-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2008, 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
+ * Copyright (c) 2001-2008, The GROMACS development team.
+ * Copyright (c) 2012,2014, 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
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, 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 www.gromacs.org.
+ * 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.
*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://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.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \file groupcoord.h
- *
- * @brief Assemble atom positions for comparison with a reference set.
+/*! \libinternal \file
+ * \brief Assemble atomic positions of a (small) subset of atoms and distribute to all nodes.
*
* This file contains functions to assemble the positions of a subset of the
* atoms and to do operations on it like determining the center of mass, or
* a subset of the positions needs to be compared to some set of reference
* positions, as e.g. done for essential dynamics.
*
+ * \inlibraryapi
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
#include <stdio.h>
-#include "typedefs.h"
-#include "types/commrec.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
/*! \brief Select local atoms of a group.
* retrieved from anrs_loc[0..nr_loc]. If you call the routine for the serial case,
* provide an array coll_ind[i] = i for i in 1..nr.
*
+ * If shifts != NULL, the PBC representation of each atom is chosen such that a
+ * continuous trajectory results. Therefore, if the group is whole at the start
+ * of the simulation, it will always stay whole.
+ * If shifts = NULL, the group positions are not made whole again, but assembled
+ * and distributed to all nodes. The variables marked "optional" are not used in
+ * that case.
+ *
* \param[in] cr Pointer to MPI communication data.
- * \param[out] xcoll Collective array of positions, idential on all nodes
+ * \param[out] xcoll Collective array of positions, identical on all nodes
* after this routine has been called.
* \param[in,out] shifts Collective array of shifts for xcoll, needed to make
* the group whole. This array remembers the shifts
* since the start of the simulation (where the group
* is whole) and must therefore not be changed outside
- * of this routine!
+ * of this routine! If NULL, the group will not be made
+ * whole and the optional variables are ignored.
* \param[out] extra_shifts Extra shifts since last time step, only needed as
- * buffer variable [0..nr].
- * \param[in] bNS Neighborsearching/domain redecomposition has been
+ * buffer variable [0..nr] (optional).
+ * \param[in] bNS Neighbor searching / domain re-decomposition has been
* performed at the begin of this time step such that
- * the shifts have changed and need to be updated.
+ * the shifts have changed and need to be updated
+ * (optional).
* \param[in] x_loc Pointer to the local atom positions this node has.
* \param[in] nr Total number of atoms in the group.
* \param[in] nr_loc Number of group atoms on the local node.
* contributions can be gmx_summed. It is provided by
* dd_make_local_group_indices.
* \param[in,out] xcoll_old Positions from the last time step, used to make the
- * group whole.
+ * group whole (optional).
* \param[in] box Simulation box matrix, needed to shift xcoll such that
- * the group becomes whole.
+ * the group becomes whole (optional).
*/
extern void communicate_group_positions(t_commrec *cr, rvec *xcoll, ivec *shifts,
ivec *extra_shifts, const gmx_bool bNS,
int *anrs_loc, int *coll_ind, rvec *xcoll_old,
matrix box);
-
/*! \brief Calculates the center of the positions x locally.
*
* Calculates the center of mass (if masses are given in the weight array) or
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff