/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
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*
- * GROningen MAchine for Chemical Simulations
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- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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- * the papers on the package - you can find them in the top README file.
- *
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+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/*! \internal \file
* \brief
* Implements the \p merge and \p plus selection modifiers.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "macros.h"
-#include "smalloc.h"
-#include "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/common.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "selmethod.h"
/*! \internal \brief
* Data structure for the merging selection modifiers.
gmx_ana_pos_t p1;
/** Other input positions. */
gmx_ana_pos_t p2;
- /** Group to store the output atom indices. */
- gmx_ana_index_t g;
/** Stride for merging (\c stride values from \c p1 for each in \c p2). */
int stride;
} t_methoddata_merge;
/** Allocates data for the merging selection modifiers. */
static void *
init_data_merge(int npar, gmx_ana_selparam_t *param);
-/** Initializes data for the merging selection modifiers. */
+/*! \brief
+ * Initializes data for the merging selection modifiers.
+ *
+ * \param[in] top Not used.
+ * \param[in] npar Not used (should be 2 or 3).
+ * \param[in] param Method parameters (should point to \ref smparams_merge).
+ * \param[in] data Should point to a \p t_methoddata_merge.
+ * \returns 0 if everything is successful, -1 on error.
+ */
static void
init_merge(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Initializes output for the \p merge selection modifier. */
/** Frees the memory allocated for the merging selection modifiers. */
static void
free_data_merge(void *data);
-/** Evaluates the \p merge selection modifier. */
+/*! \brief
+ * Evaluates the \p merge selection modifier.
+ *
+ * \param[in] top Not used.
+ * \param[in] fr Not used.
+ * \param[in] pbc Not used.
+ * \param[in] p Positions to merge (should point to \p data->p1).
+ * \param[out] out Output data structure (\p out->u.p is used).
+ * \param[in] data Should point to a \p t_methoddata_merge.
+ */
static void
evaluate_merge(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data);
-/** Evaluates the \p plus selection modifier. */
+ gmx_ana_pos_t * p, gmx_ana_selvalue_t *out, void *data);
+/*! \brief
+ * Evaluates the \p plus selection modifier.
+ *
+ * \param[in] top Not used.
+ * \param[in] fr Not used.
+ * \param[in] pbc Not used.
+ * \param[in] p Positions to merge (should point to \p data->p1).
+ * \param[out] out Output data structure (\p out->u.p is used).
+ * \param[in] data Should point to a \p t_methoddata_merge.
+ */
static void
evaluate_plus(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data);
+ gmx_ana_pos_t * p, gmx_ana_selvalue_t *out, void *data);
/** Parameters for the merging selection modifiers. */
static gmx_ana_selparam_t smparams_merge[] = {
"subexpressions.",
};
-/** \internal Selection method data for the \p plus modifier. */
+/** Selection method data for the \p plus modifier. */
gmx_ana_selmethod_t sm_merge = {
"merge", POS_VALUE, SMETH_MODIFIER,
asize(smparams_merge), smparams_merge,
{"merge POSEXPR", asize(help_merge), help_merge},
};
-/** \internal Selection method data for the \p plus modifier. */
+/** Selection method data for the \p plus modifier. */
gmx_ana_selmethod_t sm_plus = {
"plus", POS_VALUE, SMETH_MODIFIER,
asize(smparams_merge)-1, smparams_merge,
static void *
init_data_merge(int npar, gmx_ana_selparam_t *param)
{
- t_methoddata_merge *data;
-
- snew(data, 1);
- data->stride = 0;
+ t_methoddata_merge *data = new t_methoddata_merge();
+ data->stride = 0;
param[0].val.u.p = &data->p1;
param[1].val.u.p = &data->p2;
if (npar > 2)
return data;
}
-/*!
- * \param[in] top Not used.
- * \param[in] npar Not used (should be 2 or 3).
- * \param[in] param Method parameters (should point to \ref smparams_merge).
- * \param[in] data Should point to a \p t_methoddata_merge.
- * \returns 0 if everything is successful, -1 on error.
- */
static void
-init_merge(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+init_merge(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t * /* param */, void *data)
{
t_methoddata_merge *d = (t_methoddata_merge *)data;
/* If no stride given, deduce it from the input sizes */
if (d->stride == 0)
{
- d->stride = d->p1.nr / d->p2.nr;
+ d->stride = d->p1.count() / d->p2.count();
}
- if (d->p1.nr != d->stride*d->p2.nr)
+ if (d->p1.count() != d->stride*d->p2.count())
{
GMX_THROW(gmx::InconsistentInputError("The number of positions to be merged are not compatible"));
}
- /* We access the m.b.nra field instead of g->isize in the position
- * data structures to handle cases where g is NULL
- * (this occurs with constant positions. */
- gmx_ana_index_reserve(&d->g, d->p1.m.b.nra + d->p2.m.b.nra);
- d->g.isize = d->p1.m.b.nra + d->p2.m.b.nra;
}
/*! \brief
{
t_methoddata_merge *d = (t_methoddata_merge *)data;
+ GMX_UNUSED_VALUE(top);
if (d->p1.m.type != d->p2.m.type)
{
/* TODO: Maybe we could pick something else here? */
{
out->u.p->m.type = d->p1.m.type;
}
- gmx_ana_pos_reserve(out->u.p, d->p1.nr + d->p2.nr, d->g.isize);
- if (d->p1.v)
- {
- gmx_ana_pos_reserve_velocities(out->u.p);
- }
- if (d->p1.f)
- {
- gmx_ana_pos_reserve_forces(out->u.p);
- }
- gmx_ana_pos_set_evalgrp(out->u.p, &d->g);
+ gmx_ana_pos_reserve_for_append(out->u.p, d->p1.count() + d->p2.count(),
+ d->p1.m.b.nra + d->p2.m.b.nra,
+ d->p1.v != NULL, d->p1.f != NULL);
gmx_ana_pos_empty_init(out->u.p);
- d->g.isize = 0;
}
/*!
int i, j;
init_output_common(top, out, data);
- for (i = 0; i < d->p2.nr; ++i)
+ for (i = 0; i < d->p2.count(); ++i)
{
for (j = 0; j < d->stride; ++j)
{
- gmx_ana_pos_append_init(out->u.p, &d->g, &d->p1, d->stride*i+j);
+ gmx_ana_pos_append_init(out->u.p, &d->p1, d->stride * i + j);
}
- gmx_ana_pos_append_init(out->u.p, &d->g, &d->p2, i);
+ gmx_ana_pos_append_init(out->u.p, &d->p2, i);
}
}
int i;
init_output_common(top, out, data);
- for (i = 0; i < d->p1.nr; ++i)
+ for (i = 0; i < d->p1.count(); ++i)
{
- gmx_ana_pos_append_init(out->u.p, &d->g, &d->p1, i);
+ gmx_ana_pos_append_init(out->u.p, &d->p1, i);
}
- for (i = 0; i < d->p2.nr; ++i)
+ for (i = 0; i < d->p2.count(); ++i)
{
- gmx_ana_pos_append_init(out->u.p, &d->g, &d->p2, i);
+ gmx_ana_pos_append_init(out->u.p, &d->p2, i);
}
}
free_data_merge(void *data)
{
t_methoddata_merge *d = (t_methoddata_merge *)data;
-
- gmx_ana_index_deinit(&d->g);
- sfree(d);
+ delete d;
}
-/*!
- * \param[in] top Not used.
- * \param[in] fr Not used.
- * \param[in] pbc Not used.
- * \param[in] p Positions to merge (should point to \p data->p1).
- * \param[out] out Output data structure (\p out->u.p is used).
- * \param[in] data Should point to a \p t_methoddata_merge.
- */
static void
-evaluate_merge(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
+evaluate_merge(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_pos_t * /* p */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_merge *d = (t_methoddata_merge *)data;
int i, j;
int refid;
- if (d->p1.nr != d->stride*d->p2.nr)
+ if (d->p1.count() != d->stride*d->p2.count())
{
GMX_THROW(gmx::InconsistentInputError("The number of positions to be merged are not compatible"));
}
- d->g.isize = 0;
gmx_ana_pos_empty(out->u.p);
- for (i = 0; i < d->p2.nr; ++i)
+ for (i = 0; i < d->p2.count(); ++i)
{
for (j = 0; j < d->stride; ++j)
{
{
refid = (d->stride+1) * (refid / d->stride) + (refid % d->stride);
}
- gmx_ana_pos_append(out->u.p, &d->g, &d->p1, d->stride*i+j, refid);
+ gmx_ana_pos_append(out->u.p, &d->p1, d->stride*i+j, refid);
}
- refid = (d->stride+1)*d->p2.m.refid[i]+d->stride;
- gmx_ana_pos_append(out->u.p, &d->g, &d->p2, i, refid);
+ refid = (d->stride+1)*d->p2.m.refid[i] + d->stride;
+ gmx_ana_pos_append(out->u.p, &d->p2, i, refid);
}
gmx_ana_pos_append_finish(out->u.p);
}
-/*!
- * \param[in] top Not used.
- * \param[in] fr Not used.
- * \param[in] pbc Not used.
- * \param[in] p Positions to merge (should point to \p data->p1).
- * \param[out] out Output data structure (\p out->u.p is used).
- * \param[in] data Should point to a \p t_methoddata_merge.
- */
static void
-evaluate_plus(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
+evaluate_plus(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_pos_t * /* p */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_merge *d = (t_methoddata_merge *)data;
int i;
int refid;
- d->g.isize = 0;
gmx_ana_pos_empty(out->u.p);
- for (i = 0; i < d->p1.nr; ++i)
+ for (i = 0; i < d->p1.count(); ++i)
{
refid = d->p1.m.refid[i];
- gmx_ana_pos_append(out->u.p, &d->g, &d->p1, i, refid);
+ gmx_ana_pos_append(out->u.p, &d->p1, i, refid);
}
- for (i = 0; i < d->p2.nr; ++i)
+ for (i = 0; i < d->p2.count(); ++i)
{
refid = d->p2.m.refid[i];
if (refid != -1)
{
refid += d->p1.m.b.nr;
}
- gmx_ana_pos_append(out->u.p, &d->g, &d->p2, i, refid);
+ gmx_ana_pos_append(out->u.p, &d->p2, i, refid);
}
gmx_ana_pos_append_finish(out->u.p);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff