src/mdlib/groupcoord.h

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  35
  36 /*! \file groupcoord.h
  37  *
  38  *  @brief Assemble atom positions for comparison with a reference set.
  39  *
  40  *  This file contains functions to assemble the positions of a subset of the
  41  *  atoms and to do operations on it like determining the center of mass, or
  42  *  doing translations and rotations. These functions are useful when
  43  *  a subset of the positions needs to be compared to some set of reference
  44  *  positions, as e.g. done for essential dynamics.
  45  *
  46  */
  47
  48 #ifdef HAVE_CONFIG_H
  49 #include <config.h>
  50 #endif
  51
  52 #include <stdio.h>
  53 #include "typedefs.h"
  54
  55
  56 /*! \brief Select local atoms of a group.
  57 *
  58 * Selects the indices of local atoms of a group and stores them in anrs_loc[0..nr_loc].
  59 * If you need the positions of the group's atoms on all nodes, provide a coll_ind[0..nr]
  60 * array and pass it on to communicate_group_positions. Thus the collective array
  61 * will always have the same atom order (ascending indices).
  62 *
  63 *  \param ga2la[in]         Global to local atom index conversion data.
  64 *  \param nr[in]            The total number of atoms that the group contains.
  65 *  \param anrs[in]          The global atom number of the group's atoms.
  66 *  \param nr_loc[out]       The number of group atoms present on the local node.
  67 *  \param anrs_loc[out]     The local atom numbers of the group.
  68 *  \param nalloc_loc[inout] Local allocation size of anrs_loc array.
  69 *  \param coll_ind[opt]     If not NULL this array must be of size nr. It stores
  70 *                           for each local atom where it belongs in the global
  71 *                           (collective) array such that it can be gmx_summed
  72 *                           in the communicate_group_positions routine.
  73 */
  74 extern void dd_make_local_group_indices(gmx_ga2la_t ga2la,
  75                                         const int nr, int anrs[], int *nr_loc,
  76                                         int *anrs_loc[], int *nalloc_loc,
  77                                         int coll_ind[]);
  78
  79
  80 /*! \brief Assemble local positions into a collective array present on all nodes.
  81  *
  82  * Communicate the positions of the group's atoms such that every node has all of
  83  * them. Unless running on huge number of cores, this is not a big performance impact
  84  * as long as the collective subset [0..nr] is kept small. The atom indices are
  85  * retrieved from anrs_loc[0..nr_loc]. If you call the routine for the serial case,
  86  * provide an array coll_ind[i] = i for i in 1..nr.
  87  *
  88  * \param cr[in]             Pointer to MPI communication data.
  89  * \param xcoll[out]         Collective array of positions, idential on all nodes
  90  *                           after this routine has been called.
  91  * \param shifts[inout]      Collective array of shifts for xcoll, needed to make
  92  *                           the group whole. This array remembers the shifts
  93  *                           since the start of the simulation (where the group
  94  *                           is whole) and must therefore not be changed outside
  95  *                           of this routine!
  96  * \param extra_shifts[buf]  Extra shifts since last time step, only needed as
  97  *                           buffer variable [0..nr].
  98  * \param bNS[in]            Neighborsearching/domain redecomposition has been
  99  *                           performed at the begin of this time step such that
 100  *                           the shifts have changed and need to be updated.
 101  * \param x_loc[in]          Pointer to the local atom positions this node has.
 102  * \param nr[in]             Total number of atoms in the group.
 103  * \param nr_loc[in]         Number of group atoms on the local node.
 104  * \param anrs_loc[in]       Array of the local atom indices.
 105  * \param coll_ind[in]       This array of size nr stores for each local atom where
 106  *                           it belongs in the collective array so that the local
 107  *                           contributions can be gmx_summed. It is provided by
 108  *                           dd_make_local_group_indices.
 109  * \param xcoll_old[inout]   Positions from the last time step, used to make the
 110  *                           group whole.
 111  * \param box[in]            Simulation box matrix, needed to shift xcoll such that
 112  *                           the group becomes whole.
 113  */
 114 extern void communicate_group_positions(t_commrec *cr, rvec *xcoll, ivec *shifts,
 115                                         ivec *extra_shifts, const gmx_bool bNS,
 116                                         rvec *x_loc, const int nr, const int nr_loc,
 117                                         int *anrs_loc, int *coll_ind, rvec *xcoll_old,
 118                                         matrix box);
 119
 120
 121 /*! \brief Calculates the center of the positions x locally.
 122  *
 123  * Calculates the center of mass (if masses are given in the weight array) or
 124  * the geometrical center (if NULL is passed as weight).
 125  *
 126  * \param x[in]              Positions.
 127  * \param weight[in]         Can be NULL or an array of weights. If masses are
 128  *                           given as weights, the COM is calculated.
 129  * \param nr[in]             Number of positions and weights if present.
 130  * \param center[out]        The (weighted) center of the positions.
 131  *
 132  */
 133 extern void get_center(rvec x[], real weight[], const int nr, rvec center);
 134
 135
 136 /*! \brief Calculates the sum of the positions x locally.
 137  *
 138  * Calculates the (weighted) sum of position vectors and returns the sum of
 139  * weights, which is needed when local contributions shall be summed to a
 140  * global weighted center.
 141  *
 142  * \param x[in]              Array of positions.
 143  * \param weight[in]         Can be NULL or an array of weights.
 144  * \param nr[in]             Number of positions and weights if present.
 145  * \param dsumvec[out]       The (weighted) sum of the positions.
 146  * \return Sum of weights.
 147  *
 148  */
 149 extern double get_sum_of_positions(rvec x[], real weight[], const int nr, dvec dsumvec);
 150
 151
 152 /*! \brief Calculates the global center of all local arrays x.
 153  *
 154  * Get the center from local positions [0..nr_loc], this involves communication.
 155  * Not that the positions must already have the correct PBC representation. Use
 156  * this routine if no collective coordinates are assembled from which the center
 157  * could be calculated without communication.
 158  *
 159  * \param cr[in]             Pointer to MPI communication data.
 160  * \param x_loc[in]          Array of local positions [0..nr_loc].
 161  * \param weight_loc[in]     Array of local weights, these are the masses if the
 162  *                           center of mass is to be calculated.
 163  * \param nr_loc[in]         The number of positions on the local node.
 164  * \param nr_group[in]       The number of positions in the whole group. Since
 165  *                           this is known anyway, we do not need to communicate
 166  *                           and sum nr_loc if we pass it over.
 167  * \param center[out]        The (weighted) center of all x_loc from all the
 168  *                           nodes.
 169  */
 170 extern void get_center_comm(t_commrec *cr, rvec x_loc[], real weight_loc[],
 171                             int nr_loc, int nr_group, rvec center);
 172
 173
 174 /*! \brief Translate positions.
 175  *
 176  * Add a translation vector to the positions x.
 177  *
 178  * \param x[inout]           Array of positions.
 179  * \param nr[in]             Number of entries in the position array.
 180  * \param transvec[in]       Translation vector to be added to all positions.
 181  *
 182  */
 183 extern void translate_x(rvec x[], const int nr, const rvec transvec);
 184
 185
 186 /*! \brief Rotate positions.
 187  *
 188  * Rotate the positions with the rotation matrix.
 189  *
 190  * \param x[inout]           Array of positions.
 191  * \param nr[in]             Number of entries in the position array.
 192  * \param rmat[in]           Rotation matrix to operate on all positions.
 193  *
 194  */
 195 extern void rotate_x(rvec x[], const int nr, matrix rmat);
 196