/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * 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,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include "gromacs/selection/indexutil.h"
+#include "gmxpre.h"
+#include "indexutil.h"
+
+#include <cstdlib>
#include <cstring>
+#include <algorithm>
#include <string>
#include <vector>
-#include "gromacs/legacyheaders/index.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
-
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
/********************************************************************
* gmx_ana_indexgrps_t functions
}
catch (...)
{
- done_blocka(block);
- sfree(block);
for (int i = 0; i < block->nr; ++i)
{
sfree(names[i]);
}
sfree(names);
+ done_blocka(block);
+ sfree(block);
throw;
}
- done_blocka(block);
- sfree(block);
for (int i = 0; i < block->nr; ++i)
{
sfree(names[i]);
}
sfree(names);
+ done_blocka(block);
+ sfree(block);
}
/*!
int n = find_group(const_cast<char *>(name), src->nr,
const_cast<char **>(names));
sfree(names);
- if (n == NOTSET)
+ if (n < 0)
{
dest->isize = 0;
return false;
{
for (int i = 0; i < g->nr; ++i)
{
- fprintf(fp, " Group %2d \"%s\" ", i + 1, g->names[i].c_str());
+ fprintf(fp, " Group %2d \"%s\" ", i, g->names[i].c_str());
gmx_ana_index_dump(fp, &g->g[i], maxn);
}
}
fprintf(fp, "\n");
}
+int
+gmx_ana_index_get_max_index(gmx_ana_index_t *g)
+{
+ if (g->isize == 0)
+ {
+ return 0;
+ }
+ else
+ {
+ return *std::max_element(g->index, g->index + g->isize);
+ }
+}
+
/*!
* \param[in] g Index group to check.
* \returns true if the index group is sorted and has no duplicates,
return true;
}
+bool
+gmx_ana_index_check_range(gmx_ana_index_t *g, int natoms)
+{
+ for (int i = 0; i < g->isize; ++i)
+ {
+ if (g->index[i] < 0 || g->index[i] >= natoms)
+ {
+ return false;
+ }
+ }
+ return true;
+}
+
/********************************************************************
* Set operations
********************************************************************/
void
gmx_ana_index_sort(gmx_ana_index_t *g)
{
- qsort(g->index, g->isize, sizeof(*g->index), cmp_atomid);
+ std::qsort(g->index, g->isize, sizeof(*g->index), cmp_atomid);
}
/*!
break;
default: /* Should not be reached */
- gmx_bug("internal error");
+ GMX_RELEASE_ASSERT(false, "Unreachable code was reached");
break;
}
}
gmx_ana_indexmap_clear(gmx_ana_indexmap_t *m)
{
m->type = INDEX_UNKNOWN;
- m->nr = 0;
m->refid = NULL;
m->mapid = NULL;
m->mapb.nr = 0;
m->mapb.index = NULL;
m->mapb.nalloc_index = 0;
+ m->mapb.nra = 0;
+ m->mapb.a = NULL;
+ m->mapb.nalloc_a = 0;
m->orgid = NULL;
m->b.nr = 0;
m->b.index = NULL;
m->b.nalloc_index = 0;
m->b.nalloc_a = 0;
m->bStatic = true;
- m->bMapStatic = true;
}
/*!
m->type = type;
gmx_ana_index_make_block(&m->b, top, g, type, false);
gmx_ana_indexmap_reserve(m, m->b.nr, m->b.nra);
- m->nr = m->b.nr;
- for (i = mi = 0; i < m->nr; ++i)
+ for (i = mi = 0; i < m->b.nr; ++i)
{
ii = (type == INDEX_UNKNOWN ? 0 : m->b.a[m->b.index[i]]);
switch (type)
break;
}
}
- for (i = 0; i < m->nr; ++i)
+ for (i = 0; i < m->b.nr; ++i)
{
m->refid[i] = i;
m->mapid[i] = m->orgid[i];
}
- m->mapb.nr = m->nr;
- std::memcpy(m->mapb.index, m->b.index, (m->nr+1)*sizeof(*(m->mapb.index)));
- m->bStatic = true;
- m->bMapStatic = true;
+ m->mapb.nr = m->b.nr;
+ m->mapb.nra = m->b.nra;
+ m->mapb.a = m->b.a;
+ std::memcpy(m->mapb.index, m->b.index, (m->b.nr+1)*sizeof(*(m->mapb.index)));
+ m->bStatic = true;
}
/*!
gmx_ana_indexmap_set_static(gmx_ana_indexmap_t *m, t_blocka *b)
{
sfree(m->mapid);
- m->mapid = m->orgid;
- sfree(m->b.index);
- m->b.nalloc_index = 0;
- m->b.index = b->index;
sfree(m->mapb.index);
- m->mapb.nalloc_index = 0;
- m->mapb.index = m->b.index;
+ sfree(m->b.index);
sfree(m->b.a);
- m->b.nalloc_a = 0;
- m->b.a = b->a;
+ m->mapb.nalloc_index = 0;
+ m->mapb.nalloc_a = 0;
+ m->b.nalloc_index = 0;
+ m->b.nalloc_a = 0;
+ m->mapid = m->orgid;
+ m->mapb.index = b->index;
+ m->mapb.a = b->a;
+ m->b.index = b->index;
+ m->b.a = b->a;
}
/*!
std::memcpy(dest->b.index, src->b.index, (dest->b.nr+1)*sizeof(*dest->b.index));
std::memcpy(dest->b.a, src->b.a, dest->b.nra*sizeof(*dest->b.a));
}
- dest->nr = src->nr;
dest->mapb.nr = src->mapb.nr;
- std::memcpy(dest->refid, src->refid, dest->nr*sizeof(*dest->refid));
- std::memcpy(dest->mapid, src->mapid, dest->nr*sizeof(*dest->mapid));
+ dest->mapb.nra = src->mapb.nra;
+ if (src->mapb.nalloc_a > 0)
+ {
+ if (bFirst)
+ {
+ snew(dest->mapb.a, src->mapb.nalloc_a);
+ dest->mapb.nalloc_a = src->mapb.nalloc_a;
+ }
+ std::memcpy(dest->mapb.a, src->mapb.a, dest->mapb.nra*sizeof(*dest->mapb.a));
+ }
+ else
+ {
+ dest->mapb.a = src->mapb.a;
+ }
+ std::memcpy(dest->refid, src->refid, dest->mapb.nr*sizeof(*dest->refid));
+ std::memcpy(dest->mapid, src->mapid, dest->mapb.nr*sizeof(*dest->mapid));
std::memcpy(dest->mapb.index, src->mapb.index, (dest->mapb.nr+1)*sizeof(*dest->mapb.index));
- dest->bStatic = src->bStatic;
- dest->bMapStatic = src->bMapStatic;
+ dest->bStatic = src->bStatic;
+}
+
+/*! \brief
+ * Helper function to set the source atoms in an index map.
+ *
+ * \param[in,out] m Mapping structure.
+ * \param[in] isize Number of atoms in the \p index array.
+ * \param[in] index List of atoms.
+ */
+static void
+set_atoms(gmx_ana_indexmap_t *m, int isize, int *index)
+{
+ m->mapb.nra = isize;
+ if (m->mapb.nalloc_a == 0)
+ {
+ m->mapb.a = index;
+ }
+ else
+ {
+ for (int i = 0; i < isize; ++i)
+ {
+ m->mapb.a[i] = index[i];
+ }
+ }
}
/*!
bool bMaskOnly)
{
int i, j, bi, bj;
- bool bStatic;
/* Process the simple cases first */
if (m->type == INDEX_UNKNOWN && m->b.nra == 0)
}
if (m->type == INDEX_ALL)
{
+ set_atoms(m, g->isize, g->index);
if (m->b.nr > 0)
{
m->mapb.index[1] = g->isize;
return;
}
/* Reset the reference IDs and mapping if necessary */
- bStatic = (g->isize == m->b.nra && m->nr == m->b.nr);
- if (bStatic || bMaskOnly)
+ const bool bToFull = (g->isize == m->b.nra);
+ const bool bWasFull = (m->mapb.nra == m->b.nra);
+ if (bToFull || bMaskOnly)
{
if (!m->bStatic)
{
m->refid[bj] = bj;
}
}
- if (!m->bMapStatic)
+ if (!bWasFull)
{
for (bj = 0; bj < m->b.nr; ++bj)
{
{
m->mapb.index[bj] = m->b.index[bj];
}
- m->bMapStatic = true;
}
+ set_atoms(m, m->b.nra, m->b.a);
+ m->mapb.nr = m->b.nr;
}
/* Exit immediately if the group is static */
- if (bStatic)
+ if (bToFull)
{
m->bStatic = true;
return;
if (bMaskOnly)
{
- m->nr = m->b.nr;
for (i = j = bj = 0; i < g->isize; ++i, ++j)
{
/* Find the next atom in the block */
}
else
{
+ set_atoms(m, g->isize, g->index);
for (i = j = bi = 0, bj = -1; i < g->isize; ++i)
{
/* Find the next atom in the block */
}
/* Update the number of blocks */
m->mapb.index[bi] = g->isize;
- m->nr = bi;
- m->bMapStatic = false;
+ m->mapb.nr = bi;
}
- m->mapb.nr = m->nr;
m->bStatic = false;
}
{
sfree(m->mapb.index);
}
+ if (m->mapb.nalloc_a > 0)
+ {
+ sfree(m->mapb.a);
+ }
sfree(m->orgid);
if (m->b.nalloc_index > 0)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff