep", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 4590, (nbl->excl_fep), (nbl->maxnrj), sizeof(*(nbl-> excl_fep)));
4591	}
4592
4593	clear_pairlist_fep(nbl);
4594	}
4595
4596	/* Loop over the source lists and assign and copy i-entries */
4597	th_dest = 0;
4598	nbld = nbs->work[th_dest].nbl_fep;
4599	for (th = 0; th < nnbl; th++)
4600	{
4601	t_nblist *nbls;
4602	int i, j;
4603
4604	nbls = nbl_lists->nbl_fep[th];
4605
4606	for (i = 0; i < nbls->nri; i++)
4607	{
4608	int nrj;
4609
4610	/* The number of pairs in this i-entry */
4611	nrj = nbls->jindex[i+1] - nbls->jindex[i];
4612
4613	/* Decide if list th_dest is too large and we should procede
4614	* to the next destination list.
4615	*/
4616	if (th_dest+1 < nnbl && nbld->nrj > 0 &&
4617	nbld->nrj + nrj - nrj_target > nrj_target - nbld->nrj)
4618	{
4619	th_dest++;
4620	nbld = nbs->work[th_dest].nbl_fep;
4621	}
4622
4623	nbld->iinr[nbld->nri] = nbls->iinr[i];
4624	nbld->gid[nbld->nri] = nbls->gid[i];
4625	nbld->shift[nbld->nri] = nbls->shift[i];
4626
4627	for (j = nbls->jindex[i]; j < nbls->jindex[i+1]; j++)
4628	{
4629	nbld->jjnr[nbld->nrj] = nbls->jjnr[j];
4630	nbld->excl_fep[nbld->nrj] = nbls->excl_fep[j];
4631	nbld->nrj++;
4632	}
4633	nbld->nri++;
4634	nbld->jindex[nbld->nri] = nbld->nrj;
4635	}
4636	}
4637
4638	/* Swap the list pointers */
4639	for (th = 0; th < nnbl; th++)
4640	{
4641	t_nblist *nbl_tmp;
4642
4643	nbl_tmp = nbl_lists->nbl_fep[th];
4644	nbl_lists->nbl_fep[th] = nbs->work[th].nbl_fep;
4645	nbs->work[th].nbl_fep = nbl_tmp;
4646
4647	if (debug)
4648	{
4649	fprintf(debug, "nbl_fep[%d] nri %4d nrj %4d\n",
4650	th,
4651	nbl_lists->nbl_fep[th]->nri,
4652	nbl_lists->nbl_fep[th]->nrj);
4653	}
4654	}
4655	}
4656
4657	/* Returns the next ci to be processes by our thread */
4658	static gmx_bool next_ci(const nbnxn_grid_t *grid,
4659	int conv,
4660	int nth, int ci_block,
4661	int ci_x, int ci_y,
4662	int ci_b, int ci)
4663	{
4664	(*ci_b)++;
4665	(*ci)++;
4666
4667	if (*ci_b == ci_block)
4668	{
4669	/* Jump to the next block assigned to this task */
4670	ci += (nth - 1)ci_block;
4671	*ci_b = 0;
4672	}
4673
4674	if (ci >= grid->ncconv)
4675	{
4676	return FALSE0;
4677	}
4678
4679	while (ci >= grid->cxy_ind[ci_xgrid->ncy + ci_y + 1]*conv)
4680	{
4681	*ci_y += 1;
4682	if (*ci_y == grid->ncy)
4683	{
4684	*ci_x += 1;
4685	*ci_y = 0;
4686	}
4687	}
4688
4689	return TRUE1;
4690	}
4691
4692	/* Returns the distance^2 for which we put cell pairs in the list
4693	* without checking atom pair distances. This is usually < rlist^2.
4694	*/
4695	static float boundingbox_only_distance2(const nbnxn_grid_t *gridi,
4696	const nbnxn_grid_t *gridj,
4697	real rlist,
4698	gmx_bool simple)
4699	{
4700	/* If the distance between two sub-cell bounding boxes is less
4701	* than this distance, do not check the distance between
4702	* all particle pairs in the sub-cell, since then it is likely
4703	* that the box pair has atom pairs within the cut-off.
4704	* We use the nblist cut-off minus 0.5 times the average x/y diagonal
4705	* spacing of the sub-cells. Around 40% of the checked pairs are pruned.
4706	* Using more than 0.5 gains at most 0.5%.
4707	* If forces are calculated more than twice, the performance gain
4708	* in the force calculation outweighs the cost of checking.
4709	* Note that with subcell lists, the atom-pair distance check
4710	* is only performed when only 1 out of 8 sub-cells in within range,
4711	* this is because the GPU is much faster than the cpu.
4712	*/
4713	real bbx, bby;
4714	real rbb2;
4715
4716	bbx = 0.5*(gridi->sx + gridj->sx);
4717	bby = 0.5*(gridi->sy + gridj->sy);
4718	if (!simple)
4719	{
4720	bbx /= GPU_NSUBCELL_X2;
4721	bby /= GPU_NSUBCELL_Y2;
4722	}
4723
4724	rbb2 = sqr(max(0, rlist - 0.5sqrt(bbxbbx + bbybby))(((0) > (rlist - 0.5sqrt(bbxbbx + bbybby))) ? (0) : (rlist - 0.5sqrt(bbxbbx + bby*bby)) ));
4725
4726	#ifndef GMX_DOUBLE
4727	return rbb2;
4728	#else
4729	return (float)((1+GMX_FLOAT_EPS5.96046448E-08)*rbb2);
4730	#endif
4731	}
4732
4733	static int get_ci_block_size(const nbnxn_grid_t *gridi,
4734	gmx_bool bDomDec, int nth)
4735	{
4736	const int ci_block_enum = 5;
4737	const int ci_block_denom = 11;
4738	const int ci_block_min_atoms = 16;
4739	int ci_block;
4740
4741	/* Here we decide how to distribute the blocks over the threads.
4742	* We use prime numbers to try to avoid that the grid size becomes
4743	* a multiple of the number of threads, which would lead to some
4744	* threads getting "inner" pairs and others getting boundary pairs,
4745	* which in turns will lead to load imbalance between threads.
4746	* Set the block size as 5/11/ntask times the average number of cells
4747	* in a y,z slab. This should ensure a quite uniform distribution
4748	* of the grid parts of the different thread along all three grid
4749	* zone boundaries with 3D domain decomposition. At the same time
4750	* the blocks will not become too small.
4751	*/
4752	ci_block = (gridi->ncci_block_enum)/(ci_block_denomgridi->ncx*nth);
4753
4754	/* Ensure the blocks are not too small: avoids cache invalidation */
4755	if (ci_block*gridi->na_sc < ci_block_min_atoms)
4756	{
4757	ci_block = (ci_block_min_atoms + gridi->na_sc - 1)/gridi->na_sc;
4758	}
4759
4760	/* Without domain decomposition
4761	* or with less than 3 blocks per task, divide in nth blocks.
4762	*/
4763	if (!bDomDec \|\| ci_block3nth > gridi->nc)
4764	{
4765	ci_block = (gridi->nc + nth - 1)/nth;
4766	}
4767
4768	return ci_block;
4769	}
4770
4771	/* Generates the part of pair-list nbl assigned to our thread */
4772	static void nbnxn_make_pairlist_part(const nbnxn_search_t nbs,
4773	const nbnxn_grid_t *gridi,
4774	const nbnxn_grid_t *gridj,
4775	nbnxn_search_work_t *work,
4776	const nbnxn_atomdata_t *nbat,
4777	const t_blocka *excl,
4778	real rlist,
4779	int nb_kernel_type,
4780	int ci_block,
4781	gmx_bool bFBufferFlag,
4782	int nsubpair_max,
4783	gmx_bool progBal,
4784	int min_ci_balanced,
4785	int th, int nth,
4786	nbnxn_pairlist_t *nbl,
4787	t_nblist *nbl_fep)
4788	{
4789	int na_cj_2log;
4790	matrix box;
4791	real rl2, rl_fep2 = 0;
4792	float rbb2;
4793	int d;
4794	int ci_b, ci, ci_x, ci_y, ci_xy, cj;
4795	ivec shp;
4796	int tx, ty, tz;
4797	int shift;
4798	gmx_bool bMakeList;
4799	real shx, shy, shz;
4800	int conv_i, cell0_i;
4801	const nbnxn_bb_t bb_i = NULL((void)0);
4802	#ifdef NBNXN_BBXXXX
4803	const float pbb_i = NULL((void)0);
4804	#endif
4805	const float bbcz_i, bbcz_j;
4806	const int *flags_i;
4807	real bx0, bx1, by0, by1, bz0, bz1;
4808	real bz1_frac;
4809	real d2cx, d2z, d2z_cx, d2z_cy, d2zx, d2zxy, d2xy;
4810	int cxf, cxl, cyf, cyf_x, cyl;
4811	int cx, cy;
4812	int c0, c1, cs, cf, cl;
4813	int ndistc;
4814	int ncpcheck;
4815	int gridi_flag_shift = 0, gridj_flag_shift = 0;
4816	unsigned int gridj_flag = NULL((void)0);
4817	int ncj_old_i, ncj_old_j;
4818
4819	nbs_cycle_start(&work->cc[enbsCCsearch]);
4820
4821	if (gridj->bSimple != nbl->bSimple)
4822	{
4823	gmx_incons("Grid incompatible with pair-list")_gmx_error("incons", "Grid incompatible with pair-list", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 4823);
4824	}
4825
4826	sync_work(nbl);
4827	nbl->na_sc = gridj->na_sc;
4828	nbl->na_ci = gridj->na_c;
4829	nbl->na_cj = nbnxn_kernel_to_cj_size(nb_kernel_type);
4830	na_cj_2log = get_2log(nbl->na_cj);
4831
4832	nbl->rlist = rlist;
4833
4834	if (bFBufferFlag)
4835	{
4836	/* Determine conversion of clusters to flag blocks */
4837	gridi_flag_shift = 0;
4838	while ((nbl->na_ci<<gridi_flag_shift) < NBNXN_BUFFERFLAG_SIZE16)
4839	{
4840	gridi_flag_shift++;
4841	}
4842	gridj_flag_shift = 0;
4843	while ((nbl->na_cj<<gridj_flag_shift) < NBNXN_BUFFERFLAG_SIZE16)
4844	{
4845	gridj_flag_shift++;
4846	}
4847
4848	gridj_flag = work->buffer_flags.flag;
4849	}
4850
4851	copy_mat(nbs->box, box);
4852
4853	rl2 = nbl->rlist*nbl->rlist;
4854
4855	if (nbs->bFEP && !nbl->bSimple)
4856	{
4857	/* Determine an atom-pair list cut-off distance for FEP atom pairs.
4858	* We should not simply use rlist, since then we would not have
4859	* the small, effective buffering of the NxN lists.
4860	* The buffer is on overestimate, but the resulting cost for pairs
4861	* beyond rlist is neglible compared to the FEP pairs within rlist.
4862	*/
4863	rl_fep2 = nbl->rlist + effective_buffer_1x1_vs_MxN(gridi, gridj);
4864
4865	if (debug)
4866	{
4867	fprintf(debug, "nbl_fep atom-pair rlist %f\n", rl_fep2);
4868	}
4869	rl_fep2 = rl_fep2*rl_fep2;
4870	}
4871
4872	rbb2 = boundingbox_only_distance2(gridi, gridj, nbl->rlist, nbl->bSimple);
4873
4874	if (debug)
4875	{
4876	fprintf(debug, "nbl bounding box only distance %f\n", sqrt(rbb2));
4877	}
4878
4879	/* Set the shift range */
4880	for (d = 0; d < DIM3; d++)
4881	{
4882	/* Check if we need periodicity shifts.
4883	* Without PBC or with domain decomposition we don't need them.
4884	*/
4885	if (d >= ePBC2npbcdim(nbs->ePBC) \|\| nbs->dd_dim[d])
4886	{
4887	shp[d] = 0;
4888	}
4889	else
4890	{
4891	if (d == XX0 &&
4892	box[XX0][XX0] - fabs(box[YY1][XX0]) - fabs(box[ZZ2][XX0]) < sqrt(rl2))
4893	{
4894	shp[d] = 2;
4895	}
4896	else
4897	{
4898	shp[d] = 1;
4899	}
4900	}
4901	}
4902
4903	if (nbl->bSimple && !gridi->bSimple)
4904	{
4905	conv_i = gridi->na_sc/gridj->na_sc;
4906	bb_i = gridi->bb_simple;
4907	bbcz_i = gridi->bbcz_simple;
4908	flags_i = gridi->flags_simple;
4909	}
4910	else
4911	{
4912	conv_i = 1;
4913	#ifdef NBNXN_BBXXXX
4914	if (gridi->bSimple)
4915	{
4916	bb_i = gridi->bb;
4917	}
4918	else
4919	{
4920	pbb_i = gridi->pbb;
4921	}
4922	#else
4923	/* We use the normal bounding box format for both grid types */
4924	bb_i = gridi->bb;
4925	#endif
4926	bbcz_i = gridi->bbcz;
4927	flags_i = gridi->flags;
4928	}
4929	cell0_i = gridi->cell0*conv_i;
4930
4931	bbcz_j = gridj->bbcz;
4932
4933	if (conv_i != 1)
4934	{
4935	/* Blocks of the conversion factor - 1 give a large repeat count
4936	* combined with a small block size. This should result in good
4937	* load balancing for both small and large domains.
4938	*/
4939	ci_block = conv_i - 1;
4940	}
4941	if (debug)
4942	{
4943	fprintf(debug, "nbl nc_i %d col.av. %.1f ci_block %d\n",
4944	gridi->nc, gridi->nc/(double)(gridi->ncx*gridi->ncy), ci_block);
4945	}
4946
4947	ndistc = 0;
4948	ncpcheck = 0;
4949
4950	/* Initially ci_b and ci to 1 before where we want them to start,
4951	* as they will both be incremented in next_ci.
4952	*/
4953	ci_b = -1;
4954	ci = th*ci_block - 1;
4955	ci_x = 0;
4956	ci_y = 0;
4957	while (next_ci(gridi, conv_i, nth, ci_block, &ci_x, &ci_y, &ci_b, &ci))
4958	{
4959	if (nbl->bSimple && flags_i[ci] == 0)
4960	{
4961	continue;
4962	}
4963
4964	ncj_old_i = nbl->ncj;
4965
4966	d2cx = 0;
4967	if (gridj != gridi && shp[XX0] == 0)
4968	{
4969	if (nbl->bSimple)
4970	{
4971	bx1 = bb_i[ci].upper[BB_X0];
4972	}
4973	else
4974	{
4975	bx1 = gridi->c0[XX0] + (ci_x+1)*gridi->sx;
4976	}
4977	if (bx1 < gridj->c0[XX0])
4978	{
4979	d2cx = sqr(gridj->c0[XX0] - bx1);
4980
4981	if (d2cx >= rl2)
4982	{
4983	continue;
4984	}
4985	}
4986	}
4987
4988	ci_xy = ci_x*gridi->ncy + ci_y;
4989
4990	/* Loop over shift vectors in three dimensions */
4991	for (tz = -shp[ZZ2]; tz <= shp[ZZ2]; tz++)
4992	{
4993	shz = tz*box[ZZ2][ZZ2];
4994
4995	bz0 = bbcz_i[ci*NNBSBB_D2 ] + shz;
4996	bz1 = bbcz_i[ci*NNBSBB_D2+1] + shz;
4997
4998	if (tz == 0)
4999	{
5000	d2z = 0;
5001	}
5002	else if (tz < 0)
5003	{
5004	d2z = sqr(bz1);
5005	}
5006	else
5007	{
5008	d2z = sqr(bz0 - box[ZZ2][ZZ2]);
5009	}
5010
5011	d2z_cx = d2z + d2cx;
5012
5013	if (d2z_cx >= rl2)
5014	{
5015	continue;
5016	}
5017
5018	bz1_frac =
5019	bz1/((real)(gridi->cxy_ind[ci_xy+1] - gridi->cxy_ind[ci_xy]));
5020	if (bz1_frac < 0)
5021	{
5022	bz1_frac = 0;
5023	}
5024	/* The check with bz1_frac close to or larger than 1 comes later */
5025
5026	for (ty = -shp[YY1]; ty <= shp[YY1]; ty++)
5027	{
5028	shy = tybox[YY1][YY1] + tzbox[ZZ2][YY1];
5029
5030	if (nbl->bSimple)
5031	{
5032	by0 = bb_i[ci].lower[BB_Y1] + shy;
5033	by1 = bb_i[ci].upper[BB_Y1] + shy;
5034	}
5035	else
5036	{
5037	by0 = gridi->c0[YY1] + (ci_y )*gridi->sy + shy;
5038	by1 = gridi->c0[YY1] + (ci_y+1)*gridi->sy + shy;
5039	}
5040
5041	get_cell_range(by0, by1,
5042	gridj->ncy, gridj->c0[YY1], gridj->sy, gridj->inv_sy,
5043	d2z_cx, rl2,
5044	&cyf, &cyl);
5045
5046	if (cyf > cyl)
5047	{
5048	continue;
5049	}
5050
5051	d2z_cy = d2z;
5052	if (by1 < gridj->c0[YY1])
5053	{
5054	d2z_cy += sqr(gridj->c0[YY1] - by1);
5055	}
5056	else if (by0 > gridj->c1[YY1])
5057	{
5058	d2z_cy += sqr(by0 - gridj->c1[YY1]);
5059	}
5060
5061	for (tx = -shp[XX0]; tx <= shp[XX0]; tx++)
5062	{
5063	shift = XYZ2IS(tx, ty, tz)((22 +1)((21 +1)((tz)+1)+(ty)+1)+(tx)+2);
5064
5065	#ifdef NBNXN_SHIFT_BACKWARD
5066	if (gridi == gridj && shift > CENTRAL(((21 +1)(21 +1)(2*2 +1))/2))
5067	{
5068	continue;
5069	}
5070	#endif
5071
5072	shx = txbox[XX0][XX0] + tybox[YY1][XX0] + tz*box[ZZ2][XX0];
5073
5074	if (nbl->bSimple)
5075	{
5076	bx0 = bb_i[ci].lower[BB_X0] + shx;
5077	bx1 = bb_i[ci].upper[BB_X0] + shx;
5078	}
5079	else
5080	{
5081	bx0 = gridi->c0[XX0] + (ci_x )*gridi->sx + shx;
5082	bx1 = gridi->c0[XX0] + (ci_x+1)*gridi->sx + shx;
5083	}
5084
5085	get_cell_range(bx0, bx1,
5086	gridj->ncx, gridj->c0[XX0], gridj->sx, gridj->inv_sx,
5087	d2z_cy, rl2,
5088	&cxf, &cxl);
5089
5090	if (cxf > cxl)
5091	{
5092	continue;
5093	}
5094
5095	if (nbl->bSimple)
5096	{
5097	new_ci_entry(nbl, cell0_i+ci, shift, flags_i[ci]);
5098	}
5099	else
5100	{
5101	new_sci_entry(nbl, cell0_i+ci, shift);
5102	}
5103
5104	#ifndef NBNXN_SHIFT_BACKWARD
5105	if (cxf < ci_x)
5106	#else
5107	if (shift == CENTRAL(((21 +1)(21 +1)(2*2 +1))/2) && gridi == gridj &&
5108	cxf < ci_x)
5109	#endif
5110	{
5111	/* Leave the pairs with i > j.
5112	* x is the major index, so skip half of it.
5113	*/
5114	cxf = ci_x;
5115	}
5116
5117	if (nbl->bSimple)
5118	{
5119	set_icell_bb_simple(bb_i, ci, shx, shy, shz,
5120	nbl->work->bb_ci);
5121	}
5122	else
5123	{
5124	#ifdef NBNXN_BBXXXX
5125	set_icell_bbxxxx_supersub(pbb_i, ci, shx, shy, shz,
5126	nbl->work->pbb_ci);
5127	#else
5128	set_icell_bb_supersub(bb_i, ci, shx, shy, shz,
5129	nbl->work->bb_ci);
5130	#endif
5131	}
5132
5133	nbs->icell_set_x(cell0_i+ci, shx, shy, shz,
5134	gridi->na_c, nbat->xstride, nbat->x,
5135	nbl->work);
5136
5137	for (cx = cxf; cx <= cxl; cx++)
5138	{
5139	d2zx = d2z;
5140	if (gridj->c0[XX0] + cx*gridj->sx > bx1)
5141	{
5142	d2zx += sqr(gridj->c0[XX0] + cx*gridj->sx - bx1);
5143	}
5144	else if (gridj->c0[XX0] + (cx+1)*gridj->sx < bx0)
5145	{
5146	d2zx += sqr(gridj->c0[XX0] + (cx+1)*gridj->sx - bx0);
5147	}
5148
5149	#ifndef NBNXN_SHIFT_BACKWARD
5150	if (gridi == gridj &&
5151	cx == 0 && cyf < ci_y)
5152	#else
5153	if (gridi == gridj &&
5154	cx == 0 && shift == CENTRAL(((21 +1)(21 +1)(2*2 +1))/2) && cyf < ci_y)
5155	#endif
5156	{
5157	/* Leave the pairs with i > j.
5158	* Skip half of y when i and j have the same x.
5159	*/
5160	cyf_x = ci_y;
5161	}
5162	else
5163	{
5164	cyf_x = cyf;
5165	}
5166
5167	for (cy = cyf_x; cy <= cyl; cy++)
5168	{
5169	c0 = gridj->cxy_ind[cx*gridj->ncy+cy];
5170	c1 = gridj->cxy_ind[cx*gridj->ncy+cy+1];
5171	#ifdef NBNXN_SHIFT_BACKWARD
5172	if (gridi == gridj &&
5173	shift == CENTRAL(((21 +1)(21 +1)(2*2 +1))/2) && c0 < ci)
5174	{
5175	c0 = ci;
5176	}
5177	#endif
5178
5179	d2zxy = d2zx;
5180	if (gridj->c0[YY1] + cy*gridj->sy > by1)
5181	{
5182	d2zxy += sqr(gridj->c0[YY1] + cy*gridj->sy - by1);
5183	}
5184	else if (gridj->c0[YY1] + (cy+1)*gridj->sy < by0)
5185	{
5186	d2zxy += sqr(gridj->c0[YY1] + (cy+1)*gridj->sy - by0);
5187	}
5188	if (c1 > c0 && d2zxy < rl2)
5189	{
5190	cs = c0 + (int)(bz1_frac*(c1 - c0));
5191	if (cs >= c1)
5192	{
5193	cs = c1 - 1;
5194	}
5195
5196	d2xy = d2zxy - d2z;
5197
5198	/* Find the lowest cell that can possibly
5199	* be within range.
5200	*/
5201	cf = cs;
5202	while (cf > c0 &&
5203	(bbcz_j[cf*NNBSBB_D2+1] >= bz0 \|\|
5204	d2xy + sqr(bbcz_j[cf*NNBSBB_D2+1] - bz0) < rl2))
5205	{
5206	cf--;
5207	}
5208
5209	/* Find the highest cell that can possibly
5210	* be within range.
5211	*/
5212	cl = cs;
5213	while (cl < c1-1 &&
5214	(bbcz_j[cl*NNBSBB_D2] <= bz1 \|\|
5215	d2xy + sqr(bbcz_j[cl*NNBSBB_D2] - bz1) < rl2))
5216	{
5217	cl++;
5218	}
5219
5220	#ifdef NBNXN_REFCODE
5221	{
5222	/* Simple reference code, for debugging,
5223	* overrides the more complex code above.
5224	*/
5225	int k;
5226	cf = c1;
5227	cl = -1;
5228	for (k = c0; k < c1; k++)
5229	{
5230	if (box_dist2(bx0, bx1, by0, by1, bz0, bz1, bb+k) < rl2 &&
5231	k < cf)
5232	{
5233	cf = k;
5234	}
5235	if (box_dist2(bx0, bx1, by0, by1, bz0, bz1, bb+k) < rl2 &&
5236	k > cl)
5237	{
5238	cl = k;
5239	}
5240	}
5241	}
5242	#endif
5243
5244	if (gridi == gridj)
5245	{
5246	/* We want each atom/cell pair only once,
5247	* only use cj >= ci.
5248	*/
5249	#ifndef NBNXN_SHIFT_BACKWARD
5250	cf = max(cf, ci)(((cf) > (ci)) ? (cf) : (ci) );
5251	#else
5252	if (shift == CENTRAL(((21 +1)(21 +1)(2*2 +1))/2))
5253	{
5254	cf = max(cf, ci)(((cf) > (ci)) ? (cf) : (ci) );
5255	}
5256	#endif
5257	}
5258
5259	if (cf <= cl)
5260	{
5261	/* For f buffer flags with simple lists */
5262	ncj_old_j = nbl->ncj;
5263
5264	switch (nb_kernel_type)
5265	{
5266	case nbnxnk4x4_PlainC:
5267	check_subcell_list_space_simple(nbl, cl-cf+1);
5268
5269	make_cluster_list_simple(gridj,
5270	nbl, ci, cf, cl,
5271	(gridi == gridj && shift == CENTRAL(((21 +1)(21 +1)(2*2 +1))/2)),
5272	nbat->x,
5273	rl2, rbb2,
5274	&ndistc);
5275	break;
5276	#ifdef GMX_NBNXN_SIMD_4XN
5277	case nbnxnk4xN_SIMD_4xN:
5278	check_subcell_list_space_simple(nbl, ci_to_cj(na_cj_2log, cl-cf)+2);
5279	make_cluster_list_simd_4xn(gridj,
5280	nbl, ci, cf, cl,
5281	(gridi == gridj && shift == CENTRAL(((21 +1)(21 +1)(2*2 +1))/2)),
5282	nbat->x,
5283	rl2, rbb2,
5284	&ndistc);
5285	break;
5286	#endif
5287	#ifdef GMX_NBNXN_SIMD_2XNN
5288	case nbnxnk4xN_SIMD_2xNN:
5289	check_subcell_list_space_simple(nbl, ci_to_cj(na_cj_2log, cl-cf)+2);
5290	make_cluster_list_simd_2xnn(gridj,
5291	nbl, ci, cf, cl,
5292	(gridi == gridj && shift == CENTRAL(((21 +1)(21 +1)(2*2 +1))/2)),
5293	nbat->x,
5294	rl2, rbb2,
5295	&ndistc);
5296	break;
5297	#endif
5298	case nbnxnk8x8x8_PlainC:
5299	case nbnxnk8x8x8_CUDA:
5300	check_subcell_list_space_supersub(nbl, cl-cf+1);
5301	for (cj = cf; cj <= cl; cj++)
5302	{
5303	make_cluster_list_supersub(gridi, gridj,
5304	nbl, ci, cj,
5305	(gridi == gridj && shift == CENTRAL(((21 +1)(21 +1)(2*2 +1))/2) && ci == cj),
5306	nbat->xstride, nbat->x,
5307	rl2, rbb2,
5308	&ndistc);
5309	}
5310	break;
5311	}
5312	ncpcheck += cl - cf + 1;
5313
5314	if (bFBufferFlag && nbl->ncj > ncj_old_j)
5315	{
5316	int cbf, cbl, cb;
5317
5318	cbf = nbl->cj[ncj_old_j].cj >> gridj_flag_shift;
5319	cbl = nbl->cj[nbl->ncj-1].cj >> gridj_flag_shift;
5320	for (cb = cbf; cb <= cbl; cb++)
5321	{
5322	gridj_flag[cb] = 1U<<th;
5323	}
5324	}
5325	}
5326	}
5327	}
5328	}
5329
5330	/* Set the exclusions for this ci list */
5331	if (nbl->bSimple)
5332	{
5333	set_ci_top_excls(nbs,
5334	nbl,
5335	shift == CENTRAL(((21 +1)(21 +1)(2*2 +1))/2) && gridi == gridj,
5336	gridj->na_c_2log,
5337	na_cj_2log,
5338	&(nbl->ci[nbl->nci]),
5339	excl);
5340
5341	if (nbs->bFEP)
5342	{
5343	make_fep_list(nbs, nbat, nbl,
5344	shift == CENTRAL(((21 +1)(21 +1)(2*2 +1))/2) && gridi == gridj,
5345	&(nbl->ci[nbl->nci]),
5346	gridi, gridj, nbl_fep);
5347	}
5348	}
5349	else
5350	{
5351	set_sci_top_excls(nbs,
5352	nbl,
5353	shift == CENTRAL(((21 +1)(21 +1)(2*2 +1))/2) && gridi == gridj,
5354	gridj->na_c_2log,
5355	&(nbl->sci[nbl->nsci]),
5356	excl);
5357
5358	if (nbs->bFEP)
5359	{
5360	make_fep_list_supersub(nbs, nbat, nbl,
5361	shift == CENTRAL(((21 +1)(21 +1)(2*2 +1))/2) && gridi == gridj,
5362	&(nbl->sci[nbl->nsci]),
5363	shx, shy, shz,
5364	rl_fep2,
5365	gridi, gridj, nbl_fep);
5366	}
5367	}
5368
5369	/* Close this ci list */
5370	if (nbl->bSimple)
5371	{
5372	close_ci_entry_simple(nbl);
5373	}
5374	else
5375	{
5376	close_ci_entry_supersub(nbl,
5377	nsubpair_max,
5378	progBal, min_ci_balanced,
5379	th, nth);
5380	}
5381	}
5382	}
5383	}
5384
5385	if (bFBufferFlag && nbl->ncj > ncj_old_i)
5386	{
5387	work->buffer_flags.flag[(gridi->cell0+ci)>>gridi_flag_shift] = 1U<<th;
5388	}
5389	}
5390
5391	work->ndistc = ndistc;
5392
5393	nbs_cycle_stop(&work->cc[enbsCCsearch]);
5394
5395	if (debug)
5396	{
5397	fprintf(debug, "number of distance checks %d\n", ndistc);
5398	fprintf(debug, "ncpcheck %s %d\n", gridi == gridj ? "local" : "non-local",
5399	ncpcheck);
5400
5401	if (nbl->bSimple)
5402	{
5403	print_nblist_statistics_simple(debug, nbl, nbs, rlist);
5404	}
5405	else
5406	{
5407	print_nblist_statistics_supersub(debug, nbl, nbs, rlist);
5408	}
5409
5410	if (nbs->bFEP)
5411	{
5412	fprintf(debug, "nbl FEP list pairs: %d\n", nbl_fep->nrj);
5413	}
5414	}
5415	}
5416
5417	static void reduce_buffer_flags(const nbnxn_search_t nbs,
5418	int nsrc,
5419	const nbnxn_buffer_flags_t *dest)
5420	{
5421	int s, b;
5422	const unsigned int *flag;
5423
5424	for (s = 0; s < nsrc; s++)
5425	{
5426	flag = nbs->work[s].buffer_flags.flag;
5427
5428	for (b = 0; b < dest->nflag; b++)
5429	{
5430	dest->flag[b] \|= flag[b];
5431	}
5432	}
5433	}
5434
5435	static void print_reduction_cost(const nbnxn_buffer_flags_t *flags, int nout)
5436	{
5437	int nelem, nkeep, ncopy, nred, b, c, out;
5438
5439	nelem = 0;
5440	nkeep = 0;
5441	ncopy = 0;
5442	nred = 0;
5443	for (b = 0; b < flags->nflag; b++)
5444	{
5445	if (flags->flag[b] == 1)
5446	{
5447	/* Only flag 0 is set, no copy of reduction required */
5448	nelem++;
5449	nkeep++;
5450	}
5451	else if (flags->flag[b] > 0)
5452	{
5453	c = 0;
5454	for (out = 0; out < nout; out++)
5455	{
5456	if (flags->flag[b] & (1U<<out))
5457	{
5458	c++;
5459	}
5460	}
5461	nelem += c;
5462	if (c == 1)
5463	{
5464	ncopy++;
5465	}
5466	else
5467	{
5468	nred += c;
5469	}
5470	}
5471	}
5472
5473	fprintf(debug, "nbnxn reduction: #flag %d #list %d elem %4.2f, keep %4.2f copy %4.2f red %4.2f\n",
5474	flags->nflag, nout,
5475	nelem/(double)(flags->nflag),
5476	nkeep/(double)(flags->nflag),
5477	ncopy/(double)(flags->nflag),
5478	nred/(double)(flags->nflag));
5479	}
5480
5481	/* Perform a count (linear) sort to sort the smaller lists to the end.
5482	* This avoids load imbalance on the GPU, as large lists will be
5483	* scheduled and executed first and the smaller lists later.
5484	* Load balancing between multi-processors only happens at the end
5485	* and there smaller lists lead to more effective load balancing.
5486	* The sorting is done on the cj4 count, not on the actual pair counts.
5487	* Not only does this make the sort faster, but it also results in
5488	* better load balancing than using a list sorted on exact load.
5489	* This function swaps the pointer in the pair list to avoid a copy operation.
5490	*/
5491	static void sort_sci(nbnxn_pairlist_t *nbl)
5492	{
5493	nbnxn_list_work_t *work;
5494	int m, i, s, s0, s1;
5495	nbnxn_sci_t *sci_sort;
5496
5497	if (nbl->ncj4 <= nbl->nsci)
5498	{
5499	/* nsci = 0 or all sci have size 1, sorting won't change the order */
5500	return;
5501	}
5502
5503	work = nbl->work;
5504
5505	/* We will distinguish differences up to double the average */
5506	m = (2*nbl->ncj4)/nbl->nsci;
5507
5508	if (m + 1 > work->sort_nalloc)
5509	{
5510	work->sort_nalloc = over_alloc_large(m + 1)(int)(1.19*(m + 1) + 1000);
5511	srenew(work->sort, work->sort_nalloc)(work->sort) = save_realloc("work->sort", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/nbnxn_search.c" , 5511, (work->sort), (work->sort_nalloc), sizeof(*(work ->sort)));
5512	}
5513
5514	if (work->sci_sort_nalloc != nbl->sci_nalloc)
5515	{
5516	work->sci_sort_nalloc = nbl->sci_nalloc;
5517	nbnxn_realloc_void((void **)&work->sci_sort,
5518	0,
5519	work->sci_sort_nallocsizeof(work->sci_sort),
5520	nbl->alloc, nbl->free);
5521	}
5522
5523	/* Count the entries of each size */
5524	for (i = 0; i <= m; i++)
5525	{
5526	work->sort[i] = 0;
5527	}
5528	for (s = 0; s < nbl->nsci; s++)
5529	{
5530	i = min(m, nbl->sci[s].cj4_ind_end - nbl->sci[s].cj4_ind_start)(((m) < (nbl->sci[s].cj4_ind_end - nbl->sci[s].cj4_ind_start )) ? (m) : (nbl->sci[s].cj4_ind_end - nbl->sci[s].cj4_ind_start ) );
5531	work->sort[i]++;
5532	}
5533	/* Calculate the offset for each count */
5534	s0 = work->sort[m];
5535	work->sort[m] = 0;
5536	for (i = m - 1; i >= 0; i--)
5537	{
5538	s1 = work->sort[i];
5539	work->sort[i] = work->sort[i + 1] + s0;
5540	s0 = s1;
5541	}
5542
5543	/* Sort entries directly into place */
5544	sci_sort = work->sci_sort;
5545	for (s = 0; s < nbl->nsci; s++)
5546	{
5547	i = min(m, nbl->sci[s].cj4_ind_end - nbl->sci[s].cj4_ind_start)(((m) < (nbl->sci[s].cj4_ind_end - nbl->sci[s].cj4_ind_start )) ? (m) : (nbl->sci[s].cj4_ind_end - nbl->sci[s].cj4_ind_start ) );
5548	sci_sort[work->sort[i]++] = nbl->sci[s];
5549	}
5550
5551	/* Swap the sci pointers so we use the new, sorted list */
5552	work->sci_sort = nbl->sci;
5553	nbl->sci = sci_sort;
5554	}
5555
5556	/* Make a local or non-local pair-list, depending on iloc */
5557	void nbnxn_make_pairlist(const nbnxn_search_t nbs,
5558	nbnxn_atomdata_t *nbat,
5559	const t_blocka *excl,
5560	real rlist,
5561	int min_ci_balanced,
5562	nbnxn_pairlist_set_t *nbl_list,
5563	int iloc,
5564	int nb_kernel_type,
5565	t_nrnb *nrnb)
5566	{
5567	nbnxn_grid_t gridi, gridj;
5568	gmx_bool bGPUCPU;
5569	int nzi, zi, zj0, zj1, zj;
5570	int nsubpair_max;
5571	int th;
5572	int nnbl;
5573	nbnxn_pairlist_t **nbl;
5574	int ci_block;
5575	gmx_bool CombineNBLists;
5576	gmx_bool progBal;
5577	int np_tot, np_noq, np_hlj, nap;
5578
5579	/* Check if we are running hybrid GPU + CPU nbnxn mode */
5580	bGPUCPU = (!nbs->grid[0].bSimple && nbl_list->bSimple);
5581
5582	nnbl = nbl_list->nnbl;
5583	nbl = nbl_list->nbl;
5584	CombineNBLists = nbl_list->bCombined;
5585
5586	if (debug)
5587	{
5588	fprintf(debug, "ns making %d nblists\n", nnbl);
5589	}
5590
5591	nbat->bUseBufferFlags = (nbat->nout > 1);
5592	/* We should re-init the flags before making the first list */
5593	if (nbat->bUseBufferFlags && (LOCAL_I(iloc)((iloc) == eintLocal) \|\| bGPUCPU))
5594	{
5595	init_buffer_flags(&nbat->buffer_flags, nbat->natoms);
5596	}
5597
5598	if (nbl_list->bSimple)
5599	{
5600	switch (nb_kernel_type)
5601	{
5602	#ifdef GMX_NBNXN_SIMD_4XN
5603	case nbnxnk4xN_SIMD_4xN:
5604	nbs->icell_set_x = icell_set_x_simd_4xn;
5605	break;
5606	#endif
5607	#ifdef GMX_NBNXN_SIMD_2XNN
5608	case nbnxnk4xN_SIMD_2xNN:
5609	nbs->icell_set_x = icell_set_x_simd_2xnn;
5610	break;
5611	#endif
5612	default:
5613	nbs->icell_set_x = icell_set_x_simple;
5614	break;
5615	}
5616	}
5617	else
5618	{
5619	#ifdef NBNXN_SEARCH_BB_SIMD4
5620	nbs->icell_set_x = icell_set_x_supersub_simd4;
5621	#else
5622	nbs->icell_set_x = icell_set_x_supersub;
5623	#endif
5624	}
5625
5626	if (LOCAL_I(iloc)((iloc) == eintLocal))
5627	{
5628	/* Only zone (grid) 0 vs 0 */
5629	nzi = 1;
5630	zj0 = 0;
5631	zj1 = 1;
5632	}
5633	else
5634	{
5635	nzi = nbs->zones->nizone;
5636	}
5637
5638	if (!nbl_list->bSimple && min_ci_balanced > 0)
5639	{
5640	nsubpair_max = get_nsubpair_max(nbs, iloc, rlist, min_ci_balanced);
5641	}
5642	else
5643	{
5644	nsubpair_max = 0;
5645	}
5646
5647	/* Clear all pair-lists */
5648	for (th = 0; th < nnbl; th++)
5649	{
5650	clear_pairlist(nbl[th]);
5651
5652	if (nbs->bFEP)
5653	{
5654	clear_pairlist_fep(nbl_list->nbl_fep[th]);
5655	}
5656	}
5657
5658	for (zi = 0; zi < nzi; zi++)
5659	{
5660	gridi = &nbs->grid[zi];
5661
5662	if (NONLOCAL_I(iloc)((iloc) == eintNonlocal))
5663	{
5664	zj0 = nbs->zones->izone[zi].j0;
5665	zj1 = nbs->zones->izone[zi].j1;
5666	if (zi == 0)
5667	{
5668	zj0++;
5669	}
5670	}
5671	for (zj = zj0; zj < zj1; zj++)
5672	{
5673	gridj = &nbs->grid[zj];
5674
5675	if (debug)
5676	{
5677	fprintf(debug, "ns search grid %d vs %d\n", zi, zj);
5678	}
5679
5680	nbs_cycle_start(&nbs->cc[enbsCCsearch]);
5681
5682	if (nbl[0]->bSimple && !gridi->bSimple)
5683	{
5684	/* Hybrid list, determine blocking later */
5685	ci_block = 0;
5686	}
5687	else
5688	{
5689	ci_block = get_ci_block_size(gridi, nbs->DomDec, nnbl);
5690	}
5691
5692	/* With GPU: generate progressively smaller lists for
5693	* load balancing for local only or non-local with 2 zones.
5694	*/
5695	progBal = (LOCAL_I(iloc)((iloc) == eintLocal) \|\| nbs->zones->n <= 2);
5696
5697	#pragma omp parallel for num_threads(nnbl) schedule(static)
5698	for (th = 0; th < nnbl; th++)
5699	{
5700	/* Re-init the thread-local work flag data before making
5701	* the first list (not an elegant conditional).
5702	*/
5703	if (nbat->bUseBufferFlags && ((zi == 0 && zj == 0) \|\|
5704	(bGPUCPU && zi == 0 && zj == 1)))
5705	{
5706	init_buffer_flags(&nbs->work[th].buffer_flags, nbat->natoms);
5707	}
5708
5709	if (CombineNBLists && th > 0)
5710	{
5711	clear_pairlist(nbl[th]);
5712	}
5713
5714	/* Divide the i super cell equally over the nblists */
5715	nbnxn_make_pairlist_part(nbs, gridi, gridj,
5716	&nbs->work[th], nbat, excl,
5717	rlist,
5718	nb_kernel_type,
5719	ci_block,
5720	nbat->bUseBufferFlags,
5721	nsubpair_max,
5722	progBal, min_ci_balanced,
5723	th, nnbl,
5724	nbl[th],
5725	nbl_list->nbl_fep[th]);
5726	}
5727	nbs_cycle_stop(&nbs->cc[enbsCCsearch]);
5728
5729	np_tot = 0;
5730	np_noq = 0;
5731	np_hlj = 0;
5732	for (th = 0; th < nnbl; th++)
5733	{
5734	inc_nrnb(nrnb, eNR_NBNXN_DIST2, nbs->work[th].ndistc)(nrnb)->n[eNR_NBNXN_DIST2] += nbs->work[th].ndistc;
5735
5736	if (nbl_list->bSimple)
5737	{
5738	np_tot += nbl[th]->ncj;
5739	np_noq += nbl[th]->work->ncj_noq;
5740	np_hlj += nbl[th]->work->ncj_hlj;
5741	}
5742	else
5743	{
5744	/* This count ignores potential subsequent pair pruning */
5745	np_tot += nbl[th]->nci_tot;
5746	}
5747	}
5748	nap = nbl[0]->na_ci*nbl[0]->na_cj;
5749	nbl_list->natpair_ljq = (np_tot - np_noq)nap - np_hljnap/2;
5750	nbl_list->natpair_lj = np_noq*nap;
5751	nbl_list->natpair_q = np_hlj*nap/2;
5752
5753	if (CombineNBLists && nnbl > 1)
5754	{
5755	nbs_cycle_start(&nbs->cc[enbsCCcombine]);
5756
5757	combine_nblists(nnbl-1, nbl+1, nbl[0]);
5758
5759	nbs_cycle_stop(&nbs->cc[enbsCCcombine]);
5760	}
5761	}
5762	}
5763
5764	if (!nbl_list->bSimple)
5765	{
5766	/* Sort the entries on size, large ones first */
5767	if (CombineNBLists \|\| nnbl == 1)
5768	{
5769	sort_sci(nbl[0]);
5770	}
5771	else
5772	{
5773	#pragma omp parallel for num_threads(nnbl) schedule(static)
5774	for (th = 0; th < nnbl; th++)
5775	{
5776	sort_sci(nbl[th]);
5777	}
5778	}
5779	}
5780
5781	if (nbat->bUseBufferFlags)
5782	{
5783	reduce_buffer_flags(nbs, nnbl, &nbat->buffer_flags);
5784	}
5785
5786	if (nbs->bFEP)
5787	{
5788	/* Balance the free-energy lists over all the threads */
5789	balance_fep_lists(nbs, nbl_list);
5790	}
5791
5792	/* Special performance logging stuff (env.var. GMX_NBNXN_CYCLE) */
5793	if (LOCAL_I(iloc)((iloc) == eintLocal))
5794	{
5795	nbs->search_count++;
5796	}
5797	if (nbs->print_cycles &&
5798	(!nbs->DomDec \|\| (nbs->DomDec && !LOCAL_I(iloc)((iloc) == eintLocal))) &&
5799	nbs->search_count % 100 == 0)
5800	{
5801	nbs_cycle_print(stderrstderr, nbs);
5802	}
5803
5804	if (debug && (CombineNBLists && nnbl > 1))
5805	{
5806	if (nbl[0]->bSimple)
5807	{
5808	print_nblist_statistics_simple(debug, nbl[0], nbs, rlist);
5809	}
5810	else
5811	{
5812	print_nblist_statistics_supersub(debug, nbl[0], nbs, rlist);
5813	}
5814	}
5815
5816	if (debug)
5817	{
5818	if (gmx_debug_at)
5819	{
5820	if (nbl[0]->bSimple)
5821	{
5822	print_nblist_ci_cj(debug, nbl[0]);
5823	}
5824	else
5825	{
5826	print_nblist_sci_cj(debug, nbl[0]);
5827	}
5828	}
5829
5830	if (nbat->bUseBufferFlags)
5831	{
5832	print_reduction_cost(&nbat->buffer_flags, nnbl);
5833	}
5834	}
5835	}