src/gromacs/topology/block.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "block.h"
  40
  41 #include <algorithm>
  42
  43 #include "gromacs/utility/smalloc.h"
  44
  45 void init_block(t_block *block)
  46 {
  47     block->nr           = 0;
  48     block->nalloc_index = 1;
  49     snew(block->index, block->nalloc_index);
  50     block->index[0]     = 0;
  51 }
  52
  53 void init_blocka(t_blocka *block)
  54 {
  55     block->nr           = 0;
  56     block->nra          = 0;
  57     block->nalloc_index = 1;
  58     snew(block->index, block->nalloc_index);
  59     block->index[0]     = 0;
  60     block->nalloc_a     = 0;
  61     block->a            = NULL;
  62 }
  63
  64 t_blocka *new_blocka(void)
  65 {
  66     t_blocka *block;
  67
  68     snew(block, 1);
  69     snew(block->index, 1);
  70
  71     return block;
  72 }
  73
  74 void done_block(t_block *block)
  75 {
  76     block->nr    = 0;
  77     sfree(block->index);
  78     block->nalloc_index = 0;
  79 }
  80
  81 void done_blocka(t_blocka *block)
  82 {
  83     block->nr    = 0;
  84     block->nra   = 0;
  85     sfree(block->index);
  86     sfree(block->a);
  87     block->index        = NULL;
  88     block->a            = NULL;
  89     block->nalloc_index = 0;
  90     block->nalloc_a     = 0;
  91 }
  92
  93 void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup)
  94 {
  95     if (bOneIndexGroup)
  96     {
  97         grp->nalloc_index = 2;
  98         snew(grp->index, grp->nalloc_index);
  99         grp->index[0] = 0;
 100         grp->index[1] = natom;
 101         grp->nr       = 1;
 102     }
 103     else
 104     {
 105         grp->nalloc_index = natom+1;
 106         snew(grp->index, grp->nalloc_index);
 107         snew(grp->index, natom+1);
 108         for (int i = 0; i <= natom; ++i)
 109         {
 110             grp->index[i] = i;
 111         }
 112         grp->nr = natom;
 113     }
 114 }
 115
 116 void stupid_fill_blocka(t_blocka *grp, int natom)
 117 {
 118     grp->nalloc_a = natom;
 119     snew(grp->a, grp->nalloc_a);
 120     for (int i = 0; i < natom; ++i)
 121     {
 122         grp->a[i] = i;
 123     }
 124     grp->nra = natom;
 125
 126     grp->nalloc_index = natom + 1;
 127     snew(grp->index, grp->nalloc_index);
 128     for (int i = 0; i <= natom; ++i)
 129     {
 130         grp->index[i] = i;
 131     }
 132     grp->nr = natom;
 133 }
 134
 135 void copy_blocka(const t_blocka *src, t_blocka *dest)
 136 {
 137     dest->nr           = src->nr;
 138     /* Workaround for inconsistent handling of nalloc_index in
 139      * other parts of the code. Often nalloc_index and nalloc_a
 140      * are not set.
 141      */
 142     dest->nalloc_index = std::max(src->nalloc_index, dest->nr + 1);
 143     snew(dest->index, dest->nalloc_index);
 144     for (int i = 0; i < dest->nr+1; ++i)
 145     {
 146         dest->index[i] = src->index[i];
 147     }
 148     dest->nra      = src->nra;
 149     /* See above. */
 150     dest->nalloc_a = std::max(src->nalloc_a, dest->nra);
 151     snew(dest->a, dest->nalloc_a);
 152     for (int i = 0; i < dest->nra; ++i)
 153     {
 154         dest->a[i] = src->a[i];
 155     }
 156 }