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50 #include "nonbonded.h"
64 #include "gmx_omp_nthreads.h"
66 #include "gromacs/legacyheaders/types/commrec.h"
67 #include "gromacs/math/vec.h"
68 #include "gromacs/timing/wallcycle.h"
69 #include "gromacs/utility/fatalerror.h"
70 #include "gromacs/utility/smalloc.h"
81 gmx_bool bDoLongRangeNS)
87 if (!fr->ns.nblist_initialized)
89 init_neighbor_list(fp, fr, md->homenr);
97 nsearch = search_neighbours(fp, fr, box, top, groups, cr, nrnb, md,
98 bFillGrid, bDoLongRangeNS);
101 fprintf(debug, "nsearch = %d\n", nsearch);
104 /* Check whether we have to do dynamic load balancing */
105 /*if ((nsb->nstDlb > 0) && (mod(step,nsb->nstDlb) == 0))
106 count_nb(cr,nsb,&(top->blocks[ebCGS]),nns,fr->nlr,
107 &(top->idef),opts->ngener);
109 if (fr->ns.dump_nl > 0)
111 dump_nblist(fp, cr, fr, fr->ns.dump_nl);
115 static void reduce_thread_forces(int n, rvec *f,
116 tensor vir_q, tensor vir_lj,
117 real *Vcorr_q, real *Vcorr_lj,
118 real *dvdl_q, real *dvdl_lj,
119 int nthreads, f_thread_t *f_t)
123 /* This reduction can run over any number of threads */
124 #pragma omp parallel for num_threads(gmx_omp_nthreads_get(emntBonded)) private(t) schedule(static)
125 for (i = 0; i < n; i++)
127 for (t = 1; t < nthreads; t++)
129 rvec_inc(f[i], f_t[t].f[i]);
132 for (t = 1; t < nthreads; t++)
134 *Vcorr_q += f_t[t].Vcorr_q;
135 *Vcorr_lj += f_t[t].Vcorr_lj;
136 *dvdl_q += f_t[t].dvdl[efptCOUL];
137 *dvdl_lj += f_t[t].dvdl[efptVDW];
138 m_add(vir_q, f_t[t].vir_q, vir_q);
139 m_add(vir_lj, f_t[t].vir_lj, vir_lj);
143 void gmx_print_sepdvdl(FILE *fplog, const char *s, real v, real dvdlambda)
145 fprintf(fplog, " %-30s V %12.5e dVdl %12.5e\n", s, v, dvdlambda);
148 void do_force_lowlevel(FILE *fplog, gmx_int64_t step,
149 t_forcerec *fr, t_inputrec *ir,
150 t_idef *idef, t_commrec *cr,
151 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
153 rvec x[], history_t *hist,
156 gmx_enerdata_t *enerd,
173 gmx_bool bDoEpot, bSepDVDL, bSB;
179 double clam_i, vlam_i;
180 real dvdl_dum[efptNR], dvdl_nb[efptNR], lam_i[efptNR];
181 real dvdl_q, dvdl_lj;
184 double t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
187 #define PRINT_SEPDVDL(s, v, dvdlambda) if (bSepDVDL) { gmx_print_sepdvdl(fplog, s, v, dvdlambda); }
189 set_pbc(&pbc, fr->ePBC, box);
191 /* reset free energy components */
192 for (i = 0; i < efptNR; i++)
199 for (i = 0; (i < DIM); i++)
201 box_size[i] = box[i][i];
204 bSepDVDL = (fr->bSepDVDL && do_per_step(step, ir->nstlog));
207 /* do QMMM first if requested */
210 enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr);
215 fprintf(fplog, "Step %s: non-bonded V and dVdl for node %d:\n",
216 gmx_step_str(step, buf), cr->nodeid);
219 /* Call the short range functions all in one go. */
222 /*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
223 #define TAKETIME FALSE
226 MPI_Barrier(cr->mpi_comm_mygroup);
233 /* foreign lambda component for walls */
234 real dvdl_walls = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
235 enerd->grpp.ener[egLJSR], nrnb);
236 PRINT_SEPDVDL("Walls", 0.0, dvdl_walls);
237 enerd->dvdl_lin[efptVDW] += dvdl_walls;
240 /* If doing GB, reset dvda and calculate the Born radii */
241 if (ir->implicit_solvent)
243 wallcycle_sub_start(wcycle, ewcsNONBONDED);
245 for (i = 0; i < born->nr; i++)
252 calc_gb_rad(cr, fr, ir, top, x, &(fr->gblist), born, md, nrnb);
255 wallcycle_sub_stop(wcycle, ewcsNONBONDED);
259 /* We only do non-bonded calculation with group scheme here, the verlet
260 * calls are done from do_force_cutsVERLET(). */
261 if (fr->cutoff_scheme == ecutsGROUP && (flags & GMX_FORCE_NONBONDED))
264 /* Add short-range interactions */
265 donb_flags |= GMX_NONBONDED_DO_SR;
267 /* Currently all group scheme kernels always calculate (shift-)forces */
268 if (flags & GMX_FORCE_FORCES)
270 donb_flags |= GMX_NONBONDED_DO_FORCE;
272 if (flags & GMX_FORCE_VIRIAL)
274 donb_flags |= GMX_NONBONDED_DO_SHIFTFORCE;
276 if (flags & GMX_FORCE_ENERGY)
278 donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
280 if (flags & GMX_FORCE_DO_LR)
282 donb_flags |= GMX_NONBONDED_DO_LR;
285 wallcycle_sub_start(wcycle, ewcsNONBONDED);
286 do_nonbonded(fr, x, f, f_longrange, md, excl,
288 lambda, dvdl_nb, -1, -1, donb_flags);
290 /* If we do foreign lambda and we have soft-core interactions
291 * we have to recalculate the (non-linear) energies contributions.
293 if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) && fepvals->sc_alpha != 0)
295 for (i = 0; i < enerd->n_lambda; i++)
297 for (j = 0; j < efptNR; j++)
299 lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
301 reset_foreign_enerdata(enerd);
302 do_nonbonded(fr, x, f, f_longrange, md, excl,
303 &(enerd->foreign_grpp), nrnb,
304 lam_i, dvdl_dum, -1, -1,
305 (donb_flags & ~GMX_NONBONDED_DO_FORCE) | GMX_NONBONDED_DO_FOREIGNLAMBDA);
306 sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
307 enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
310 wallcycle_sub_stop(wcycle, ewcsNONBONDED);
314 /* If we are doing GB, calculate bonded forces and apply corrections
315 * to the solvation forces */
316 /* MRS: Eventually, many need to include free energy contribution here! */
317 if (ir->implicit_solvent)
319 wallcycle_sub_start(wcycle, ewcsBONDED);
320 calc_gb_forces(cr, md, born, top, x, f, fr, idef,
321 ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
322 wallcycle_sub_stop(wcycle, ewcsBONDED);
333 if (fepvals->sc_alpha != 0)
335 enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
339 enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
342 if (fepvals->sc_alpha != 0)
344 /* even though coulomb part is linear, we already added it, beacuse we
345 need to go through the vdw calculation anyway */
347 enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
351 enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
356 real V_short_range = 0;
357 real dvdl_short_range = 0;
359 for (i = 0; i < enerd->grpp.nener; i++)
363 enerd->grpp.ener[egBHAMSR][i] :
364 enerd->grpp.ener[egLJSR][i])
365 + enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
367 dvdl_short_range = dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
368 PRINT_SEPDVDL("VdW and Coulomb SR particle-p.",
377 pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
380 /* Shift the coordinates. Must be done before bonded forces and PPPM,
381 * but is also necessary for SHAKE and update, therefore it can NOT
382 * go when no bonded forces have to be evaluated.
385 /* Here sometimes we would not need to shift with NBFonly,
386 * but we do so anyhow for consistency of the returned coordinates.
390 shift_self(graph, box, x);
393 inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
397 inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
400 /* Check whether we need to do bondeds or correct for exclusions */
402 ((flags & GMX_FORCE_BONDED)
403 || EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype)))
405 /* Since all atoms are in the rectangular or triclinic unit-cell,
406 * only single box vector shifts (2 in x) are required.
408 set_pbc_dd(&pbc, fr->ePBC, cr->dd, TRUE, box);
412 if (flags & GMX_FORCE_BONDED)
414 wallcycle_sub_start(wcycle, ewcsBONDED);
415 calc_bonds(fplog, cr->ms,
416 idef, x, hist, f, fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
417 DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL, atype, born,
419 fr->bSepDVDL && do_per_step(step, ir->nstlog), step);
421 /* Check if we have to determine energy differences
422 * at foreign lambda's.
424 if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) &&
425 idef->ilsort != ilsortNO_FE)
427 if (idef->ilsort != ilsortFE_SORTED)
429 gmx_incons("The bonded interactions are not sorted for free energy");
431 for (i = 0; i < enerd->n_lambda; i++)
433 reset_foreign_enerdata(enerd);
434 for (j = 0; j < efptNR; j++)
436 lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
438 calc_bonds_lambda(fplog, idef, x, fr, &pbc, graph, &(enerd->foreign_grpp), enerd->foreign_term, nrnb, lam_i, md,
439 fcd, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
440 sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
441 enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
446 wallcycle_sub_stop(wcycle, ewcsBONDED);
452 clear_mat(fr->vir_el_recip);
453 clear_mat(fr->vir_lj_recip);
455 /* Do long-range electrostatics and/or LJ-PME, including related short-range
458 if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
460 real Vlr = 0, Vcorr = 0;
461 real dvdl_long_range = 0;
463 real Vlr_q = 0, Vlr_lj = 0, Vcorr_q = 0, Vcorr_lj = 0;
464 real dvdl_long_range_q = 0, dvdl_long_range_lj = 0;
466 bSB = (ir->nwall == 2);
470 svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
471 box_size[ZZ] *= ir->wall_ewald_zfac;
474 if (EEL_PME_EWALD(fr->eeltype) || EVDW_PME(fr->vdwtype))
476 real dvdl_long_range_correction_q = 0;
477 real dvdl_long_range_correction_lj = 0;
478 /* With the Verlet scheme exclusion forces are calculated
479 * in the non-bonded kernel.
481 /* The TPI molecule does not have exclusions with the rest
482 * of the system and no intra-molecular PME grid
483 * contributions will be calculated in
484 * gmx_pme_calc_energy.
486 if ((ir->cutoff_scheme == ecutsGROUP && fr->n_tpi == 0) ||
487 ir->ewald_geometry != eewg3D ||
488 ir->epsilon_surface != 0)
492 wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
496 gmx_fatal(FARGS, "TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
499 nthreads = gmx_omp_nthreads_get(emntBonded);
500 #pragma omp parallel for num_threads(nthreads) schedule(static)
501 for (t = 0; t < nthreads; t++)
505 tensor *vir_q, *vir_lj;
506 real *Vcorrt_q, *Vcorrt_lj, *dvdlt_q, *dvdlt_lj;
509 fnv = fr->f_novirsum;
510 vir_q = &fr->vir_el_recip;
511 vir_lj = &fr->vir_lj_recip;
513 Vcorrt_lj = &Vcorr_lj;
514 dvdlt_q = &dvdl_long_range_correction_q;
515 dvdlt_lj = &dvdl_long_range_correction_lj;
520 vir_q = &fr->f_t[t].vir_q;
521 vir_lj = &fr->f_t[t].vir_lj;
522 Vcorrt_q = &fr->f_t[t].Vcorr_q;
523 Vcorrt_lj = &fr->f_t[t].Vcorr_lj;
524 dvdlt_q = &fr->f_t[t].dvdl[efptCOUL];
525 dvdlt_lj = &fr->f_t[t].dvdl[efptVDW];
526 for (i = 0; i < fr->natoms_force; i++)
536 ewald_LRcorrection(fr->excl_load[t], fr->excl_load[t+1],
539 md->nChargePerturbed ? md->chargeB : NULL,
541 md->nTypePerturbed ? md->sqrt_c6B : NULL,
543 md->nTypePerturbed ? md->sigmaB : NULL,
545 md->nTypePerturbed ? md->sigma3B : NULL,
546 ir->cutoff_scheme != ecutsVERLET,
547 excl, x, bSB ? boxs : box, mu_tot,
550 fnv, *vir_q, *vir_lj,
552 lambda[efptCOUL], lambda[efptVDW],
557 reduce_thread_forces(fr->natoms_force, fr->f_novirsum,
558 fr->vir_el_recip, fr->vir_lj_recip,
560 &dvdl_long_range_correction_q,
561 &dvdl_long_range_correction_lj,
564 wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
567 if (EEL_PME_EWALD(fr->eeltype) && fr->n_tpi == 0)
569 Vcorr_q += ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
570 &dvdl_long_range_correction_q,
574 PRINT_SEPDVDL("Ewald excl./charge/dip. corr.", Vcorr_q, dvdl_long_range_correction_q);
575 PRINT_SEPDVDL("Ewald excl. corr. LJ", Vcorr_lj, dvdl_long_range_correction_lj);
576 enerd->dvdl_lin[efptCOUL] += dvdl_long_range_correction_q;
577 enerd->dvdl_lin[efptVDW] += dvdl_long_range_correction_lj;
579 if ((EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype)) && (cr->duty & DUTY_PME))
581 /* Do reciprocal PME for Coulomb and/or LJ. */
582 assert(fr->n_tpi >= 0);
583 if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
585 pme_flags = GMX_PME_SPREAD | GMX_PME_SOLVE;
586 if (EEL_PME(fr->eeltype))
588 pme_flags |= GMX_PME_DO_COULOMB;
590 if (EVDW_PME(fr->vdwtype))
592 pme_flags |= GMX_PME_DO_LJ;
594 if (flags & GMX_FORCE_FORCES)
596 pme_flags |= GMX_PME_CALC_F;
598 if (flags & GMX_FORCE_VIRIAL)
600 pme_flags |= GMX_PME_CALC_ENER_VIR;
604 /* We don't calculate f, but we do want the potential */
605 pme_flags |= GMX_PME_CALC_POT;
607 wallcycle_start(wcycle, ewcPMEMESH);
608 status = gmx_pme_do(fr->pmedata,
609 0, md->homenr - fr->n_tpi,
611 md->chargeA, md->chargeB,
612 md->sqrt_c6A, md->sqrt_c6B,
613 md->sigmaA, md->sigmaB,
614 bSB ? boxs : box, cr,
615 DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
616 DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
618 fr->vir_el_recip, fr->ewaldcoeff_q,
619 fr->vir_lj_recip, fr->ewaldcoeff_lj,
621 lambda[efptCOUL], lambda[efptVDW],
622 &dvdl_long_range_q, &dvdl_long_range_lj, pme_flags);
623 *cycles_pme = wallcycle_stop(wcycle, ewcPMEMESH);
626 gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
628 /* We should try to do as little computation after
629 * this as possible, because parallel PME synchronizes
630 * the nodes, so we want all load imbalance of the
631 * rest of the force calculation to be before the PME
632 * call. DD load balancing is done on the whole time
633 * of the force call (without PME).
638 if (EVDW_PME(ir->vdwtype))
641 gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
643 /* Determine the PME grid energy of the test molecule
644 * with the PME grid potential of the other charges.
646 gmx_pme_calc_energy(fr->pmedata, fr->n_tpi,
647 x + md->homenr - fr->n_tpi,
648 md->chargeA + md->homenr - fr->n_tpi,
651 PRINT_SEPDVDL("PME mesh", Vlr_q + Vlr_lj, dvdl_long_range_q+dvdl_long_range_lj);
655 if (!EEL_PME(fr->eeltype) && EEL_PME_EWALD(fr->eeltype))
657 Vlr_q = do_ewald(ir, x, fr->f_novirsum,
658 md->chargeA, md->chargeB,
659 box_size, cr, md->homenr,
660 fr->vir_el_recip, fr->ewaldcoeff_q,
661 lambda[efptCOUL], &dvdl_long_range_q, fr->ewald_table);
662 PRINT_SEPDVDL("Ewald long-range", Vlr_q, dvdl_long_range_q);
665 /* Note that with separate PME nodes we get the real energies later */
666 enerd->dvdl_lin[efptCOUL] += dvdl_long_range_q;
667 enerd->dvdl_lin[efptVDW] += dvdl_long_range_lj;
668 enerd->term[F_COUL_RECIP] = Vlr_q + Vcorr_q;
669 enerd->term[F_LJ_RECIP] = Vlr_lj + Vcorr_lj;
672 fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
673 Vlr_q, Vcorr_q, enerd->term[F_COUL_RECIP]);
674 pr_rvecs(debug, 0, "vir_el_recip after corr", fr->vir_el_recip, DIM);
675 pr_rvecs(debug, 0, "fshift after LR Corrections", fr->fshift, SHIFTS);
676 fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n",
677 Vlr_lj, Vcorr_lj, enerd->term[F_LJ_RECIP]);
678 pr_rvecs(debug, 0, "vir_lj_recip after corr", fr->vir_lj_recip, DIM);
683 /* Is there a reaction-field exclusion correction needed? */
684 if (EEL_RF(fr->eeltype) && eelRF_NEC != fr->eeltype)
686 /* With the Verlet scheme, exclusion forces are calculated
687 * in the non-bonded kernel.
689 if (ir->cutoff_scheme != ecutsVERLET)
691 real dvdl_rf_excl = 0;
692 enerd->term[F_RF_EXCL] =
693 RF_excl_correction(fr, graph, md, excl, x, f,
694 fr->fshift, &pbc, lambda[efptCOUL], &dvdl_rf_excl);
696 enerd->dvdl_lin[efptCOUL] += dvdl_rf_excl;
697 PRINT_SEPDVDL("RF exclusion correction",
698 enerd->term[F_RF_EXCL], dvdl_rf_excl);
707 print_nrnb(debug, nrnb);
715 MPI_Barrier(cr->mpi_comm_mygroup);
718 if (fr->timesteps == 11)
720 fprintf(stderr, "* PP load balancing info: node %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
721 cr->nodeid, gmx_step_str(fr->timesteps, buf),
722 100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
723 (fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
731 pr_rvecs(debug, 0, "fshift after bondeds", fr->fshift, SHIFTS);
736 void init_enerdata(int ngener, int n_lambda, gmx_enerdata_t *enerd)
740 for (i = 0; i < F_NRE; i++)
743 enerd->foreign_term[i] = 0;
747 for (i = 0; i < efptNR; i++)
749 enerd->dvdl_lin[i] = 0;
750 enerd->dvdl_nonlin[i] = 0;
756 fprintf(debug, "Creating %d sized group matrix for energies\n", n2);
758 enerd->grpp.nener = n2;
759 enerd->foreign_grpp.nener = n2;
760 for (i = 0; (i < egNR); i++)
762 snew(enerd->grpp.ener[i], n2);
763 snew(enerd->foreign_grpp.ener[i], n2);
768 enerd->n_lambda = 1 + n_lambda;
769 snew(enerd->enerpart_lambda, enerd->n_lambda);
777 void destroy_enerdata(gmx_enerdata_t *enerd)
781 for (i = 0; (i < egNR); i++)
783 sfree(enerd->grpp.ener[i]);
786 for (i = 0; (i < egNR); i++)
788 sfree(enerd->foreign_grpp.ener[i]);
793 sfree(enerd->enerpart_lambda);
797 static real sum_v(int n, real v[])
803 for (i = 0; (i < n); i++)
811 void sum_epot(gmx_grppairener_t *grpp, real *epot)
815 /* Accumulate energies */
816 epot[F_COUL_SR] = sum_v(grpp->nener, grpp->ener[egCOULSR]);
817 epot[F_LJ] = sum_v(grpp->nener, grpp->ener[egLJSR]);
818 epot[F_LJ14] = sum_v(grpp->nener, grpp->ener[egLJ14]);
819 epot[F_COUL14] = sum_v(grpp->nener, grpp->ener[egCOUL14]);
820 epot[F_COUL_LR] = sum_v(grpp->nener, grpp->ener[egCOULLR]);
821 epot[F_LJ_LR] = sum_v(grpp->nener, grpp->ener[egLJLR]);
822 /* We have already added 1-2,1-3, and 1-4 terms to F_GBPOL */
823 epot[F_GBPOL] += sum_v(grpp->nener, grpp->ener[egGB]);
825 /* lattice part of LR doesnt belong to any group
826 * and has been added earlier
828 epot[F_BHAM] = sum_v(grpp->nener, grpp->ener[egBHAMSR]);
829 epot[F_BHAM_LR] = sum_v(grpp->nener, grpp->ener[egBHAMLR]);
832 for (i = 0; (i < F_EPOT); i++)
834 if (i != F_DISRESVIOL && i != F_ORIRESDEV)
836 epot[F_EPOT] += epot[i];
841 void sum_dhdl(gmx_enerdata_t *enerd, real *lambda, t_lambda *fepvals)
846 enerd->dvdl_lin[efptVDW] += enerd->term[F_DVDL_VDW]; /* include dispersion correction */
847 enerd->term[F_DVDL] = 0.0;
848 for (i = 0; i < efptNR; i++)
850 if (fepvals->separate_dvdl[i])
852 /* could this be done more readably/compactly? */
865 index = F_DVDL_BONDED;
867 case (efptRESTRAINT):
868 index = F_DVDL_RESTRAINT;
874 enerd->term[index] = enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
877 fprintf(debug, "dvdl-%s[%2d]: %f: non-linear %f + linear %f\n",
878 efpt_names[i], i, enerd->term[index], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
883 enerd->term[F_DVDL] += enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
886 fprintf(debug, "dvd-%sl[%2d]: %f: non-linear %f + linear %f\n",
887 efpt_names[0], i, enerd->term[F_DVDL], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
892 /* Notes on the foreign lambda free energy difference evaluation:
893 * Adding the potential and ekin terms that depend linearly on lambda
894 * as delta lam * dvdl to the energy differences is exact.
895 * For the constraints this is not exact, but we have no other option
896 * without literally changing the lengths and reevaluating the energies at each step.
897 * (try to remedy this post 4.6 - MRS)
898 * For the non-bonded LR term we assume that the soft-core (if present)
899 * no longer affects the energy beyond the short-range cut-off,
900 * which is a very good approximation (except for exotic settings).
901 * (investigate how to overcome this post 4.6 - MRS)
903 if (fepvals->separate_dvdl[efptBONDED])
905 enerd->term[F_DVDL_BONDED] += enerd->term[F_DVDL_CONSTR];
909 enerd->term[F_DVDL] += enerd->term[F_DVDL_CONSTR];
911 enerd->term[F_DVDL_CONSTR] = 0;
913 for (i = 0; i < fepvals->n_lambda; i++)
915 /* note we are iterating over fepvals here!
916 For the current lam, dlam = 0 automatically,
917 so we don't need to add anything to the
918 enerd->enerpart_lambda[0] */
920 /* we don't need to worry about dvdl_lin contributions to dE at
921 current lambda, because the contributions to the current
922 lambda are automatically zeroed */
924 for (j = 0; j < efptNR; j++)
926 /* Note that this loop is over all dhdl components, not just the separated ones */
927 dlam = (fepvals->all_lambda[j][i]-lambda[j]);
928 enerd->enerpart_lambda[i+1] += dlam*enerd->dvdl_lin[j];
931 fprintf(debug, "enerdiff lam %g: (%15s), non-linear %f linear %f*%f\n",
932 fepvals->all_lambda[j][i], efpt_names[j],
933 (enerd->enerpart_lambda[i+1] - enerd->enerpart_lambda[0]),
934 dlam, enerd->dvdl_lin[j]);
941 void reset_foreign_enerdata(gmx_enerdata_t *enerd)
945 /* First reset all foreign energy components. Foreign energies always called on
946 neighbor search steps */
947 for (i = 0; (i < egNR); i++)
949 for (j = 0; (j < enerd->grpp.nener); j++)
951 enerd->foreign_grpp.ener[i][j] = 0.0;
955 /* potential energy components */
956 for (i = 0; (i <= F_EPOT); i++)
958 enerd->foreign_term[i] = 0.0;
962 void reset_enerdata(t_forcerec *fr, gmx_bool bNS,
963 gmx_enerdata_t *enerd,
969 /* First reset all energy components, except for the long range terms
970 * on the master at non neighbor search steps, since the long range
971 * terms have already been summed at the last neighbor search step.
973 bKeepLR = (fr->bTwinRange && !bNS);
974 for (i = 0; (i < egNR); i++)
976 if (!(bKeepLR && bMaster && (i == egCOULLR || i == egLJLR)))
978 for (j = 0; (j < enerd->grpp.nener); j++)
980 enerd->grpp.ener[i][j] = 0.0;
984 for (i = 0; i < efptNR; i++)
986 enerd->dvdl_lin[i] = 0.0;
987 enerd->dvdl_nonlin[i] = 0.0;
990 /* Normal potential energy components */
991 for (i = 0; (i <= F_EPOT); i++)
993 enerd->term[i] = 0.0;
995 /* Initialize the dVdlambda term with the long range contribution */
996 /* Initialize the dvdl term with the long range contribution */
997 enerd->term[F_DVDL] = 0.0;
998 enerd->term[F_DVDL_COUL] = 0.0;
999 enerd->term[F_DVDL_VDW] = 0.0;
1000 enerd->term[F_DVDL_BONDED] = 0.0;
1001 enerd->term[F_DVDL_RESTRAINT] = 0.0;
1002 enerd->term[F_DKDL] = 0.0;
1003 if (enerd->n_lambda > 0)
1005 for (i = 0; i < enerd->n_lambda; i++)
1007 enerd->enerpart_lambda[i] = 0.0;
1010 /* reset foreign energy data - separate function since we also call it elsewhere */
1011 reset_foreign_enerdata(enerd);