src/gromacs/awh/coordstate.cpp

   1 /*
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   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  35
  36 /*! \internal \file
  37  * \brief
  38  * Implements the CoordState class.
  39  *
  40  * \author Viveca Lindahl
  41  * \author Berk Hess <hess@kth.se>
  42  * \ingroup module_awh
  43  */
  44
  45 #include "gmxpre.h"
  46
  47 #include "coordstate.h"
  48
  49 #include <algorithm>
  50
  51 #include "gromacs/math/utilities.h"
  52 #include "gromacs/mdtypes/awh_history.h"
  53 #include "gromacs/mdtypes/awh_params.h"
  54 #include "gromacs/random/threefry.h"
  55 #include "gromacs/random/uniformrealdistribution.h"
  56 #include "gromacs/utility/arrayref.h"
  57 #include "gromacs/utility/exceptions.h"
  58 #include "gromacs/utility/gmxassert.h"
  59 #include "gromacs/utility/stringutil.h"
  60
  61 #include "grid.h"
  62
  63 namespace gmx
  64 {
  65
  66 CoordState::CoordState(const AwhBiasParams          &awhBiasParams,
  67                        const std::vector<DimParams> &dimParams,
  68                        const Grid                   &grid)
  69 {
  70     for (size_t d = 0; d < dimParams.size(); d++)
  71     {
  72         coordValue_[d] = dimParams[d].scaleUserInputToInternal(awhBiasParams.dimParams[d].coordValueInit);
  73     }
  74
  75     /* The grid-point index is always the nearest point to the coordinate.
  76      * We initialize the umbrella location to the same nearest point.
  77      * More correctly one would sample from the biased distribution,
  78      * but it doesn't really matter, as this will happen after a few steps.
  79      */
  80     gridpointIndex_    = grid.nearestIndex(coordValue_);
  81     umbrellaGridpoint_ = gridpointIndex_;
  82 }
  83
  84 namespace
  85 {
  86
  87 /*! \brief Generate a sample from a discrete probability distribution defined on [0, distr.size() - 1].
  88  *
  89  * The pair (indexSeed0,indexSeed1) should be different for every invocation.
  90  *
  91  * \param[in] distr       Normalized probability distribution to generate a sample from.
  92  * \param[in] seed        Random seed for initializing the random number generator.
  93  * \param[in] indexSeed0  Random seed needed by the random number generator.
  94  * \param[in] indexSeed1  Random seed needed by the random number generator.
  95  * \returns a sample index in [0, distr.size() - 1]
  96  */
  97 int getSampleFromDistribution(ArrayRef<const double> distr,
  98                               int64_t                seed,
  99                               int64_t                indexSeed0,
 100                               int64_t                indexSeed1)
 101 {
 102     gmx::ThreeFry2x64<0>               rng(seed, gmx::RandomDomain::AwhBiasing);
 103     gmx::UniformRealDistribution<real> uniformRealDistr;
 104
 105     GMX_RELEASE_ASSERT(!distr.empty(), "We need a non-zero length distribution to sample from");
 106
 107     /* Generate the cumulative probability distribution function */
 108     std::vector<double> cumulativeDistribution(distr.size());
 109
 110     cumulativeDistribution[0] = distr[0];
 111
 112     for (gmx::index i = 1; i < distr.ssize(); i++)
 113     {
 114         cumulativeDistribution[i] = cumulativeDistribution[i - 1] + distr[i];
 115     }
 116
 117     GMX_RELEASE_ASSERT(gmx_within_tol(cumulativeDistribution.back(), 1.0, 0.01), "Attempt to get sample from non-normalized/zero distribution");
 118
 119     /* Use binary search to convert the real value to an integer in [0, ndistr - 1] distributed according to distr. */
 120     rng.restart(indexSeed0, indexSeed1);
 121
 122     double value  = uniformRealDistr(rng);
 123     int    sample = std::upper_bound(cumulativeDistribution.begin(), cumulativeDistribution.end() - 1, value) - cumulativeDistribution.begin();
 124
 125     return sample;
 126 }
 127
 128 }   // namespace
 129
 130 void
 131 CoordState::sampleUmbrellaGridpoint(const Grid                  &grid,
 132                                     int                          gridpointIndex,
 133                                     gmx::ArrayRef<const double>  probWeightNeighbor,
 134                                     int64_t                      step,
 135                                     int64_t                      seed,
 136                                     int                          indexSeed)
 137 {
 138     /* Sample new umbrella reference value from the probability distribution
 139      * which is defined for the neighboring points of the current coordinate.
 140      */
 141     const std::vector<int> &neighbor = grid.point(gridpointIndex).neighbor;
 142
 143     /* In order to use the same seed for all AWH biases and get independent
 144        samples we use the index of the bias. */
 145     int localIndex     = getSampleFromDistribution(probWeightNeighbor,
 146                                                    seed, step, indexSeed);
 147
 148     umbrellaGridpoint_ = neighbor[localIndex];
 149 }
 150
 151 void CoordState::setCoordValue(const Grid     &grid,
 152                                const awh_dvec  coordValue)
 153 {
 154     /* We need to check for valid (probable) coordinate values, to give
 155      * a clear error message instead of a low-level assertion failure.
 156      * We allow values up to 10*sigma beyond the bounds. For points at
 157      * the bounds this means a chance of less than 2*10-45 of a false positive
 158      * in the usual case that the PMF is flat or goes up beyond the bounds.
 159      * In the worst reasonable case of the PMF curving down with a curvature
 160      * of half the harmonic force constant, the chance is 1.5*10-12.
 161      */
 162     constexpr int c_marginInSigma = 10;
 163
 164     for (int dim = 0; dim < grid.numDimensions(); dim++)
 165     {
 166         const GridAxis &axis = grid.axis(dim);
 167         /* We do not check periodic coordinates, since that is more complicated
 168          * and those cases are less likely to cause problems.
 169          */
 170         if (!axis.isPeriodic())
 171         {
 172             const double margin = axis.spacing()*c_marginInSigma/Grid::c_numPointsPerSigma;
 173             if (coordValue[dim] < axis.origin() - margin ||
 174                 coordValue[dim] > axis.origin() + axis.length() + margin)
 175             {
 176                 std::string mesg = gmx::formatString("Coordinate %d of an AWH bias has a value %f which is more than %d sigma out of the AWH range of [%f, %f]. You seem to have an unstable reaction coordinate setup or an unequilibrated system.",
 177                                                      dim + 1,
 178                                                      coordValue[dim],
 179                                                      c_marginInSigma,
 180                                                      axis.origin(),
 181                                                      axis.origin() + axis.length());
 182                 GMX_THROW(SimulationInstabilityError(mesg));
 183             }
 184         }
 185
 186         coordValue_[dim] = coordValue[dim];
 187     }
 188
 189     /* The grid point closest to the coordinate value defines the current
 190      * neighborhood of points. Besides at steps when global updates and/or
 191      * checks are performed, only the neighborhood will be touched.
 192      */
 193     gridpointIndex_ = grid.nearestIndex(coordValue_);
 194 }
 195
 196 void
 197 CoordState::restoreFromHistory(const AwhBiasStateHistory &stateHistory)
 198 {
 199     umbrellaGridpoint_ = stateHistory.umbrellaGridpoint;
 200 }
 201
 202 } // namespace gmx