/*! \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] data Data for the current frame.
* \param[in] sel Selection element being evaluated.
* \param[in] g Group for which \p sel should be evaluated.
* \returns 0 on success, a non-zero error code on error.
*
* If this is the first call for this frame, evaluates the child element
* there should be exactly one in \p g.
* The compiler has taken care that the child actually stores the evaluated
* value in the value pointer of this element.
* Assumes that \p g is persistent for the duration of the whole evaluation.
*
* This function is used as \c t_selelem::evaluate for \ref SEL_SUBEXPR
* elements that have a static evaluation group, and hence do not need full
* subexpression handling.
*/
void
_gmx_sel_evaluate_subexpr_staticeval(gmx_sel_evaluate_t *data, t_selelem *sel, gmx_ana_index_t *g)
{
if (sel->u.cgrp.isize == 0)
{
sel->child->evaluate(data, sel->child, g);
sel->v.nr = sel->child->v.nr;
gmx_ana_index_set(&sel->u.cgrp, g->isize, g->index, sel->u.cgrp.name, 0);
}
}
void SelectionTreeElement::resolveIndexGroupReference(
gmx_ana_indexgrps_t *grps, int natoms)
{
GMX_RELEASE_ASSERT(type == SEL_GROUPREF,
"Should only be called for index group reference elements");
if (grps == NULL)
{
std::string message = formatString(
"Cannot match '%s', because index groups are not available.",
name().c_str());
GMX_THROW(InconsistentInputError(message));
}
gmx_ana_index_t foundGroup;
std::string foundName;
if (u.gref.name != NULL)
{
if (!gmx_ana_indexgrps_find(&foundGroup, &foundName, grps, u.gref.name))
{
std::string message = formatString(
"Cannot match '%s', because no such index group can be found.",
name().c_str());
GMX_THROW(InconsistentInputError(message));
}
}
else
{
if (!gmx_ana_indexgrps_extract(&foundGroup, &foundName, grps, u.gref.id))
{
std::string message = formatString(
"Cannot match '%s', because no such index group can be found.",
name().c_str());
GMX_THROW(InconsistentInputError(message));
}
}
if (!gmx_ana_index_check_sorted(&foundGroup))
{
flags |= SEL_UNSORTED;
}
sfree(u.gref.name);
type = SEL_CONST;
gmx_ana_index_set(&u.cgrp, foundGroup.isize, foundGroup.index,
foundGroup.nalloc_index);
setName(foundName);
if (natoms > 0)
{
checkIndexGroup(natoms);
}
}
/*!
* \param[out] g Index group structure.
* \param[in] ngrps Number of index groups.
* \param[in] isize Array of index group sizes.
* \param[in] index Array of pointers to indices of each group.
* \param[in] name Array of names of the groups.
* \param[in] bFree If TRUE, the \p isize, \p index and \p name arrays
* are freed after they have been copied.
*/
void
gmx_ana_indexgrps_set(gmx_ana_indexgrps_t **g, int ngrps, int *isize,
atom_id **index, char **name, bool bFree)
{
int i;
gmx_ana_indexgrps_alloc(g, ngrps);
for (i = 0; i < ngrps; ++i)
{
gmx_ana_index_set(&(*g)->g[i], isize[i], index[i], name[i], isize[i]);
}
if (bFree)
{
sfree(isize);
sfree(index);
sfree(name);
}
}
/*! \brief
* Checks whether two position calculations should use a common base.
*
* \param[in] pc1 Calculation 1 to check for.
* \param[in] pc2 Calculation 2 to check for.
* \param[in] g1 Index group structure that contains the atoms from
* \p pc1.
* \param[in,out] g Working space, should have enough allocated memory to
* contain the intersection of the atoms in \p pc1 and \p pc2.
* \returns TRUE if the two calculations should be merged to use a common
* base, FALSE otherwise.
*/
static bool
should_merge(gmx_ana_poscalc_t *pc1, gmx_ana_poscalc_t *pc2,
gmx_ana_index_t *g1, gmx_ana_index_t *g)
{
gmx_ana_index_t g2;
/* Do not merge calculations with different mass weighting. */
if ((pc1->flags & POS_MASS) != (pc2->flags & POS_MASS))
{
return FALSE;
}
/* Avoid messing up complete calculations. */
if ((pc1->flags & POS_COMPLWHOLE) != (pc2->flags & POS_COMPLWHOLE))
{
return FALSE;
}
/* Find the overlap between the calculations. */
gmx_ana_index_set(&g2, pc2->b.nra, pc2->b.a, NULL, 0);
gmx_ana_index_intersection(g, g1, &g2);
/* Do not merge if there is no overlap. */
if (g->isize == 0)
{
return FALSE;
}
/* Full completion calculations always match if the type is correct. */
if ((pc1->flags & POS_COMPLWHOLE) && (pc2->flags & POS_COMPLWHOLE)
&& pc1->type == pc2->type)
{
return TRUE;
}
/* The calculations also match if the intersection consists of full
* blocks. */
if (gmx_ana_index_has_full_ablocks(g, &pc1->b)
&& gmx_ana_index_has_full_ablocks(g, &pc2->b))
{
return TRUE;
}
return FALSE;
}
/*! \brief
* Setups the static base calculation for a position calculation.
*
* \param[in,out] pc Position calculation to setup the base for.
*/
static void
setup_base(gmx_ana_poscalc_t *pc)
{
gmx_ana_poscalc_t *base, *pbase, *next;
gmx_ana_index_t gp, g;
/* Exit immediately if pc should not have a base. */
if (!can_use_base(pc))
{
return;
}
gmx_ana_index_set(&gp, pc->b.nra, pc->b.a, NULL, 0);
gmx_ana_index_clear(&g);
gmx_ana_index_reserve(&g, pc->b.nra);
pbase = pc;
base = pc->coll->first;
while (base)
{
/* Save the next calculation so that we can safely delete base */
next = base->next;
/* Skip pc, calculations that already have a base (we should match the
* base instead), as well as calculations that should not have a base.
* If the above conditions are met, check whether we should do a
* merge.
*/
if (base != pc && !base->sbase && can_use_base(base)
&& should_merge(pbase, base, &gp, &g))
{
/* Check whether this is the first base found */
if (pbase == pc)
{
/* Create a real base if one is not present */
if (!base->p)
{
pbase = create_simple_base(base);
}
else
{
pbase = base;
}
/* Make it a base for pc as well */
merge_to_base(pbase, pc);
pc->sbase = pbase;
pbase->refcount++;
}
else /* This was not the first base */
{
if (!base->p)
{
/* If it is not a real base, just make the new base as
* the base for it as well. */
merge_to_base(pbase, base);
base->sbase = pbase;
pbase->refcount++;
}
else
{
/* If base is a real base, merge it with the new base
* and delete it. */
merge_bases(pbase, base);
}
}
gmx_ana_index_set(&gp, pbase->b.nra, pbase->b.a, NULL, 0);
gmx_ana_index_reserve(&g, pc->b.nra);
}
/* Proceed to the next unchecked calculation */
base = next;
}
gmx_ana_index_deinit(&g);
/* If no base was found, create one if one is required */
if (!pc->sbase && (pc->flags & POS_DYNAMIC)
&& (pc->flags & (POS_COMPLMAX | POS_COMPLWHOLE)))
{
create_simple_base(pc);
}
}
/*! \brief
* Merges a calculation into another calculation such that the new calculation
* can be used as a base.
*
* \param[in,out] base Base calculation to merge to.
* \param[in,out] pc Position calculation to merge to \p base.
*
* After the call, \p base can be used as a base for \p pc (or any calculation
* that used it as a base).
* It is assumed that any overlap between \p base and \p pc is in complete
* blocks, i.e., that the merge is possible.
*/
static void
merge_to_base(gmx_ana_poscalc_t *base, gmx_ana_poscalc_t *pc)
{
gmx_ana_index_t gp, gb, g;
int isize, bnr;
int i, j, bi, bj, bo;
gmx_ana_index_set(&gp, pc->b.nra, pc->b.a, NULL, 0);
gmx_ana_index_set(&gb, base->b.nra, base->b.a, NULL, 0);
isize = gmx_ana_index_difference_size(&gp, &gb);
if (isize > 0)
{
gmx_ana_index_clear(&g);
gmx_ana_index_reserve(&g, base->b.nra + isize);
/* Find the new blocks */
gmx_ana_index_difference(&g, &gp, &gb);
/* Count the blocks in g */
i = bi = bnr = 0;
while (i < g.isize)
{
while (pc->b.a[pc->b.index[bi]] != g.index[i])
{
++bi;
}
i += pc->b.index[bi+1] - pc->b.index[bi];
++bnr;
++bi;
}
/* Merge the atoms into a temporary structure */
gmx_ana_index_merge(&g, &gb, &g);
/* Merge the blocks */
srenew(base->b.index, base->b.nr + bnr + 1);
i = g.isize - 1;
bi = base->b.nr - 1;
bj = pc->b.nr - 1;
bo = base->b.nr + bnr - 1;
base->b.index[bo+1] = i + 1;
while (bo >= 0)
{
if (bi < 0 || base->b.a[base->b.index[bi+1]-1] != g.index[i])
{
i -= pc->b.index[bj+1] - pc->b.index[bj];
--bj;
}
else
{
if (bj >= 0 && pc->b.a[pc->b.index[bj+1]-1] == g.index[i])
{
--bj;
}
i -= base->b.index[bi+1] - base->b.index[bi];
--bi;
}
base->b.index[bo] = i + 1;
--bo;
}
base->b.nr += bnr;
base->b.nalloc_index += bnr;
sfree(base->b.a);
base->b.nra = g.isize;
base->b.a = g.index;
base->b.nalloc_a = g.isize;
/* Refresh the gmax field */
gmx_ana_index_set(&base->gmax, base->b.nra, base->b.a, NULL, 0);
}
}
void
Selection::printDebugInfo(FILE *fp, int nmaxind) const
{
const gmx_ana_pos_t &p = data().rawPositions_;
fprintf(fp, " ");
printInfo(fp);
fprintf(fp, " Group ");
gmx_ana_index_t g;
gmx_ana_index_set(&g, p.m.mapb.nra, p.m.mapb.a, 0);
gmx_ana_index_dump(fp, &g, nmaxind);
fprintf(fp, " Block (size=%d):", p.m.mapb.nr);
if (!p.m.mapb.index)
{
fprintf(fp, " (null)");
}
else
{
int n = p.m.mapb.nr;
if (nmaxind >= 0 && n > nmaxind)
{
n = nmaxind;
}
for (int i = 0; i <= n; ++i)
{
fprintf(fp, " %d", p.m.mapb.index[i]);
}
if (n < p.m.mapb.nr)
{
fprintf(fp, " ...");
}
}
fprintf(fp, "\n");
int n = posCount();
if (nmaxind >= 0 && n > nmaxind)
{
n = nmaxind;
}
fprintf(fp, " RefId:");
if (!p.m.refid)
{
fprintf(fp, " (null)");
}
else
{
for (int i = 0; i < n; ++i)
{
fprintf(fp, " %d", p.m.refid[i]);
}
if (n < posCount())
{
fprintf(fp, " ...");
}
}
fprintf(fp, "\n");
fprintf(fp, " MapId:");
if (!p.m.mapid)
{
fprintf(fp, " (null)");
}
else
{
for (int i = 0; i < n; ++i)
{
fprintf(fp, " %d", p.m.mapid[i]);
}
if (n < posCount())
{
fprintf(fp, " ...");
}
}
fprintf(fp, "\n");
}