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*
- * This source code is part of
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+ * the research papers on the package. Check out http://www.gromacs.org.
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/*! \internal \file
* \brief
* Implements the \p permute selection modifier.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/vec.h"
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
#include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
+#include "selmethod.h"
+
/*! \internal \brief
* Data structure for the \p permute selection modifier.
*/
{
/** Positions to permute. */
gmx_ana_pos_t p;
- /** Group to receive the output permutation. */
- gmx_ana_index_t g;
/** Number of elements in the permutation. */
int n;
/** Array describing the permutation. */
int *rperm;
} t_methoddata_permute;
-/** Allocates data for the \p permute selection modifier. */
+/*! \brief
+ * Allocates data for the \p permute selection modifier.
+ *
+ * \param[in] npar Not used (should be 2).
+ * \param[in,out] param Method parameters (should point to a copy of
+ * \ref smparams_permute).
+ * \returns Pointer to the allocated data (\p t_methoddata_permute).
+ *
+ * Allocates memory for a \p t_methoddata_permute structure.
+ */
static void *
init_data_permute(int npar, gmx_ana_selparam_t *param);
-/** Initializes data for the \p permute selection modifier. */
+/*! \brief
+ * Initializes data for the \p permute selection modifier.
+ *
+ * \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);
-/** Initializes output for the \p permute selection modifier. */
+/*! \brief
+ * Initializes output for the \p permute selection modifier.
+ *
+ * \param[in] top Topology data structure.
+ * \param[in,out] out Pointer to output data structure.
+ * \param[in,out] data Should point to \c t_methoddata_permute.
+ */
static void
init_output_permute(t_topology *top, gmx_ana_selvalue_t *out, void *data);
/** Frees the memory allocated for the \p permute selection modifier. */
static void
free_data_permute(void *data);
-/** Evaluates the \p permute selection modifier. */
static void
+/*! \brief
+ * Evaluates the \p permute selection modifier.
+ *
+ * \param[in] top Not used.
+ * \param[in] fr Not used.
+ * \param[in] pbc Not used.
+ * \param[in] p Positions to permute (should point to \p data->p).
+ * \param[out] out Output data structure (\p out->u.p is used).
+ * \param[in] data Should point to a \p t_methoddata_permute.
+ * \returns 0 if \p p could be permuted, -1 on error.
+ *
+ * Returns -1 if the size of \p p is not divisible by the number of
+ * elements in the permutation.
+ */
evaluate_permute(t_topology *top, t_trxframe *fr, t_pbc *pbc,
gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data);
"a selection.",
};
-/** \internal Selection method data for the \p permute modifier. */
+/** Selection method data for the \p permute modifier. */
gmx_ana_selmethod_t sm_permute = {
"permute", POS_VALUE, SMETH_MODIFIER,
asize(smparams_permute), smparams_permute,
{"permute P1 ... PN", asize(help_permute), help_permute},
};
-/*!
- * \param[in] npar Not used (should be 2).
- * \param[in,out] param Method parameters (should point to a copy of
- * \ref smparams_permute).
- * \returns Pointer to the allocated data (\p t_methoddata_permute).
- *
- * Allocates memory for a \p t_methoddata_permute structure.
- */
static void *
-init_data_permute(int npar, gmx_ana_selparam_t *param)
+init_data_permute(int /* npar */, gmx_ana_selparam_t *param)
{
- t_methoddata_permute *data;
-
- snew(data, 1);
+ t_methoddata_permute *data = new t_methoddata_permute();
+ data->n = 0;
+ data->perm = NULL;
+ data->rperm = NULL;
param[0].val.u.p = &data->p;
return data;
}
-/*!
- * \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)
+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)
+ if (d->p.count() % d->n != 0)
{
GMX_THROW(gmx::InconsistentInputError(
- gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
+ 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)
}
}
-/*!
- * \param[in] top Topology data structure.
- * \param[in,out] out Pointer to output data structure.
- * \param[in,out] data Should point to \c t_methoddata_permute.
- */
static void
-init_output_permute(t_topology *top, gmx_ana_selvalue_t *out, void *data)
+init_output_permute(t_topology * /* top */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_permute *d = (t_methoddata_permute *)data;
int i, j, b;
- gmx_ana_pos_copy(out->u.p, &d->p, true);
- gmx_ana_pos_set_evalgrp(out->u.p, &d->g);
- d->g.isize = 0;
+ out->u.p->m.type = d->p.m.type;
+ gmx_ana_pos_reserve_for_append(out->u.p, d->p.count(), d->p.m.b.nra,
+ d->p.v != NULL, d->p.f != NULL);
gmx_ana_pos_empty_init(out->u.p);
- for (i = 0; i < d->p.nr; i += d->n)
+ for (i = 0; i < d->p.count(); i += d->n)
{
for (j = 0; j < d->n; ++j)
{
b = i + d->rperm[j];
- gmx_ana_pos_append_init(out->u.p, &d->g, &d->p, b);
+ gmx_ana_pos_append_init(out->u.p, &d->p, b);
}
}
}
{
t_methoddata_permute *d = (t_methoddata_permute *)data;
- gmx_ana_index_deinit(&d->g);
sfree(d->rperm);
- sfree(d);
+ delete d;
}
-/*!
- * \param[in] top Not used.
- * \param[in] fr Not used.
- * \param[in] pbc Not used.
- * \param[in] p Positions to permute (should point to \p data->p).
- * \param[out] out Output data structure (\p out->u.p is used).
- * \param[in] data Should point to a \p t_methoddata_permute.
- * \returns 0 if \p p could be permuted, -1 on error.
- *
- * Returns -1 if the size of \p p is not divisible by the number of
- * elements in the permutation.
- */
static void
-evaluate_permute(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_permute(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_permute *d = (t_methoddata_permute *)data;
int i, j, b;
int refid;
- if (d->p.nr % d->n != 0)
+ if (d->p.count() % d->n != 0)
{
GMX_THROW(gmx::InconsistentInputError(
- gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
+ gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
}
- d->g.isize = 0;
gmx_ana_pos_empty(out->u.p);
- for (i = 0; i < d->p.nr; i += d->n)
+ for (i = 0; i < d->p.count(); i += d->n)
{
for (j = 0; j < d->n; ++j)
{
- b = i + d->rperm[j];
+ b = i + d->rperm[j];
refid = d->p.m.refid[b];
if (refid != -1)
{
/* De-permute the reference ID */
refid = refid - (refid % d->n) + d->perm[refid % d->n];
}
- gmx_ana_pos_append(out->u.p, &d->g, p, b, refid);
+ gmx_ana_pos_append(out->u.p, p, b, refid);
}
}
gmx_ana_pos_append_finish(out->u.p);
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