src/gromacs/nbnxm/kernel_common.cpp

   1 /*
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   5  * Copyright (c) 2019,2020, by the GROMACS development team, led by
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  36
  37 /*! \internal \file
  38  *
  39  * \brief
  40  * Implements utility functions used by all nbnxm CPU kernels.
  41  *
  42  * \author Berk Hess <hess@kth.se>
  43  * \ingroup module_nbnxm
  44  */
  45
  46 #include "gmxpre.h"
  47
  48 #include "kernel_common.h"
  49
  50 #include "gromacs/pbcutil/ishift.h"
  51 #include "gromacs/utility/gmxassert.h"
  52
  53 //! Clears all elements of buffer
  54 static void clearBufferAll(gmx::ArrayRef<real> buffer)
  55 {
  56     for (real& elem : buffer)
  57     {
  58         elem = 0;
  59     }
  60 }
  61
  62 /*! \brief Clears elements of size and stride \p numComponentsPerElement
  63  *
  64  * Only elements with flags in \p nbat set for index \p outputIndex
  65  * are cleared.
  66  */
  67 template<int numComponentsPerElement>
  68 static void clearBufferFlagged(const nbnxn_atomdata_t& nbat, int outputIndex, gmx::ArrayRef<real> buffer)
  69 {
  70     const nbnxn_buffer_flags_t& flags = nbat.buffer_flags;
  71     gmx_bitmask_t               our_flag;
  72     bitmask_init_bit(&our_flag, outputIndex);
  73
  74     constexpr size_t numComponentsPerBlock = NBNXN_BUFFERFLAG_SIZE * numComponentsPerElement;
  75
  76     for (int b = 0; b < flags.nflag; b++)
  77     {
  78         if (!bitmask_is_disjoint(flags.flag[b], our_flag))
  79         {
  80             clearBufferAll(buffer.subArray(b * numComponentsPerBlock, numComponentsPerBlock));
  81         }
  82     }
  83 }
  84
  85 void clearForceBuffer(nbnxn_atomdata_t* nbat, int outputIndex)
  86 {
  87     if (nbat->bUseBufferFlags)
  88     {
  89         GMX_ASSERT(nbat->fstride == DIM, "Only fstride=3 is currently handled here");
  90
  91         clearBufferFlagged<DIM>(*nbat, outputIndex, nbat->out[outputIndex].f);
  92     }
  93     else
  94     {
  95         clearBufferAll(nbat->out[outputIndex].f);
  96     }
  97 }
  98
  99 void clear_fshift(real* fshift)
 100 {
 101     int i;
 102
 103     for (i = 0; i < SHIFTS * DIM; i++)
 104     {
 105         fshift[i] = 0;
 106     }
 107 }
 108
 109 void reduce_energies_over_lists(const nbnxn_atomdata_t* nbat, int nlist, real* Vvdw, real* Vc)
 110 {
 111     const int nenergrp = nbat->params().nenergrp;
 112
 113     for (int nb = 0; nb < nlist; nb++)
 114     {
 115         for (int i = 0; i < nenergrp; i++)
 116         {
 117             /* Reduce the diagonal terms */
 118             int ind = i * nenergrp + i;
 119             Vvdw[ind] += nbat->out[nb].Vvdw[ind];
 120             Vc[ind] += nbat->out[nb].Vc[ind];
 121
 122             /* Reduce the off-diagonal terms */
 123             for (int j = i + 1; j < nenergrp; j++)
 124             {
 125                 /* The output should contain only one off-diagonal part */
 126                 int ind  = i * nenergrp + j;
 127                 int indr = j * nenergrp + i;
 128                 Vvdw[ind] += nbat->out[nb].Vvdw[ind] + nbat->out[nb].Vvdw[indr];
 129                 Vc[ind] += nbat->out[nb].Vc[ind] + nbat->out[nb].Vc[indr];
 130             }
 131         }
 132     }
 133 }