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38 * \brief This file defines high-level functions for mdrun to compute
39 * energies and forces for listed interactions.
41 * \author Mark Abraham <mark.j.abraham@gmail.com>
43 * \ingroup module_listed_forces
47 #include "listed_forces.h"
54 #include "gromacs/gmxlib/network.h"
55 #include "gromacs/gmxlib/nrnb.h"
56 #include "gromacs/listed_forces/bonded.h"
57 #include "gromacs/listed_forces/disre.h"
58 #include "gromacs/listed_forces/orires.h"
59 #include "gromacs/listed_forces/pairs.h"
60 #include "gromacs/listed_forces/position_restraints.h"
61 #include "gromacs/math/vec.h"
62 #include "gromacs/mdlib/enerdata_utils.h"
63 #include "gromacs/mdlib/force.h"
64 #include "gromacs/mdtypes/commrec.h"
65 #include "gromacs/mdtypes/fcdata.h"
66 #include "gromacs/mdtypes/forceoutput.h"
67 #include "gromacs/mdtypes/forcerec.h"
68 #include "gromacs/mdtypes/inputrec.h"
69 #include "gromacs/mdtypes/md_enums.h"
70 #include "gromacs/mdtypes/simulation_workload.h"
71 #include "gromacs/pbcutil/ishift.h"
72 #include "gromacs/pbcutil/pbc.h"
73 #include "gromacs/timing/wallcycle.h"
74 #include "gromacs/topology/topology.h"
75 #include "gromacs/utility/exceptions.h"
76 #include "gromacs/utility/fatalerror.h"
77 #include "gromacs/utility/smalloc.h"
79 #include "listed_internal.h"
80 #include "utilities.h"
87 /*! \brief Return true if ftype is an explicit pair-listed LJ or
88 * COULOMB interaction type: bonded LJ (usually 1-4), or special
89 * listed non-bonded for FEP. */
90 bool isPairInteraction(int ftype)
92 return ((ftype) >= F_LJ14 && (ftype) <= F_LJC_PAIRS_NB);
95 /*! \brief Zero thread-local output buffers */
96 void zero_thread_output(f_thread_t* f_t)
98 constexpr int nelem_fa = sizeof(f_t->f[0]) / sizeof(real);
100 for (int i = 0; i < f_t->nblock_used; i++)
102 int a0 = f_t->block_index[i] * reduction_block_size;
103 int a1 = a0 + reduction_block_size;
104 for (int a = a0; a < a1; a++)
106 for (int d = 0; d < nelem_fa; d++)
113 for (int i = 0; i < SHIFTS; i++)
115 clear_rvec(f_t->fshift[i]);
117 for (int i = 0; i < F_NRE; i++)
121 for (int i = 0; i < egNR; i++)
123 for (int j = 0; j < f_t->grpp.nener; j++)
125 f_t->grpp.ener[i][j] = 0;
128 for (int i = 0; i < efptNR; i++)
134 /*! \brief The max thread number is arbitrary, we used a fixed number
135 * to avoid memory management. Using more than 16 threads is probably
136 * never useful performance wise. */
137 #define MAX_BONDED_THREADS 256
139 /*! \brief Reduce thread-local force buffers */
140 void reduce_thread_forces(int n, gmx::ArrayRef<gmx::RVec> force, const bonded_threading_t* bt, int nthreads)
142 if (nthreads > MAX_BONDED_THREADS)
144 gmx_fatal(FARGS, "Can not reduce bonded forces on more than %d threads", MAX_BONDED_THREADS);
147 rvec* gmx_restrict f = as_rvec_array(force.data());
149 /* This reduction can run on any number of threads,
150 * independently of bt->nthreads.
151 * But if nthreads matches bt->nthreads (which it currently does)
152 * the uniform distribution of the touched blocks over nthreads will
153 * match the distribution of bonded over threads well in most cases,
154 * which means that threads mostly reduce their own data which increases
155 * the number of cache hits.
157 #pragma omp parallel for num_threads(nthreads) schedule(static)
158 for (int b = 0; b < bt->nblock_used; b++)
162 int ind = bt->block_index[b];
163 rvec4* fp[MAX_BONDED_THREADS];
165 /* Determine which threads contribute to this block */
167 for (int ft = 0; ft < bt->nthreads; ft++)
169 if (bitmask_is_set(bt->mask[ind], ft))
171 fp[nfb++] = bt->f_t[ft]->f;
176 /* Reduce force buffers for threads that contribute */
177 int a0 = ind * reduction_block_size;
178 int a1 = (ind + 1) * reduction_block_size;
179 /* It would be nice if we could pad f to avoid this min */
180 a1 = std::min(a1, n);
181 for (int a = a0; a < a1; a++)
183 for (int fb = 0; fb < nfb; fb++)
185 rvec_inc(f[a], fp[fb][a]);
190 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
194 /*! \brief Reduce thread-local forces, shift forces and energies */
195 void reduce_thread_output(int n,
196 gmx::ForceWithShiftForces* forceWithShiftForces,
198 gmx_grppairener_t* grpp,
200 const bonded_threading_t* bt,
201 const gmx::StepWorkload& stepWork)
203 assert(bt->haveBondeds);
205 if (bt->nblock_used > 0)
207 /* Reduce the bonded force buffer */
208 reduce_thread_forces(n, forceWithShiftForces->force(), bt, bt->nthreads);
211 rvec* gmx_restrict fshift = as_rvec_array(forceWithShiftForces->shiftForces().data());
213 /* When necessary, reduce energy and virial using one thread only */
214 if ((stepWork.computeEnergy || stepWork.computeVirial || stepWork.computeDhdl) && bt->nthreads > 1)
216 gmx::ArrayRef<const std::unique_ptr<f_thread_t>> f_t = bt->f_t;
218 if (stepWork.computeVirial)
220 for (int i = 0; i < SHIFTS; i++)
222 for (int t = 1; t < bt->nthreads; t++)
224 rvec_inc(fshift[i], f_t[t]->fshift[i]);
228 if (stepWork.computeEnergy)
230 for (int i = 0; i < F_NRE; i++)
232 for (int t = 1; t < bt->nthreads; t++)
234 ener[i] += f_t[t]->ener[i];
237 for (int i = 0; i < egNR; i++)
239 for (int j = 0; j < f_t[1]->grpp.nener; j++)
241 for (int t = 1; t < bt->nthreads; t++)
243 grpp->ener[i][j] += f_t[t]->grpp.ener[i][j];
248 if (stepWork.computeDhdl)
250 for (int i = 0; i < efptNR; i++)
253 for (int t = 1; t < bt->nthreads; t++)
255 dvdl[i] += f_t[t]->dvdl[i];
262 /*! \brief Returns the bonded kernel flavor
264 * Note that energies are always requested when the virial
265 * is requested (performance gain would be small).
266 * Note that currently we do not have bonded kernels that
267 * do not compute forces.
269 BondedKernelFlavor selectBondedKernelFlavor(const gmx::StepWorkload& stepWork,
270 const bool useSimdKernels,
271 const bool havePerturbedInteractions)
273 BondedKernelFlavor flavor;
274 if (stepWork.computeEnergy || stepWork.computeVirial)
276 if (stepWork.computeVirial)
278 flavor = BondedKernelFlavor::ForcesAndVirialAndEnergy;
282 flavor = BondedKernelFlavor::ForcesAndEnergy;
287 if (useSimdKernels && !havePerturbedInteractions)
289 flavor = BondedKernelFlavor::ForcesSimdWhenAvailable;
293 flavor = BondedKernelFlavor::ForcesNoSimd;
300 /*! \brief Calculate one element of the list of bonded interactions
302 real calc_one_bond(int thread,
304 const InteractionDefinitions& idef,
305 ArrayRef<const int> iatoms,
306 const int numNonperturbedInteractions,
307 const WorkDivision& workDivision,
311 const t_forcerec* fr,
314 gmx_grppairener_t* grpp,
320 const gmx::StepWorkload& stepWork,
321 int* global_atom_index)
323 GMX_ASSERT(idef.ilsort == ilsortNO_FE || idef.ilsort == ilsortFE_SORTED,
324 "The topology should be marked either as no FE or sorted on FE");
326 const bool havePerturbedInteractions =
327 (idef.ilsort == ilsortFE_SORTED && numNonperturbedInteractions < iatoms.ssize());
328 BondedKernelFlavor flavor =
329 selectBondedKernelFlavor(stepWork, fr->use_simd_kernels, havePerturbedInteractions);
331 if (IS_RESTRAINT_TYPE(ftype))
333 efptFTYPE = efptRESTRAINT;
337 efptFTYPE = efptBONDED;
340 const int nat1 = interaction_function[ftype].nratoms + 1;
341 const int nbonds = iatoms.ssize() / nat1;
343 GMX_ASSERT(fr->gpuBonded != nullptr || workDivision.end(ftype) == iatoms.ssize(),
344 "The thread division should match the topology");
346 const int nb0 = workDivision.bound(ftype, thread);
347 const int nbn = workDivision.bound(ftype, thread + 1) - nb0;
349 ArrayRef<const t_iparams> iparams = idef.iparams;
352 if (!isPairInteraction(ftype))
356 /* TODO The execution time for CMAP dihedrals might be
357 nice to account to its own subtimer, but first
358 wallcycle needs to be extended to support calling from
360 v = cmap_dihs(nbn, iatoms.data() + nb0, iparams.data(), &idef.cmap_grid, x, f, fshift,
361 pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]), md, fcd, global_atom_index);
365 v = calculateSimpleBond(ftype, nbn, iatoms.data() + nb0, iparams.data(), x, f, fshift,
366 pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]), md, fcd,
367 global_atom_index, flavor);
372 /* TODO The execution time for pairs might be nice to account
373 to its own subtimer, but first wallcycle needs to be
374 extended to support calling from multiple threads. */
375 do_pairs(ftype, nbn, iatoms.data() + nb0, iparams.data(), x, f, fshift, pbc, g, lambda,
376 dvdl, md, fr, havePerturbedInteractions, stepWork, grpp, global_atom_index);
381 inc_nrnb(nrnb, nrnbIndex(ftype), nbonds);
389 /*! \brief Compute the bonded part of the listed forces, parallelized over threads
391 static void calcBondedForces(const InteractionDefinitions& idef,
393 const t_forcerec* fr,
394 const t_pbc* pbc_null,
396 rvec* fshiftMasterBuffer,
397 gmx_enerdata_t* enerd,
403 const gmx::StepWorkload& stepWork,
404 int* global_atom_index)
406 bonded_threading_t* bt = fr->bondedThreading;
408 #pragma omp parallel for num_threads(bt->nthreads) schedule(static)
409 for (int thread = 0; thread < bt->nthreads; thread++)
413 f_thread_t& threadBuffers = *bt->f_t[thread];
419 gmx_grppairener_t* grpp;
421 zero_thread_output(&threadBuffers);
423 rvec4* ft = threadBuffers.f;
425 /* Thread 0 writes directly to the main output buffers.
426 * We might want to reconsider this.
430 fshift = fshiftMasterBuffer;
437 fshift = threadBuffers.fshift;
438 epot = threadBuffers.ener;
439 grpp = &threadBuffers.grpp;
440 dvdlt = threadBuffers.dvdl;
442 /* Loop over all bonded force types to calculate the bonded forces */
443 for (ftype = 0; (ftype < F_NRE); ftype++)
445 const InteractionList& ilist = idef.il[ftype];
446 if (!ilist.empty() && ftype_is_bonded_potential(ftype))
448 ArrayRef<const int> iatoms = gmx::makeConstArrayRef(ilist.iatoms);
450 thread, ftype, idef, iatoms, idef.numNonperturbedInteractions[ftype],
451 fr->bondedThreading->workDivision, x, ft, fshift, fr, pbc_null, g, grpp,
452 nrnb, lambda, dvdlt, md, fcd, stepWork, global_atom_index);
457 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
461 bool haveRestraints(const InteractionDefinitions& idef, const t_fcdata& fcd)
463 return (!idef.il[F_POSRES].empty() || !idef.il[F_FBPOSRES].empty() || fcd.orires.nr > 0
464 || fcd.disres.nres > 0);
467 bool haveCpuBondeds(const t_forcerec& fr)
469 return fr.bondedThreading->haveBondeds;
472 bool haveCpuListedForces(const t_forcerec& fr, const InteractionDefinitions& idef, const t_fcdata& fcd)
474 return haveCpuBondeds(fr) || haveRestraints(idef, fcd);
480 /*! \brief Calculates all listed force interactions.
482 * Note that pbc_full is used only for position restraints, and is
483 * not initialized if there are none.
485 void calc_listed(const t_commrec* cr,
486 const gmx_multisim_t* ms,
487 struct gmx_wallcycle* wcycle,
488 const InteractionDefinitions& idef,
490 ArrayRef<const gmx::RVec> xWholeMolecules,
492 gmx::ForceOutputs* forceOutputs,
493 const t_forcerec* fr,
494 const struct t_pbc* pbc,
495 const struct t_pbc* pbc_full,
496 const struct t_graph* g,
497 gmx_enerdata_t* enerd,
502 int* global_atom_index,
503 const gmx::StepWorkload& stepWork)
505 const t_pbc* pbc_null;
506 bonded_threading_t* bt = fr->bondedThreading;
517 if (haveRestraints(idef, *fcd))
519 /* TODO Use of restraints triggers further function calls
520 inside the loop over calc_one_bond(), but those are too
521 awkward to account to this subtimer properly in the present
522 code. We don't test / care much about performance with
523 restraints, anyway. */
524 wallcycle_sub_start(wcycle, ewcsRESTRAINTS);
526 if (!idef.il[F_POSRES].empty())
528 posres_wrapper(nrnb, idef, pbc_full, x, enerd, lambda, fr, &forceOutputs->forceWithVirial());
531 if (!idef.il[F_FBPOSRES].empty())
533 fbposres_wrapper(nrnb, idef, pbc_full, x, enerd, fr, &forceOutputs->forceWithVirial());
536 /* Do pre force calculation stuff which might require communication */
537 if (fcd->orires.nr > 0)
539 GMX_ASSERT(!xWholeMolecules.empty(), "Need whole molecules for orienation restraints");
540 enerd->term[F_ORIRESDEV] =
541 calc_orires_dev(ms, idef.il[F_ORIRES].size(), idef.il[F_ORIRES].iatoms.data(),
542 idef.iparams.data(), md, xWholeMolecules, x, pbc_null, fcd, hist);
544 if (fcd->disres.nres > 0)
546 calc_disres_R_6(cr, ms, idef.il[F_DISRES].size(), idef.il[F_DISRES].iatoms.data(), x,
547 pbc_null, fcd, hist);
550 wallcycle_sub_stop(wcycle, ewcsRESTRAINTS);
553 if (haveCpuBondeds(*fr))
555 gmx::ForceWithShiftForces& forceWithShiftForces = forceOutputs->forceWithShiftForces();
557 wallcycle_sub_start(wcycle, ewcsLISTED);
558 /* The dummy array is to have a place to store the dhdl at other values
559 of lambda, which will be thrown away in the end */
560 real dvdl[efptNR] = { 0 };
561 calcBondedForces(idef, x, fr, pbc_null, g,
562 as_rvec_array(forceWithShiftForces.shiftForces().data()), enerd, nrnb,
563 lambda, dvdl, md, fcd, stepWork, global_atom_index);
564 wallcycle_sub_stop(wcycle, ewcsLISTED);
566 wallcycle_sub_start(wcycle, ewcsLISTED_BUF_OPS);
567 reduce_thread_output(fr->natoms_force, &forceWithShiftForces, enerd->term, &enerd->grpp,
570 if (stepWork.computeDhdl)
572 for (int i = 0; i < efptNR; i++)
574 enerd->dvdl_nonlin[i] += dvdl[i];
577 wallcycle_sub_stop(wcycle, ewcsLISTED_BUF_OPS);
580 /* Copy the sum of violations for the distance restraints from fcd */
583 enerd->term[F_DISRESVIOL] = fcd->disres.sumviol;
587 /*! \brief As calc_listed(), but only determines the potential energy
588 * for the perturbed interactions.
590 * The shift forces in fr are not affected.
592 void calc_listed_lambda(const InteractionDefinitions& idef,
594 const t_forcerec* fr,
595 const struct t_pbc* pbc,
596 const struct t_graph* g,
597 gmx_grppairener_t* grpp,
599 gmx::ArrayRef<real> dvdl,
604 int* global_atom_index)
609 const t_pbc* pbc_null;
610 WorkDivision& workDivision = fr->bondedThreading->foreignLambdaWorkDivision;
621 /* We already have the forces, so we use temp buffers here */
622 // TODO: Get rid of these allocations by using permanent force buffers
623 snew(f, fr->natoms_force);
624 snew(fshift, SHIFTS);
626 /* Loop over all bonded force types to calculate the bonded energies */
627 for (int ftype = 0; (ftype < F_NRE); ftype++)
629 if (ftype_is_bonded_potential(ftype))
631 const InteractionList& ilist = idef.il[ftype];
632 /* Create a temporary iatom list with only perturbed interactions */
633 const int numNonperturbed = idef.numNonperturbedInteractions[ftype];
634 ArrayRef<const int> iatomsPerturbed = gmx::constArrayRefFromArray(
635 ilist.iatoms.data() + numNonperturbed, ilist.size() - numNonperturbed);
636 if (!iatomsPerturbed.empty())
638 /* Set the work range of thread 0 to the perturbed bondeds */
639 workDivision.setBound(ftype, 0, 0);
640 workDivision.setBound(ftype, 1, iatomsPerturbed.ssize());
642 gmx::StepWorkload tempFlags;
643 tempFlags.computeEnergy = true;
644 v = calc_one_bond(0, ftype, idef, iatomsPerturbed, iatomsPerturbed.ssize(),
645 workDivision, x, f, fshift, fr, pbc_null, g, grpp, nrnb, lambda,
646 dvdl.data(), md, fcd, tempFlags, global_atom_index);
658 void do_force_listed(struct gmx_wallcycle* wcycle,
660 const t_lambda* fepvals,
662 const gmx_multisim_t* ms,
663 const InteractionDefinitions& idef,
665 gmx::ArrayRef<const gmx::RVec> xWholeMolecules,
667 gmx::ForceOutputs* forceOutputs,
668 const t_forcerec* fr,
669 const struct t_pbc* pbc,
670 const struct t_graph* graph,
671 gmx_enerdata_t* enerd,
676 int* global_atom_index,
677 const gmx::StepWorkload& stepWork)
679 t_pbc pbc_full; /* Full PBC is needed for position restraints */
681 if (!stepWork.computeListedForces)
686 if (!idef.il[F_POSRES].empty() || !idef.il[F_FBPOSRES].empty())
688 /* Not enough flops to bother counting */
689 set_pbc(&pbc_full, fr->pbcType, box);
691 calc_listed(cr, ms, wcycle, idef, x, xWholeMolecules, hist, forceOutputs, fr, pbc, &pbc_full,
692 graph, enerd, nrnb, lambda, md, fcd, global_atom_index, stepWork);
694 /* Check if we have to determine energy differences
695 * at foreign lambda's.
697 if (fepvals->n_lambda > 0 && stepWork.computeDhdl)
699 real dvdl[efptNR] = { 0 };
700 posres_wrapper_lambda(wcycle, fepvals, idef, &pbc_full, x, enerd, lambda, fr);
702 if (idef.ilsort != ilsortNO_FE)
704 wallcycle_sub_start(wcycle, ewcsLISTED_FEP);
705 if (idef.ilsort != ilsortFE_SORTED)
707 gmx_incons("The bonded interactions are not sorted for free energy");
709 for (size_t i = 0; i < enerd->enerpart_lambda.size(); i++)
713 reset_foreign_enerdata(enerd);
714 for (int j = 0; j < efptNR; j++)
716 lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i - 1]);
718 calc_listed_lambda(idef, x, fr, pbc, graph, &(enerd->foreign_grpp),
719 enerd->foreign_term, dvdl, nrnb, lam_i, md, fcd, global_atom_index);
720 sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
721 enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
722 for (int j = 0; j < efptNR; j++)
724 enerd->dhdlLambda[i] += dvdl[j];
728 wallcycle_sub_stop(wcycle, ewcsLISTED_FEP);