/*! \brief
* Initializes position calculation using the maximum possible input index.
*
* \param[in,out] pc Position calculation data structure.
* \param[in] g Maximum index group for the calculation.
* \param[in] bBase Whether \p pc will be used as a base or not.
*
* \p bBase affects on how the \p pc->gmax field is initialized.
*/
static void
set_poscalc_maxindex(gmx_ana_poscalc_t *pc, gmx_ana_index_t *g, bool bBase)
{
e_index_t ptype;
ptype = index_type_for_poscalc(pc->type);
gmx_ana_index_make_block(&pc->b, pc->coll->top, g, ptype, pc->flags & POS_COMPLWHOLE);
/* Set the type to POS_ATOM if the calculation in fact is such. */
if (pc->b.nr == pc->b.nra)
{
pc->type = POS_ATOM;
pc->flags &= ~(POS_MASS | POS_COMPLMAX | POS_COMPLWHOLE);
}
/* Set the POS_COMPLWHOLE flag if the calculation in fact always uses
* complete residues and molecules. */
if (!(pc->flags & POS_COMPLWHOLE)
&& (!(pc->flags & POS_DYNAMIC) || (pc->flags & POS_COMPLMAX))
&& (pc->type == POS_RES || pc->type == POS_MOL)
&& gmx_ana_index_has_complete_elems(g, ptype, pc->coll->top))
{
pc->flags &= ~POS_COMPLMAX;
pc->flags |= POS_COMPLWHOLE;
}
/* Setup the gmax field */
if ((pc->flags & POS_COMPLWHOLE) && !bBase && pc->b.nra > g->isize)
{
gmx_ana_index_copy(&pc->gmax, g, TRUE);
sfree(pc->gmax.name);
pc->gmax.name = NULL;
}
else
{
gmx_ana_index_set(&pc->gmax, pc->b.nra, pc->b.a, NULL, 0);
}
}
/*!
* \param[in] pc Position calculation data structure.
* \param[out] p Output positions.
*
* Calls to gmx_ana_poscalc_update() using \p pc should use only positions
* initialized with this function.
* The \c p->g pointer is initialized to point to an internal group that
* contains the maximum index group set with gmx_ana_poscalc_set_maxindex().
*/
void
gmx_ana_poscalc_init_pos(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p)
{
e_index_t ptype;
ptype = index_type_for_poscalc(pc->type);
gmx_ana_indexmap_init(&p->m, &pc->gmax, pc->coll->top, ptype);
gmx_ana_pos_reserve(p, p->m.nr, 0);
p->g = &pc->gmax;
}
gmx_ana_poscalc_t *
PositionCalculationCollection::Impl::createCalculation(e_poscalc_t type, int flags)
{
gmx_ana_poscalc_t *pc;
snew(pc, 1);
pc->type = type;
pc->itype = index_type_for_poscalc(type);
gmx_ana_poscalc_set_flags(pc, flags);
pc->refcount = 1;
pc->coll = this;
insertCalculation(pc, NULL);
return pc;
}
void
PositionCalculationCollection::printTree(FILE *fp) const
{
gmx_ana_poscalc_t *pc;
int i, j;
fprintf(fp, "Position calculations:\n");
i = 1;
pc = impl_->first_;
while (pc)
{
fprintf(fp, "%2d ", i);
switch (pc->type)
{
case POS_ATOM: fprintf(fp, "ATOM"); break;
case POS_RES: fprintf(fp, "RES"); break;
case POS_MOL: fprintf(fp, "MOL"); break;
case POS_ALL: fprintf(fp, "ALL"); break;
case POS_ALL_PBC: fprintf(fp, "ALL_PBC"); break;
}
if (pc->itype != index_type_for_poscalc(pc->type))
{
fprintf(fp, " (");
switch (pc->itype)
{
case INDEX_UNKNOWN: fprintf(fp, "???"); break;
case INDEX_ATOM: fprintf(fp, "ATOM"); break;
case INDEX_RES: fprintf(fp, "RES"); break;
case INDEX_MOL: fprintf(fp, "MOL"); break;
case INDEX_ALL: fprintf(fp, "ALL"); break;
}
fprintf(fp, ")");
}
fprintf(fp, " flg=");
if (pc->flags & POS_MASS)
{
fprintf(fp, "M");
}
if (pc->flags & POS_DYNAMIC)
{
fprintf(fp, "D");
}
if (pc->flags & POS_MASKONLY)
{
fprintf(fp, "A");
}
if (pc->flags & POS_COMPLMAX)
{
fprintf(fp, "Cm");
}
if (pc->flags & POS_COMPLWHOLE)
{
fprintf(fp, "Cw");
}
if (!pc->flags)
{
fprintf(fp, "0");
}
fprintf(fp, " nr=%d nra=%d", pc->b.nr, pc->b.nra);
fprintf(fp, " refc=%d", pc->refcount);
fprintf(fp, "\n");
if (pc->gmax.nalloc_index > 0)
{
fprintf(fp, " Group: ");
if (pc->gmax.isize > 20)
{
fprintf(fp, " %d atoms", pc->gmax.isize);
}
else
{
for (j = 0; j < pc->gmax.isize; ++j)
{
fprintf(fp, " %d", pc->gmax.index[j] + 1);
}
}
fprintf(fp, "\n");
}
if (pc->b.nalloc_a > 0)
{
fprintf(fp, " Atoms: ");
if (pc->b.nra > 20)
{
fprintf(fp, " %d atoms", pc->b.nra);
}
else
{
for (j = 0; j < pc->b.nra; ++j)
{
fprintf(fp, " %d", pc->b.a[j] + 1);
}
}
fprintf(fp, "\n");
}
if (pc->b.nalloc_index > 0)
{
fprintf(fp, " Blocks:");
if (pc->b.nr > 20)
{
fprintf(fp, " %d pcs", pc->b.nr);
}
else
{
for (j = 0; j <= pc->b.nr; ++j)
{
fprintf(fp, " %d", pc->b.index[j]);
}
}
fprintf(fp, "\n");
}
if (pc->sbase)
{
gmx_ana_poscalc_t *base;
fprintf(fp, " Base: ");
j = 1;
base = impl_->first_;
while (base && base != pc->sbase)
{
++j;
base = base->next;
}
fprintf(fp, "%d", j);
if (pc->baseid && pc->b.nr <= 20)
{
fprintf(fp, " id:");
for (j = 0; j < pc->b.nr; ++j)
{
fprintf(fp, " %d", pc->baseid[j]+1);
}
}
fprintf(fp, "\n");
}
++i;
pc = pc->next;
}
}
