/*
+ * 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,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * G R O M A C S
+ * GROMACS is free software; you can redistribute it and/or
+ * 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
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
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+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * If you want to redistribute modifications, please consider that
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- * files - if they are missing, get the official version at www.gromacs.org.
+ * 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 simple keyword selection methods.
*
- * \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 "gmxpre.h"
#include <cctype>
#include "gromacs/legacyheaders/macros.h"
-
#include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/exceptions.h"
+#include "selmethod.h"
+
/** Evaluates the \p all selection keyword. */
static void
evaluate_all(t_topology *top, t_trxframe *fr, t_pbc *pbc,
static void
evaluate_resindex(t_topology *top, t_trxframe *fr, t_pbc *pbc,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
-/** Checks whether molecule information is present in the topology. */
+/*! \brief
+ * Checks whether molecule information is present in the topology.
+ *
+ * \param[in] top Topology structure.
+ * \param npar Not used.
+ * \param param Not used.
+ * \param data Not used.
+ * \returns 0 if molecule info is present in the topology, -1 otherwise.
+ *
+ * If molecule information is not found, also prints an error message.
+ */
static void
check_molecules(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Evaluates the \p molindex selection keyword. */
static void
evaluate_pdbatomname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
-/** Checks whether atom types are present in the topology. */
+/*! \brief
+ * Checks whether atom types are present in the topology.
+ *
+ * \param[in] top Topology structure.
+ * \param npar Not used.
+ * \param param Not used.
+ * \param data Not used.
+ * \returns 0 if atom types are present in the topology, -1 otherwise.
+ *
+ * If the atom types are not found, also prints an error message.
+ */
static void
check_atomtype(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Evaluates the \p atomtype selection keyword. */
static void
evaluate_charge(t_topology *top, t_trxframe *fr, t_pbc *pbc,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
-/** Checks whether PDB info is present in the topology. */
+/*! \brief
+ * Checks whether PDB info is present in the topology.
+ *
+ * \param[in] top Topology structure.
+ * \param npar Not used.
+ * \param param Not used.
+ * \param data Not used.
+ * \returns 0 if PDB info is present in the topology, -1 otherwise.
+ *
+ * If PDB info is not found, also prints an error message.
+ */
static void
check_pdbinfo(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Evaluates the \p altloc selection keyword. */
"keywords."
};
-/** \internal Selection method data for \p all selection keyword. */
+/** Selection method data for \p all selection keyword. */
gmx_ana_selmethod_t sm_all = {
"all", GROUP_VALUE, 0,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p none selection keyword. */
+/** Selection method data for \p none selection keyword. */
gmx_ana_selmethod_t sm_none = {
"none", GROUP_VALUE, 0,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p atomnr selection keyword. */
+/** Selection method data for \p atomnr selection keyword. */
gmx_ana_selmethod_t sm_atomnr = {
"atomnr", INT_VALUE, 0,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p resnr selection keyword. */
+/** Selection method data for \p resnr selection keyword. */
gmx_ana_selmethod_t sm_resnr = {
"resnr", INT_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p resindex selection keyword. */
+/** Selection method data for \p resindex selection keyword. */
gmx_ana_selmethod_t sm_resindex = {
"resindex", INT_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p molindex selection keyword. */
+/** Selection method data for \p molindex selection keyword. */
gmx_ana_selmethod_t sm_molindex = {
"molindex", INT_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p atomname selection keyword. */
+/** Selection method data for \p atomname selection keyword. */
gmx_ana_selmethod_t sm_atomname = {
"atomname", STR_VALUE, SMETH_REQTOP,
0, NULL,
{NULL, asize(help_atomname), help_atomname}
};
-/** \internal Selection method data for \p pdbatomname selection keyword. */
+/** Selection method data for \p pdbatomname selection keyword. */
gmx_ana_selmethod_t sm_pdbatomname = {
"pdbatomname", STR_VALUE, SMETH_REQTOP,
0, NULL,
{NULL, asize(help_atomname), help_atomname}
};
-/** \internal Selection method data for \p atomtype selection keyword. */
+/** Selection method data for \p atomtype selection keyword. */
gmx_ana_selmethod_t sm_atomtype = {
"atomtype", STR_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p resname selection keyword. */
+/** Selection method data for \p resname selection keyword. */
gmx_ana_selmethod_t sm_resname = {
"resname", STR_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p chain selection keyword. */
+/** Selection method data for \p chain selection keyword. */
gmx_ana_selmethod_t sm_insertcode = {
"insertcode", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p chain selection keyword. */
+/** Selection method data for \p chain selection keyword. */
gmx_ana_selmethod_t sm_chain = {
"chain", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p mass selection keyword. */
+/** Selection method data for \p mass selection keyword. */
gmx_ana_selmethod_t sm_mass = {
"mass", REAL_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p charge selection keyword. */
+/** Selection method data for \p charge selection keyword. */
gmx_ana_selmethod_t sm_charge = {
"charge", REAL_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p chain selection keyword. */
+/** Selection method data for \p chain selection keyword. */
gmx_ana_selmethod_t sm_altloc = {
"altloc", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p occupancy selection keyword. */
+/** Selection method data for \p occupancy selection keyword. */
gmx_ana_selmethod_t sm_occupancy = {
"occupancy", REAL_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p betafactor selection keyword. */
+/** Selection method data for \p betafactor selection keyword. */
gmx_ana_selmethod_t sm_betafactor = {
"betafactor", REAL_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p x selection keyword. */
+/** Selection method data for \p x selection keyword. */
gmx_ana_selmethod_t sm_x = {
"x", REAL_VALUE, SMETH_DYNAMIC,
0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ NULL,
+ NULL,
+ NULL,
+ NULL,
+ NULL,
+ NULL,
+ NULL,
&evaluate_x,
};
-/** \internal Selection method data for \p y selection keyword. */
+/** Selection method data for \p y selection keyword. */
gmx_ana_selmethod_t sm_y = {
"y", REAL_VALUE, SMETH_DYNAMIC,
0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ NULL,
+ NULL,
+ NULL,
+ NULL,
+ NULL,
+ NULL,
+ NULL,
&evaluate_y,
};
-/** \internal Selection method data for \p z selection keyword. */
+/** Selection method data for \p z selection keyword. */
gmx_ana_selmethod_t sm_z = {
"z", REAL_VALUE, SMETH_DYNAMIC,
0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ NULL,
+ NULL,
+ NULL,
+ NULL,
+ NULL,
+ NULL,
+ NULL,
&evaluate_z,
};
* Copies \p g to \p out->u.g.
*/
static void
-evaluate_all(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_all(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
gmx_ana_index_copy(out->u.g, g, false);
}
* Returns an empty \p out->u.g.
*/
static void
-evaluate_none(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_none(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void * /* data */)
{
out->u.g->isize = 0;
}
* Returns the indices for each atom in \p out->u.i.
*/
static void
-evaluate_atomnr(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_atomnr(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Returns the residue numbers for each atom in \p out->u.i.
*/
static void
-evaluate_resnr(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_resnr(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
int resind;
out->nr = g->isize;
for (i = 0; i < g->isize; ++i)
{
- resind = top->atoms.atom[g->index[i]].resind;
+ resind = top->atoms.atom[g->index[i]].resind;
out->u.i[i] = top->atoms.resinfo[resind].nr;
}
}
* Returns the residue indices for each atom in \p out->u.i.
*/
static void
-evaluate_resindex(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_resindex(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
}
}
-/*!
- * \param[in] top Topology structure.
- * \param npar Not used.
- * \param param Not used.
- * \param data Not used.
- * \returns 0 if molecule info is present in the topology, -1 otherwise.
- *
- * If molecule information is not found, also prints an error message.
- */
static void
-check_molecules(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+check_molecules(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
{
bool bOk;
* Returns the molecule indices for each atom in \p out->u.i.
*/
static void
-evaluate_molindex(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_molindex(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i, j;
out->nr = g->isize;
for (i = j = 0; i < g->isize; ++i)
{
- while (top->mols.index[j + 1] <= g->index[i]) ++j;
+ while (top->mols.index[j + 1] <= g->index[i])
+ {
+ ++j;
+ }
out->u.i[i] = j + 1;
}
}
* Returns the atom name for each atom in \p out->u.s.
*/
static void
-evaluate_atomname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_atomname(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Returns the PDB atom name for each atom in \p out->u.s.
*/
static void
-evaluate_pdbatomname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_pdbatomname(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
}
}
-/*!
- * \param[in] top Topology structure.
- * \param npar Not used.
- * \param param Not used.
- * \param data Not used.
- * \returns 0 if atom types are present in the topology, -1 otherwise.
- *
- * If the atom types are not found, also prints an error message.
- */
static void
-check_atomtype(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+check_atomtype(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
{
bool bOk;
* Segfaults if atom types are not found in the topology.
*/
static void
-evaluate_atomtype(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_atomtype(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Returns the residue name for each atom in \p out->u.s.
*/
static void
-evaluate_resname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_resname(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
int resind;
out->nr = g->isize;
for (i = 0; i < g->isize; ++i)
{
- resind = top->atoms.atom[g->index[i]].resind;
+ resind = top->atoms.atom[g->index[i]].resind;
out->u.s[i] = *top->atoms.resinfo[resind].name;
}
}
* Returns the insertion code for each atom in \p out->u.s.
*/
static void
-evaluate_insertcode(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_insertcode(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
int resind;
out->nr = g->isize;
for (i = 0; i < g->isize; ++i)
{
- resind = top->atoms.atom[g->index[i]].resind;
+ resind = top->atoms.atom[g->index[i]].resind;
out->u.s[i][0] = top->atoms.resinfo[resind].ic;
}
}
* Returns the chain for each atom in \p out->u.s.
*/
static void
-evaluate_chain(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_chain(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
int resind;
out->nr = g->isize;
for (i = 0; i < g->isize; ++i)
{
- resind = top->atoms.atom[g->index[i]].resind;
+ resind = top->atoms.atom[g->index[i]].resind;
out->u.s[i][0] = top->atoms.resinfo[resind].chainid;
}
}
* Returns the mass for each atom in \p out->u.r.
*/
static void
-evaluate_mass(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_mass(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Returns the charge for each atom in \p out->u.r.
*/
static void
-evaluate_charge(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_charge(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
}
}
-/*!
- * \param[in] top Topology structure.
- * \param npar Not used.
- * \param param Not used.
- * \param data Not used.
- * \returns 0 if PDB info is present in the topology, -1 otherwise.
- *
- * If PDB info is not found, also prints an error message.
- */
static void
-check_pdbinfo(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+check_pdbinfo(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
{
bool bOk;
* Returns the alternate location identifier for each atom in \p out->u.s.
*/
static void
-evaluate_altloc(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_altloc(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Segfaults if PDB info is not found in the topology.
*/
static void
-evaluate_occupancy(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_occupancy(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Segfaults if PDB info is not found in the topology.
*/
static void
-evaluate_betafactor(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_betafactor(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
/*! \brief
* Internal utility function for position keyword evaluation.
*
- * \param[in] fr Current frame.
- * \param[in] g Index group for which the coordinates should be evaluated.
* \param[out] out Output array.
* \param[in] pos Position data to use instead of atomic coordinates
* (can be NULL).
* evaluate_z() to do the actual evaluation.
*/
static void
-evaluate_coord(t_trxframe *fr, gmx_ana_index_t *g, real out[],
- gmx_ana_pos_t *pos, int d)
+evaluate_coord(real out[], gmx_ana_pos_t *pos, int d)
{
- int b, i;
- real v;
-
- if (pos)
+ for (int b = 0; b < pos->count(); ++b)
{
- for (b = 0; b < pos->nr; ++b)
+ const real v = pos->x[b][d];
+ for (int i = pos->m.mapb.index[b]; i < pos->m.mapb.index[b+1]; ++i)
{
- v = pos->x[b][d];
- for (i = pos->m.mapb.index[b]; i < pos->m.mapb.index[b+1]; ++i)
- {
- out[i] = v;
- }
- }
- }
- else
- {
- for (i = 0; i < g->isize; ++i)
- {
- out[i] = fr->x[g->index[i]][d];
+ out[i] = v;
}
}
+ // TODO: Make this more efficient by directly extracting the coordinates
+ // from the frame coordinates for atomic positions instead of going through
+ // a position calculation.
}
/*!
* Returns the \p x coordinate for each atom in \p out->u.r.
*/
static void
-evaluate_x(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
+evaluate_x(t_topology * /*top*/, t_trxframe * /*fr*/, t_pbc * /*pbc*/,
+ gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
{
- out->nr = pos->g->isize;
- evaluate_coord(fr, pos->g, out->u.r, pos, XX);
+ out->nr = pos->m.mapb.nra;
+ evaluate_coord(out->u.r, pos, XX);
}
/*!
* Returns the \p y coordinate for each atom in \p out->u.r.
*/
static void
-evaluate_y(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
+evaluate_y(t_topology * /*top*/, t_trxframe * /*fr*/, t_pbc * /*pbc*/,
+ gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
{
- out->nr = pos->g->isize;
- evaluate_coord(fr, pos->g, out->u.r, pos, YY);
+ out->nr = pos->m.mapb.nra;
+ evaluate_coord(out->u.r, pos, YY);
}
/*!
* Returns the \p z coordinate for each atom in \p out->u.r.
*/
static void
-evaluate_z(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
+evaluate_z(t_topology * /*top*/, t_trxframe * /*fr*/, t_pbc * /*pbc*/,
+ gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
{
- out->nr = pos->g->isize;
- evaluate_coord(fr, pos->g, out->u.r, pos, ZZ);
+ out->nr = pos->m.mapb.nra;
+ evaluate_coord(out->u.r, pos, ZZ);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff