pele::NGT Class Reference

#include <ngt.hpp>

List of all members.

Public Types
typedef std::map< std::pair < node_id, node_id >, double >	rate_map_t
Public Member Functions
	~NGT ()
template<class Acontainer , class Bcontainer >
	NGT (std::shared_ptr< Graph > graph, Acontainer const &A, Bcontainer const &B)
void	set_debug ()
std::map< node_id, double > const &	get_committors ()
template<class Acontainer , class Bcontainer >
	NGT (rate_map_t &rate_constants, Acontainer const &A, Bcontainer const &B)
void	set_node_occupation_probabilities (std::map< node_id, double > &Peq)
void	sort_intermediates ()
double	get_tau (node_ptr u)
double	get_P (edge_ptr edge)
void	set_tau (node_ptr u, double tau)
void	set_P (edge_ptr edge, double P)
double	get_node_P (node_ptr u)
double	get_node_one_minus_P (node_ptr u)
void	update_node (edge_ptr ux, double omPxx, double tau_x)
edge_ptr	add_edge (node_ptr u, node_ptr v)
void	update_edge (node_ptr u, node_ptr v, edge_ptr ux, edge_ptr xv, double omPxx)
void	remove_node (node_ptr x)
void	remove_intermediates ()
void	phase_one ()
void	reduce_all_in_group (std::set< node_ptr > &to_remove, std::set< node_ptr > &to_keep)
void	phase_two ()
void	compute_rates ()
double	_get_rate_final (std::set< node_ptr > &A)
double	get_rate_AB ()
double	get_rate_BA ()
double	_get_rate_SS (std::set< node_ptr > &A, std::set< node_ptr > &B)
double	get_rate_AB_SS ()
double	get_rate_BA_SS ()
double	get_PxB (node_ptr x, std::set< node_id > &B)
void	_remove_nodes_and_compute_committors (std::list< node_ptr > &to_remove, std::set< node_ptr > &to_keep, std::set< node_ptr > const &committor_targets)
void	compute_rates_and_committors ()
Public Attributes
std::shared_ptr< Graph >	_graph
std::set< node_ptr >	_A
std::set< node_ptr >	_B
std::list< node_ptr >	intermediates
bool	debug
std::map< node_id, double >	initial_tau
std::map< node_id, double >	final_omPxx
std::map< node_id, double >	final_tau
std::map< node_id, double >	final_committors
std::map< node_id, double >	weights

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Detailed Description

Definition at line 33 of file ngt.hpp.

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Member Typedef Documentation

typedef std::map<std::pair<node_id, node_id>, double> pele::NGT::rate_map_t

Definition at line 35 of file ngt.hpp.

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Constructor & Destructor Documentation

pele::NGT::~NGT

(

)

[inline]

Definition at line 61 of file ngt.hpp.

template<class Acontainer , class Bcontainer >

pele::NGT::NGT	(	std::shared_ptr< Graph >	graph,
		Acontainer const &	A,
		Bcontainer const &	B
	)		[inline]

Definition at line 72 of file ngt.hpp.

template<class Acontainer , class Bcontainer >

pele::NGT::NGT	(	rate_map_t &	rate_constants,
		Acontainer const &	A,
		Bcontainer const &	B
	)		[inline]

Definition at line 106 of file ngt.hpp.

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Member Function Documentation

double pele::NGT::_get_rate_final

(

std::set< node_ptr > &

A

)

[inline]

Definition at line 444 of file ngt.hpp.

double pele::NGT::_get_rate_SS	(	std::set< node_ptr > &	A,
		std::set< node_ptr > &	B
	)		[inline]

Definition at line 474 of file ngt.hpp.

void pele::NGT::_remove_nodes_and_compute_committors	(	std::list< node_ptr > &	to_remove,
		std::set< node_ptr > &	to_keep,
		std::set< node_ptr > const &	committor_targets
	)		[inline]

Definition at line 553 of file ngt.hpp.

edge_ptr pele::NGT::add_edge	(	node_ptr	u,
		node_ptr	v
	)		[inline]

Definition at line 260 of file ngt.hpp.

void pele::NGT::compute_rates

(

)

[inline]

Definition at line 436 of file ngt.hpp.

void pele::NGT::compute_rates_and_committors

(

)

[inline]

Definition at line 616 of file ngt.hpp.

std::map<node_id, double> const& pele::NGT::get_committors

(

)

[inline]

Definition at line 100 of file ngt.hpp.

double pele::NGT::get_node_one_minus_P

(

node_ptr

u

)

[inline]

Definition at line 222 of file ngt.hpp.

double pele::NGT::get_node_P

(

node_ptr

u

)

[inline]

Definition at line 213 of file ngt.hpp.

double pele::NGT::get_P

(

edge_ptr

edge

)

[inline]

Definition at line 206 of file ngt.hpp.

double pele::NGT::get_PxB	(	node_ptr	x,
		std::set< node_id > &	B
	)		[inline]

Definition at line 518 of file ngt.hpp.

double pele::NGT::get_rate_AB

(

)

[inline]

Definition at line 463 of file ngt.hpp.

double pele::NGT::get_rate_AB_SS

(

)

[inline]

Definition at line 502 of file ngt.hpp.

double pele::NGT::get_rate_BA

(

)

[inline]

Definition at line 470 of file ngt.hpp.

double pele::NGT::get_rate_BA_SS

(

)

[inline]

Definition at line 511 of file ngt.hpp.

double pele::NGT::get_tau

(

node_ptr

u

)

[inline]

Definition at line 205 of file ngt.hpp.

void pele::NGT::phase_one

(

)

[inline]

Definition at line 352 of file ngt.hpp.

void pele::NGT::phase_two

(

)

[inline]

Definition at line 428 of file ngt.hpp.

void pele::NGT::reduce_all_in_group	(	std::set< node_ptr > &	to_remove,
		std::set< node_ptr > &	to_keep
	)		[inline]

Definition at line 362 of file ngt.hpp.

void pele::NGT::remove_intermediates

(

)

[inline]

Definition at line 338 of file ngt.hpp.

void pele::NGT::remove_node

(

node_ptr

x

)

[inline]

Definition at line 295 of file ngt.hpp.

void pele::NGT::set_debug

(

)

[inline]

Definition at line 99 of file ngt.hpp.

void pele::NGT::set_node_occupation_probabilities

(

std::map< node_id, double > &

Peq

)

[inline]

Definition at line 183 of file ngt.hpp.

void pele::NGT::set_P	(	edge_ptr	edge,
		double	P
	)		[inline]

Definition at line 208 of file ngt.hpp.

void pele::NGT::set_tau	(	node_ptr	u,
		double	tau
	)		[inline]

Definition at line 207 of file ngt.hpp.

void pele::NGT::sort_intermediates

(

)

[inline]

Definition at line 192 of file ngt.hpp.

void pele::NGT::update_edge	(	node_ptr	u,
		node_ptr	v,
		edge_ptr	ux,
		edge_ptr	xv,
		double	omPxx
	)		[inline]

Definition at line 271 of file ngt.hpp.

void pele::NGT::update_node	(	edge_ptr	ux,
		double	omPxx,
		double	tau_x
	)		[inline]

Definition at line 246 of file ngt.hpp.

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Member Data Documentation

std::set<node_ptr> pele::NGT::_A

Definition at line 38 of file ngt.hpp.

std::set<node_ptr> pele::NGT::_B

Definition at line 39 of file ngt.hpp.

std::shared_ptr<Graph> pele::NGT::_graph

Definition at line 37 of file ngt.hpp.

bool pele::NGT::debug

Definition at line 41 of file ngt.hpp.

std::map<node_id, double> pele::NGT::final_committors

Definition at line 56 of file ngt.hpp.

std::map<node_id, double> pele::NGT::final_omPxx

Final values of 1-Pxx for node x after the graph transformation.

Definition at line 51 of file ngt.hpp.

std::map<node_id, double> pele::NGT::final_tau

Final values of tau for node x after the graph transformation.

Definition at line 55 of file ngt.hpp.

std::map<node_id, double> pele::NGT::initial_tau

the initial waiting time before any graph transformation. Used to compute steady state rates.

Definition at line 47 of file ngt.hpp.

std::list<node_ptr> pele::NGT::intermediates

Definition at line 40 of file ngt.hpp.

std::map<node_id, double> pele::NGT::weights

Definition at line 57 of file ngt.hpp.

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

• /home/js850/projects/pele/source/pele/ngt.hpp