src/kernel/sorting.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
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   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
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  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
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  35
  36 #ifndef _sorting_h
  37 #define _sorting_h
  38
  39 #include "typedefs.h"
  40 typedef atom_id t_bond[2];
  41
  42 extern void sort_bonds(t_topology *top);
  43 /*
  44  * Sort_bonds sorts all bonded force parameters in order of ascending
  45  * atom id of the maximum atom id specified in a bond per type bond.
  46  *
  47  * If, for example, for a specific bond type the following bonds are specified:
  48  *    bond1 between atoms 15, 16, 12, 18 and 20
  49  *    bond2 between atoms 14, 13, 12, 18 and 19
  50  *    bond3 between atoms 17, 11, 19, 21 and 15
  51  * then the maximum atom id for each bond would be:
  52  *    bond1: 20
  53  *    bond2: 19
  54  *    bond3: 21
  55  * so order in which the bonds will be sorted is bond2, bond1, bond3
  56  *
  57  * This routine is used to determine to which node a bonds should be
  58  * allocated. For the distribution of bonds it is necessary to keep all
  59  * the needed atoms when calculating a bonded force on one node. In
  60  * this way we prevent communication overhead in bonded force calculations.
  61  *
  62  */
  63
  64 extern void sort_xblock(t_block *block,rvec x[],int renum[]);
  65 /*
  66  * Sort_xblock returns a renumber table which can be used to sort the
  67  * blocks specified in block in an order dependent of the coordinates.
  68  */
  69
  70 extern void sort_bond_list(t_bond bonds[],int nr);
  71 /*
  72  * Sort_bond_list sort the list of bonds, specified by bonds in order
  73  * of ascending atom id. The bonds are specified as pairs of atom ids.
  74  * Where nr specifies the number of bonds (the length of the array).
  75  */
  76
  77 #endif  /* _sorting_h */