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47 #include "gromacs/math/functions.h"
48 #include "gromacs/math/utilities.h"
49 #include "gromacs/math/vec.h"
50 #include "gromacs/mdlib/gmx_omp_nthreads.h"
51 #include "gromacs/mdtypes/forcerec.h" // only for GET_CGINFO_*
52 #include "gromacs/mdtypes/md_enums.h"
53 #include "gromacs/nbnxm/nbnxm.h"
54 #include "gromacs/pbcutil/ishift.h"
55 #include "gromacs/simd/simd.h"
56 #include "gromacs/utility/exceptions.h"
57 #include "gromacs/utility/fatalerror.h"
58 #include "gromacs/utility/gmxomp.h"
59 #include "gromacs/utility/logger.h"
60 #include "gromacs/utility/strconvert.h"
61 #include "gromacs/utility/stringutil.h"
65 #include "nbnxm_geometry.h"
66 #include "nbnxm_gpu.h"
69 using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
72 const char* enumValueToString(LJCombinationRule enumValue)
74 static constexpr gmx::EnumerationArray<LJCombinationRule, const char*> s_ljCombinationRuleNames = {
75 "Geometric", "Lorentz-Berthelot", "None"
77 return s_ljCombinationRuleNames[enumValue];
80 void nbnxn_atomdata_t::resizeCoordinateBuffer(int numAtoms)
84 x_.resize(numAtoms * xstride);
87 void nbnxn_atomdata_t::resizeForceBuffers()
89 /* Force buffers need padding up to a multiple of the buffer flag size */
90 const int paddedSize =
91 (numAtoms() + NBNXN_BUFFERFLAG_SIZE - 1) / NBNXN_BUFFERFLAG_SIZE * NBNXN_BUFFERFLAG_SIZE;
93 /* Should we let each thread allocate it's own data instead? */
94 for (nbnxn_atomdata_output_t& outBuffer : out)
96 outBuffer.f.resize(paddedSize * fstride);
100 /* Initializes an nbnxn_atomdata_output_t data structure */
101 nbnxn_atomdata_output_t::nbnxn_atomdata_output_t(Nbnxm::KernelType kernelType,
103 int simdEnergyBufferStride,
104 gmx::PinningPolicy pinningPolicy) :
105 f({}, { pinningPolicy }),
106 fshift({}, { pinningPolicy }),
107 Vvdw({}, { pinningPolicy }),
108 Vc({}, { pinningPolicy })
110 fshift.resize(gmx::c_numShiftVectors * DIM);
111 Vvdw.resize(numEnergyGroups * numEnergyGroups);
112 Vc.resize(numEnergyGroups * numEnergyGroups);
114 if (Nbnxm::kernelTypeIsSimd(kernelType))
116 int cj_size = Nbnxm::JClusterSizePerKernelType[kernelType];
118 numEnergyGroups * numEnergyGroups * simdEnergyBufferStride * (cj_size / 2) * cj_size;
119 VSvdw.resize(numElements);
120 VSc.resize(numElements);
124 static void copy_int_to_nbat_int(const int* a, int na, int na_round, const int* in, int fill, int* innb)
127 for (int i = 0; i < na; i++)
129 innb[j++] = in[a[i]];
131 /* Complete the partially filled last cell with fill */
132 for (int i = na; i < na_round; i++)
138 void copy_rvec_to_nbat_real(const int* a, int na, int na_round, const rvec* x, int nbatFormat, real* xnb, int a0)
140 /* We complete partially filled cells, can only be the last one in each
141 * column, with coordinates farAway. The actual coordinate value does
142 * not influence the results, since these filler particles do not interact.
143 * Clusters with normal atoms + fillers have a bounding box based only
144 * on the coordinates of the atoms. Clusters with only fillers have as
145 * the bounding box the coordinates of the first filler. Such clusters
146 * are not considered as i-entries, but they are considered as j-entries.
147 * So for performance it is better to have their bounding boxes far away,
148 * such that filler only clusters don't end up in the pair list.
150 const real farAway = -1000000;
152 if (nbatFormat == nbatXYZ)
155 int j = a0 * STRIDE_XYZ;
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++)
170 else if (nbatFormat == nbatXYZQ)
173 int j = a0 * STRIDE_XYZQ;
176 xnb[j++] = x[a[i]][XX];
177 xnb[j++] = x[a[i]][YY];
178 xnb[j++] = x[a[i]][ZZ];
181 /* Complete the partially filled last cell with zeros */
182 for (; i < na_round; i++)
190 else if (nbatFormat == nbatX4)
193 int j = atom_to_x_index<c_packX4>(a0);
194 int c = a0 & (c_packX4 - 1);
197 xnb[j + XX * c_packX4] = x[a[i]][XX];
198 xnb[j + YY * c_packX4] = x[a[i]][YY];
199 xnb[j + ZZ * c_packX4] = x[a[i]][ZZ];
204 j += (DIM - 1) * c_packX4;
208 /* Complete the partially filled last cell with zeros */
209 for (; i < na_round; i++)
211 xnb[j + XX * c_packX4] = farAway;
212 xnb[j + YY * c_packX4] = farAway;
213 xnb[j + ZZ * c_packX4] = farAway;
218 j += (DIM - 1) * c_packX4;
223 else if (nbatFormat == nbatX8)
226 int j = atom_to_x_index<c_packX8>(a0);
227 int c = a0 & (c_packX8 - 1);
230 xnb[j + XX * c_packX8] = x[a[i]][XX];
231 xnb[j + YY * c_packX8] = x[a[i]][YY];
232 xnb[j + ZZ * c_packX8] = x[a[i]][ZZ];
237 j += (DIM - 1) * c_packX8;
241 /* Complete the partially filled last cell with zeros */
242 for (; i < na_round; i++)
244 xnb[j + XX * c_packX8] = farAway;
245 xnb[j + YY * c_packX8] = farAway;
246 xnb[j + ZZ * c_packX8] = farAway;
251 j += (DIM - 1) * c_packX8;
258 gmx_incons("Unsupported nbnxn_atomdata_t format");
262 /* Stores the LJ parameter data in a format convenient for different kernels */
263 static void set_lj_parameter_data(nbnxn_atomdata_t::Params* params, gmx_bool bSIMD)
265 int nt = params->numTypes;
270 /* nbfp_aligned stores two parameters using the stride most suitable
271 * for the present SIMD architecture, as specified by the constant
272 * c_simdBestPairAlignment from the SIMD header.
273 * There's a slight inefficiency in allocating and initializing nbfp_aligned
274 * when it might not be used, but introducing the conditional code is not
277 params->nbfp_aligned.resize(nt * nt * c_simdBestPairAlignment);
279 for (int i = 0; i < nt; i++)
281 for (int j = 0; j < nt; j++)
283 params->nbfp_aligned[(i * nt + j) * c_simdBestPairAlignment + 0] =
284 params->nbfp[(i * nt + j) * 2 + 0];
285 params->nbfp_aligned[(i * nt + j) * c_simdBestPairAlignment + 1] =
286 params->nbfp[(i * nt + j) * 2 + 1];
287 if (c_simdBestPairAlignment > 2)
289 params->nbfp_aligned[(i * nt + j) * c_simdBestPairAlignment + 2] = 0;
290 params->nbfp_aligned[(i * nt + j) * c_simdBestPairAlignment + 3] = 0;
297 /* We use combination rule data for SIMD combination rule kernels
298 * and with LJ-PME kernels. We then only need parameters per atom type,
299 * not per pair of atom types.
301 params->nbfp_comb.resize(nt * 2);
302 switch (params->ljCombinationRule)
304 case LJCombinationRule::Geometric:
305 for (int i = 0; i < nt; i++)
307 /* Store the sqrt of the diagonal from the nbfp matrix */
308 params->nbfp_comb[i * 2] = std::sqrt(params->nbfp[(i * nt + i) * 2]);
309 params->nbfp_comb[i * 2 + 1] = std::sqrt(params->nbfp[(i * nt + i) * 2 + 1]);
312 case LJCombinationRule::LorentzBerthelot:
313 for (int i = 0; i < nt; i++)
315 /* Get 6*C6 and 12*C12 from the diagonal of the nbfp matrix */
316 const real c6 = params->nbfp[(i * nt + i) * 2];
317 const real c12 = params->nbfp[(i * nt + i) * 2 + 1];
318 if (c6 > 0 && c12 > 0)
320 /* We store 0.5*2^1/6*sigma and sqrt(4*3*eps),
321 * so we get 6*C6 and 12*C12 after combining.
323 params->nbfp_comb[i * 2] = 0.5 * gmx::sixthroot(c12 / c6);
324 params->nbfp_comb[i * 2 + 1] = std::sqrt(c6 * c6 / c12);
328 params->nbfp_comb[i * 2] = 0;
329 params->nbfp_comb[i * 2 + 1] = 0;
333 case LJCombinationRule::None:
334 /* We always store the full matrix (see code above) */
336 default: gmx_incons("Unknown combination rule");
340 nbnxn_atomdata_t::SimdMasks::SimdMasks()
343 constexpr int simd_width = GMX_SIMD_REAL_WIDTH;
344 /* Set the diagonal cluster pair exclusion mask setup data.
345 * In the kernel we check 0 < j - i to generate the masks.
346 * Here we store j - i for generating the mask for the first i,
347 * we subtract 0.5 to avoid rounding issues.
348 * In the kernel we can subtract 1 to generate the subsequent mask.
350 const int simd_4xn_diag_size = std::max(c_nbnxnCpuIClusterSize, simd_width);
351 diagonal_4xn_j_minus_i.resize(simd_4xn_diag_size);
352 for (int j = 0; j < simd_4xn_diag_size; j++)
354 diagonal_4xn_j_minus_i[j] = j - 0.5;
357 diagonal_2xnn_j_minus_i.resize(simd_width);
358 for (int j = 0; j < simd_width / 2; j++)
360 /* The j-cluster size is half the SIMD width */
361 diagonal_2xnn_j_minus_i[j] = j - 0.5;
362 /* The next half of the SIMD width is for i + 1 */
363 diagonal_2xnn_j_minus_i[simd_width / 2 + j] = j - 1 - 0.5;
366 /* We use up to 32 bits for exclusion masking.
367 * The same masks are used for the 4xN and 2x(N+N) kernels.
368 * The masks are read either into integer SIMD registers or into
369 * real SIMD registers (together with a cast).
370 * In single precision this means the real and integer SIMD registers
373 const int simd_excl_size = c_nbnxnCpuIClusterSize * simd_width;
374 # if GMX_DOUBLE && !GMX_SIMD_HAVE_INT32_LOGICAL
375 exclusion_filter64.resize(simd_excl_size);
377 exclusion_filter.resize(simd_excl_size);
380 for (int j = 0; j < simd_excl_size; j++)
382 /* Set the consecutive bits for masking pair exclusions */
383 # if GMX_DOUBLE && !GMX_SIMD_HAVE_INT32_LOGICAL
384 exclusion_filter64[j] = (1U << j);
386 exclusion_filter[j] = (1U << j);
390 if (!GMX_SIMD_HAVE_LOGICAL && !GMX_SIMD_HAVE_INT32_LOGICAL) // NOLINT(misc-redundant-expression)
392 // If the SIMD implementation has no bitwise logical operation support
393 // whatsoever we cannot use the normal masking. Instead,
394 // we generate a vector of all 2^4 possible ways an i atom
395 // interacts with its 4 j atoms. Each array entry contains
396 // GMX_SIMD_REAL_WIDTH values that are read with a single aligned SIMD load.
397 // Since there is no logical value representation in this case, we use
398 // any nonzero value to indicate 'true', while zero mean 'false'.
399 // This can then be converted to a SIMD boolean internally in the SIMD
400 // module by comparing to zero.
401 // Each array entry encodes how this i atom will interact with the 4 j atoms.
402 // Matching code exists in set_ci_top_excls() to generate indices into this array.
403 // Those indices are used in the kernels.
405 const int simd_excl_size = c_nbnxnCpuIClusterSize * c_nbnxnCpuIClusterSize;
406 const real simdFalse = 0.0;
407 const real simdTrue = 1.0;
409 interaction_array.resize(simd_excl_size * GMX_SIMD_REAL_WIDTH);
410 for (int j = 0; j < simd_excl_size; j++)
412 const int index = j * GMX_SIMD_REAL_WIDTH;
413 for (int i = 0; i < GMX_SIMD_REAL_WIDTH; i++)
415 interaction_array[index + i] = (j & (1 << i)) ? simdTrue : simdFalse;
422 nbnxn_atomdata_t::Params::Params(gmx::PinningPolicy pinningPolicy) :
424 nbfp({}, { pinningPolicy }),
425 nbfp_comb({}, { pinningPolicy }),
426 type({}, { pinningPolicy }),
427 lj_comb({}, { pinningPolicy }),
428 q({}, { pinningPolicy }),
431 energrp({}, { pinningPolicy })
435 /* Initializes an nbnxn_atomdata_t::Params data structure */
436 static void nbnxn_atomdata_params_init(const gmx::MDLogger& mdlog,
437 nbnxn_atomdata_t::Params* params,
438 const Nbnxm::KernelType kernelType,
439 int enbnxninitcombrule,
441 ArrayRef<const real> nbfp,
446 fprintf(debug, "There are %d atom types in the system, adding one for nbnxn_atomdata_t\n", ntype);
448 params->numTypes = ntype + 1;
449 params->nbfp.resize(params->numTypes * params->numTypes * 2);
450 params->nbfp_comb.resize(params->numTypes * 2);
452 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
453 * force-field floating point parameters.
456 const char* tolOverrideString = getenv("GMX_LJCOMB_TOL");
457 if (tolOverrideString != nullptr)
459 double tolOverride = std::strtod(tolOverrideString, nullptr);
462 bool bCombGeom = true;
465 /* Temporarily fill params->nbfp_comb with sigma and epsilon
466 * to check for the LB rule.
468 for (int i = 0; i < ntype; i++)
470 const real c6 = nbfp[(i * ntype + i) * 2] / 6.0;
471 const real c12 = nbfp[(i * ntype + i) * 2 + 1] / 12.0;
472 if (c6 > 0 && c12 > 0)
474 params->nbfp_comb[i * 2] = gmx::sixthroot(c12 / c6);
475 params->nbfp_comb[i * 2 + 1] = 0.25 * c6 * c6 / c12;
477 else if (c6 == 0 && c12 == 0)
479 params->nbfp_comb[i * 2] = 0;
480 params->nbfp_comb[i * 2 + 1] = 0;
484 /* Can not use LB rule with only dispersion or repulsion */
489 for (int i = 0; i < params->numTypes; i++)
491 for (int j = 0; j < params->numTypes; j++)
493 if (i < ntype && j < ntype)
495 /* fr->nbfp has been updated, so that array too now stores c6/c12 including
496 * the 6.0/12.0 prefactors to save 2 flops in the most common case (force-only).
498 real c6 = nbfp[(i * ntype + j) * 2];
499 real c12 = nbfp[(i * ntype + j) * 2 + 1];
501 params->nbfp[(i * params->numTypes + j) * 2] = c6;
502 params->nbfp[(i * params->numTypes + j) * 2 + 1] = c12;
504 /* Compare 6*C6 and 12*C12 for geometric cobination rule */
507 && gmx_within_tol(c6 * c6, nbfp[(i * ntype + i) * 2] * nbfp[(j * ntype + j) * 2], tol)
508 && gmx_within_tol(c12 * c12,
509 nbfp[(i * ntype + i) * 2 + 1] * nbfp[(j * ntype + j) * 2 + 1],
512 /* Compare C6 and C12 for Lorentz-Berthelot combination rule */
517 && ((c6 == 0 && c12 == 0
518 && (params->nbfp_comb[i * 2 + 1] == 0 || params->nbfp_comb[j * 2 + 1] == 0))
519 || (c6 > 0 && c12 > 0
520 && gmx_within_tol(gmx::sixthroot(c12 / c6),
521 0.5 * (params->nbfp_comb[i * 2] + params->nbfp_comb[j * 2]),
523 && gmx_within_tol(0.25 * c6 * c6 / c12,
524 std::sqrt(params->nbfp_comb[i * 2 + 1]
525 * params->nbfp_comb[j * 2 + 1]),
530 /* Add zero parameters for the additional dummy atom type */
531 params->nbfp[(i * params->numTypes + j) * 2] = 0;
532 params->nbfp[(i * params->numTypes + j) * 2 + 1] = 0;
539 "Combination rules: geometric %s Lorentz-Berthelot %s\n",
540 gmx::boolToString(bCombGeom),
541 gmx::boolToString(bCombLB));
544 const bool simple = Nbnxm::kernelTypeUsesSimplePairlist(kernelType);
546 switch (enbnxninitcombrule)
548 case enbnxninitcombruleDETECT:
549 /* We prefer the geometric combination rule,
550 * as that gives a slightly faster kernel than the LB rule.
554 params->ljCombinationRule = LJCombinationRule::Geometric;
558 params->ljCombinationRule = LJCombinationRule::LorentzBerthelot;
562 params->ljCombinationRule = LJCombinationRule::None;
564 params->nbfp_comb.clear();
569 if (params->ljCombinationRule == LJCombinationRule::None)
571 mesg = "Using full Lennard-Jones parameter combination matrix";
575 mesg = gmx::formatString("Using %s Lennard-Jones combination rule",
576 enumValueToString(params->ljCombinationRule));
578 GMX_LOG(mdlog.info).asParagraph().appendText(mesg);
581 case enbnxninitcombruleGEOM:
582 params->ljCombinationRule = LJCombinationRule::Geometric;
584 case enbnxninitcombruleLB:
585 params->ljCombinationRule = LJCombinationRule::LorentzBerthelot;
587 case enbnxninitcombruleNONE:
588 params->ljCombinationRule = LJCombinationRule::None;
590 params->nbfp_comb.clear();
592 default: gmx_incons("Unknown enbnxninitcombrule");
595 const bool bSIMD = Nbnxm::kernelTypeIsSimd(kernelType);
597 set_lj_parameter_data(params, bSIMD);
599 params->nenergrp = n_energygroups;
602 // We now check for energy groups already when starting mdrun
603 GMX_RELEASE_ASSERT(n_energygroups == 1, "GPU kernels do not support energy groups");
605 /* Temporary storage goes as #grp^3*simd_width^2/2, so limit to 64 */
606 if (params->nenergrp > 64)
608 gmx_fatal(FARGS, "With NxN kernels not more than 64 energy groups are supported\n");
610 params->neg_2log = 1;
611 while (params->nenergrp > (1 << params->neg_2log))
617 /* Initializes an nbnxn_atomdata_t data structure */
618 nbnxn_atomdata_t::nbnxn_atomdata_t(gmx::PinningPolicy pinningPolicy,
619 const gmx::MDLogger& mdlog,
620 const Nbnxm::KernelType kernelType,
621 int enbnxninitcombrule,
623 ArrayRef<const real> nbfp,
626 params_(pinningPolicy),
629 shift_vec({}, { pinningPolicy }),
630 x_({}, { pinningPolicy }),
632 bUseBufferFlags(FALSE)
634 nbnxn_atomdata_params_init(
635 mdlog, ¶msDeprecated(), kernelType, enbnxninitcombrule, ntype, nbfp, n_energygroups);
637 const bool simple = Nbnxm::kernelTypeUsesSimplePairlist(kernelType);
638 const bool bSIMD = Nbnxm::kernelTypeIsSimd(kernelType);
644 int pack_x = std::max(c_nbnxnCpuIClusterSize, Nbnxm::JClusterSizePerKernelType[kernelType]);
647 case 4: XFormat = nbatX4; break;
648 case 8: XFormat = nbatX8; break;
649 default: gmx_incons("Unsupported packing width");
665 shift_vec.resize(gmx::c_numShiftVectors);
667 xstride = (XFormat == nbatXYZQ ? STRIDE_XYZQ : DIM);
668 fstride = (FFormat == nbatXYZQ ? STRIDE_XYZQ : DIM);
670 /* Initialize the output data structures */
671 for (int i = 0; i < nout; i++)
673 const auto& pinningPolicy = params().type.get_allocator().pinningPolicy();
674 out.emplace_back(kernelType, params().nenergrp, 1 << params().neg_2log, pinningPolicy);
677 buffer_flags.clear();
680 template<int packSize>
681 static void copy_lj_to_nbat_lj_comb(gmx::ArrayRef<const real> ljparam_type, const int* type, int na, real* ljparam_at)
683 /* The LJ params follow the combination rule:
684 * copy the params for the type array to the atom array.
686 for (int is = 0; is < na; is += packSize)
688 for (int k = 0; k < packSize; k++)
691 ljparam_at[is * 2 + k] = ljparam_type[type[i] * 2];
692 ljparam_at[is * 2 + packSize + k] = ljparam_type[type[i] * 2 + 1];
697 /* Sets the atom type in nbnxn_atomdata_t */
698 static void nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t::Params* params,
699 const Nbnxm::GridSet& gridSet,
700 ArrayRef<const int> atomTypes)
702 params->type.resize(gridSet.numGridAtomsTotal());
704 for (const Nbnxm::Grid& grid : gridSet.grids())
706 /* Loop over all columns and copy and fill */
707 for (int i = 0; i < grid.numColumns(); i++)
709 const int numAtoms = grid.paddedNumAtomsInColumn(i);
710 const int atomOffset = grid.firstAtomInColumn(i);
712 copy_int_to_nbat_int(gridSet.atomIndices().data() + atomOffset,
713 grid.numAtomsInColumn(i),
716 params->numTypes - 1,
717 params->type.data() + atomOffset);
722 /* Sets the LJ combination rule parameters in nbnxn_atomdata_t */
723 static void nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t::Params* params,
725 const Nbnxm::GridSet& gridSet)
727 params->lj_comb.resize(gridSet.numGridAtomsTotal() * 2);
729 if (params->ljCombinationRule != LJCombinationRule::None)
731 for (const Nbnxm::Grid& grid : gridSet.grids())
733 /* Loop over all columns and copy and fill */
734 for (int i = 0; i < grid.numColumns(); i++)
736 const int numAtoms = grid.paddedNumAtomsInColumn(i);
737 const int atomOffset = grid.firstAtomInColumn(i);
739 if (XFormat == nbatX4)
741 copy_lj_to_nbat_lj_comb<c_packX4>(params->nbfp_comb,
742 params->type.data() + atomOffset,
744 params->lj_comb.data() + atomOffset * 2);
746 else if (XFormat == nbatX8)
748 copy_lj_to_nbat_lj_comb<c_packX8>(params->nbfp_comb,
749 params->type.data() + atomOffset,
751 params->lj_comb.data() + atomOffset * 2);
753 else if (XFormat == nbatXYZQ)
755 copy_lj_to_nbat_lj_comb<1>(params->nbfp_comb,
756 params->type.data() + atomOffset,
758 params->lj_comb.data() + atomOffset * 2);
765 /* Sets the charges in nbnxn_atomdata_t *nbat */
766 static void nbnxn_atomdata_set_charges(nbnxn_atomdata_t* nbat,
767 const Nbnxm::GridSet& gridSet,
768 ArrayRef<const real> charges)
770 if (nbat->XFormat != nbatXYZQ)
772 nbat->paramsDeprecated().q.resize(nbat->numAtoms());
775 for (const Nbnxm::Grid& grid : gridSet.grids())
777 /* Loop over all columns and copy and fill */
778 for (int cxy = 0; cxy < grid.numColumns(); cxy++)
780 const int atomOffset = grid.firstAtomInColumn(cxy);
781 const int numAtoms = grid.numAtomsInColumn(cxy);
782 const int paddedNumAtoms = grid.paddedNumAtomsInColumn(cxy);
784 if (nbat->XFormat == nbatXYZQ)
786 real* q = nbat->x().data() + atomOffset * STRIDE_XYZQ + ZZ + 1;
787 for (int i = 0; i < numAtoms; i++)
789 *q = charges[gridSet.atomIndices()[atomOffset + i]];
792 /* Complete the partially filled last cell with zeros */
793 for (int i = numAtoms; i < paddedNumAtoms; i++)
801 real* q = nbat->paramsDeprecated().q.data() + atomOffset;
802 for (int i = 0; i < numAtoms; i++)
804 *q = charges[gridSet.atomIndices()[atomOffset + i]];
807 /* Complete the partially filled last cell with zeros */
808 for (int i = numAtoms; i < paddedNumAtoms; i++)
818 /* Set the charges of perturbed atoms in nbnxn_atomdata_t to 0.
819 * This is to automatically remove the RF/PME self term in the nbnxn kernels.
820 * Part of the zero interactions are still calculated in the normal kernels.
821 * All perturbed interactions are calculated in the free energy kernel,
822 * using the original charge and LJ data, not nbnxn_atomdata_t.
824 static void nbnxn_atomdata_mask_fep(nbnxn_atomdata_t* nbat, const Nbnxm::GridSet& gridSet)
826 nbnxn_atomdata_t::Params& params = nbat->paramsDeprecated();
828 const bool formatIsXYZQ = (nbat->XFormat == nbatXYZQ);
830 real* q = formatIsXYZQ ? (nbat->x().data() + ZZ + 1) : params.q.data();
831 int stride_q = formatIsXYZQ ? STRIDE_XYZQ : 1;
833 for (const Nbnxm::Grid& grid : gridSet.grids())
835 const int nsubc = (grid.geometry().isSimple) ? 1 : c_gpuNumClusterPerCell;
837 const int c_offset = grid.firstAtomInColumn(0);
839 /* Loop over all columns and copy and fill */
840 for (int c = 0; c < grid.numCells() * nsubc; c++)
842 /* Does this cluster contain perturbed particles? */
843 if (grid.clusterIsPerturbed(c))
845 const int numAtomsPerCluster = grid.geometry().numAtomsICluster;
846 for (int i = 0; i < numAtomsPerCluster; i++)
848 /* Is this a perturbed particle? */
849 if (grid.atomIsPerturbed(c, i))
851 int ind = c_offset + c * numAtomsPerCluster + i;
852 /* Set atom type and charge to non-interacting */
853 params.type[ind] = params.numTypes - 1;
854 q[ind * stride_q] = 0;
862 /* Copies the energy group indices to a reordered and packed array */
864 copy_egp_to_nbat_egps(const int* a, int na, int na_round, int na_c, int bit_shift, const int* in, int* innb)
867 for (; i < na; i += na_c)
869 /* Store na_c energy group numbers into one int */
871 for (int sa = 0; sa < na_c; sa++)
876 comb |= (GET_CGINFO_GID(in[at]) << (sa * bit_shift));
881 /* Complete the partially filled last cell with fill */
882 for (; i < na_round; i += na_c)
888 /* Set the energy group indices for atoms in nbnxn_atomdata_t */
889 static void nbnxn_atomdata_set_energygroups(nbnxn_atomdata_t::Params* params,
890 const Nbnxm::GridSet& gridSet,
891 ArrayRef<const int> atomInfo)
893 if (params->nenergrp == 1)
898 params->energrp.resize(gridSet.numGridAtomsTotal());
900 for (const Nbnxm::Grid& grid : gridSet.grids())
902 /* Loop over all columns and copy and fill */
903 for (int i = 0; i < grid.numColumns(); i++)
905 const int numAtoms = grid.paddedNumAtomsInColumn(i);
906 const int atomOffset = grid.firstAtomInColumn(i);
908 copy_egp_to_nbat_egps(gridSet.atomIndices().data() + atomOffset,
909 grid.numAtomsInColumn(i),
911 c_nbnxnCpuIClusterSize,
914 params->energrp.data() + grid.atomToCluster(atomOffset));
919 /* Sets all required atom parameter data in nbnxn_atomdata_t */
920 void nbnxn_atomdata_set(nbnxn_atomdata_t* nbat,
921 const Nbnxm::GridSet& gridSet,
922 ArrayRef<const int> atomTypes,
923 ArrayRef<const real> atomCharges,
924 ArrayRef<const int> atomInfo)
926 nbnxn_atomdata_t::Params& params = nbat->paramsDeprecated();
928 nbnxn_atomdata_set_atomtypes(¶ms, gridSet, atomTypes);
930 nbnxn_atomdata_set_charges(nbat, gridSet, atomCharges);
932 if (gridSet.haveFep())
934 nbnxn_atomdata_mask_fep(nbat, gridSet);
937 /* This must be done after masking types for FEP */
938 nbnxn_atomdata_set_ljcombparams(¶ms, nbat->XFormat, gridSet);
940 nbnxn_atomdata_set_energygroups(¶ms, gridSet, atomInfo);
943 /* Copies the shift vector array to nbnxn_atomdata_t */
944 void nbnxn_atomdata_copy_shiftvec(gmx_bool bDynamicBox, gmx::ArrayRef<gmx::RVec> shift_vec, nbnxn_atomdata_t* nbat)
946 nbat->bDynamicBox = bDynamicBox;
947 std::copy(shift_vec.begin(), shift_vec.end(), nbat->shift_vec.begin());
950 // This is slightly different from nbnxn_get_atom_range(...) at the end of the file
951 // TODO: Combine if possible
952 static void getAtomRanges(const Nbnxm::GridSet& gridSet,
953 const gmx::AtomLocality locality,
959 case gmx::AtomLocality::All:
961 *gridEnd = gridSet.grids().size();
963 case gmx::AtomLocality::Local:
967 case gmx::AtomLocality::NonLocal:
969 *gridEnd = gridSet.grids().size();
971 case gmx::AtomLocality::Count:
972 GMX_ASSERT(false, "Count is invalid locality specifier");
977 /* Copies (and reorders) the coordinates to nbnxn_atomdata_t */
978 void nbnxn_atomdata_copy_x_to_nbat_x(const Nbnxm::GridSet& gridSet,
979 const gmx::AtomLocality locality,
980 const rvec* coordinates,
981 nbnxn_atomdata_t* nbat)
986 getAtomRanges(gridSet, locality, &gridBegin, &gridEnd);
988 const int nth = gmx_omp_nthreads_get(ModuleMultiThread::Pairsearch);
989 #pragma omp parallel for num_threads(nth) schedule(static)
990 for (int th = 0; th < nth; th++)
994 for (int g = gridBegin; g < gridEnd; g++)
996 const Nbnxm::Grid& grid = gridSet.grids()[g];
997 const int numCellsXY = grid.numColumns();
999 const int cxy0 = (numCellsXY * th + nth - 1) / nth;
1000 const int cxy1 = (numCellsXY * (th + 1) + nth - 1) / nth;
1002 for (int cxy = cxy0; cxy < cxy1; cxy++)
1004 const int na = grid.numAtomsInColumn(cxy);
1005 const int ash = grid.firstAtomInColumn(cxy);
1007 copy_rvec_to_nbat_real(gridSet.atomIndices().data() + ash,
1017 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1021 /* Copies (and reorders) the coordinates to nbnxn_atomdata_t on the GPU*/
1022 void nbnxn_atomdata_x_to_nbat_x_gpu(const Nbnxm::GridSet& gridSet,
1023 const gmx::AtomLocality locality,
1025 DeviceBuffer<RVec> d_x,
1026 GpuEventSynchronizer* xReadyOnDevice)
1028 GMX_ASSERT(xReadyOnDevice != nullptr, "Need a valid GpuEventSynchronizer object");
1032 getAtomRanges(gridSet, locality, &gridBegin, &gridEnd);
1034 for (int g = gridBegin; g < gridEnd; g++)
1036 nbnxn_gpu_x_to_nbat_x(gridSet.grids()[g],
1039 (g == gridBegin) ? xReadyOnDevice : nullptr, // Sync on first iteration only
1042 gridSet.numColumnsMax(),
1043 (g == gridEnd - 1));
1047 static void nbnxn_atomdata_clear_reals(gmx::ArrayRef<real> dest, int i0, int i1)
1049 for (int i = i0; i < i1; i++)
1055 gmx_unused static void nbnxn_atomdata_reduce_reals(real* gmx_restrict dest,
1057 const real** gmx_restrict src,
1064 /* The destination buffer contains data, add to it */
1065 for (int i = i0; i < i1; i++)
1067 for (int s = 0; s < nsrc; s++)
1069 dest[i] += src[s][i];
1075 /* The destination buffer is uninitialized, set it first */
1076 for (int i = i0; i < i1; i++)
1078 dest[i] = src[0][i];
1079 for (int s = 1; s < nsrc; s++)
1081 dest[i] += src[s][i];
1087 gmx_unused static void nbnxn_atomdata_reduce_reals_simd(real gmx_unused* gmx_restrict dest,
1088 gmx_bool gmx_unused bDestSet,
1089 const gmx_unused real** gmx_restrict src,
1090 int gmx_unused nsrc,
1095 /* The SIMD width here is actually independent of that in the kernels,
1096 * but we use the same width for simplicity (usually optimal anyhow).
1098 SimdReal dest_SSE, src_SSE;
1102 for (int i = i0; i < i1; i += GMX_SIMD_REAL_WIDTH)
1104 dest_SSE = load<SimdReal>(dest + i);
1105 for (int s = 0; s < nsrc; s++)
1107 src_SSE = load<SimdReal>(src[s] + i);
1108 dest_SSE = dest_SSE + src_SSE;
1110 store(dest + i, dest_SSE);
1115 for (int i = i0; i < i1; i += GMX_SIMD_REAL_WIDTH)
1117 dest_SSE = load<SimdReal>(src[0] + i);
1118 for (int s = 1; s < nsrc; s++)
1120 src_SSE = load<SimdReal>(src[s] + i);
1121 dest_SSE = dest_SSE + src_SSE;
1123 store(dest + i, dest_SSE);
1129 /* Add part of the force array(s) from nbnxn_atomdata_t to f
1131 * Note: Adding restrict to f makes this function 50% slower with gcc 7.3
1133 static void nbnxn_atomdata_add_nbat_f_to_f_part(const Nbnxm::GridSet& gridSet,
1134 const nbnxn_atomdata_t& nbat,
1135 const nbnxn_atomdata_output_t& out,
1140 gmx::ArrayRef<const int> cell = gridSet.cells();
1141 // Note: Using ArrayRef instead makes this code 25% slower with gcc 7.3
1142 const real* fnb = out.f.data();
1144 /* Loop over all columns and copy and fill */
1145 switch (nbat.FFormat)
1149 for (int a = a0; a < a1; a++)
1151 int i = cell[a] * nbat.fstride;
1154 f[a][YY] += fnb[i + 1];
1155 f[a][ZZ] += fnb[i + 2];
1159 for (int a = a0; a < a1; a++)
1161 int i = atom_to_x_index<c_packX4>(cell[a]);
1163 f[a][XX] += fnb[i + XX * c_packX4];
1164 f[a][YY] += fnb[i + YY * c_packX4];
1165 f[a][ZZ] += fnb[i + ZZ * c_packX4];
1169 for (int a = a0; a < a1; a++)
1171 int i = atom_to_x_index<c_packX8>(cell[a]);
1173 f[a][XX] += fnb[i + XX * c_packX8];
1174 f[a][YY] += fnb[i + YY * c_packX8];
1175 f[a][ZZ] += fnb[i + ZZ * c_packX8];
1178 default: gmx_incons("Unsupported nbnxn_atomdata_t format");
1182 static void nbnxn_atomdata_add_nbat_f_to_f_reduce(nbnxn_atomdata_t* nbat, int nth)
1184 #pragma omp parallel for num_threads(nth) schedule(static)
1185 for (int th = 0; th < nth; th++)
1189 const real* fptr[NBNXN_BUFFERFLAG_MAX_THREADS];
1191 gmx::ArrayRef<const gmx_bitmask_t> flags = nbat->buffer_flags;
1193 /* Calculate the cell-block range for our thread */
1194 const int b0 = (flags.size() * th) / nth;
1195 const int b1 = (flags.size() * (th + 1)) / nth;
1197 for (int b = b0; b < b1; b++)
1199 const int i0 = b * NBNXN_BUFFERFLAG_SIZE * nbat->fstride;
1200 const int i1 = (b + 1) * NBNXN_BUFFERFLAG_SIZE * nbat->fstride;
1203 for (gmx::index out = 1; out < gmx::ssize(nbat->out); out++)
1205 if (bitmask_is_set(flags[b], out))
1207 fptr[nfptr++] = nbat->out[out].f.data();
1213 nbnxn_atomdata_reduce_reals_simd
1215 nbnxn_atomdata_reduce_reals
1217 (nbat->out[0].f.data(), bitmask_is_set(flags[b], 0), fptr, nfptr, i0, i1);
1219 else if (!bitmask_is_set(flags[b], 0))
1221 nbnxn_atomdata_clear_reals(nbat->out[0].f, i0, i1);
1225 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1230 /* Add the force array(s) from nbnxn_atomdata_t to f */
1231 void reduceForces(nbnxn_atomdata_t* nbat, const gmx::AtomLocality locality, const Nbnxm::GridSet& gridSet, rvec* f)
1236 nbnxn_get_atom_range(locality, gridSet, &a0, &na);
1240 /* The are no atoms for this reduction, avoid some overhead */
1244 int nth = gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded);
1246 if (nbat->out.size() > 1)
1248 if (locality != gmx::AtomLocality::All)
1250 gmx_incons("add_f_to_f called with nout>1 and locality!=eatAll");
1253 /* Reduce the force thread output buffers into buffer 0, before adding
1254 * them to the, differently ordered, "real" force buffer.
1256 nbnxn_atomdata_add_nbat_f_to_f_reduce(nbat, nth);
1258 #pragma omp parallel for num_threads(nth) schedule(static)
1259 for (int th = 0; th < nth; th++)
1263 nbnxn_atomdata_add_nbat_f_to_f_part(
1264 gridSet, *nbat, nbat->out[0], a0 + ((th + 0) * na) / nth, a0 + ((th + 1) * na) / nth, f);
1266 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1270 void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
1272 gmx::ArrayRef<const nbnxn_atomdata_output_t> outputBuffers = nbat.out;
1274 for (int s = 0; s < gmx::c_numShiftVectors; s++)
1278 for (const nbnxn_atomdata_output_t& out : outputBuffers)
1280 sum[XX] += out.fshift[s * DIM + XX];
1281 sum[YY] += out.fshift[s * DIM + YY];
1282 sum[ZZ] += out.fshift[s * DIM + ZZ];
1288 void nbnxn_get_atom_range(const gmx::AtomLocality atomLocality,
1289 const Nbnxm::GridSet& gridSet,
1294 switch (atomLocality)
1296 case gmx::AtomLocality::All:
1298 *nAtoms = gridSet.numRealAtomsTotal();
1300 case gmx::AtomLocality::Local:
1302 *nAtoms = gridSet.numRealAtomsLocal();
1304 case gmx::AtomLocality::NonLocal:
1305 *atomStart = gridSet.numRealAtomsLocal();
1306 *nAtoms = gridSet.numRealAtomsTotal() - gridSet.numRealAtomsLocal();
1308 case gmx::AtomLocality::Count:
1309 GMX_ASSERT(false, "Count is invalid locality specifier");