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 blockaToExclusionBlocks(const t_blocka *b, gmx::ArrayRef<ExclusionBlock> b2)
  52 {
  53     for (int i = 0; (i < b->nr); i++)
  54     {
  55         for (int j = b->index[i]; (j < b->index[i+1]); j++)
  56         {
  57             b2[i].atomNumber.push_back(b->a[j]);
  58         }
  59     }
  60 }
  61
  62 void exclusionBlocksToBlocka(gmx::ArrayRef<const ExclusionBlock> b2, t_blocka *b)
  63 {
  64     int nra = 0;
  65     int i   = 0;
  66     for (const auto &block : b2)
  67     {
  68         b->index[i] = nra;
  69         int j = 0;
  70         for (const auto &entry : block.atomNumber)
  71         {
  72             b->a[nra+j] = entry;
  73             j++;
  74         }
  75         nra += block.nra();
  76         i++;
  77     }
  78     /* terminate list */
  79     b->index[i] = nra;
  80 }
  81
  82 void mergeExclusions(t_blocka *excl, gmx::ArrayRef<ExclusionBlock> b2)
  83 {
  84     if (b2.empty())
  85     {
  86         return;
  87     }
  88     GMX_RELEASE_ASSERT(b2.ssize() == excl->nr, "Cannot merge exclusions for "
  89                        "blocks that do not describe the same number "
  90                        "of particles");
  91
  92     /* Convert the t_blocka entries to ExclusionBlock form */
  93     blockaToExclusionBlocks(excl, b2);
  94
  95     /* Count and sort the exclusions */
  96     int nra = 0;
  97     for (auto &block : b2)
  98     {
  99         if (block.nra() > 0)
 100         {
 101             /* remove double entries */
 102             std::sort(block.atomNumber.begin(), block.atomNumber.end());
 103             for (auto atom = block.atomNumber.begin() + 1; atom != block.atomNumber.end(); )
 104             {
 105                 GMX_RELEASE_ASSERT(atom < block.atomNumber.end(), "Need to stay in range of the size of the blocks");
 106                 auto prev = atom - 1;
 107                 if (*prev == *atom)
 108                 {
 109                     atom = block.atomNumber.erase(atom);
 110                 }
 111                 else
 112                 {
 113                     ++atom;
 114                 }
 115             }
 116             nra       += block.nra();
 117         }
 118     }
 119     excl->nra = nra;
 120     srenew(excl->a, excl->nra);
 121
 122     exclusionBlocksToBlocka(b2, excl);
 123 }
 124
 125 } // namespace gmx