/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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+ * top-level source directory and at http://www.gromacs.org.
*
- * G R O M A C S
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+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
*
- * GROningen MAchine for Chemical Simulations
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+ * Lesser General Public License for more details.
*
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
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+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/*! \internal \file
* \brief
* Implements functions in position.h.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include <string.h>
+#include "gmxpre.h"
+
+#include "position.h"
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vec.h"
+#include <string.h>
+#include "gromacs/math/vec.h"
#include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/position.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
-/*!
- * \param[out] pos Output structure.
- *
- * Any contents of \p pos are discarded without freeing.
- */
-void
-gmx_ana_pos_clear(gmx_ana_pos_t *pos)
+gmx_ana_pos_t::gmx_ana_pos_t()
+{
+ x = NULL;
+ v = NULL;
+ f = NULL;
+ gmx_ana_indexmap_clear(&m);
+ nalloc_x = 0;
+}
+
+gmx_ana_pos_t::~gmx_ana_pos_t()
{
- pos->nr = 0;
- pos->x = NULL;
- pos->v = NULL;
- pos->f = NULL;
- gmx_ana_indexmap_clear(&pos->m);
- pos->g = NULL;
- pos->nalloc_x = 0;
+ sfree(x);
+ sfree(v);
+ sfree(f);
+ gmx_ana_indexmap_deinit(&m);
}
/*!
}
}
+/*!
+ * \param[in,out] pos Position data structure.
+ * \param[in] n Maximum number of positions.
+ * \param[in] isize Maximum number of atoms.
+ * \param[in] bVelocities Whether to reserve space for velocities.
+ * \param[in] bForces Whether to reserve space for forces.
+ *
+ * Ensures that enough memory is allocated in \p pos to calculate \p n
+ * positions from \p isize atoms.
+ *
+ * This method needs to be called instead of gmx_ana_pos_reserve() if the
+ * intent is to use gmx_ana_pos_append_init()/gmx_ana_pos_append().
+ */
+void
+gmx_ana_pos_reserve_for_append(gmx_ana_pos_t *pos, int n, int isize,
+ bool bVelocities, bool bForces)
+{
+ gmx_ana_pos_reserve(pos, n, isize);
+ snew(pos->m.mapb.a, isize);
+ pos->m.mapb.nalloc_a = isize;
+ if (bVelocities)
+ {
+ gmx_ana_pos_reserve_velocities(pos);
+ }
+ if (bForces)
+ {
+ gmx_ana_pos_reserve_forces(pos);
+ }
+}
+
/*!
* \param[out] pos Position data structure to initialize.
* \param[in] x Position vector to use.
void
gmx_ana_pos_init_const(gmx_ana_pos_t *pos, const rvec x)
{
- gmx_ana_pos_clear(pos);
- pos->nr = 1;
snew(pos->x, 1);
snew(pos->v, 1);
snew(pos->f, 1);
gmx_ana_indexmap_init(&pos->m, NULL, NULL, INDEX_UNKNOWN);
}
-/*!
- * \param[in,out] pos Position data structure.
- *
- * Frees any memory allocated within \p pos.
- * The pointer \p pos itself is not freed.
- *
- * \see gmx_ana_pos_free()
- */
-void
-gmx_ana_pos_deinit(gmx_ana_pos_t *pos)
-{
- pos->nr = 0;
- sfree(pos->x); pos->x = NULL;
- sfree(pos->v); pos->v = NULL;
- sfree(pos->f); pos->f = NULL;
- pos->nalloc_x = 0;
- gmx_ana_indexmap_deinit(&pos->m);
-}
-
-/*!
- * \param[in,out] pos Position data structure.
- *
- * Frees any memory allocated for \p pos.
- * The pointer \p pos is also freed, and is invalid after the call.
- *
- * \see gmx_ana_pos_deinit()
- */
-void
-gmx_ana_pos_free(gmx_ana_pos_t *pos)
-{
- gmx_ana_pos_deinit(pos);
- sfree(pos);
-}
-
/*!
* \param[in,out] dest Destination positions.
* \param[in] src Source positions.
{
if (bFirst)
{
- gmx_ana_pos_reserve(dest, src->nr, 0);
+ gmx_ana_pos_reserve(dest, src->count(), 0);
if (src->v)
{
gmx_ana_pos_reserve_velocities(dest);
gmx_ana_pos_reserve_forces(dest);
}
}
- dest->nr = src->nr;
- memcpy(dest->x, src->x, dest->nr*sizeof(*dest->x));
+ memcpy(dest->x, src->x, src->count()*sizeof(*dest->x));
if (dest->v)
{
GMX_ASSERT(src->v, "src velocities should be non-null if dest velocities are allocated");
- memcpy(dest->v, src->v, dest->nr*sizeof(*dest->v));
+ memcpy(dest->v, src->v, src->count()*sizeof(*dest->v));
}
if (dest->f)
{
GMX_ASSERT(src->f, "src forces should be non-null if dest forces are allocated");
- memcpy(dest->f, src->f, dest->nr*sizeof(*dest->f));
+ memcpy(dest->f, src->f, src->count()*sizeof(*dest->f));
}
gmx_ana_indexmap_copy(&dest->m, &src->m, bFirst);
- dest->g = src->g;
}
/*!
void
gmx_ana_pos_set_nr(gmx_ana_pos_t *pos, int nr)
{
- pos->nr = nr;
-}
-
-/*!
- * \param[in,out] pos Position data structure.
- * \param g Evaluation group.
- *
- * The old group, if any, is discarded.
- * Note that only a pointer to \p g is stored; it is the responsibility of
- * the caller to ensure that \p g is not freed while it can be accessed
- * through \p pos.
- */
-void
-gmx_ana_pos_set_evalgrp(gmx_ana_pos_t *pos, gmx_ana_index_t *g)
-{
- pos->g = g;
+ // TODO: This puts the mapping in a somewhat inconsistent state.
+ pos->m.mapb.nr = nr;
}
/*!
void
gmx_ana_pos_empty_init(gmx_ana_pos_t *pos)
{
- pos->nr = 0;
- pos->m.nr = 0;
- pos->m.mapb.nr = 0;
- pos->m.b.nr = 0;
- pos->m.b.nra = 0;
+ pos->m.mapb.nr = 0;
+ pos->m.mapb.nra = 0;
+ pos->m.b.nr = 0;
+ pos->m.b.nra = 0;
/* This should not really be necessary, but do it for safety... */
pos->m.mapb.index[0] = 0;
pos->m.b.index[0] = 0;
/* This function should only be used to construct all the possible
* positions, so the result should always be static. */
- pos->m.bStatic = true;
- pos->m.bMapStatic = true;
+ pos->m.bStatic = true;
}
/*!
void
gmx_ana_pos_empty(gmx_ana_pos_t *pos)
{
- pos->nr = 0;
- pos->m.nr = 0;
- pos->m.mapb.nr = 0;
+ pos->m.mapb.nr = 0;
+ pos->m.mapb.nra = 0;
/* This should not really be necessary, but do it for safety... */
pos->m.mapb.index[0] = 0;
- /* We set the flags to true, although really in the empty state they
- * should be false. This makes it possible to update the flags in
+ /* We set the flag to true, although really in the empty state it
+ * should be false. This makes it possible to update the flag in
* gmx_ana_pos_append(), and just make a simple check in
* gmx_ana_pos_append_finish(). */
- pos->m.bStatic = true;
- pos->m.bMapStatic = true;
+ pos->m.bStatic = true;
}
/*!
* \param[in,out] dest Data structure to which the new position is appended.
- * \param[in,out] g Data structure to which the new atoms are appended.
* \param[in] src Data structure from which the position is copied.
* \param[in] i Index in \p from to copy.
*/
void
-gmx_ana_pos_append_init(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
- gmx_ana_pos_t *src, int i)
+gmx_ana_pos_append_init(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, int i)
{
int j, k;
- j = dest->nr;
+ j = dest->count();
copy_rvec(src->x[i], dest->x[j]);
if (dest->v)
{
dest->m.orgid[j] = src->m.orgid[i];
for (k = src->m.mapb.index[i]; k < src->m.mapb.index[i+1]; ++k)
{
- g->index[g->isize++] = src->g->index[k];
- dest->m.b.a[dest->m.b.nra++] = src->m.b.a[k];
+ dest->m.mapb.a[dest->m.mapb.nra++] = src->m.mapb.a[k];
+ dest->m.b.a[dest->m.b.nra++] = src->m.b.a[k];
}
- dest->m.mapb.index[j+1] = g->isize;
- dest->m.b.index[j+1] = g->isize;
- dest->nr++;
- dest->m.nr = dest->nr;
- dest->m.mapb.nr = dest->nr;
- dest->m.b.nr = dest->nr;
+ dest->m.mapb.index[j+1] = dest->m.mapb.nra;
+ dest->m.b.index[j+1] = dest->m.mapb.nra;
+ dest->m.mapb.nr++;
+ dest->m.b.nr++;
}
/*!
- * \param[in,out] dest Data structure to which the new position is appended
- * (can be NULL, in which case only \p g is updated).
- * \param[in,out] g Data structure to which the new atoms are appended.
+ * \param[in,out] dest Data structure to which the new position is appended.
* \param[in] src Data structure from which the position is copied.
* \param[in] i Index in \p src to copy.
* \param[in] refid Reference ID in \p out
* (all negative values are treated as -1).
- *
- * If \p dest is NULL, the value of \p refid is not used.
*/
void
-gmx_ana_pos_append(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
- gmx_ana_pos_t *src, int i, int refid)
+gmx_ana_pos_append(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, int i, int refid)
{
- int j, k;
-
- for (k = src->m.mapb.index[i]; k < src->m.mapb.index[i+1]; ++k)
+ for (int k = src->m.mapb.index[i]; k < src->m.mapb.index[i+1]; ++k)
{
- g->index[g->isize++] = src->g->index[k];
+ dest->m.mapb.a[dest->m.mapb.nra++] = src->m.mapb.a[k];
}
- if (dest)
+ const int j = dest->count();
+ if (dest->v)
{
- j = dest->nr;
- if (dest->v)
+ if (src->v)
{
- if (src->v)
- {
- copy_rvec(src->v[i], dest->v[j]);
- }
- else
- {
- clear_rvec(dest->v[j]);
- }
+ copy_rvec(src->v[i], dest->v[j]);
}
- if (dest->f)
+ else
{
- if (src->f)
- {
- copy_rvec(src->f[i], dest->f[j]);
- }
- else
- {
- clear_rvec(dest->f[j]);
- }
+ clear_rvec(dest->v[j]);
}
- copy_rvec(src->x[i], dest->x[j]);
- if (refid < 0)
+ }
+ if (dest->f)
+ {
+ if (src->f)
{
- dest->m.refid[j] = -1;
- dest->m.bStatic = false;
- /* If we are using masks, there is no need to alter the
- * mapid field. */
+ copy_rvec(src->f[i], dest->f[j]);
}
else
{
- if (refid != j)
- {
- dest->m.bStatic = false;
- dest->m.bMapStatic = false;
- }
- dest->m.refid[j] = refid;
- /* Use the original IDs from the output structure to correctly
- * handle user customization. */
- dest->m.mapid[j] = dest->m.orgid[refid];
+ clear_rvec(dest->f[j]);
+ }
+ }
+ copy_rvec(src->x[i], dest->x[j]);
+ if (refid < 0)
+ {
+ dest->m.refid[j] = -1;
+ dest->m.bStatic = false;
+ /* If we are using masks, there is no need to alter the
+ * mapid field. */
+ }
+ else
+ {
+ if (refid != j)
+ {
+ dest->m.bStatic = false;
}
- dest->m.mapb.index[j+1] = g->isize;
- dest->nr++;
- dest->m.nr = dest->nr;
- dest->m.mapb.nr = dest->nr;
+ dest->m.refid[j] = refid;
+ /* Use the original IDs from the output structure to correctly
+ * handle user customization. */
+ dest->m.mapid[j] = dest->m.orgid[refid];
}
+ dest->m.mapb.index[j+1] = dest->m.mapb.nra;
+ dest->m.mapb.nr++;
}
/*!
void
gmx_ana_pos_append_finish(gmx_ana_pos_t *pos)
{
- if (pos->m.nr != pos->m.b.nr)
+ if (pos->m.mapb.nr != pos->m.b.nr)
+ {
+ pos->m.bStatic = false;
+ }
+}
+
+/*!
+ * \param[in,out] g Data structure to which the new atoms are appended.
+ * \param[in] src Data structure from which the position is copied.
+ * \param[in] i Index in \p src to copy.
+ */
+void
+gmx_ana_pos_add_to_group(gmx_ana_index_t *g, gmx_ana_pos_t *src, int i)
+{
+ for (int k = src->m.mapb.index[i]; k < src->m.mapb.index[i+1]; ++k)
{
- pos->m.bStatic = false;
- pos->m.bMapStatic = false;
+ g->index[g->isize++] = src->m.mapb.a[k];
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff