void count_bonded_distances(gmx_mtop_t *mtop, const t_inputrec *ir,
double *ndistance_c, double *ndistance_simd)
{
gmx_bool bExcl;
int nst_ener_or_vir;
double nonsimd_step_frac;
int mb, nmol, ftype;
gmx_moltype_t *molt;
double ndtot_c, ndtot_simd;
#ifdef GMX_SIMD_HAVE_REAL
gmx_bool bSimdBondeds = TRUE;
#else
gmx_bool bSimdBondeds = FALSE;
#endif
bExcl = (ir->cutoff_scheme == ecutsGROUP && IR_EXCL_FORCES(*ir)
&& !EEL_FULL(ir->coulombtype));
if (bSimdBondeds)
{
/* We only have SIMD versions of these bondeds without energy and
* without shift-forces, we take that into account here.
*/
if (ir->nstcalcenergy > 0)
{
nonsimd_step_frac = 1.0/ir->nstcalcenergy;
}
else
{
nonsimd_step_frac = 0;
}
if (ir->epc != epcNO && 1.0/ir->nstpcouple > nonsimd_step_frac)
{
nonsimd_step_frac = 1.0/ir->nstpcouple;
}
}
else
{
nonsimd_step_frac = 1;
}
/* Count the number of pbc_rvec_sub calls required for bonded interactions.
* This number is also roughly proportional to the computational cost.
*/
ndtot_c = 0;
ndtot_simd = 0;
#if defined _ICC && __ICC == 1400 || defined __ICL && __ICL == 1400
#pragma novector /* Work-around for incorrect vectorization */
#endif
for (mb = 0; mb < mtop->nmolblock; mb++)
{
molt = &mtop->moltype[mtop->molblock[mb].type];
nmol = mtop->molblock[mb].nmol;
for (ftype = 0; ftype < F_NRE; ftype++)
{
int nbonds;
if (interaction_function[ftype].flags & IF_BOND)
{
double nd_c, nd_simd;
nd_c = 0;
nd_simd = 0;
/* For all interactions, except for the three exceptions
* in the switch below, #distances = #atoms - 1.
*/
switch (ftype)
{
case F_POSRES:
case F_FBPOSRES:
nd_c = 1;
break;
case F_CONNBONDS:
break;
/* These bonded potentially use SIMD */
case F_ANGLES:
case F_PDIHS:
case F_RBDIHS:
nd_c = nonsimd_step_frac *(NRAL(ftype) - 1);
nd_simd = (1 - nonsimd_step_frac)*(NRAL(ftype) - 1);
break;
default:
nd_c = NRAL(ftype) - 1;
break;
}
nbonds = nmol*molt->ilist[ftype].nr/(1 + NRAL(ftype));
ndtot_c += nbonds*nd_c;
ndtot_simd += nbonds*nd_simd;
}
}
if (bExcl)
{
ndtot_c += nmol*(molt->excls.nra - molt->atoms.nr)/2;
}
}
if (debug)
{
fprintf(debug, "nr. of distance calculations in bondeds: C %.1f SIMD %.1f\n", ndtot_c, ndtot_simd);
}
if (ndistance_c != NULL)
{
*ndistance_c = ndtot_c;
}
if (ndistance_simd != NULL)
{
*ndistance_simd = ndtot_simd;
}
}
static real optimize_ncells(FILE *fplog,
int nnodes_tot,int npme_only,
gmx_bool bDynLoadBal,real dlb_scale,
gmx_mtop_t *mtop,matrix box,gmx_ddbox_t *ddbox,
t_inputrec *ir,
gmx_domdec_t *dd,
real cellsize_limit,real cutoff,
gmx_bool bInterCGBondeds,gmx_bool bInterCGMultiBody,
ivec nc)
{
int npp,npme,ndiv,*div,*mdiv,d,nmax;
gmx_bool bExcl_pbcdx;
float pbcdxr;
real limit;
ivec itry;
limit = cellsize_limit;
dd->nc[XX] = 1;
dd->nc[YY] = 1;
dd->nc[ZZ] = 1;
npp = nnodes_tot - npme_only;
if (EEL_PME(ir->coulombtype))
{
npme = (npme_only > 0 ? npme_only : npp);
}
else
{
npme = 0;
}
if (bInterCGBondeds)
{
/* For Ewald exclusions pbc_dx is not called */
bExcl_pbcdx =
(IR_EXCL_FORCES(*ir) && !EEL_FULL(ir->coulombtype));
pbcdxr = (double)n_bonded_dx(mtop,bExcl_pbcdx)/(double)mtop->natoms;
}
else
{
/* Every molecule is a single charge group: no pbc required */
pbcdxr = 0;
}
/* Add a margin for DLB and/or pressure scaling */
if (bDynLoadBal)
{
if (dlb_scale >= 1.0)
{
gmx_fatal(FARGS,"The value for option -dds should be smaller than 1");
}
if (fplog)
{
fprintf(fplog,"Scaling the initial minimum size with 1/%g (option -dds) = %g\n",dlb_scale,1/dlb_scale);
}
limit /= dlb_scale;
}
else if (ir->epc != epcNO)
{
if (fplog)
{
fprintf(fplog,"To account for pressure scaling, scaling the initial minimum size with %g\n",DD_GRID_MARGIN_PRES_SCALE);
limit *= DD_GRID_MARGIN_PRES_SCALE;
}
}
if (fplog)
{
fprintf(fplog,"Optimizing the DD grid for %d cells with a minimum initial size of %.3f nm\n",npp,limit);
if (inhomogeneous_z(ir))
{
fprintf(fplog,"Ewald_geometry=%s: assuming inhomogeneous particle distribution in z, will not decompose in z.\n",eewg_names[ir->ewald_geometry]);
}
if (limit > 0)
{
fprintf(fplog,"The maximum allowed number of cells is:");
for(d=0; d<DIM; d++)
{
nmax = (int)(ddbox->box_size[d]*ddbox->skew_fac[d]/limit);
if (d >= ddbox->npbcdim && nmax < 2)
{
nmax = 2;
}
if (d == ZZ && inhomogeneous_z(ir))
{
nmax = 1;
}
fprintf(fplog," %c %d",'X' + d,nmax);
}
fprintf(fplog,"\n");
}
}
if (debug)
{
fprintf(debug,"Average nr of pbc_dx calls per atom %.2f\n",pbcdxr);
}
/* Decompose npp in factors */
ndiv = factorize(npp,&div,&mdiv);
itry[XX] = 1;
itry[YY] = 1;
itry[ZZ] = 1;
clear_ivec(nc);
assign_factors(dd,limit,cutoff,box,ddbox,mtop->natoms,ir,pbcdxr,
npme,ndiv,div,mdiv,itry,nc);
sfree(div);
sfree(mdiv);
return limit;
}
