void ns(FILE *fp,
t_forcerec *fr,
matrix box,
gmx_groups_t *groups,
gmx_localtop_t *top,
t_mdatoms *md,
t_commrec *cr,
t_nrnb *nrnb,
gmx_bool bFillGrid)
{
int nsearch;
if (!fr->ns->nblist_initialized)
{
init_neighbor_list(fp, fr, md->homenr);
}
nsearch = search_neighbours(fp, fr, box, top, groups, cr, nrnb, md,
bFillGrid);
if (debug)
{
fprintf(debug, "nsearch = %d\n", nsearch);
}
/* Check whether we have to do dynamic load balancing */
/*if ((nsb->nstDlb > 0) && (mod(step,nsb->nstDlb) == 0))
count_nb(cr,nsb,&(top->blocks[ebCGS]),nns,fr->nlr,
&(top->idef),opts->ngener);
*/
if (fr->ns->dump_nl > 0)
{
dump_nblist(fp, cr, fr, fr->ns->dump_nl);
}
}
void ns(FILE *fp,
t_forcerec *fr,
rvec x[],
matrix box,
gmx_groups_t *groups,
t_grpopts *opts,
gmx_localtop_t *top,
t_mdatoms *md,
t_commrec *cr,
t_nrnb *nrnb,
real *lambda,
real *dvdlambda,
gmx_grppairener_t *grppener,
gmx_bool bFillGrid,
gmx_bool bDoLongRangeNS)
{
char *ptr;
int nsearch;
GMX_MPE_LOG(ev_ns_start);
if (!fr->ns.nblist_initialized)
{
init_neighbor_list(fp, fr, md->homenr);
}
if (fr->bTwinRange)
{
fr->nlr = 0;
}
nsearch = search_neighbours(fp, fr, x, box, top, groups, cr, nrnb, md,
lambda, dvdlambda, grppener,
bFillGrid, bDoLongRangeNS, TRUE);
if (debug)
{
fprintf(debug, "nsearch = %d\n", nsearch);
}
/* Check whether we have to do dynamic load balancing */
/*if ((nsb->nstDlb > 0) && (mod(step,nsb->nstDlb) == 0))
count_nb(cr,nsb,&(top->blocks[ebCGS]),nns,fr->nlr,
&(top->idef),opts->ngener);
*/
if (fr->ns.dump_nl > 0)
{
dump_nblist(fp, cr, fr, fr->ns.dump_nl);
}
GMX_MPE_LOG(ev_ns_finish);
}
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 ns(FILE *fp,
t_forcerec *fr,
rvec x[],
rvec f[],
matrix box,
t_groups *grps,
t_grpopts *opts,
t_topology *top,
t_mdatoms *md,
t_commrec *cr,
t_nrnb *nrnb,
t_nsborder *nsb,
int step,
real lambda,
real *dvdlambda)
{
static bool bFirst=TRUE;
static int nDNL;
char *ptr;
int nsearch;
if (bFirst) {
#ifdef SPEC_CPU
ptr = NULL;
#else
ptr=getenv("DUMPNL");
#endif
if (ptr) {
nDNL=atoi(ptr);
fprintf(fp,"nDNL = %d\n",nDNL);
} else
nDNL=0;
/* Allocate memory for the neighbor lists */
init_neighbor_list(fp,fr,HOMENR(nsb));
bFirst=FALSE;
}
if (fr->bTwinRange)
fr->nlr=0;
/* Whether or not we do dynamic load balancing,
* workload contains the proper numbers of charge groups
* to be searched.
*/
if (cr->nodeid == 0)
fr->cg0=0;
else
fr->cg0=nsb->workload[cr->nodeid-1];
fr->hcg=nsb->workload[cr->nodeid];
nsearch = search_neighbours(fp,fr,x,box,top,grps,cr,nsb,nrnb,md,
lambda,dvdlambda);
if (debug)
fprintf(debug,"nsearch = %d\n",nsearch);
/* Check whether we have to do dynamic load balancing */
/*if ((nsb->nstDlb > 0) && (mod(step,nsb->nstDlb) == 0))
count_nb(cr,nsb,&(top->blocks[ebCGS]),nns,fr->nlr,
&(top->idef),opts->ngener);
*/
if (nDNL > 0)
dump_nblist(fp,fr,nDNL);
}