biasstate.cpp File Reference

#include "gmxpre.h"
#include "biasstate.h"
#include <assert.h>
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <algorithm>
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/utilities.h"
#include "gromacs/mdtypes/awh-history.h"
#include "gromacs/mdtypes/awh-params.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/simd/simd.h"
#include "gromacs/simd/simd_math.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "grid.h"
#include "pointstate.h"

Include dependency graph for biasstate.cpp:

Description

Implements the BiasState class.

Author

Viveca Lindahl

Berk Hess hess@.nosp@m.kth..nosp@m.se

Functions
void	gmx::anonymous_namespace{biasstate.cpp}::sumOverSimulations (gmx::ArrayRef< int > arrayRef, const gmx_multisim_t *multiSimComm)
	Sum an array over all simulations on the master rank of each simulation. More...
void	gmx::anonymous_namespace{biasstate.cpp}::sumOverSimulations (gmx::ArrayRef< double > arrayRef, const gmx_multisim_t *multiSimComm)
	Sum an array over all simulations on the master rank of each simulation. More...
template<typename T >
void	gmx::anonymous_namespace{biasstate.cpp}::sumOverSimulations (gmx::ArrayRef< T > arrayRef, const t_commrec *commRecord, const gmx_multisim_t *multiSimComm)
	Sum an array over all simulations on all ranks of each simulation. More...
void	gmx::anonymous_namespace{biasstate.cpp}::sumPmf (gmx::ArrayRef< PointState > pointState, int numSharedUpdate, const t_commrec *commRecord, const gmx_multisim_t *multiSimComm)
	Sum PMF over multiple simulations, when requested. More...
double	gmx::anonymous_namespace{biasstate.cpp}::freeEnergyMinimumValue (gmx::ArrayRef< const PointState > pointState)
	Find the minimum free energy value. More...
double	gmx::anonymous_namespace{biasstate.cpp}::biasedLogWeightFromPoint (const std::vector< DimParams > &dimParams, const std::vector< PointState > &points, const Grid &grid, int pointIndex, double pointBias, const awh_dvec value)
	Find and return the log of the probability weight of a point given a coordinate value. More...
void	gmx::anonymous_namespace{biasstate.cpp}::updateTargetDistribution (gmx::ArrayRef< PointState > pointState, const BiasParams &params)
	Updates the target distribution for all points. More...
std::string	gmx::anonymous_namespace{biasstate.cpp}::gridPointValueString (const Grid &grid, int point)
	Puts together a string describing a grid point. More...
void	gmx::anonymous_namespace{biasstate.cpp}::setHistogramUpdateScaleFactors (const BiasParams &params, double newHistogramSize, double oldHistogramSize, double *weightHistScaling, double *logPmfSumScaling)
	Sets the histogram rescaling factors needed to control the histogram size. More...
void	gmx::anonymous_namespace{biasstate.cpp}::mergeSharedUpdateLists (std::vector< int > *updateList, int numPoints, const t_commrec *commRecord, const gmx_multisim_t *multiSimComm)
	Merge update lists from multiple sharing simulations. More...
void	gmx::anonymous_namespace{biasstate.cpp}::makeLocalUpdateList (const Grid &grid, const std::vector< PointState > &points, const awh_ivec originUpdatelist, const awh_ivec endUpdatelist, std::vector< int > *updateList)
	Generate an update list of points sampled since the last update. More...
void	gmx::anonymous_namespace{biasstate.cpp}::sumHistograms (gmx::ArrayRef< PointState > pointState, gmx::ArrayRef< double > weightSumCovering, int numSharedUpdate, const t_commrec *commRecord, const gmx_multisim_t *multiSimComm, const std::vector< int > &localUpdateList)
	Add partial histograms (accumulating between updates) to accumulating histograms. More...
void	gmx::anonymous_namespace{biasstate.cpp}::labelCoveredPoints (const std::vector< bool > &visited, const std::vector< bool > &checkCovering, int numPoints, int period, int coverRadius, gmx::ArrayRef< int > covered)
	Label points along an axis as covered or not. More...
static void	gmx::normalizeFreeEnergyAndPmfSum (std::vector< PointState > *pointState)
	Normalizes the free energy and PMF sum. More...
static int	gmx::countTrailingZeroRows (const double *const *data, int numRows, int numColumns)
	Count trailing data rows containing only zeros. More...
static void	gmx::readUserPmfAndTargetDistribution (const std::vector< DimParams > &dimParams, const Grid &grid, const std::string &filename, int numBias, int biasIndex, std::vector< PointState > *pointState)
	Initializes the PMF and target with data read from an input table. More...