src/gromacs/math/densityfittingforce.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements density fitting forces.
  38  *
  39  * \author Christian Blau <blau@kth.se>
  40  * \ingroup module_math
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "densityfittingforce.h"
  45
  46 #include "gromacs/math/functions.h"
  47 #include "gromacs/math/multidimarray.h"
  48
  49 namespace gmx
  50 {
  51
  52 /********************************************************************
  53  * DensityFittingForce::Impl
  54  */
  55
  56 /*! \internal \brief
  57  * Private implementation class for DensityFittingForce.
  58  */
  59 class DensityFittingForce::Impl
  60 {
  61 public:
  62     /*! \brief Construct densityfitting force implementation from
  63      * spread of function used to generate the density and spread range.
  64      * \param[in] kernelShapeParameters determine the shape of the spreading kernel
  65      */
  66     explicit Impl(const GaussianSpreadKernelParameters::Shape& kernelShapeParameters);
  67     //! \copydoc DensityFittingForce::evaluateForce(const DensitySpreadKernelParameters::PositionAndAmplitude & localParameters, basic_mdspan<const float, dynamicExtents3D> densityDerivative)
  68     RVec evaluateForce(const GaussianSpreadKernelParameters::PositionAndAmplitude& localParameters,
  69                        basic_mdspan<const float, dynamicExtents3D> densityDerivative);
  70     //! The width of the Gaussian in lattice spacing units
  71     DVec sigma_;
  72     //! The spread range in lattice points
  73     IVec latticeSpreadRange_;
  74     //! The three one-dimensional Gaussians that are used in the force calculation
  75     std::array<GaussianOn1DLattice, DIM> gauss1d_;
  76     //! The outer product of a Gaussian along the z and y dimension
  77     OuterProductEvaluator outerProductZY_;
  78 };
  79
  80 DensityFittingForce::Impl::Impl(const GaussianSpreadKernelParameters::Shape& kernelShapeParameters) :
  81     sigma_{ kernelShapeParameters.sigma_ },
  82     latticeSpreadRange_{ kernelShapeParameters.latticeSpreadRange()[XX],
  83                          kernelShapeParameters.latticeSpreadRange()[YY],
  84                          kernelShapeParameters.latticeSpreadRange()[ZZ] },
  85     gauss1d_({ GaussianOn1DLattice(latticeSpreadRange_[XX], sigma_[XX]),
  86                GaussianOn1DLattice(latticeSpreadRange_[YY], sigma_[YY]),
  87                GaussianOn1DLattice(latticeSpreadRange_[ZZ], sigma_[ZZ]) })
  88 {
  89 }
  90
  91 RVec DensityFittingForce::Impl::evaluateForce(const GaussianSpreadKernelParameters::PositionAndAmplitude& localParameters,
  92                                               basic_mdspan<const float, dynamicExtents3D> densityDerivative)
  93 {
  94     const IVec closestLatticePoint(roundToInt(localParameters.coordinate_[XX]),
  95                                    roundToInt(localParameters.coordinate_[YY]),
  96                                    roundToInt(localParameters.coordinate_[ZZ]));
  97     const auto spreadRange = spreadRangeWithinLattice(
  98             closestLatticePoint, densityDerivative.extents(), latticeSpreadRange_);
  99
 100     // do nothing if the added Gaussian will never reach the lattice
 101     if (spreadRange.empty())
 102     {
 103         return {};
 104     }
 105
 106     for (int dimension = XX; dimension <= ZZ; ++dimension)
 107     {
 108         // multiply with amplitude so that Gauss3D = (amplitude * Gauss_x) * Gauss_y * Gauss_z
 109         const float gauss1DAmplitude = dimension > XX ? 1.0 : localParameters.amplitude_;
 110         gauss1d_[dimension].spread(gauss1DAmplitude, localParameters.coordinate_[dimension]
 111                                                              - closestLatticePoint[dimension]);
 112     }
 113
 114     const auto spreadZY = outerProductZY_(gauss1d_[ZZ].view(), gauss1d_[YY].view());
 115     const auto spreadX  = gauss1d_[XX].view();
 116     const IVec spreadGridOffset(latticeSpreadRange_[XX] - closestLatticePoint[XX],
 117                                 latticeSpreadRange_[YY] - closestLatticePoint[YY],
 118                                 latticeSpreadRange_[ZZ] - closestLatticePoint[ZZ]);
 119
 120     const DVec differenceVectorScale  = { 1. / (square(sigma_[XX])), 1. / (square(sigma_[YY])),
 121                                          1. / (square(sigma_[ZZ])) };
 122     const DVec differenceVectorOffset = scaleByVector(
 123             spreadRange.begin().toDVec() - localParameters.coordinate_.toDVec(), differenceVectorScale);
 124
 125     DVec differenceVector = differenceVectorOffset;
 126
 127     DVec force = { 0., 0., 0. };
 128
 129     for (int zLatticeIndex = spreadRange.begin()[ZZ]; zLatticeIndex < spreadRange.end()[ZZ];
 130          ++zLatticeIndex, differenceVector[ZZ] += differenceVectorScale[ZZ])
 131     {
 132         auto zSliceOfDerivative = densityDerivative[zLatticeIndex];
 133
 134         differenceVector[YY] = differenceVectorOffset[YY];
 135         for (int yLatticeIndex = spreadRange.begin()[YY]; yLatticeIndex < spreadRange.end()[YY];
 136              ++yLatticeIndex, differenceVector[YY] += differenceVectorScale[YY])
 137         {
 138             auto       ySliceOfDerivative = zSliceOfDerivative[yLatticeIndex];
 139             const auto zyPrefactor        = spreadZY(zLatticeIndex + spreadGridOffset[ZZ],
 140                                               yLatticeIndex + spreadGridOffset[YY]);
 141
 142             differenceVector[XX] = differenceVectorOffset[XX];
 143             for (int xLatticeIndex = spreadRange.begin()[XX]; xLatticeIndex < spreadRange.end()[XX];
 144                  ++xLatticeIndex, differenceVector[XX] += differenceVectorScale[XX])
 145             {
 146                 const double preFactor = zyPrefactor * spreadX[xLatticeIndex + spreadGridOffset[XX]]
 147                                          * ySliceOfDerivative[xLatticeIndex];
 148                 force += preFactor * differenceVector;
 149             }
 150         }
 151     }
 152     return localParameters.amplitude_ * force.toRVec();
 153 }
 154
 155 /********************************************************************
 156  * DensityFittingForce
 157  */
 158
 159 DensityFittingForce::DensityFittingForce(const GaussianSpreadKernelParameters::Shape& kernelShapeParameters) :
 160     impl_(new Impl(kernelShapeParameters))
 161 {
 162 }
 163
 164 RVec DensityFittingForce::evaluateForce(const GaussianSpreadKernelParameters::PositionAndAmplitude& localParameters,
 165                                         basic_mdspan<const float, dynamicExtents3D> densityDerivative)
 166 {
 167     return impl_->evaluateForce(localParameters, densityDerivative);
 168 }
 169
 170 DensityFittingForce::~DensityFittingForce() {}
 171
 172 DensityFittingForce::DensityFittingForce(const DensityFittingForce& other) :
 173     impl_(new Impl(*other.impl_))
 174 {
 175 }
 176
 177 DensityFittingForce& DensityFittingForce::operator=(const DensityFittingForce& other)
 178 {
 179     *impl_ = *other.impl_;
 180     return *this;
 181 }
 182
 183 DensityFittingForce::DensityFittingForce(DensityFittingForce&&) noexcept = default;
 184
 185 DensityFittingForce& DensityFittingForce::operator=(DensityFittingForce&&) noexcept = default;
 186
 187 } // namespace gmx