/*!
* \param[in] top Not used.
* \param[in] npar Not used (should be 2).
* \param[in] param Method parameters (should point to \ref smparams_permute).
* \param[in] data Should point to a \p t_methoddata_permute.
* \returns 0 if the input permutation is valid, -1 on error.
*/
static void
init_permute(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_permute *d = (t_methoddata_permute *)data;
int i;
gmx_ana_index_reserve(&d->g, d->p.g->isize);
d->n = param[1].val.nr;
d->perm = param[1].val.u.i;
if (d->p.nr % d->n != 0)
{
GMX_THROW(gmx::InconsistentInputError(
gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
}
snew(d->rperm, d->n);
for (i = 0; i < d->n; ++i)
{
d->rperm[i] = -1;
}
for (i = 0; i < d->n; ++i)
{
d->perm[i]--;
if (d->perm[i] < 0 || d->perm[i] >= d->n)
{
GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
}
if (d->rperm[d->perm[i]] >= 0)
{
GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
}
d->rperm[d->perm[i]] = i;
}
}
/*!
* \param[in] top Not used.
* \param[in] npar Not used (should be 2).
* \param[in] param Method parameters (should point to \ref smparams_permute).
* \param[in] data Should point to a \p t_methoddata_permute.
* \returns 0 if the input permutation is valid, -1 on error.
*/
static int
init_permute(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_permute *d = (t_methoddata_permute *)data;
int i;
gmx_ana_index_reserve(&d->g, d->p.g->isize);
d->n = param[1].val.nr;
d->perm = param[1].val.u.i;
if (d->p.nr % d->n != 0)
{
fprintf(stderr, "error: the number of positions to be permuted is not divisible by %d\n",
d->n);
return -1;
}
snew(d->rperm, d->n);
for (i = 0; i < d->n; ++i)
{
d->rperm[i] = -1;
}
for (i = 0; i < d->n; ++i)
{
d->perm[i]--;
if (d->perm[i] < 0 || d->perm[i] >= d->n)
{
fprintf(stderr, "invalid permutation");
return -1;
}
if (d->rperm[d->perm[i]] >= 0)
{
fprintf(stderr, "invalid permutation");
return -1;
}
d->rperm[d->perm[i]] = i;
}
return 0;
}
/*! \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);
}
}
