t_graph *mk_graph(FILE *fplog,
const t_idef *idef, int at_start, int at_end,
gmx_bool bShakeOnly, gmx_bool bSettle)
{
t_graph *g;
snew(g, 1);
mk_graph_ilist(fplog, idef->il, at_start, at_end, bShakeOnly, bSettle, g);
return g;
}
static void low_do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
gmx_mtop_t *mtop,rvec x[],
bool bFirst)
{
t_graph *graph;
int mb,as,mol;
gmx_molblock_t *molb;
if (bFirst && fplog)
fprintf(fplog,"Removing pbc first time\n");
snew(graph,1);
as = 0;
for(mb=0; mb<mtop->nmolblock; mb++) {
molb = &mtop->molblock[mb];
if (molb->natoms_mol == 1 ||
(!bFirst && mtop->moltype[molb->type].cgs.nr == 1)) {
/* Just one atom or charge group in the molecule, no PBC required */
as += molb->nmol*molb->natoms_mol;
} else {
/* Pass NULL iso fplog to avoid graph prints for each molecule type */
mk_graph_ilist(NULL,mtop->moltype[molb->type].ilist,
0,molb->natoms_mol,FALSE,FALSE,graph);
for(mol=0; mol<molb->nmol; mol++) {
mk_mshift(fplog,graph,ePBC,box,x+as);
shift_self(graph,box,x+as);
/* The molecule is whole now.
* We don't need the second mk_mshift call as in do_pbc_first,
* since we no longer need this graph.
*/
as += molb->natoms_mol;
}
done_graph(graph);
}
}
sfree(graph);
}
