src/gromacs/nbnxm/kernel_common.cpp

   1 /*
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  35
  36 /*! \internal \file
  37  *
  38  * \brief
  39  * Implements utility functions used by all nbnxm CPU kernels.
  40  *
  41  * \author Berk Hess <hess@kth.se>
  42  */
  43
  44 #include "gmxpre.h"
  45
  46 #include "kernel_common.h"
  47
  48 #include "gromacs/pbcutil/ishift.h"
  49 #include "gromacs/utility/gmxassert.h"
  50
  51 //! Clears all elements of buffer
  52 static void
  53 clearBufferAll(gmx::ArrayRef<real> buffer)
  54 {
  55     for (real &elem : buffer)
  56     {
  57         elem = 0;
  58     }
  59 }
  60
  61 /*! \brief Clears elements of size and stride \p numComponentsPerElement
  62  *
  63  * Only elements with flags in \p nbat set for index \p outputIndex
  64  * are cleared.
  65  */
  66 template <int numComponentsPerElement>
  67 static void
  68 clearBufferFlagged(const nbnxn_atomdata_t &nbat,
  69                    int                     outputIndex,
  70                    gmx::ArrayRef<real>     buffer)
  71 {
  72     const nbnxn_buffer_flags_t &flags = nbat.buffer_flags;
  73     gmx_bitmask_t               our_flag;
  74     bitmask_init_bit(&our_flag, outputIndex);
  75
  76     constexpr size_t numComponentsPerBlock = NBNXN_BUFFERFLAG_SIZE*numComponentsPerElement;
  77
  78     for (int b = 0; b < flags.nflag; b++)
  79     {
  80         if (!bitmask_is_disjoint(flags.flag[b], our_flag))
  81         {
  82             clearBufferAll(buffer.subArray(b*numComponentsPerBlock, numComponentsPerBlock));
  83         }
  84     }
  85 }
  86
  87 void
  88 clearForceBuffer(nbnxn_atomdata_t *nbat,
  89                  int               outputIndex)
  90 {
  91     if (nbat->bUseBufferFlags)
  92     {
  93         GMX_ASSERT(nbat->fstride == DIM, "Only fstride=3 is currently handled here");
  94
  95         clearBufferFlagged<DIM>(*nbat, outputIndex, nbat->out[outputIndex].f);
  96     }
  97     else
  98     {
  99         clearBufferAll(nbat->out[outputIndex].f);
 100     }
 101 }
 102
 103 void
 104 clear_fshift(real *fshift)
 105 {
 106     int i;
 107
 108     for (i = 0; i < SHIFTS*DIM; i++)
 109     {
 110         fshift[i] = 0;
 111     }
 112 }
 113
 114 void
 115 reduce_energies_over_lists(const nbnxn_atomdata_t     *nbat,
 116                            int                         nlist,
 117                            real                       *Vvdw,
 118                            real                       *Vc)
 119 {
 120     const int nenergrp = nbat->params().nenergrp;
 121
 122     for (int nb = 0; nb < nlist; nb++)
 123     {
 124         for (int i = 0; i < nenergrp; i++)
 125         {
 126             /* Reduce the diagonal terms */
 127             int ind    = i*nenergrp + i;
 128             Vvdw[ind] += nbat->out[nb].Vvdw[ind];
 129             Vc[ind]   += nbat->out[nb].Vc[ind];
 130
 131             /* Reduce the off-diagonal terms */
 132             for (int j = i + 1; j < nenergrp; j++)
 133             {
 134                 /* The output should contain only one off-diagonal part */
 135                 int ind    = i*nenergrp + j;
 136                 int indr   = j*nenergrp + i;
 137                 Vvdw[ind] += nbat->out[nb].Vvdw[ind] + nbat->out[nb].Vvdw[indr];
 138                 Vc[ind]   += nbat->out[nb].Vc[ind]   + nbat->out[nb].Vc[indr];
 139             }
 140         }
 141     }
 142 }