gmx_lincsdata_t init_lincs(FILE *fplog,gmx_mtop_t *mtop,
int nflexcon_global,t_blocka *at2con,
gmx_bool bPLINCS,int nIter,int nProjOrder)
{
struct gmx_lincsdata *li;
int mb;
gmx_moltype_t *molt;
if (fplog)
{
fprintf(fplog,"\nInitializing%s LINear Constraint Solver\n",
bPLINCS ? " Parallel" : "");
}
snew(li,1);
li->ncg =
gmx_mtop_ftype_count(mtop,F_CONSTR) +
gmx_mtop_ftype_count(mtop,F_CONSTRNC);
li->ncg_flex = nflexcon_global;
li->ncg_triangle = 0;
for(mb=0; mb<mtop->nmolblock; mb++)
{
molt = &mtop->moltype[mtop->molblock[mb].type];
li->ncg_triangle +=
mtop->molblock[mb].nmol*
count_triangle_constraints(molt->ilist,
&at2con[mtop->molblock[mb].type]);
}
li->nIter = nIter;
li->nOrder = nProjOrder;
if (bPLINCS || li->ncg_triangle > 0)
{
please_cite(fplog,"Hess2008a");
}
else
{
please_cite(fplog,"Hess97a");
}
if (fplog)
{
fprintf(fplog,"The number of constraints is %d\n",li->ncg);
if (bPLINCS)
{
fprintf(fplog,"There are inter charge-group constraints,\n"
"will communicate selected coordinates each lincs iteration\n");
}
if (li->ncg_triangle > 0)
{
fprintf(fplog,
"%d constraints are involved in constraint triangles,\n"
"will apply an additional matrix expansion of order %d for couplings\n"
"between constraints inside triangles\n",
li->ncg_triangle,li->nOrder);
}
}
return li;
}
gmx_lincsdata_t init_lincs(FILE *fplog,gmx_mtop_t *mtop,
int nflexcon_global,t_blocka *at2con,
gmx_bool bPLINCS,int nIter,int nProjOrder)
{
struct gmx_lincsdata *li;
int mb;
gmx_moltype_t *molt;
if (fplog)
{
fprintf(fplog,"\nInitializing%s LINear Constraint Solver\n",
bPLINCS ? " Parallel" : "");
}
snew(li,1);
li->ncg =
gmx_mtop_ftype_count(mtop,F_CONSTR) +
gmx_mtop_ftype_count(mtop,F_CONSTRNC);
li->ncg_flex = nflexcon_global;
li->ncg_triangle = 0;
for(mb=0; mb<mtop->nmolblock; mb++)
{
molt = &mtop->moltype[mtop->molblock[mb].type];
li->ncg_triangle +=
mtop->molblock[mb].nmol*
count_triangle_constraints(molt->ilist,
&at2con[mtop->molblock[mb].type]);
}
li->nIter = nIter;
li->nOrder = nProjOrder;
/* LINCS can run on any number of threads.
* Currently the number is fixed for the whole simulation,
* but it could be set in set_lincs().
*/
li->nth = gmx_omp_nthreads_get(emntLINCS);
if (li->nth == 1)
{
snew(li->th,1);
}
else
{
/* Allocate an extra elements for "thread-overlap" constraints */
snew(li->th,li->nth+1);
}
if (debug)
{
fprintf(debug,"LINCS: using %d threads\n",li->nth);
}
if (bPLINCS || li->ncg_triangle > 0)
{
please_cite(fplog,"Hess2008a");
}
else
{
please_cite(fplog,"Hess97a");
}
if (fplog)
{
fprintf(fplog,"The number of constraints is %d\n",li->ncg);
if (bPLINCS)
{
fprintf(fplog,"There are inter charge-group constraints,\n"
"will communicate selected coordinates each lincs iteration\n");
}
if (li->ncg_triangle > 0)
{
fprintf(fplog,
"%d constraints are involved in constraint triangles,\n"
"will apply an additional matrix expansion of order %d for couplings\n"
"between constraints inside triangles\n",
li->ncg_triangle,li->nOrder);
}
}
return li;
}
