/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright 2015- The GROMACS Authors
 * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
 * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
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/*! \internal \file
 *
 * \brief
 * Declares the BiasState class.
 *
 * The data members of this class are the state variables of the bias.
 * All interaction from the outside happens through the Bias class, which
 * holds important helper classes such as DimParams and BiasGrid.
 * This class holds many methods, but more are const methods that compute
 * properties of the state.
 *
 * \author Viveca Lindahl
 * \author Berk Hess <hess@kth.se>
 * \ingroup module_awh
 */

#ifndef GMX_AWH_BIASSTATE_H
#define GMX_AWH_BIASSTATE_H

#include <cstdio>

#include <string>
#include <vector>

#include "gromacs/math/vectypes.h"
#include "gromacs/utility/alignedallocator.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"

#include "coordstate.h"
#include "dimparams.h"
#include "histogramsize.h"

struct t_commrec;

namespace gmx
{

template<typename>
class ArrayRef;
struct AwhBiasHistory;
class BiasParams;
class BiasGrid;
class BiasSharing;
class CorrelationGrid;
class GridAxis;
class PointState;

/*! \internal
 * \brief The state of a bias.
 *
 * The bias state has the current coordinate state: its value and the grid point
 * it maps to (the grid point of the umbrella potential if needed). It contains
 * a vector with the state for each point on the grid. It also
 * counts the number of updates issued and tracks which points have been sampled
 * since last update. Finally, the convergence state is a global property set
 * ultimately by the histogram size histogramSize in the sub-class HistogramSize,
 * since the update sizes are ~ 1/histogramSize.
 */
class BiasState
{
public:
    /*! \brief Constructor.
     *
     * Constructs the global state and the point states on a provided
     * geometric grid passed in \p grid.
     *
     * \param[in] awhBiasParams         The Bias parameters from inputrec.
     * \param[in] histogramSizeInitial  The estimated initial histogram size.
     *                                  This is floating-point, since histograms use weighted
     *                                  entries and grow by a floating-point scaling factor.
     * \param[in] dimParams             The dimension parameters.
     * \param[in] grid                  The bias grid.
     * \param[in] biasSharing           Multisim bias sharing object, can be nullptrx
     */
    BiasState(const AwhBiasParams&      awhBiasParams,
              double                    histogramSizeInitial,
              ArrayRef<const DimParams> dimParams,
              const BiasGrid&           grid,
              const BiasSharing*        biasSharing);

    /*! \brief
     * Restore the bias state from history.
     *
     * \param[in] biasHistory  Bias history struct.
     * \param[in] grid         The bias grid.
     */
    void restoreFromHistory(const AwhBiasHistory& biasHistory, const BiasGrid& grid);

    /*! \brief
     * Broadcast the bias state over the MPI ranks in this simulation.
     *
     * \param[in] commRecord  Struct for communication.
     */
    void broadcast(const t_commrec* commRecord);

    /*! \brief
     * Allocate and initialize a bias history with the given bias state.
     *
     * This function will be called at the start of a new simulation.
     * Note that this only sets the correct size and does produce
     * a valid history object, but with all data set to zero.
     * Actual history data is set by \ref updateHistory.
     *
     * \param[in,out] biasHistory  AWH history to initialize.
     */
    void initHistoryFromState(AwhBiasHistory* biasHistory) const;

    /*! \brief
     * Update the bias state history with the current state.
     *
     * \param[out] biasHistory  Bias history struct.
     * \param[in]  grid         The bias grid.
     */
    void updateHistory(AwhBiasHistory* biasHistory, const BiasGrid& grid) const;

private:
    /*! \brief Convolves the given PMF using the given AWH bias.
     *
     * \note: The PMF is in single precision, because it is a statistical
     *        quantity and therefore never reaches full float precision.
     *
     * \param[in] dimParams     The bias dimensions parameters
     * \param[in] grid          The grid.
     * \param[in,out] convolvedPmf  Array returned will be of the same length as the AWH grid to store the convolved PMF in.
     */
    void calcConvolvedPmf(ArrayRef<const DimParams> dimParams,
                          const BiasGrid&           grid,
                          std::vector<float>*       convolvedPmf) const;

    /*! \brief
     * Convolves the PMF and sets the initial free energy to its convolution.
     *
     * \param[in] dimParams  The bias dimensions parameters
     * \param[in] grid       The bias grid.
     */
    void setFreeEnergyToConvolvedPmf(ArrayRef<const DimParams> dimParams, const BiasGrid& grid);

    /*! \brief
     * Normalize the PMF histogram.
     *
     * \param[in] numSharingSims  The number of simulations sharing the bias.
     */
    void normalizePmf(int numSharingSims);

public:
    /*! \brief
     * Initialize the state of grid coordinate points.
     *
     * \param[in] awhBiasParams   Bias parameters from inputrec.
     * \param[in] dimParams       The dimension parameters.
     * \param[in] grid            The grid.
     * \param[in] params          The bias parameters.
     * \param[in] filename        Name of file to read PMF and target from.
     * \param[in] numBias         The number of biases.
     */
    void initGridPointState(const AwhBiasParams&      awhBiasParams,
                            ArrayRef<const DimParams> dimParams,
                            const BiasGrid&           grid,
                            const BiasParams&         params,
                            const std::string&        filename,
                            int                       numBias);

    /*! \brief
     * Performs statistical checks on the collected histograms and warns if issues are detected.
     *
     * \param[in]     grid            The grid.
     * \param[in]     biasIndex       The index of the bias we are checking for.
     * \param[in]     t               Time.
     * \param[in,out] fplog           Output file for warnings.
     * \param[in]     maxNumWarnings  Don't issue more than this number of warnings.
     * \returns the number of warnings issued.
     */
    int warnForHistogramAnomalies(const BiasGrid& grid, int biasIndex, double t, FILE* fplog, int maxNumWarnings) const;

    /*! \brief
     * Calculates and sets the force the coordinate experiences from an umbrella centered at the given point.
     *
     * The umbrella potential is an harmonic potential given by 0.5k(coord value - point value)^2. This
     * value is also returned.
     *
     * \param[in]     dimParams  The bias dimensions parameters.
     * \param[in]     grid       The grid.
     * \param[in]     point      Point for umbrella center.
     * \param[in]     neighborLambdaDhdl     An array containing the dHdL at the neighboring lambda
     * points. The array is of length numLambdas+1, where numLambdas is the number of free
     * energy lambda states. Element 0 in the array is the dHdL
     * of the current state and elements 1..numLambdas contain the dHdL of the system in the
     * neighboring lambda states (also including the current state). When there are no free
     * energy lambda state dimensions this can be empty.
     * \param[in,out] force      Force vector to set.
     * Returns the umbrella potential.
     */
    double calcUmbrellaForceAndPotential(ArrayRef<const DimParams> dimParams,
                                         const BiasGrid&           grid,
                                         int                       point,
                                         ArrayRef<const double>    neighborLambdaDhdl,
                                         ArrayRef<double>          force) const;

    /*! \brief
     * Calculates and sets the convolved force acting on the coordinate.
     *
     * The convolved force is the weighted sum of forces from umbrellas
     * located at each point in the grid.
     *
     * \param[in]     dimParams           The bias dimensions parameters.
     * \param[in]     grid                The grid.
     * \param[in]     probWeightNeighbor  Probability weights of the neighbors.
     * \param[in]     neighborLambdaDhdl     An array containing the dHdL at the neighboring lambda
     * points. The array is of length numLambdas+1, where numLambdas is the number of free
     * energy lambda states. Element 0 in the array is the dHdL
     * of the current state and elements 1..numLambdas contain the dHdL of the system in the
     * neighboring lambda states (also including the current state). When there are no free
     * energy lambda state dimensions this can be empty.
     * \param[in]     forceWorkBuffer     Force work buffer, values only used internally.
     * \param[in,out] force               Bias force vector to set.
     */
    void calcConvolvedForce(ArrayRef<const DimParams> dimParams,
                            const BiasGrid&           grid,
                            ArrayRef<const double>    probWeightNeighbor,
                            ArrayRef<const double>    neighborLambdaDhdl,
                            ArrayRef<double>          forceWorkBuffer,
                            ArrayRef<double>          force) const;

    /*! \brief
     * Move the center point of the umbrella potential.
     *
     * A new umbrella center is sampled from the biased distibution. Also, the bias
     * force is updated and the new potential is return.
     *
     * This function should only be called when the bias force is not being convolved.
     * It is assumed that the probability distribution has been updated.
     *
     * \param[in] dimParams                   Bias dimension parameters.
     * \param[in] grid                        The grid.
     * \param[in] probWeightNeighbor          Probability weights of the neighbors.
     * \param[in] neighborLambdaDhdl          An array containing the dHdL at the neighboring lambda
     * points. The array is of length numLambdas+1, where numLambdas is the number of free
     * energy lambda states. Element 0 in the array is the dHdL
     * of the current state and elements 1..numLambdas contain the dHdL of the system in the
     * neighboring lambda states (also including the current state). When there are no free
     * energy lambda state dimensions this can be empty.
     * \param[in,out] biasForce               The AWH bias force.
     * \param[in] step                        Step number, needed for the random number generator.
     * \param[in] seed                        Random seed.
     * \param[in] indexSeed                   Second random seed, should be the bias Index.
     * \param[in] onlySampleUmbrellaGridpoint Only sample the umbrella gridpoint without calculating
     * force and potential.
     * \returns the new potential value.
     */
    double moveUmbrella(ArrayRef<const DimParams> dimParams,
                        const BiasGrid&           grid,
                        ArrayRef<const double>    probWeightNeighbor,
                        ArrayRef<const double>    neighborLambdaDhdl,
                        ArrayRef<double>          biasForce,
                        int64_t                   step,
                        int64_t                   seed,
                        int                       indexSeed,
                        bool                      onlySampleUmbrellaGridpoint);

private:
    /*! \brief
     * Gets the histogram rescaling factors needed for skipped updates.
     *
     * \param[in]  params             The bias parameters.
     * \param[out] weighthistScaling  Scaling factor for the reference weight histogram.
     * \param[out] logPmfsumScaling   Log of the scaling factor for the PMF histogram.
     */
    void getSkippedUpdateHistogramScaleFactors(const BiasParams& params,
                                               double*           weighthistScaling,
                                               double*           logPmfsumScaling) const;

public:
    /*! \brief
     * Do all previously skipped updates.
     * Public for use by tests.
     *
     * \param[in] params  The bias parameters.
     */
    void doSkippedUpdatesForAllPoints(const BiasParams& params);

    /*! \brief
     * Do previously skipped updates in this neighborhood.
     *
     * \param[in] params  The bias parameters.
     * \param[in] grid    The grid.
     */
    void doSkippedUpdatesInNeighborhood(const BiasParams& params, const BiasGrid& grid);

private:
    /*! \brief
     * Reset the range used to make the local update list.
     *
     * \param[in] grid  The grid.
     */
    void resetLocalUpdateRange(const BiasGrid& grid);

    /*! \brief
     * Check if the sampling region has been covered "enough" or not.
     *
     * A one-dimensional interval is defined as covered if each point has
     * accumulated the same weight as is in the peak of a discretized normal
     * distribution. For multiple dimensions, the weights are simply projected
     * onto each dimension and the multidimensional space is covered if each
     * dimension is.
     *
     * \note The covering criterion for multiple dimensions could improved, e.g.
     * by using a path finding algorithm.
     *
     * \param[in] params        The bias parameters.
     * \param[in] dimParams     Bias dimension parameters.
     * \param[in] grid          The grid.
     * \returns true if covered.
     */
    bool isSamplingRegionCovered(const BiasParams&         params,
                                 ArrayRef<const DimParams> dimParams,
                                 const BiasGrid&           grid) const;

public:
    /*! \brief
     * Update the reaction coordinate value.
     *
     * \param[in] grid        The bias grid.
     * \param[in] coordValue  The current reaction coordinate value (there are no limits on allowed values).
     */
    void setCoordValue(const BiasGrid& grid, const awh_dvec coordValue)
    {
        coordState_.setCoordValue(grid, coordValue);
    }

    /*! \brief
     * Performs an update of the bias.
     *
     * The objective of the update is to use collected samples (probability weights)
     * to improve the free energy estimate. For sake of efficiency, the update is
     * local whenever possible, meaning that only points that have actually been sampled
     * are accessed and updated here. For certain AWH settings or at certain steps
     * however, global need to be performed. Besides the actual free energy update, this
     * function takes care of ensuring future convergence of the free energy. Convergence
     * is obtained by increasing the size of the reference weight histogram in a controlled
     * (sometimes dynamic) manner. Also, there are AWH variables that are direct functions
     * of the free energy or sampling history that need to be updated here, namely the target
     * distribution and the bias function.
     *
     * \param[in]     dimParams   The dimension parameters.
     * \param[in]     grid        The grid.
     * \param[in]     params      The bias parameters.
     * \param[in]     t           Time.
     * \param[in]     step        Time step.
     * \param[in,out] fplog       Log file.
     * \param[in,out] updateList  Work space to store a temporary list.
     */
    void updateFreeEnergyAndAddSamplesToHistogram(ArrayRef<const DimParams> dimParams,
                                                  const BiasGrid&           grid,
                                                  const BiasParams&         params,
                                                  double                    t,
                                                  int64_t                   step,
                                                  FILE*                     fplog,
                                                  std::vector<int>*         updateList);

    /*! \brief
     * Update the probability weights and the convolved bias.
     *
     * Given a coordinate value, each grid point is assigned a probability
     * weight, w(point|value), that depends on the current bias function. The sum
     * of these weights is needed for normalizing the probability sum to 1 but
     * also equals the effective, or convolved, biasing weight for this coordinate
     * value. The convolved bias is needed e.g. for extracting the PMF, so we save
     * it here since this saves us from doing extra exponential function evaluations
     * later on.
     *
     * \param[in]  dimParams              The bias dimensions parameters
     * \param[in]  grid                   The grid.
     * \param[in]  neighborLambdaEnergies An array containing the energy of the system
     * in neighboring lambdas. The array is of length numLambdas+1, where numLambdas is
     * the number of free energy lambda states. Element 0 in the array is the energy
     * of the current state and elements 1..numLambdas contain the energy of the system in the
     * neighboring lambda states (also including the current state). When there are no free
     * energy lambda state dimensions this can be empty.
     * \param[out] weight                 Probability weights of the neighbors, SIMD aligned.
     * \returns the convolved bias.
     */

    double updateProbabilityWeightsAndConvolvedBias(ArrayRef<const DimParams> dimParams,
                                                    const BiasGrid&           grid,
                                                    ArrayRef<const double> neighborLambdaEnergies,
                                                    std::vector<double, AlignedAllocator<double>>* weight) const;

    /*! \brief
     * Take samples of the current probability weights for future updates and analysis.
     *
     * Points in the current neighborhood will now have data meaning they
     * need to be included in the local update list of the next update.
     * Therefore, the local update range is also update here.
     *
     * \param[in] grid                The grid.
     * \param[in] probWeightNeighbor  Probability weights of the neighbors.
     */
    void sampleProbabilityWeights(const BiasGrid& grid, ArrayRef<const double> probWeightNeighbor);

    /*! \brief
     * Sample the reaction coordinate and PMF for future updates or analysis.
     *
     * These samples do not affect the (future) sampling and are thus
     * pure observables. Statisics of these are stored in the energy file.
     *
     * \param[in] dimParams           The bias dimensions parameters
     * \param[in] grid                The grid.
     * \param[in] probWeightNeighbor  Probability weights of the neighbors.
     * \param[in] convolvedBias       The convolved bias.
     */
    void sampleCoordAndPmf(const std::vector<DimParams>& dimParams,
                           const BiasGrid&               grid,
                           ArrayRef<const double>        probWeightNeighbor,
                           double                        convolvedBias);
    /*! \brief
     * Calculates the convolved bias for a given coordinate value.
     *
     * The convolved bias is the effective bias acting on the coordinate.
     * Since the bias here has arbitrary normalization, this only makes
     * sense as a relative, to other coordinate values, measure of the bias.
     *
     * \note If it turns out to be costly to calculate this pointwise
     * the convolved bias for the whole grid could be returned instead.
     *
     * \param[in] dimParams   The bias dimensions parameters
     * \param[in] grid        The grid.
     * \param[in] coordValue  Coordinate value.
     * \returns the convolved bias >= -GMX_FLOAT_MAX.
     */
    double calcConvolvedBias(ArrayRef<const DimParams> dimParams,
                             const BiasGrid&           grid,
                             const awh_dvec&           coordValue) const;

    /*! \brief
     * Fills the given array with PMF values.
     *
     * Points outside of the biasing target region will get PMF = GMX_FLOAT_MAX.
     * \note: The PMF is in single precision, because it is a statistical
     *        quantity and therefore never reaches full float precision.
     *
     * \param[out] pmf  Array(ref) to be filled with the PMF values, should have the same size as the bias grid.
     */
    void getPmf(ArrayRef<float> /*pmf*/) const;

    /*! \brief Returns the current coordinate state.
     */
    const CoordState& coordState() const { return coordState_; }

    /*! \brief Returns a const reference to the point state.
     */
    const std::vector<PointState>& points() const { return points_; }

    /*! \brief Returns true if we are in the initial stage.
     */
    bool inInitialStage() const { return histogramSize_.inInitialStage(); }

    /*! \brief Returns the current histogram size.
     */
    inline HistogramSize histogramSize() const { return histogramSize_; }

    /*! \brief Sets the umbrella grid point to the current grid point
     */
    void setUmbrellaGridpointToGridpoint() { coordState_.setUmbrellaGridpointToGridpoint(); }

    /*! \brief Updates sharedCorrelationTensorTimeIntegral_ for all points.
     *
     * \param[in] biasParams       The bias parameters.
     * \param[in] forceCorrelation The force correlation grid.
     */
    void updateSharedCorrelationTensorTimeIntegral(const BiasParams&      biasParams,
                                                   const CorrelationGrid& forceCorrelation);

    /*! \brief Gets the time integral, shared across all ranks, of a tensor of a correlation grid point.
     *
     * \param[in] gridPointIndex         The index of the grid point from which to retrieve the tensor
     * volume.
     * \param[in] correlationTensorIndex The index of the tensor.
     */
    double getSharedCorrelationTensorTimeIntegral(int gridPointIndex, int correlationTensorIndex) const;

    /*! \brief Gets the time integral (all tensors), shared across all ranks, of a correlation grid point.
     *
     * \param[in] gridPointIndex         The index of the grid point from which to retrieve the tensor
     * volume.
     */
    const std::vector<double>& getSharedPointCorrelationIntegral(int gridPointIndex) const;

    /*! \brief Gets the volume element, shared across all ranks, of a correlation grid point.
     *
     * \param[in] gridPointIndex   The index of the grid point from which to retrieve the tensor
     * volume.
     * \param[in] numCorrelation   Number of force correlation tensors.
     */
    double getSharedCorrelationTensorVolumeElement(int gridPointIndex, int numCorrelation) const;

    /* Data members */
private:
    CoordState coordState_; /**< The Current coordinate state */

    /* The grid point state */
    std::vector<PointState> points_; /**< Vector of state of the grid points */

    /* Covering values for each point on the grid */
    std::vector<double> weightSumCovering_; /**< Accumulated weights for covering checks */

    HistogramSize histogramSize_; /**< Global histogram size related values. */

    /* Track the part of the grid sampled since the last update. */
    awh_ivec originUpdatelist_; /**< The origin of the rectangular region that has been sampled since last update. */
    awh_ivec endUpdatelist_; /**< The end of the rectangular region that has been sampled since last update. */

    //! Object for sharing biases over multiple simulations, can be nullptr
    const BiasSharing* biasSharing_;

    /* Correlation tensor time integral, for all points, shared across all ranks (weighted based on
     * the local weight contribution). The structure is [points][correlationTensorIndex].
     * This is only updated on the main MPI ranks.*/
    std::vector<std::vector<double>> sharedCorrelationTensorTimeIntegral_;
};

//! Linewidth used for warning output
static const int c_linewidth = 80 - 2;

} // namespace gmx

#endif /* GMX_AWH_BIASSTATE_H */
