t_mdebin *init_mdebin(ener_file_t fp_ene, const gmx_mtop_t *mtop, const t_inputrec *ir, FILE *fp_dhdl) { const char *ener_nm[F_NRE]; static const char *vir_nm[] = { "Vir-XX", "Vir-XY", "Vir-XZ", "Vir-YX", "Vir-YY", "Vir-YZ", "Vir-ZX", "Vir-ZY", "Vir-ZZ" }; static const char *sv_nm[] = { "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ", "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ", "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ" }; static const char *fv_nm[] = { "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ", "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ", "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ" }; static const char *pres_nm[] = { "Pres-XX","Pres-XY","Pres-XZ", "Pres-YX","Pres-YY","Pres-YZ", "Pres-ZX","Pres-ZY","Pres-ZZ" }; static const char *surft_nm[] = { "#Surf*SurfTen" }; static const char *mu_nm[] = { "Mu-X", "Mu-Y", "Mu-Z" }; static const char *vcos_nm[] = { "2CosZ*Vel-X" }; static const char *visc_nm[] = { "1/Viscosity" }; static const char *baro_nm[] = { "Barostat" }; char **grpnms; const gmx_groups_t *groups; char **gnm; char buf[256]; const char *bufi; t_mdebin *md; int i,j,ni,nj,n,nh,k,kk,ncon,nset; gmx_bool bBHAM,bNoseHoover,b14; snew(md,1); if (EI_DYNAMICS(ir->eI)) { md->delta_t = ir->delta_t; } else { md->delta_t = 0; } groups = &mtop->groups; bBHAM = (mtop->ffparams.functype[0] == F_BHAM); b14 = (gmx_mtop_ftype_count(mtop,F_LJ14) > 0 || gmx_mtop_ftype_count(mtop,F_LJC14_Q) > 0); ncon = gmx_mtop_ftype_count(mtop,F_CONSTR); nset = gmx_mtop_ftype_count(mtop,F_SETTLE); md->bConstr = (ncon > 0 || nset > 0); md->bConstrVir = FALSE; if (md->bConstr) { if (ncon > 0 && ir->eConstrAlg == econtLINCS) { if (ir->eI == eiSD2) md->nCrmsd = 2; else md->nCrmsd = 1; } md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL); } else { md->nCrmsd = 0; } /* Energy monitoring */ for(i=0;i<egNR;i++) { md->bEInd[i]=FALSE; } #ifndef GMX_OPENMM for(i=0; i<F_NRE; i++) { md->bEner[i] = FALSE; if (i == F_LJ) md->bEner[i] = !bBHAM; else if (i == F_BHAM) md->bEner[i] = bBHAM; else if (i == F_EQM) md->bEner[i] = ir->bQMMM; else if (i == F_COUL_LR) md->bEner[i] = (ir->rcoulomb > ir->rlist); else if (i == F_LJ_LR) md->bEner[i] = (!bBHAM && ir->rvdw > ir->rlist); else if (i == F_BHAM_LR) md->bEner[i] = (bBHAM && ir->rvdw > ir->rlist); else if (i == F_RF_EXCL) md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC); else if (i == F_COUL_RECIP) md->bEner[i] = EEL_FULL(ir->coulombtype); else if (i == F_LJ14) md->bEner[i] = b14; else if (i == F_COUL14) md->bEner[i] = b14; else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB) md->bEner[i] = FALSE; else if ((i == F_DVDL) || (i == F_DKDL)) md->bEner[i] = (ir->efep != efepNO); else if (i == F_DHDL_CON) md->bEner[i] = (ir->efep != efepNO && md->bConstr); else if ((interaction_function[i].flags & IF_VSITE) || (i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE)) md->bEner[i] = FALSE; else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i==F_EQM)) md->bEner[i] = TRUE; else if ((i == F_GBPOL) && ir->implicit_solvent==eisGBSA) md->bEner[i] = TRUE; else if ((i == F_NPSOLVATION) && ir->implicit_solvent==eisGBSA && (ir->sa_algorithm != esaNO)) md->bEner[i] = TRUE; else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14)) md->bEner[i] = FALSE; else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP)) md->bEner[i] = EI_DYNAMICS(ir->eI); else if (i==F_VTEMP) md->bEner[i] = (EI_DYNAMICS(ir->eI) && getenv("GMX_VIRIAL_TEMPERATURE")); else if (i == F_DISPCORR || i == F_PDISPCORR) md->bEner[i] = (ir->eDispCorr != edispcNO); else if (i == F_DISRESVIOL) md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0); else if (i == F_ORIRESDEV) md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0); else if (i == F_CONNBONDS) md->bEner[i] = FALSE; else if (i == F_COM_PULL) md->bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F); else if (i == F_ECONSERVED) md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) && (ir->epc == epcNO || ir->epc==epcMTTK)); else md->bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0); } #else /* OpenMM always produces only the following 4 energy terms */ md->bEner[F_EPOT] = TRUE; md->bEner[F_EKIN] = TRUE; md->bEner[F_ETOT] = TRUE; md->bEner[F_TEMP] = TRUE; #endif md->f_nre=0; for(i=0; i<F_NRE; i++) { if (md->bEner[i]) { /* FIXME: The constness should not be cast away */ /*ener_nm[f_nre]=(char *)interaction_function[i].longname;*/ ener_nm[md->f_nre]=interaction_function[i].longname; md->f_nre++; } } md->epc = ir->epc; for (i=0;i<DIM;i++) { for (j=0;j<DIM;j++) { md->ref_p[i][j] = ir->ref_p[i][j]; } } md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform); md->bDynBox = DYNAMIC_BOX(*ir); md->etc = ir->etc; md->bNHC_trotter = IR_NVT_TROTTER(ir); md->bMTTK = IR_NPT_TROTTER(ir); md->ebin = mk_ebin(); /* Pass NULL for unit to let get_ebin_space determine the units * for interaction_function[i].longname */ md->ie = get_ebin_space(md->ebin,md->f_nre,ener_nm,NULL); if (md->nCrmsd) { /* This should be called directly after the call for md->ie, * such that md->iconrmsd follows directly in the list. */ md->iconrmsd = get_ebin_space(md->ebin,md->nCrmsd,conrmsd_nm,""); } if (md->bDynBox) { md->ib = get_ebin_space(md->ebin, md->bTricl ? NTRICLBOXS : NBOXS, md->bTricl ? tricl_boxs_nm : boxs_nm, unit_length); md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume); md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI); md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy); md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy); } if (md->bConstrVir) { md->isvir = get_ebin_space(md->ebin,asize(sv_nm),sv_nm,unit_energy); md->ifvir = get_ebin_space(md->ebin,asize(fv_nm),fv_nm,unit_energy); } md->ivir = get_ebin_space(md->ebin,asize(vir_nm),vir_nm,unit_energy); md->ipres = get_ebin_space(md->ebin,asize(pres_nm),pres_nm,unit_pres_bar); md->isurft = get_ebin_space(md->ebin,asize(surft_nm),surft_nm, unit_surft_bar); if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK) { md->ipc = get_ebin_space(md->ebin,md->bTricl ? 6 : 3, boxvel_nm,unit_vel); } md->imu = get_ebin_space(md->ebin,asize(mu_nm),mu_nm,unit_dipole_D); if (ir->cos_accel != 0) { md->ivcos = get_ebin_space(md->ebin,asize(vcos_nm),vcos_nm,unit_vel); md->ivisc = get_ebin_space(md->ebin,asize(visc_nm),visc_nm, unit_invvisc_SI); } /* Energy monitoring */ for(i=0;i<egNR;i++) { md->bEInd[i] = FALSE; } md->bEInd[egCOULSR] = TRUE; md->bEInd[egLJSR ] = TRUE; if (ir->rcoulomb > ir->rlist) { md->bEInd[egCOULLR] = TRUE; } if (!bBHAM) { if (ir->rvdw > ir->rlist) { md->bEInd[egLJLR] = TRUE; } } else { md->bEInd[egLJSR] = FALSE; md->bEInd[egBHAMSR] = TRUE; if (ir->rvdw > ir->rlist) { md->bEInd[egBHAMLR] = TRUE; } } if (b14) { md->bEInd[egLJ14] = TRUE; md->bEInd[egCOUL14] = TRUE; } md->nEc=0; for(i=0; (i<egNR); i++) { if (md->bEInd[i]) { md->nEc++; } } n=groups->grps[egcENER].nr; md->nEg=n; md->nE=(n*(n+1))/2; snew(md->igrp,md->nE); if (md->nE > 1) { n=0; snew(gnm,md->nEc); for(k=0; (k<md->nEc); k++) { snew(gnm[k],STRLEN); } for(i=0; (i<groups->grps[egcENER].nr); i++) { ni=groups->grps[egcENER].nm_ind[i]; for(j=i; (j<groups->grps[egcENER].nr); j++) { nj=groups->grps[egcENER].nm_ind[j]; for(k=kk=0; (k<egNR); k++) { if (md->bEInd[k]) { sprintf(gnm[kk],"%s:%s-%s",egrp_nm[k], *(groups->grpname[ni]),*(groups->grpname[nj])); kk++; } } md->igrp[n]=get_ebin_space(md->ebin,md->nEc, (const char **)gnm,unit_energy); n++; } } for(k=0; (k<md->nEc); k++) { sfree(gnm[k]); } sfree(gnm); if (n != md->nE) { gmx_incons("Number of energy terms wrong"); } } md->nTC=groups->grps[egcTC].nr; md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */ if (md->bMTTK) { md->nTCP = 1; /* assume only one possible coupling system for barostat for now */ } else { md->nTCP = 0; } if (md->etc == etcNOSEHOOVER) { if (md->bNHC_trotter) { md->mde_n = 2*md->nNHC*md->nTC; } else { md->mde_n = 2*md->nTC; } if (md->epc == epcMTTK) { md->mdeb_n = 2*md->nNHC*md->nTCP; } } else { md->mde_n = md->nTC; md->mdeb_n = 0; } snew(md->tmp_r,md->mde_n); snew(md->tmp_v,md->mde_n); snew(md->grpnms,md->mde_n); grpnms = md->grpnms; for(i=0; (i<md->nTC); i++) { ni=groups->grps[egcTC].nm_ind[i]; sprintf(buf,"T-%s",*(groups->grpname[ni])); grpnms[i]=strdup(buf); } md->itemp=get_ebin_space(md->ebin,md->nTC,(const char **)grpnms, unit_temp_K); bNoseHoover = (getenv("GMX_NOSEHOOVER_CHAINS") != NULL); /* whether to print Nose-Hoover chains */ if (md->etc == etcNOSEHOOVER) { if (bNoseHoover) { if (md->bNHC_trotter) { for(i=0; (i<md->nTC); i++) { ni=groups->grps[egcTC].nm_ind[i]; bufi = *(groups->grpname[ni]); for(j=0; (j<md->nNHC); j++) { sprintf(buf,"Xi-%d-%s",j,bufi); grpnms[2*(i*md->nNHC+j)]=strdup(buf); sprintf(buf,"vXi-%d-%s",j,bufi); grpnms[2*(i*md->nNHC+j)+1]=strdup(buf); } } md->itc=get_ebin_space(md->ebin,md->mde_n, (const char **)grpnms,unit_invtime); if (md->bMTTK) { for(i=0; (i<md->nTCP); i++) { bufi = baro_nm[0]; /* All barostat DOF's together for now. */ for(j=0; (j<md->nNHC); j++) { sprintf(buf,"Xi-%d-%s",j,bufi); grpnms[2*(i*md->nNHC+j)]=strdup(buf); sprintf(buf,"vXi-%d-%s",j,bufi); grpnms[2*(i*md->nNHC+j)+1]=strdup(buf); } } md->itcb=get_ebin_space(md->ebin,md->mdeb_n, (const char **)grpnms,unit_invtime); } } else { for(i=0; (i<md->nTC); i++) { ni=groups->grps[egcTC].nm_ind[i]; bufi = *(groups->grpname[ni]); sprintf(buf,"Xi-%s",bufi); grpnms[2*i]=strdup(buf); sprintf(buf,"vXi-%s",bufi); grpnms[2*i+1]=strdup(buf); } md->itc=get_ebin_space(md->ebin,md->mde_n, (const char **)grpnms,unit_invtime); } } } else if (md->etc == etcBERENDSEN || md->etc == etcYES || md->etc == etcVRESCALE) { for(i=0; (i<md->nTC); i++) { ni=groups->grps[egcTC].nm_ind[i]; sprintf(buf,"Lamb-%s",*(groups->grpname[ni])); grpnms[i]=strdup(buf); } md->itc=get_ebin_space(md->ebin,md->mde_n,(const char **)grpnms,""); } sfree(grpnms); md->nU=groups->grps[egcACC].nr; if (md->nU > 1) { snew(grpnms,3*md->nU); for(i=0; (i<md->nU); i++) { ni=groups->grps[egcACC].nm_ind[i]; sprintf(buf,"Ux-%s",*(groups->grpname[ni])); grpnms[3*i+XX]=strdup(buf); sprintf(buf,"Uy-%s",*(groups->grpname[ni])); grpnms[3*i+YY]=strdup(buf); sprintf(buf,"Uz-%s",*(groups->grpname[ni])); grpnms[3*i+ZZ]=strdup(buf); } md->iu=get_ebin_space(md->ebin,3*md->nU,(const char **)grpnms,unit_vel); sfree(grpnms); } if ( fp_ene ) { do_enxnms(fp_ene,&md->ebin->nener,&md->ebin->enm); } md->print_grpnms=NULL; /* check whether we're going to write dh histograms */ md->dhc=NULL; if (ir->separate_dhdl_file == sepdhdlfileNO ) { int i; snew(md->dhc, 1); mde_delta_h_coll_init(md->dhc, ir); md->fp_dhdl = NULL; } else { md->fp_dhdl = fp_dhdl; } md->dhdl_derivatives = (ir->dhdl_derivatives==dhdlderivativesYES); return md; }
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); }
t_mdebin *init_mdebin(int fp_ene, const gmx_mtop_t *mtop, const t_inputrec *ir) { char *ener_nm[F_NRE]; static char *vir_nm[] = { "Vir-XX", "Vir-XY", "Vir-XZ", "Vir-YX", "Vir-YY", "Vir-YZ", "Vir-ZX", "Vir-ZY", "Vir-ZZ" }; static char *sv_nm[] = { "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ", "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ", "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ" }; static char *fv_nm[] = { "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ", "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ", "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ" }; static char *pres_nm[] = { "Pres-XX (bar)","Pres-XY (bar)","Pres-XZ (bar)", "Pres-YX (bar)","Pres-YY (bar)","Pres-YZ (bar)", "Pres-ZX (bar)","Pres-ZY (bar)","Pres-ZZ (bar)" }; static char *surft_nm[] = { "#Surf*SurfTen" }; static char *mu_nm[] = { "Mu-X", "Mu-Y", "Mu-Z" }; static char *vcos_nm[] = { "2CosZ*Vel-X" }; static char *visc_nm[] = { "1/Viscosity (SI)" }; static char **grpnms; const gmx_groups_t *groups; char **gnm; char buf[256]; t_mdebin *md; int i,j,ni,nj,n,k,kk,ncon,nset; bool bBHAM,b14; f_nre = 0; // otherwise, multiple calls to mdrunner_integrate are not possible!NnCrmsd; groups = &mtop->groups; bBHAM = (mtop->ffparams.functype[0] == F_BHAM); b14 = (gmx_mtop_ftype_count(mtop,F_LJ14) > 0 || gmx_mtop_ftype_count(mtop,F_LJC14_Q) > 0); ncon = gmx_mtop_ftype_count(mtop,F_CONSTR); nset = gmx_mtop_ftype_count(mtop,F_SETTLE); bConstr = (ncon > 0 || nset > 0); bConstrVir = FALSE; if (bConstr) { if (ncon > 0 && ir->eConstrAlg == econtLINCS) { if (ir->eI == eiSD2) nCrmsd = 2; else nCrmsd = 1; } bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL); } else { nCrmsd = 0; } for(i=0; i<F_NRE; i++) { bEner[i] = FALSE; if (i == F_LJ) bEner[i] = !bBHAM; else if (i == F_BHAM) bEner[i] = bBHAM; else if (i == F_EQM) bEner[i] = ir->bQMMM; else if (i == F_COUL_LR) bEner[i] = (ir->rcoulomb > ir->rlist); else if (i == F_LJ_LR) bEner[i] = (!bBHAM && ir->rvdw > ir->rlist); else if (i == F_BHAM_LR) bEner[i] = (bBHAM && ir->rvdw > ir->rlist); else if (i == F_RF_EXCL) bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC); else if (i == F_COUL_RECIP) bEner[i] = EEL_FULL(ir->coulombtype); else if (i == F_LJ14) bEner[i] = b14; else if (i == F_COUL14) bEner[i] = b14; else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB) bEner[i] = FALSE; else if ((i == F_DVDL) || (i == F_DKDL)) bEner[i] = (ir->efep != efepNO); else if (i == F_DGDL_CON) bEner[i] = (ir->efep != efepNO && bConstr); else if ((interaction_function[i].flags & IF_VSITE) || (i == F_CONSTR) || (i == F_SETTLE)) bEner[i] = FALSE; else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i==F_EQM)) bEner[i] = TRUE; else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP)) bEner[i] = EI_DYNAMICS(ir->eI); else if (i == F_DISPCORR) bEner[i] = (ir->eDispCorr != edispcNO); else if (i == F_DISRESVIOL) bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0); else if (i == F_ORIRESDEV) bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0); else if (i == F_CONNBONDS) bEner[i] = FALSE; else if (i == F_COM_PULL) bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F); else if (i == F_ECONSERVED) bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) && ir->epc == epcNO); else bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0); } for(i=0; i<F_NRE; i++) if (bEner[i]) { ener_nm[f_nre]=interaction_function[i].longname; f_nre++; } epc = ir->epc; bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform); bDynBox = DYNAMIC_BOX(*ir); etc = ir->etc; /* Energy monitoring */ snew(md,1); md->ebin = mk_ebin(); md->ie = get_ebin_space(md->ebin,f_nre,ener_nm); if (nCrmsd) { /* This should be called directly after the call for md->ie, * such that md->iconrmsd follows directly in the list. */ md->iconrmsd = get_ebin_space(md->ebin,nCrmsd,conrmsd_nm); } if (bDynBox) md->ib = get_ebin_space(md->ebin, bTricl ? NTRICLBOXS : NBOXS, bTricl ? tricl_boxs_nm : boxs_nm); if (bConstrVir) { md->isvir = get_ebin_space(md->ebin,asize(sv_nm),sv_nm); md->ifvir = get_ebin_space(md->ebin,asize(fv_nm),fv_nm); } md->ivir = get_ebin_space(md->ebin,asize(vir_nm),vir_nm); md->ipres = get_ebin_space(md->ebin,asize(pres_nm),pres_nm); md->isurft = get_ebin_space(md->ebin,asize(surft_nm),surft_nm); if (epc == epcPARRINELLORAHMAN) { md->ipc = get_ebin_space(md->ebin,bTricl ? 6 : 3,boxvel_nm); } md->imu = get_ebin_space(md->ebin,asize(mu_nm),mu_nm); if (ir->cos_accel != 0) { md->ivcos = get_ebin_space(md->ebin,asize(vcos_nm),vcos_nm); md->ivisc = get_ebin_space(md->ebin,asize(visc_nm),visc_nm); } if (ir->rcoulomb > ir->rlist) bEInd[egCOULLR] = TRUE; if (!bBHAM) { if (ir->rvdw > ir->rlist) bEInd[egLJLR] = TRUE; } else { bEInd[egLJSR] = FALSE; bEInd[egBHAMSR] = TRUE; if (ir->rvdw > ir->rlist) bEInd[egBHAMLR] = TRUE; } if (b14) { bEInd[egLJ14] = TRUE; bEInd[egCOUL14] = TRUE; } md->nEc=0; for(i=0; (i<egNR); i++) if (bEInd[i]) md->nEc++; n=groups->grps[egcENER].nr; md->nEg=n; md->nE=(n*(n+1))/2; snew(md->igrp,md->nE); if (md->nE > 1) { n=0; snew(gnm,md->nEc); for(k=0; (k<md->nEc); k++) snew(gnm[k],STRLEN); for(i=0; (i<groups->grps[egcENER].nr); i++) { ni=groups->grps[egcENER].nm_ind[i]; for(j=i; (j<groups->grps[egcENER].nr); j++) { nj=groups->grps[egcENER].nm_ind[j]; for(k=kk=0; (k<egNR); k++) { if (bEInd[k]) { sprintf(gnm[kk],"%s:%s-%s",egrp_nm[k], *(groups->grpname[ni]),*(groups->grpname[nj])); kk++; } } md->igrp[n]=get_ebin_space(md->ebin,md->nEc,gnm); n++; } } for(k=0; (k<md->nEc); k++) sfree(gnm[k]); sfree(gnm); if (n != md->nE) gmx_incons("Number of energy terms wrong"); } md->nTC=groups->grps[egcTC].nr; snew(grpnms,md->nTC); for(i=0; (i<md->nTC); i++) { ni=groups->grps[egcTC].nm_ind[i]; sprintf(buf,"T-%s",*(groups->grpname[ni])); grpnms[i]=strdup(buf); } md->itemp=get_ebin_space(md->ebin,md->nTC,grpnms); sfree(*grpnms); if (etc == etcNOSEHOOVER) { for(i=0; (i<md->nTC); i++) { ni=groups->grps[egcTC].nm_ind[i]; sprintf(buf,"Xi-%s",*(groups->grpname[ni])); grpnms[i]=strdup(buf); } md->itc=get_ebin_space(md->ebin,md->nTC,grpnms); sfree(*grpnms); } else if (etc == etcBERENDSEN || etc == etcYES || etc == etcVRESCALE) { for(i=0; (i<md->nTC); i++) { ni=groups->grps[egcTC].nm_ind[i]; sprintf(buf,"Lamb-%s",*(groups->grpname[ni])); grpnms[i]=strdup(buf); } md->itc=get_ebin_space(md->ebin,md->nTC,grpnms); sfree(*grpnms); } sfree(grpnms); md->nU=groups->grps[egcACC].nr; if (md->nU > 1) { snew(grpnms,3*md->nU); for(i=0; (i<md->nU); i++) { ni=groups->grps[egcACC].nm_ind[i]; sprintf(buf,"Ux-%s",*(groups->grpname[ni])); grpnms[3*i+XX]=strdup(buf); sprintf(buf,"Uy-%s",*(groups->grpname[ni])); grpnms[3*i+YY]=strdup(buf); sprintf(buf,"Uz-%s",*(groups->grpname[ni])); grpnms[3*i+ZZ]=strdup(buf); } md->iu=get_ebin_space(md->ebin,3*md->nU,grpnms); sfree(*grpnms); sfree(grpnms); } if (fp_ene != -1) do_enxnms(fp_ene,&md->ebin->nener,&md->ebin->enm); return md; }