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38 #include "nbnxn_atomdata.h"
47 #include "thread_mpi/atomic.h"
49 #include "gromacs/math/functions.h"
50 #include "gromacs/math/utilities.h"
51 #include "gromacs/math/vec.h"
52 #include "gromacs/mdlib/gmx_omp_nthreads.h"
53 #include "gromacs/mdlib/nb_verlet.h"
54 #include "gromacs/mdlib/nbnxn_consts.h"
55 #include "gromacs/mdlib/nbnxn_internal.h"
56 #include "gromacs/mdlib/nbnxn_search.h"
57 #include "gromacs/mdlib/nbnxn_util.h"
58 #include "gromacs/mdtypes/forcerec.h" // only for GET_CGINFO_*
59 #include "gromacs/mdtypes/mdatom.h"
60 #include "gromacs/pbcutil/ishift.h"
61 #include "gromacs/simd/simd.h"
62 #include "gromacs/timing/wallcycle.h"
63 #include "gromacs/utility/exceptions.h"
64 #include "gromacs/utility/fatalerror.h"
65 #include "gromacs/utility/gmxomp.h"
66 #include "gromacs/utility/logger.h"
67 #include "gromacs/utility/smalloc.h"
68 #include "gromacs/utility/strconvert.h"
69 #include "gromacs/utility/stringutil.h"
71 using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
74 void nbnxn_atomdata_t::resizeCoordinateBuffer(int numAtoms)
78 x_.resize(numAtoms*xstride);
81 void nbnxn_atomdata_t::resizeForceBuffers()
83 /* Force buffers need padding up to a multiple of the buffer flag size */
84 const int paddedSize = (numAtoms() + NBNXN_BUFFERFLAG_SIZE - 1)/NBNXN_BUFFERFLAG_SIZE*NBNXN_BUFFERFLAG_SIZE;
86 /* Should we let each thread allocate it's own data instead? */
87 for (nbnxn_atomdata_output_t &outBuffer : out)
89 outBuffer.f.resize(paddedSize*fstride);
93 /* Initializes an nbnxn_atomdata_output_t data structure */
94 nbnxn_atomdata_output_t::nbnxn_atomdata_output_t(int nb_kernel_type,
96 int simdEnergyBufferStride,
97 gmx::PinningPolicy pinningPolicy) :
98 f({}, {pinningPolicy}),
99 fshift({}, {pinningPolicy}),
100 Vvdw({}, {pinningPolicy}),
101 Vc({}, {pinningPolicy})
103 fshift.resize(SHIFTS*DIM);
104 Vvdw.resize(numEnergyGroups*numEnergyGroups);
105 Vc.resize(numEnergyGroups*numEnergyGroups);
107 if (nb_kernel_type == nbnxnk4xN_SIMD_4xN ||
108 nb_kernel_type == nbnxnk4xN_SIMD_2xNN)
110 int cj_size = nbnxn_kernel_to_cluster_j_size(nb_kernel_type);
111 int numElements = numEnergyGroups*numEnergyGroups*simdEnergyBufferStride*(cj_size/2)*cj_size;
112 VSvdw.resize(numElements);
113 VSc.resize(numElements);
117 static void copy_int_to_nbat_int(const int *a, int na, int na_round,
118 const int *in, int fill, int *innb)
123 for (i = 0; i < na; i++)
125 innb[j++] = in[a[i]];
127 /* Complete the partially filled last cell with fill */
128 for (; i < na_round; i++)
134 void copy_rvec_to_nbat_real(const int *a, int na, int na_round,
135 const rvec *x, int nbatFormat,
138 /* We complete partially filled cells, can only be the last one in each
139 * column, with coordinates farAway. The actual coordinate value does
140 * not influence the results, since these filler particles do not interact.
141 * Clusters with normal atoms + fillers have a bounding box based only
142 * on the coordinates of the atoms. Clusters with only fillers have as
143 * the bounding box the coordinates of the first filler. Such clusters
144 * are not considered as i-entries, but they are considered as j-entries.
145 * So for performance it is better to have their bounding boxes far away,
146 * such that filler only clusters don't end up in the pair list.
148 const real farAway = -1000000;
156 for (i = 0; i < na; i++)
158 xnb[j++] = x[a[i]][XX];
159 xnb[j++] = x[a[i]][YY];
160 xnb[j++] = x[a[i]][ZZ];
162 /* Complete the partially filled last cell with farAway elements */
163 for (; i < na_round; i++)
172 for (i = 0; i < na; i++)
174 xnb[j++] = x[a[i]][XX];
175 xnb[j++] = x[a[i]][YY];
176 xnb[j++] = x[a[i]][ZZ];
179 /* Complete the partially filled last cell with zeros */
180 for (; i < na_round; i++)
189 j = atom_to_x_index<c_packX4>(a0);
190 c = a0 & (c_packX4-1);
191 for (i = 0; i < na; i++)
193 xnb[j+XX*c_packX4] = x[a[i]][XX];
194 xnb[j+YY*c_packX4] = x[a[i]][YY];
195 xnb[j+ZZ*c_packX4] = x[a[i]][ZZ];
200 j += (DIM-1)*c_packX4;
204 /* Complete the partially filled last cell with zeros */
205 for (; i < na_round; i++)
207 xnb[j+XX*c_packX4] = farAway;
208 xnb[j+YY*c_packX4] = farAway;
209 xnb[j+ZZ*c_packX4] = farAway;
214 j += (DIM-1)*c_packX4;
220 j = atom_to_x_index<c_packX8>(a0);
221 c = a0 & (c_packX8 - 1);
222 for (i = 0; i < na; i++)
224 xnb[j+XX*c_packX8] = x[a[i]][XX];
225 xnb[j+YY*c_packX8] = x[a[i]][YY];
226 xnb[j+ZZ*c_packX8] = x[a[i]][ZZ];
231 j += (DIM-1)*c_packX8;
235 /* Complete the partially filled last cell with zeros */
236 for (; i < na_round; i++)
238 xnb[j+XX*c_packX8] = farAway;
239 xnb[j+YY*c_packX8] = farAway;
240 xnb[j+ZZ*c_packX8] = farAway;
245 j += (DIM-1)*c_packX8;
251 gmx_incons("Unsupported nbnxn_atomdata_t format");
255 /* Stores the LJ parameter data in a format convenient for different kernels */
256 static void set_lj_parameter_data(nbnxn_atomdata_t::Params *params, gmx_bool bSIMD)
258 int nt = params->numTypes;
263 /* nbfp_aligned stores two parameters using the stride most suitable
264 * for the present SIMD architecture, as specified by the constant
265 * c_simdBestPairAlignment from the SIMD header.
266 * There's a slight inefficiency in allocating and initializing nbfp_aligned
267 * when it might not be used, but introducing the conditional code is not
270 params->nbfp_aligned.resize(nt*nt*c_simdBestPairAlignment);
272 for (int i = 0; i < nt; i++)
274 for (int j = 0; j < nt; j++)
276 params->nbfp_aligned[(i*nt+j)*c_simdBestPairAlignment+0] = params->nbfp[(i*nt+j)*2+0];
277 params->nbfp_aligned[(i*nt+j)*c_simdBestPairAlignment+1] = params->nbfp[(i*nt+j)*2+1];
278 params->nbfp_aligned[(i*nt+j)*c_simdBestPairAlignment+2] = 0;
279 params->nbfp_aligned[(i*nt+j)*c_simdBestPairAlignment+3] = 0;
285 /* We use combination rule data for SIMD combination rule kernels
286 * and with LJ-PME kernels. We then only need parameters per atom type,
287 * not per pair of atom types.
289 params->nbfp_comb.resize(nt*2);
290 switch (params->comb_rule)
293 params->comb_rule = ljcrGEOM;
295 for (int i = 0; i < nt; i++)
297 /* Store the sqrt of the diagonal from the nbfp matrix */
298 params->nbfp_comb[i*2 ] = std::sqrt(params->nbfp[(i*nt+i)*2 ]);
299 params->nbfp_comb[i*2+1] = std::sqrt(params->nbfp[(i*nt+i)*2+1]);
303 for (int i = 0; i < nt; i++)
305 /* Get 6*C6 and 12*C12 from the diagonal of the nbfp matrix */
306 const real c6 = params->nbfp[(i*nt+i)*2 ];
307 const real c12 = params->nbfp[(i*nt+i)*2+1];
308 if (c6 > 0 && c12 > 0)
310 /* We store 0.5*2^1/6*sigma and sqrt(4*3*eps),
311 * so we get 6*C6 and 12*C12 after combining.
313 params->nbfp_comb[i*2 ] = 0.5*gmx::sixthroot(c12/c6);
314 params->nbfp_comb[i*2+1] = std::sqrt(c6*c6/c12);
318 params->nbfp_comb[i*2 ] = 0;
319 params->nbfp_comb[i*2+1] = 0;
324 /* We always store the full matrix (see code above) */
327 gmx_incons("Unknown combination rule");
331 nbnxn_atomdata_t::SimdMasks::SimdMasks()
334 constexpr int simd_width = GMX_SIMD_REAL_WIDTH;
335 /* Set the diagonal cluster pair exclusion mask setup data.
336 * In the kernel we check 0 < j - i to generate the masks.
337 * Here we store j - i for generating the mask for the first i,
338 * we substract 0.5 to avoid rounding issues.
339 * In the kernel we can subtract 1 to generate the subsequent mask.
341 const int simd_4xn_diag_size = std::max(c_nbnxnCpuIClusterSize, simd_width);
342 diagonal_4xn_j_minus_i.resize(simd_4xn_diag_size);
343 for (int j = 0; j < simd_4xn_diag_size; j++)
345 diagonal_4xn_j_minus_i[j] = j - 0.5;
348 diagonal_2xnn_j_minus_i.resize(simd_width);
349 for (int j = 0; j < simd_width/2; j++)
351 /* The j-cluster size is half the SIMD width */
352 diagonal_2xnn_j_minus_i[j] = j - 0.5;
353 /* The next half of the SIMD width is for i + 1 */
354 diagonal_2xnn_j_minus_i[simd_width/2 + j] = j - 1 - 0.5;
357 /* We use up to 32 bits for exclusion masking.
358 * The same masks are used for the 4xN and 2x(N+N) kernels.
359 * The masks are read either into integer SIMD registers or into
360 * real SIMD registers (together with a cast).
361 * In single precision this means the real and integer SIMD registers
364 const int simd_excl_size = c_nbnxnCpuIClusterSize*simd_width;
365 #if GMX_DOUBLE && !GMX_SIMD_HAVE_INT32_LOGICAL
366 exclusion_filter64.resize(simd_excl_size);
368 exclusion_filter.resize(simd_excl_size);
371 for (int j = 0; j < simd_excl_size; j++)
373 /* Set the consecutive bits for masking pair exclusions */
374 #if GMX_DOUBLE && !GMX_SIMD_HAVE_INT32_LOGICAL
375 exclusion_filter64[j] = (1U << j);
377 exclusion_filter[j] = (1U << j);
381 if (!GMX_SIMD_HAVE_LOGICAL && !GMX_SIMD_HAVE_INT32_LOGICAL)
383 // If the SIMD implementation has no bitwise logical operation support
384 // whatsoever we cannot use the normal masking. Instead,
385 // we generate a vector of all 2^4 possible ways an i atom
386 // interacts with its 4 j atoms. Each array entry contains
387 // GMX_SIMD_REAL_WIDTH values that are read with a single aligned SIMD load.
388 // Since there is no logical value representation in this case, we use
389 // any nonzero value to indicate 'true', while zero mean 'false'.
390 // This can then be converted to a SIMD boolean internally in the SIMD
391 // module by comparing to zero.
392 // Each array entry encodes how this i atom will interact with the 4 j atoms.
393 // Matching code exists in set_ci_top_excls() to generate indices into this array.
394 // Those indices are used in the kernels.
396 const int simd_excl_size = c_nbnxnCpuIClusterSize*c_nbnxnCpuIClusterSize;
397 const real simdFalse = 0.0;
398 const real simdTrue = 1.0;
400 interaction_array.resize(simd_excl_size * GMX_SIMD_REAL_WIDTH);
401 for (int j = 0; j < simd_excl_size; j++)
403 const int index = j * GMX_SIMD_REAL_WIDTH;
404 for (int i = 0; i < GMX_SIMD_REAL_WIDTH; i++)
406 interaction_array[index + i] = (j & (1 << i)) ? simdTrue : simdFalse;
413 nbnxn_atomdata_t::Params::Params(gmx::PinningPolicy pinningPolicy) :
415 nbfp({}, {pinningPolicy}),
416 nbfp_comb({}, {pinningPolicy}),
417 type({}, {pinningPolicy}),
418 lj_comb({}, {pinningPolicy}),
419 q({}, {pinningPolicy}),
422 energrp({}, {pinningPolicy})
426 nbnxn_atomdata_t::nbnxn_atomdata_t(gmx::PinningPolicy pinningPolicy) :
427 params_(pinningPolicy),
430 shift_vec({}, {pinningPolicy}),
431 x_({}, {pinningPolicy}),
433 bUseBufferFlags(FALSE),
434 bUseTreeReduce(FALSE)
438 /* Initializes an nbnxn_atomdata_t::Params data structure */
439 static void nbnxn_atomdata_params_init(const gmx::MDLogger &mdlog,
440 nbnxn_atomdata_t::Params *params,
442 int enbnxninitcombrule,
443 int ntype, const real *nbfp,
448 gmx_bool simple, bCombGeom, bCombLB, bSIMD;
452 fprintf(debug, "There are %d atom types in the system, adding one for nbnxn_atomdata_t\n", ntype);
454 params->numTypes = ntype + 1;
455 params->nbfp.resize(params->numTypes*params->numTypes*2);
456 params->nbfp_comb.resize(params->numTypes*2);
458 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
459 * force-field floating point parameters.
462 ptr = getenv("GMX_LJCOMB_TOL");
467 sscanf(ptr, "%lf", &dbl);
473 /* Temporarily fill params->nbfp_comb with sigma and epsilon
474 * to check for the LB rule.
476 for (int i = 0; i < ntype; i++)
478 c6 = nbfp[(i*ntype+i)*2 ]/6.0;
479 c12 = nbfp[(i*ntype+i)*2 + 1]/12.0;
480 if (c6 > 0 && c12 > 0)
482 params->nbfp_comb[i*2 ] = gmx::sixthroot(c12/c6);
483 params->nbfp_comb[i*2 + 1] = 0.25*c6*c6/c12;
485 else if (c6 == 0 && c12 == 0)
487 params->nbfp_comb[i*2 ] = 0;
488 params->nbfp_comb[i*2 + 1] = 0;
492 /* Can not use LB rule with only dispersion or repulsion */
497 for (int i = 0; i < params->numTypes; i++)
499 for (int j = 0; j < params->numTypes; j++)
501 if (i < ntype && j < ntype)
503 /* fr->nbfp has been updated, so that array too now stores c6/c12 including
504 * the 6.0/12.0 prefactors to save 2 flops in the most common case (force-only).
506 c6 = nbfp[(i*ntype+j)*2 ];
507 c12 = nbfp[(i*ntype+j)*2 + 1];
508 params->nbfp[(i*params->numTypes+j)*2 ] = c6;
509 params->nbfp[(i*params->numTypes+j)*2 + 1] = c12;
511 /* Compare 6*C6 and 12*C12 for geometric cobination rule */
512 bCombGeom = bCombGeom &&
513 gmx_within_tol(c6*c6, nbfp[(i*ntype+i)*2 ]*nbfp[(j*ntype+j)*2 ], tol) &&
514 gmx_within_tol(c12*c12, nbfp[(i*ntype+i)*2 + 1]*nbfp[(j*ntype+j)*2 + 1], tol);
516 /* Compare C6 and C12 for Lorentz-Berthelot combination rule */
520 ((c6 == 0 && c12 == 0 &&
521 (params->nbfp_comb[i*2 + 1] == 0 || params->nbfp_comb[j*2 + 1] == 0)) ||
522 (c6 > 0 && c12 > 0 &&
523 gmx_within_tol(gmx::sixthroot(c12/c6),
524 0.5*(params->nbfp_comb[i*2]+params->nbfp_comb[j*2]), tol) &&
525 gmx_within_tol(0.25*c6*c6/c12, std::sqrt(params->nbfp_comb[i*2 + 1]*params->nbfp_comb[j*2 + 1]), tol)));
529 /* Add zero parameters for the additional dummy atom type */
530 params->nbfp[(i*params->numTypes + j)*2 ] = 0;
531 params->nbfp[(i*params->numTypes + j)*2+1] = 0;
537 fprintf(debug, "Combination rules: geometric %s Lorentz-Berthelot %s\n",
538 gmx::boolToString(bCombGeom), gmx::boolToString(bCombLB));
541 simple = nbnxn_kernel_pairlist_simple(nb_kernel_type);
543 switch (enbnxninitcombrule)
545 case enbnxninitcombruleDETECT:
546 /* We prefer the geometic combination rule,
547 * as that gives a slightly faster kernel than the LB rule.
551 params->comb_rule = ljcrGEOM;
555 params->comb_rule = ljcrLB;
559 params->comb_rule = ljcrNONE;
561 params->nbfp_comb.clear();
566 if (params->comb_rule == ljcrNONE)
568 mesg = "Using full Lennard-Jones parameter combination matrix";
572 mesg = gmx::formatString("Using %s Lennard-Jones combination rule",
573 params->comb_rule == ljcrGEOM ? "geometric" : "Lorentz-Berthelot");
575 GMX_LOG(mdlog.info).asParagraph().appendText(mesg);
578 case enbnxninitcombruleGEOM:
579 params->comb_rule = ljcrGEOM;
581 case enbnxninitcombruleLB:
582 params->comb_rule = ljcrLB;
584 case enbnxninitcombruleNONE:
585 params->comb_rule = ljcrNONE;
587 params->nbfp_comb.clear();
590 gmx_incons("Unknown enbnxninitcombrule");
593 bSIMD = (nb_kernel_type == nbnxnk4xN_SIMD_4xN ||
594 nb_kernel_type == nbnxnk4xN_SIMD_2xNN);
596 set_lj_parameter_data(params, bSIMD);
598 params->nenergrp = n_energygroups;
601 // We now check for energy groups already when starting mdrun
602 GMX_RELEASE_ASSERT(n_energygroups == 1, "GPU kernels do not support energy groups");
604 /* Temporary storage goes as #grp^3*simd_width^2/2, so limit to 64 */
605 if (params->nenergrp > 64)
607 gmx_fatal(FARGS, "With NxN kernels not more than 64 energy groups are supported\n");
609 params->neg_2log = 1;
610 while (params->nenergrp > (1<<params->neg_2log))
616 /* Initializes an nbnxn_atomdata_t data structure */
617 void nbnxn_atomdata_init(const gmx::MDLogger &mdlog,
618 nbnxn_atomdata_t *nbat,
620 int enbnxninitcombrule,
621 int ntype, const real *nbfp,
625 nbnxn_atomdata_params_init(mdlog, &nbat->paramsDeprecated(), nb_kernel_type,
626 enbnxninitcombrule, ntype, nbfp, n_energygroups);
628 const gmx_bool simple = nbnxn_kernel_pairlist_simple(nb_kernel_type);
629 const gmx_bool bSIMD = (nb_kernel_type == nbnxnk4xN_SIMD_4xN ||
630 nb_kernel_type == nbnxnk4xN_SIMD_2xNN);
638 pack_x = std::max(c_nbnxnCpuIClusterSize,
639 nbnxn_kernel_to_cluster_j_size(nb_kernel_type));
643 nbat->XFormat = nbatX4;
646 nbat->XFormat = nbatX8;
649 gmx_incons("Unsupported packing width");
654 nbat->XFormat = nbatXYZ;
657 nbat->FFormat = nbat->XFormat;
661 nbat->XFormat = nbatXYZQ;
662 nbat->FFormat = nbatXYZ;
665 nbat->shift_vec.resize(SHIFTS);
667 nbat->xstride = (nbat->XFormat == nbatXYZQ ? STRIDE_XYZQ : DIM);
668 nbat->fstride = (nbat->FFormat == nbatXYZQ ? STRIDE_XYZQ : DIM);
670 /* Initialize the output data structures */
671 for (int i = 0; i < nout; i++)
673 const auto &pinningPolicy = nbat->params().type.get_allocator().pinningPolicy();
674 nbat->out.emplace_back(nb_kernel_type, nbat->params().nenergrp, 1 << nbat->params().neg_2log,
678 nbat->buffer_flags.flag = nullptr;
679 nbat->buffer_flags.flag_nalloc = 0;
681 const int nth = gmx_omp_nthreads_get(emntNonbonded);
683 const char *ptr = getenv("GMX_USE_TREEREDUCE");
686 nbat->bUseTreeReduce = (strtol(ptr, nullptr, 10) != 0);
689 else if (nth > 8) /*on the CPU we currently don't benefit even at 32*/
691 nbat->bUseTreeReduce = 1;
696 nbat->bUseTreeReduce = false;
698 if (nbat->bUseTreeReduce)
700 GMX_LOG(mdlog.info).asParagraph().appendText("Using tree force reduction");
702 nbat->syncStep = new tMPI_Atomic[nth];
706 template<int packSize>
707 static void copy_lj_to_nbat_lj_comb(gmx::ArrayRef<const real> ljparam_type,
708 const int *type, int na,
711 /* The LJ params follow the combination rule:
712 * copy the params for the type array to the atom array.
714 for (int is = 0; is < na; is += packSize)
716 for (int k = 0; k < packSize; k++)
719 ljparam_at[is*2 + k] = ljparam_type[type[i]*2 ];
720 ljparam_at[is*2 + packSize + k] = ljparam_type[type[i]*2 + 1];
725 static int numAtomsFromGrids(const nbnxn_search &nbs)
727 const nbnxn_grid_t &lastGrid = nbs.grid.back();
729 return (lastGrid.cell0 + lastGrid.nc)*lastGrid.na_sc;
732 /* Sets the atom type in nbnxn_atomdata_t */
733 static void nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t::Params *params,
734 const nbnxn_search *nbs,
737 params->type.resize(numAtomsFromGrids(*nbs));
739 for (const nbnxn_grid_t &grid : nbs->grid)
741 /* Loop over all columns and copy and fill */
742 for (int i = 0; i < grid.numCells[XX]*grid.numCells[YY]; i++)
744 int ncz = grid.cxy_ind[i+1] - grid.cxy_ind[i];
745 int ash = (grid.cell0 + grid.cxy_ind[i])*grid.na_sc;
747 copy_int_to_nbat_int(nbs->a.data() + ash, grid.cxy_na[i], ncz*grid.na_sc,
748 type, params->numTypes - 1, params->type.data() + ash);
753 /* Sets the LJ combination rule parameters in nbnxn_atomdata_t */
754 static void nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t::Params *params,
756 const nbnxn_search *nbs)
758 params->lj_comb.resize(numAtomsFromGrids(*nbs)*2);
760 if (params->comb_rule != ljcrNONE)
762 for (const nbnxn_grid_t &grid : nbs->grid)
764 /* Loop over all columns and copy and fill */
765 for (int i = 0; i < grid.numCells[XX]*grid.numCells[YY]; i++)
767 int ncz = grid.cxy_ind[i+1] - grid.cxy_ind[i];
768 int ash = (grid.cell0 + grid.cxy_ind[i])*grid.na_sc;
770 if (XFormat == nbatX4)
772 copy_lj_to_nbat_lj_comb<c_packX4>(params->nbfp_comb,
773 params->type.data() + ash,
775 params->lj_comb.data() + ash*2);
777 else if (XFormat == nbatX8)
779 copy_lj_to_nbat_lj_comb<c_packX8>(params->nbfp_comb,
780 params->type.data() + ash,
782 params->lj_comb.data() + ash*2);
784 else if (XFormat == nbatXYZQ)
786 copy_lj_to_nbat_lj_comb<1>(params->nbfp_comb,
787 params->type.data() + ash,
789 params->lj_comb.data() + ash*2);
796 /* Sets the charges in nbnxn_atomdata_t *nbat */
797 static void nbnxn_atomdata_set_charges(nbnxn_atomdata_t *nbat,
798 const nbnxn_search *nbs,
801 if (nbat->XFormat != nbatXYZQ)
803 nbat->paramsDeprecated().q.resize(nbat->numAtoms());
806 for (const nbnxn_grid_t &grid : nbs->grid)
808 /* Loop over all columns and copy and fill */
809 for (int cxy = 0; cxy < grid.numCells[XX]*grid.numCells[YY]; cxy++)
811 int ash = (grid.cell0 + grid.cxy_ind[cxy])*grid.na_sc;
812 int na = grid.cxy_na[cxy];
813 int na_round = (grid.cxy_ind[cxy+1] - grid.cxy_ind[cxy])*grid.na_sc;
815 if (nbat->XFormat == nbatXYZQ)
817 real *q = nbat->x().data() + ash*STRIDE_XYZQ + ZZ + 1;
819 for (i = 0; i < na; i++)
821 *q = charge[nbs->a[ash+i]];
824 /* Complete the partially filled last cell with zeros */
825 for (; i < na_round; i++)
833 real *q = nbat->paramsDeprecated().q.data() + ash;
835 for (i = 0; i < na; i++)
837 *q = charge[nbs->a[ash+i]];
840 /* Complete the partially filled last cell with zeros */
841 for (; i < na_round; i++)
851 /* Set the charges of perturbed atoms in nbnxn_atomdata_t to 0.
852 * This is to automatically remove the RF/PME self term in the nbnxn kernels.
853 * Part of the zero interactions are still calculated in the normal kernels.
854 * All perturbed interactions are calculated in the free energy kernel,
855 * using the original charge and LJ data, not nbnxn_atomdata_t.
857 static void nbnxn_atomdata_mask_fep(nbnxn_atomdata_t *nbat,
858 const nbnxn_search *nbs)
860 nbnxn_atomdata_t::Params ¶ms = nbat->paramsDeprecated();
864 if (nbat->XFormat == nbatXYZQ)
866 q = nbat->x().data() + ZZ + 1;
867 stride_q = STRIDE_XYZQ;
875 for (const nbnxn_grid_t &grid : nbs->grid)
884 nsubc = c_gpuNumClusterPerCell;
887 int c_offset = grid.cell0*grid.na_sc;
889 /* Loop over all columns and copy and fill */
890 for (int c = 0; c < grid.nc*nsubc; c++)
892 /* Does this cluster contain perturbed particles? */
893 if (grid.fep[c] != 0)
895 for (int i = 0; i < grid.na_c; i++)
897 /* Is this a perturbed particle? */
898 if (grid.fep[c] & (1 << i))
900 int ind = c_offset + c*grid.na_c + i;
901 /* Set atom type and charge to non-interacting */
902 params.type[ind] = params.numTypes - 1;
911 /* Copies the energy group indices to a reordered and packed array */
912 static void copy_egp_to_nbat_egps(const int *a, int na, int na_round,
913 int na_c, int bit_shift,
914 const int *in, int *innb)
920 for (i = 0; i < na; i += na_c)
922 /* Store na_c energy group numbers into one int */
924 for (int sa = 0; sa < na_c; sa++)
929 comb |= (GET_CGINFO_GID(in[at]) << (sa*bit_shift));
934 /* Complete the partially filled last cell with fill */
935 for (; i < na_round; i += na_c)
941 /* Set the energy group indices for atoms in nbnxn_atomdata_t */
942 static void nbnxn_atomdata_set_energygroups(nbnxn_atomdata_t::Params *params,
943 const nbnxn_search *nbs,
946 if (params->nenergrp == 1)
951 params->energrp.resize(numAtomsFromGrids(*nbs));
953 for (const nbnxn_grid_t &grid : nbs->grid)
955 /* Loop over all columns and copy and fill */
956 for (int i = 0; i < grid.numCells[XX]*grid.numCells[YY]; i++)
958 int ncz = grid.cxy_ind[i+1] - grid.cxy_ind[i];
959 int ash = (grid.cell0 + grid.cxy_ind[i])*grid.na_sc;
961 copy_egp_to_nbat_egps(nbs->a.data() + ash, grid.cxy_na[i], ncz*grid.na_sc,
962 c_nbnxnCpuIClusterSize, params->neg_2log,
964 params->energrp.data() + (ash >> grid.na_c_2log));
969 /* Sets all required atom parameter data in nbnxn_atomdata_t */
970 void nbnxn_atomdata_set(nbnxn_atomdata_t *nbat,
971 const nbnxn_search *nbs,
972 const t_mdatoms *mdatoms,
975 nbnxn_atomdata_t::Params ¶ms = nbat->paramsDeprecated();
977 nbnxn_atomdata_set_atomtypes(¶ms, nbs, mdatoms->typeA);
979 nbnxn_atomdata_set_charges(nbat, nbs, mdatoms->chargeA);
983 nbnxn_atomdata_mask_fep(nbat, nbs);
986 /* This must be done after masking types for FEP */
987 nbnxn_atomdata_set_ljcombparams(¶ms, nbat->XFormat, nbs);
989 nbnxn_atomdata_set_energygroups(¶ms, nbs, atinfo);
992 /* Copies the shift vector array to nbnxn_atomdata_t */
993 void nbnxn_atomdata_copy_shiftvec(gmx_bool bDynamicBox,
995 nbnxn_atomdata_t *nbat)
999 nbat->bDynamicBox = bDynamicBox;
1000 for (i = 0; i < SHIFTS; i++)
1002 copy_rvec(shift_vec[i], nbat->shift_vec[i]);
1006 /* Copies (and reorders) the coordinates to nbnxn_atomdata_t */
1007 void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search *nbs,
1011 nbnxn_atomdata_t *nbat,
1012 gmx_wallcycle *wcycle)
1014 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1015 wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
1024 g1 = nbs->grid.size();
1032 g1 = nbs->grid.size();
1038 nbat->natoms_local = nbs->grid[0].nc*nbs->grid[0].na_sc;
1041 nth = gmx_omp_nthreads_get(emntPairsearch);
1043 #pragma omp parallel for num_threads(nth) schedule(static)
1044 for (th = 0; th < nth; th++)
1048 for (int g = g0; g < g1; g++)
1050 const nbnxn_grid_t &grid = nbs->grid[g];
1051 const int numCellsXY = grid.numCells[XX]*grid.numCells[YY];
1053 const int cxy0 = (numCellsXY* th + nth - 1)/nth;
1054 const int cxy1 = (numCellsXY*(th + 1) + nth - 1)/nth;
1056 for (int cxy = cxy0; cxy < cxy1; cxy++)
1058 int na, ash, na_fill;
1060 na = grid.cxy_na[cxy];
1061 ash = (grid.cell0 + grid.cxy_ind[cxy])*grid.na_sc;
1063 if (g == 0 && FillLocal)
1066 (grid.cxy_ind[cxy+1] - grid.cxy_ind[cxy])*grid.na_sc;
1070 /* We fill only the real particle locations.
1071 * We assume the filling entries at the end have been
1072 * properly set before during pair-list generation.
1076 copy_rvec_to_nbat_real(nbs->a.data() + ash, na, na_fill, x,
1077 nbat->XFormat, nbat->x().data(), ash);
1081 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1084 wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
1085 wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1089 nbnxn_atomdata_clear_reals(gmx::ArrayRef<real> dest,
1092 for (int i = i0; i < i1; i++)
1098 gmx_unused static void
1099 nbnxn_atomdata_reduce_reals(real * gmx_restrict dest,
1101 const real ** gmx_restrict src,
1107 /* The destination buffer contains data, add to it */
1108 for (int i = i0; i < i1; i++)
1110 for (int s = 0; s < nsrc; s++)
1112 dest[i] += src[s][i];
1118 /* The destination buffer is unitialized, set it first */
1119 for (int i = i0; i < i1; i++)
1121 dest[i] = src[0][i];
1122 for (int s = 1; s < nsrc; s++)
1124 dest[i] += src[s][i];
1130 gmx_unused static void
1131 nbnxn_atomdata_reduce_reals_simd(real gmx_unused * gmx_restrict dest,
1132 gmx_bool gmx_unused bDestSet,
1133 const gmx_unused real ** gmx_restrict src,
1134 int gmx_unused nsrc,
1135 int gmx_unused i0, int gmx_unused i1)
1138 /* The SIMD width here is actually independent of that in the kernels,
1139 * but we use the same width for simplicity (usually optimal anyhow).
1141 SimdReal dest_SSE, src_SSE;
1145 for (int i = i0; i < i1; i += GMX_SIMD_REAL_WIDTH)
1147 dest_SSE = load<SimdReal>(dest+i);
1148 for (int s = 0; s < nsrc; s++)
1150 src_SSE = load<SimdReal>(src[s]+i);
1151 dest_SSE = dest_SSE + src_SSE;
1153 store(dest+i, dest_SSE);
1158 for (int i = i0; i < i1; i += GMX_SIMD_REAL_WIDTH)
1160 dest_SSE = load<SimdReal>(src[0]+i);
1161 for (int s = 1; s < nsrc; s++)
1163 src_SSE = load<SimdReal>(src[s]+i);
1164 dest_SSE = dest_SSE + src_SSE;
1166 store(dest+i, dest_SSE);
1172 /* Add part of the force array(s) from nbnxn_atomdata_t to f */
1174 nbnxn_atomdata_add_nbat_f_to_f_part(const nbnxn_search *nbs,
1175 const nbnxn_atomdata_t *nbat,
1176 gmx::ArrayRef<nbnxn_atomdata_output_t> out,
1181 gmx::ArrayRef<const int> cell = nbs->cell;
1183 /* Loop over all columns and copy and fill */
1184 switch (nbat->FFormat)
1190 const real *fnb = out[0].f.data();
1192 for (int a = a0; a < a1; a++)
1194 int i = cell[a]*nbat->fstride;
1197 f[a][YY] += fnb[i+1];
1198 f[a][ZZ] += fnb[i+2];
1203 for (int a = a0; a < a1; a++)
1205 int i = cell[a]*nbat->fstride;
1207 for (int fa = 0; fa < nfa; fa++)
1209 f[a][XX] += out[fa].f[i];
1210 f[a][YY] += out[fa].f[i+1];
1211 f[a][ZZ] += out[fa].f[i+2];
1219 const real *fnb = out[0].f.data();
1221 for (int a = a0; a < a1; a++)
1223 int i = atom_to_x_index<c_packX4>(cell[a]);
1225 f[a][XX] += fnb[i+XX*c_packX4];
1226 f[a][YY] += fnb[i+YY*c_packX4];
1227 f[a][ZZ] += fnb[i+ZZ*c_packX4];
1232 for (int a = a0; a < a1; a++)
1234 int i = atom_to_x_index<c_packX4>(cell[a]);
1236 for (int fa = 0; fa < nfa; fa++)
1238 f[a][XX] += out[fa].f[i+XX*c_packX4];
1239 f[a][YY] += out[fa].f[i+YY*c_packX4];
1240 f[a][ZZ] += out[fa].f[i+ZZ*c_packX4];
1248 const real *fnb = out[0].f.data();
1250 for (int a = a0; a < a1; a++)
1252 int i = atom_to_x_index<c_packX8>(cell[a]);
1254 f[a][XX] += fnb[i+XX*c_packX8];
1255 f[a][YY] += fnb[i+YY*c_packX8];
1256 f[a][ZZ] += fnb[i+ZZ*c_packX8];
1261 for (int a = a0; a < a1; a++)
1263 int i = atom_to_x_index<c_packX8>(cell[a]);
1265 for (int fa = 0; fa < nfa; fa++)
1267 f[a][XX] += out[fa].f[i+XX*c_packX8];
1268 f[a][YY] += out[fa].f[i+YY*c_packX8];
1269 f[a][ZZ] += out[fa].f[i+ZZ*c_packX8];
1275 gmx_incons("Unsupported nbnxn_atomdata_t format");
1279 static inline unsigned char reverse_bits(unsigned char b)
1281 /* http://graphics.stanford.edu/~seander/bithacks.html#ReverseByteWith64BitsDiv */
1282 return (b * 0x0202020202ULL & 0x010884422010ULL) % 1023;
1285 static void nbnxn_atomdata_add_nbat_f_to_f_treereduce(nbnxn_atomdata_t *nbat,
1288 const nbnxn_buffer_flags_t *flags = &nbat->buffer_flags;
1290 int next_pow2 = 1<<(gmx::log2I(nth-1)+1);
1292 const int numOutputBuffers = nbat->out.size();
1293 GMX_ASSERT(numOutputBuffers == nth,
1294 "tree-reduce currently only works for numOutputBuffers==nth");
1296 memset(nbat->syncStep, 0, sizeof(*(nbat->syncStep))*nth);
1298 #pragma omp parallel num_threads(nth)
1306 th = gmx_omp_get_thread_num();
1308 for (group_size = 2; group_size < 2*next_pow2; group_size *= 2)
1310 int index[2], group_pos, partner_pos, wu;
1311 int partner_th = th ^ (group_size/2);
1316 /* wait on partner thread - replaces full barrier */
1317 int sync_th, sync_group_size;
1319 tMPI_Atomic_memory_barrier(); /* gurantee data is saved before marking work as done */
1320 tMPI_Atomic_set(&(nbat->syncStep[th]), group_size/2); /* mark previous step as completed */
1322 /* find thread to sync with. Equal to partner_th unless nth is not a power of two. */
1323 for (sync_th = partner_th, sync_group_size = group_size; sync_th >= nth && sync_group_size > 2; sync_group_size /= 2)
1325 sync_th &= ~(sync_group_size/4);
1327 if (sync_th < nth) /* otherwise nothing to sync index[1] will be >=nout */
1329 /* wait on the thread which computed input data in previous step */
1330 while (tMPI_Atomic_get(static_cast<volatile tMPI_Atomic_t*>(&(nbat->syncStep[sync_th]))) < group_size/2)
1334 /* guarantee that no later load happens before wait loop is finisehd */
1335 tMPI_Atomic_memory_barrier();
1337 #else /* TMPI_ATOMICS */
1342 /* Calculate buffers to sum (result goes into first buffer) */
1343 group_pos = th % group_size;
1344 index[0] = th - group_pos;
1345 index[1] = index[0] + group_size/2;
1347 /* If no second buffer, nothing to do */
1348 if (index[1] >= numOutputBuffers && group_size > 2)
1353 #if NBNXN_BUFFERFLAG_MAX_THREADS > 256
1354 #error reverse_bits assumes max 256 threads
1356 /* Position is permuted so that one of the 2 vectors being added was computed on the same thread in the previous step.
1357 This improves locality and enables to sync with just a single thread between steps (=the levels in the btree).
1358 The permutation which allows this corresponds to reversing the bits of the group position.
1360 group_pos = reverse_bits(group_pos)/(256/group_size);
1362 partner_pos = group_pos ^ 1;
1364 /* loop over two work-units (own and partner) */
1365 for (wu = 0; wu < 2; wu++)
1369 if (partner_th < nth)
1371 break; /* partner exists we don't have to do his work */
1375 group_pos = partner_pos;
1379 /* Calculate the cell-block range for our thread */
1380 b0 = (flags->nflag* group_pos )/group_size;
1381 b1 = (flags->nflag*(group_pos+1))/group_size;
1383 for (b = b0; b < b1; b++)
1385 i0 = b *NBNXN_BUFFERFLAG_SIZE*nbat->fstride;
1386 i1 = (b+1)*NBNXN_BUFFERFLAG_SIZE*nbat->fstride;
1388 if (bitmask_is_set(flags->flag[b], index[1]) || group_size > 2)
1390 const real *fIndex1 = nbat->out[index[1]].f.data();
1392 nbnxn_atomdata_reduce_reals_simd
1394 nbnxn_atomdata_reduce_reals
1396 (nbat->out[index[0]].f.data(),
1397 bitmask_is_set(flags->flag[b], index[0]) || group_size > 2,
1398 &fIndex1, 1, i0, i1);
1401 else if (!bitmask_is_set(flags->flag[b], index[0]))
1403 nbnxn_atomdata_clear_reals(nbat->out[index[0]].f,
1410 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1415 static void nbnxn_atomdata_add_nbat_f_to_f_stdreduce(nbnxn_atomdata_t *nbat,
1418 #pragma omp parallel for num_threads(nth) schedule(static)
1419 for (int th = 0; th < nth; th++)
1423 const nbnxn_buffer_flags_t *flags;
1425 const real *fptr[NBNXN_BUFFERFLAG_MAX_THREADS];
1427 flags = &nbat->buffer_flags;
1429 /* Calculate the cell-block range for our thread */
1430 int b0 = (flags->nflag* th )/nth;
1431 int b1 = (flags->nflag*(th+1))/nth;
1433 for (int b = b0; b < b1; b++)
1435 int i0 = b *NBNXN_BUFFERFLAG_SIZE*nbat->fstride;
1436 int i1 = (b+1)*NBNXN_BUFFERFLAG_SIZE*nbat->fstride;
1439 for (int out = 1; out < static_cast<gmx::index>(nbat->out.size()); out++)
1441 if (bitmask_is_set(flags->flag[b], out))
1443 fptr[nfptr++] = nbat->out[out].f.data();
1449 nbnxn_atomdata_reduce_reals_simd
1451 nbnxn_atomdata_reduce_reals
1453 (nbat->out[0].f.data(),
1454 bitmask_is_set(flags->flag[b], 0),
1458 else if (!bitmask_is_set(flags->flag[b], 0))
1460 nbnxn_atomdata_clear_reals(nbat->out[0].f,
1465 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1469 /* Add the force array(s) from nbnxn_atomdata_t to f */
1470 void nbnxn_atomdata_add_nbat_f_to_f(nbnxn_search *nbs,
1472 nbnxn_atomdata_t *nbat,
1474 gmx_wallcycle *wcycle)
1476 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1477 wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
1481 nbs_cycle_start(&nbs->cc[enbsCCreducef]);
1487 na = nbs->natoms_nonlocal;
1491 na = nbs->natoms_local;
1494 a0 = nbs->natoms_local;
1495 na = nbs->natoms_nonlocal - nbs->natoms_local;
1499 int nth = gmx_omp_nthreads_get(emntNonbonded);
1501 if (nbat->out.size() > 1)
1503 if (locality != eatAll)
1505 gmx_incons("add_f_to_f called with nout>1 and locality!=eatAll");
1508 /* Reduce the force thread output buffers into buffer 0, before adding
1509 * them to the, differently ordered, "real" force buffer.
1511 if (nbat->bUseTreeReduce)
1513 nbnxn_atomdata_add_nbat_f_to_f_treereduce(nbat, nth);
1517 nbnxn_atomdata_add_nbat_f_to_f_stdreduce(nbat, nth);
1520 #pragma omp parallel for num_threads(nth) schedule(static)
1521 for (int th = 0; th < nth; th++)
1525 nbnxn_atomdata_add_nbat_f_to_f_part(nbs, nbat,
1532 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1535 nbs_cycle_stop(&nbs->cc[enbsCCreducef]);
1537 wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
1538 wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1541 /* Adds the shift forces from nbnxn_atomdata_t to fshift */
1542 void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t *nbat,
1545 gmx::ArrayRef<const nbnxn_atomdata_output_t> outputBuffers = nbat->out;
1547 for (int s = 0; s < SHIFTS; s++)
1551 for (const nbnxn_atomdata_output_t &out : outputBuffers)
1553 sum[XX] += out.fshift[s*DIM+XX];
1554 sum[YY] += out.fshift[s*DIM+YY];
1555 sum[ZZ] += out.fshift[s*DIM+ZZ];
1557 rvec_inc(fshift[s], sum);