int relax_shell_flexcon(FILE *fplog, t_commrec *cr, gmx_bool bVerbose, gmx_int64_t mdstep, t_inputrec *inputrec, gmx_bool bDoNS, int force_flags, gmx_localtop_t *top, gmx_constr_t constr, gmx_enerdata_t *enerd, t_fcdata *fcd, t_state *state, rvec f[], tensor force_vir, t_mdatoms *md, t_nrnb *nrnb, gmx_wallcycle_t wcycle, t_graph *graph, gmx_groups_t *groups, struct gmx_shellfc *shfc, t_forcerec *fr, gmx_bool bBornRadii, double t, rvec mu_tot, gmx_bool *bConverged, gmx_vsite_t *vsite, FILE *fp_field) { int nshell; t_shell *shell; t_idef *idef; rvec *pos[2], *force[2], *acc_dir = NULL, *x_old = NULL; real Epot[2], df[2]; rvec dx; real sf_dir, invdt; real ftol, xiH, xiS, dum = 0; char sbuf[22]; gmx_bool bCont, bInit; int nat, dd_ac0, dd_ac1 = 0, i; int start = 0, homenr = md->homenr, end = start+homenr, cg0, cg1; int nflexcon, g, number_steps, d, Min = 0, count = 0; #define Try (1-Min) /* At start Try = 1 */ bCont = (mdstep == inputrec->init_step) && inputrec->bContinuation; bInit = (mdstep == inputrec->init_step) || shfc->bRequireInit; ftol = inputrec->em_tol; number_steps = inputrec->niter; nshell = shfc->nshell; shell = shfc->shell; nflexcon = shfc->nflexcon; idef = &top->idef; if (DOMAINDECOMP(cr)) { nat = dd_natoms_vsite(cr->dd); if (nflexcon > 0) { dd_get_constraint_range(cr->dd, &dd_ac0, &dd_ac1); nat = max(nat, dd_ac1); } } else { nat = state->natoms; } if (nat > shfc->x_nalloc) { /* Allocate local arrays */ shfc->x_nalloc = over_alloc_dd(nat); for (i = 0; (i < 2); i++) { srenew(shfc->x[i], shfc->x_nalloc); srenew(shfc->f[i], shfc->x_nalloc); } } for (i = 0; (i < 2); i++) { pos[i] = shfc->x[i]; force[i] = shfc->f[i]; } /* When we had particle decomposition, this code only worked with * PD when all particles involved with each shell were in the same * charge group. Not sure if this is still relevant. */ if (bDoNS && inputrec->ePBC != epbcNONE && !DOMAINDECOMP(cr)) { /* This is the only time where the coordinates are used * before do_force is called, which normally puts all * charge groups in the box. */ cg0 = 0; cg1 = top->cgs.nr; put_charge_groups_in_box(fplog, cg0, cg1, fr->ePBC, state->box, &(top->cgs), state->x, fr->cg_cm); if (graph) { mk_mshift(fplog, graph, fr->ePBC, state->box, state->x); } } /* After this all coordinate arrays will contain whole molecules */ if (graph) { shift_self(graph, state->box, state->x); } if (nflexcon) { if (nat > shfc->flex_nalloc) { shfc->flex_nalloc = over_alloc_dd(nat); srenew(shfc->acc_dir, shfc->flex_nalloc); srenew(shfc->x_old, shfc->flex_nalloc); } acc_dir = shfc->acc_dir; x_old = shfc->x_old; for (i = 0; i < homenr; i++) { for (d = 0; d < DIM; d++) { shfc->x_old[i][d] = state->x[start+i][d] - state->v[start+i][d]*inputrec->delta_t; } } } /* Do a prediction of the shell positions */ if (shfc->bPredict && !bCont) { predict_shells(fplog, state->x, state->v, inputrec->delta_t, nshell, shell, md->massT, NULL, bInit); } /* do_force expected the charge groups to be in the box */ if (graph) { unshift_self(graph, state->box, state->x); } /* Calculate the forces first time around */ if (gmx_debug_at) { pr_rvecs(debug, 0, "x b4 do_force", state->x + start, homenr); } do_force(fplog, cr, inputrec, mdstep, nrnb, wcycle, top, groups, state->box, state->x, &state->hist, force[Min], force_vir, md, enerd, fcd, state->lambda, graph, fr, vsite, mu_tot, t, fp_field, NULL, bBornRadii, (bDoNS ? GMX_FORCE_NS : 0) | force_flags); sf_dir = 0; if (nflexcon) { init_adir(fplog, shfc, constr, idef, inputrec, cr, dd_ac1, mdstep, md, start, end, shfc->x_old-start, state->x, state->x, force[Min], shfc->acc_dir-start, fr->bMolPBC, state->box, state->lambda, &dum, nrnb); for (i = start; i < end; i++) { sf_dir += md->massT[i]*norm2(shfc->acc_dir[i-start]); } } Epot[Min] = enerd->term[F_EPOT]; df[Min] = rms_force(cr, shfc->f[Min], nshell, shell, nflexcon, &sf_dir, &Epot[Min]); df[Try] = 0; if (debug) { fprintf(debug, "df = %g %g\n", df[Min], df[Try]); } if (gmx_debug_at) { pr_rvecs(debug, 0, "force0", force[Min], md->nr); } if (nshell+nflexcon > 0) { /* Copy x to pos[Min] & pos[Try]: during minimization only the * shell positions are updated, therefore the other particles must * be set here. */ memcpy(pos[Min], state->x, nat*sizeof(state->x[0])); memcpy(pos[Try], state->x, nat*sizeof(state->x[0])); } if (bVerbose && MASTER(cr)) { print_epot(stdout, mdstep, 0, Epot[Min], df[Min], nflexcon, sf_dir); } if (debug) { fprintf(debug, "%17s: %14.10e\n", interaction_function[F_EKIN].longname, enerd->term[F_EKIN]); fprintf(debug, "%17s: %14.10e\n", interaction_function[F_EPOT].longname, enerd->term[F_EPOT]); fprintf(debug, "%17s: %14.10e\n", interaction_function[F_ETOT].longname, enerd->term[F_ETOT]); fprintf(debug, "SHELLSTEP %s\n", gmx_step_str(mdstep, sbuf)); } /* First check whether we should do shells, or whether the force is * low enough even without minimization. */ *bConverged = (df[Min] < ftol); for (count = 1; (!(*bConverged) && (count < number_steps)); count++) { if (vsite) { construct_vsites(vsite, pos[Min], inputrec->delta_t, state->v, idef->iparams, idef->il, fr->ePBC, fr->bMolPBC, cr, state->box); } if (nflexcon) { init_adir(fplog, shfc, constr, idef, inputrec, cr, dd_ac1, mdstep, md, start, end, x_old-start, state->x, pos[Min], force[Min], acc_dir-start, fr->bMolPBC, state->box, state->lambda, &dum, nrnb); directional_sd(pos[Min], pos[Try], acc_dir-start, start, end, fr->fc_stepsize); } /* New positions, Steepest descent */ shell_pos_sd(pos[Min], pos[Try], force[Min], nshell, shell, count); /* do_force expected the charge groups to be in the box */ if (graph) { unshift_self(graph, state->box, pos[Try]); } if (gmx_debug_at) { pr_rvecs(debug, 0, "RELAX: pos[Min] ", pos[Min] + start, homenr); pr_rvecs(debug, 0, "RELAX: pos[Try] ", pos[Try] + start, homenr); } /* Try the new positions */ do_force(fplog, cr, inputrec, 1, nrnb, wcycle, top, groups, state->box, pos[Try], &state->hist, force[Try], force_vir, md, enerd, fcd, state->lambda, graph, fr, vsite, mu_tot, t, fp_field, NULL, bBornRadii, force_flags); if (gmx_debug_at) { pr_rvecs(debug, 0, "RELAX: force[Min]", force[Min] + start, homenr); pr_rvecs(debug, 0, "RELAX: force[Try]", force[Try] + start, homenr); } sf_dir = 0; if (nflexcon) { init_adir(fplog, shfc, constr, idef, inputrec, cr, dd_ac1, mdstep, md, start, end, x_old-start, state->x, pos[Try], force[Try], acc_dir-start, fr->bMolPBC, state->box, state->lambda, &dum, nrnb); for (i = start; i < end; i++) { sf_dir += md->massT[i]*norm2(acc_dir[i-start]); } } Epot[Try] = enerd->term[F_EPOT]; df[Try] = rms_force(cr, force[Try], nshell, shell, nflexcon, &sf_dir, &Epot[Try]); if (debug) { fprintf(debug, "df = %g %g\n", df[Min], df[Try]); } if (debug) { if (gmx_debug_at) { pr_rvecs(debug, 0, "F na do_force", force[Try] + start, homenr); } if (gmx_debug_at) { fprintf(debug, "SHELL ITER %d\n", count); dump_shells(debug, pos[Try], force[Try], ftol, nshell, shell); } } if (bVerbose && MASTER(cr)) { print_epot(stdout, mdstep, count, Epot[Try], df[Try], nflexcon, sf_dir); } *bConverged = (df[Try] < ftol); if ((df[Try] < df[Min])) { if (debug) { fprintf(debug, "Swapping Min and Try\n"); } if (nflexcon) { /* Correct the velocities for the flexible constraints */ invdt = 1/inputrec->delta_t; for (i = start; i < end; i++) { for (d = 0; d < DIM; d++) { state->v[i][d] += (pos[Try][i][d] - pos[Min][i][d])*invdt; } } } Min = Try; } else { decrease_step_size(nshell, shell); } } if (MASTER(cr) && !(*bConverged)) { /* Note that the energies and virial are incorrect when not converged */ if (fplog) { fprintf(fplog, "step %s: EM did not converge in %d iterations, RMS force %.3f\n", gmx_step_str(mdstep, sbuf), number_steps, df[Min]); } fprintf(stderr, "step %s: EM did not converge in %d iterations, RMS force %.3f\n", gmx_step_str(mdstep, sbuf), number_steps, df[Min]); } /* Copy back the coordinates and the forces */ memcpy(state->x, pos[Min], nat*sizeof(state->x[0])); memcpy(f, force[Min], nat*sizeof(f[0])); return count; }
void do_force(FILE *fplog,t_commrec *cr, t_inputrec *inputrec, int step,t_nrnb *nrnb,gmx_wallcycle_t wcycle, gmx_localtop_t *top, gmx_groups_t *groups, matrix box,rvec x[],history_t *hist, rvec f[],rvec buf[], tensor vir_force, t_mdatoms *mdatoms, gmx_enerdata_t *enerd,t_fcdata *fcd, real lambda,t_graph *graph, t_forcerec *fr,gmx_vsite_t *vsite,rvec mu_tot, real t,FILE *field,gmx_edsam_t ed, int flags) { static rvec box_size; int cg0,cg1,i,j; int start,homenr; static double mu[2*DIM]; rvec mu_tot_AB[2]; bool bSepDVDL,bStateChanged,bNS,bFillGrid,bCalcCGCM,bBS,bDoForces; matrix boxs; real e,v,dvdl; t_pbc pbc; float cycles_ppdpme,cycles_pme,cycles_force; start = mdatoms->start; homenr = mdatoms->homenr; bSepDVDL = (fr->bSepDVDL && do_per_step(step,inputrec->nstlog)); clear_mat(vir_force); if (PARTDECOMP(cr)) { pd_cg_range(cr,&cg0,&cg1); } else { cg0 = 0; if (DOMAINDECOMP(cr)) cg1 = cr->dd->ncg_tot; else cg1 = top->cgs.nr; if (fr->n_tpi > 0) cg1--; } bStateChanged = (flags & GMX_FORCE_STATECHANGED); bNS = (flags & GMX_FORCE_NS); bFillGrid = (bNS && bStateChanged); bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr)); bDoForces = (flags & GMX_FORCE_FORCES); if (bStateChanged) { update_forcerec(fplog,fr,box); /* Calculate total (local) dipole moment in a temporary common array. * This makes it possible to sum them over nodes faster. */ calc_mu(start,homenr, x,mdatoms->chargeA,mdatoms->chargeB,mdatoms->nChargePerturbed, mu,mu+DIM); } if (fr->ePBC != epbcNONE) { /* Compute shift vectors every step, * because of pressure coupling or box deformation! */ if (DYNAMIC_BOX(*inputrec) && bStateChanged) calc_shifts(box,fr->shift_vec); if (bCalcCGCM) { put_charge_groups_in_box(fplog,cg0,cg1,fr->ePBC,box, &(top->cgs),x,fr->cg_cm); inc_nrnb(nrnb,eNR_CGCM,homenr); inc_nrnb(nrnb,eNR_RESETX,cg1-cg0); } else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph) { unshift_self(graph,box,x); } } else if (bCalcCGCM) { calc_cgcm(fplog,cg0,cg1,&(top->cgs),x,fr->cg_cm); inc_nrnb(nrnb,eNR_CGCM,homenr); } if (bCalcCGCM) { if (PAR(cr)) { move_cgcm(fplog,cr,fr->cg_cm); } if (gmx_debug_at) pr_rvecs(debug,0,"cgcm",fr->cg_cm,top->cgs.nr); } #ifdef GMX_MPI if (!(cr->duty & DUTY_PME)) { /* Send particle coordinates to the pme nodes. * Since this is only implemented for domain decomposition * and domain decomposition does not use the graph, * we do not need to worry about shifting. */ wallcycle_start(wcycle,ewcPP_PMESENDX); GMX_MPE_LOG(ev_send_coordinates_start); bBS = (inputrec->nwall == 2); if (bBS) { copy_mat(box,boxs); svmul(inputrec->wall_ewald_zfac,boxs[ZZ],boxs[ZZ]); } gmx_pme_send_x(cr,bBS ? boxs : box,x,mdatoms->nChargePerturbed,lambda); GMX_MPE_LOG(ev_send_coordinates_finish); wallcycle_stop(wcycle,ewcPP_PMESENDX); } #endif /* GMX_MPI */ /* Communicate coordinates and sum dipole if necessary */ if (PAR(cr)) { wallcycle_start(wcycle,ewcMOVEX); if (DOMAINDECOMP(cr)) { dd_move_x(cr->dd,box,x,buf); } else { move_x(fplog,cr,GMX_LEFT,GMX_RIGHT,x,nrnb); } /* When we don't need the total dipole we sum it in global_stat */ if (NEED_MUTOT(*inputrec)) gmx_sumd(2*DIM,mu,cr); wallcycle_stop(wcycle,ewcMOVEX); } for(i=0; i<2; i++) for(j=0;j<DIM;j++) mu_tot_AB[i][j] = mu[i*DIM + j]; if (fr->efep == efepNO) copy_rvec(mu_tot_AB[0],mu_tot); else for(j=0; j<DIM; j++) mu_tot[j] = (1.0 - lambda)*mu_tot_AB[0][j] + lambda*mu_tot_AB[1][j]; /* Reset energies */ reset_energies(&(inputrec->opts),fr,bNS,enerd,MASTER(cr)); if (bNS) { wallcycle_start(wcycle,ewcNS); if (graph && bStateChanged) /* Calculate intramolecular shift vectors to make molecules whole */ mk_mshift(fplog,graph,fr->ePBC,box,x); /* Reset long range forces if necessary */ if (fr->bTwinRange) { clear_rvecs(fr->f_twin_n,fr->f_twin); clear_rvecs(SHIFTS,fr->fshift_twin); } /* Do the actual neighbour searching and if twin range electrostatics * also do the calculation of long range forces and energies. */ dvdl = 0; ns(fplog,fr,x,f,box,groups,&(inputrec->opts),top,mdatoms, cr,nrnb,step,lambda,&dvdl,&enerd->grpp,bFillGrid,bDoForces); if (bSepDVDL) fprintf(fplog,sepdvdlformat,"LR non-bonded",0,dvdl); enerd->dvdl_lr = dvdl; enerd->term[F_DVDL] += dvdl; wallcycle_stop(wcycle,ewcNS); } if (DOMAINDECOMP(cr)) { if (!(cr->duty & DUTY_PME)) { wallcycle_start(wcycle,ewcPPDURINGPME); dd_force_flop_start(cr->dd,nrnb); } } /* Start the force cycle counter. * This counter is stopped in do_forcelow_level. * No parallel communication should occur while this counter is running, * since that will interfere with the dynamic load balancing. */ wallcycle_start(wcycle,ewcFORCE); if (bDoForces) { /* Reset PME/Ewald forces if necessary */ if (fr->bF_NoVirSum) { GMX_BARRIER(cr->mpi_comm_mygroup); if (fr->bDomDec) clear_rvecs(fr->f_novirsum_n,fr->f_novirsum); else clear_rvecs(homenr,fr->f_novirsum+start); GMX_BARRIER(cr->mpi_comm_mygroup); } /* Copy long range forces into normal buffers */ if (fr->bTwinRange) { for(i=0; i<fr->f_twin_n; i++) copy_rvec(fr->f_twin[i],f[i]); for(i=0; i<SHIFTS; i++) copy_rvec(fr->fshift_twin[i],fr->fshift[i]); } else { if (DOMAINDECOMP(cr)) clear_rvecs(cr->dd->nat_tot,f); else clear_rvecs(mdatoms->nr,f); clear_rvecs(SHIFTS,fr->fshift); } clear_rvec(fr->vir_diag_posres); GMX_BARRIER(cr->mpi_comm_mygroup); } if (inputrec->ePull == epullCONSTRAINT) clear_pull_forces(inputrec->pull); /* update QMMMrec, if necessary */ if(fr->bQMMM) update_QMMMrec(cr,fr,x,mdatoms,box,top); if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0) { /* Position restraints always require full pbc */ set_pbc(&pbc,inputrec->ePBC,box); v = posres(top->idef.il[F_POSRES].nr,top->idef.il[F_POSRES].iatoms, top->idef.iparams_posres, (const rvec*)x,fr->f_novirsum,fr->vir_diag_posres, inputrec->ePBC==epbcNONE ? NULL : &pbc,lambda,&dvdl, fr->rc_scaling,fr->ePBC,fr->posres_com,fr->posres_comB); if (bSepDVDL) { fprintf(fplog,sepdvdlformat, interaction_function[F_POSRES].longname,v,dvdl); } enerd->term[F_POSRES] += v; enerd->term[F_DVDL] += dvdl; inc_nrnb(nrnb,eNR_POSRES,top->idef.il[F_POSRES].nr/2); } /* Compute the bonded and non-bonded forces */ do_force_lowlevel(fplog,step,fr,inputrec,&(top->idef), cr,nrnb,wcycle,mdatoms,&(inputrec->opts), x,hist,f,enerd,fcd,box,lambda,graph,&(top->excls),mu_tot_AB, flags,&cycles_force); GMX_BARRIER(cr->mpi_comm_mygroup); if (ed) { do_flood(fplog,cr,x,f,ed,box,step); } if (DOMAINDECOMP(cr)) { dd_force_flop_stop(cr->dd,nrnb); if (wcycle) dd_cycles_add(cr->dd,cycles_force,ddCyclF); } if (bDoForces) { /* Compute forces due to electric field */ calc_f_el(MASTER(cr) ? field : NULL, start,homenr,mdatoms->chargeA,x,f,inputrec->ex,inputrec->et,t); /* When using PME/Ewald we compute the long range virial there. * otherwise we do it based on long range forces from twin range * cut-off based calculation (or not at all). */ /* Communicate the forces */ if (PAR(cr)) { wallcycle_start(wcycle,ewcMOVEF); if (DOMAINDECOMP(cr)) { dd_move_f(cr->dd,f,buf,fr->fshift); /* Position restraint do not introduce inter-cg forces */ if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl) dd_move_f(cr->dd,fr->f_novirsum,buf,NULL); } else { move_f(fplog,cr,GMX_LEFT,GMX_RIGHT,f,buf,nrnb); } wallcycle_stop(wcycle,ewcMOVEF); } } if (bDoForces) { if (vsite) { wallcycle_start(wcycle,ewcVSITESPREAD); spread_vsite_f(fplog,vsite,x,f,fr->fshift,nrnb, &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr); wallcycle_stop(wcycle,ewcVSITESPREAD); } /* Calculation of the virial must be done after vsites! */ calc_virial(fplog,mdatoms->start,mdatoms->homenr,x,f, vir_force,graph,box,nrnb,fr,inputrec->ePBC); } if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F) { /* Calculate the center of mass forces, this requires communication, * which is why pull_potential is called close to other communication. * The virial contribution is calculated directly, * which is why we call pull_potential after calc_virial. */ set_pbc(&pbc,inputrec->ePBC,box); dvdl = 0; enerd->term[F_COM_PULL] = pull_potential(inputrec->ePull,inputrec->pull,mdatoms,&pbc, cr,t,lambda,x,f,vir_force,&dvdl); if (bSepDVDL) fprintf(fplog,sepdvdlformat,"Com pull",enerd->term[F_COM_PULL],dvdl); enerd->term[F_DVDL] += dvdl; } if (!(cr->duty & DUTY_PME)) { cycles_ppdpme = wallcycle_stop(wcycle,ewcPPDURINGPME); dd_cycles_add(cr->dd,cycles_ppdpme,ddCyclPPduringPME); } #ifdef GMX_MPI if (PAR(cr) && !(cr->duty & DUTY_PME)) { /* In case of node-splitting, the PP nodes receive the long-range * forces, virial and energy from the PME nodes here. */ wallcycle_start(wcycle,ewcPP_PMEWAITRECVF); dvdl = 0; gmx_pme_receive_f(cr,fr->f_novirsum,fr->vir_el_recip,&e,&dvdl, &cycles_pme); if (bSepDVDL) fprintf(fplog,sepdvdlformat,"PME mesh",e,dvdl); enerd->term[F_COUL_RECIP] += e; enerd->term[F_DVDL] += dvdl; if (wcycle) dd_cycles_add(cr->dd,cycles_pme,ddCyclPME); wallcycle_stop(wcycle,ewcPP_PMEWAITRECVF); } #endif if (bDoForces && fr->bF_NoVirSum) { if (vsite) { /* Spread the mesh force on virtual sites to the other particles... * This is parallellized. MPI communication is performed * if the constructing atoms aren't local. */ wallcycle_start(wcycle,ewcVSITESPREAD); spread_vsite_f(fplog,vsite,x,fr->f_novirsum,NULL,nrnb, &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr); wallcycle_stop(wcycle,ewcVSITESPREAD); } /* Now add the forces, this is local */ if (fr->bDomDec) { sum_forces(0,fr->f_novirsum_n,f,fr->f_novirsum); } else { sum_forces(start,start+homenr,f,fr->f_novirsum); } if (EEL_FULL(fr->eeltype)) { /* Add the mesh contribution to the virial */ m_add(vir_force,fr->vir_el_recip,vir_force); } if (debug) pr_rvecs(debug,0,"vir_force",vir_force,DIM); } /* Sum the potential energy terms from group contributions */ sum_epot(&(inputrec->opts),enerd); if (fr->print_force >= 0 && bDoForces) print_large_forces(stderr,mdatoms,cr,step,fr->print_force,x,f); }
void do_nsgrid(FILE *fp, gmx_bool bVerbose, matrix box, rvec x[], t_atoms *atoms, real rlong, const output_env_t oenv) { gmx_mtop_t *mtop; gmx_localtop_t *top; t_mdatoms *md; t_block *cgs; t_inputrec *ir; t_nrnb nrnb; t_commrec *cr; int *cg_index; gmx_moltype_t *molt; gmx_ffparams_t *ffp; ivec *nFreeze; int i, m, natoms; rvec box_size; real *lambda, *dvdl; natoms = atoms->nr; /* Charge group index */ snew(cg_index, natoms); for (i = 0; (i < natoms); i++) { cg_index[i] = i; } /* Topology needs charge groups and exclusions */ snew(mtop, 1); init_mtop(mtop); mtop->natoms = natoms; /* Make one moltype that contains the whol system */ mtop->nmoltype = 1; snew(mtop->moltype, mtop->nmoltype); molt = &mtop->moltype[0]; molt->name = mtop->name; molt->atoms = *atoms; stupid_fill_block(&molt->cgs, mtop->natoms, FALSE); stupid_fill_blocka(&molt->excls, natoms); /* Make one molblock for the whole system */ mtop->nmolblock = 1; snew(mtop->molblock, mtop->nmolblock); mtop->molblock[0].type = 0; mtop->molblock[0].nmol = 1; mtop->molblock[0].natoms_mol = natoms; /* Initialize a single energy group */ mtop->groups.grps[egcENER].nr = 1; mtop->groups.ngrpnr[egcENER] = 0; mtop->groups.grpnr[egcENER] = NULL; ffp = &mtop->ffparams; ffp->ntypes = 1; ffp->atnr = 1; ffp->reppow = 12; snew(ffp->functype, 1); snew(ffp->iparams, 1); ffp->iparams[0].lj.c6 = 1; ffp->iparams[0].lj.c12 = 1; /* inputrec structure */ snew(ir, 1); ir->coulombtype = eelCUT; ir->vdwtype = evdwCUT; ir->ndelta = 2; ir->ns_type = ensGRID; snew(ir->opts.egp_flags, 1); top = gmx_mtop_generate_local_top(mtop, ir); /* Some nasty shortcuts */ cgs = &(top->cgs); /* mdatoms structure */ snew(nFreeze, 2); snew(md, 1); md = init_mdatoms(fp, mtop, FALSE); atoms2md(mtop, ir, 0, NULL, 0, mtop->natoms, md); sfree(nFreeze); /* forcerec structure */ if (fr == NULL) { fr = mk_forcerec(); } snew(cr, 1); cr->nnodes = 1; /* cr->nthreads = 1; */ /* ir->rlist = ir->rcoulomb = ir->rvdw = rlong; printf("Neighborsearching with a cut-off of %g\n",rlong); init_forcerec(stdout,fr,ir,top,cr,md,box,FALSE,NULL,NULL,NULL,TRUE);*/ fr->cg0 = 0; fr->hcg = top->cgs.nr; fr->nWatMol = 0; /* Prepare for neighboursearching */ init_nrnb(&nrnb); /* Init things dependent on parameters */ ir->rlistlong = ir->rlist = ir->rcoulomb = ir->rvdw = rlong; /* create free energy data to avoid NULLs */ snew(ir->fepvals, 1); printf("Neighborsearching with a cut-off of %g\n", rlong); init_forcerec(stdout, oenv, fr, NULL, ir, mtop, cr, box, FALSE, NULL, NULL, NULL, NULL, NULL, TRUE, -1); if (debug) { pr_forcerec(debug, fr, cr); } /* Calculate new stuff dependent on coords and box */ for (m = 0; (m < DIM); m++) { box_size[m] = box[m][m]; } calc_shifts(box, fr->shift_vec); put_charge_groups_in_box(fp, 0, cgs->nr, fr->ePBC, box, cgs, x, fr->cg_cm); /* Do the actual neighboursearching */ snew(lambda, efptNR); snew(dvdl, efptNR); init_neighbor_list(fp, fr, md->homenr); search_neighbours(fp, fr, x, box, top, &mtop->groups, cr, &nrnb, md, lambda, dvdl, NULL, TRUE, FALSE, FALSE); if (debug) { dump_nblist(debug, cr, fr, 0); } if (bVerbose) { fprintf(stderr, "Successfully made neighbourlist\n"); } }
void do_force(FILE *log,t_commrec *cr,t_commrec *mcr, t_parm *parm,t_nsborder *nsb,tensor vir_part,tensor pme_vir, int step,t_nrnb *nrnb,t_topology *top,t_groups *grps, rvec x[],rvec v[],rvec f[],rvec buf[], t_mdatoms *mdatoms,real ener[],t_fcdata *fcd,bool bVerbose, real lambda,t_graph *graph, bool bNS,bool bNBFonly,t_forcerec *fr, rvec mu_tot, bool bGatherOnly) { static rvec box_size; static real dvdl_lr = 0; int cg0,cg1,i,j; int start,homenr; static real mu_and_q[DIM+1]; real qsum; start = START(nsb); homenr = HOMENR(nsb); cg0 = CG0(nsb); cg1 = CG1(nsb); update_forcerec(log,fr,parm->box); /* Calculate total (local) dipole moment in a temporary common array. * This makes it possible to sum them over nodes faster. */ calc_mu_and_q(nsb,x,mdatoms->chargeT,mu_and_q,mu_and_q+DIM); if (fr->ePBC != epbcNONE) { /* Compute shift vectors every step, because of pressure coupling! */ if (parm->ir.epc != epcNO) calc_shifts(parm->box,box_size,fr->shift_vec); if (bNS) { put_charge_groups_in_box(log,cg0,cg1,parm->box,box_size, &(top->blocks[ebCGS]),x,fr->cg_cm); inc_nrnb(nrnb,eNR_RESETX,homenr); } else if (parm->ir.eI==eiSteep || parm->ir.eI==eiCG) unshift_self(graph,parm->box,x); } else if (bNS) calc_cgcm(log,cg0,cg1,&(top->blocks[ebCGS]),x,fr->cg_cm); if (bNS) { inc_nrnb(nrnb,eNR_CGCM,cg1-cg0); if (PAR(cr)) move_cgcm(log,cr,fr->cg_cm,nsb->workload); if (debug) pr_rvecs(debug,0,"cgcm",fr->cg_cm,nsb->cgtotal); } /* Communicate coordinates and sum dipole and net charge if necessary */ if (PAR(cr)) { move_x(log,cr->left,cr->right,x,nsb,nrnb); gmx_sum(DIM+1,mu_and_q,cr); } for(i=0;i<DIM;i++) mu_tot[i]=mu_and_q[i]; qsum=mu_and_q[DIM]; /* Reset energies */ reset_energies(&(parm->ir.opts),grps,fr,bNS,ener); if (bNS) { if (fr->ePBC != epbcNONE) /* Calculate intramolecular shift vectors to make molecules whole */ mk_mshift(log,graph,parm->box,x); /* Reset long range forces if necessary */ if (fr->bTwinRange) { clear_rvecs(nsb->natoms,fr->f_twin); clear_rvecs(SHIFTS,fr->fshift_twin); } /* Do the actual neighbour searching and if twin range electrostatics * also do the calculation of long range forces and energies. */ dvdl_lr = 0; ns(log,fr,x,f,parm->box,grps,&(parm->ir.opts),top,mdatoms, cr,nrnb,nsb,step,lambda,&dvdl_lr); } /* Reset PME/Ewald forces if necessary */ if (EEL_LR(fr->eeltype)) clear_rvecs(homenr,fr->f_pme+start); /* Copy long range forces into normal buffers */ if (fr->bTwinRange) { for(i=0; i<nsb->natoms; i++) copy_rvec(fr->f_twin[i],f[i]); for(i=0; i<SHIFTS; i++) copy_rvec(fr->fshift_twin[i],fr->fshift[i]); } else { clear_rvecs(nsb->natoms,f); clear_rvecs(SHIFTS,fr->fshift); } /* Compute the forces */ force(log,step,fr,&(parm->ir),&(top->idef),nsb,cr,mcr,nrnb,grps,mdatoms, top->atoms.grps[egcENER].nr,&(parm->ir.opts), x,f,ener,fcd,bVerbose,parm->box,lambda,graph,&(top->atoms.excl), bNBFonly,pme_vir,mu_tot,qsum,bGatherOnly); /* Take long range contribution to free energy into account */ ener[F_DVDL] += dvdl_lr; #ifdef DEBUG if (bNS) print_nrnb(log,nrnb); #endif /* The short-range virial from surrounding boxes */ clear_mat(vir_part); calc_vir(log,SHIFTS,fr->shift_vec,fr->fshift,vir_part); inc_nrnb(nrnb,eNR_VIRIAL,SHIFTS); if (debug) pr_rvecs(debug,0,"vir_shifts",vir_part,DIM); /* Compute forces due to electric field */ calc_f_el(start,homenr,mdatoms->chargeT,f,parm->ir.ex); /* When using PME/Ewald we compute the long range virial (pme_vir) there. * otherwise we do it based on long range forces from twin range * cut-off based calculation (or not at all). */ /* Communicate the forces */ if (PAR(cr)) move_f(log,cr->left,cr->right,f,buf,nsb,nrnb); }