{
if (gmx_debug_at)
{
- 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);
+ fprintf(debug,"reallocating neigborlist (ielec=%d, ivdw=%d, igeometry=%d, type=%d), maxnri=%d\n",
+ nl->ielec,nl->ivdw,nl->igeometry,nl->type,nl->maxnri);
}
srenew(nl->iinr, nl->maxnri);
if (nl->igeometry == GMX_NBLIST_GEOMETRY_CG_CG)
int maxsr,int maxlr,
int ivdw, int ivdwmod,
int ielec, int ielecmod,
- gmx_bool bfree, int igeometry)
+ int igeometry, int type)
{
t_nblist *nl;
int homenr;
nl->ivdwmod = ivdwmod;
nl->ielec = ielec;
nl->ielecmod = ielecmod;
- nl->free_energy = bfree;
+ nl->type = type;
nl->igeometry = igeometry;
- if (bfree)
+ if (nl->type==GMX_NBLIST_INTERACTION_FREE_ENERGY)
{
nl->igeometry = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
}
-
+
/* This will also set the simd_padding_width field */
gmx_nonbonded_set_kernel_pointers( (i==0) ? log : NULL,nl);
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);
+ fprintf(debug,"Initiating neighbourlist (ielec=%d, ivdw=%d, type=%d) for %s interactions,\nwith %d SR, %d LR atoms.\n",
+ nl->ielec,nl->ivdw,nl->type,gmx_nblist_geometry_names[nl->igeometry],maxsr,maxlr);
}
}
}
* cache trashing.
*/
int maxsr,maxsr_wat,maxlr,maxlr_wat;
- int ielec,ielecf,ivdw,ielecmod,ielecmodf,ivdwmod;
+ int ielec,ielecf,ivdw,ielecmod,ielecmodf,ivdwmod,type;
int solvent;
int igeometry_def,igeometry_w,igeometry_ww;
int i;
ivdw = fr->nbkernel_vdw_interaction;
ielecmod = fr->nbkernel_elec_modifier;
ivdwmod = fr->nbkernel_vdw_modifier;
+ type = GMX_NBLIST_INTERACTION_STANDARD;
fr->ns.bCGlist = (getenv("GMX_NBLISTCG") != 0);
if (!fr->ns.bCGlist)
for(i=0; i<fr->nnblists; i++)
{
nbl = &(fr->nblists[i]);
+
+ if ((fr->adress_type!=eAdressOff) && (i>=fr->nnblists/2)){
+ type=GMX_NBLIST_INTERACTION_ADRESS;
+ }
init_nblist(log,&nbl->nlist_sr[eNL_VDWQQ],&nbl->nlist_lr[eNL_VDWQQ],
- maxsr,maxlr,ivdw,ivdwmod,ielec,ielecmod,FALSE,igeometry_def);
+ maxsr,maxlr,ivdw,ivdwmod,ielec,ielecmod,igeometry_def, type);
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);
+ maxsr,maxlr,ivdw,ivdwmod,GMX_NBKERNEL_ELEC_NONE,eintmodNONE,igeometry_def, type);
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);
+ maxsr,maxlr,GMX_NBKERNEL_VDW_NONE,eintmodNONE,ielec,ielecmod,igeometry_def, type);
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);
+ maxsr_wat,maxlr_wat,ivdw,ivdwmod,ielec,ielecmod, igeometry_w, type);
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);
+ maxsr_wat,maxlr_wat,GMX_NBKERNEL_VDW_NONE,eintmodNONE,ielec,ielecmod, igeometry_w, type);
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);
+ maxsr_wat,maxlr_wat,ivdw,ivdwmod,ielec,ielecmod, igeometry_ww, type);
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);
+ maxsr_wat,maxlr_wat,GMX_NBKERNEL_VDW_NONE,eintmodNONE,ielec,ielecmod, igeometry_ww, type);
/* Did we get the solvent loops so we can use optimized water kernels? */
if(nbl->nlist_sr[eNL_VDWQQ_WATER].kernelptr_vf==NULL
}
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);
+ maxsr,maxlr,ivdw,ivdwmod,ielecf,ielecmod,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY);
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);
+ maxsr,maxlr,ivdw,ivdwmod,GMX_NBKERNEL_ELEC_NONE,eintmodNONE,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY);
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);
+ maxsr,maxlr,GMX_NBKERNEL_VDW_NONE,eintmodNONE,ielecf,ielecmod,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY);
}
}
/* QMMM MM list */
if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
{
init_nblist(log,&fr->QMMMlist,NULL,
- maxsr,maxlr,0,0,ielec,ielecmod,FALSE,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE);
+ maxsr,maxlr,0,0,ielec,ielecmod,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_STANDARD);
}
if(log!=NULL)
nlist->maxnrj = round_up_to_simd_width(over_alloc_small(nlist->nrj + 1),nlist->simd_padding_width);
if (gmx_debug_at)
- 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);
+ fprintf(debug,"Increasing %s nblist (ielec=%d,ivdw=%d,type=%d,igeometry=%d) j size to %d\n",
+ bLR ? "LR" : "SR",nlist->ielec,nlist->ivdw,nlist->type,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 (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);
+ fprintf(debug,"Increasing %s nblist (ielec=%d,ivdw=%d,type=%d,igeometry=%d) j size to %d\n",
+ bLR ? "LR" : "SR",nlist->ielec,nlist->ivdw,nlist->type,nlist->igeometry,nlist->maxnrj);
srenew(nlist->jjnr ,nlist->maxnrj);
srenew(nlist->jjnr_end,nlist->maxnrj);
{
continue;
}
-
+
jj0 = index[jcg];
jwater = GET_CGINFO_SOLOPT(cginfo[jcg]);
#endif
}
}
- else if (iwater == esolTIP4P && jwater == esolTIP4P)
+ else if (iwater == esolTIP4P && jwater == esolTIP4P)
{
/* Interaction between two TIP4p molecules */
if (!bDoCoul)
}
}
+static void
+put_in_list_adress(gmx_bool bHaveVdW[],
+ int ngid,
+ t_mdatoms * md,
+ int icg,
+ int jgid,
+ int nj,
+ atom_id jjcg[],
+ atom_id index[],
+ t_excl bExcl[],
+ int shift,
+ t_forcerec * fr,
+ 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].
+ */
+ t_nblist * vdwc;
+ t_nblist * vdw;
+ t_nblist * coul;
+ t_nblist * vdwc_adress = NULL;
+ t_nblist * vdw_adress = NULL;
+ t_nblist * coul_adress = NULL;
+ t_nblist * vdwc_ww = NULL;
+ t_nblist * coul_ww = NULL;
+
+ int i,j,jcg,igid,gid,nbl_ind,nbl_ind_adress;
+ atom_id jj,jj0,jj1,i_atom;
+ int i0,nicg,len;
+
+ int *cginfo;
+ int *type,*typeB;
+ real *charge,*chargeB;
+ real *wf;
+ real qi,qiB,qq,rlj;
+ gmx_bool bFreeEnergy,bFree,bFreeJ,bNotEx,*bPert;
+ gmx_bool bDoVdW_i,bDoCoul_i,bDoCoul_i_sol;
+ gmx_bool b_hybrid;
+ gmx_bool j_all_atom;
+ int iwater,jwater;
+ t_nblist *nlist, *nlist_adress;
+
+ /* Copy some pointers */
+ cginfo = fr->cginfo;
+ charge = md->chargeA;
+ chargeB = md->chargeB;
+ type = md->typeA;
+ typeB = md->typeB;
+ bPert = md->bPerturbed;
+ wf = md->wf;
+
+ /* Get atom range */
+ i0 = index[icg];
+ nicg = index[icg+1]-i0;
+
+ /* Get the i charge group info */
+ igid = GET_CGINFO_GID(cginfo[icg]);
+
+ iwater = (solvent_opt!=esolNO) ? GET_CGINFO_SOLOPT(cginfo[icg]) : esolNO;
+
+ if (md->nPerturbed)
+ {
+ gmx_fatal(FARGS,"AdResS does not support free energy pertubation\n");
+ }
+
+ /* Unpack pointers to neighbourlist structs */
+ if (fr->nnblists == 2)
+ {
+ nbl_ind = 0;
+ nbl_ind_adress = 1;
+ }
+ else
+ {
+ nbl_ind = fr->gid2nblists[GID(igid,jgid,ngid)];
+ nbl_ind_adress = nbl_ind+fr->nnblists/2;
+ }
+ if (bLR)
+ {
+ nlist = fr->nblists[nbl_ind].nlist_lr;
+ nlist_adress= fr->nblists[nbl_ind_adress].nlist_lr;
+ }
+ else
+ {
+ nlist = fr->nblists[nbl_ind].nlist_sr;
+ nlist_adress = fr->nblists[nbl_ind_adress].nlist_sr;
+ }
+
+
+ vdwc = &nlist[eNL_VDWQQ];
+ vdw = &nlist[eNL_VDW];
+ coul = &nlist[eNL_QQ];
+
+ vdwc_adress = &nlist_adress[eNL_VDWQQ];
+ vdw_adress = &nlist_adress[eNL_VDW];
+ coul_adress = &nlist_adress[eNL_QQ];
+
+ /* We do not support solvent optimization with AdResS for now.
+ For this we would need hybrid solvent-other kernels */
+
+ /* no solvent as i charge group */
+ /* Loop over the atoms in the i charge group */
+ for(i=0; i<nicg; i++)
+ {
+ i_atom = i0+i;
+ gid = GID(igid,jgid,ngid);
+ qi = charge[i_atom];
+
+ /* Create new i_atom for each energy group */
+ if (bDoVdW && bDoCoul)
+ {
+ new_i_nblist(vdwc,bLR,i_atom,shift,gid);
+ new_i_nblist(vdwc_adress,bLR,i_atom,shift,gid);
+
+ }
+ if (bDoVdW)
+ {
+ new_i_nblist(vdw,bLR,i_atom,shift,gid);
+ new_i_nblist(vdw_adress,bLR,i_atom,shift,gid);
+
+ }
+ if (bDoCoul)
+ {
+ new_i_nblist(coul,bLR,i_atom,shift,gid);
+ new_i_nblist(coul_adress,bLR,i_atom,shift,gid);
+ }
+ bDoVdW_i = (bDoVdW && bHaveVdW[type[i_atom]]);
+ bDoCoul_i = (bDoCoul && qi!=0);
+
+ if (bDoVdW_i || bDoCoul_i)
+ {
+ /* Loop over the j charge groups */
+ for(j=0; (j<nj); j++)
+ {
+ jcg=jjcg[j];
+
+ /* Check for large charge groups */
+ if (jcg == icg)
+ {
+ jj0 = i0 + i + 1;
+ }
+ else
+ {
+ jj0 = index[jcg];
+ }
+
+ jj1=index[jcg+1];
+ /* Finally loop over the atoms in the j-charge group */
+ for(jj=jj0; jj<jj1; jj++)
+ {
+ bNotEx = NOTEXCL(bExcl,i,jj);
+
+ b_hybrid=!((wf[i_atom]==1&&wf[jj]==1)||(wf[i_atom] ==0 && wf[jj]==0));
+
+ if (bNotEx)
+ {
+ if (!bDoVdW_i)
+ {
+ if (charge[jj] != 0)
+ {
+ if(!b_hybrid){
+ add_j_to_nblist(coul,jj,bLR);
+ }else{
+ add_j_to_nblist(coul_adress,jj,bLR);
+ }
+ }
+ }
+ else if (!bDoCoul_i)
+ {
+ if (bHaveVdW[type[jj]])
+ {
+ if(!b_hybrid){
+ add_j_to_nblist(vdw,jj,bLR);
+ }else{
+ add_j_to_nblist(vdw_adress,jj,bLR);
+ }
+ }
+ }
+ else
+ {
+ if (bHaveVdW[type[jj]])
+ {
+ if (charge[jj] != 0)
+ {
+ if(!b_hybrid){
+ add_j_to_nblist(vdwc,jj,bLR);
+ }else{
+ add_j_to_nblist(vdwc_adress,jj,bLR);
+ }
+ }
+ else
+ {
+ if(!b_hybrid){
+ add_j_to_nblist(vdw,jj,bLR);
+ }else{
+ add_j_to_nblist(vdw_adress,jj,bLR);
+ }
+
+ }
+ }
+ else if (charge[jj] != 0)
+ {
+ if(!b_hybrid){
+ add_j_to_nblist(coul,jj,bLR);
+ }else{
+ add_j_to_nblist(coul_adress,jj,bLR);
+ }
+
+ }
+ }
+ }
+ }
+ }
+
+ close_i_nblist(vdw);
+ close_i_nblist(coul);
+ close_i_nblist(vdwc);
+ close_i_nblist(vdw_adress);
+ close_i_nblist(coul_adress);
+ close_i_nblist(vdwc_adress);
+ }
+ }
+}
+
static void
put_in_list_qmmm(gmx_bool bHaveVdW[],
int ngid,
fill_grid(log,NULL,ns->grid,fr->hcg,fr->hcg-1,fr->hcg,fr->cg_cm);
}
debug_gmx();
-
- if (!fr->ns.bCGlist)
- {
- put_in_list = put_in_list_at;
- }
- else
- {
- put_in_list = put_in_list_cg;
+
+ if (fr->adress_type == eAdressOff){
+ if (!fr->ns.bCGlist)
+ {
+ put_in_list = put_in_list_at;
+ }
+ else
+ {
+ put_in_list = put_in_list_cg;
+ }
+ }else{
+ put_in_list = put_in_list_adress;
}
/* Do the core! */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff