t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx)
{
t_cluster_ndx *c;
int i;
snew(c, 1);
c->clust = init_index(ndx, &c->grpname);
c->maxframe = -1;
for (i = 0; (i < c->clust->nra); i++)
{
c->maxframe = max(c->maxframe, c->clust->a[i]);
}
fprintf(fplog ? fplog : stdout,
"There are %d clusters containing %d structures, highest framenr is %d\n",
c->clust->nr, c->clust->nra, c->maxframe);
if (debug)
{
pr_blocka(debug, 0, "clust", c->clust, TRUE);
for (i = 0; (i < c->clust->nra); i++)
{
if ((c->clust->a[i] < 0) || (c->clust->a[i] > c->maxframe))
{
gmx_fatal(FARGS, "Range check error for c->clust->a[%d] = %d\n"
"should be within 0 and %d", i, c->clust->a[i], c->maxframe+1);
}
}
}
c->inv_clust = make_invblocka(c->clust, c->maxframe);
return c;
}
void chk_ndx(const char *fn)
{
t_blocka *grps;
char **grpname;
int i, j;
grps = init_index(fn, &grpname);
if (debug)
{
pr_blocka(debug, 0, fn, grps, FALSE);
}
else
{
printf("Contents of index file %s\n", fn);
printf("--------------------------------------------------\n");
printf("Nr. Group #Entries First Last\n");
for (i = 0; (i < grps->nr); i++)
{
printf("%4d %-20s%8d%8d%8d\n", i, grpname[i],
grps->index[i+1]-grps->index[i],
grps->a[grps->index[i]]+1,
grps->a[grps->index[i+1]-1]+1);
}
}
for (i = 0; (i < grps->nr); i++)
{
sfree(grpname[i]);
}
sfree(grpname);
done_blocka(grps);
}
void pr_top(FILE *fp,int indent,const char *title,t_topology *top, gmx_bool bShowNumbers)
{
if (available(fp,top,indent,title)) {
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"name=\"%s\"\n",*(top->name));
pr_atoms(fp,indent,"atoms",&(top->atoms),bShowNumbers);
pr_atomtypes(fp,indent,"atomtypes",&(top->atomtypes),bShowNumbers);
pr_block(fp,indent,"cgs",&top->cgs, bShowNumbers);
pr_block(fp,indent,"mols",&top->mols, bShowNumbers);
pr_blocka(fp,indent,"excls",&top->excls, bShowNumbers);
pr_idef(fp,indent,"idef",&top->idef,bShowNumbers);
}
}
void pr_top(FILE *fp, int indent, const char *title, const t_topology *top, gmx_bool bShowNumbers)
{
if (available(fp, top, indent, title))
{
indent = pr_title(fp, indent, title);
pr_indent(fp, indent);
fprintf(fp, "name=\"%s\"\n", *(top->name));
pr_atoms(fp, indent, "atoms", &(top->atoms), bShowNumbers);
pr_atomtypes(fp, indent, "atomtypes", &(top->atomtypes), bShowNumbers);
pr_block(fp, indent, "cgs", &top->cgs, bShowNumbers);
pr_block(fp, indent, "mols", &top->mols, bShowNumbers);
pr_str(fp, indent, "bIntermolecularInteractions",
gmx::boolToString(top->bIntermolecularInteractions));
pr_blocka(fp, indent, "excls", &top->excls, bShowNumbers);
pr_idef(fp, indent, "idef", &top->idef, bShowNumbers);
}
}
static void pr_moltype(FILE *fp,int indent,const char *title,
gmx_moltype_t *molt,int n,
gmx_ffparams_t *ffparams,
gmx_bool bShowNumbers)
{
int j;
indent = pr_title_n(fp,indent,title,n);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"name=\"%s\"\n",*(molt->name));
pr_atoms(fp,indent,"atoms",&(molt->atoms),bShowNumbers);
pr_block(fp,indent,"cgs",&molt->cgs, bShowNumbers);
pr_blocka(fp,indent,"excls",&molt->excls, bShowNumbers);
for(j=0; (j<F_NRE); j++) {
pr_ilist(fp,indent,interaction_function[j].longname,
ffparams->functype,&molt->ilist[j],bShowNumbers);
}
}
