gmx::BiasGrid Class Reference

#include <gromacs/applied_forces/awh/biasgrid.h>

Description

The grid for a single bias, generally multidimensional and periodic.

The grid discretizes a multidimensional space with some given resolution. Each dimension is represented by an axis which sets the spatial extent, point spacing and periodicity of the grid in that direction.

Public Member Functions
	BiasGrid (ArrayRef< const DimParams > dimParams, ArrayRef< const AwhDimParams > awhDimParams)
	Construct a grid using AWH input parameters. More...
size_t	numPoints () const
	Returns the number of points in the grid. More...
const GridPoint &	point (size_t pointIndex) const
	Returns a reference to a point on the grid. More...
int	numDimensions () const
	Returns the dimensionality of the grid. More...
ArrayRef< const GridAxis >	axis () const
	Returns the grid axes. More...
const GridAxis &	axis (int dim) const
	Returns a grid axis. More...
int	nearestIndex (const awh_dvec value) const
	Find the grid point with value nearest to the given value. More...
bool	covers (const awh_dvec value) const
	Query if the value is in the grid. More...
bool	hasLambdaAxis () const
	Returns true if the grid has a free energy lambda state axis at all.
std::optional< int >	lambdaAxisIndex () const
	Returns the index of a free energy lambda state axis (there can be no more than one) if there is one.
int	numFepLambdaStates () const
	Returns the number of free energy lambda states in the grid (the number of points along a free energy lambda state axis) or 0 if there are no free energy lambda state axes.

Static Public Attributes
static constexpr double	c_numPointsPerSigma = 1.0
	The point density per sigma of the Gaussian distribution in an umbrella. More...
static constexpr double	c_scopeCutoff = 5.5
	Cut-off in sigma for considering points, neglects 4e-8 of the density.

Constructor & Destructor Documentation

gmx::BiasGrid::BiasGrid	(	ArrayRef< const DimParams >	dimParams,
		ArrayRef< const AwhDimParams >	awhDimParams
	)

Construct a grid using AWH input parameters.

Parameters

[in]	dimParams	Dimension parameters including the expected inverse variance of the coordinate living on the grid (determines the grid spacing).
[in]	awhDimParams	Dimension params from inputrec.

Member Function Documentation

ArrayRef<const GridAxis> gmx::BiasGrid::axis ( ) const

inline

Returns the grid axes.

Returns

a constant reference to the grid axes.

const GridAxis& gmx::BiasGrid::axis ( int  dim ) const

inline

Returns a grid axis.

param[in] dim Dimension to return the grid axis for.

Returns

a constant reference to the grid axis.

bool gmx::BiasGrid::covers

(

const awh_dvec

value

)

const

Query if the value is in the grid.

Parameters

[in]

value

Value vector.

Returns

true if the value is in the grid.

Note

It is assumed that any periodicity of value has already been taken care of.

int gmx::BiasGrid::nearestIndex

(

const awh_dvec

value

)

const

Find the grid point with value nearest to the given value.

Parameters

[in]

value

Value vector.

Returns

the grid point index.

int gmx::BiasGrid::numDimensions ( ) const

inline

Returns the dimensionality of the grid.

Returns

the dimensionality of the grid.

size_t gmx::BiasGrid::numPoints ( ) const

inline

Returns the number of points in the grid.

Returns

the number of points in the grid.

const GridPoint& gmx::BiasGrid::point ( size_t  pointIndex ) const

inline

Returns a reference to a point on the grid.

Returns

a constant reference to a point on the grid.

Member Data Documentation

constexpr double gmx::BiasGrid::c_numPointsPerSigma = 1.0

static

The point density per sigma of the Gaussian distribution in an umbrella.

This value should be at least 1 to uniformly cover the reaction coordinate range with density and having it larger than 1 does not add information.

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The documentation for this class was generated from the following files:

• src/gromacs/applied_forces/awh/biasgrid.h
• src/gromacs/applied_forces/awh/biasgrid.cpp