Adaptive force scaling for densityfitting

[gromacs.git] / src / gromacs / applied_forces / densityfittingforceprovider.cpp

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/*! \internal \file
 * \brief
 * Implements force provider for density fitting
 *
 * \author Christian Blau <blau@kth.se>
 * \ingroup module_applied_forces
 */
#include "gmxpre.h"

#include "densityfittingforceprovider.h"

#include <numeric>

#include "gromacs/compat/optional.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/densityfit.h"
#include "gromacs/math/densityfittingforce.h"
#include "gromacs/math/exponentialmovingaverage.h"
#include "gromacs/math/gausstransform.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/forceoutput.h"
#include "gromacs/mdtypes/iforceprovider.h"
#include "gromacs/pbcutil/pbc.h"

#include "densityfittingamplitudelookup.h"
#include "densityfittingparameters.h"

namespace gmx
{

namespace
{

/*! \internal \brief Generate the spread kernel from Gaussian parameters.
 *
 * \param[in] sigma the width of the Gaussian to be spread
 * \param[in] nSigma the range of the Gaussian in multiples of sigma
 * \param[in] scaleToLattice the coordinate transformation into the spreading lattice
 * \returns A Gauss-transform kernel shape
 */
GaussianSpreadKernelParameters::Shape
makeSpreadKernel(real sigma, real nSigma, const ScaleCoordinates &scaleToLattice)
{
    RVec sigmaInLatticeCoordinates {
        sigma, sigma, sigma
    };
    scaleToLattice( { &sigmaInLatticeCoordinates, &sigmaInLatticeCoordinates + 1 });
    return {
               DVec {
                   sigmaInLatticeCoordinates[XX], sigmaInLatticeCoordinates[YY], sigmaInLatticeCoordinates[ZZ]
               }, nSigma
    };
}

}   // namespace

/********************************************************************
 * DensityFittingForceProvider::Impl
 */

class DensityFittingForceProvider::Impl
{
    public:
        //! \copydoc DensityFittingForceProvider(const DensityFittingParameters &parameters)
        Impl(const DensityFittingParameters &parameters,
             basic_mdspan<const float, dynamicExtents3D> referenceDensity,
             const TranslateAndScale &transformationToDensityLattice,
             const LocalAtomSet &localAtomSet,
             int pbcType,
             double simulationTimeStep,
             const DensityFittingForceProviderState &state);
        ~Impl();
        void calculateForces(const ForceProviderInput &forceProviderInput, ForceProviderOutput *forceProviderOutput);

        DensityFittingForceProviderState state();

    private:
        const DensityFittingParameters       &parameters_;
        DensityFittingForceProviderState      state_;
        LocalAtomSet                          localAtomSet_;

        GaussianSpreadKernelParameters::Shape spreadKernel_;
        GaussTransform3D                      gaussTransform_;
        DensitySimilarityMeasure              measure_;
        DensityFittingForce                   densityFittingForce_;
        //! the local atom coordinates transformed into the grid coordinate system
        std::vector<RVec>                     transformedCoordinates_;
        std::vector<RVec>                     forces_;
        DensityFittingAmplitudeLookup         amplitudeLookup_;
        TranslateAndScale                     transformationToDensityLattice_;
        RVec                                  referenceDensityCenter_;
        int                                   pbcType_;

        //! Optionally scale the force according to a moving average of the similarity
        compat::optional<ExponentialMovingAverage> expAverageSimilarity_;
};

DensityFittingForceProvider::Impl::~Impl() = default;

DensityFittingForceProvider::Impl::Impl(const DensityFittingParameters &parameters,
                                        basic_mdspan<const float, dynamicExtents3D> referenceDensity,
                                        const TranslateAndScale &transformationToDensityLattice,
                                        const LocalAtomSet &localAtomSet,
                                        int pbcType,
                                        double simulationTimeStep,
                                        const DensityFittingForceProviderState &state) :
    parameters_(parameters),
    state_(state),
    localAtomSet_(localAtomSet),
    spreadKernel_(makeSpreadKernel(parameters_.gaussianTransformSpreadingWidth_,
                                   parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_,
                                   transformationToDensityLattice.scaleOperationOnly())),
    gaussTransform_(referenceDensity.extents(), spreadKernel_),
    measure_(parameters.similarityMeasureMethod_, referenceDensity),
    densityFittingForce_(spreadKernel_),
    transformedCoordinates_(localAtomSet_.numAtomsLocal()),
    amplitudeLookup_(parameters_.amplitudeLookupMethod_),
    transformationToDensityLattice_(transformationToDensityLattice),
    pbcType_(pbcType),
    expAverageSimilarity_(compat::nullopt)
{
    if (parameters_.adaptiveForceScaling_)
    {
        GMX_ASSERT(simulationTimeStep > 0, "Simulation time step must be larger than zero for adaptive for scaling.");
        expAverageSimilarity_.emplace(ExponentialMovingAverage(
                                              parameters_.adaptiveForceScalingTimeConstant_
                                              / (simulationTimeStep * parameters_.calculationIntervalInSteps_),
                                              state.exponentialMovingAverageState_));
    }
    referenceDensityCenter_  = {
        real(referenceDensity.extent(XX))/2,
        real(referenceDensity.extent(YY))/2,
        real(referenceDensity.extent(ZZ))/2
    };
    transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
            { &referenceDensityCenter_, &referenceDensityCenter_ + 1 });
    // correct the reference density center for a shift
    // if the reference density does not have its origin at (0,0,0)
    RVec referenceDensityOriginShift(0, 0, 0);
    transformationToDensityLattice_({ &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
    transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
            { &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
    referenceDensityCenter_ -= referenceDensityOriginShift;
}

void DensityFittingForceProvider::Impl::calculateForces(const ForceProviderInput &forceProviderInput,
                                                        ForceProviderOutput      *forceProviderOutput)
{
    // do nothing but count number of steps when not in density fitting step
    if (state_.stepsSinceLastCalculation_ % parameters_.calculationIntervalInSteps_ != 0)
    {
        ++(state_.stepsSinceLastCalculation_);
        return;
    }

    state_.stepsSinceLastCalculation_ = 0;

    // do nothing if there are no density fitting atoms on this node
    if (localAtomSet_.numAtomsLocal() == 0)
    {
        return;
    }
    transformedCoordinates_.resize(localAtomSet_.numAtomsLocal());
    // pick and copy atom coordinates
    std::transform(std::cbegin(localAtomSet_.localIndex()),
                   std::cend(localAtomSet_.localIndex()),
                   std::begin(transformedCoordinates_),
                   [&forceProviderInput](int index) { return forceProviderInput.x_[index]; });

    // pick periodic image that is closest to the center of the reference density
    {
        t_pbc pbc;
        set_pbc(&pbc, pbcType_, forceProviderInput.box_);
        for (RVec &x : transformedCoordinates_)
        {
            rvec dx;
            pbc_dx(&pbc, x, referenceDensityCenter_, dx);
            x = referenceDensityCenter_ + dx;
        }
    }

    // transform local atom coordinates to density grid coordinates
    transformationToDensityLattice_(transformedCoordinates_);

    // spread atoms on grid
    gaussTransform_.setZero();

    std::vector<real> amplitudes = amplitudeLookup_(forceProviderInput.mdatoms_, localAtomSet_.localIndex());

    if (parameters_.normalizeDensities_)
    {
        real sum = std::accumulate(std::begin(amplitudes), std::end(amplitudes), 0.);
        if (PAR(&forceProviderInput.cr_))
        {
            gmx_sum(1, &sum, &forceProviderInput.cr_);
        }
        for (real &amplitude : amplitudes)
        {
            amplitude /= sum;
        }
    }

    auto amplitudeIterator = amplitudes.cbegin();

    for (const auto &r : transformedCoordinates_)
    {
        gaussTransform_.add({ r, *amplitudeIterator });
        ++amplitudeIterator;
    }

    // communicate grid
    if (PAR(&forceProviderInput.cr_))
    {
        // \todo update to real once GaussTransform class returns real
        gmx_sumf(gaussTransform_.view().mapping().required_span_size(),
                 gaussTransform_.view().data(), &forceProviderInput.cr_);
    }

    // calculate grid derivative
    const DensitySimilarityMeasure::density &densityDerivative =
        measure_.gradient(gaussTransform_.constView());
    // calculate forces
    forces_.resize(localAtomSet_.numAtomsLocal());
    std::transform(
            std::begin(transformedCoordinates_),
            std::end(transformedCoordinates_),
            std::begin(amplitudes),
            std::begin(forces_),
            [&densityDerivative, this](const RVec r, real amplitude)
            {
                return densityFittingForce_.evaluateForce({r, amplitude}, densityDerivative);
            }
            );

    transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(forces_);

    auto       densityForceIterator   = forces_.cbegin();
    const real effectiveForceConstant = state_.adaptiveForceConstantScale_ *
        parameters_.calculationIntervalInSteps_ * parameters_.forceConstant_;
    for (const auto localAtomIndex : localAtomSet_.localIndex())
    {
        forceProviderOutput->forceWithVirial_.force_[localAtomIndex]
            += effectiveForceConstant * *densityForceIterator;
        ++densityForceIterator;
    }

    // calculate corresponding potential energy
    const float similarity  = measure_.similarity(gaussTransform_.constView());
    const real  energy      = -similarity * parameters_.forceConstant_ * state_.adaptiveForceConstantScale_;
    forceProviderOutput->enerd_.term[F_DENSITYFITTING] += energy;

    if (expAverageSimilarity_.has_value())
    {
        expAverageSimilarity_->updateWithDataPoint(similarity);

        if (expAverageSimilarity_->increasing())
        {
            state_.adaptiveForceConstantScale_ /= 1._real + expAverageSimilarity_->inverseTimeConstant();
        }
        else
        {
            state_.adaptiveForceConstantScale_ *= 1._real + expAverageSimilarity_->inverseTimeConstant();
        }
    }
}

DensityFittingForceProviderState
DensityFittingForceProvider::Impl::state()
{
    if (expAverageSimilarity_.has_value())
    {
        state_.exponentialMovingAverageState_ = expAverageSimilarity_->state();
    }
    return state_;
}

/********************************************************************
 * DensityFittingForceProvider
 */

DensityFittingForceProvider::~DensityFittingForceProvider() = default;

DensityFittingForceProvider::DensityFittingForceProvider(const DensityFittingParameters &parameters,
                                                         basic_mdspan<const float, dynamicExtents3D> referenceDensity,
                                                         const TranslateAndScale &transformationToDensityLattice,
                                                         const LocalAtomSet &localAtomSet,
                                                         int pbcType,
                                                         double simulationTimeStep,
                                                         const DensityFittingForceProviderState &state)
    : impl_(new Impl(parameters, referenceDensity, transformationToDensityLattice, localAtomSet, pbcType, simulationTimeStep, state))
{}

void DensityFittingForceProvider::calculateForces(const ForceProviderInput  &forceProviderInput,
                                                  ForceProviderOutput      * forceProviderOutput)
{
    impl_->calculateForces(forceProviderInput, forceProviderOutput);
}

DensityFittingForceProviderState DensityFittingForceProvider::state()
{
    return impl_->state();
}

} // namespace gmx