/usr/include/gromacs/math/paddedvector.h is in libgromacs-dev 2018.1-1.
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* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
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/*! \file
* \brief
* Declares gmx::PaddedRVecVector
*
* \author Mark Abraham <mark.j.abraham@gmail.com>
* \inpublicapi
* \ingroup module_math
*/
#ifndef GMX_MATH_PADDEDVECTOR_H
#define GMX_MATH_PADDEDVECTOR_H
#include <algorithm>
#include <vector>
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/alignedallocator.h"
#include "gromacs/utility/arrayref.h"
namespace gmx
{
/*! \brief Temporary definition of a type usable for SIMD-style loads of RVec quantities.
*
* \note When resizing paddedRVecVector, the size should be chosen with
paddedRVecVectorSize() to ensure correct padding.
* \todo Consider replacing the padding applied in resizePaddedRVecVector()
* by automated padding on resize() of the vector.
* \todo Undo the move of allocator.h and alignedallocator.h from the internal
* to be public API applied in Change-Id: Ifb8dacf, needed to use
* AlignedAllocationPolicy here, when replacing std::vector here.
*/
using PaddedRVecVector = std::vector < RVec, Allocator < RVec, AlignedAllocationPolicy > >;
/*! \brief Returns the padded size for PaddedRVecVector given the number of atoms
*
* \param[in] numAtoms The number of atoms for which data will be stored in a PaddedRVecVector
*/
static inline size_t paddedRVecVectorSize(size_t numAtoms)
{
/* We need one real extra for 4-wide SIMD load/store of RVec.
* But because the vector contains RVecs, we need to add 1 RVec.
*/
size_t simdScatterAccessSize;
if (numAtoms > 0)
{
simdScatterAccessSize = numAtoms + 1;
}
else
{
simdScatterAccessSize = 0;
}
/* We need padding up to a multiple of the SIMD real width.
* But because we don't want a dependence on the SIMD module,
* we use GMX_REAL_MAX_SIMD_WIDTH here.
*/
size_t simdFlatAccesSize = ((numAtoms + (GMX_REAL_MAX_SIMD_WIDTH - 1))/GMX_REAL_MAX_SIMD_WIDTH)*GMX_REAL_MAX_SIMD_WIDTH;
return std::max(simdScatterAccessSize, simdFlatAccesSize);
}
/*! \brief Temporary definition of a type usable for SIMD-style loads of RVec quantities from a view.
*
* \todo Find a more permanent solution that permits the update code to safely
* use a padded, aligned array-ref type. */
template <typename T>
using PaddedArrayRef = ArrayRef<T>;
} // namespace gmx
// TODO These are hacks to avoid littering gmx:: all over code that is
// almost all destined to move into the gmx namespace at some point.
// An alternative would be about 20 files with using statements.
using gmx::PaddedRVecVector;
#endif
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