#include <Histogram.h>

Inheritance diagram for SSAGES::Histogram< T >:

Classes
class	HistIterator
	Custom Iterator. More...

Public Types
typedef HistIterator< T >	iterator
	Custom iterator over a histogram.

typedef HistIterator< const T >	const_iterator
	Custom constant iterator over a histogram.

Public Member Functions
	Histogram (std::vector< int > numPoints, std::vector< double > lower, std::vector< double > upper, std::vector< bool > isPeriodic)
	Constructor. More...

iterator	begin ()
	Return iterator at first bin of histogram. More...

iterator	end ()
	Return iterator after last valid bin. More...

std::vector< T >::const_iterator	begin () const
	Return const iterator at first bin of histogram. More...

std::vector< T >::const_iterator	end () const
	Return const iterator after last valid bin. More...

Public Member Functions inherited from SSAGES::GridBase< T >
size_t	GetDimension () const
	Get the dimension. More...

const std::vector< int > &	GetNumPoints () const
	Get the number of points for all dimensions. More...

int	GetNumPoints (size_t dim) const
	Get the number of points for a specific dimension. More...

const std::vector< double > &	GetLower () const
	Return the lower edges of the Grid. More...

double	GetLower (size_t dim) const
	Get the lower edge for a specific dimension. More...

const std::vector< double > &	GetUpper () const
	Return the upper edges of the Grid. More...

double	GetUpper (size_t dim) const
	Get the upper edge for a specific dimension. More...

const std::vector< bool > &	GetPeriodic () const
	Return the periodicity of the Grid. More...

bool	GetPeriodic (size_t dim) const
	Get the periodicity in a specific dimension. More...

size_t	size () const
	Get the size of the internal storage vector. More...

T *	data ()
	Get pointer to the internal data storage vector. More...

T const *	data () const
	Get pointer to const of the internal data storage vector. More...

std::vector< int >	GetIndices (const std::vector< double > &x) const
	Return the Grid indices for a given point. More...

double	GetInterpolated (const std::vector< double > &x)
	Return linear interpolation on a coordinate. More...

int	GetIndex (double x) const
	Return the Grid index for a one-dimensional grid. More...

std::vector< double >	GetCoordinates (const std::vector< int > &indices)
	Return coordinates of the grid center points. More...

double	GetCoordinate (int index)
	Return center point of 1d-grid. More...

const T &	at (const std::vector< int > &indices) const
	Access Grid element read-only. More...

T &	at (const std::vector< int > &indices)
	Access Grid element read/write. More...

template<typename R >
const T &	at (std::initializer_list< R > &&x) const
	Const access of Grid element via initializer list. More...

template<typename R >
T &	at (std::initializer_list< R > &&x)
	Access Grid element via initializer list. More...

const T &	at (int index) const
	Access 1d Grid by index, read-only. More...

T &	at (int index)
	Access 1d Grid by index, read-write. More...

const T &	at (const std::vector< double > &x) const
	Access Grid element pertaining to a specific point – read-only. More...

T &	at (const std::vector< double > &x)
	Access Grid element pertaining to a specific point – read/write. More...

const T &	at (double x) const
	Access 1d-Grid by point - read-only. More...

T &	at (double x)
	Access 1d-Grid by point - read-write. More...

const T &	operator[] (const std::vector< int > &indices) const
	Access Grid element per [] read-only. More...

T &	operator[] (const std::vector< int > &indices)
	Access Grid element per [] read-write. More...

template<typename R >
const T &	operator[] (std::initializer_list< R > &&x) const
	Const access of Grid element via initializer list. More...

template<typename R >
T &	operator[] (std::initializer_list< R > &&x)
	Access Grid element via initializer list. More...

const T &	operator[] (int index) const
	Access 1d-Grid per [] operator, read-only. More...

T &	operator[] (int index)
	Access 1d-Grid per [] operator, read-write. More...

const T &	operator[] (const std::vector< double > &x) const
	Access Grid element pertaining to a specific point per [] read-only. More...

T &	operator[] (const std::vector< double > &x)
	Access Grid element pertaining to a specific point per [] read-write. More...

const T &	operator[] (double x) const
	Access 1d-Grid via specific point, read-only. More...

T &	operator[] (double x)
	Access 1d-Grid via specific point, read-write. More...

Static Public Member Functions
static Histogram< T > *	BuildHistogram (const Json::Value &json)
	Set up the histogram. More...

static Histogram< T > *	BuildHistogram (const Json::Value &json, const std::string &path)
	Set up the histogram. More...

Private Member Functions
size_t	mapTo1d (const std::vector< int > &indices) const override
	Map d-dimensional indices to 1-d data vector. More...

Additional Inherited Members
Protected Member Functions inherited from SSAGES::GridBase< T >
std::vector< int >	wrapIndices (const std::vector< int > &indices) const
	Wrap the index around periodic boundaries.

	GridBase (std::vector< int > numPoints, std::vector< double > lower, std::vector< double > upper, std::vector< bool > isPeriodic)
	Constructor. More...

Protected Attributes inherited from SSAGES::GridBase< T >
std::vector< T >	data_
	Internal storage of the data.

size_t	dimension_
	Dimension of the grid.

std::vector< int >	numPoints_
	Number of points in each dimension.

std::pair< std::vector< double > , std::vector< double > >	edges_
	Edges of the Grid in each dimension.

std::vector< bool >	isPeriodic_
	Periodicity of the Grid.

Detailed Description

template<typename T>
class SSAGES::Histogram< T >

Basic Histogram.

Template Parameters

T	type of data to be stored in the histogram.

A Histogram is a method to store data in SSAGES. It is used to discretize a continuous number, typically a collective variable, into number_points bins. For each bin, an arbitrary type of data can be stored, specified via the template parameter T.

The histogram can be of arbitrary dimension. For each dimension, the lower bound, the upper bound and the number of grid points need to be specified. Furthermore, the histogram can be defined as periodic or non-periodic in the respective dimension. By default, the histogram is non-periodic. The bins are indexed from 0 to number_points-1 following the standard C/C++ convention. In contrast to the Grid, a Histogram additionally includes an under- and an overflow bin in each non-periodic dimension. These can be accessed via the indices -1 an number_points (see below).

The bin width Delta is given by (upper - lower)/number_points. Thus, bin n corresponds to the interval [lower + n*Delta, lower + (n+1)*Delta). Note that n follows the C/C++ convention, i.e. n = 0 for the first interval. The bin indices pertaining to a given point can be obtained via GetIndices().

In non-periodic dimensions, an overflow and an underflow interval exist. The underflow interval corresponds to the interval (-infinity, lower), i.e. all points below lower. Similarly, the overflow interval corresponds to the interval [upper, infinity). The underflow grid point can be accessed via the index -1, the overflow grid point via the index number_points.

Definition at line 64 of file Histogram.h.

Constructor & Destructor Documentation

template<typename T>

SSAGES::Histogram< T >::Histogram	(	std::vector< int >	numPoints,
		std::vector< double >	lower,
		std::vector< double >	upper,
		std::vector< bool >	isPeriodic
	)

inline

Constructor.

Parameters

numPoints	Number of grid points in each dimension.
lower	Lower edges of the grid.
upper	Upper edges of the grid.
isPeriodic	Bools specifying the periodicity in the respective dimension.

The dimension of the grid is determined by the size of the parameter vectors.

Definition at line 116 of file Histogram.h.

Referenced by SSAGES::Histogram< int >::BuildHistogram().

       : GridBase<T>(numPoints, lower, upper, isPeriodic)
     {
         size_t data_size = 1;
         for (size_t d = 0; d < GridBase<T>::GetDimension(); ++d) {
             size_t storage_size = GridBase<T>::GetNumPoints(d);
             if (!GridBase<T>::GetPeriodic(d)) { storage_size += 2; }
             data_size *= storage_size;
         }
 
         GridBase<T>::data_.resize(data_size);
     }

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Member Function Documentation

template<typename T>

iterator SSAGES::Histogram< T >::begin ( )

inline

Return iterator at first bin of histogram.

Returns: Iterator at first bin of the histogram.

The first bin is the bin that has the lowest allowed index in all dimensions, i.e. 0 in periodic and -1 in non-periodic dimensions.

Definition at line 549 of file Histogram.h.

Referenced by SSAGES::Basis::PrintBias(), and SSAGES::Basis::UpdateBias().

     {
         std::vector<int> indices(GridBase<T>::GetDimension());
         for (size_t i = 0; i < indices.size(); ++i) {
             if(GridBase<T>::GetPeriodic(i)) {
                 indices.at(i) = 0;
             } else {
                 indices.at(i) = -1;
             }
         }
 
         return iterator(indices, this);
     }

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template<typename T>

std::vector<T>::const_iterator SSAGES::Histogram< T >::begin ( ) const

inline

Return const iterator at first bin of histogram.

Returns: Const iterator at first bin of the histogram.

The first bin is the bin that has the lowest allowed index in all dimensions, i.e. 0 in periodic and -1 in non-periodic dimensions.

Definition at line 593 of file Histogram.h.

     {
         std::vector<int> indices(GridBase<T>::GetDimension());
         for (size_t i = 0; i < indices.size(); ++i) {
             if(GridBase<T>::GetPeriodic(i)) {
                 indices.at(i) = 0;
             } else {
                 indices.at(i) = -1;
             }
         }
 
         return iterator(indices, this);
     }

template<typename T>

static Histogram<T>* SSAGES::Histogram< T >::BuildHistogram ( const Json::Value & json )

inlinestatic

Set up the histogram.

Parameters

json	JSON value containing all input information.

Returns: Pointer to the newly built histogram.

This function builds a histogram from a JSON node. It will return a nullptr if an unknown error occured, but generally, it will throw a BuildException of failure.

Definition at line 141 of file Histogram.h.

Referenced by SSAGES::Histogram< int >::BuildHistogram().

     {
         return BuildHistogram(json, "#/Histogram");
     }

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template<typename T>

static Histogram<T>* SSAGES::Histogram< T >::BuildHistogram	(	const Json::Value &	json,
		const std::string &	path
	)

inlinestatic

Set up the histogram.

Parameters

json	JSON Value containing all input information.
path	Path for JSON path specification.

Returns: Pointer to the newly built histogram.

This function builds a histogram from a JSON node. It will return a nullptr if an unknown error occured, but generally, it will throw a BuildException on failure.

Definition at line 156 of file Histogram.h.

     {
         Json::ObjectRequirement validator;
         Json::Value schema;
         Json::Reader reader;
 
         reader.parse(JsonSchema::grid, schema);
         validator.Parse(schema, path);
 
         // Validate inputs.
         validator.Validate(json, path);
         if (validator.HasErrors()) {
             throw BuildException(validator.GetErrors());
         }
 
         // Read in Lower Grid edges.
         std::vector<double> lower;
         for (auto &lv : json["lower"]) {
            lower.push_back(lv.asDouble());
         }
 
         size_t dimension = lower.size();
 
         // Read in upper grid edges.
         std::vector<double> upper;
         for (auto &uv : json["upper"]) {
             upper.push_back(uv.asDouble());
         }
 
         if (upper.size() != dimension) {
             throw BuildException({"Number of upper values does not match "
                                   "number of lower values!"});
         }
 
         // Read in number of points.
         std::vector<int> number_points;
         for (auto &np : json["number_points"]) {
             number_points.push_back(np.asInt());
         }
 
         if (number_points.size() != dimension) {
             throw BuildException({"Arrays \"lower\" and \"number_points\" do "
                                   "not have the same size!"});
         }
 
         // Read in periodicity.
         std::vector<bool> isPeriodic;
         for (auto &periodic : json["periodic"]) {
             isPeriodic.push_back(periodic.asBool());
         }
 
         if (isPeriodic.size() == 0) {
             isPeriodic = std::vector<bool>(dimension, false);
         } else if (isPeriodic.size() != dimension) {
             throw BuildException({"Arrays \"lower\" and \"periodic\" do not "
                                   "have the same size!"});
         }
 
         // Construct the grid.
         Histogram<T>* hist = new Histogram(number_points, lower, upper, isPeriodic);
 
         return hist;
     }

template<typename T>

iterator SSAGES::Histogram< T >::end ( )

inline

Return iterator after last valid bin.

Returns: Iterator after last valid bin.

The last valid bin is the bin that has the highest allowed index in all dimensions, i.e. num_points - 1 in periodic and num_points in non-periodic dimensions.

Definition at line 571 of file Histogram.h.

     {
         std::vector<int> indices(GridBase<T>::GetDimension());
         for (size_t i = 0; i < indices.size(); ++i) {
             if (GridBase<T>::GetPeriodic(i)) {
                 indices.at(i) = GridBase<T>::GetNumPoints(i) - 1;
             } else {
                 indices.at(i) = GridBase<T>::GetNumPoints(i);
             }
         }
 
         iterator it(indices, this);
         return ++it;
     }

template<typename T>

std::vector<T>::const_iterator SSAGES::Histogram< T >::end ( ) const

inline

Return const iterator after last valid bin.

Returns: Const iterator after last valid bin.

The last valid bin is the bin that has the highest allowed index in all dimensions, i.e. num_points - 1 in periodic and num_points in non-periodic dimensions.

Definition at line 615 of file Histogram.h.

     {
         std::vector<int> indices(GridBase<T>::GetDimension());
         for (size_t i = 0; i < indices.size(); ++i) {
             if (GridBase<T>::GetPeriodic(i)) {
                 indices.at(i) = GridBase<T>::GetNumPoints(i) - 1;
             } else {
                 indices.at(i) = GridBase<T>::GetNumPoints(i);
             }
         }
 
         iterator it(indices, this);
         return ++it;
     }

template<typename T>

size_t SSAGES::Histogram< T >::mapTo1d ( const std::vector< int > & indices ) const

inlineoverrideprivatevirtual

Map d-dimensional indices to 1-d data vector.

Parameters

indices Vector specifying the grid point.

Returns: Index of 1d data vector.

Map a set of indices to the index of the 1d data vector. Keep in mind, that the data includes underflow (index -1) and overflow (index numPoints) bins in periodic dimension.

Implements SSAGES::GridBase< T >.

Definition at line 76 of file Histogram.h.

     {
         // Check if an index is out of bounds
         for (size_t i=0; i < GridBase<T>::GetDimension(); ++i) {
             int index = indices.at(i);
             bool periodic = GridBase<T>::GetPeriodic(i);
             int numpoints = GridBase<T>::GetNumPoints(i);
             if ( (periodic && (index < 0 || index >= numpoints)) ||
                  (periodic && (index < -1 || index > numpoints)) )
             {
                 throw std::out_of_range("Bin index out of range.");
             }
         }
 
         size_t idx = 0;
         size_t fac = 1;
         for (size_t i=0; i < GridBase<T>::GetDimension(); ++i) {
             if (GridBase<T>::GetPeriodic(i)) {
                 idx += indices.at(i) * fac;
                 fac *= GridBase<T>::GetNumPoints(i);
             } else {
                 idx += (indices.at(i) + 1) * fac;
                 fac *= GridBase<T>::GetNumPoints(i) + 2;
             }
         }
         return idx;
     }

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

/home/cody/SSAGES/src/Grids/Histogram.h

Classes

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

template<typename T> class SSAGES::Histogram< T >

Constructor & Destructor Documentation

Member Function Documentation

template<typename T>
class SSAGES::Histogram< T >