Class NGT#

Class Documentation#

class NGT#

Public Types

typedef std::map<std::pair<node_id, node_id>, double> rate_map_t#

Public Functions

inline ~NGT()#
template<class Acontainer, class Bcontainer>
inline NGT(
std::shared_ptr<Graph> graph,
Acontainer const &A,
Bcontainer const &B
)#
inline void set_debug()#
inline std::map<node_id, double> const &get_committors()#
template<class Acontainer, class Bcontainer>
inline NGT(
rate_map_t &rate_constants,
Acontainer const &A,
Bcontainer const &B
)#
inline void set_node_occupation_probabilities(std::map<node_id, double> &Peq)#
inline void sort_intermediates()#
inline double get_tau(node_ptr u)#
inline double get_P(edge_ptr edge)#
inline void set_tau(node_ptr u, double tau)#
inline void set_P(edge_ptr edge, double P)#
inline double get_node_P(node_ptr u)#
inline double get_node_one_minus_P(node_ptr u)#
inline void update_node(edge_ptr ux, double omPxx, double tau_x)#
inline edge_ptr add_edge(node_ptr u, node_ptr v)#
inline void update_edge(node_ptr u, node_ptr v, edge_ptr ux, edge_ptr xv, double omPxx)#
inline void remove_node(node_ptr x)#
inline void remove_intermediates()#
inline void phase_one()#
inline void reduce_all_in_group(
std::set<node_ptr> &to_remove,
std::set<node_ptr> &to_keep
)#
inline void phase_two()#
inline void compute_rates()#
inline double get_rate_AB()#
inline double get_rate_BA()#
inline double get_rate_AB_SS()#
inline double get_rate_BA_SS()#
inline double get_PxB(node_ptr x, std::set<node_id> &B)#
inline void compute_rates_and_committors()#

Public Members

std::list<node_ptr> intermediates#
bool debug#
std::map<node_id, double> initial_tau#

the initial waiting time before any graph transformation.

Used to compute steady state rates.

std::map<node_id, double> final_omPxx#

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

std::map<node_id, double> final_tau#

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

std::map<node_id, double> final_committors#
std::map<node_id, double> weights#