Reaction path diagrams (graphs). More...

#include <ReactionPath.h>

Detailed Description

Reaction path diagrams (graphs).

Definition at line 159 of file ReactionPath.h.

Public Member Functions
virtual	~ReactionPathDiagram ()
	Destructor.

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

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

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

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

void	writeData (std::ostream &s)

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

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 string &nm, double x=0.0)

void	displayOnly (size_t k=npos)

void	linkNodes (size_t k1, size_t k2, size_t rxn, double value, string legend="")

void	include (const string &aaname)

void	exclude (const string &aaname)

void	include (vector< string > &names)

void	exclude (vector< string > &names)

vector< string > &	included ()

vector< string > &	excluded ()

vector< size_t >	species ()

vector< int >	reactions ()

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

void	setFont (const string &font)

Public Attributes
string	title

string	bold_color = "blue"

string	normal_color = "steelblue"

string	dashed_color = "gray"

string	element

string	m_font = "Helvetica"

double	threshold = 0.005

double	bold_min = 0.2

double	dashed_max = 0.0

double	label_min = 0.0

double	x_size = -1.0

double	y_size = -1.0

string	name = "reaction_paths"

string	dot_options = "center=1;"

flow_t	flow_type = NetFlow

double	scale = -1

double	arrow_width = -5.0

bool	show_details = false

double	arrow_hue = 0.6666

Protected Attributes
double	m_flxmax = 0.0

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

map< size_t, SpeciesNode * >	m_nodes
	map of species index to SpeciesNode

vector< Path * >	m_pathlist

vector< string >	m_include

vector< string >	m_exclude

vector< size_t >	m_speciesNumber

set< size_t >	m_rxns
	Indices of reactions that are included in the diagram.

size_t	m_local = npos

Constructor & Destructor Documentation

◆ ~ReactionPathDiagram()

~ReactionPathDiagram ( )

virtual

Destructor.

Deletes all nodes and paths in the diagram.

Definition at line 81 of file ReactionPath.cpp.

Member Function Documentation

◆ maxFlow()

double maxFlow ( )

inline

The largest one-way flow value in any path.

Definition at line 170 of file ReactionPath.h.

◆ netFlow()

double netFlow	(	size_t	k1,
		size_t	k2
	)

inline

The net flow from node k1 to node k2.

Definition at line 175 of file ReactionPath.h.

◆ flow()

double flow	(	size_t	k1,
		size_t	k2
	)

inline

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

Definition at line 180 of file ReactionPath.h.

◆ hasNode()

bool hasNode ( size_t k )

inline

True if a node for species k exists.

Definition at line 185 of file ReactionPath.h.

◆ writeData()

void writeData ( std::ostream & s )

Definition at line 151 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

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

Function that calculates a templated inner product.

Definition utilities.h:82

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

Definition at line 171 of file ReactionPath.cpp.

◆ add()

void add ( ReactionPathDiagram & d )

Definition at line 118 of file ReactionPath.cpp.

◆ node()

SpeciesNode * node ( size_t k )

inline

Definition at line 206 of file ReactionPath.h.

◆ path() [1/2]

Path * path	(	size_t	k1,
		size_t	k2
	)

inline

Definition at line 209 of file ReactionPath.h.

◆ path() [2/2]

Path * path ( size_t n )

inline

Definition at line 212 of file ReactionPath.h.

◆ nPaths()

size_t nPaths ( )

inline

Definition at line 215 of file ReactionPath.h.

◆ nNodes()

size_t nNodes ( )

inline

Definition at line 218 of file ReactionPath.h.

◆ addNode()

void addNode	(	size_t	k,
		const string &	nm,
		double	x = `0.0`
	)

Definition at line 354 of file ReactionPath.cpp.

◆ displayOnly()

void displayOnly ( size_t k = npos )

inline

Definition at line 224 of file ReactionPath.h.

◆ linkNodes()

void linkNodes	(	size_t	k1,
		size_t	k2,
		size_t	rxn,
		double	value,
		string	legend = `""`
	)

Definition at line 365 of file ReactionPath.cpp.

◆ include() [1/2]

void include ( const string & aaname )

inline

Definition at line 230 of file ReactionPath.h.

◆ exclude() [1/2]

void exclude ( const string & aaname )

inline

Definition at line 233 of file ReactionPath.h.

◆ include() [2/2]

void include ( vector< string > & names )

inline

Definition at line 236 of file ReactionPath.h.

◆ exclude() [2/2]

void exclude ( vector< string > & names )

inline

Definition at line 241 of file ReactionPath.h.

◆ included()

vector< string > & included ( )

inline

Definition at line 246 of file ReactionPath.h.

◆ excluded()

vector< string > & excluded ( )

inline

Definition at line 249 of file ReactionPath.h.

◆ species()

vector< size_t > species ( )

Definition at line 379 of file ReactionPath.cpp.

◆ reactions()

vector< int > reactions ( )

Definition at line 95 of file ReactionPath.cpp.

◆ findMajorPaths()

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

Definition at line 128 of file ReactionPath.cpp.

◆ setFont()

void setFont ( const string & font )

inline

Definition at line 255 of file ReactionPath.h.

Member Data Documentation

◆ title

string title

Definition at line 260 of file ReactionPath.h.

◆ bold_color

string bold_color = "blue"

Definition at line 261 of file ReactionPath.h.

◆ normal_color

string normal_color = "steelblue"

Definition at line 262 of file ReactionPath.h.

◆ dashed_color

string dashed_color = "gray"

Definition at line 263 of file ReactionPath.h.

◆ element

string element

Definition at line 264 of file ReactionPath.h.

◆ m_font

string m_font = "Helvetica"

Definition at line 265 of file ReactionPath.h.

◆ threshold

double threshold = 0.005

Definition at line 266 of file ReactionPath.h.

◆ bold_min

double bold_min = 0.2

Definition at line 267 of file ReactionPath.h.

◆ dashed_max

double dashed_max = 0.0

Definition at line 268 of file ReactionPath.h.

◆ label_min

double label_min = 0.0

Definition at line 269 of file ReactionPath.h.

◆ x_size

double x_size = -1.0

Definition at line 270 of file ReactionPath.h.

◆ y_size

double y_size = -1.0

Definition at line 271 of file ReactionPath.h.

◆ name

string name = "reaction_paths"

Definition at line 272 of file ReactionPath.h.

◆ dot_options

string dot_options = "center=1;"

Definition at line 273 of file ReactionPath.h.

◆ flow_type

flow_t flow_type = NetFlow

Definition at line 274 of file ReactionPath.h.

◆ scale

double scale = -1

Definition at line 275 of file ReactionPath.h.

◆ arrow_width

double arrow_width = -5.0

Definition at line 276 of file ReactionPath.h.

◆ show_details

bool show_details = false

Definition at line 277 of file ReactionPath.h.

◆ arrow_hue

double arrow_hue = 0.6666

Definition at line 278 of file ReactionPath.h.

◆ m_flxmax

double m_flxmax = 0.0

protected

Definition at line 281 of file ReactionPath.h.

◆ m_paths

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

protected

Definition at line 282 of file ReactionPath.h.

◆ m_nodes

map<size_t, SpeciesNode*> m_nodes

protected

map of species index to SpeciesNode

Definition at line 285 of file ReactionPath.h.

◆ m_pathlist

vector<Path*> m_pathlist

protected

Definition at line 286 of file ReactionPath.h.

◆ m_include

vector<string> m_include

protected

Definition at line 287 of file ReactionPath.h.

◆ m_exclude

vector<string> m_exclude

protected

Definition at line 288 of file ReactionPath.h.

◆ m_speciesNumber

vector<size_t> m_speciesNumber

protected

Definition at line 289 of file ReactionPath.h.

◆ m_rxns

set<size_t> m_rxns

protected

Indices of reactions that are included in the diagram.

Definition at line 292 of file ReactionPath.h.

◆ m_local

size_t m_local = npos

protected

Definition at line 293 of file ReactionPath.h.

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

Detailed Description

Public Member Functions

Public Attributes

Protected Attributes

Constructor & Destructor Documentation

◆ ~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