src/gromacs/topology/exclusionblocks.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "exclusionblocks.h"
  40
  41 #include <algorithm>
  42
  43 #include "gromacs/topology/block.h"
  44 #include "gromacs/utility/fatalerror.h"
  45 #include "gromacs/utility/smalloc.h"
  46 #include "gromacs/utility/stringutil.h"
  47
  48 namespace gmx
  49 {
  50
  51 void initExclusionBlocks(ExclusionBlocks *b2, int natom)
  52 {
  53     int i;
  54
  55     b2->nr = natom;
  56     snew(b2->nra, b2->nr);
  57     snew(b2->a, b2->nr);
  58     for (i = 0; (i < b2->nr); i++)
  59     {
  60         b2->a[i] = nullptr;
  61     }
  62 }
  63
  64 void doneExclusionBlocks(ExclusionBlocks *b2)
  65 {
  66     int i;
  67
  68     if (b2->nr)
  69     {
  70         for (i = 0; (i < b2->nr); i++)
  71         {
  72             sfree(b2->a[i]);
  73         }
  74         sfree(b2->a);
  75         sfree(b2->nra);
  76         b2->nr = 0;
  77     }
  78 }
  79
  80 void blockaToExclusionBlocks(t_blocka *b, ExclusionBlocks *b2)
  81 {
  82     int     i;
  83     int     j, a;
  84
  85     for (i = 0; (i < b->nr); i++)
  86     {
  87         for (j = b->index[i]; (j < b->index[i+1]); j++)
  88         {
  89             a = b->a[j];
  90             srenew(b2->a[i], ++b2->nra[i]);
  91             b2->a[i][b2->nra[i]-1] = a;
  92         }
  93     }
  94 }
  95
  96 void exclusionBlocksToBlocka(ExclusionBlocks *b2, t_blocka *b)
  97 {
  98     int     i, nra;
  99     int     j;
 100
 101     nra = 0;
 102     for (i = 0; (i < b2->nr); i++)
 103     {
 104         b->index[i] = nra;
 105         for (j = 0; (j < b2->nra[i]); j++)
 106         {
 107             b->a[nra+j] = b2->a[i][j];
 108         }
 109         nra += b2->nra[i];
 110     }
 111     /* terminate list */
 112     b->index[i] = nra;
 113 }
 114
 115 void mergeExclusions(t_blocka *excl, ExclusionBlocks *b2)
 116 {
 117     int     i, k;
 118     int     j;
 119     int     nra;
 120
 121     if (!b2->nr)
 122     {
 123         return;
 124     }
 125     GMX_RELEASE_ASSERT(b2->nr == excl->nr, "Cannot merge exclusions for "
 126                        "blocks that do not describe the same number "
 127                        "of particles");
 128
 129     /* First copy all entries from excl to b2 */
 130     blockaToExclusionBlocks(excl, b2);
 131
 132     /* Count and sort the exclusions */
 133     nra = 0;
 134     for (i = 0; (i < b2->nr); i++)
 135     {
 136         if (b2->nra[i] > 0)
 137         {
 138             /* remove double entries */
 139             std::sort(b2->a[i], b2->a[i]+b2->nra[i]);
 140             k = 1;
 141             for (j = 1; (j < b2->nra[i]); j++)
 142             {
 143                 if (b2->a[i][j] != b2->a[i][k-1])
 144                 {
 145                     b2->a[i][k] = b2->a[i][j];
 146                     k++;
 147                 }
 148             }
 149             b2->nra[i] = k;
 150             nra       += b2->nra[i];
 151         }
 152     }
 153     excl->nra = nra;
 154     srenew(excl->a, excl->nra);
 155
 156     exclusionBlocksToBlocka(b2, excl);
 157 }
 158
 159 } // namespace gmx