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39 #include "gromacs/legacyheaders/sim_util.h"
48 #ifdef HAVE_SYS_TIME_H
52 #include "gromacs/bonded/bonded.h"
53 #include "gromacs/essentialdynamics/edsam.h"
54 #include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
55 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
56 #include "gromacs/imd/imd.h"
57 #include "gromacs/legacyheaders/calcmu.h"
58 #include "gromacs/legacyheaders/chargegroup.h"
59 #include "gromacs/legacyheaders/constr.h"
60 #include "gromacs/legacyheaders/copyrite.h"
61 #include "gromacs/legacyheaders/disre.h"
62 #include "gromacs/legacyheaders/domdec.h"
63 #include "gromacs/legacyheaders/force.h"
64 #include "gromacs/legacyheaders/genborn.h"
65 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
66 #include "gromacs/legacyheaders/mdatoms.h"
67 #include "gromacs/legacyheaders/mdrun.h"
68 #include "gromacs/legacyheaders/names.h"
69 #include "gromacs/legacyheaders/network.h"
70 #include "gromacs/legacyheaders/nonbonded.h"
71 #include "gromacs/legacyheaders/nrnb.h"
72 #include "gromacs/legacyheaders/orires.h"
73 #include "gromacs/legacyheaders/pme.h"
74 #include "gromacs/legacyheaders/qmmm.h"
75 #include "gromacs/legacyheaders/txtdump.h"
76 #include "gromacs/legacyheaders/typedefs.h"
77 #include "gromacs/legacyheaders/update.h"
78 #include "gromacs/legacyheaders/types/commrec.h"
79 #include "gromacs/math/units.h"
80 #include "gromacs/math/vec.h"
81 #include "gromacs/mdlib/nb_verlet.h"
82 #include "gromacs/mdlib/nbnxn_atomdata.h"
83 #include "gromacs/mdlib/nbnxn_search.h"
84 #include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h"
85 #include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
86 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
87 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.h"
88 #include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
89 #include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
90 #include "gromacs/pbcutil/ishift.h"
91 #include "gromacs/pbcutil/mshift.h"
92 #include "gromacs/pbcutil/pbc.h"
93 #include "gromacs/pulling/pull.h"
94 #include "gromacs/pulling/pull_rotation.h"
95 #include "gromacs/timing/wallcycle.h"
96 #include "gromacs/timing/walltime_accounting.h"
97 #include "gromacs/utility/cstringutil.h"
98 #include "gromacs/utility/gmxmpi.h"
99 #include "gromacs/utility/smalloc.h"
103 void print_time(FILE *out,
104 gmx_walltime_accounting_t walltime_accounting,
107 t_commrec gmx_unused *cr)
110 char timebuf[STRLEN];
111 double dt, elapsed_seconds, time_per_step;
114 #ifndef GMX_THREAD_MPI
120 fprintf(out, "step %s", gmx_step_str(step, buf));
121 if ((step >= ir->nstlist))
123 double seconds_since_epoch = gmx_gettime();
124 elapsed_seconds = seconds_since_epoch - walltime_accounting_get_start_time_stamp(walltime_accounting);
125 time_per_step = elapsed_seconds/(step - ir->init_step + 1);
126 dt = (ir->nsteps + ir->init_step - step) * time_per_step;
132 finish = (time_t) (seconds_since_epoch + dt);
133 gmx_ctime_r(&finish, timebuf, STRLEN);
134 sprintf(buf, "%s", timebuf);
135 buf[strlen(buf)-1] = '\0';
136 fprintf(out, ", will finish %s", buf);
140 fprintf(out, ", remaining wall clock time: %5d s ", (int)dt);
145 fprintf(out, " performance: %.1f ns/day ",
146 ir->delta_t/1000*24*60*60/time_per_step);
149 #ifndef GMX_THREAD_MPI
159 void print_date_and_time(FILE *fplog, int nodeid, const char *title,
162 char time_string[STRLEN];
171 char timebuf[STRLEN];
172 time_t temp_time = (time_t) the_time;
174 gmx_ctime_r(&temp_time, timebuf, STRLEN);
175 for (i = 0; timebuf[i] >= ' '; i++)
177 time_string[i] = timebuf[i];
179 time_string[i] = '\0';
182 fprintf(fplog, "%s on rank %d %s\n", title, nodeid, time_string);
185 void print_start(FILE *fplog, t_commrec *cr,
186 gmx_walltime_accounting_t walltime_accounting,
191 sprintf(buf, "Started %s", name);
192 print_date_and_time(fplog, cr->nodeid, buf,
193 walltime_accounting_get_start_time_stamp(walltime_accounting));
196 static void sum_forces(int start, int end, rvec f[], rvec flr[])
202 pr_rvecs(debug, 0, "fsr", f+start, end-start);
203 pr_rvecs(debug, 0, "flr", flr+start, end-start);
205 for (i = start; (i < end); i++)
207 rvec_inc(f[i], flr[i]);
212 * calc_f_el calculates forces due to an electric field.
214 * force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e
216 * Et[] contains the parameters for the time dependent
217 * part of the field (not yet used).
218 * Ex[] contains the parameters for
219 * the spatial dependent part of the field. You can have cool periodic
220 * fields in principle, but only a constant field is supported
222 * The function should return the energy due to the electric field
223 * (if any) but for now returns 0.
226 * There can be problems with the virial.
227 * Since the field is not self-consistent this is unavoidable.
228 * For neutral molecules the virial is correct within this approximation.
229 * For neutral systems with many charged molecules the error is small.
230 * But for systems with a net charge or a few charged molecules
231 * the error can be significant when the field is high.
232 * Solution: implement a self-consitent electric field into PME.
234 static void calc_f_el(FILE *fp, int start, int homenr,
235 real charge[], rvec f[],
236 t_cosines Ex[], t_cosines Et[], double t)
242 for (m = 0; (m < DIM); m++)
249 Ext[m] = cos(Et[m].a[0]*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(Et[m].a[2])));
253 Ext[m] = cos(Et[m].a[0]*t);
262 /* Convert the field strength from V/nm to MD-units */
263 Ext[m] *= Ex[m].a[0]*FIELDFAC;
264 for (i = start; (i < start+homenr); i++)
266 f[i][m] += charge[i]*Ext[m];
276 fprintf(fp, "%10g %10g %10g %10g #FIELD\n", t,
277 Ext[XX]/FIELDFAC, Ext[YY]/FIELDFAC, Ext[ZZ]/FIELDFAC);
281 static void calc_virial(int start, int homenr, rvec x[], rvec f[],
282 tensor vir_part, t_graph *graph, matrix box,
283 t_nrnb *nrnb, const t_forcerec *fr, int ePBC)
288 /* The short-range virial from surrounding boxes */
290 calc_vir(SHIFTS, fr->shift_vec, fr->fshift, vir_part, ePBC == epbcSCREW, box);
291 inc_nrnb(nrnb, eNR_VIRIAL, SHIFTS);
293 /* Calculate partial virial, for local atoms only, based on short range.
294 * Total virial is computed in global_stat, called from do_md
296 f_calc_vir(start, start+homenr, x, f, vir_part, graph, box);
297 inc_nrnb(nrnb, eNR_VIRIAL, homenr);
299 /* Add position restraint contribution */
300 for (i = 0; i < DIM; i++)
302 vir_part[i][i] += fr->vir_diag_posres[i];
305 /* Add wall contribution */
306 for (i = 0; i < DIM; i++)
308 vir_part[i][ZZ] += fr->vir_wall_z[i];
313 pr_rvecs(debug, 0, "vir_part", vir_part, DIM);
317 static void posres_wrapper(int flags,
321 matrix box, rvec x[],
322 gmx_enerdata_t *enerd,
330 /* Position restraints always require full pbc */
331 set_pbc(&pbc, ir->ePBC, box);
333 v = posres(top->idef.il[F_POSRES].nr, top->idef.il[F_POSRES].iatoms,
334 top->idef.iparams_posres,
335 (const rvec*)x, fr->f_novirsum, fr->vir_diag_posres,
336 ir->ePBC == epbcNONE ? NULL : &pbc,
337 lambda[efptRESTRAINT], &dvdl,
338 fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
339 enerd->term[F_POSRES] += v;
340 /* If just the force constant changes, the FEP term is linear,
341 * but if k changes, it is not.
343 enerd->dvdl_nonlin[efptRESTRAINT] += dvdl;
344 inc_nrnb(nrnb, eNR_POSRES, top->idef.il[F_POSRES].nr/2);
346 if ((ir->fepvals->n_lambda > 0) && (flags & GMX_FORCE_DHDL))
348 for (i = 0; i < enerd->n_lambda; i++)
350 real dvdl_dum, lambda_dum;
352 lambda_dum = (i == 0 ? lambda[efptRESTRAINT] : ir->fepvals->all_lambda[efptRESTRAINT][i-1]);
353 v = posres(top->idef.il[F_POSRES].nr, top->idef.il[F_POSRES].iatoms,
354 top->idef.iparams_posres,
355 (const rvec*)x, NULL, NULL,
356 ir->ePBC == epbcNONE ? NULL : &pbc, lambda_dum, &dvdl,
357 fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
358 enerd->enerpart_lambda[i] += v;
363 static void fbposres_wrapper(t_inputrec *ir,
366 matrix box, rvec x[],
367 gmx_enerdata_t *enerd,
373 /* Flat-bottomed position restraints always require full pbc */
374 set_pbc(&pbc, ir->ePBC, box);
375 v = fbposres(top->idef.il[F_FBPOSRES].nr, top->idef.il[F_FBPOSRES].iatoms,
376 top->idef.iparams_fbposres,
377 (const rvec*)x, fr->f_novirsum, fr->vir_diag_posres,
378 ir->ePBC == epbcNONE ? NULL : &pbc,
379 fr->rc_scaling, fr->ePBC, fr->posres_com);
380 enerd->term[F_FBPOSRES] += v;
381 inc_nrnb(nrnb, eNR_FBPOSRES, top->idef.il[F_FBPOSRES].nr/2);
384 static void pull_potential_wrapper(t_commrec *cr,
386 matrix box, rvec x[],
390 gmx_enerdata_t *enerd,
393 gmx_wallcycle_t wcycle)
398 /* Calculate the center of mass forces, this requires communication,
399 * which is why pull_potential is called close to other communication.
400 * The virial contribution is calculated directly,
401 * which is why we call pull_potential after calc_virial.
403 wallcycle_start(wcycle, ewcPULLPOT);
404 set_pbc(&pbc, ir->ePBC, box);
406 enerd->term[F_COM_PULL] +=
407 pull_potential(ir->ePull, ir->pull, mdatoms, &pbc,
408 cr, t, lambda[efptRESTRAINT], x, f, vir_force, &dvdl);
409 enerd->dvdl_lin[efptRESTRAINT] += dvdl;
410 wallcycle_stop(wcycle, ewcPULLPOT);
413 static void pme_receive_force_ener(t_commrec *cr,
414 gmx_wallcycle_t wcycle,
415 gmx_enerdata_t *enerd,
418 real e_q, e_lj, v, dvdl_q, dvdl_lj;
419 float cycles_ppdpme, cycles_seppme;
421 cycles_ppdpme = wallcycle_stop(wcycle, ewcPPDURINGPME);
422 dd_cycles_add(cr->dd, cycles_ppdpme, ddCyclPPduringPME);
424 /* In case of node-splitting, the PP nodes receive the long-range
425 * forces, virial and energy from the PME nodes here.
427 wallcycle_start(wcycle, ewcPP_PMEWAITRECVF);
430 gmx_pme_receive_f(cr, fr->f_novirsum, fr->vir_el_recip, &e_q,
431 fr->vir_lj_recip, &e_lj, &dvdl_q, &dvdl_lj,
433 enerd->term[F_COUL_RECIP] += e_q;
434 enerd->term[F_LJ_RECIP] += e_lj;
435 enerd->dvdl_lin[efptCOUL] += dvdl_q;
436 enerd->dvdl_lin[efptVDW] += dvdl_lj;
440 dd_cycles_add(cr->dd, cycles_seppme, ddCyclPME);
442 wallcycle_stop(wcycle, ewcPP_PMEWAITRECVF);
445 static void print_large_forces(FILE *fp, t_mdatoms *md, t_commrec *cr,
446 gmx_int64_t step, real pforce, rvec *x, rvec *f)
450 char buf[STEPSTRSIZE];
453 for (i = 0; i < md->homenr; i++)
456 /* We also catch NAN, if the compiler does not optimize this away. */
457 if (fn2 >= pf2 || fn2 != fn2)
459 fprintf(fp, "step %s atom %6d x %8.3f %8.3f %8.3f force %12.5e\n",
460 gmx_step_str(step, buf),
461 ddglatnr(cr->dd, i), x[i][XX], x[i][YY], x[i][ZZ], sqrt(fn2));
466 static void post_process_forces(t_commrec *cr,
468 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
470 matrix box, rvec x[],
475 t_forcerec *fr, gmx_vsite_t *vsite,
482 /* Spread the mesh force on virtual sites to the other particles...
483 * This is parallellized. MPI communication is performed
484 * if the constructing atoms aren't local.
486 wallcycle_start(wcycle, ewcVSITESPREAD);
487 spread_vsite_f(vsite, x, fr->f_novirsum, NULL,
488 (flags & GMX_FORCE_VIRIAL), fr->vir_el_recip,
490 &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
491 wallcycle_stop(wcycle, ewcVSITESPREAD);
493 if (flags & GMX_FORCE_VIRIAL)
495 /* Now add the forces, this is local */
498 sum_forces(0, fr->f_novirsum_n, f, fr->f_novirsum);
502 sum_forces(0, mdatoms->homenr,
505 if (EEL_FULL(fr->eeltype))
507 /* Add the mesh contribution to the virial */
508 m_add(vir_force, fr->vir_el_recip, vir_force);
510 if (EVDW_PME(fr->vdwtype))
512 /* Add the mesh contribution to the virial */
513 m_add(vir_force, fr->vir_lj_recip, vir_force);
517 pr_rvecs(debug, 0, "vir_force", vir_force, DIM);
522 if (fr->print_force >= 0)
524 print_large_forces(stderr, mdatoms, cr, step, fr->print_force, x, f);
528 static void do_nb_verlet(t_forcerec *fr,
529 interaction_const_t *ic,
530 gmx_enerdata_t *enerd,
531 int flags, int ilocality,
534 gmx_wallcycle_t wcycle)
536 int nnbl, kernel_type, enr_nbnxn_kernel_ljc, enr_nbnxn_kernel_lj;
538 nonbonded_verlet_group_t *nbvg;
541 if (!(flags & GMX_FORCE_NONBONDED))
543 /* skip non-bonded calculation */
547 nbvg = &fr->nbv->grp[ilocality];
549 /* CUDA kernel launch overhead is already timed separately */
550 if (fr->cutoff_scheme != ecutsVERLET)
552 gmx_incons("Invalid cut-off scheme passed!");
555 bCUDA = (nbvg->kernel_type == nbnxnk8x8x8_CUDA);
559 wallcycle_sub_start(wcycle, ewcsNONBONDED);
561 switch (nbvg->kernel_type)
563 case nbnxnk4x4_PlainC:
564 nbnxn_kernel_ref(&nbvg->nbl_lists,
570 enerd->grpp.ener[egCOULSR],
572 enerd->grpp.ener[egBHAMSR] :
573 enerd->grpp.ener[egLJSR]);
576 case nbnxnk4xN_SIMD_4xN:
577 nbnxn_kernel_simd_4xn(&nbvg->nbl_lists,
584 enerd->grpp.ener[egCOULSR],
586 enerd->grpp.ener[egBHAMSR] :
587 enerd->grpp.ener[egLJSR]);
589 case nbnxnk4xN_SIMD_2xNN:
590 nbnxn_kernel_simd_2xnn(&nbvg->nbl_lists,
597 enerd->grpp.ener[egCOULSR],
599 enerd->grpp.ener[egBHAMSR] :
600 enerd->grpp.ener[egLJSR]);
603 case nbnxnk8x8x8_CUDA:
604 nbnxn_cuda_launch_kernel(fr->nbv->cu_nbv, nbvg->nbat, flags, ilocality);
607 case nbnxnk8x8x8_PlainC:
608 nbnxn_kernel_gpu_ref(nbvg->nbl_lists.nbl[0],
613 nbvg->nbat->out[0].f,
615 enerd->grpp.ener[egCOULSR],
617 enerd->grpp.ener[egBHAMSR] :
618 enerd->grpp.ener[egLJSR]);
622 gmx_incons("Invalid nonbonded kernel type passed!");
627 wallcycle_sub_stop(wcycle, ewcsNONBONDED);
630 if (EEL_RF(ic->eeltype) || ic->eeltype == eelCUT)
632 enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_RF;
634 else if ((!bCUDA && nbvg->ewald_excl == ewaldexclAnalytical) ||
635 (bCUDA && nbnxn_cuda_is_kernel_ewald_analytical(fr->nbv->cu_nbv)))
637 enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_EWALD;
641 enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_TAB;
643 enr_nbnxn_kernel_lj = eNR_NBNXN_LJ;
644 if (flags & GMX_FORCE_ENERGY)
646 /* In eNR_??? the nbnxn F+E kernels are always the F kernel + 1 */
647 enr_nbnxn_kernel_ljc += 1;
648 enr_nbnxn_kernel_lj += 1;
651 inc_nrnb(nrnb, enr_nbnxn_kernel_ljc,
652 nbvg->nbl_lists.natpair_ljq);
653 inc_nrnb(nrnb, enr_nbnxn_kernel_lj,
654 nbvg->nbl_lists.natpair_lj);
655 /* The Coulomb-only kernels are offset -eNR_NBNXN_LJ_RF+eNR_NBNXN_RF */
656 inc_nrnb(nrnb, enr_nbnxn_kernel_ljc-eNR_NBNXN_LJ_RF+eNR_NBNXN_RF,
657 nbvg->nbl_lists.natpair_q);
659 if (ic->vdw_modifier == eintmodFORCESWITCH)
661 /* We add up the switch cost separately */
662 inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_FSW+((flags & GMX_FORCE_ENERGY) ? 1 : 0),
663 nbvg->nbl_lists.natpair_ljq + nbvg->nbl_lists.natpair_lj);
665 if (ic->vdw_modifier == eintmodPOTSWITCH)
667 /* We add up the switch cost separately */
668 inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_PSW+((flags & GMX_FORCE_ENERGY) ? 1 : 0),
669 nbvg->nbl_lists.natpair_ljq + nbvg->nbl_lists.natpair_lj);
671 if (ic->vdwtype == evdwPME)
673 /* We add up the LJ Ewald cost separately */
674 inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_EWALD+((flags & GMX_FORCE_ENERGY) ? 1 : 0),
675 nbvg->nbl_lists.natpair_ljq + nbvg->nbl_lists.natpair_lj);
679 static void do_nb_verlet_fep(nbnxn_pairlist_set_t *nbl_lists,
686 gmx_enerdata_t *enerd,
689 gmx_wallcycle_t wcycle)
692 nb_kernel_data_t kernel_data;
694 real dvdl_nb[efptNR];
699 /* Add short-range interactions */
700 donb_flags |= GMX_NONBONDED_DO_SR;
702 /* Currently all group scheme kernels always calculate (shift-)forces */
703 if (flags & GMX_FORCE_FORCES)
705 donb_flags |= GMX_NONBONDED_DO_FORCE;
707 if (flags & GMX_FORCE_VIRIAL)
709 donb_flags |= GMX_NONBONDED_DO_SHIFTFORCE;
711 if (flags & GMX_FORCE_ENERGY)
713 donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
715 if (flags & GMX_FORCE_DO_LR)
717 donb_flags |= GMX_NONBONDED_DO_LR;
720 kernel_data.flags = donb_flags;
721 kernel_data.lambda = lambda;
722 kernel_data.dvdl = dvdl_nb;
724 kernel_data.energygrp_elec = enerd->grpp.ener[egCOULSR];
725 kernel_data.energygrp_vdw = enerd->grpp.ener[egLJSR];
727 /* reset free energy components */
728 for (i = 0; i < efptNR; i++)
733 assert(gmx_omp_nthreads_get(emntNonbonded) == nbl_lists->nnbl);
735 wallcycle_sub_start(wcycle, ewcsNONBONDED);
736 #pragma omp parallel for schedule(static) num_threads(nbl_lists->nnbl)
737 for (th = 0; th < nbl_lists->nnbl; th++)
739 gmx_nb_free_energy_kernel(nbl_lists->nbl_fep[th],
740 x, f, fr, mdatoms, &kernel_data, nrnb);
743 if (fepvals->sc_alpha != 0)
745 enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
746 enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
750 enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
751 enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
754 /* If we do foreign lambda and we have soft-core interactions
755 * we have to recalculate the (non-linear) energies contributions.
757 if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) && fepvals->sc_alpha != 0)
759 kernel_data.flags = (donb_flags & ~(GMX_NONBONDED_DO_FORCE | GMX_NONBONDED_DO_SHIFTFORCE)) | GMX_NONBONDED_DO_FOREIGNLAMBDA;
760 kernel_data.lambda = lam_i;
761 kernel_data.energygrp_elec = enerd->foreign_grpp.ener[egCOULSR];
762 kernel_data.energygrp_vdw = enerd->foreign_grpp.ener[egLJSR];
763 /* Note that we add to kernel_data.dvdl, but ignore the result */
765 for (i = 0; i < enerd->n_lambda; i++)
767 for (j = 0; j < efptNR; j++)
769 lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
771 reset_foreign_enerdata(enerd);
772 #pragma omp parallel for schedule(static) num_threads(nbl_lists->nnbl)
773 for (th = 0; th < nbl_lists->nnbl; th++)
775 gmx_nb_free_energy_kernel(nbl_lists->nbl_fep[th],
776 x, f, fr, mdatoms, &kernel_data, nrnb);
779 sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
780 enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
784 wallcycle_sub_stop(wcycle, ewcsNONBONDED);
787 gmx_bool use_GPU(const nonbonded_verlet_t *nbv)
789 return nbv != NULL && nbv->bUseGPU;
792 void do_force_cutsVERLET(FILE *fplog, t_commrec *cr,
793 t_inputrec *inputrec,
794 gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
796 gmx_groups_t gmx_unused *groups,
797 matrix box, rvec x[], history_t *hist,
801 gmx_enerdata_t *enerd, t_fcdata *fcd,
802 real *lambda, t_graph *graph,
803 t_forcerec *fr, interaction_const_t *ic,
804 gmx_vsite_t *vsite, rvec mu_tot,
805 double t, FILE *field, gmx_edsam_t ed,
813 gmx_bool bStateChanged, bNS, bFillGrid, bCalcCGCM, bBS;
814 gmx_bool bDoLongRange, bDoForces, bSepLRF, bUseGPU, bUseOrEmulGPU;
815 gmx_bool bDiffKernels = FALSE;
817 rvec vzero, box_diag;
819 float cycles_pme, cycles_force, cycles_wait_gpu;
820 nonbonded_verlet_t *nbv;
825 nb_kernel_type = fr->nbv->grp[0].kernel_type;
828 homenr = mdatoms->homenr;
830 clear_mat(vir_force);
833 if (DOMAINDECOMP(cr))
835 cg1 = cr->dd->ncg_tot;
846 bStateChanged = (flags & GMX_FORCE_STATECHANGED);
847 bNS = (flags & GMX_FORCE_NS) && (fr->bAllvsAll == FALSE);
848 bFillGrid = (bNS && bStateChanged);
849 bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
850 bDoLongRange = (fr->bTwinRange && bNS && (flags & GMX_FORCE_DO_LR));
851 bDoForces = (flags & GMX_FORCE_FORCES);
852 bSepLRF = (bDoLongRange && bDoForces && (flags & GMX_FORCE_SEPLRF));
853 bUseGPU = fr->nbv->bUseGPU;
854 bUseOrEmulGPU = bUseGPU || (nbv->grp[0].kernel_type == nbnxnk8x8x8_PlainC);
858 update_forcerec(fr, box);
860 if (NEED_MUTOT(*inputrec))
862 /* Calculate total (local) dipole moment in a temporary common array.
863 * This makes it possible to sum them over nodes faster.
865 calc_mu(start, homenr,
866 x, mdatoms->chargeA, mdatoms->chargeB, mdatoms->nChargePerturbed,
871 if (fr->ePBC != epbcNONE)
873 /* Compute shift vectors every step,
874 * because of pressure coupling or box deformation!
876 if ((flags & GMX_FORCE_DYNAMICBOX) && bStateChanged)
878 calc_shifts(box, fr->shift_vec);
883 put_atoms_in_box_omp(fr->ePBC, box, homenr, x);
884 inc_nrnb(nrnb, eNR_SHIFTX, homenr);
886 else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph)
888 unshift_self(graph, box, x);
892 nbnxn_atomdata_copy_shiftvec(flags & GMX_FORCE_DYNAMICBOX,
893 fr->shift_vec, nbv->grp[0].nbat);
896 if (!(cr->duty & DUTY_PME))
898 /* Send particle coordinates to the pme nodes.
899 * Since this is only implemented for domain decomposition
900 * and domain decomposition does not use the graph,
901 * we do not need to worry about shifting.
906 wallcycle_start(wcycle, ewcPP_PMESENDX);
908 bBS = (inputrec->nwall == 2);
912 svmul(inputrec->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
915 if (EEL_PME(fr->eeltype))
917 pme_flags |= GMX_PME_DO_COULOMB;
920 if (EVDW_PME(fr->vdwtype))
922 pme_flags |= GMX_PME_DO_LJ;
925 gmx_pme_send_coordinates(cr, bBS ? boxs : box, x,
926 mdatoms->nChargePerturbed, mdatoms->nTypePerturbed, lambda[efptCOUL], lambda[efptVDW],
927 (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY)),
930 wallcycle_stop(wcycle, ewcPP_PMESENDX);
934 /* do gridding for pair search */
937 if (graph && bStateChanged)
939 /* Calculate intramolecular shift vectors to make molecules whole */
940 mk_mshift(fplog, graph, fr->ePBC, box, x);
944 box_diag[XX] = box[XX][XX];
945 box_diag[YY] = box[YY][YY];
946 box_diag[ZZ] = box[ZZ][ZZ];
948 wallcycle_start(wcycle, ewcNS);
951 wallcycle_sub_start(wcycle, ewcsNBS_GRID_LOCAL);
952 nbnxn_put_on_grid(nbv->nbs, fr->ePBC, box,
954 0, mdatoms->homenr, -1, fr->cginfo, x,
956 nbv->grp[eintLocal].kernel_type,
957 nbv->grp[eintLocal].nbat);
958 wallcycle_sub_stop(wcycle, ewcsNBS_GRID_LOCAL);
962 wallcycle_sub_start(wcycle, ewcsNBS_GRID_NONLOCAL);
963 nbnxn_put_on_grid_nonlocal(nbv->nbs, domdec_zones(cr->dd),
965 nbv->grp[eintNonlocal].kernel_type,
966 nbv->grp[eintNonlocal].nbat);
967 wallcycle_sub_stop(wcycle, ewcsNBS_GRID_NONLOCAL);
970 if (nbv->ngrp == 1 ||
971 nbv->grp[eintNonlocal].nbat == nbv->grp[eintLocal].nbat)
973 nbnxn_atomdata_set(nbv->grp[eintLocal].nbat, eatAll,
974 nbv->nbs, mdatoms, fr->cginfo);
978 nbnxn_atomdata_set(nbv->grp[eintLocal].nbat, eatLocal,
979 nbv->nbs, mdatoms, fr->cginfo);
980 nbnxn_atomdata_set(nbv->grp[eintNonlocal].nbat, eatAll,
981 nbv->nbs, mdatoms, fr->cginfo);
983 wallcycle_stop(wcycle, ewcNS);
986 /* initialize the GPU atom data and copy shift vector */
991 wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
992 nbnxn_cuda_init_atomdata(nbv->cu_nbv, nbv->grp[eintLocal].nbat);
993 wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
996 wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
997 nbnxn_cuda_upload_shiftvec(nbv->cu_nbv, nbv->grp[eintLocal].nbat);
998 wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
1001 /* do local pair search */
1004 wallcycle_start_nocount(wcycle, ewcNS);
1005 wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_LOCAL);
1006 nbnxn_make_pairlist(nbv->nbs, nbv->grp[eintLocal].nbat,
1009 nbv->min_ci_balanced,
1010 &nbv->grp[eintLocal].nbl_lists,
1012 nbv->grp[eintLocal].kernel_type,
1014 wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_LOCAL);
1018 /* initialize local pair-list on the GPU */
1019 nbnxn_cuda_init_pairlist(nbv->cu_nbv,
1020 nbv->grp[eintLocal].nbl_lists.nbl[0],
1023 wallcycle_stop(wcycle, ewcNS);
1027 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1028 wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
1029 nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs, eatLocal, FALSE, x,
1030 nbv->grp[eintLocal].nbat);
1031 wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
1032 wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1037 wallcycle_start(wcycle, ewcLAUNCH_GPU_NB);
1038 /* launch local nonbonded F on GPU */
1039 do_nb_verlet(fr, ic, enerd, flags, eintLocal, enbvClearFNo,
1041 wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
1044 /* Communicate coordinates and sum dipole if necessary +
1045 do non-local pair search */
1046 if (DOMAINDECOMP(cr))
1048 bDiffKernels = (nbv->grp[eintNonlocal].kernel_type !=
1049 nbv->grp[eintLocal].kernel_type);
1053 /* With GPU+CPU non-bonded calculations we need to copy
1054 * the local coordinates to the non-local nbat struct
1055 * (in CPU format) as the non-local kernel call also
1056 * calculates the local - non-local interactions.
1058 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1059 wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
1060 nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs, eatLocal, TRUE, x,
1061 nbv->grp[eintNonlocal].nbat);
1062 wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
1063 wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1068 wallcycle_start_nocount(wcycle, ewcNS);
1069 wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_NONLOCAL);
1073 nbnxn_grid_add_simple(nbv->nbs, nbv->grp[eintNonlocal].nbat);
1076 nbnxn_make_pairlist(nbv->nbs, nbv->grp[eintNonlocal].nbat,
1079 nbv->min_ci_balanced,
1080 &nbv->grp[eintNonlocal].nbl_lists,
1082 nbv->grp[eintNonlocal].kernel_type,
1085 wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_NONLOCAL);
1087 if (nbv->grp[eintNonlocal].kernel_type == nbnxnk8x8x8_CUDA)
1089 /* initialize non-local pair-list on the GPU */
1090 nbnxn_cuda_init_pairlist(nbv->cu_nbv,
1091 nbv->grp[eintNonlocal].nbl_lists.nbl[0],
1094 wallcycle_stop(wcycle, ewcNS);
1098 wallcycle_start(wcycle, ewcMOVEX);
1099 dd_move_x(cr->dd, box, x);
1101 /* When we don't need the total dipole we sum it in global_stat */
1102 if (bStateChanged && NEED_MUTOT(*inputrec))
1104 gmx_sumd(2*DIM, mu, cr);
1106 wallcycle_stop(wcycle, ewcMOVEX);
1108 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1109 wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
1110 nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs, eatNonlocal, FALSE, x,
1111 nbv->grp[eintNonlocal].nbat);
1112 wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
1113 cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1116 if (bUseGPU && !bDiffKernels)
1118 wallcycle_start(wcycle, ewcLAUNCH_GPU_NB);
1119 /* launch non-local nonbonded F on GPU */
1120 do_nb_verlet(fr, ic, enerd, flags, eintNonlocal, enbvClearFNo,
1122 cycles_force += wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
1128 /* launch D2H copy-back F */
1129 wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
1130 if (DOMAINDECOMP(cr) && !bDiffKernels)
1132 nbnxn_cuda_launch_cpyback(nbv->cu_nbv, nbv->grp[eintNonlocal].nbat,
1133 flags, eatNonlocal);
1135 nbnxn_cuda_launch_cpyback(nbv->cu_nbv, nbv->grp[eintLocal].nbat,
1137 cycles_force += wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
1140 if (bStateChanged && NEED_MUTOT(*inputrec))
1144 gmx_sumd(2*DIM, mu, cr);
1147 for (i = 0; i < 2; i++)
1149 for (j = 0; j < DIM; j++)
1151 fr->mu_tot[i][j] = mu[i*DIM + j];
1155 if (fr->efep == efepNO)
1157 copy_rvec(fr->mu_tot[0], mu_tot);
1161 for (j = 0; j < DIM; j++)
1164 (1.0 - lambda[efptCOUL])*fr->mu_tot[0][j] +
1165 lambda[efptCOUL]*fr->mu_tot[1][j];
1169 /* Reset energies */
1170 reset_enerdata(fr, bNS, enerd, MASTER(cr));
1171 clear_rvecs(SHIFTS, fr->fshift);
1173 if (DOMAINDECOMP(cr) && !(cr->duty & DUTY_PME))
1175 wallcycle_start(wcycle, ewcPPDURINGPME);
1176 dd_force_flop_start(cr->dd, nrnb);
1181 /* Enforced rotation has its own cycle counter that starts after the collective
1182 * coordinates have been communicated. It is added to ddCyclF to allow
1183 * for proper load-balancing */
1184 wallcycle_start(wcycle, ewcROT);
1185 do_rotation(cr, inputrec, box, x, t, step, wcycle, bNS);
1186 wallcycle_stop(wcycle, ewcROT);
1189 /* Start the force cycle counter.
1190 * This counter is stopped in do_forcelow_level.
1191 * No parallel communication should occur while this counter is running,
1192 * since that will interfere with the dynamic load balancing.
1194 wallcycle_start(wcycle, ewcFORCE);
1197 /* Reset forces for which the virial is calculated separately:
1198 * PME/Ewald forces if necessary */
1199 if (fr->bF_NoVirSum)
1201 if (flags & GMX_FORCE_VIRIAL)
1203 fr->f_novirsum = fr->f_novirsum_alloc;
1206 clear_rvecs(fr->f_novirsum_n, fr->f_novirsum);
1210 clear_rvecs(homenr, fr->f_novirsum+start);
1215 /* We are not calculating the pressure so we do not need
1216 * a separate array for forces that do not contribute
1223 /* Clear the short- and long-range forces */
1224 clear_rvecs(fr->natoms_force_constr, f);
1225 if (bSepLRF && do_per_step(step, inputrec->nstcalclr))
1227 clear_rvecs(fr->natoms_force_constr, fr->f_twin);
1230 clear_rvec(fr->vir_diag_posres);
1233 if (inputrec->ePull == epullCONSTRAINT)
1235 clear_pull_forces(inputrec->pull);
1238 /* We calculate the non-bonded forces, when done on the CPU, here.
1239 * We do this before calling do_force_lowlevel, as in there bondeds
1240 * forces are calculated before PME, which does communication.
1241 * With this order, non-bonded and bonded force calculation imbalance
1242 * can be balanced out by the domain decomposition load balancing.
1247 /* Maybe we should move this into do_force_lowlevel */
1248 do_nb_verlet(fr, ic, enerd, flags, eintLocal, enbvClearFYes,
1252 if (fr->efep != efepNO)
1254 /* Calculate the local and non-local free energy interactions here.
1255 * Happens here on the CPU both with and without GPU.
1257 if (fr->nbv->grp[eintLocal].nbl_lists.nbl_fep[0]->nrj > 0)
1259 do_nb_verlet_fep(&fr->nbv->grp[eintLocal].nbl_lists,
1261 inputrec->fepvals, lambda,
1262 enerd, flags, nrnb, wcycle);
1265 if (DOMAINDECOMP(cr) &&
1266 fr->nbv->grp[eintNonlocal].nbl_lists.nbl_fep[0]->nrj > 0)
1268 do_nb_verlet_fep(&fr->nbv->grp[eintNonlocal].nbl_lists,
1270 inputrec->fepvals, lambda,
1271 enerd, flags, nrnb, wcycle);
1275 if (!bUseOrEmulGPU || bDiffKernels)
1279 if (DOMAINDECOMP(cr))
1281 do_nb_verlet(fr, ic, enerd, flags, eintNonlocal,
1282 bDiffKernels ? enbvClearFYes : enbvClearFNo,
1292 aloc = eintNonlocal;
1295 /* Add all the non-bonded force to the normal force array.
1296 * This can be split into a local a non-local part when overlapping
1297 * communication with calculation with domain decomposition.
1299 cycles_force += wallcycle_stop(wcycle, ewcFORCE);
1300 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1301 wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
1302 nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs, eatAll, nbv->grp[aloc].nbat, f);
1303 wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
1304 cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1305 wallcycle_start_nocount(wcycle, ewcFORCE);
1307 /* if there are multiple fshift output buffers reduce them */
1308 if ((flags & GMX_FORCE_VIRIAL) &&
1309 nbv->grp[aloc].nbl_lists.nnbl > 1)
1311 nbnxn_atomdata_add_nbat_fshift_to_fshift(nbv->grp[aloc].nbat,
1316 /* update QMMMrec, if necessary */
1319 update_QMMMrec(cr, fr, x, mdatoms, box, top);
1322 if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
1324 posres_wrapper(flags, inputrec, nrnb, top, box, x,
1328 if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_FBPOSRES].nr > 0)
1330 fbposres_wrapper(inputrec, nrnb, top, box, x, enerd, fr);
1333 /* Compute the bonded and non-bonded energies and optionally forces */
1334 do_force_lowlevel(fr, inputrec, &(top->idef),
1335 cr, nrnb, wcycle, mdatoms,
1336 x, hist, f, bSepLRF ? fr->f_twin : f, enerd, fcd, top, fr->born,
1338 inputrec->fepvals, lambda, graph, &(top->excls), fr->mu_tot,
1339 flags, &cycles_pme);
1343 if (do_per_step(step, inputrec->nstcalclr))
1345 /* Add the long range forces to the short range forces */
1346 for (i = 0; i < fr->natoms_force_constr; i++)
1348 rvec_add(fr->f_twin[i], f[i], f[i]);
1353 cycles_force += wallcycle_stop(wcycle, ewcFORCE);
1357 do_flood(cr, inputrec, x, f, ed, box, step, bNS);
1360 if (bUseOrEmulGPU && !bDiffKernels)
1362 /* wait for non-local forces (or calculate in emulation mode) */
1363 if (DOMAINDECOMP(cr))
1369 wallcycle_start(wcycle, ewcWAIT_GPU_NB_NL);
1370 nbnxn_cuda_wait_gpu(nbv->cu_nbv,
1371 nbv->grp[eintNonlocal].nbat,
1373 enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
1375 cycles_tmp = wallcycle_stop(wcycle, ewcWAIT_GPU_NB_NL);
1376 cycles_wait_gpu += cycles_tmp;
1377 cycles_force += cycles_tmp;
1381 wallcycle_start_nocount(wcycle, ewcFORCE);
1382 do_nb_verlet(fr, ic, enerd, flags, eintNonlocal, enbvClearFYes,
1384 cycles_force += wallcycle_stop(wcycle, ewcFORCE);
1386 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1387 wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
1388 /* skip the reduction if there was no non-local work to do */
1389 if (nbv->grp[eintLocal].nbl_lists.nbl[0]->nsci > 0)
1391 nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs, eatNonlocal,
1392 nbv->grp[eintNonlocal].nbat, f);
1394 wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
1395 cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1399 if (bDoForces && DOMAINDECOMP(cr))
1401 /* Communicate the forces */
1402 wallcycle_start(wcycle, ewcMOVEF);
1403 dd_move_f(cr->dd, f, fr->fshift);
1404 /* Do we need to communicate the separate force array
1405 * for terms that do not contribute to the single sum virial?
1406 * Position restraints and electric fields do not introduce
1407 * inter-cg forces, only full electrostatics methods do.
1408 * When we do not calculate the virial, fr->f_novirsum = f,
1409 * so we have already communicated these forces.
1411 if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl &&
1412 (flags & GMX_FORCE_VIRIAL))
1414 dd_move_f(cr->dd, fr->f_novirsum, NULL);
1418 /* We should not update the shift forces here,
1419 * since f_twin is already included in f.
1421 dd_move_f(cr->dd, fr->f_twin, NULL);
1423 wallcycle_stop(wcycle, ewcMOVEF);
1428 /* wait for local forces (or calculate in emulation mode) */
1431 wallcycle_start(wcycle, ewcWAIT_GPU_NB_L);
1432 nbnxn_cuda_wait_gpu(nbv->cu_nbv,
1433 nbv->grp[eintLocal].nbat,
1435 enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
1437 cycles_wait_gpu += wallcycle_stop(wcycle, ewcWAIT_GPU_NB_L);
1439 /* now clear the GPU outputs while we finish the step on the CPU */
1441 wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
1442 nbnxn_cuda_clear_outputs(nbv->cu_nbv, flags);
1443 wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
1447 wallcycle_start_nocount(wcycle, ewcFORCE);
1448 do_nb_verlet(fr, ic, enerd, flags, eintLocal,
1449 DOMAINDECOMP(cr) ? enbvClearFNo : enbvClearFYes,
1451 wallcycle_stop(wcycle, ewcFORCE);
1453 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1454 wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
1455 if (nbv->grp[eintLocal].nbl_lists.nbl[0]->nsci > 0)
1457 /* skip the reduction if there was no non-local work to do */
1458 nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs, eatLocal,
1459 nbv->grp[eintLocal].nbat, f);
1461 wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
1462 wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1465 if (DOMAINDECOMP(cr))
1467 dd_force_flop_stop(cr->dd, nrnb);
1470 dd_cycles_add(cr->dd, cycles_force-cycles_pme, ddCyclF);
1473 dd_cycles_add(cr->dd, cycles_wait_gpu, ddCyclWaitGPU);
1480 if (IR_ELEC_FIELD(*inputrec))
1482 /* Compute forces due to electric field */
1483 calc_f_el(MASTER(cr) ? field : NULL,
1484 start, homenr, mdatoms->chargeA, fr->f_novirsum,
1485 inputrec->ex, inputrec->et, t);
1488 /* If we have NoVirSum forces, but we do not calculate the virial,
1489 * we sum fr->f_novirum=f later.
1491 if (vsite && !(fr->bF_NoVirSum && !(flags & GMX_FORCE_VIRIAL)))
1493 wallcycle_start(wcycle, ewcVSITESPREAD);
1494 spread_vsite_f(vsite, x, f, fr->fshift, FALSE, NULL, nrnb,
1495 &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
1496 wallcycle_stop(wcycle, ewcVSITESPREAD);
1500 wallcycle_start(wcycle, ewcVSITESPREAD);
1501 spread_vsite_f(vsite, x, fr->f_twin, NULL, FALSE, NULL,
1503 &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
1504 wallcycle_stop(wcycle, ewcVSITESPREAD);
1508 if (flags & GMX_FORCE_VIRIAL)
1510 /* Calculation of the virial must be done after vsites! */
1511 calc_virial(0, mdatoms->homenr, x, f,
1512 vir_force, graph, box, nrnb, fr, inputrec->ePBC);
1516 if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
1518 /* Since the COM pulling is always done mass-weighted, no forces are
1519 * applied to vsites and this call can be done after vsite spreading.
1521 pull_potential_wrapper(cr, inputrec, box, x,
1522 f, vir_force, mdatoms, enerd, lambda, t,
1526 /* Add the forces from enforced rotation potentials (if any) */
1529 wallcycle_start(wcycle, ewcROTadd);
1530 enerd->term[F_COM_PULL] += add_rot_forces(inputrec->rot, f, cr, step, t);
1531 wallcycle_stop(wcycle, ewcROTadd);
1534 /* Add forces from interactive molecular dynamics (IMD), if bIMD == TRUE. */
1535 IMD_apply_forces(inputrec->bIMD, inputrec->imd, cr, f, wcycle);
1537 if (PAR(cr) && !(cr->duty & DUTY_PME))
1539 /* In case of node-splitting, the PP nodes receive the long-range
1540 * forces, virial and energy from the PME nodes here.
1542 pme_receive_force_ener(cr, wcycle, enerd, fr);
1547 post_process_forces(cr, step, nrnb, wcycle,
1548 top, box, x, f, vir_force, mdatoms, graph, fr, vsite,
1552 /* Sum the potential energy terms from group contributions */
1553 sum_epot(&(enerd->grpp), enerd->term);
1556 void do_force_cutsGROUP(FILE *fplog, t_commrec *cr,
1557 t_inputrec *inputrec,
1558 gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
1559 gmx_localtop_t *top,
1560 gmx_groups_t *groups,
1561 matrix box, rvec x[], history_t *hist,
1565 gmx_enerdata_t *enerd, t_fcdata *fcd,
1566 real *lambda, t_graph *graph,
1567 t_forcerec *fr, gmx_vsite_t *vsite, rvec mu_tot,
1568 double t, FILE *field, gmx_edsam_t ed,
1569 gmx_bool bBornRadii,
1575 gmx_bool bStateChanged, bNS, bFillGrid, bCalcCGCM, bBS;
1576 gmx_bool bDoLongRangeNS, bDoForces, bDoPotential, bSepLRF;
1577 gmx_bool bDoAdressWF;
1579 rvec vzero, box_diag;
1580 real e, v, dvdlambda[efptNR];
1582 float cycles_pme, cycles_force;
1585 homenr = mdatoms->homenr;
1587 clear_mat(vir_force);
1590 if (DOMAINDECOMP(cr))
1592 cg1 = cr->dd->ncg_tot;
1603 bStateChanged = (flags & GMX_FORCE_STATECHANGED);
1604 bNS = (flags & GMX_FORCE_NS) && (fr->bAllvsAll == FALSE);
1605 /* Should we update the long-range neighborlists at this step? */
1606 bDoLongRangeNS = fr->bTwinRange && bNS;
1607 /* Should we perform the long-range nonbonded evaluation inside the neighborsearching? */
1608 bFillGrid = (bNS && bStateChanged);
1609 bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
1610 bDoForces = (flags & GMX_FORCE_FORCES);
1611 bDoPotential = (flags & GMX_FORCE_ENERGY);
1612 bSepLRF = ((inputrec->nstcalclr > 1) && bDoForces &&
1613 (flags & GMX_FORCE_SEPLRF) && (flags & GMX_FORCE_DO_LR));
1615 /* should probably move this to the forcerec since it doesn't change */
1616 bDoAdressWF = ((fr->adress_type != eAdressOff));
1620 update_forcerec(fr, box);
1622 if (NEED_MUTOT(*inputrec))
1624 /* Calculate total (local) dipole moment in a temporary common array.
1625 * This makes it possible to sum them over nodes faster.
1627 calc_mu(start, homenr,
1628 x, mdatoms->chargeA, mdatoms->chargeB, mdatoms->nChargePerturbed,
1633 if (fr->ePBC != epbcNONE)
1635 /* Compute shift vectors every step,
1636 * because of pressure coupling or box deformation!
1638 if ((flags & GMX_FORCE_DYNAMICBOX) && bStateChanged)
1640 calc_shifts(box, fr->shift_vec);
1645 put_charge_groups_in_box(fplog, cg0, cg1, fr->ePBC, box,
1646 &(top->cgs), x, fr->cg_cm);
1647 inc_nrnb(nrnb, eNR_CGCM, homenr);
1648 inc_nrnb(nrnb, eNR_RESETX, cg1-cg0);
1650 else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph)
1652 unshift_self(graph, box, x);
1657 calc_cgcm(fplog, cg0, cg1, &(top->cgs), x, fr->cg_cm);
1658 inc_nrnb(nrnb, eNR_CGCM, homenr);
1661 if (bCalcCGCM && gmx_debug_at)
1663 pr_rvecs(debug, 0, "cgcm", fr->cg_cm, top->cgs.nr);
1667 if (!(cr->duty & DUTY_PME))
1669 /* Send particle coordinates to the pme nodes.
1670 * Since this is only implemented for domain decomposition
1671 * and domain decomposition does not use the graph,
1672 * we do not need to worry about shifting.
1677 wallcycle_start(wcycle, ewcPP_PMESENDX);
1679 bBS = (inputrec->nwall == 2);
1682 copy_mat(box, boxs);
1683 svmul(inputrec->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
1686 if (EEL_PME(fr->eeltype))
1688 pme_flags |= GMX_PME_DO_COULOMB;
1691 if (EVDW_PME(fr->vdwtype))
1693 pme_flags |= GMX_PME_DO_LJ;
1696 gmx_pme_send_coordinates(cr, bBS ? boxs : box, x,
1697 mdatoms->nChargePerturbed, mdatoms->nTypePerturbed, lambda[efptCOUL], lambda[efptVDW],
1698 (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY)),
1701 wallcycle_stop(wcycle, ewcPP_PMESENDX);
1703 #endif /* GMX_MPI */
1705 /* Communicate coordinates and sum dipole if necessary */
1706 if (DOMAINDECOMP(cr))
1708 wallcycle_start(wcycle, ewcMOVEX);
1709 dd_move_x(cr->dd, box, x);
1710 wallcycle_stop(wcycle, ewcMOVEX);
1713 /* update adress weight beforehand */
1714 if (bStateChanged && bDoAdressWF)
1716 /* need pbc for adress weight calculation with pbc_dx */
1717 set_pbc(&pbc, inputrec->ePBC, box);
1718 if (fr->adress_site == eAdressSITEcog)
1720 update_adress_weights_cog(top->idef.iparams, top->idef.il, x, fr, mdatoms,
1721 inputrec->ePBC == epbcNONE ? NULL : &pbc);
1723 else if (fr->adress_site == eAdressSITEcom)
1725 update_adress_weights_com(fplog, cg0, cg1, &(top->cgs), x, fr, mdatoms,
1726 inputrec->ePBC == epbcNONE ? NULL : &pbc);
1728 else if (fr->adress_site == eAdressSITEatomatom)
1730 update_adress_weights_atom_per_atom(cg0, cg1, &(top->cgs), x, fr, mdatoms,
1731 inputrec->ePBC == epbcNONE ? NULL : &pbc);
1735 update_adress_weights_atom(cg0, cg1, &(top->cgs), x, fr, mdatoms,
1736 inputrec->ePBC == epbcNONE ? NULL : &pbc);
1740 if (NEED_MUTOT(*inputrec))
1747 gmx_sumd(2*DIM, mu, cr);
1749 for (i = 0; i < 2; i++)
1751 for (j = 0; j < DIM; j++)
1753 fr->mu_tot[i][j] = mu[i*DIM + j];
1757 if (fr->efep == efepNO)
1759 copy_rvec(fr->mu_tot[0], mu_tot);
1763 for (j = 0; j < DIM; j++)
1766 (1.0 - lambda[efptCOUL])*fr->mu_tot[0][j] + lambda[efptCOUL]*fr->mu_tot[1][j];
1771 /* Reset energies */
1772 reset_enerdata(fr, bNS, enerd, MASTER(cr));
1773 clear_rvecs(SHIFTS, fr->fshift);
1777 wallcycle_start(wcycle, ewcNS);
1779 if (graph && bStateChanged)
1781 /* Calculate intramolecular shift vectors to make molecules whole */
1782 mk_mshift(fplog, graph, fr->ePBC, box, x);
1785 /* Do the actual neighbour searching */
1787 groups, top, mdatoms,
1788 cr, nrnb, bFillGrid,
1791 wallcycle_stop(wcycle, ewcNS);
1794 if (inputrec->implicit_solvent && bNS)
1796 make_gb_nblist(cr, inputrec->gb_algorithm,
1797 x, box, fr, &top->idef, graph, fr->born);
1800 if (DOMAINDECOMP(cr) && !(cr->duty & DUTY_PME))
1802 wallcycle_start(wcycle, ewcPPDURINGPME);
1803 dd_force_flop_start(cr->dd, nrnb);
1808 /* Enforced rotation has its own cycle counter that starts after the collective
1809 * coordinates have been communicated. It is added to ddCyclF to allow
1810 * for proper load-balancing */
1811 wallcycle_start(wcycle, ewcROT);
1812 do_rotation(cr, inputrec, box, x, t, step, wcycle, bNS);
1813 wallcycle_stop(wcycle, ewcROT);
1816 /* Start the force cycle counter.
1817 * This counter is stopped in do_forcelow_level.
1818 * No parallel communication should occur while this counter is running,
1819 * since that will interfere with the dynamic load balancing.
1821 wallcycle_start(wcycle, ewcFORCE);
1825 /* Reset forces for which the virial is calculated separately:
1826 * PME/Ewald forces if necessary */
1827 if (fr->bF_NoVirSum)
1829 if (flags & GMX_FORCE_VIRIAL)
1831 fr->f_novirsum = fr->f_novirsum_alloc;
1834 clear_rvecs(fr->f_novirsum_n, fr->f_novirsum);
1838 clear_rvecs(homenr, fr->f_novirsum+start);
1843 /* We are not calculating the pressure so we do not need
1844 * a separate array for forces that do not contribute
1851 /* Clear the short- and long-range forces */
1852 clear_rvecs(fr->natoms_force_constr, f);
1853 if (bSepLRF && do_per_step(step, inputrec->nstcalclr))
1855 clear_rvecs(fr->natoms_force_constr, fr->f_twin);
1858 clear_rvec(fr->vir_diag_posres);
1860 if (inputrec->ePull == epullCONSTRAINT)
1862 clear_pull_forces(inputrec->pull);
1865 /* update QMMMrec, if necessary */
1868 update_QMMMrec(cr, fr, x, mdatoms, box, top);
1871 if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
1873 posres_wrapper(flags, inputrec, nrnb, top, box, x,
1877 if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_FBPOSRES].nr > 0)
1879 fbposres_wrapper(inputrec, nrnb, top, box, x, enerd, fr);
1882 /* Compute the bonded and non-bonded energies and optionally forces */
1883 do_force_lowlevel(fr, inputrec, &(top->idef),
1884 cr, nrnb, wcycle, mdatoms,
1885 x, hist, f, bSepLRF ? fr->f_twin : f, enerd, fcd, top, fr->born,
1887 inputrec->fepvals, lambda,
1888 graph, &(top->excls), fr->mu_tot,
1894 if (do_per_step(step, inputrec->nstcalclr))
1896 /* Add the long range forces to the short range forces */
1897 for (i = 0; i < fr->natoms_force_constr; i++)
1899 rvec_add(fr->f_twin[i], f[i], f[i]);
1904 cycles_force = wallcycle_stop(wcycle, ewcFORCE);
1908 do_flood(cr, inputrec, x, f, ed, box, step, bNS);
1911 if (DOMAINDECOMP(cr))
1913 dd_force_flop_stop(cr->dd, nrnb);
1916 dd_cycles_add(cr->dd, cycles_force-cycles_pme, ddCyclF);
1922 if (IR_ELEC_FIELD(*inputrec))
1924 /* Compute forces due to electric field */
1925 calc_f_el(MASTER(cr) ? field : NULL,
1926 start, homenr, mdatoms->chargeA, fr->f_novirsum,
1927 inputrec->ex, inputrec->et, t);
1930 if (bDoAdressWF && fr->adress_icor == eAdressICThermoForce)
1932 /* Compute thermodynamic force in hybrid AdResS region */
1933 adress_thermo_force(start, homenr, &(top->cgs), x, fr->f_novirsum, fr, mdatoms,
1934 inputrec->ePBC == epbcNONE ? NULL : &pbc);
1937 /* Communicate the forces */
1938 if (DOMAINDECOMP(cr))
1940 wallcycle_start(wcycle, ewcMOVEF);
1941 dd_move_f(cr->dd, f, fr->fshift);
1942 /* Do we need to communicate the separate force array
1943 * for terms that do not contribute to the single sum virial?
1944 * Position restraints and electric fields do not introduce
1945 * inter-cg forces, only full electrostatics methods do.
1946 * When we do not calculate the virial, fr->f_novirsum = f,
1947 * so we have already communicated these forces.
1949 if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl &&
1950 (flags & GMX_FORCE_VIRIAL))
1952 dd_move_f(cr->dd, fr->f_novirsum, NULL);
1956 /* We should not update the shift forces here,
1957 * since f_twin is already included in f.
1959 dd_move_f(cr->dd, fr->f_twin, NULL);
1961 wallcycle_stop(wcycle, ewcMOVEF);
1964 /* If we have NoVirSum forces, but we do not calculate the virial,
1965 * we sum fr->f_novirum=f later.
1967 if (vsite && !(fr->bF_NoVirSum && !(flags & GMX_FORCE_VIRIAL)))
1969 wallcycle_start(wcycle, ewcVSITESPREAD);
1970 spread_vsite_f(vsite, x, f, fr->fshift, FALSE, NULL, nrnb,
1971 &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
1972 wallcycle_stop(wcycle, ewcVSITESPREAD);
1976 wallcycle_start(wcycle, ewcVSITESPREAD);
1977 spread_vsite_f(vsite, x, fr->f_twin, NULL, FALSE, NULL,
1979 &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
1980 wallcycle_stop(wcycle, ewcVSITESPREAD);
1984 if (flags & GMX_FORCE_VIRIAL)
1986 /* Calculation of the virial must be done after vsites! */
1987 calc_virial(0, mdatoms->homenr, x, f,
1988 vir_force, graph, box, nrnb, fr, inputrec->ePBC);
1992 if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
1994 pull_potential_wrapper(cr, inputrec, box, x,
1995 f, vir_force, mdatoms, enerd, lambda, t,
1999 /* Add the forces from enforced rotation potentials (if any) */
2002 wallcycle_start(wcycle, ewcROTadd);
2003 enerd->term[F_COM_PULL] += add_rot_forces(inputrec->rot, f, cr, step, t);
2004 wallcycle_stop(wcycle, ewcROTadd);
2007 /* Add forces from interactive molecular dynamics (IMD), if bIMD == TRUE. */
2008 IMD_apply_forces(inputrec->bIMD, inputrec->imd, cr, f, wcycle);
2010 if (PAR(cr) && !(cr->duty & DUTY_PME))
2012 /* In case of node-splitting, the PP nodes receive the long-range
2013 * forces, virial and energy from the PME nodes here.
2015 pme_receive_force_ener(cr, wcycle, enerd, fr);
2020 post_process_forces(cr, step, nrnb, wcycle,
2021 top, box, x, f, vir_force, mdatoms, graph, fr, vsite,
2025 /* Sum the potential energy terms from group contributions */
2026 sum_epot(&(enerd->grpp), enerd->term);
2029 void do_force(FILE *fplog, t_commrec *cr,
2030 t_inputrec *inputrec,
2031 gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
2032 gmx_localtop_t *top,
2033 gmx_groups_t *groups,
2034 matrix box, rvec x[], history_t *hist,
2038 gmx_enerdata_t *enerd, t_fcdata *fcd,
2039 real *lambda, t_graph *graph,
2041 gmx_vsite_t *vsite, rvec mu_tot,
2042 double t, FILE *field, gmx_edsam_t ed,
2043 gmx_bool bBornRadii,
2046 /* modify force flag if not doing nonbonded */
2047 if (!fr->bNonbonded)
2049 flags &= ~GMX_FORCE_NONBONDED;
2052 switch (inputrec->cutoff_scheme)
2055 do_force_cutsVERLET(fplog, cr, inputrec,
2071 do_force_cutsGROUP(fplog, cr, inputrec,
2086 gmx_incons("Invalid cut-off scheme passed!");
2091 void do_constrain_first(FILE *fplog, gmx_constr_t constr,
2092 t_inputrec *ir, t_mdatoms *md,
2093 t_state *state, t_commrec *cr, t_nrnb *nrnb,
2094 t_forcerec *fr, gmx_localtop_t *top)
2096 int i, m, start, end;
2098 real dt = ir->delta_t;
2102 snew(savex, state->natoms);
2109 fprintf(debug, "vcm: start=%d, homenr=%d, end=%d\n",
2110 start, md->homenr, end);
2112 /* Do a first constrain to reset particles... */
2113 step = ir->init_step;
2116 char buf[STEPSTRSIZE];
2117 fprintf(fplog, "\nConstraining the starting coordinates (step %s)\n",
2118 gmx_step_str(step, buf));
2122 /* constrain the current position */
2123 constrain(NULL, TRUE, FALSE, constr, &(top->idef),
2124 ir, NULL, cr, step, 0, 1.0, md,
2125 state->x, state->x, NULL,
2126 fr->bMolPBC, state->box,
2127 state->lambda[efptBONDED], &dvdl_dum,
2128 NULL, NULL, nrnb, econqCoord,
2129 ir->epc == epcMTTK, state->veta, state->veta);
2132 /* constrain the inital velocity, and save it */
2133 /* also may be useful if we need the ekin from the halfstep for velocity verlet */
2134 /* might not yet treat veta correctly */
2135 constrain(NULL, TRUE, FALSE, constr, &(top->idef),
2136 ir, NULL, cr, step, 0, 1.0, md,
2137 state->x, state->v, state->v,
2138 fr->bMolPBC, state->box,
2139 state->lambda[efptBONDED], &dvdl_dum,
2140 NULL, NULL, nrnb, econqVeloc,
2141 ir->epc == epcMTTK, state->veta, state->veta);
2143 /* constrain the inital velocities at t-dt/2 */
2144 if (EI_STATE_VELOCITY(ir->eI) && ir->eI != eiVV)
2146 for (i = start; (i < end); i++)
2148 for (m = 0; (m < DIM); m++)
2150 /* Reverse the velocity */
2151 state->v[i][m] = -state->v[i][m];
2152 /* Store the position at t-dt in buf */
2153 savex[i][m] = state->x[i][m] + dt*state->v[i][m];
2156 /* Shake the positions at t=-dt with the positions at t=0
2157 * as reference coordinates.
2161 char buf[STEPSTRSIZE];
2162 fprintf(fplog, "\nConstraining the coordinates at t0-dt (step %s)\n",
2163 gmx_step_str(step, buf));
2166 constrain(NULL, TRUE, FALSE, constr, &(top->idef),
2167 ir, NULL, cr, step, -1, 1.0, md,
2168 state->x, savex, NULL,
2169 fr->bMolPBC, state->box,
2170 state->lambda[efptBONDED], &dvdl_dum,
2171 state->v, NULL, nrnb, econqCoord,
2172 ir->epc == epcMTTK, state->veta, state->veta);
2174 for (i = start; i < end; i++)
2176 for (m = 0; m < DIM; m++)
2178 /* Re-reverse the velocities */
2179 state->v[i][m] = -state->v[i][m];
2188 integrate_table(real vdwtab[], real scale, int offstart, int rstart, int rend,
2189 double *enerout, double *virout)
2191 double enersum, virsum;
2192 double invscale, invscale2, invscale3;
2193 double r, ea, eb, ec, pa, pb, pc, pd;
2195 int ri, offset, tabfactor;
2197 invscale = 1.0/scale;
2198 invscale2 = invscale*invscale;
2199 invscale3 = invscale*invscale2;
2201 /* Following summation derived from cubic spline definition,
2202 * Numerical Recipies in C, second edition, p. 113-116. Exact for
2203 * the cubic spline. We first calculate the negative of the
2204 * energy from rvdw to rvdw_switch, assuming that g(r)=1, and then
2205 * add the more standard, abrupt cutoff correction to that result,
2206 * yielding the long-range correction for a switched function. We
2207 * perform both the pressure and energy loops at the same time for
2208 * simplicity, as the computational cost is low. */
2212 /* Since the dispersion table has been scaled down a factor
2213 * 6.0 and the repulsion a factor 12.0 to compensate for the
2214 * c6/c12 parameters inside nbfp[] being scaled up (to save
2215 * flops in kernels), we need to correct for this.
2226 for (ri = rstart; ri < rend; ++ri)
2230 eb = 2.0*invscale2*r;
2234 pb = 3.0*invscale2*r;
2235 pc = 3.0*invscale*r*r;
2238 /* this "8" is from the packing in the vdwtab array - perhaps
2239 should be defined? */
2241 offset = 8*ri + offstart;
2242 y0 = vdwtab[offset];
2243 f = vdwtab[offset+1];
2244 g = vdwtab[offset+2];
2245 h = vdwtab[offset+3];
2247 enersum += y0*(ea/3 + eb/2 + ec) + f*(ea/4 + eb/3 + ec/2) + g*(ea/5 + eb/4 + ec/3) + h*(ea/6 + eb/5 + ec/4);
2248 virsum += f*(pa/4 + pb/3 + pc/2 + pd) + 2*g*(pa/5 + pb/4 + pc/3 + pd/2) + 3*h*(pa/6 + pb/5 + pc/4 + pd/3);
2250 *enerout = 4.0*M_PI*enersum*tabfactor;
2251 *virout = 4.0*M_PI*virsum*tabfactor;
2254 void calc_enervirdiff(FILE *fplog, int eDispCorr, t_forcerec *fr)
2256 double eners[2], virs[2], enersum, virsum, y0, f, g, h;
2257 double r0, r1, r, rc3, rc9, ea, eb, ec, pa, pb, pc, pd;
2258 double invscale, invscale2, invscale3;
2259 int ri0, ri1, ri, i, offstart, offset;
2260 real scale, *vdwtab, tabfactor, tmp;
2262 fr->enershiftsix = 0;
2263 fr->enershifttwelve = 0;
2264 fr->enerdiffsix = 0;
2265 fr->enerdifftwelve = 0;
2267 fr->virdifftwelve = 0;
2269 if (eDispCorr != edispcNO)
2271 for (i = 0; i < 2; i++)
2276 if ((fr->vdw_modifier == eintmodPOTSHIFT) ||
2277 (fr->vdw_modifier == eintmodPOTSWITCH) ||
2278 (fr->vdw_modifier == eintmodFORCESWITCH) ||
2279 (fr->vdwtype == evdwSHIFT) ||
2280 (fr->vdwtype == evdwSWITCH))
2282 if (((fr->vdw_modifier == eintmodPOTSWITCH) ||
2283 (fr->vdw_modifier == eintmodFORCESWITCH) ||
2284 (fr->vdwtype == evdwSWITCH)) && fr->rvdw_switch == 0)
2287 "With dispersion correction rvdw-switch can not be zero "
2288 "for vdw-type = %s", evdw_names[fr->vdwtype]);
2291 scale = fr->nblists[0].table_vdw.scale;
2292 vdwtab = fr->nblists[0].table_vdw.data;
2294 /* Round the cut-offs to exact table values for precision */
2295 ri0 = floor(fr->rvdw_switch*scale);
2296 ri1 = ceil(fr->rvdw*scale);
2298 /* The code below has some support for handling force-switching, i.e.
2299 * when the force (instead of potential) is switched over a limited
2300 * region. This leads to a constant shift in the potential inside the
2301 * switching region, which we can handle by adding a constant energy
2302 * term in the force-switch case just like when we do potential-shift.
2304 * For now this is not enabled, but to keep the functionality in the
2305 * code we check separately for switch and shift. When we do force-switch
2306 * the shifting point is rvdw_switch, while it is the cutoff when we
2307 * have a classical potential-shift.
2309 * For a pure potential-shift the potential has a constant shift
2310 * all the way out to the cutoff, and that is it. For other forms
2311 * we need to calculate the constant shift up to the point where we
2312 * start modifying the potential.
2314 ri0 = (fr->vdw_modifier == eintmodPOTSHIFT) ? ri1 : ri0;
2321 if ((fr->vdw_modifier == eintmodFORCESWITCH) ||
2322 (fr->vdwtype == evdwSHIFT))
2324 /* Determine the constant energy shift below rvdw_switch.
2325 * Table has a scale factor since we have scaled it down to compensate
2326 * for scaling-up c6/c12 with the derivative factors to save flops in analytical kernels.
2328 fr->enershiftsix = (real)(-1.0/(rc3*rc3)) - 6.0*vdwtab[8*ri0];
2329 fr->enershifttwelve = (real)( 1.0/(rc9*rc3)) - 12.0*vdwtab[8*ri0 + 4];
2331 else if (fr->vdw_modifier == eintmodPOTSHIFT)
2333 fr->enershiftsix = (real)(-1.0/(rc3*rc3));
2334 fr->enershifttwelve = (real)( 1.0/(rc9*rc3));
2337 /* Add the constant part from 0 to rvdw_switch.
2338 * This integration from 0 to rvdw_switch overcounts the number
2339 * of interactions by 1, as it also counts the self interaction.
2340 * We will correct for this later.
2342 eners[0] += 4.0*M_PI*fr->enershiftsix*rc3/3.0;
2343 eners[1] += 4.0*M_PI*fr->enershifttwelve*rc3/3.0;
2345 /* Calculate the contribution in the range [r0,r1] where we
2346 * modify the potential. For a pure potential-shift modifier we will
2347 * have ri0==ri1, and there will not be any contribution here.
2349 for (i = 0; i < 2; i++)
2353 integrate_table(vdwtab, scale, (i == 0 ? 0 : 4), ri0, ri1, &enersum, &virsum);
2354 eners[i] -= enersum;
2358 /* Alright: Above we compensated by REMOVING the parts outside r0
2359 * corresponding to the ideal VdW 1/r6 and /r12 potentials.
2361 * Regardless of whether r0 is the point where we start switching,
2362 * or the cutoff where we calculated the constant shift, we include
2363 * all the parts we are missing out to infinity from r0 by
2364 * calculating the analytical dispersion correction.
2366 eners[0] += -4.0*M_PI/(3.0*rc3);
2367 eners[1] += 4.0*M_PI/(9.0*rc9);
2368 virs[0] += 8.0*M_PI/rc3;
2369 virs[1] += -16.0*M_PI/(3.0*rc9);
2371 else if (fr->vdwtype == evdwCUT ||
2372 EVDW_PME(fr->vdwtype) ||
2373 fr->vdwtype == evdwUSER)
2375 if (fr->vdwtype == evdwUSER && fplog)
2378 "WARNING: using dispersion correction with user tables\n");
2381 /* Note that with LJ-PME, the dispersion correction is multiplied
2382 * by the difference between the actual C6 and the value of C6
2383 * that would produce the combination rule.
2384 * This means the normal energy and virial difference formulas
2388 rc3 = fr->rvdw*fr->rvdw*fr->rvdw;
2390 /* Contribution beyond the cut-off */
2391 eners[0] += -4.0*M_PI/(3.0*rc3);
2392 eners[1] += 4.0*M_PI/(9.0*rc9);
2393 if (fr->vdw_modifier == eintmodPOTSHIFT)
2395 /* Contribution within the cut-off */
2396 eners[0] += -4.0*M_PI/(3.0*rc3);
2397 eners[1] += 4.0*M_PI/(3.0*rc9);
2399 /* Contribution beyond the cut-off */
2400 virs[0] += 8.0*M_PI/rc3;
2401 virs[1] += -16.0*M_PI/(3.0*rc9);
2406 "Dispersion correction is not implemented for vdw-type = %s",
2407 evdw_names[fr->vdwtype]);
2410 /* When we deprecate the group kernels the code below can go too */
2411 if (fr->vdwtype == evdwPME && fr->cutoff_scheme == ecutsGROUP)
2413 /* Calculate self-interaction coefficient (assuming that
2414 * the reciprocal-space contribution is constant in the
2415 * region that contributes to the self-interaction).
2417 fr->enershiftsix = pow(fr->ewaldcoeff_lj, 6) / 6.0;
2419 eners[0] += -pow(sqrt(M_PI)*fr->ewaldcoeff_lj, 3)/3.0;
2420 virs[0] += pow(sqrt(M_PI)*fr->ewaldcoeff_lj, 3);
2423 fr->enerdiffsix = eners[0];
2424 fr->enerdifftwelve = eners[1];
2425 /* The 0.5 is due to the Gromacs definition of the virial */
2426 fr->virdiffsix = 0.5*virs[0];
2427 fr->virdifftwelve = 0.5*virs[1];
2431 void calc_dispcorr(t_inputrec *ir, t_forcerec *fr,
2433 matrix box, real lambda, tensor pres, tensor virial,
2434 real *prescorr, real *enercorr, real *dvdlcorr)
2436 gmx_bool bCorrAll, bCorrPres;
2437 real dvdlambda, invvol, dens, ninter, avcsix, avctwelve, enerdiff, svir = 0, spres = 0;
2447 if (ir->eDispCorr != edispcNO)
2449 bCorrAll = (ir->eDispCorr == edispcAllEner ||
2450 ir->eDispCorr == edispcAllEnerPres);
2451 bCorrPres = (ir->eDispCorr == edispcEnerPres ||
2452 ir->eDispCorr == edispcAllEnerPres);
2454 invvol = 1/det(box);
2457 /* Only correct for the interactions with the inserted molecule */
2458 dens = (natoms - fr->n_tpi)*invvol;
2463 dens = natoms*invvol;
2464 ninter = 0.5*natoms;
2467 if (ir->efep == efepNO)
2469 avcsix = fr->avcsix[0];
2470 avctwelve = fr->avctwelve[0];
2474 avcsix = (1 - lambda)*fr->avcsix[0] + lambda*fr->avcsix[1];
2475 avctwelve = (1 - lambda)*fr->avctwelve[0] + lambda*fr->avctwelve[1];
2478 enerdiff = ninter*(dens*fr->enerdiffsix - fr->enershiftsix);
2479 *enercorr += avcsix*enerdiff;
2481 if (ir->efep != efepNO)
2483 dvdlambda += (fr->avcsix[1] - fr->avcsix[0])*enerdiff;
2487 enerdiff = ninter*(dens*fr->enerdifftwelve - fr->enershifttwelve);
2488 *enercorr += avctwelve*enerdiff;
2489 if (fr->efep != efepNO)
2491 dvdlambda += (fr->avctwelve[1] - fr->avctwelve[0])*enerdiff;
2497 svir = ninter*dens*avcsix*fr->virdiffsix/3.0;
2498 if (ir->eDispCorr == edispcAllEnerPres)
2500 svir += ninter*dens*avctwelve*fr->virdifftwelve/3.0;
2502 /* The factor 2 is because of the Gromacs virial definition */
2503 spres = -2.0*invvol*svir*PRESFAC;
2505 for (m = 0; m < DIM; m++)
2507 virial[m][m] += svir;
2508 pres[m][m] += spres;
2513 /* Can't currently control when it prints, for now, just print when degugging */
2518 fprintf(debug, "Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
2524 "Long Range LJ corr.: Epot %10g, Pres: %10g, Vir: %10g\n",
2525 *enercorr, spres, svir);
2529 fprintf(debug, "Long Range LJ corr.: Epot %10g\n", *enercorr);
2533 if (fr->efep != efepNO)
2535 *dvdlcorr += dvdlambda;
2540 void do_pbc_first(FILE *fplog, matrix box, t_forcerec *fr,
2541 t_graph *graph, rvec x[])
2545 fprintf(fplog, "Removing pbc first time\n");
2547 calc_shifts(box, fr->shift_vec);
2550 mk_mshift(fplog, graph, fr->ePBC, box, x);
2553 p_graph(debug, "do_pbc_first 1", graph);
2555 shift_self(graph, box, x);
2556 /* By doing an extra mk_mshift the molecules that are broken
2557 * because they were e.g. imported from another software
2558 * will be made whole again. Such are the healing powers
2561 mk_mshift(fplog, graph, fr->ePBC, box, x);
2564 p_graph(debug, "do_pbc_first 2", graph);
2569 fprintf(fplog, "Done rmpbc\n");
2573 static void low_do_pbc_mtop(FILE *fplog, int ePBC, matrix box,
2574 gmx_mtop_t *mtop, rvec x[],
2579 gmx_molblock_t *molb;
2581 if (bFirst && fplog)
2583 fprintf(fplog, "Removing pbc first time\n");
2588 for (mb = 0; mb < mtop->nmolblock; mb++)
2590 molb = &mtop->molblock[mb];
2591 if (molb->natoms_mol == 1 ||
2592 (!bFirst && mtop->moltype[molb->type].cgs.nr == 1))
2594 /* Just one atom or charge group in the molecule, no PBC required */
2595 as += molb->nmol*molb->natoms_mol;
2599 /* Pass NULL iso fplog to avoid graph prints for each molecule type */
2600 mk_graph_ilist(NULL, mtop->moltype[molb->type].ilist,
2601 0, molb->natoms_mol, FALSE, FALSE, graph);
2603 for (mol = 0; mol < molb->nmol; mol++)
2605 mk_mshift(fplog, graph, ePBC, box, x+as);
2607 shift_self(graph, box, x+as);
2608 /* The molecule is whole now.
2609 * We don't need the second mk_mshift call as in do_pbc_first,
2610 * since we no longer need this graph.
2613 as += molb->natoms_mol;
2621 void do_pbc_first_mtop(FILE *fplog, int ePBC, matrix box,
2622 gmx_mtop_t *mtop, rvec x[])
2624 low_do_pbc_mtop(fplog, ePBC, box, mtop, x, TRUE);
2627 void do_pbc_mtop(FILE *fplog, int ePBC, matrix box,
2628 gmx_mtop_t *mtop, rvec x[])
2630 low_do_pbc_mtop(fplog, ePBC, box, mtop, x, FALSE);
2633 void finish_run(FILE *fplog, t_commrec *cr,
2634 t_inputrec *inputrec,
2635 t_nrnb nrnb[], gmx_wallcycle_t wcycle,
2636 gmx_walltime_accounting_t walltime_accounting,
2637 nonbonded_verlet_t *nbv,
2638 gmx_bool bWriteStat)
2641 t_nrnb *nrnb_tot = NULL;
2644 double elapsed_time,
2645 elapsed_time_over_all_ranks,
2646 elapsed_time_over_all_threads,
2647 elapsed_time_over_all_threads_over_all_ranks;
2648 wallcycle_sum(cr, wcycle);
2654 MPI_Allreduce(nrnb->n, nrnb_tot->n, eNRNB, MPI_DOUBLE, MPI_SUM,
2655 cr->mpi_comm_mysim);
2663 elapsed_time = walltime_accounting_get_elapsed_time(walltime_accounting);
2664 elapsed_time_over_all_ranks = elapsed_time;
2665 elapsed_time_over_all_threads = walltime_accounting_get_elapsed_time_over_all_threads(walltime_accounting);
2666 elapsed_time_over_all_threads_over_all_ranks = elapsed_time_over_all_threads;
2670 /* reduce elapsed_time over all MPI ranks in the current simulation */
2671 MPI_Allreduce(&elapsed_time,
2672 &elapsed_time_over_all_ranks,
2673 1, MPI_DOUBLE, MPI_SUM,
2674 cr->mpi_comm_mysim);
2675 elapsed_time_over_all_ranks /= cr->nnodes;
2676 /* Reduce elapsed_time_over_all_threads over all MPI ranks in the
2677 * current simulation. */
2678 MPI_Allreduce(&elapsed_time_over_all_threads,
2679 &elapsed_time_over_all_threads_over_all_ranks,
2680 1, MPI_DOUBLE, MPI_SUM,
2681 cr->mpi_comm_mysim);
2687 print_flop(fplog, nrnb_tot, &nbfs, &mflop);
2694 if ((cr->duty & DUTY_PP) && DOMAINDECOMP(cr))
2696 print_dd_statistics(cr, inputrec, fplog);
2701 wallclock_gpu_t* gputimes = use_GPU(nbv) ?
2702 nbnxn_cuda_get_timings(nbv->cu_nbv) : NULL;
2703 wallcycle_print(fplog, cr->nnodes, cr->npmenodes,
2704 elapsed_time_over_all_ranks,
2707 if (EI_DYNAMICS(inputrec->eI))
2709 delta_t = inputrec->delta_t;
2718 print_perf(fplog, elapsed_time_over_all_threads_over_all_ranks,
2719 elapsed_time_over_all_ranks,
2720 walltime_accounting_get_nsteps_done(walltime_accounting),
2721 delta_t, nbfs, mflop);
2725 print_perf(stderr, elapsed_time_over_all_threads_over_all_ranks,
2726 elapsed_time_over_all_ranks,
2727 walltime_accounting_get_nsteps_done(walltime_accounting),
2728 delta_t, nbfs, mflop);
2733 extern void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, real *lambda, double *lam0)
2735 /* this function works, but could probably use a logic rewrite to keep all the different
2736 types of efep straight. */
2739 t_lambda *fep = ir->fepvals;
2741 if ((ir->efep == efepNO) && (ir->bSimTemp == FALSE))
2743 for (i = 0; i < efptNR; i++)
2755 *fep_state = fep->init_fep_state; /* this might overwrite the checkpoint
2756 if checkpoint is set -- a kludge is in for now
2758 for (i = 0; i < efptNR; i++)
2760 /* overwrite lambda state with init_lambda for now for backwards compatibility */
2761 if (fep->init_lambda >= 0) /* if it's -1, it was never initializd */
2763 lambda[i] = fep->init_lambda;
2766 lam0[i] = lambda[i];
2771 lambda[i] = fep->all_lambda[i][*fep_state];
2774 lam0[i] = lambda[i];
2780 /* need to rescale control temperatures to match current state */
2781 for (i = 0; i < ir->opts.ngtc; i++)
2783 if (ir->opts.ref_t[i] > 0)
2785 ir->opts.ref_t[i] = ir->simtempvals->temperatures[*fep_state];
2791 /* Send to the log the information on the current lambdas */
2794 fprintf(fplog, "Initial vector of lambda components:[ ");
2795 for (i = 0; i < efptNR; i++)
2797 fprintf(fplog, "%10.4f ", lambda[i]);
2799 fprintf(fplog, "]\n");
2805 void init_md(FILE *fplog,
2806 t_commrec *cr, t_inputrec *ir, const output_env_t oenv,
2807 double *t, double *t0,
2808 real *lambda, int *fep_state, double *lam0,
2809 t_nrnb *nrnb, gmx_mtop_t *mtop,
2811 int nfile, const t_filenm fnm[],
2812 gmx_mdoutf_t *outf, t_mdebin **mdebin,
2813 tensor force_vir, tensor shake_vir, rvec mu_tot,
2814 gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags,
2815 gmx_wallcycle_t wcycle)
2820 /* Initial values */
2821 *t = *t0 = ir->init_t;
2824 for (i = 0; i < ir->opts.ngtc; i++)
2826 /* set bSimAnn if any group is being annealed */
2827 if (ir->opts.annealing[i] != eannNO)
2834 update_annealing_target_temp(&(ir->opts), ir->init_t);
2837 /* Initialize lambda variables */
2838 initialize_lambdas(fplog, ir, fep_state, lambda, lam0);
2842 *upd = init_update(ir);
2848 *vcm = init_vcm(fplog, &mtop->groups, ir);
2851 if (EI_DYNAMICS(ir->eI) && !(Flags & MD_APPENDFILES))
2853 if (ir->etc == etcBERENDSEN)
2855 please_cite(fplog, "Berendsen84a");
2857 if (ir->etc == etcVRESCALE)
2859 please_cite(fplog, "Bussi2007a");
2861 if (ir->eI == eiSD1)
2863 please_cite(fplog, "Goga2012");
2871 *outf = init_mdoutf(fplog, nfile, fnm, Flags, cr, ir, mtop, oenv, wcycle);
2873 *mdebin = init_mdebin((Flags & MD_APPENDFILES) ? NULL : mdoutf_get_fp_ene(*outf),
2874 mtop, ir, mdoutf_get_fp_dhdl(*outf));
2879 please_cite(fplog, "Fritsch12");
2880 please_cite(fplog, "Junghans10");
2882 /* Initiate variables */
2883 clear_mat(force_vir);
2884 clear_mat(shake_vir);