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45 #include "gromacs/domdec/dlbtiming.h"
46 #include "gromacs/domdec/domdec.h"
47 #include "gromacs/domdec/domdec_struct.h"
48 #include "gromacs/ewald/ewald.h"
49 #include "gromacs/ewald/long_range_correction.h"
50 #include "gromacs/ewald/pme.h"
51 #include "gromacs/gmxlib/network.h"
52 #include "gromacs/gmxlib/nrnb.h"
53 #include "gromacs/listed_forces/listed_forces.h"
54 #include "gromacs/math/vec.h"
55 #include "gromacs/math/vecdump.h"
56 #include "gromacs/mdlib/force_flags.h"
57 #include "gromacs/mdlib/forcerec_threading.h"
58 #include "gromacs/mdlib/qmmm.h"
59 #include "gromacs/mdlib/rf_util.h"
60 #include "gromacs/mdlib/wall.h"
61 #include "gromacs/mdtypes/commrec.h"
62 #include "gromacs/mdtypes/enerdata.h"
63 #include "gromacs/mdtypes/forceoutput.h"
64 #include "gromacs/mdtypes/forcerec.h"
65 #include "gromacs/mdtypes/inputrec.h"
66 #include "gromacs/mdtypes/md_enums.h"
67 #include "gromacs/mdtypes/mdatom.h"
68 #include "gromacs/pbcutil/ishift.h"
69 #include "gromacs/pbcutil/mshift.h"
70 #include "gromacs/pbcutil/pbc.h"
71 #include "gromacs/timing/wallcycle.h"
72 #include "gromacs/utility/exceptions.h"
73 #include "gromacs/utility/fatalerror.h"
74 #include "gromacs/utility/smalloc.h"
76 static void clearEwaldThreadOutput(ewald_corr_thread_t *ewc_t)
80 ewc_t->dvdl[efptCOUL] = 0;
81 ewc_t->dvdl[efptVDW] = 0;
82 clear_mat(ewc_t->vir_q);
83 clear_mat(ewc_t->vir_lj);
86 static void reduceEwaldThreadOuput(int nthreads, ewald_corr_thread_t *ewc_t)
88 ewald_corr_thread_t &dest = ewc_t[0];
90 for (int t = 1; t < nthreads; t++)
92 dest.Vcorr_q += ewc_t[t].Vcorr_q;
93 dest.Vcorr_lj += ewc_t[t].Vcorr_lj;
94 dest.dvdl[efptCOUL] += ewc_t[t].dvdl[efptCOUL];
95 dest.dvdl[efptVDW] += ewc_t[t].dvdl[efptVDW];
96 m_add(dest.vir_q, ewc_t[t].vir_q, dest.vir_q);
97 m_add(dest.vir_lj, ewc_t[t].vir_lj, dest.vir_lj);
102 do_force_lowlevel(t_forcerec *fr,
103 const t_inputrec *ir,
106 const gmx_multisim_t *ms,
108 gmx_wallcycle_t wcycle,
110 gmx::ArrayRefWithPadding<gmx::RVec> coordinates,
112 gmx::ForceOutputs *forceOutputs,
113 gmx_enerdata_t *enerd,
117 const t_graph *graph,
120 const DDBalanceRegionHandler &ddBalanceRegionHandler)
122 // TODO: Replace all uses of x by const coordinates
123 rvec *x = as_rvec_array(coordinates.paddedArrayRef().data());
125 auto &forceWithVirial = forceOutputs->forceWithVirial();
127 /* do QMMM first if requested */
130 enerd->term[F_EQM] = calculate_QMMM(cr, &forceOutputs->forceWithShiftForces(), fr);
133 /* Call the short range functions all in one go. */
137 /* foreign lambda component for walls */
138 real dvdl_walls = do_walls(*ir, *fr, box, *md, x,
139 &forceWithVirial, lambda[efptVDW],
140 enerd->grpp.ener[egLJSR].data(), nrnb);
141 enerd->dvdl_lin[efptVDW] += dvdl_walls;
144 /* Shift the coordinates. Must be done before listed forces and PPPM,
145 * but is also necessary for SHAKE and update, therefore it can NOT
146 * go when no listed forces have to be evaluated.
148 * The shifting and PBC code is deliberately not timed, since with
149 * the Verlet scheme it only takes non-zero time with triclinic
150 * boxes, and even then the time is around a factor of 100 less
151 * than the next smallest counter.
155 /* Here sometimes we would not need to shift with NBFonly,
156 * but we do so anyhow for consistency of the returned coordinates.
160 shift_self(graph, box, x);
163 inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
167 inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
174 /* Check whether we need to take into account PBC in listed interactions. */
175 const auto needPbcForListedForces = fr->bMolPBC && bool(flags & GMX_FORCE_LISTED) && haveCpuListedForces(*fr, *idef, *fcd);
176 if (needPbcForListedForces)
178 /* Since all atoms are in the rectangular or triclinic unit-cell,
179 * only single box vector shifts (2 in x) are required.
181 set_pbc_dd(&pbc, fr->ePBC, DOMAINDECOMP(cr) ? cr->dd->nc : nullptr,
185 do_force_listed(wcycle, box, ir->fepvals, cr, ms,
188 fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
189 DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr,
193 const bool computePmeOnCpu =
194 (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype)) &&
195 thisRankHasDuty(cr, DUTY_PME) &&
196 (pme_run_mode(fr->pmedata) == PmeRunMode::CPU);
198 const bool haveEwaldSurfaceTerms =
199 EEL_PME_EWALD(fr->ic->eeltype) &&
200 (ir->ewald_geometry != eewg3D || ir->epsilon_surface != 0);
202 /* Do long-range electrostatics and/or LJ-PME
203 * and compute PME surface terms when necessary.
205 if (computePmeOnCpu ||
206 fr->ic->eeltype == eelEWALD ||
207 haveEwaldSurfaceTerms)
210 real Vlr_q = 0, Vlr_lj = 0;
212 /* We reduce all virial, dV/dlambda and energy contributions, except
213 * for the reciprocal energies (Vlr_q, Vlr_lj) into the same struct.
215 ewald_corr_thread_t &ewaldOutput = fr->ewc_t[0];
216 clearEwaldThreadOutput(&ewaldOutput);
218 if (EEL_PME_EWALD(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
220 /* Calculate Ewald surface terms, when necessary */
221 if (haveEwaldSurfaceTerms)
223 wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
227 gmx_fatal(FARGS, "TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
230 int nthreads = fr->nthread_ewc;
231 #pragma omp parallel for num_threads(nthreads) schedule(static)
232 for (int t = 0; t < nthreads; t++)
236 ewald_corr_thread_t &ewc_t = fr->ewc_t[t];
239 clearEwaldThreadOutput(&ewc_t);
242 /* Threading is only supported with the Verlet cut-off
243 * scheme and then only single particle forces (no
244 * exclusion forces) are calculated, so we can store
245 * the forces in the normal, single forceWithVirial->force_ array.
247 ewald_LRcorrection(md->homenr, cr, nthreads, t, fr, ir,
248 md->chargeA, md->chargeB,
249 (md->nChargePerturbed != 0),
253 as_rvec_array(forceWithVirial.force_.data()),
256 &ewc_t.dvdl[efptCOUL]);
258 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
262 reduceEwaldThreadOuput(nthreads, fr->ewc_t);
264 wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
267 if (EEL_PME_EWALD(fr->ic->eeltype) && fr->n_tpi == 0)
269 /* This is not in a subcounter because it takes a
270 negligible and constant-sized amount of time */
271 ewaldOutput.Vcorr_q +=
272 ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
273 &ewaldOutput.dvdl[efptCOUL],
279 /* Do reciprocal PME for Coulomb and/or LJ. */
280 assert(fr->n_tpi >= 0);
281 if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
283 int pme_flags = GMX_PME_SPREAD | GMX_PME_SOLVE;
285 if (flags & GMX_FORCE_FORCES)
287 pme_flags |= GMX_PME_CALC_F;
289 if (flags & GMX_FORCE_VIRIAL)
291 pme_flags |= GMX_PME_CALC_ENER_VIR;
295 /* We don't calculate f, but we do want the potential */
296 pme_flags |= GMX_PME_CALC_POT;
299 /* With domain decomposition we close the CPU side load
300 * balancing region here, because PME does global
301 * communication that acts as a global barrier.
303 ddBalanceRegionHandler.closeAfterForceComputationCpu();
305 wallcycle_start(wcycle, ewcPMEMESH);
306 status = gmx_pme_do(fr->pmedata,
307 gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(), md->homenr - fr->n_tpi),
308 forceWithVirial.force_,
309 md->chargeA, md->chargeB,
310 md->sqrt_c6A, md->sqrt_c6B,
311 md->sigmaA, md->sigmaB,
313 DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
314 DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
316 ewaldOutput.vir_q, ewaldOutput.vir_lj,
318 lambda[efptCOUL], lambda[efptVDW],
319 &ewaldOutput.dvdl[efptCOUL],
320 &ewaldOutput.dvdl[efptVDW],
322 wallcycle_stop(wcycle, ewcPMEMESH);
325 gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
328 /* We should try to do as little computation after
329 * this as possible, because parallel PME synchronizes
330 * the nodes, so we want all load imbalance of the
331 * rest of the force calculation to be before the PME
332 * call. DD load balancing is done on the whole time
333 * of the force call (without PME).
338 if (EVDW_PME(ir->vdwtype))
341 gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
343 /* Determine the PME grid energy of the test molecule
344 * with the PME grid potential of the other charges.
346 gmx_pme_calc_energy(fr->pmedata,
347 coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
348 gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
354 if (fr->ic->eeltype == eelEWALD)
356 Vlr_q = do_ewald(ir, x, as_rvec_array(forceWithVirial.force_.data()),
357 md->chargeA, md->chargeB,
359 ewaldOutput.vir_q, fr->ic->ewaldcoeff_q,
360 lambda[efptCOUL], &ewaldOutput.dvdl[efptCOUL],
364 /* Note that with separate PME nodes we get the real energies later */
365 // TODO it would be simpler if we just accumulated a single
366 // long-range virial contribution.
367 forceWithVirial.addVirialContribution(ewaldOutput.vir_q);
368 forceWithVirial.addVirialContribution(ewaldOutput.vir_lj);
369 enerd->dvdl_lin[efptCOUL] += ewaldOutput.dvdl[efptCOUL];
370 enerd->dvdl_lin[efptVDW] += ewaldOutput.dvdl[efptVDW];
371 enerd->term[F_COUL_RECIP] = Vlr_q + ewaldOutput.Vcorr_q;
372 enerd->term[F_LJ_RECIP] = Vlr_lj + ewaldOutput.Vcorr_lj;
376 fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
377 Vlr_q, ewaldOutput.Vcorr_q, enerd->term[F_COUL_RECIP]);
378 pr_rvecs(debug, 0, "vir_el_recip after corr", ewaldOutput.vir_q, DIM);
379 rvec *fshift = as_rvec_array(forceOutputs->forceWithShiftForces().shiftForces().data());
380 pr_rvecs(debug, 0, "fshift after LR Corrections", fshift, SHIFTS);
381 fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n",
382 Vlr_lj, ewaldOutput.Vcorr_lj, enerd->term[F_LJ_RECIP]);
383 pr_rvecs(debug, 0, "vir_lj_recip after corr", ewaldOutput.vir_lj, DIM);
389 print_nrnb(debug, nrnb);
394 rvec *fshift = as_rvec_array(forceOutputs->forceWithShiftForces().shiftForces().data());
395 pr_rvecs(debug, 0, "fshift after bondeds", fshift, SHIFTS);