Reaction path diagrams (graphs). More...

#include <ReactionPath.h>

Public Member Functions
virtual	~ReactionPathDiagram ()
	Destructor. More...

doublereal	maxFlow ()
	The largest one-way flow value in any path. More...

doublereal	netFlow (size_t k1, size_t k2)
	The net flow from node `k1` to node `k2`. More...

doublereal	flow (size_t k1, size_t k2)
	The one-way flow from node `k1` to node `k2`. More...

bool	hasNode (size_t k)
	True if a node for species k exists. More...

void	writeData (std::ostream &s)

void	exportToDot (std::ostream &s)
	Export the reaction path diagram. More...

void	add (ReactionPathDiagram &d)

SpeciesNode *	node (size_t k)

Path *	path (size_t k1, size_t k2)

Path *	path (size_t n)

size_t	nPaths ()

size_t	nNodes ()

void	addNode (size_t k, const std::string &nm, doublereal x=0.0)

void	displayOnly (size_t k=npos)

void	linkNodes (size_t k1, size_t k2, size_t rxn, doublereal value, std::string legend="")

void	include (const std::string &aaname)

void	exclude (const std::string &aaname)

void	include (std::vector< std::string > &names)

void	exclude (std::vector< std::string > &names)

std::vector< std::string > &	included ()

std::vector< std::string > &	excluded ()

std::vector< size_t >	species ()

vector_int	reactions ()

void	findMajorPaths (doublereal threshold, size_t lda, doublereal *a)

void	setFont (const std::string &font)

Public Attributes
std::string	title

std::string	bold_color

std::string	normal_color

std::string	dashed_color

std::string	element

std::string	m_font

doublereal	threshold

doublereal	bold_min

doublereal	dashed_max

doublereal	label_min

doublereal	x_size

doublereal	y_size

std::string	name

std::string	dot_options

flow_t	flow_type

doublereal	scale

doublereal	arrow_width

bool	show_details

doublereal	arrow_hue

Protected Attributes
doublereal	m_flxmax

std::map< size_t, std::map< size_t, Path * > >	m_paths

std::map< size_t, SpeciesNode * >	m_nodes

std::vector< Path * >	m_pathlist

std::vector< std::string >	m_include

std::vector< std::string >	m_exclude

std::vector< size_t >	m_speciesNumber

std::map< size_t, int >	m_rxns

size_t	m_local

Detailed Description

Reaction path diagrams (graphs).

Definition at line 162 of file ReactionPath.h.

Constructor & Destructor Documentation

◆ ReactionPathDiagram()

ReactionPathDiagram ( )

Definition at line 82 of file ReactionPath.cpp.

◆ ~ReactionPathDiagram()

~ReactionPathDiagram ( )

virtual

Destructor.

Deletes all nodes and paths in the diagram.

Definition at line 106 of file ReactionPath.cpp.

Member Function Documentation

◆ maxFlow()

doublereal maxFlow ( )

inline

The largest one-way flow value in any path.

Definition at line 173 of file ReactionPath.h.

◆ netFlow()

doublereal netFlow	(	size_t	k1,
		size_t	k2
	)

inline

The net flow from node k1 to node k2.

Definition at line 178 of file ReactionPath.h.

References ReactionPathDiagram::flow().

Referenced by ReactionPathDiagram::exportToDot().

◆ flow()

doublereal flow	(	size_t	k1,
		size_t	k2
	)

inline

The one-way flow from node k1 to node k2.

Definition at line 183 of file ReactionPath.h.

References ReactionPathDiagram::flow().

Referenced by ReactionPathDiagram::exportToDot(), ReactionPathDiagram::flow(), and ReactionPathDiagram::netFlow().

◆ hasNode()

bool hasNode ( size_t k )

inline

True if a node for species k exists.

Definition at line 188 of file ReactionPath.h.

◆ writeData()

void writeData ( std::ostream & s )

Definition at line 177 of file ReactionPath.cpp.

◆ exportToDot()

void exportToDot ( std::ostream & s )

Export the reaction path diagram.

This method writes to stream s the commands for the 'dot' program in the GraphViz package from AT&T. (GraphViz may be downloaded from www.graphviz.org.)

To generate a postscript reaction path diagram from the output of this method saved in file paths.dot, for example, give the command:

dot -Tps paths.dot > paths.ps

Cantera::dot

doublereal dot(InputIter x_begin, InputIter x_end, InputIter2 y_begin)

Function that calculates a templated inner product.

Definition: utilities.h:77

To generate a GIF image, replace -Tps with -Tgif

Definition at line 197 of file ReactionPath.cpp.

References ReactionPathDiagram::flow(), SpeciesNode::name, ReactionPathDiagram::netFlow(), Cantera::npos, and SpeciesNode::visible.

◆ add()

void add ( ReactionPathDiagram & d )

Definition at line 143 of file ReactionPath.cpp.

◆ node()

SpeciesNode * node ( size_t k )

inline

Definition at line 209 of file ReactionPath.h.

◆ path() [1/2]

Path * path	(	size_t	k1,
		size_t	k2
	)

inline

Definition at line 212 of file ReactionPath.h.

◆ path() [2/2]

Path * path ( size_t n )

inline

Definition at line 215 of file ReactionPath.h.

◆ nPaths()

size_t nPaths ( )

inline

Definition at line 218 of file ReactionPath.h.

◆ nNodes()

size_t nNodes ( )

inline

Definition at line 221 of file ReactionPath.h.

◆ addNode()

void addNode	(	size_t	k,
		const std::string &	nm,
		doublereal	x = `0.0`
	)

Definition at line 380 of file ReactionPath.cpp.

◆ displayOnly()

void displayOnly ( size_t k = npos )

inline

Definition at line 227 of file ReactionPath.h.

◆ linkNodes()

void linkNodes	(	size_t	k1,
		size_t	k2,
		size_t	rxn,
		doublereal	value,
		std::string	legend = `""`
	)

Definition at line 391 of file ReactionPath.cpp.

◆ include() [1/2]

void include ( const std::string & aaname )

inline

Definition at line 234 of file ReactionPath.h.

◆ exclude() [1/2]

void exclude ( const std::string & aaname )

inline

Definition at line 237 of file ReactionPath.h.

◆ include() [2/2]

void include ( std::vector< std::string > & names )

inline

Definition at line 240 of file ReactionPath.h.

◆ exclude() [2/2]

void exclude ( std::vector< std::string > & names )

inline

Definition at line 245 of file ReactionPath.h.

◆ included()

std::vector< std::string > & included ( )

inline

Definition at line 250 of file ReactionPath.h.

◆ excluded()

std::vector< std::string > & excluded ( )

inline

Definition at line 253 of file ReactionPath.h.

◆ species()

std::vector< size_t > species ( )

Definition at line 405 of file ReactionPath.cpp.

◆ reactions()

vector_int reactions ( )

Definition at line 120 of file ReactionPath.cpp.

◆ findMajorPaths()

void findMajorPaths	(	doublereal	threshold,
		size_t	lda,
		doublereal *	a
	)

Definition at line 153 of file ReactionPath.cpp.

◆ setFont()

void setFont ( const std::string & font )

inline

Definition at line 259 of file ReactionPath.h.

Member Data Documentation

◆ title

std::string title

Definition at line 264 of file ReactionPath.h.

◆ bold_color

std::string bold_color

Definition at line 265 of file ReactionPath.h.

◆ normal_color

std::string normal_color

Definition at line 266 of file ReactionPath.h.

◆ dashed_color

std::string dashed_color

Definition at line 267 of file ReactionPath.h.

◆ element

std::string element

Definition at line 268 of file ReactionPath.h.

◆ m_font

std::string m_font

Definition at line 269 of file ReactionPath.h.

◆ threshold

doublereal threshold

Definition at line 270 of file ReactionPath.h.

◆ bold_min

doublereal bold_min

Definition at line 270 of file ReactionPath.h.

◆ dashed_max

doublereal dashed_max

Definition at line 270 of file ReactionPath.h.

◆ label_min

doublereal label_min

Definition at line 270 of file ReactionPath.h.

◆ x_size

doublereal x_size

Definition at line 271 of file ReactionPath.h.

◆ y_size

doublereal y_size

Definition at line 271 of file ReactionPath.h.

◆ name

std::string name

Definition at line 272 of file ReactionPath.h.

◆ dot_options

std::string dot_options

Definition at line 272 of file ReactionPath.h.

◆ flow_type

flow_t flow_type

Definition at line 273 of file ReactionPath.h.

◆ scale

doublereal scale

Definition at line 274 of file ReactionPath.h.

◆ arrow_width

doublereal arrow_width

Definition at line 275 of file ReactionPath.h.

◆ show_details

bool show_details

Definition at line 276 of file ReactionPath.h.

◆ arrow_hue

doublereal arrow_hue

Definition at line 277 of file ReactionPath.h.

◆ m_flxmax

doublereal m_flxmax

protected

Definition at line 280 of file ReactionPath.h.

◆ m_paths

std::map<size_t, std::map<size_t, Path*> > m_paths

protected

Definition at line 281 of file ReactionPath.h.

◆ m_nodes

std::map<size_t, SpeciesNode*> m_nodes

protected

Definition at line 282 of file ReactionPath.h.

◆ m_pathlist

std::vector<Path*> m_pathlist

protected

Definition at line 283 of file ReactionPath.h.

◆ m_include

std::vector<std::string> m_include

protected

Definition at line 284 of file ReactionPath.h.

◆ m_exclude

std::vector<std::string> m_exclude

protected

Definition at line 285 of file ReactionPath.h.

◆ m_speciesNumber

std::vector<size_t> m_speciesNumber

protected

Definition at line 286 of file ReactionPath.h.

◆ m_rxns

std::map<size_t, int> m_rxns

protected

Definition at line 287 of file ReactionPath.h.

◆ m_local

size_t m_local

protected

Definition at line 288 of file ReactionPath.h.

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

Public Member Functions

Public Attributes

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ReactionPathDiagram()

◆ ~ReactionPathDiagram()

Member Function Documentation

◆ maxFlow()

◆ netFlow()

◆ flow()

◆ hasNode()

◆ writeData()

◆ exportToDot()

◆ add()

◆ node()

◆ path() [1/2]

◆ path() [2/2]

◆ nPaths()

◆ nNodes()

◆ addNode()

◆ displayOnly()

◆ linkNodes()

◆ include() [1/2]

◆ exclude() [1/2]

◆ include() [2/2]

◆ exclude() [2/2]

◆ included()

◆ excluded()

◆ species()

◆ reactions()

◆ findMajorPaths()

◆ setFont()

Member Data Documentation

◆ title

◆ bold_color

◆ normal_color

◆ dashed_color

◆ element

◆ m_font

◆ threshold

◆ bold_min

◆ dashed_max

◆ label_min

◆ x_size

◆ y_size

◆ name

◆ dot_options

◆ flow_type

◆ scale

◆ arrow_width

◆ show_details

◆ arrow_hue

◆ m_flxmax

◆ m_paths

◆ m_nodes

◆ m_pathlist

◆ m_include

◆ m_exclude

◆ m_speciesNumber

◆ m_rxns

◆ m_local