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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/forcerec_threading.h"
57 #include "gromacs/mdlib/qmmm.h"
58 #include "gromacs/mdlib/rf_util.h"
59 #include "gromacs/mdlib/wall.h"
60 #include "gromacs/mdtypes/commrec.h"
61 #include "gromacs/mdtypes/enerdata.h"
62 #include "gromacs/mdtypes/forceoutput.h"
63 #include "gromacs/mdtypes/forcerec.h"
64 #include "gromacs/mdtypes/inputrec.h"
65 #include "gromacs/mdtypes/md_enums.h"
66 #include "gromacs/mdtypes/mdatom.h"
67 #include "gromacs/mdtypes/simulation_workload.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);
101 void do_force_lowlevel(t_forcerec* fr,
102 const t_inputrec* ir,
105 const gmx_multisim_t* ms,
107 gmx_wallcycle_t wcycle,
109 gmx::ArrayRefWithPadding<gmx::RVec> coordinates,
111 gmx::ForceOutputs* forceOutputs,
112 gmx_enerdata_t* enerd,
116 const t_graph* graph,
118 const gmx::StepWorkload& stepWork,
119 const DDBalanceRegionHandler& ddBalanceRegionHandler)
121 // TODO: Replace all uses of x by const coordinates
122 rvec* x = as_rvec_array(coordinates.paddedArrayRef().data());
124 auto& forceWithVirial = forceOutputs->forceWithVirial();
126 /* do QMMM first if requested */
129 enerd->term[F_EQM] = calculate_QMMM(cr, &forceOutputs->forceWithShiftForces(), fr);
132 /* Call the short range functions all in one go. */
136 /* foreign lambda component for walls */
137 real dvdl_walls = do_walls(*ir, *fr, box, *md, x, &forceWithVirial, lambda[efptVDW],
138 enerd->grpp.ener[egLJSR].data(), nrnb);
139 enerd->dvdl_lin[efptVDW] += dvdl_walls;
142 /* Shift the coordinates. Must be done before listed forces and PPPM,
143 * but is also necessary for SHAKE and update, therefore it can NOT
144 * go when no listed forces have to be evaluated.
146 * The shifting and PBC code is deliberately not timed, since with
147 * the Verlet scheme it only takes non-zero time with triclinic
148 * boxes, and even then the time is around a factor of 100 less
149 * than the next smallest counter.
153 /* Here sometimes we would not need to shift with NBFonly,
154 * but we do so anyhow for consistency of the returned coordinates.
158 shift_self(graph, box, x);
161 inc_nrnb(nrnb, eNR_SHIFTX, 2 * graph->nnodes);
165 inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
172 /* Check whether we need to take into account PBC in listed interactions. */
173 const auto needPbcForListedForces =
174 fr->bMolPBC && stepWork.computeListedForces && haveCpuListedForces(*fr, *idef, *fcd);
175 if (needPbcForListedForces)
177 /* Since all atoms are in the rectangular or triclinic unit-cell,
178 * only single box vector shifts (2 in x) are required.
180 set_pbc_dd(&pbc, fr->ePBC, DOMAINDECOMP(cr) ? cr->dd->nc : nullptr, TRUE, box);
183 do_force_listed(wcycle, box, ir->fepvals, cr, ms, idef, x, hist, forceOutputs, fr, &pbc,
184 graph, enerd, nrnb, lambda, md, fcd,
185 DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr, stepWork);
188 const bool computePmeOnCpu = (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
189 && thisRankHasDuty(cr, DUTY_PME)
190 && (pme_run_mode(fr->pmedata) == PmeRunMode::CPU);
192 const bool haveEwaldSurfaceTerm = haveEwaldSurfaceContribution(*ir);
194 /* Do long-range electrostatics and/or LJ-PME
195 * and compute PME surface terms when necessary.
197 if (computePmeOnCpu || fr->ic->eeltype == eelEWALD || haveEwaldSurfaceTerm)
200 real Vlr_q = 0, Vlr_lj = 0;
202 /* We reduce all virial, dV/dlambda and energy contributions, except
203 * for the reciprocal energies (Vlr_q, Vlr_lj) into the same struct.
205 ewald_corr_thread_t& ewaldOutput = fr->ewc_t[0];
206 clearEwaldThreadOutput(&ewaldOutput);
208 if (EEL_PME_EWALD(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
210 /* Calculate the Ewald surface force and energy contributions, when necessary */
211 if (haveEwaldSurfaceTerm)
213 wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
218 "TPI with PME currently only works in a 3D geometry with tin-foil "
219 "boundary conditions");
222 int nthreads = fr->nthread_ewc;
223 #pragma omp parallel for num_threads(nthreads) schedule(static)
224 for (int t = 0; t < nthreads; t++)
228 ewald_corr_thread_t& ewc_t = fr->ewc_t[t];
231 clearEwaldThreadOutput(&ewc_t);
234 /* Threading is only supported with the Verlet cut-off
235 * scheme and then only single particle forces (no
236 * exclusion forces) are calculated, so we can store
237 * the forces in the normal, single forceWithVirial->force_ array.
239 ewald_LRcorrection(md->homenr, cr, nthreads, t, *fr, *ir, md->chargeA,
240 md->chargeB, (md->nChargePerturbed != 0), x, box, mu_tot,
241 as_rvec_array(forceWithVirial.force_.data()),
242 &ewc_t.Vcorr_q, lambda[efptCOUL], &ewc_t.dvdl[efptCOUL]);
244 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
248 reduceEwaldThreadOuput(nthreads, fr->ewc_t);
250 wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
253 if (EEL_PME_EWALD(fr->ic->eeltype) && fr->n_tpi == 0)
255 /* This is not in a subcounter because it takes a
256 negligible and constant-sized amount of time */
257 ewaldOutput.Vcorr_q += ewald_charge_correction(
258 cr, fr, lambda[efptCOUL], box, &ewaldOutput.dvdl[efptCOUL], ewaldOutput.vir_q);
263 /* Do reciprocal PME for Coulomb and/or LJ. */
264 assert(fr->n_tpi >= 0);
265 if (fr->n_tpi == 0 || stepWork.stateChanged)
267 int pme_flags = GMX_PME_SPREAD | GMX_PME_SOLVE;
269 if (stepWork.computeForces)
271 pme_flags |= GMX_PME_CALC_F;
273 if (stepWork.computeVirial)
275 pme_flags |= GMX_PME_CALC_ENER_VIR;
279 /* We don't calculate f, but we do want the potential */
280 pme_flags |= GMX_PME_CALC_POT;
283 /* With domain decomposition we close the CPU side load
284 * balancing region here, because PME does global
285 * communication that acts as a global barrier.
287 ddBalanceRegionHandler.closeAfterForceComputationCpu();
289 wallcycle_start(wcycle, ewcPMEMESH);
292 gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(),
293 md->homenr - fr->n_tpi),
294 forceWithVirial.force_, md->chargeA, md->chargeB, md->sqrt_c6A,
295 md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
296 DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
297 DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
298 ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
299 lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
300 &ewaldOutput.dvdl[efptVDW], pme_flags);
301 wallcycle_stop(wcycle, ewcPMEMESH);
304 gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
307 /* We should try to do as little computation after
308 * this as possible, because parallel PME synchronizes
309 * the nodes, so we want all load imbalance of the
310 * rest of the force calculation to be before the PME
311 * call. DD load balancing is done on the whole time
312 * of the force call (without PME).
317 if (EVDW_PME(ir->vdwtype))
320 gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
322 /* Determine the PME grid energy of the test molecule
323 * with the PME grid potential of the other charges.
327 coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
328 gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
334 if (fr->ic->eeltype == eelEWALD)
336 Vlr_q = do_ewald(ir, x, as_rvec_array(forceWithVirial.force_.data()), md->chargeA,
337 md->chargeB, box, cr, md->homenr, ewaldOutput.vir_q, fr->ic->ewaldcoeff_q,
338 lambda[efptCOUL], &ewaldOutput.dvdl[efptCOUL], fr->ewald_table);
341 /* Note that with separate PME nodes we get the real energies later */
342 // TODO it would be simpler if we just accumulated a single
343 // long-range virial contribution.
344 forceWithVirial.addVirialContribution(ewaldOutput.vir_q);
345 forceWithVirial.addVirialContribution(ewaldOutput.vir_lj);
346 enerd->dvdl_lin[efptCOUL] += ewaldOutput.dvdl[efptCOUL];
347 enerd->dvdl_lin[efptVDW] += ewaldOutput.dvdl[efptVDW];
348 enerd->term[F_COUL_RECIP] = Vlr_q + ewaldOutput.Vcorr_q;
349 enerd->term[F_LJ_RECIP] = Vlr_lj + ewaldOutput.Vcorr_lj;
353 fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n", Vlr_q,
354 ewaldOutput.Vcorr_q, enerd->term[F_COUL_RECIP]);
355 pr_rvecs(debug, 0, "vir_el_recip after corr", ewaldOutput.vir_q, DIM);
356 rvec* fshift = as_rvec_array(forceOutputs->forceWithShiftForces().shiftForces().data());
357 pr_rvecs(debug, 0, "fshift after LR Corrections", fshift, SHIFTS);
358 fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n", Vlr_lj,
359 ewaldOutput.Vcorr_lj, enerd->term[F_LJ_RECIP]);
360 pr_rvecs(debug, 0, "vir_lj_recip after corr", ewaldOutput.vir_lj, DIM);
366 print_nrnb(debug, nrnb);
371 rvec* fshift = as_rvec_array(forceOutputs->forceWithShiftForces().shiftForces().data());
372 pr_rvecs(debug, 0, "fshift after bondeds", fshift, SHIFTS);