* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
{
if (gmx_debug_at)
{
- fprintf(debug,"reallocating neigborlist il_code=%d, maxnri=%d\n",
- nl->il_code,nl->maxnri);
+ fprintf(debug,"reallocating neigborlist (ielec=%d, ivdw=%d, igeometry=%d, free_energy=%d), maxnri=%d\n",
+ nl->ielec,nl->ivdw,nl->igeometry,nl->free_energy,nl->maxnri);
}
srenew(nl->iinr, nl->maxnri);
- if (nl->enlist == enlistCG_CG)
+ if (nl->igeometry == GMX_NBLIST_GEOMETRY_CG_CG)
{
srenew(nl->iinr_end,nl->maxnri);
}
srenew(nl->jindex, nl->maxnri+1);
}
-/* ivdw/icoul are used to determine the type of interaction, so we
- * can set an innerloop index here. The obvious choice for this would have
- * been the vdwtype/coultype values in the forcerecord, but unfortunately
- * those types are braindead - for instance both Buckingham and normal
- * Lennard-Jones use the same value (evdwCUT), and a separate gmx_boolean variable
- * to determine which interaction is used. There is further no special value
- * for 'no interaction'. For backward compatibility with old TPR files we won't
- * change this in the 3.x series, so when calling this routine you should use:
- *
- * icoul=0 no coulomb interaction
- * icoul=1 cutoff standard coulomb
- * icoul=2 reaction-field coulomb
- * icoul=3 tabulated coulomb
- *
- * ivdw=0 no vdw interaction
- * ivdw=1 standard L-J interaction
- * ivdw=2 Buckingham
- * ivdw=3 tabulated vdw.
- *
- * Kind of ugly, but it works.
- */
-static void init_nblist(t_nblist *nl_sr,t_nblist *nl_lr,
+
+static void init_nblist(FILE *log, t_nblist *nl_sr,t_nblist *nl_lr,
int maxsr,int maxlr,
- int ivdw, int icoul,
- gmx_bool bfree, int enlist)
+ int ivdw, int ivdwmod,
+ int ielec, int ielecmod,
+ gmx_bool bfree, int igeometry)
{
t_nblist *nl;
int homenr;
int i,nn;
- int inloop[20] =
- {
- eNR_NBKERNEL_NONE,
- eNR_NBKERNEL010,
- eNR_NBKERNEL020,
- eNR_NBKERNEL030,
- eNR_NBKERNEL100,
- eNR_NBKERNEL110,
- eNR_NBKERNEL120,
- eNR_NBKERNEL130,
- eNR_NBKERNEL200,
- eNR_NBKERNEL210,
- eNR_NBKERNEL220,
- eNR_NBKERNEL230,
- eNR_NBKERNEL300,
- eNR_NBKERNEL310,
- eNR_NBKERNEL320,
- eNR_NBKERNEL330,
- eNR_NBKERNEL400,
- eNR_NBKERNEL410,
- eNR_NBKERNEL_NONE,
- eNR_NBKERNEL430
- };
-
for(i=0; (i<2); i++)
{
nl = (i == 0) ? nl_sr : nl_lr;
{
continue;
}
-
+
+
/* Set coul/vdw in neighborlist, and for the normal loops we determine
* an index of which one to call.
*/
- nl->ivdw = ivdw;
- nl->icoul = icoul;
+ nl->ivdw = ivdw;
+ nl->ivdwmod = ivdwmod;
+ nl->ielec = ielec;
+ nl->ielecmod = ielecmod;
nl->free_energy = bfree;
-
+ nl->igeometry = igeometry;
+
if (bfree)
{
- nl->enlist = enlistATOM_ATOM;
- nl->il_code = eNR_NBKERNEL_FREE_ENERGY;
+ nl->igeometry = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
}
- else
- {
- nl->enlist = enlist;
-
- nn = inloop[4*icoul + ivdw];
-
- /* solvent loops follow directly after the corresponding
- * ordinary loops, in the order:
- *
- * SPC, SPC-SPC, TIP4p, TIP4p-TIP4p
- *
- */
- switch (enlist) {
- case enlistATOM_ATOM:
- case enlistCG_CG:
- break;
- case enlistSPC_ATOM: nn += 1; break;
- case enlistSPC_SPC: nn += 2; break;
- case enlistTIP4P_ATOM: nn += 3; break;
- case enlistTIP4P_TIP4P: nn += 4; break;
- }
-
- nl->il_code = nn;
- }
-
- if (debug)
- fprintf(debug,"Initiating neighbourlist type %d for %s interactions,\nwith %d SR, %d LR atoms.\n",
- nl->il_code,ENLISTTYPE(enlist),maxsr,maxlr);
+
+ gmx_nonbonded_set_kernel_pointers( (i==0) ? log : NULL,nl);
/* maxnri is influenced by the number of shifts (maximum is 8)
* and the number of energy groups.
nl->jindex = NULL;
reallocate_nblist(nl);
nl->jindex[0] = 0;
+
+ if(debug)
+ {
+ fprintf(debug,"Initiating neighbourlist (ielec=%d, ivdw=%d, free=%d) for %s interactions,\nwith %d SR, %d LR atoms.\n",
+ nl->ielec,nl->ivdw,nl->free_energy,gmx_nblist_geometry_names[nl->igeometry],maxsr,maxlr);
+ }
+
#ifdef GMX_THREAD_SHM_FDECOMP
nl->counter = 0;
snew(nl->mtx,1);
* cache trashing.
*/
int maxsr,maxsr_wat,maxlr,maxlr_wat;
- int icoul,icoulf,ivdw;
+ int ielec,ielecf,ivdw,ielecmod,ielecmodf,ivdwmod;
int solvent;
- int enlist_def,enlist_w,enlist_ww;
+ int igeometry_def,igeometry_w,igeometry_ww;
int i;
t_nblists *nbl;
maxlr = maxlr_wat = 0;
}
- /* Determine the values for icoul/ivdw. */
- /* Start with GB */
- if(fr->bGB)
- {
- icoul=enbcoulGB;
- }
- else if (fr->bcoultab)
- {
- icoul = enbcoulTAB;
- }
- else if (EEL_RF(fr->eeltype))
- {
- icoul = enbcoulRF;
- }
- else
- {
- icoul = enbcoulOOR;
- }
-
- if (fr->bvdwtab)
- {
- ivdw = enbvdwTAB;
- }
- else if (fr->bBHAM)
- {
- ivdw = enbvdwBHAM;
- }
- else
- {
- ivdw = enbvdwLJ;
- }
+ /* Determine the values for ielec/ivdw. */
+ ielec = fr->nbkernel_elec_interaction;
+ ivdw = fr->nbkernel_vdw_interaction;
+ ielecmod = fr->nbkernel_elec_modifier;
+ ivdwmod = fr->nbkernel_vdw_modifier;
fr->ns.bCGlist = (getenv("GMX_NBLISTCG") != 0);
if (!fr->ns.bCGlist)
{
- enlist_def = enlistATOM_ATOM;
+ igeometry_def = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
}
else
{
- enlist_def = enlistCG_CG;
+ igeometry_def = GMX_NBLIST_GEOMETRY_CG_CG;
if (log != NULL)
{
fprintf(log,"\nUsing charge-group - charge-group neighbor lists and kernels\n\n");
}
if (fr->solvent_opt == esolTIP4P) {
- enlist_w = enlistTIP4P_ATOM;
- enlist_ww = enlistTIP4P_TIP4P;
+ igeometry_w = GMX_NBLIST_GEOMETRY_WATER4_PARTICLE;
+ igeometry_ww = GMX_NBLIST_GEOMETRY_WATER4_WATER4;
} else {
- enlist_w = enlistSPC_ATOM;
- enlist_ww = enlistSPC_SPC;
+ igeometry_w = GMX_NBLIST_GEOMETRY_WATER3_PARTICLE;
+ igeometry_ww = GMX_NBLIST_GEOMETRY_WATER3_WATER3;
}
for(i=0; i<fr->nnblists; i++)
{
nbl = &(fr->nblists[i]);
- init_nblist(&nbl->nlist_sr[eNL_VDWQQ],&nbl->nlist_lr[eNL_VDWQQ],
- maxsr,maxlr,ivdw,icoul,FALSE,enlist_def);
- init_nblist(&nbl->nlist_sr[eNL_VDW],&nbl->nlist_lr[eNL_VDW],
- maxsr,maxlr,ivdw,0,FALSE,enlist_def);
- init_nblist(&nbl->nlist_sr[eNL_QQ],&nbl->nlist_lr[eNL_QQ],
- maxsr,maxlr,0,icoul,FALSE,enlist_def);
- init_nblist(&nbl->nlist_sr[eNL_VDWQQ_WATER],&nbl->nlist_lr[eNL_VDWQQ_WATER],
- maxsr_wat,maxlr_wat,ivdw,icoul, FALSE,enlist_w);
- init_nblist(&nbl->nlist_sr[eNL_QQ_WATER],&nbl->nlist_lr[eNL_QQ_WATER],
- maxsr_wat,maxlr_wat,0,icoul, FALSE,enlist_w);
- init_nblist(&nbl->nlist_sr[eNL_VDWQQ_WATERWATER],&nbl->nlist_lr[eNL_VDWQQ_WATERWATER],
- maxsr_wat,maxlr_wat,ivdw,icoul, FALSE,enlist_ww);
- init_nblist(&nbl->nlist_sr[eNL_QQ_WATERWATER],&nbl->nlist_lr[eNL_QQ_WATERWATER],
- maxsr_wat,maxlr_wat,0,icoul, FALSE,enlist_ww);
+ init_nblist(log,&nbl->nlist_sr[eNL_VDWQQ],&nbl->nlist_lr[eNL_VDWQQ],
+ maxsr,maxlr,ivdw,ivdwmod,ielec,ielecmod,FALSE,igeometry_def);
+ init_nblist(log,&nbl->nlist_sr[eNL_VDW],&nbl->nlist_lr[eNL_VDW],
+ maxsr,maxlr,ivdw,ivdwmod,GMX_NBKERNEL_ELEC_NONE,eintmodNONE,FALSE,igeometry_def);
+ init_nblist(log,&nbl->nlist_sr[eNL_QQ],&nbl->nlist_lr[eNL_QQ],
+ maxsr,maxlr,GMX_NBKERNEL_VDW_NONE,eintmodNONE,ielec,ielecmod,FALSE,igeometry_def);
+ init_nblist(log,&nbl->nlist_sr[eNL_VDWQQ_WATER],&nbl->nlist_lr[eNL_VDWQQ_WATER],
+ maxsr_wat,maxlr_wat,ivdw,ivdwmod,ielec,ielecmod, FALSE,igeometry_w);
+ init_nblist(log,&nbl->nlist_sr[eNL_QQ_WATER],&nbl->nlist_lr[eNL_QQ_WATER],
+ maxsr_wat,maxlr_wat,GMX_NBKERNEL_VDW_NONE,eintmodNONE,ielec,ielecmod, FALSE,igeometry_w);
+ init_nblist(log,&nbl->nlist_sr[eNL_VDWQQ_WATERWATER],&nbl->nlist_lr[eNL_VDWQQ_WATERWATER],
+ maxsr_wat,maxlr_wat,ivdw,ivdwmod,ielec,ielecmod, FALSE,igeometry_ww);
+ init_nblist(log,&nbl->nlist_sr[eNL_QQ_WATERWATER],&nbl->nlist_lr[eNL_QQ_WATERWATER],
+ maxsr_wat,maxlr_wat,GMX_NBKERNEL_VDW_NONE,eintmodNONE,ielec,ielecmod, FALSE,igeometry_ww);
+
+ /* Did we get the solvent loops so we can use optimized water kernels? */
+ if(nbl->nlist_sr[eNL_VDWQQ_WATER].kernelptr_vf==NULL
+ || nbl->nlist_sr[eNL_QQ_WATER].kernelptr_vf==NULL
+#ifndef DISABLE_WATERWATER_NLIST
+ || nbl->nlist_sr[eNL_VDWQQ_WATERWATER].kernelptr_vf==NULL
+ || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf==NULL
+#endif
+ )
+ {
+ fr->solvent_opt = esolNO;
+ fprintf(log,"Note: The available nonbonded kernels do not support water optimization - disabling.\n");
+ }
if (fr->efep != efepNO)
{
if ((fr->bEwald) && (fr->sc_alphacoul > 0)) /* need to handle long range differently if using softcore */
{
- icoulf = enbcoulFEWALD;
+ ielecf = GMX_NBKERNEL_ELEC_EWALD;
+ ielecmodf = eintmodNONE;
}
else
{
- icoulf = icoul;
+ ielecf = ielec;
+ ielecmodf = ielecmod;
}
- init_nblist(&nbl->nlist_sr[eNL_VDWQQ_FREE],&nbl->nlist_lr[eNL_VDWQQ_FREE],
- maxsr,maxlr,ivdw,icoulf,TRUE,enlistATOM_ATOM);
- init_nblist(&nbl->nlist_sr[eNL_VDW_FREE],&nbl->nlist_lr[eNL_VDW_FREE],
- maxsr,maxlr,ivdw,0,TRUE,enlistATOM_ATOM);
- init_nblist(&nbl->nlist_sr[eNL_QQ_FREE],&nbl->nlist_lr[eNL_QQ_FREE],
- maxsr,maxlr,0,icoulf,TRUE,enlistATOM_ATOM);
+ init_nblist(log,&nbl->nlist_sr[eNL_VDWQQ_FREE],&nbl->nlist_lr[eNL_VDWQQ_FREE],
+ maxsr,maxlr,ivdw,ivdwmod,ielecf,ielecmod,TRUE,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE);
+ init_nblist(log,&nbl->nlist_sr[eNL_VDW_FREE],&nbl->nlist_lr[eNL_VDW_FREE],
+ maxsr,maxlr,ivdw,ivdwmod,GMX_NBKERNEL_ELEC_NONE,eintmodNONE,TRUE,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE);
+ init_nblist(log,&nbl->nlist_sr[eNL_QQ_FREE],&nbl->nlist_lr[eNL_QQ_FREE],
+ maxsr,maxlr,GMX_NBKERNEL_VDW_NONE,eintmodNONE,ielecf,ielecmod,TRUE,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE);
}
}
/* QMMM MM list */
if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
{
- init_nblist(&fr->QMMMlist,NULL,
- maxsr,maxlr,0,icoul,FALSE,enlistATOM_ATOM);
+ init_nblist(log,&fr->QMMMlist,NULL,
+ maxsr,maxlr,0,0,ielec,ielecmod,FALSE,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE);
+ }
+
+ if(log!=NULL)
+ {
+ fprintf(log,"\n");
}
fr->ns.nblist_initialized=TRUE;
}
}
-static void reset_neighbor_list(t_forcerec *fr,gmx_bool bLR,int nls,int eNL)
+static void reset_neighbor_lists(t_forcerec *fr,gmx_bool bResetSR, gmx_bool bResetLR)
{
int n,i;
- if (bLR)
+ if (fr->bQMMM)
{
- reset_nblist(&(fr->nblists[nls].nlist_lr[eNL]));
+ /* only reset the short-range nblist */
+ reset_nblist(&(fr->QMMMlist));
}
- else
+
+ for(n=0; n<fr->nnblists; n++)
{
- for(n=0; n<fr->nnblists; n++)
+ for(i=0; i<eNL_NR; i++)
{
- for(i=0; i<eNL_NR; i++)
+ if(bResetSR)
{
- reset_nblist(&(fr->nblists[n].nlist_sr[i]));
+ reset_nblist( &(fr->nblists[n].nlist_sr[i]) );
+ }
+ if(bResetLR)
+ {
+ reset_nblist( &(fr->nblists[n].nlist_lr[i]) );
}
- }
- if (fr->bQMMM)
- {
- /* only reset the short-range nblist */
- reset_nblist(&(fr->QMMMlist));
}
}
}
}
}
-static inline void close_neighbor_list(t_forcerec *fr,gmx_bool bLR,int nls,int eNL,
- gmx_bool bMakeQMMMnblist)
+static inline void close_neighbor_lists(t_forcerec *fr,gmx_bool bMakeQMMMnblist)
{
int n,i;
- if (bMakeQMMMnblist) {
- if (!bLR)
- {
+ if (bMakeQMMMnblist)
+ {
close_nblist(&(fr->QMMMlist));
- }
}
- else
+
+ for(n=0; n<fr->nnblists; n++)
{
- if (bLR)
+ for(i=0; (i<eNL_NR); i++)
{
- close_nblist(&(fr->nblists[nls].nlist_lr[eNL]));
- }
- else
- {
- for(n=0; n<fr->nnblists; n++)
- {
- for(i=0; (i<eNL_NR); i++)
- {
- close_nblist(&(fr->nblists[n].nlist_sr[i]));
- }
- }
+ close_nblist(&(fr->nblists[n].nlist_sr[i]));
+ close_nblist(&(fr->nblists[n].nlist_lr[i]));
}
}
}
+
static inline void add_j_to_nblist(t_nblist *nlist,atom_id j_atom,gmx_bool bLR)
{
int nrj=nlist->nrj;
{
nlist->maxnrj = over_alloc_small(nlist->nrj + 1);
if (gmx_debug_at)
- fprintf(debug,"Increasing %s nblist %s j size to %d\n",
- bLR ? "LR" : "SR",nrnb_str(nlist->il_code),nlist->maxnrj);
+ fprintf(debug,"Increasing %s nblist (ielec=%d,ivdw=%d,free=%d,igeometry=%d) j size to %d\n",
+ bLR ? "LR" : "SR",nlist->ielec,nlist->ivdw,nlist->free_energy,nlist->igeometry,nlist->maxnrj);
srenew(nlist->jjnr,nlist->maxnrj);
}
{
nlist->maxnrj = over_alloc_small(nlist->nrj + 1);
if (gmx_debug_at)
- fprintf(debug,"Increasing %s nblist %s j size to %d\n",
- bLR ? "LR" : "SR",nrnb_str(nlist->il_code),nlist->maxnrj);
+ fprintf(debug,"Increasing %s nblist (ielec=%d,ivdw=%d,free=%d,igeometry=%d) j size to %d\n",
+ bLR ? "LR" : "SR",nlist->ielec,nlist->ivdw,nlist->free_energy,nlist->igeometry,nlist->maxnrj);
srenew(nlist->jjnr ,nlist->maxnrj);
srenew(nlist->jjnr_end,nlist->maxnrj);
t_excl bExcl[],
int shift,
t_forcerec * fr,
- gmx_bool bLR,
- gmx_bool bDoVdW,
- gmx_bool bDoCoul);
+ gmx_bool bLR,
+ gmx_bool bDoVdW,
+ gmx_bool bDoCoul,
+ int solvent_opt);
static void
put_in_list_at(gmx_bool bHaveVdW[],
t_excl bExcl[],
int shift,
t_forcerec * fr,
- gmx_bool bLR,
- gmx_bool bDoVdW,
- gmx_bool bDoCoul)
+ gmx_bool bLR,
+ gmx_bool bDoVdW,
+ gmx_bool bDoCoul,
+ int solvent_opt)
{
/* The a[] index has been removed,
* to put it back in i_atom should be a[i0] and jj should be a[jj].
/* Get the i charge group info */
igid = GET_CGINFO_GID(cginfo[icg]);
- iwater = GET_CGINFO_SOLOPT(cginfo[icg]);
+
+ iwater = (solvent_opt!=esolNO) ? GET_CGINFO_SOLOPT(cginfo[icg]) : esolNO;
bFreeEnergy = FALSE;
if (md->nPerturbed)
t_excl bExcl[],
int shift,
t_forcerec * fr,
- gmx_bool bLR,
- gmx_bool bDoVdW,
- gmx_bool bDoCoul)
+ gmx_bool bLR,
+ gmx_bool bDoVdW,
+ gmx_bool bDoCoul,
+ int solvent_opt)
{
t_nblist * coul;
int i,j,jcg,igid,gid;
t_excl bExcl[],
int shift,
t_forcerec * fr,
- gmx_bool bLR,
- gmx_bool bDoVdW,
- gmx_bool bDoCoul)
+ gmx_bool bLR,
+ gmx_bool bDoVdW,
+ gmx_bool bDoCoul,
+ int solvent_opt)
{
int cginfo;
int igid,gid,nbl_ind;
if (nsbuf->nj + nrj > MAX_CG)
{
put_in_list(bHaveVdW,ngid,md,icg,jgid,nsbuf->ncg,nsbuf->jcg,
- cgs->index,bexcl,shift,fr,FALSE,TRUE,TRUE);
+ cgs->index,bexcl,shift,fr,FALSE,TRUE,TRUE,fr->solvent_opt);
/* Reset buffer contents */
nsbuf->ncg = nsbuf->nj = 0;
}
}
}
}
- }
+ }
else
{
for(j=0; (j<njcg); j++)
if (nsbuf->ncg > 0)
{
put_in_list(bHaveVdW,ngid,md,icg,nn,nsbuf->ncg,nsbuf->jcg,
- cgs->index,bexcl,k,fr,FALSE,TRUE,TRUE);
+ cgs->index,bexcl,k,fr,FALSE,TRUE,TRUE,fr->solvent_opt);
nsbuf->ncg=nsbuf->nj=0;
}
}
/* setexcl(nri,i_atoms,excl,FALSE,bexcl); */
setexcl(cgs->index[icg],cgs->index[icg+1],excl,FALSE,bexcl);
}
- close_neighbor_list(fr,FALSE,-1,-1,FALSE);
+ close_neighbor_lists(fr,FALSE);
return nsearch;
}
*
****************************************************/
-static void do_longrange(t_commrec *cr,gmx_localtop_t *top,t_forcerec *fr,
- int ngid,t_mdatoms *md,int icg,
- int jgid,int nlr,
- atom_id lr[],t_excl bexcl[],int shift,
- rvec x[],rvec box_size,t_nrnb *nrnb,
- real *lambda,real *dvdlambda,
- gmx_grppairener_t *grppener,
- gmx_bool bDoVdW,gmx_bool bDoCoul,
- gmx_bool bEvaluateNow,put_in_list_t *put_in_list,
- gmx_bool bHaveVdW[],
- gmx_bool bDoForces,rvec *f)
-{
- int n,i;
- t_nblist *nl;
-
- for(n=0; n<fr->nnblists; n++)
- {
- for(i=0; (i<eNL_NR); i++)
- {
- nl = &fr->nblists[n].nlist_lr[i];
- if ((nl->nri > nl->maxnri-32) || bEvaluateNow)
- {
- close_neighbor_list(fr,TRUE,n,i,FALSE);
- /* Evaluate the energies and forces */
- do_nonbonded(cr,fr,x,f,md,NULL,
- grppener->ener[fr->bBHAM ? egBHAMLR : egLJLR],
- grppener->ener[egCOULLR],
- grppener->ener[egGB],box_size,
- nrnb,lambda,dvdlambda,n,i,
- GMX_DONB_LR | GMX_DONB_FORCES);
-
- reset_neighbor_list(fr,TRUE,n,i);
- }
- }
- }
-
- if (!bEvaluateNow)
- {
- /* Put the long range particles in a list */
- /* do_longrange is never called for QMMM */
- put_in_list(bHaveVdW,ngid,md,icg,jgid,nlr,lr,top->cgs.index,
- bexcl,shift,fr,TRUE,bDoVdW,bDoCoul);
- }
-}
static void get_cutoff2(t_forcerec *fr,gmx_bool bDoLongRange,
real *rvdw2,real *rcoul2,
real *rs2,real *rm2,real *rl2)
{
*rs2 = sqr(fr->rlist);
+
if (bDoLongRange && fr->bTwinRange)
{
/* The VdW and elec. LR cut-off's could be different,
snew(ns->nlr_ljc,ngid);
snew(ns->nlr_one,ngid);
- if (rm2 > rs2)
- {
- /* Long range VdW and Coul buffers */
- snew(ns->nl_lr_ljc,ngid);
- }
- if (rl2 > rm2)
- {
- /* Long range VdW or Coul only buffers */
- snew(ns->nl_lr_one,ngid);
- }
+ /* Always allocate both list types, since rcoulomb might now change with PME load balancing */
+ /* Long range VdW and Coul buffers */
+ snew(ns->nl_lr_ljc,ngid);
+ /* Long range VdW or Coul only buffers */
+ snew(ns->nl_lr_one,ngid);
+
for(j=0; (j<ngid); j++) {
snew(ns->nl_sr[j],MAX_CG);
- if (rm2 > rs2)
- {
- snew(ns->nl_lr_ljc[j],MAX_CG);
- }
- if (rl2 > rm2)
- {
- snew(ns->nl_lr_one[j],MAX_CG);
- }
+ snew(ns->nl_lr_ljc[j],MAX_CG);
+ snew(ns->nl_lr_one[j],MAX_CG);
}
if (debug)
{
gmx_grppairener_t *grppener,
put_in_list_t *put_in_list,
gmx_bool bHaveVdW[],
- gmx_bool bDoLongRange,gmx_bool bDoForces,rvec *f,
- gmx_bool bMakeQMMMnblist)
+ gmx_bool bDoLongRange,gmx_bool bMakeQMMMnblist)
{
gmx_ns_t *ns;
atom_id **nl_lr_ljc,**nl_lr_one,**nl_sr;
{
if (nsr[jgid] >= MAX_CG)
{
+ /* Add to short-range list */
put_in_list(bHaveVdW,ngid,md,icg,jgid,
nsr[jgid],nl_sr[jgid],
cgs->index,/* cgsatoms, */ bexcl,
- shift,fr,FALSE,TRUE,TRUE);
+ shift,fr,FALSE,TRUE,TRUE,fr->solvent_opt);
nsr[jgid]=0;
}
nl_sr[jgid][nsr[jgid]++]=jjcg;
{
if (nlr_ljc[jgid] >= MAX_CG)
{
- do_longrange(cr,top,fr,ngid,md,icg,jgid,
- nlr_ljc[jgid],
- nl_lr_ljc[jgid],bexcl,shift,x,
- box_size,nrnb,
- lambda,dvdlambda,
- grppener,
- TRUE,TRUE,FALSE,
- put_in_list,
- bHaveVdW,
- bDoForces,f);
+ /* Add to LJ+coulomb long-range list */
+ put_in_list(bHaveVdW,ngid,md,icg,jgid,
+ nlr_ljc[jgid],nl_lr_ljc[jgid],top->cgs.index,
+ bexcl,shift,fr,TRUE,TRUE,TRUE,fr->solvent_opt);
nlr_ljc[jgid]=0;
}
nl_lr_ljc[jgid][nlr_ljc[jgid]++]=jjcg;
}
else
{
- if (nlr_one[jgid] >= MAX_CG) {
- do_longrange(cr,top,fr,ngid,md,icg,jgid,
- nlr_one[jgid],
- nl_lr_one[jgid],bexcl,shift,x,
- box_size,nrnb,
- lambda,dvdlambda,
- grppener,
- rvdw_lt_rcoul,rcoul_lt_rvdw,FALSE,
- put_in_list,
- bHaveVdW,
- bDoForces,f);
+ if (nlr_one[jgid] >= MAX_CG)
+ {
+ /* Add to long-range list with only coul, or only LJ */
+ put_in_list(bHaveVdW,ngid,md,icg,jgid,
+ nlr_one[jgid],nl_lr_one[jgid],top->cgs.index,
+ bexcl,shift,fr,TRUE,rvdw_lt_rcoul,rcoul_lt_rvdw,fr->solvent_opt);
nlr_one[jgid]=0;
}
nl_lr_one[jgid][nlr_one[jgid]++]=jjcg;
{
put_in_list(bHaveVdW,ngid,md,icg,nn,nsr[nn],nl_sr[nn],
cgs->index, /* cgsatoms, */ bexcl,
- shift,fr,FALSE,TRUE,TRUE);
+ shift,fr,FALSE,TRUE,TRUE,fr->solvent_opt);
}
if (nlr_ljc[nn] > 0)
{
- do_longrange(cr,top,fr,ngid,md,icg,nn,nlr_ljc[nn],
- nl_lr_ljc[nn],bexcl,shift,x,box_size,nrnb,
- lambda,dvdlambda,grppener,TRUE,TRUE,FALSE,
- put_in_list,bHaveVdW,bDoForces,f);
+ put_in_list(bHaveVdW,ngid,md,icg,nn,nlr_ljc[nn],
+ nl_lr_ljc[nn],top->cgs.index,
+ bexcl,shift,fr,TRUE,TRUE,TRUE,fr->solvent_opt);
}
if (nlr_one[nn] > 0)
{
- do_longrange(cr,top,fr,ngid,md,icg,nn,nlr_one[nn],
- nl_lr_one[nn],bexcl,shift,x,box_size,nrnb,
- lambda,dvdlambda,grppener,
- rvdw_lt_rcoul,rcoul_lt_rvdw,FALSE,
- put_in_list,bHaveVdW,bDoForces,f);
+ put_in_list(bHaveVdW,ngid,md,icg,nn,nlr_one[nn],
+ nl_lr_one[nn],top->cgs.index,
+ bexcl,shift,fr,TRUE,rvdw_lt_rcoul,rcoul_lt_rvdw,fr->solvent_opt);
}
}
}
/* setexcl(nri,i_atoms,&top->atoms.excl,FALSE,bexcl); */
setexcl(cgs->index[icg],cgs->index[icg+1],&top->excls,FALSE,bexcl);
}
- /* Perform any left over force calculations */
- for (nn=0; (nn<ngid); nn++)
- {
- if (rm2 > rs2)
- {
- do_longrange(cr,top,fr,0,md,icg,nn,nlr_ljc[nn],
- nl_lr_ljc[nn],bexcl,shift,x,box_size,nrnb,
- lambda,dvdlambda,grppener,
- TRUE,TRUE,TRUE,put_in_list,bHaveVdW,bDoForces,f);
- }
- if (rl2 > rm2) {
- do_longrange(cr,top,fr,0,md,icg,nn,nlr_one[nn],
- nl_lr_one[nn],bexcl,shift,x,box_size,nrnb,
- lambda,dvdlambda,grppener,
- rvdw_lt_rcoul,rcoul_lt_rvdw,
- TRUE,put_in_list,bHaveVdW,bDoForces,f);
- }
- }
+ /* No need to perform any left-over force calculations anymore (as we used to do here)
+ * since we now save the proper long-range lists for later evaluation.
+ */
+
debug_gmx();
-
- /* Close off short range neighbourlists */
- close_neighbor_list(fr,FALSE,-1,-1,bMakeQMMMnblist);
+
+ /* Close neighbourlists */
+ close_neighbor_lists(fr,bMakeQMMMnblist);
return nns;
}
real *lambda,real *dvdlambda,
gmx_grppairener_t *grppener,
gmx_bool bFillGrid,
- gmx_bool bDoLongRange,
- gmx_bool bDoForces,rvec *f)
+ gmx_bool bDoLongRangeNS)
{
t_block *cgs=&(top->cgs);
rvec box_size,grid_x0,grid_x1;
t_grid *grid;
gmx_domdec_zones_t *dd_zones;
put_in_list_t *put_in_list;
-
+
ns = &fr->ns;
/* Set some local variables */
debug_gmx();
/* Reset the neighbourlists */
- reset_neighbor_list(fr,FALSE,-1,-1);
+ reset_neighbor_lists(fr,TRUE,TRUE);
if (bGrid && bFillGrid)
{
grid,x,ns->bexcl,ns->bExcludeAlleg,
nrnb,md,lambda,dvdlambda,grppener,
put_in_list,ns->bHaveVdW,
- bDoLongRange,bDoForces,f,
- FALSE);
+ bDoLongRangeNS,FALSE);
/* neighbour searching withouth QMMM! QM atoms have zero charge in
* the classical calculation. The charge-charge interaction
grid,x,ns->bexcl,ns->bExcludeAlleg,
nrnb,md,lambda,dvdlambda,grppener,
put_in_list_qmmm,ns->bHaveVdW,
- bDoLongRange,bDoForces,f,
- TRUE);
+ bDoLongRangeNS,TRUE);
}
}
else
ngid,ns->ns_buf,put_in_list,ns->bHaveVdW);
}
debug_gmx();
-
+
#ifdef DEBUG
pr_nsblock(log);
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff