2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
45 #ifdef HAVE_SYS_TIME_H
50 #include "gromacs/utility/cstringutil.h"
51 #include "gromacs/utility/smalloc.h"
55 #include "chargegroup.h"
77 #include "nbnxn_atomdata.h"
78 #include "nbnxn_search.h"
79 #include "nbnxn_kernels/nbnxn_kernel_ref.h"
80 #include "nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
81 #include "nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
82 #include "nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
83 #include "nonbonded.h"
84 #include "../gmxlib/nonbonded/nb_kernel.h"
85 #include "../gmxlib/nonbonded/nb_free_energy.h"
87 #include "gromacs/timing/wallcycle.h"
88 #include "gromacs/timing/walltime_accounting.h"
89 #include "gromacs/utility/gmxmpi.h"
90 #include "gromacs/essentialdynamics/edsam.h"
91 #include "gromacs/pulling/pull.h"
92 #include "gromacs/pulling/pull_rotation.h"
93 #include "gromacs/imd/imd.h"
97 #include "gmx_omp_nthreads.h"
99 #include "nbnxn_cuda_data_mgmt.h"
100 #include "nbnxn_cuda/nbnxn_cuda.h"
102 void print_time(FILE *out,
103 gmx_walltime_accounting_t walltime_accounting,
106 t_commrec gmx_unused *cr)
109 char timebuf[STRLEN];
110 double dt, elapsed_seconds, time_per_step;
113 #ifndef GMX_THREAD_MPI
119 fprintf(out, "step %s", gmx_step_str(step, buf));
120 if ((step >= ir->nstlist))
122 double seconds_since_epoch = gmx_gettime();
123 elapsed_seconds = seconds_since_epoch - walltime_accounting_get_start_time_stamp(walltime_accounting);
124 time_per_step = elapsed_seconds/(step - ir->init_step + 1);
125 dt = (ir->nsteps + ir->init_step - step) * time_per_step;
131 finish = (time_t) (seconds_since_epoch + dt);
132 gmx_ctime_r(&finish, timebuf, STRLEN);
133 sprintf(buf, "%s", timebuf);
134 buf[strlen(buf)-1] = '\0';
135 fprintf(out, ", will finish %s", buf);
139 fprintf(out, ", remaining wall clock time: %5d s ", (int)dt);
144 fprintf(out, " performance: %.1f ns/day ",
145 ir->delta_t/1000*24*60*60/time_per_step);
148 #ifndef GMX_THREAD_MPI
158 void print_date_and_time(FILE *fplog, int nodeid, const char *title,
161 char time_string[STRLEN];
170 char timebuf[STRLEN];
171 time_t temp_time = (time_t) the_time;
173 gmx_ctime_r(&temp_time, timebuf, STRLEN);
174 for (i = 0; timebuf[i] >= ' '; i++)
176 time_string[i] = timebuf[i];
178 time_string[i] = '\0';
181 fprintf(fplog, "%s on rank %d %s\n", title, nodeid, time_string);
184 void print_start(FILE *fplog, t_commrec *cr,
185 gmx_walltime_accounting_t walltime_accounting,
190 sprintf(buf, "Started %s", name);
191 print_date_and_time(fplog, cr->nodeid, buf,
192 walltime_accounting_get_start_time_stamp(walltime_accounting));
195 static void sum_forces(int start, int end, rvec f[], rvec flr[])
201 pr_rvecs(debug, 0, "fsr", f+start, end-start);
202 pr_rvecs(debug, 0, "flr", flr+start, end-start);
204 for (i = start; (i < end); i++)
206 rvec_inc(f[i], flr[i]);
211 * calc_f_el calculates forces due to an electric field.
213 * force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e
215 * Et[] contains the parameters for the time dependent
216 * part of the field (not yet used).
217 * Ex[] contains the parameters for
218 * the spatial dependent part of the field. You can have cool periodic
219 * fields in principle, but only a constant field is supported
221 * The function should return the energy due to the electric field
222 * (if any) but for now returns 0.
225 * There can be problems with the virial.
226 * Since the field is not self-consistent this is unavoidable.
227 * For neutral molecules the virial is correct within this approximation.
228 * For neutral systems with many charged molecules the error is small.
229 * But for systems with a net charge or a few charged molecules
230 * the error can be significant when the field is high.
231 * Solution: implement a self-consitent electric field into PME.
233 static void calc_f_el(FILE *fp, int start, int homenr,
234 real charge[], rvec f[],
235 t_cosines Ex[], t_cosines Et[], double t)
241 for (m = 0; (m < DIM); m++)
248 Ext[m] = cos(Et[m].a[0]*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(Et[m].a[2])));
252 Ext[m] = cos(Et[m].a[0]*t);
261 /* Convert the field strength from V/nm to MD-units */
262 Ext[m] *= Ex[m].a[0]*FIELDFAC;
263 for (i = start; (i < start+homenr); i++)
265 f[i][m] += charge[i]*Ext[m];
275 fprintf(fp, "%10g %10g %10g %10g #FIELD\n", t,
276 Ext[XX]/FIELDFAC, Ext[YY]/FIELDFAC, Ext[ZZ]/FIELDFAC);
280 static void calc_virial(int start, int homenr, rvec x[], rvec f[],
281 tensor vir_part, t_graph *graph, matrix box,
282 t_nrnb *nrnb, const t_forcerec *fr, int ePBC)
287 /* The short-range virial from surrounding boxes */
289 calc_vir(SHIFTS, fr->shift_vec, fr->fshift, vir_part, ePBC == epbcSCREW, box);
290 inc_nrnb(nrnb, eNR_VIRIAL, SHIFTS);
292 /* Calculate partial virial, for local atoms only, based on short range.
293 * Total virial is computed in global_stat, called from do_md
295 f_calc_vir(start, start+homenr, x, f, vir_part, graph, box);
296 inc_nrnb(nrnb, eNR_VIRIAL, homenr);
298 /* Add position restraint contribution */
299 for (i = 0; i < DIM; i++)
301 vir_part[i][i] += fr->vir_diag_posres[i];
304 /* Add wall contribution */
305 for (i = 0; i < DIM; i++)
307 vir_part[i][ZZ] += fr->vir_wall_z[i];
312 pr_rvecs(debug, 0, "vir_part", vir_part, DIM);
316 static void posres_wrapper(FILE *fplog,
322 matrix box, rvec x[],
323 gmx_enerdata_t *enerd,
331 /* Position restraints always require full pbc */
332 set_pbc(&pbc, ir->ePBC, box);
334 v = posres(top->idef.il[F_POSRES].nr, top->idef.il[F_POSRES].iatoms,
335 top->idef.iparams_posres,
336 (const rvec*)x, fr->f_novirsum, fr->vir_diag_posres,
337 ir->ePBC == epbcNONE ? NULL : &pbc,
338 lambda[efptRESTRAINT], &dvdl,
339 fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
342 gmx_print_sepdvdl(fplog, interaction_function[F_POSRES].longname, v, dvdl);
344 enerd->term[F_POSRES] += v;
345 /* If just the force constant changes, the FEP term is linear,
346 * but if k changes, it is not.
348 enerd->dvdl_nonlin[efptRESTRAINT] += dvdl;
349 inc_nrnb(nrnb, eNR_POSRES, top->idef.il[F_POSRES].nr/2);
351 if ((ir->fepvals->n_lambda > 0) && (flags & GMX_FORCE_DHDL))
353 for (i = 0; i < enerd->n_lambda; i++)
355 real dvdl_dum, lambda_dum;
357 lambda_dum = (i == 0 ? lambda[efptRESTRAINT] : ir->fepvals->all_lambda[efptRESTRAINT][i-1]);
358 v = posres(top->idef.il[F_POSRES].nr, top->idef.il[F_POSRES].iatoms,
359 top->idef.iparams_posres,
360 (const rvec*)x, NULL, NULL,
361 ir->ePBC == epbcNONE ? NULL : &pbc, lambda_dum, &dvdl,
362 fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
363 enerd->enerpart_lambda[i] += v;
368 static void fbposres_wrapper(t_inputrec *ir,
371 matrix box, rvec x[],
372 gmx_enerdata_t *enerd,
378 /* Flat-bottomed position restraints always require full pbc */
379 set_pbc(&pbc, ir->ePBC, box);
380 v = fbposres(top->idef.il[F_FBPOSRES].nr, top->idef.il[F_FBPOSRES].iatoms,
381 top->idef.iparams_fbposres,
382 (const rvec*)x, fr->f_novirsum, fr->vir_diag_posres,
383 ir->ePBC == epbcNONE ? NULL : &pbc,
384 fr->rc_scaling, fr->ePBC, fr->posres_com);
385 enerd->term[F_FBPOSRES] += v;
386 inc_nrnb(nrnb, eNR_FBPOSRES, top->idef.il[F_FBPOSRES].nr/2);
389 static void pull_potential_wrapper(FILE *fplog,
393 matrix box, rvec x[],
397 gmx_enerdata_t *enerd,
400 gmx_wallcycle_t wcycle)
405 /* Calculate the center of mass forces, this requires communication,
406 * which is why pull_potential is called close to other communication.
407 * The virial contribution is calculated directly,
408 * which is why we call pull_potential after calc_virial.
410 wallcycle_start(wcycle, ewcPULLPOT);
411 set_pbc(&pbc, ir->ePBC, box);
413 enerd->term[F_COM_PULL] +=
414 pull_potential(ir->ePull, ir->pull, mdatoms, &pbc,
415 cr, t, lambda[efptRESTRAINT], x, f, vir_force, &dvdl);
418 gmx_print_sepdvdl(fplog, "Com pull", enerd->term[F_COM_PULL], dvdl);
420 enerd->dvdl_lin[efptRESTRAINT] += dvdl;
421 wallcycle_stop(wcycle, ewcPULLPOT);
424 static void pme_receive_force_ener(FILE *fplog,
427 gmx_wallcycle_t wcycle,
428 gmx_enerdata_t *enerd,
431 real e_q, e_lj, v, dvdl_q, dvdl_lj;
432 float cycles_ppdpme, cycles_seppme;
434 cycles_ppdpme = wallcycle_stop(wcycle, ewcPPDURINGPME);
435 dd_cycles_add(cr->dd, cycles_ppdpme, ddCyclPPduringPME);
437 /* In case of node-splitting, the PP nodes receive the long-range
438 * forces, virial and energy from the PME nodes here.
440 wallcycle_start(wcycle, ewcPP_PMEWAITRECVF);
443 gmx_pme_receive_f(cr, fr->f_novirsum, fr->vir_el_recip, &e_q,
444 fr->vir_lj_recip, &e_lj, &dvdl_q, &dvdl_lj,
448 gmx_print_sepdvdl(fplog, "Electrostatic PME mesh", e_q, dvdl_q);
449 gmx_print_sepdvdl(fplog, "Lennard-Jones PME mesh", e_lj, dvdl_lj);
451 enerd->term[F_COUL_RECIP] += e_q;
452 enerd->term[F_LJ_RECIP] += e_lj;
453 enerd->dvdl_lin[efptCOUL] += dvdl_q;
454 enerd->dvdl_lin[efptVDW] += dvdl_lj;
458 dd_cycles_add(cr->dd, cycles_seppme, ddCyclPME);
460 wallcycle_stop(wcycle, ewcPP_PMEWAITRECVF);
463 static void print_large_forces(FILE *fp, t_mdatoms *md, t_commrec *cr,
464 gmx_int64_t step, real pforce, rvec *x, rvec *f)
468 char buf[STEPSTRSIZE];
471 for (i = 0; i < md->homenr; i++)
474 /* We also catch NAN, if the compiler does not optimize this away. */
475 if (fn2 >= pf2 || fn2 != fn2)
477 fprintf(fp, "step %s atom %6d x %8.3f %8.3f %8.3f force %12.5e\n",
478 gmx_step_str(step, buf),
479 ddglatnr(cr->dd, i), x[i][XX], x[i][YY], x[i][ZZ], sqrt(fn2));
484 static void post_process_forces(t_commrec *cr,
486 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
488 matrix box, rvec x[],
493 t_forcerec *fr, gmx_vsite_t *vsite,
500 /* Spread the mesh force on virtual sites to the other particles...
501 * This is parallellized. MPI communication is performed
502 * if the constructing atoms aren't local.
504 wallcycle_start(wcycle, ewcVSITESPREAD);
505 spread_vsite_f(vsite, x, fr->f_novirsum, NULL,
506 (flags & GMX_FORCE_VIRIAL), fr->vir_el_recip,
508 &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
509 wallcycle_stop(wcycle, ewcVSITESPREAD);
511 if (flags & GMX_FORCE_VIRIAL)
513 /* Now add the forces, this is local */
516 sum_forces(0, fr->f_novirsum_n, f, fr->f_novirsum);
520 sum_forces(0, mdatoms->homenr,
523 if (EEL_FULL(fr->eeltype))
525 /* Add the mesh contribution to the virial */
526 m_add(vir_force, fr->vir_el_recip, vir_force);
528 if (EVDW_PME(fr->vdwtype))
530 /* Add the mesh contribution to the virial */
531 m_add(vir_force, fr->vir_lj_recip, vir_force);
535 pr_rvecs(debug, 0, "vir_force", vir_force, DIM);
540 if (fr->print_force >= 0)
542 print_large_forces(stderr, mdatoms, cr, step, fr->print_force, x, f);
546 static void do_nb_verlet(t_forcerec *fr,
547 interaction_const_t *ic,
548 gmx_enerdata_t *enerd,
549 int flags, int ilocality,
552 gmx_wallcycle_t wcycle)
554 int nnbl, kernel_type, enr_nbnxn_kernel_ljc, enr_nbnxn_kernel_lj;
556 nonbonded_verlet_group_t *nbvg;
559 if (!(flags & GMX_FORCE_NONBONDED))
561 /* skip non-bonded calculation */
565 nbvg = &fr->nbv->grp[ilocality];
567 /* CUDA kernel launch overhead is already timed separately */
568 if (fr->cutoff_scheme != ecutsVERLET)
570 gmx_incons("Invalid cut-off scheme passed!");
573 bCUDA = (nbvg->kernel_type == nbnxnk8x8x8_CUDA);
577 wallcycle_sub_start(wcycle, ewcsNONBONDED);
579 switch (nbvg->kernel_type)
581 case nbnxnk4x4_PlainC:
582 nbnxn_kernel_ref(&nbvg->nbl_lists,
588 enerd->grpp.ener[egCOULSR],
590 enerd->grpp.ener[egBHAMSR] :
591 enerd->grpp.ener[egLJSR]);
594 case nbnxnk4xN_SIMD_4xN:
595 nbnxn_kernel_simd_4xn(&nbvg->nbl_lists,
602 enerd->grpp.ener[egCOULSR],
604 enerd->grpp.ener[egBHAMSR] :
605 enerd->grpp.ener[egLJSR]);
607 case nbnxnk4xN_SIMD_2xNN:
608 nbnxn_kernel_simd_2xnn(&nbvg->nbl_lists,
615 enerd->grpp.ener[egCOULSR],
617 enerd->grpp.ener[egBHAMSR] :
618 enerd->grpp.ener[egLJSR]);
621 case nbnxnk8x8x8_CUDA:
622 nbnxn_cuda_launch_kernel(fr->nbv->cu_nbv, nbvg->nbat, flags, ilocality);
625 case nbnxnk8x8x8_PlainC:
626 nbnxn_kernel_gpu_ref(nbvg->nbl_lists.nbl[0],
631 nbvg->nbat->out[0].f,
633 enerd->grpp.ener[egCOULSR],
635 enerd->grpp.ener[egBHAMSR] :
636 enerd->grpp.ener[egLJSR]);
640 gmx_incons("Invalid nonbonded kernel type passed!");
645 wallcycle_sub_stop(wcycle, ewcsNONBONDED);
648 if (EEL_RF(ic->eeltype) || ic->eeltype == eelCUT)
650 enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_RF;
652 else if ((!bCUDA && nbvg->ewald_excl == ewaldexclAnalytical) ||
653 (bCUDA && nbnxn_cuda_is_kernel_ewald_analytical(fr->nbv->cu_nbv)))
655 enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_EWALD;
659 enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_TAB;
661 enr_nbnxn_kernel_lj = eNR_NBNXN_LJ;
662 if (flags & GMX_FORCE_ENERGY)
664 /* In eNR_??? the nbnxn F+E kernels are always the F kernel + 1 */
665 enr_nbnxn_kernel_ljc += 1;
666 enr_nbnxn_kernel_lj += 1;
669 inc_nrnb(nrnb, enr_nbnxn_kernel_ljc,
670 nbvg->nbl_lists.natpair_ljq);
671 inc_nrnb(nrnb, enr_nbnxn_kernel_lj,
672 nbvg->nbl_lists.natpair_lj);
673 /* The Coulomb-only kernels are offset -eNR_NBNXN_LJ_RF+eNR_NBNXN_RF */
674 inc_nrnb(nrnb, enr_nbnxn_kernel_ljc-eNR_NBNXN_LJ_RF+eNR_NBNXN_RF,
675 nbvg->nbl_lists.natpair_q);
677 if (ic->vdw_modifier == eintmodFORCESWITCH)
679 /* We add up the switch cost separately */
680 inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_FSW+((flags & GMX_FORCE_ENERGY) ? 1 : 0),
681 nbvg->nbl_lists.natpair_ljq + nbvg->nbl_lists.natpair_lj);
683 if (ic->vdw_modifier == eintmodPOTSWITCH)
685 /* We add up the switch cost separately */
686 inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_PSW+((flags & GMX_FORCE_ENERGY) ? 1 : 0),
687 nbvg->nbl_lists.natpair_ljq + nbvg->nbl_lists.natpair_lj);
689 if (ic->vdwtype == evdwPME)
691 /* We add up the LJ Ewald cost separately */
692 inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_EWALD+((flags & GMX_FORCE_ENERGY) ? 1 : 0),
693 nbvg->nbl_lists.natpair_ljq + nbvg->nbl_lists.natpair_lj);
697 static void do_nb_verlet_fep(nbnxn_pairlist_set_t *nbl_lists,
704 gmx_enerdata_t *enerd,
707 gmx_wallcycle_t wcycle)
710 nb_kernel_data_t kernel_data;
712 real dvdl_nb[efptNR];
717 /* Add short-range interactions */
718 donb_flags |= GMX_NONBONDED_DO_SR;
720 /* Currently all group scheme kernels always calculate (shift-)forces */
721 if (flags & GMX_FORCE_FORCES)
723 donb_flags |= GMX_NONBONDED_DO_FORCE;
725 if (flags & GMX_FORCE_VIRIAL)
727 donb_flags |= GMX_NONBONDED_DO_SHIFTFORCE;
729 if (flags & GMX_FORCE_ENERGY)
731 donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
733 if (flags & GMX_FORCE_DO_LR)
735 donb_flags |= GMX_NONBONDED_DO_LR;
738 kernel_data.flags = donb_flags;
739 kernel_data.lambda = lambda;
740 kernel_data.dvdl = dvdl_nb;
742 kernel_data.energygrp_elec = enerd->grpp.ener[egCOULSR];
743 kernel_data.energygrp_vdw = enerd->grpp.ener[egLJSR];
745 /* reset free energy components */
746 for (i = 0; i < efptNR; i++)
751 assert(gmx_omp_nthreads_get(emntNonbonded) == nbl_lists->nnbl);
753 wallcycle_sub_start(wcycle, ewcsNONBONDED);
754 #pragma omp parallel for schedule(static) num_threads(nbl_lists->nnbl)
755 for (th = 0; th < nbl_lists->nnbl; th++)
757 gmx_nb_free_energy_kernel(nbl_lists->nbl_fep[th],
758 x, f, fr, mdatoms, &kernel_data, nrnb);
761 if (fepvals->sc_alpha != 0)
763 enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
764 enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
768 enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
769 enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
772 /* If we do foreign lambda and we have soft-core interactions
773 * we have to recalculate the (non-linear) energies contributions.
775 if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) && fepvals->sc_alpha != 0)
777 kernel_data.flags = (donb_flags & ~(GMX_NONBONDED_DO_FORCE | GMX_NONBONDED_DO_SHIFTFORCE)) | GMX_NONBONDED_DO_FOREIGNLAMBDA;
778 kernel_data.lambda = lam_i;
779 kernel_data.energygrp_elec = enerd->foreign_grpp.ener[egCOULSR];
780 kernel_data.energygrp_vdw = enerd->foreign_grpp.ener[egLJSR];
781 /* Note that we add to kernel_data.dvdl, but ignore the result */
783 for (i = 0; i < enerd->n_lambda; i++)
785 for (j = 0; j < efptNR; j++)
787 lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
789 reset_foreign_enerdata(enerd);
790 #pragma omp parallel for schedule(static) num_threads(nbl_lists->nnbl)
791 for (th = 0; th < nbl_lists->nnbl; th++)
793 gmx_nb_free_energy_kernel(nbl_lists->nbl_fep[th],
794 x, f, fr, mdatoms, &kernel_data, nrnb);
797 sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
798 enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
802 wallcycle_sub_stop(wcycle, ewcsNONBONDED);
805 void do_force_cutsVERLET(FILE *fplog, t_commrec *cr,
806 t_inputrec *inputrec,
807 gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
809 gmx_groups_t gmx_unused *groups,
810 matrix box, rvec x[], history_t *hist,
814 gmx_enerdata_t *enerd, t_fcdata *fcd,
815 real *lambda, t_graph *graph,
816 t_forcerec *fr, interaction_const_t *ic,
817 gmx_vsite_t *vsite, rvec mu_tot,
818 double t, FILE *field, gmx_edsam_t ed,
826 gmx_bool bSepDVDL, bStateChanged, bNS, bFillGrid, bCalcCGCM, bBS;
827 gmx_bool bDoLongRange, bDoForces, bSepLRF, bUseGPU, bUseOrEmulGPU;
828 gmx_bool bDiffKernels = FALSE;
830 rvec vzero, box_diag;
832 float cycles_pme, cycles_force, cycles_wait_gpu;
833 nonbonded_verlet_t *nbv;
838 nb_kernel_type = fr->nbv->grp[0].kernel_type;
841 homenr = mdatoms->homenr;
843 bSepDVDL = (fr->bSepDVDL && do_per_step(step, inputrec->nstlog));
845 clear_mat(vir_force);
848 if (DOMAINDECOMP(cr))
850 cg1 = cr->dd->ncg_tot;
861 bStateChanged = (flags & GMX_FORCE_STATECHANGED);
862 bNS = (flags & GMX_FORCE_NS) && (fr->bAllvsAll == FALSE);
863 bFillGrid = (bNS && bStateChanged);
864 bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
865 bDoLongRange = (fr->bTwinRange && bNS && (flags & GMX_FORCE_DO_LR));
866 bDoForces = (flags & GMX_FORCE_FORCES);
867 bSepLRF = (bDoLongRange && bDoForces && (flags & GMX_FORCE_SEPLRF));
868 bUseGPU = fr->nbv->bUseGPU;
869 bUseOrEmulGPU = bUseGPU || (nbv->grp[0].kernel_type == nbnxnk8x8x8_PlainC);
873 update_forcerec(fr, box);
875 if (NEED_MUTOT(*inputrec))
877 /* Calculate total (local) dipole moment in a temporary common array.
878 * This makes it possible to sum them over nodes faster.
880 calc_mu(start, homenr,
881 x, mdatoms->chargeA, mdatoms->chargeB, mdatoms->nChargePerturbed,
886 if (fr->ePBC != epbcNONE)
888 /* Compute shift vectors every step,
889 * because of pressure coupling or box deformation!
891 if ((flags & GMX_FORCE_DYNAMICBOX) && bStateChanged)
893 calc_shifts(box, fr->shift_vec);
898 put_atoms_in_box_omp(fr->ePBC, box, homenr, x);
899 inc_nrnb(nrnb, eNR_SHIFTX, homenr);
901 else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph)
903 unshift_self(graph, box, x);
907 nbnxn_atomdata_copy_shiftvec(flags & GMX_FORCE_DYNAMICBOX,
908 fr->shift_vec, nbv->grp[0].nbat);
911 if (!(cr->duty & DUTY_PME))
913 /* Send particle coordinates to the pme nodes.
914 * Since this is only implemented for domain decomposition
915 * and domain decomposition does not use the graph,
916 * we do not need to worry about shifting.
921 wallcycle_start(wcycle, ewcPP_PMESENDX);
923 bBS = (inputrec->nwall == 2);
927 svmul(inputrec->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
930 if (EEL_PME(fr->eeltype))
932 pme_flags |= GMX_PME_DO_COULOMB;
935 if (EVDW_PME(fr->vdwtype))
937 pme_flags |= GMX_PME_DO_LJ;
940 gmx_pme_send_coordinates(cr, bBS ? boxs : box, x,
941 mdatoms->nChargePerturbed, mdatoms->nTypePerturbed, lambda[efptCOUL], lambda[efptVDW],
942 (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY)),
945 wallcycle_stop(wcycle, ewcPP_PMESENDX);
949 /* do gridding for pair search */
952 if (graph && bStateChanged)
954 /* Calculate intramolecular shift vectors to make molecules whole */
955 mk_mshift(fplog, graph, fr->ePBC, box, x);
959 box_diag[XX] = box[XX][XX];
960 box_diag[YY] = box[YY][YY];
961 box_diag[ZZ] = box[ZZ][ZZ];
963 wallcycle_start(wcycle, ewcNS);
966 wallcycle_sub_start(wcycle, ewcsNBS_GRID_LOCAL);
967 nbnxn_put_on_grid(nbv->nbs, fr->ePBC, box,
969 0, mdatoms->homenr, -1, fr->cginfo, x,
971 nbv->grp[eintLocal].kernel_type,
972 nbv->grp[eintLocal].nbat);
973 wallcycle_sub_stop(wcycle, ewcsNBS_GRID_LOCAL);
977 wallcycle_sub_start(wcycle, ewcsNBS_GRID_NONLOCAL);
978 nbnxn_put_on_grid_nonlocal(nbv->nbs, domdec_zones(cr->dd),
980 nbv->grp[eintNonlocal].kernel_type,
981 nbv->grp[eintNonlocal].nbat);
982 wallcycle_sub_stop(wcycle, ewcsNBS_GRID_NONLOCAL);
985 if (nbv->ngrp == 1 ||
986 nbv->grp[eintNonlocal].nbat == nbv->grp[eintLocal].nbat)
988 nbnxn_atomdata_set(nbv->grp[eintLocal].nbat, eatAll,
989 nbv->nbs, mdatoms, fr->cginfo);
993 nbnxn_atomdata_set(nbv->grp[eintLocal].nbat, eatLocal,
994 nbv->nbs, mdatoms, fr->cginfo);
995 nbnxn_atomdata_set(nbv->grp[eintNonlocal].nbat, eatAll,
996 nbv->nbs, mdatoms, fr->cginfo);
998 wallcycle_stop(wcycle, ewcNS);
1001 /* initialize the GPU atom data and copy shift vector */
1006 wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
1007 nbnxn_cuda_init_atomdata(nbv->cu_nbv, nbv->grp[eintLocal].nbat);
1008 wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
1011 wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
1012 nbnxn_cuda_upload_shiftvec(nbv->cu_nbv, nbv->grp[eintLocal].nbat);
1013 wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
1016 /* do local pair search */
1019 wallcycle_start_nocount(wcycle, ewcNS);
1020 wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_LOCAL);
1021 nbnxn_make_pairlist(nbv->nbs, nbv->grp[eintLocal].nbat,
1024 nbv->min_ci_balanced,
1025 &nbv->grp[eintLocal].nbl_lists,
1027 nbv->grp[eintLocal].kernel_type,
1029 wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_LOCAL);
1033 /* initialize local pair-list on the GPU */
1034 nbnxn_cuda_init_pairlist(nbv->cu_nbv,
1035 nbv->grp[eintLocal].nbl_lists.nbl[0],
1038 wallcycle_stop(wcycle, ewcNS);
1042 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1043 wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
1044 nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs, eatLocal, FALSE, x,
1045 nbv->grp[eintLocal].nbat);
1046 wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
1047 wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1052 wallcycle_start(wcycle, ewcLAUNCH_GPU_NB);
1053 /* launch local nonbonded F on GPU */
1054 do_nb_verlet(fr, ic, enerd, flags, eintLocal, enbvClearFNo,
1056 wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
1059 /* Communicate coordinates and sum dipole if necessary +
1060 do non-local pair search */
1061 if (DOMAINDECOMP(cr))
1063 bDiffKernels = (nbv->grp[eintNonlocal].kernel_type !=
1064 nbv->grp[eintLocal].kernel_type);
1068 /* With GPU+CPU non-bonded calculations we need to copy
1069 * the local coordinates to the non-local nbat struct
1070 * (in CPU format) as the non-local kernel call also
1071 * calculates the local - non-local interactions.
1073 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1074 wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
1075 nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs, eatLocal, TRUE, x,
1076 nbv->grp[eintNonlocal].nbat);
1077 wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
1078 wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1083 wallcycle_start_nocount(wcycle, ewcNS);
1084 wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_NONLOCAL);
1088 nbnxn_grid_add_simple(nbv->nbs, nbv->grp[eintNonlocal].nbat);
1091 nbnxn_make_pairlist(nbv->nbs, nbv->grp[eintNonlocal].nbat,
1094 nbv->min_ci_balanced,
1095 &nbv->grp[eintNonlocal].nbl_lists,
1097 nbv->grp[eintNonlocal].kernel_type,
1100 wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_NONLOCAL);
1102 if (nbv->grp[eintNonlocal].kernel_type == nbnxnk8x8x8_CUDA)
1104 /* initialize non-local pair-list on the GPU */
1105 nbnxn_cuda_init_pairlist(nbv->cu_nbv,
1106 nbv->grp[eintNonlocal].nbl_lists.nbl[0],
1109 wallcycle_stop(wcycle, ewcNS);
1113 wallcycle_start(wcycle, ewcMOVEX);
1114 dd_move_x(cr->dd, box, x);
1116 /* When we don't need the total dipole we sum it in global_stat */
1117 if (bStateChanged && NEED_MUTOT(*inputrec))
1119 gmx_sumd(2*DIM, mu, cr);
1121 wallcycle_stop(wcycle, ewcMOVEX);
1123 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1124 wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
1125 nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs, eatNonlocal, FALSE, x,
1126 nbv->grp[eintNonlocal].nbat);
1127 wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
1128 cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1131 if (bUseGPU && !bDiffKernels)
1133 wallcycle_start(wcycle, ewcLAUNCH_GPU_NB);
1134 /* launch non-local nonbonded F on GPU */
1135 do_nb_verlet(fr, ic, enerd, flags, eintNonlocal, enbvClearFNo,
1137 cycles_force += wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
1143 /* launch D2H copy-back F */
1144 wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
1145 if (DOMAINDECOMP(cr) && !bDiffKernels)
1147 nbnxn_cuda_launch_cpyback(nbv->cu_nbv, nbv->grp[eintNonlocal].nbat,
1148 flags, eatNonlocal);
1150 nbnxn_cuda_launch_cpyback(nbv->cu_nbv, nbv->grp[eintLocal].nbat,
1152 cycles_force += wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
1155 if (bStateChanged && NEED_MUTOT(*inputrec))
1159 gmx_sumd(2*DIM, mu, cr);
1162 for (i = 0; i < 2; i++)
1164 for (j = 0; j < DIM; j++)
1166 fr->mu_tot[i][j] = mu[i*DIM + j];
1170 if (fr->efep == efepNO)
1172 copy_rvec(fr->mu_tot[0], mu_tot);
1176 for (j = 0; j < DIM; j++)
1179 (1.0 - lambda[efptCOUL])*fr->mu_tot[0][j] +
1180 lambda[efptCOUL]*fr->mu_tot[1][j];
1184 /* Reset energies */
1185 reset_enerdata(fr, bNS, enerd, MASTER(cr));
1186 clear_rvecs(SHIFTS, fr->fshift);
1188 if (DOMAINDECOMP(cr) && !(cr->duty & DUTY_PME))
1190 wallcycle_start(wcycle, ewcPPDURINGPME);
1191 dd_force_flop_start(cr->dd, nrnb);
1196 /* Enforced rotation has its own cycle counter that starts after the collective
1197 * coordinates have been communicated. It is added to ddCyclF to allow
1198 * for proper load-balancing */
1199 wallcycle_start(wcycle, ewcROT);
1200 do_rotation(cr, inputrec, box, x, t, step, wcycle, bNS);
1201 wallcycle_stop(wcycle, ewcROT);
1204 /* Start the force cycle counter.
1205 * This counter is stopped in do_forcelow_level.
1206 * No parallel communication should occur while this counter is running,
1207 * since that will interfere with the dynamic load balancing.
1209 wallcycle_start(wcycle, ewcFORCE);
1212 /* Reset forces for which the virial is calculated separately:
1213 * PME/Ewald forces if necessary */
1214 if (fr->bF_NoVirSum)
1216 if (flags & GMX_FORCE_VIRIAL)
1218 fr->f_novirsum = fr->f_novirsum_alloc;
1221 clear_rvecs(fr->f_novirsum_n, fr->f_novirsum);
1225 clear_rvecs(homenr, fr->f_novirsum+start);
1230 /* We are not calculating the pressure so we do not need
1231 * a separate array for forces that do not contribute
1238 /* Clear the short- and long-range forces */
1239 clear_rvecs(fr->natoms_force_constr, f);
1240 if (bSepLRF && do_per_step(step, inputrec->nstcalclr))
1242 clear_rvecs(fr->natoms_force_constr, fr->f_twin);
1245 clear_rvec(fr->vir_diag_posres);
1248 if (inputrec->ePull == epullCONSTRAINT)
1250 clear_pull_forces(inputrec->pull);
1253 /* We calculate the non-bonded forces, when done on the CPU, here.
1254 * We do this before calling do_force_lowlevel, as in there bondeds
1255 * forces are calculated before PME, which does communication.
1256 * With this order, non-bonded and bonded force calculation imbalance
1257 * can be balanced out by the domain decomposition load balancing.
1262 /* Maybe we should move this into do_force_lowlevel */
1263 do_nb_verlet(fr, ic, enerd, flags, eintLocal, enbvClearFYes,
1267 if (fr->efep != efepNO)
1269 /* Calculate the local and non-local free energy interactions here.
1270 * Happens here on the CPU both with and without GPU.
1272 if (fr->nbv->grp[eintLocal].nbl_lists.nbl_fep[0]->nrj > 0)
1274 do_nb_verlet_fep(&fr->nbv->grp[eintLocal].nbl_lists,
1276 inputrec->fepvals, lambda,
1277 enerd, flags, nrnb, wcycle);
1280 if (DOMAINDECOMP(cr) &&
1281 fr->nbv->grp[eintNonlocal].nbl_lists.nbl_fep[0]->nrj > 0)
1283 do_nb_verlet_fep(&fr->nbv->grp[eintNonlocal].nbl_lists,
1285 inputrec->fepvals, lambda,
1286 enerd, flags, nrnb, wcycle);
1290 if (!bUseOrEmulGPU || bDiffKernels)
1294 if (DOMAINDECOMP(cr))
1296 do_nb_verlet(fr, ic, enerd, flags, eintNonlocal,
1297 bDiffKernels ? enbvClearFYes : enbvClearFNo,
1307 aloc = eintNonlocal;
1310 /* Add all the non-bonded force to the normal force array.
1311 * This can be split into a local a non-local part when overlapping
1312 * communication with calculation with domain decomposition.
1314 cycles_force += wallcycle_stop(wcycle, ewcFORCE);
1315 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1316 wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
1317 nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs, eatAll, nbv->grp[aloc].nbat, f);
1318 wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
1319 cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1320 wallcycle_start_nocount(wcycle, ewcFORCE);
1322 /* if there are multiple fshift output buffers reduce them */
1323 if ((flags & GMX_FORCE_VIRIAL) &&
1324 nbv->grp[aloc].nbl_lists.nnbl > 1)
1326 nbnxn_atomdata_add_nbat_fshift_to_fshift(nbv->grp[aloc].nbat,
1331 /* update QMMMrec, if necessary */
1334 update_QMMMrec(cr, fr, x, mdatoms, box, top);
1337 if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
1339 posres_wrapper(fplog, flags, bSepDVDL, inputrec, nrnb, top, box, x,
1343 if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_FBPOSRES].nr > 0)
1345 fbposres_wrapper(inputrec, nrnb, top, box, x, enerd, fr);
1348 /* Compute the bonded and non-bonded energies and optionally forces */
1349 do_force_lowlevel(fplog, step, fr, inputrec, &(top->idef),
1350 cr, nrnb, wcycle, mdatoms,
1351 x, hist, f, bSepLRF ? fr->f_twin : f, enerd, fcd, top, fr->born,
1352 &(top->atomtypes), bBornRadii, box,
1353 inputrec->fepvals, lambda, graph, &(top->excls), fr->mu_tot,
1354 flags, &cycles_pme);
1358 if (do_per_step(step, inputrec->nstcalclr))
1360 /* Add the long range forces to the short range forces */
1361 for (i = 0; i < fr->natoms_force_constr; i++)
1363 rvec_add(fr->f_twin[i], f[i], f[i]);
1368 cycles_force += wallcycle_stop(wcycle, ewcFORCE);
1372 do_flood(cr, inputrec, x, f, ed, box, step, bNS);
1375 if (bUseOrEmulGPU && !bDiffKernels)
1377 /* wait for non-local forces (or calculate in emulation mode) */
1378 if (DOMAINDECOMP(cr))
1384 wallcycle_start(wcycle, ewcWAIT_GPU_NB_NL);
1385 nbnxn_cuda_wait_gpu(nbv->cu_nbv,
1386 nbv->grp[eintNonlocal].nbat,
1388 enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
1390 cycles_tmp = wallcycle_stop(wcycle, ewcWAIT_GPU_NB_NL);
1391 cycles_wait_gpu += cycles_tmp;
1392 cycles_force += cycles_tmp;
1396 wallcycle_start_nocount(wcycle, ewcFORCE);
1397 do_nb_verlet(fr, ic, enerd, flags, eintNonlocal, enbvClearFYes,
1399 cycles_force += wallcycle_stop(wcycle, ewcFORCE);
1401 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1402 wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
1403 /* skip the reduction if there was no non-local work to do */
1404 if (nbv->grp[eintLocal].nbl_lists.nbl[0]->nsci > 0)
1406 nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs, eatNonlocal,
1407 nbv->grp[eintNonlocal].nbat, f);
1409 wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
1410 cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1414 if (bDoForces && DOMAINDECOMP(cr))
1416 /* Communicate the forces */
1417 wallcycle_start(wcycle, ewcMOVEF);
1418 dd_move_f(cr->dd, f, fr->fshift);
1419 /* Do we need to communicate the separate force array
1420 * for terms that do not contribute to the single sum virial?
1421 * Position restraints and electric fields do not introduce
1422 * inter-cg forces, only full electrostatics methods do.
1423 * When we do not calculate the virial, fr->f_novirsum = f,
1424 * so we have already communicated these forces.
1426 if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl &&
1427 (flags & GMX_FORCE_VIRIAL))
1429 dd_move_f(cr->dd, fr->f_novirsum, NULL);
1433 /* We should not update the shift forces here,
1434 * since f_twin is already included in f.
1436 dd_move_f(cr->dd, fr->f_twin, NULL);
1438 wallcycle_stop(wcycle, ewcMOVEF);
1443 /* wait for local forces (or calculate in emulation mode) */
1446 wallcycle_start(wcycle, ewcWAIT_GPU_NB_L);
1447 nbnxn_cuda_wait_gpu(nbv->cu_nbv,
1448 nbv->grp[eintLocal].nbat,
1450 enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
1452 cycles_wait_gpu += wallcycle_stop(wcycle, ewcWAIT_GPU_NB_L);
1454 /* now clear the GPU outputs while we finish the step on the CPU */
1456 wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
1457 nbnxn_cuda_clear_outputs(nbv->cu_nbv, flags);
1458 wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
1462 wallcycle_start_nocount(wcycle, ewcFORCE);
1463 do_nb_verlet(fr, ic, enerd, flags, eintLocal,
1464 DOMAINDECOMP(cr) ? enbvClearFNo : enbvClearFYes,
1466 wallcycle_stop(wcycle, ewcFORCE);
1468 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1469 wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
1470 if (nbv->grp[eintLocal].nbl_lists.nbl[0]->nsci > 0)
1472 /* skip the reduction if there was no non-local work to do */
1473 nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs, eatLocal,
1474 nbv->grp[eintLocal].nbat, f);
1476 wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
1477 wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1480 if (DOMAINDECOMP(cr))
1482 dd_force_flop_stop(cr->dd, nrnb);
1485 dd_cycles_add(cr->dd, cycles_force-cycles_pme, ddCyclF);
1488 dd_cycles_add(cr->dd, cycles_wait_gpu, ddCyclWaitGPU);
1495 if (IR_ELEC_FIELD(*inputrec))
1497 /* Compute forces due to electric field */
1498 calc_f_el(MASTER(cr) ? field : NULL,
1499 start, homenr, mdatoms->chargeA, fr->f_novirsum,
1500 inputrec->ex, inputrec->et, t);
1503 /* If we have NoVirSum forces, but we do not calculate the virial,
1504 * we sum fr->f_novirum=f later.
1506 if (vsite && !(fr->bF_NoVirSum && !(flags & GMX_FORCE_VIRIAL)))
1508 wallcycle_start(wcycle, ewcVSITESPREAD);
1509 spread_vsite_f(vsite, x, f, fr->fshift, FALSE, NULL, nrnb,
1510 &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
1511 wallcycle_stop(wcycle, ewcVSITESPREAD);
1515 wallcycle_start(wcycle, ewcVSITESPREAD);
1516 spread_vsite_f(vsite, x, fr->f_twin, NULL, FALSE, NULL,
1518 &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
1519 wallcycle_stop(wcycle, ewcVSITESPREAD);
1523 if (flags & GMX_FORCE_VIRIAL)
1525 /* Calculation of the virial must be done after vsites! */
1526 calc_virial(0, mdatoms->homenr, x, f,
1527 vir_force, graph, box, nrnb, fr, inputrec->ePBC);
1531 if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
1533 /* Since the COM pulling is always done mass-weighted, no forces are
1534 * applied to vsites and this call can be done after vsite spreading.
1536 pull_potential_wrapper(fplog, bSepDVDL, cr, inputrec, box, x,
1537 f, vir_force, mdatoms, enerd, lambda, t,
1541 /* Add the forces from enforced rotation potentials (if any) */
1544 wallcycle_start(wcycle, ewcROTadd);
1545 enerd->term[F_COM_PULL] += add_rot_forces(inputrec->rot, f, cr, step, t);
1546 wallcycle_stop(wcycle, ewcROTadd);
1549 /* Add forces from interactive molecular dynamics (IMD), if bIMD == TRUE. */
1550 IMD_apply_forces(inputrec->bIMD, inputrec->imd, cr, f, wcycle);
1552 if (PAR(cr) && !(cr->duty & DUTY_PME))
1554 /* In case of node-splitting, the PP nodes receive the long-range
1555 * forces, virial and energy from the PME nodes here.
1557 pme_receive_force_ener(fplog, bSepDVDL, cr, wcycle, enerd, fr);
1562 post_process_forces(cr, step, nrnb, wcycle,
1563 top, box, x, f, vir_force, mdatoms, graph, fr, vsite,
1567 /* Sum the potential energy terms from group contributions */
1568 sum_epot(&(enerd->grpp), enerd->term);
1571 void do_force_cutsGROUP(FILE *fplog, t_commrec *cr,
1572 t_inputrec *inputrec,
1573 gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
1574 gmx_localtop_t *top,
1575 gmx_groups_t *groups,
1576 matrix box, rvec x[], history_t *hist,
1580 gmx_enerdata_t *enerd, t_fcdata *fcd,
1581 real *lambda, t_graph *graph,
1582 t_forcerec *fr, gmx_vsite_t *vsite, rvec mu_tot,
1583 double t, FILE *field, gmx_edsam_t ed,
1584 gmx_bool bBornRadii,
1590 gmx_bool bSepDVDL, bStateChanged, bNS, bFillGrid, bCalcCGCM, bBS;
1591 gmx_bool bDoLongRangeNS, bDoForces, bDoPotential, bSepLRF;
1592 gmx_bool bDoAdressWF;
1594 rvec vzero, box_diag;
1595 real e, v, dvdlambda[efptNR];
1597 float cycles_pme, cycles_force;
1600 homenr = mdatoms->homenr;
1602 bSepDVDL = (fr->bSepDVDL && do_per_step(step, inputrec->nstlog));
1604 clear_mat(vir_force);
1607 if (DOMAINDECOMP(cr))
1609 cg1 = cr->dd->ncg_tot;
1620 bStateChanged = (flags & GMX_FORCE_STATECHANGED);
1621 bNS = (flags & GMX_FORCE_NS) && (fr->bAllvsAll == FALSE);
1622 /* Should we update the long-range neighborlists at this step? */
1623 bDoLongRangeNS = fr->bTwinRange && bNS;
1624 /* Should we perform the long-range nonbonded evaluation inside the neighborsearching? */
1625 bFillGrid = (bNS && bStateChanged);
1626 bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
1627 bDoForces = (flags & GMX_FORCE_FORCES);
1628 bDoPotential = (flags & GMX_FORCE_ENERGY);
1629 bSepLRF = ((inputrec->nstcalclr > 1) && bDoForces &&
1630 (flags & GMX_FORCE_SEPLRF) && (flags & GMX_FORCE_DO_LR));
1632 /* should probably move this to the forcerec since it doesn't change */
1633 bDoAdressWF = ((fr->adress_type != eAdressOff));
1637 update_forcerec(fr, box);
1639 if (NEED_MUTOT(*inputrec))
1641 /* Calculate total (local) dipole moment in a temporary common array.
1642 * This makes it possible to sum them over nodes faster.
1644 calc_mu(start, homenr,
1645 x, mdatoms->chargeA, mdatoms->chargeB, mdatoms->nChargePerturbed,
1650 if (fr->ePBC != epbcNONE)
1652 /* Compute shift vectors every step,
1653 * because of pressure coupling or box deformation!
1655 if ((flags & GMX_FORCE_DYNAMICBOX) && bStateChanged)
1657 calc_shifts(box, fr->shift_vec);
1662 put_charge_groups_in_box(fplog, cg0, cg1, fr->ePBC, box,
1663 &(top->cgs), x, fr->cg_cm);
1664 inc_nrnb(nrnb, eNR_CGCM, homenr);
1665 inc_nrnb(nrnb, eNR_RESETX, cg1-cg0);
1667 else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph)
1669 unshift_self(graph, box, x);
1674 calc_cgcm(fplog, cg0, cg1, &(top->cgs), x, fr->cg_cm);
1675 inc_nrnb(nrnb, eNR_CGCM, homenr);
1678 if (bCalcCGCM && gmx_debug_at)
1680 pr_rvecs(debug, 0, "cgcm", fr->cg_cm, top->cgs.nr);
1684 if (!(cr->duty & DUTY_PME))
1686 /* Send particle coordinates to the pme nodes.
1687 * Since this is only implemented for domain decomposition
1688 * and domain decomposition does not use the graph,
1689 * we do not need to worry about shifting.
1694 wallcycle_start(wcycle, ewcPP_PMESENDX);
1696 bBS = (inputrec->nwall == 2);
1699 copy_mat(box, boxs);
1700 svmul(inputrec->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
1703 if (EEL_PME(fr->eeltype))
1705 pme_flags |= GMX_PME_DO_COULOMB;
1708 if (EVDW_PME(fr->vdwtype))
1710 pme_flags |= GMX_PME_DO_LJ;
1713 gmx_pme_send_coordinates(cr, bBS ? boxs : box, x,
1714 mdatoms->nChargePerturbed, mdatoms->nTypePerturbed, lambda[efptCOUL], lambda[efptVDW],
1715 (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY)),
1718 wallcycle_stop(wcycle, ewcPP_PMESENDX);
1720 #endif /* GMX_MPI */
1722 /* Communicate coordinates and sum dipole if necessary */
1723 if (DOMAINDECOMP(cr))
1725 wallcycle_start(wcycle, ewcMOVEX);
1726 dd_move_x(cr->dd, box, x);
1727 wallcycle_stop(wcycle, ewcMOVEX);
1730 /* update adress weight beforehand */
1731 if (bStateChanged && bDoAdressWF)
1733 /* need pbc for adress weight calculation with pbc_dx */
1734 set_pbc(&pbc, inputrec->ePBC, box);
1735 if (fr->adress_site == eAdressSITEcog)
1737 update_adress_weights_cog(top->idef.iparams, top->idef.il, x, fr, mdatoms,
1738 inputrec->ePBC == epbcNONE ? NULL : &pbc);
1740 else if (fr->adress_site == eAdressSITEcom)
1742 update_adress_weights_com(fplog, cg0, cg1, &(top->cgs), x, fr, mdatoms,
1743 inputrec->ePBC == epbcNONE ? NULL : &pbc);
1745 else if (fr->adress_site == eAdressSITEatomatom)
1747 update_adress_weights_atom_per_atom(cg0, cg1, &(top->cgs), x, fr, mdatoms,
1748 inputrec->ePBC == epbcNONE ? NULL : &pbc);
1752 update_adress_weights_atom(cg0, cg1, &(top->cgs), x, fr, mdatoms,
1753 inputrec->ePBC == epbcNONE ? NULL : &pbc);
1757 if (NEED_MUTOT(*inputrec))
1764 gmx_sumd(2*DIM, mu, cr);
1766 for (i = 0; i < 2; i++)
1768 for (j = 0; j < DIM; j++)
1770 fr->mu_tot[i][j] = mu[i*DIM + j];
1774 if (fr->efep == efepNO)
1776 copy_rvec(fr->mu_tot[0], mu_tot);
1780 for (j = 0; j < DIM; j++)
1783 (1.0 - lambda[efptCOUL])*fr->mu_tot[0][j] + lambda[efptCOUL]*fr->mu_tot[1][j];
1788 /* Reset energies */
1789 reset_enerdata(fr, bNS, enerd, MASTER(cr));
1790 clear_rvecs(SHIFTS, fr->fshift);
1794 wallcycle_start(wcycle, ewcNS);
1796 if (graph && bStateChanged)
1798 /* Calculate intramolecular shift vectors to make molecules whole */
1799 mk_mshift(fplog, graph, fr->ePBC, box, x);
1802 /* Do the actual neighbour searching */
1804 groups, top, mdatoms,
1805 cr, nrnb, bFillGrid,
1808 wallcycle_stop(wcycle, ewcNS);
1811 if (inputrec->implicit_solvent && bNS)
1813 make_gb_nblist(cr, inputrec->gb_algorithm,
1814 x, box, fr, &top->idef, graph, fr->born);
1817 if (DOMAINDECOMP(cr) && !(cr->duty & DUTY_PME))
1819 wallcycle_start(wcycle, ewcPPDURINGPME);
1820 dd_force_flop_start(cr->dd, nrnb);
1825 /* Enforced rotation has its own cycle counter that starts after the collective
1826 * coordinates have been communicated. It is added to ddCyclF to allow
1827 * for proper load-balancing */
1828 wallcycle_start(wcycle, ewcROT);
1829 do_rotation(cr, inputrec, box, x, t, step, wcycle, bNS);
1830 wallcycle_stop(wcycle, ewcROT);
1833 /* Start the force cycle counter.
1834 * This counter is stopped in do_forcelow_level.
1835 * No parallel communication should occur while this counter is running,
1836 * since that will interfere with the dynamic load balancing.
1838 wallcycle_start(wcycle, ewcFORCE);
1842 /* Reset forces for which the virial is calculated separately:
1843 * PME/Ewald forces if necessary */
1844 if (fr->bF_NoVirSum)
1846 if (flags & GMX_FORCE_VIRIAL)
1848 fr->f_novirsum = fr->f_novirsum_alloc;
1851 clear_rvecs(fr->f_novirsum_n, fr->f_novirsum);
1855 clear_rvecs(homenr, fr->f_novirsum+start);
1860 /* We are not calculating the pressure so we do not need
1861 * a separate array for forces that do not contribute
1868 /* Clear the short- and long-range forces */
1869 clear_rvecs(fr->natoms_force_constr, f);
1870 if (bSepLRF && do_per_step(step, inputrec->nstcalclr))
1872 clear_rvecs(fr->natoms_force_constr, fr->f_twin);
1875 clear_rvec(fr->vir_diag_posres);
1877 if (inputrec->ePull == epullCONSTRAINT)
1879 clear_pull_forces(inputrec->pull);
1882 /* update QMMMrec, if necessary */
1885 update_QMMMrec(cr, fr, x, mdatoms, box, top);
1888 if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
1890 posres_wrapper(fplog, flags, bSepDVDL, inputrec, nrnb, top, box, x,
1894 if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_FBPOSRES].nr > 0)
1896 fbposres_wrapper(inputrec, nrnb, top, box, x, enerd, fr);
1899 /* Compute the bonded and non-bonded energies and optionally forces */
1900 do_force_lowlevel(fplog, step, fr, inputrec, &(top->idef),
1901 cr, nrnb, wcycle, mdatoms,
1902 x, hist, f, bSepLRF ? fr->f_twin : f, enerd, fcd, top, fr->born,
1903 &(top->atomtypes), bBornRadii, box,
1904 inputrec->fepvals, lambda,
1905 graph, &(top->excls), fr->mu_tot,
1911 if (do_per_step(step, inputrec->nstcalclr))
1913 /* Add the long range forces to the short range forces */
1914 for (i = 0; i < fr->natoms_force_constr; i++)
1916 rvec_add(fr->f_twin[i], f[i], f[i]);
1921 cycles_force = wallcycle_stop(wcycle, ewcFORCE);
1925 do_flood(cr, inputrec, x, f, ed, box, step, bNS);
1928 if (DOMAINDECOMP(cr))
1930 dd_force_flop_stop(cr->dd, nrnb);
1933 dd_cycles_add(cr->dd, cycles_force-cycles_pme, ddCyclF);
1939 if (IR_ELEC_FIELD(*inputrec))
1941 /* Compute forces due to electric field */
1942 calc_f_el(MASTER(cr) ? field : NULL,
1943 start, homenr, mdatoms->chargeA, fr->f_novirsum,
1944 inputrec->ex, inputrec->et, t);
1947 if (bDoAdressWF && fr->adress_icor == eAdressICThermoForce)
1949 /* Compute thermodynamic force in hybrid AdResS region */
1950 adress_thermo_force(start, homenr, &(top->cgs), x, fr->f_novirsum, fr, mdatoms,
1951 inputrec->ePBC == epbcNONE ? NULL : &pbc);
1954 /* Communicate the forces */
1955 if (DOMAINDECOMP(cr))
1957 wallcycle_start(wcycle, ewcMOVEF);
1958 dd_move_f(cr->dd, f, fr->fshift);
1959 /* Do we need to communicate the separate force array
1960 * for terms that do not contribute to the single sum virial?
1961 * Position restraints and electric fields do not introduce
1962 * inter-cg forces, only full electrostatics methods do.
1963 * When we do not calculate the virial, fr->f_novirsum = f,
1964 * so we have already communicated these forces.
1966 if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl &&
1967 (flags & GMX_FORCE_VIRIAL))
1969 dd_move_f(cr->dd, fr->f_novirsum, NULL);
1973 /* We should not update the shift forces here,
1974 * since f_twin is already included in f.
1976 dd_move_f(cr->dd, fr->f_twin, NULL);
1978 wallcycle_stop(wcycle, ewcMOVEF);
1981 /* If we have NoVirSum forces, but we do not calculate the virial,
1982 * we sum fr->f_novirum=f later.
1984 if (vsite && !(fr->bF_NoVirSum && !(flags & GMX_FORCE_VIRIAL)))
1986 wallcycle_start(wcycle, ewcVSITESPREAD);
1987 spread_vsite_f(vsite, x, f, fr->fshift, FALSE, NULL, nrnb,
1988 &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
1989 wallcycle_stop(wcycle, ewcVSITESPREAD);
1993 wallcycle_start(wcycle, ewcVSITESPREAD);
1994 spread_vsite_f(vsite, x, fr->f_twin, NULL, FALSE, NULL,
1996 &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
1997 wallcycle_stop(wcycle, ewcVSITESPREAD);
2001 if (flags & GMX_FORCE_VIRIAL)
2003 /* Calculation of the virial must be done after vsites! */
2004 calc_virial(0, mdatoms->homenr, x, f,
2005 vir_force, graph, box, nrnb, fr, inputrec->ePBC);
2009 if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
2011 pull_potential_wrapper(fplog, bSepDVDL, cr, inputrec, box, x,
2012 f, vir_force, mdatoms, enerd, lambda, t,
2016 /* Add the forces from enforced rotation potentials (if any) */
2019 wallcycle_start(wcycle, ewcROTadd);
2020 enerd->term[F_COM_PULL] += add_rot_forces(inputrec->rot, f, cr, step, t);
2021 wallcycle_stop(wcycle, ewcROTadd);
2024 /* Add forces from interactive molecular dynamics (IMD), if bIMD == TRUE. */
2025 IMD_apply_forces(inputrec->bIMD, inputrec->imd, cr, f, wcycle);
2027 if (PAR(cr) && !(cr->duty & DUTY_PME))
2029 /* In case of node-splitting, the PP nodes receive the long-range
2030 * forces, virial and energy from the PME nodes here.
2032 pme_receive_force_ener(fplog, bSepDVDL, cr, wcycle, enerd, fr);
2037 post_process_forces(cr, step, nrnb, wcycle,
2038 top, box, x, f, vir_force, mdatoms, graph, fr, vsite,
2042 /* Sum the potential energy terms from group contributions */
2043 sum_epot(&(enerd->grpp), enerd->term);
2046 void do_force(FILE *fplog, t_commrec *cr,
2047 t_inputrec *inputrec,
2048 gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
2049 gmx_localtop_t *top,
2050 gmx_groups_t *groups,
2051 matrix box, rvec x[], history_t *hist,
2055 gmx_enerdata_t *enerd, t_fcdata *fcd,
2056 real *lambda, t_graph *graph,
2058 gmx_vsite_t *vsite, rvec mu_tot,
2059 double t, FILE *field, gmx_edsam_t ed,
2060 gmx_bool bBornRadii,
2063 /* modify force flag if not doing nonbonded */
2064 if (!fr->bNonbonded)
2066 flags &= ~GMX_FORCE_NONBONDED;
2069 switch (inputrec->cutoff_scheme)
2072 do_force_cutsVERLET(fplog, cr, inputrec,
2088 do_force_cutsGROUP(fplog, cr, inputrec,
2103 gmx_incons("Invalid cut-off scheme passed!");
2108 void do_constrain_first(FILE *fplog, gmx_constr_t constr,
2109 t_inputrec *ir, t_mdatoms *md,
2110 t_state *state, t_commrec *cr, t_nrnb *nrnb,
2111 t_forcerec *fr, gmx_localtop_t *top)
2113 int i, m, start, end;
2115 real dt = ir->delta_t;
2119 snew(savex, state->natoms);
2126 fprintf(debug, "vcm: start=%d, homenr=%d, end=%d\n",
2127 start, md->homenr, end);
2129 /* Do a first constrain to reset particles... */
2130 step = ir->init_step;
2133 char buf[STEPSTRSIZE];
2134 fprintf(fplog, "\nConstraining the starting coordinates (step %s)\n",
2135 gmx_step_str(step, buf));
2139 /* constrain the current position */
2140 constrain(NULL, TRUE, FALSE, constr, &(top->idef),
2141 ir, NULL, cr, step, 0, 1.0, md,
2142 state->x, state->x, NULL,
2143 fr->bMolPBC, state->box,
2144 state->lambda[efptBONDED], &dvdl_dum,
2145 NULL, NULL, nrnb, econqCoord,
2146 ir->epc == epcMTTK, state->veta, state->veta);
2149 /* constrain the inital velocity, and save it */
2150 /* also may be useful if we need the ekin from the halfstep for velocity verlet */
2151 /* might not yet treat veta correctly */
2152 constrain(NULL, TRUE, FALSE, constr, &(top->idef),
2153 ir, NULL, cr, step, 0, 1.0, md,
2154 state->x, state->v, state->v,
2155 fr->bMolPBC, state->box,
2156 state->lambda[efptBONDED], &dvdl_dum,
2157 NULL, NULL, nrnb, econqVeloc,
2158 ir->epc == epcMTTK, state->veta, state->veta);
2160 /* constrain the inital velocities at t-dt/2 */
2161 if (EI_STATE_VELOCITY(ir->eI) && ir->eI != eiVV)
2163 for (i = start; (i < end); i++)
2165 for (m = 0; (m < DIM); m++)
2167 /* Reverse the velocity */
2168 state->v[i][m] = -state->v[i][m];
2169 /* Store the position at t-dt in buf */
2170 savex[i][m] = state->x[i][m] + dt*state->v[i][m];
2173 /* Shake the positions at t=-dt with the positions at t=0
2174 * as reference coordinates.
2178 char buf[STEPSTRSIZE];
2179 fprintf(fplog, "\nConstraining the coordinates at t0-dt (step %s)\n",
2180 gmx_step_str(step, buf));
2183 constrain(NULL, TRUE, FALSE, constr, &(top->idef),
2184 ir, NULL, cr, step, -1, 1.0, md,
2185 state->x, savex, NULL,
2186 fr->bMolPBC, state->box,
2187 state->lambda[efptBONDED], &dvdl_dum,
2188 state->v, NULL, nrnb, econqCoord,
2189 ir->epc == epcMTTK, state->veta, state->veta);
2191 for (i = start; i < end; i++)
2193 for (m = 0; m < DIM; m++)
2195 /* Re-reverse the velocities */
2196 state->v[i][m] = -state->v[i][m];
2205 integrate_table(real vdwtab[], real scale, int offstart, int rstart, int rend,
2206 double *enerout, double *virout)
2208 double enersum, virsum;
2209 double invscale, invscale2, invscale3;
2210 double r, ea, eb, ec, pa, pb, pc, pd;
2212 int ri, offset, tabfactor;
2214 invscale = 1.0/scale;
2215 invscale2 = invscale*invscale;
2216 invscale3 = invscale*invscale2;
2218 /* Following summation derived from cubic spline definition,
2219 * Numerical Recipies in C, second edition, p. 113-116. Exact for
2220 * the cubic spline. We first calculate the negative of the
2221 * energy from rvdw to rvdw_switch, assuming that g(r)=1, and then
2222 * add the more standard, abrupt cutoff correction to that result,
2223 * yielding the long-range correction for a switched function. We
2224 * perform both the pressure and energy loops at the same time for
2225 * simplicity, as the computational cost is low. */
2229 /* Since the dispersion table has been scaled down a factor
2230 * 6.0 and the repulsion a factor 12.0 to compensate for the
2231 * c6/c12 parameters inside nbfp[] being scaled up (to save
2232 * flops in kernels), we need to correct for this.
2243 for (ri = rstart; ri < rend; ++ri)
2247 eb = 2.0*invscale2*r;
2251 pb = 3.0*invscale2*r;
2252 pc = 3.0*invscale*r*r;
2255 /* this "8" is from the packing in the vdwtab array - perhaps
2256 should be defined? */
2258 offset = 8*ri + offstart;
2259 y0 = vdwtab[offset];
2260 f = vdwtab[offset+1];
2261 g = vdwtab[offset+2];
2262 h = vdwtab[offset+3];
2264 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);
2265 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);
2267 *enerout = 4.0*M_PI*enersum*tabfactor;
2268 *virout = 4.0*M_PI*virsum*tabfactor;
2271 void calc_enervirdiff(FILE *fplog, int eDispCorr, t_forcerec *fr)
2273 double eners[2], virs[2], enersum, virsum, y0, f, g, h;
2274 double r0, r1, r, rc3, rc9, ea, eb, ec, pa, pb, pc, pd;
2275 double invscale, invscale2, invscale3;
2276 int ri0, ri1, ri, i, offstart, offset;
2277 real scale, *vdwtab, tabfactor, tmp;
2279 fr->enershiftsix = 0;
2280 fr->enershifttwelve = 0;
2281 fr->enerdiffsix = 0;
2282 fr->enerdifftwelve = 0;
2284 fr->virdifftwelve = 0;
2286 if (eDispCorr != edispcNO)
2288 for (i = 0; i < 2; i++)
2293 if ((fr->vdw_modifier == eintmodPOTSHIFT) ||
2294 (fr->vdw_modifier == eintmodPOTSWITCH) ||
2295 (fr->vdw_modifier == eintmodFORCESWITCH) ||
2296 (fr->vdwtype == evdwSHIFT) ||
2297 (fr->vdwtype == evdwSWITCH))
2299 if (((fr->vdw_modifier == eintmodPOTSWITCH) ||
2300 (fr->vdw_modifier == eintmodFORCESWITCH) ||
2301 (fr->vdwtype == evdwSWITCH)) && fr->rvdw_switch == 0)
2304 "With dispersion correction rvdw-switch can not be zero "
2305 "for vdw-type = %s", evdw_names[fr->vdwtype]);
2308 scale = fr->nblists[0].table_vdw.scale;
2309 vdwtab = fr->nblists[0].table_vdw.data;
2311 /* Round the cut-offs to exact table values for precision */
2312 ri0 = floor(fr->rvdw_switch*scale);
2313 ri1 = ceil(fr->rvdw*scale);
2315 /* The code below has some support for handling force-switching, i.e.
2316 * when the force (instead of potential) is switched over a limited
2317 * region. This leads to a constant shift in the potential inside the
2318 * switching region, which we can handle by adding a constant energy
2319 * term in the force-switch case just like when we do potential-shift.
2321 * For now this is not enabled, but to keep the functionality in the
2322 * code we check separately for switch and shift. When we do force-switch
2323 * the shifting point is rvdw_switch, while it is the cutoff when we
2324 * have a classical potential-shift.
2326 * For a pure potential-shift the potential has a constant shift
2327 * all the way out to the cutoff, and that is it. For other forms
2328 * we need to calculate the constant shift up to the point where we
2329 * start modifying the potential.
2331 ri0 = (fr->vdw_modifier == eintmodPOTSHIFT) ? ri1 : ri0;
2338 if ((fr->vdw_modifier == eintmodFORCESWITCH) ||
2339 (fr->vdwtype == evdwSHIFT))
2341 /* Determine the constant energy shift below rvdw_switch.
2342 * Table has a scale factor since we have scaled it down to compensate
2343 * for scaling-up c6/c12 with the derivative factors to save flops in analytical kernels.
2345 fr->enershiftsix = (real)(-1.0/(rc3*rc3)) - 6.0*vdwtab[8*ri0];
2346 fr->enershifttwelve = (real)( 1.0/(rc9*rc3)) - 12.0*vdwtab[8*ri0 + 4];
2348 else if (fr->vdw_modifier == eintmodPOTSHIFT)
2350 fr->enershiftsix = (real)(-1.0/(rc3*rc3));
2351 fr->enershifttwelve = (real)( 1.0/(rc9*rc3));
2354 /* Add the constant part from 0 to rvdw_switch.
2355 * This integration from 0 to rvdw_switch overcounts the number
2356 * of interactions by 1, as it also counts the self interaction.
2357 * We will correct for this later.
2359 eners[0] += 4.0*M_PI*fr->enershiftsix*rc3/3.0;
2360 eners[1] += 4.0*M_PI*fr->enershifttwelve*rc3/3.0;
2362 /* Calculate the contribution in the range [r0,r1] where we
2363 * modify the potential. For a pure potential-shift modifier we will
2364 * have ri0==ri1, and there will not be any contribution here.
2366 for (i = 0; i < 2; i++)
2370 integrate_table(vdwtab, scale, (i == 0 ? 0 : 4), ri0, ri1, &enersum, &virsum);
2371 eners[i] -= enersum;
2375 /* Alright: Above we compensated by REMOVING the parts outside r0
2376 * corresponding to the ideal VdW 1/r6 and /r12 potentials.
2378 * Regardless of whether r0 is the point where we start switching,
2379 * or the cutoff where we calculated the constant shift, we include
2380 * all the parts we are missing out to infinity from r0 by
2381 * calculating the analytical dispersion correction.
2383 eners[0] += -4.0*M_PI/(3.0*rc3);
2384 eners[1] += 4.0*M_PI/(9.0*rc9);
2385 virs[0] += 8.0*M_PI/rc3;
2386 virs[1] += -16.0*M_PI/(3.0*rc9);
2388 else if (fr->vdwtype == evdwCUT ||
2389 EVDW_PME(fr->vdwtype) ||
2390 fr->vdwtype == evdwUSER)
2392 if (fr->vdwtype == evdwUSER && fplog)
2395 "WARNING: using dispersion correction with user tables\n");
2398 /* Note that with LJ-PME, the dispersion correction is multiplied
2399 * by the difference between the actual C6 and the value of C6
2400 * that would produce the combination rule.
2401 * This means the normal energy and virial difference formulas
2405 rc3 = fr->rvdw*fr->rvdw*fr->rvdw;
2407 /* Contribution beyond the cut-off */
2408 eners[0] += -4.0*M_PI/(3.0*rc3);
2409 eners[1] += 4.0*M_PI/(9.0*rc9);
2410 if (fr->vdw_modifier == eintmodPOTSHIFT)
2412 /* Contribution within the cut-off */
2413 eners[0] += -4.0*M_PI/(3.0*rc3);
2414 eners[1] += 4.0*M_PI/(3.0*rc9);
2416 /* Contribution beyond the cut-off */
2417 virs[0] += 8.0*M_PI/rc3;
2418 virs[1] += -16.0*M_PI/(3.0*rc9);
2423 "Dispersion correction is not implemented for vdw-type = %s",
2424 evdw_names[fr->vdwtype]);
2427 /* When we deprecate the group kernels the code below can go too */
2428 if (fr->vdwtype == evdwPME && fr->cutoff_scheme == ecutsGROUP)
2430 /* Calculate self-interaction coefficient (assuming that
2431 * the reciprocal-space contribution is constant in the
2432 * region that contributes to the self-interaction).
2434 fr->enershiftsix = pow(fr->ewaldcoeff_lj, 6) / 6.0;
2436 eners[0] += -pow(sqrt(M_PI)*fr->ewaldcoeff_lj, 3)/3.0;
2437 virs[0] += pow(sqrt(M_PI)*fr->ewaldcoeff_lj, 3);
2440 fr->enerdiffsix = eners[0];
2441 fr->enerdifftwelve = eners[1];
2442 /* The 0.5 is due to the Gromacs definition of the virial */
2443 fr->virdiffsix = 0.5*virs[0];
2444 fr->virdifftwelve = 0.5*virs[1];
2448 void calc_dispcorr(FILE *fplog, t_inputrec *ir, t_forcerec *fr,
2449 gmx_int64_t step, int natoms,
2450 matrix box, real lambda, tensor pres, tensor virial,
2451 real *prescorr, real *enercorr, real *dvdlcorr)
2453 gmx_bool bCorrAll, bCorrPres;
2454 real dvdlambda, invvol, dens, ninter, avcsix, avctwelve, enerdiff, svir = 0, spres = 0;
2464 if (ir->eDispCorr != edispcNO)
2466 bCorrAll = (ir->eDispCorr == edispcAllEner ||
2467 ir->eDispCorr == edispcAllEnerPres);
2468 bCorrPres = (ir->eDispCorr == edispcEnerPres ||
2469 ir->eDispCorr == edispcAllEnerPres);
2471 invvol = 1/det(box);
2474 /* Only correct for the interactions with the inserted molecule */
2475 dens = (natoms - fr->n_tpi)*invvol;
2480 dens = natoms*invvol;
2481 ninter = 0.5*natoms;
2484 if (ir->efep == efepNO)
2486 avcsix = fr->avcsix[0];
2487 avctwelve = fr->avctwelve[0];
2491 avcsix = (1 - lambda)*fr->avcsix[0] + lambda*fr->avcsix[1];
2492 avctwelve = (1 - lambda)*fr->avctwelve[0] + lambda*fr->avctwelve[1];
2495 enerdiff = ninter*(dens*fr->enerdiffsix - fr->enershiftsix);
2496 *enercorr += avcsix*enerdiff;
2498 if (ir->efep != efepNO)
2500 dvdlambda += (fr->avcsix[1] - fr->avcsix[0])*enerdiff;
2504 enerdiff = ninter*(dens*fr->enerdifftwelve - fr->enershifttwelve);
2505 *enercorr += avctwelve*enerdiff;
2506 if (fr->efep != efepNO)
2508 dvdlambda += (fr->avctwelve[1] - fr->avctwelve[0])*enerdiff;
2514 svir = ninter*dens*avcsix*fr->virdiffsix/3.0;
2515 if (ir->eDispCorr == edispcAllEnerPres)
2517 svir += ninter*dens*avctwelve*fr->virdifftwelve/3.0;
2519 /* The factor 2 is because of the Gromacs virial definition */
2520 spres = -2.0*invvol*svir*PRESFAC;
2522 for (m = 0; m < DIM; m++)
2524 virial[m][m] += svir;
2525 pres[m][m] += spres;
2530 /* Can't currently control when it prints, for now, just print when degugging */
2535 fprintf(debug, "Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
2541 "Long Range LJ corr.: Epot %10g, Pres: %10g, Vir: %10g\n",
2542 *enercorr, spres, svir);
2546 fprintf(debug, "Long Range LJ corr.: Epot %10g\n", *enercorr);
2550 if (fr->bSepDVDL && do_per_step(step, ir->nstlog))
2552 gmx_print_sepdvdl(fplog, "Dispersion correction", *enercorr, dvdlambda);
2554 if (fr->efep != efepNO)
2556 *dvdlcorr += dvdlambda;
2561 void do_pbc_first(FILE *fplog, matrix box, t_forcerec *fr,
2562 t_graph *graph, rvec x[])
2566 fprintf(fplog, "Removing pbc first time\n");
2568 calc_shifts(box, fr->shift_vec);
2571 mk_mshift(fplog, graph, fr->ePBC, box, x);
2574 p_graph(debug, "do_pbc_first 1", graph);
2576 shift_self(graph, box, x);
2577 /* By doing an extra mk_mshift the molecules that are broken
2578 * because they were e.g. imported from another software
2579 * will be made whole again. Such are the healing powers
2582 mk_mshift(fplog, graph, fr->ePBC, box, x);
2585 p_graph(debug, "do_pbc_first 2", graph);
2590 fprintf(fplog, "Done rmpbc\n");
2594 static void low_do_pbc_mtop(FILE *fplog, int ePBC, matrix box,
2595 gmx_mtop_t *mtop, rvec x[],
2600 gmx_molblock_t *molb;
2602 if (bFirst && fplog)
2604 fprintf(fplog, "Removing pbc first time\n");
2609 for (mb = 0; mb < mtop->nmolblock; mb++)
2611 molb = &mtop->molblock[mb];
2612 if (molb->natoms_mol == 1 ||
2613 (!bFirst && mtop->moltype[molb->type].cgs.nr == 1))
2615 /* Just one atom or charge group in the molecule, no PBC required */
2616 as += molb->nmol*molb->natoms_mol;
2620 /* Pass NULL iso fplog to avoid graph prints for each molecule type */
2621 mk_graph_ilist(NULL, mtop->moltype[molb->type].ilist,
2622 0, molb->natoms_mol, FALSE, FALSE, graph);
2624 for (mol = 0; mol < molb->nmol; mol++)
2626 mk_mshift(fplog, graph, ePBC, box, x+as);
2628 shift_self(graph, box, x+as);
2629 /* The molecule is whole now.
2630 * We don't need the second mk_mshift call as in do_pbc_first,
2631 * since we no longer need this graph.
2634 as += molb->natoms_mol;
2642 void do_pbc_first_mtop(FILE *fplog, int ePBC, matrix box,
2643 gmx_mtop_t *mtop, rvec x[])
2645 low_do_pbc_mtop(fplog, ePBC, box, mtop, x, TRUE);
2648 void do_pbc_mtop(FILE *fplog, int ePBC, matrix box,
2649 gmx_mtop_t *mtop, rvec x[])
2651 low_do_pbc_mtop(fplog, ePBC, box, mtop, x, FALSE);
2654 void finish_run(FILE *fplog, t_commrec *cr,
2655 t_inputrec *inputrec,
2656 t_nrnb nrnb[], gmx_wallcycle_t wcycle,
2657 gmx_walltime_accounting_t walltime_accounting,
2658 wallclock_gpu_t *gputimes,
2659 gmx_bool bWriteStat)
2662 t_nrnb *nrnb_tot = NULL;
2665 double elapsed_time,
2666 elapsed_time_over_all_ranks,
2667 elapsed_time_over_all_threads,
2668 elapsed_time_over_all_threads_over_all_ranks;
2669 wallcycle_sum(cr, wcycle);
2675 MPI_Allreduce(nrnb->n, nrnb_tot->n, eNRNB, MPI_DOUBLE, MPI_SUM,
2676 cr->mpi_comm_mysim);
2684 elapsed_time = walltime_accounting_get_elapsed_time(walltime_accounting);
2685 elapsed_time_over_all_ranks = elapsed_time;
2686 elapsed_time_over_all_threads = walltime_accounting_get_elapsed_time_over_all_threads(walltime_accounting);
2687 elapsed_time_over_all_threads_over_all_ranks = elapsed_time_over_all_threads;
2691 /* reduce elapsed_time over all MPI ranks in the current simulation */
2692 MPI_Allreduce(&elapsed_time,
2693 &elapsed_time_over_all_ranks,
2694 1, MPI_DOUBLE, MPI_SUM,
2695 cr->mpi_comm_mysim);
2696 elapsed_time_over_all_ranks /= cr->nnodes;
2697 /* Reduce elapsed_time_over_all_threads over all MPI ranks in the
2698 * current simulation. */
2699 MPI_Allreduce(&elapsed_time_over_all_threads,
2700 &elapsed_time_over_all_threads_over_all_ranks,
2701 1, MPI_DOUBLE, MPI_SUM,
2702 cr->mpi_comm_mysim);
2708 print_flop(fplog, nrnb_tot, &nbfs, &mflop);
2715 if ((cr->duty & DUTY_PP) && DOMAINDECOMP(cr))
2717 print_dd_statistics(cr, inputrec, fplog);
2722 wallcycle_print(fplog, cr->nnodes, cr->npmenodes,
2723 elapsed_time_over_all_ranks,
2726 if (EI_DYNAMICS(inputrec->eI))
2728 delta_t = inputrec->delta_t;
2737 print_perf(fplog, elapsed_time_over_all_threads_over_all_ranks,
2738 elapsed_time_over_all_ranks,
2739 walltime_accounting_get_nsteps_done(walltime_accounting),
2740 delta_t, nbfs, mflop);
2744 print_perf(stderr, elapsed_time_over_all_threads_over_all_ranks,
2745 elapsed_time_over_all_ranks,
2746 walltime_accounting_get_nsteps_done(walltime_accounting),
2747 delta_t, nbfs, mflop);
2752 extern void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, real *lambda, double *lam0)
2754 /* this function works, but could probably use a logic rewrite to keep all the different
2755 types of efep straight. */
2758 t_lambda *fep = ir->fepvals;
2760 if ((ir->efep == efepNO) && (ir->bSimTemp == FALSE))
2762 for (i = 0; i < efptNR; i++)
2774 *fep_state = fep->init_fep_state; /* this might overwrite the checkpoint
2775 if checkpoint is set -- a kludge is in for now
2777 for (i = 0; i < efptNR; i++)
2779 /* overwrite lambda state with init_lambda for now for backwards compatibility */
2780 if (fep->init_lambda >= 0) /* if it's -1, it was never initializd */
2782 lambda[i] = fep->init_lambda;
2785 lam0[i] = lambda[i];
2790 lambda[i] = fep->all_lambda[i][*fep_state];
2793 lam0[i] = lambda[i];
2799 /* need to rescale control temperatures to match current state */
2800 for (i = 0; i < ir->opts.ngtc; i++)
2802 if (ir->opts.ref_t[i] > 0)
2804 ir->opts.ref_t[i] = ir->simtempvals->temperatures[*fep_state];
2810 /* Send to the log the information on the current lambdas */
2813 fprintf(fplog, "Initial vector of lambda components:[ ");
2814 for (i = 0; i < efptNR; i++)
2816 fprintf(fplog, "%10.4f ", lambda[i]);
2818 fprintf(fplog, "]\n");
2824 void init_md(FILE *fplog,
2825 t_commrec *cr, t_inputrec *ir, const output_env_t oenv,
2826 double *t, double *t0,
2827 real *lambda, int *fep_state, double *lam0,
2828 t_nrnb *nrnb, gmx_mtop_t *mtop,
2830 int nfile, const t_filenm fnm[],
2831 gmx_mdoutf_t *outf, t_mdebin **mdebin,
2832 tensor force_vir, tensor shake_vir, rvec mu_tot,
2833 gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags)
2838 /* Initial values */
2839 *t = *t0 = ir->init_t;
2842 for (i = 0; i < ir->opts.ngtc; i++)
2844 /* set bSimAnn if any group is being annealed */
2845 if (ir->opts.annealing[i] != eannNO)
2852 update_annealing_target_temp(&(ir->opts), ir->init_t);
2855 /* Initialize lambda variables */
2856 initialize_lambdas(fplog, ir, fep_state, lambda, lam0);
2860 *upd = init_update(ir);
2866 *vcm = init_vcm(fplog, &mtop->groups, ir);
2869 if (EI_DYNAMICS(ir->eI) && !(Flags & MD_APPENDFILES))
2871 if (ir->etc == etcBERENDSEN)
2873 please_cite(fplog, "Berendsen84a");
2875 if (ir->etc == etcVRESCALE)
2877 please_cite(fplog, "Bussi2007a");
2879 if (ir->eI == eiSD1)
2881 please_cite(fplog, "Goga2012");
2889 *outf = init_mdoutf(fplog, nfile, fnm, Flags, cr, ir, mtop, oenv);
2891 *mdebin = init_mdebin((Flags & MD_APPENDFILES) ? NULL : mdoutf_get_fp_ene(*outf),
2892 mtop, ir, mdoutf_get_fp_dhdl(*outf));
2897 please_cite(fplog, "Fritsch12");
2898 please_cite(fplog, "Junghans10");
2900 /* Initiate variables */
2901 clear_mat(force_vir);
2902 clear_mat(shake_vir);