| Cantera 3.0.0

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Public Member Functions | Public Attributes | Protected Attributes | List of all members
ReactionPathDiagram Class Reference

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:

- ReactionPath.h
- ReactionPath.cpp