src/gromacs/math/paddedvector.h

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  35 /*! \file
  36  * \brief
  37  * Declares gmx::PaddedRVecVector
  38  *
  39  * \author Mark Abraham <mark.j.abraham@gmail.com>
  40  * \inpublicapi
  41  * \ingroup module_math
  42  */
  43 #ifndef GMX_MATH_PADDEDVECTOR_H
  44 #define GMX_MATH_PADDEDVECTOR_H
  45
  46 #include <algorithm>
  47 #include <vector>
  48
  49 #include "gromacs/math/vectypes.h"
  50 #include "gromacs/utility/alignedallocator.h"
  51 #include "gromacs/utility/arrayref.h"
  52
  53 namespace gmx
  54 {
  55
  56 /*! \brief Temporary definition of a type usable for SIMD-style loads of RVec quantities.
  57  *
  58  * \note When resizing paddedRVecVector, the size should be chosen with
  59          paddedRVecVectorSize() to ensure correct padding.
  60  * \todo Consider replacing the padding applied in resizePaddedRVecVector()
  61  *       by automated padding on resize() of the vector.
  62  * \todo Undo the move of allocator.h and alignedallocator.h from the internal
  63  *       to be public API applied in Change-Id: Ifb8dacf, needed to use
  64  *       AlignedAllocationPolicy here, when replacing std::vector here.
  65  */
  66 using PaddedRVecVector = std::vector < RVec, Allocator < RVec, AlignedAllocationPolicy > >;
  67
  68 /*! \brief Returns the padded size for PaddedRVecVector given the number of atoms
  69  *
  70  * \param[in] numAtoms  The number of atoms for which data will be stored in a PaddedRVecVector
  71  */
  72 static inline size_t paddedRVecVectorSize(size_t numAtoms)
  73 {
  74     /* We need one real extra for 4-wide SIMD load/store of RVec.
  75      * But because the vector contains RVecs, we need to add 1 RVec.
  76      */
  77     size_t simdScatterAccessSize;
  78     if (numAtoms > 0)
  79     {
  80         simdScatterAccessSize = numAtoms + 1;
  81     }
  82     else
  83     {
  84         simdScatterAccessSize = 0;
  85     }
  86
  87     /* We need padding up to a multiple of the SIMD real width.
  88      * But because we don't want a dependence on the SIMD module,
  89      * we use GMX_REAL_MAX_SIMD_WIDTH here.
  90      */
  91     size_t simdFlatAccesSize  = ((numAtoms + (GMX_REAL_MAX_SIMD_WIDTH - 1))/GMX_REAL_MAX_SIMD_WIDTH)*GMX_REAL_MAX_SIMD_WIDTH;
  92
  93     return std::max(simdScatterAccessSize, simdFlatAccesSize);
  94 }
  95
  96 /*! \brief Temporary definition of a type usable for SIMD-style loads of RVec quantities from a view.
  97  *
  98  * \todo Find a more permanent solution that permits the update code to safely
  99  * use a padded, aligned array-ref type. */
 100 template <typename T>
 101 using PaddedArrayRef = ArrayRef<T>;
 102
 103 } // namespace gmx
 104
 105 // TODO These are hacks to avoid littering gmx:: all over code that is
 106 // almost all destined to move into the gmx namespace at some point.
 107 // An alternative would be about 20 files with using statements.
 108 using gmx::PaddedRVecVector;
 109
 110 #endif