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- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+/*
+ * This file is part of the GROMACS molecular simulation package.
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* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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-/*! \file groupcoord.h
+/*! \libinternal \file
+ * \brief Assemble atomic positions of a (small) subset of atoms and distribute to all nodes.
*
- * @brief Assemble atom positions for comparison with a reference set.
- *
- * This file contains functions to assemble the positions of a subset of the
+ * 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
* doing translations and rotations. These functions are useful when
* 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.
-*
-* Selects the indices of local atoms of a group and stores them in anrs_loc[0..nr_loc].
-* If you need the positions of the group's atoms on all nodes, provide a coll_ind[0..nr]
-* array and pass it on to communicate_group_positions. Thus the collective array
-* will always have the same atom order (ascending indices).
-*
-* \param[in] ga2la Global to local atom index conversion data.
-* \param[in] nr The total number of atoms that the group contains.
-* \param[in] anrs The global atom number of the group's atoms.
-* \param[out] nr_loc The number of group atoms present on the local node.
-* \param[out] anrs_loc The local atom numbers of the group.
-* \param[in,out] nalloc_loc Local allocation size of anrs_loc array.
-* \param[out] coll_ind If not NULL this array must be of size nr. It stores
-* for each local atom where it belongs in the global
-* (collective) array such that it can be gmx_summed
-* in the communicate_group_positions routine.
-*/
+ *
+ * Selects the indices of local atoms of a group and stores them in anrs_loc[0..nr_loc].
+ * If you need the positions of the group's atoms on all nodes, provide a coll_ind[0..nr]
+ * array and pass it on to communicate_group_positions. Thus the collective array
+ * will always have the same atom order (ascending indices).
+ *
+ * \param[in] ga2la Global to local atom index conversion data.
+ * \param[in] nr The total number of atoms that the group contains.
+ * \param[in] anrs The global atom number of the group's atoms.
+ * \param[out] nr_loc The number of group atoms present on the local node.
+ * \param[out] anrs_loc The local atom numbers of the group.
+ * \param[in,out] nalloc_loc Local allocation size of anrs_loc array.
+ * \param[out] coll_ind If not NULL this array must be of size nr. It stores
+ * for each local atom where it belongs in the global
+ * (collective) array such that it can be gmx_summed
+ * in the communicate_group_positions routine.
+ */
extern void dd_make_local_group_indices(gmx_ga2la_t ga2la,
const int nr, int anrs[], int *nr_loc,
int *anrs_loc[], int *nalloc_loc,
/*! \brief Assemble local positions into a collective array present on all nodes.
- *
- * Communicate the positions of the group's atoms such that every node has all of
+ *
+ * Communicate the positions of the group's atoms such that every node has all of
* them. Unless running on huge number of cores, this is not a big performance impact
- * as long as the collective subset [0..nr] is kept small. The atom indices are
+ * as long as the collective subset [0..nr] is kept small. The atom indices are
* 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
* the geometrical center (if NULL is passed as weight).
- *
+ *
* \param[in] x Positions.
* \param[in] weight Can be NULL or an array of weights. If masses are
* given as weights, the COM is calculated.
* \param[in] nr Number of positions and weights if present.
* \param[out] center The (weighted) center of the positions.
- *
+ *
*/
extern void get_center(rvec x[], real weight[], const int nr, rvec center);
/*! \brief Calculates the sum of the positions x locally.
- *
- * Calculates the (weighted) sum of position vectors and returns the sum of
- * weights, which is needed when local contributions shall be summed to a
+ *
+ * Calculates the (weighted) sum of position vectors and returns the sum of
+ * weights, which is needed when local contributions shall be summed to a
* global weighted center.
- *
+ *
* \param[in] x Array of positions.
* \param[in] weight Can be NULL or an array of weights.
* \param[in] nr Number of positions and weights if present.
* \param[out] dsumvec The (weighted) sum of the positions.
* \return Sum of weights.
- *
+ *
*/
extern double get_sum_of_positions(rvec x[], real weight[], const int nr, dvec dsumvec);
-/*! \brief Calculates the global center of all local arrays x.
- *
+/*! \brief Calculates the global center of all local arrays x.
+ *
* Get the center from local positions [0..nr_loc], this involves communication.
* Not that the positions must already have the correct PBC representation. Use
- * this routine if no collective coordinates are assembled from which the center
+ * this routine if no collective coordinates are assembled from which the center
* could be calculated without communication.
- *
+ *
* \param[in] cr Pointer to MPI communication data.
* \param[in] x_loc Array of local positions [0..nr_loc].
* \param[in] weight_loc Array of local weights, these are the masses if the
/*! \brief Translate positions.
- *
+ *
* Add a translation vector to the positions x.
- *
+ *
* \param[in,out] x Array of positions.
* \param[in] nr Number of entries in the position array.
* \param[in] transvec Translation vector to be added to all positions.
- *
+ *
*/
extern void translate_x(rvec x[], const int nr, const rvec transvec);
/*! \brief Rotate positions.
- *
+ *
* Rotate the positions with the rotation matrix.
- *
+ *
* \param[in,out] x Array of positions.
* \param[in] nr Number of entries in the position array.
* \param[in] rmat Rotation matrix to operate on all positions.
- *
+ *
*/
extern void rotate_x(rvec x[], const int nr, matrix rmat);
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff