transferOperator.hpp File Reference

Calculate discretized approximation of transfer operators from time series. More...

#include <iostream>
#include <vector>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_vector_uint.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_matrix_uint.h>
#include <Eigen/Dense>
#include <Eigen/Sparse>
#include <ATSuite/atmatrix.hpp>
#include <ATSuite/atmarkov.hpp>
#include <ATSuite/atio.hpp>

Go to the source code of this file.

Classes
class	Grid
	Grid class. More...
class	transferOperator
	Transfer operator class. More...

Typedefs
typedef Eigen::Triplet< double >	triplet
	Eigen triplet of double.
typedef std::vector< triplet >	tripletVector
	STD vector of Eigen triplet of double.
typedef Eigen::Triplet< size_t >	tripletUInt
	Eigen triplet of integer.
typedef std::vector< tripletUInt >	tripletUIntVector
	STD vector of Eigen triplet of integer.
typedef Eigen::SparseMatrix< double, Eigen::ColMajor >	SpMatCSC
	Eigen CSC matrix of double type.
typedef Eigen::SparseMatrix< double, Eigen::RowMajor >	SpMatCSR
	Eigen CSR matrix of double type.

Functions
gsl_matrix_uint *	getGridMemMatrix (const gsl_matrix *, const gsl_matrix *, const Grid *)
	Get membership matrix from initial and final states for a grid. More...
gsl_matrix_uint *	getGridMemMatrix (const gsl_matrix *, const Grid *, const size_t)
	Get the grid membership vector from a single long trajectory. More...
gsl_vector_uint *	getGridMemVector (const gsl_matrix *, const Grid *)
	Get the grid membership matrix from a single long trajectory. More...
gsl_matrix_uint *	memVector2memMatrix (const gsl_vector_uint *, size_t)
	Get the grid membership matrix from the membership vector for a given lag.
gsl_matrix_uint *	memVectorList2memMatrix (const std::vector< gsl_vector_uint * > *, size_t)
	Concatenate a list of membership vectors into one membership matrix. More...
int	getBoxMembership (const gsl_vector *, const Grid *)
	Get membership to a grid box of a single realization. More...
tripletUIntVector *	getTransitionCountTriplet (const gsl_matrix_uint *, size_t)
	Get triplet vector from membership matrix. More...
gsl_matrix_uint *	memVector2memMatrix (gsl_vector_uint *gridMemVect, size_t tauStep)

Detailed Description

Calculate discretized approximation of transfer operators from time series. The result is given as forward and backward Markov transition matrices and their distributions.

Definition in file transferOperator.hpp.

Function Documentation

int getBoxMembership	(	const gsl_vector *	state,
		const Grid *	grid
	)

Get membership to a grid box of a single realization.

Parameters

[in]	state	GSL vector of a single state.
[in]	grid	Pointer to Grid object.

Returns

Box index to which the state belongs.

Definition at line 716 of file transferOperator.hpp.

References Grid::dim, Grid::gridBounds, and Grid::N.

Referenced by getGridMemMatrix(), getGridMemVector(), and transferOperator::transferOperator().

gsl_matrix_uint * getGridMemMatrix	(	const gsl_matrix *	initStates,
		const gsl_matrix *	finalStates,
		const Grid *	grid
	)

Get membership matrix from initial and final states for a grid.

Parameters

[in]	initStates	GSL matrix of initial states.
[in]	finalStates	GSL matrix of final states.
[in]	grid	Pointer to Grid object.

Returns

GSL grid membership matrix.

Definition at line 563 of file transferOperator.hpp.

References Grid::dim, getBoxMembership(), and Grid::N.

Referenced by transferOperator::transferOperator().

gsl_matrix_uint * getGridMemMatrix	(	const gsl_matrix *	states,
		const Grid *	grid,
		const size_t	tauStep
	)

Get the grid membership matrix from a single long trajectory.

Parameters

[in]	states	GSL matrix of states for each time step.
[in]	grid	Pointer to Grid object.
[in]	tauStep	Lag used to calculate the transitions.

Returns

GSL grid membership matrix.

Definition at line 658 of file transferOperator.hpp.

References getGridMemVector(), and memVector2memMatrix().

gsl_vector_uint * getGridMemVector	(	const gsl_matrix *	states,
		const Grid *	grid
	)

Get the grid membership vector from a single long trajectory.

Parameters

[in]	states	GSL matrix of states for each time step.
[in]	grid	Pointer to Grid object.

Returns

GSL grid membership vector.

Definition at line 601 of file transferOperator.hpp.

References Grid::dim, and getBoxMembership().

Referenced by getGridMemMatrix(), and transferOperator::transferOperator().

tripletUIntVector * getTransitionCountTriplet	(	const gsl_matrix_uint *	gridMem,
		size_t	N
	)

Get the triplet vector counting the transitions from pairs of grid boxes from the grid membership matrix.

Parameters

[in]	gridMem	Grid membership matrix.
[in]	N	Size of the grid.

Returns

Triplet vector counting the transitions.

Definition at line 757 of file transferOperator.hpp.

Referenced by transferOperator::transferOperator(), and Grid::~Grid().

gsl_matrix_uint* memVector2memMatrix	(	gsl_vector_uint *	gridMemVect,
		size_t	tauStep
	)

Get the grid membership matrix from the membership vector for a given lag.

Parameters

[in]	gridMemVect	Grid membership vector of a long trajectory for a grid.
[in]	tauStep	Lag used to calculate the transitions.

Returns

GSL grid membership matrix.

Definition at line 634 of file transferOperator.hpp.

gsl_matrix_uint * memVectorList2memMatrix	(	const std::vector< gsl_vector_uint * > *	memList,
		size_t	tauStep
	)

Concatenate a list of membership vectors into one membership matrix.

Parameters

[in]	memList	STD vector of membership GSL vectors each of them associated with a single long trajectory.
[in]	tauStep	Lag used to calculate the transitions.

Returns

GSL grid membership matrix.

Definition at line 680 of file transferOperator.hpp.

References memVector2memMatrix().

Referenced by transferOperator::transferOperator().