Cantera  3.1.0a1
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ReactionPath.h
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1/**
2 * @file ReactionPath.h
3 * Classes for reaction path analysis.
4 */
5
6// This file is part of Cantera. See License.txt in the top-level directory or
7// at https://cantera.org/license.txt for license and copyright information.
8
9#ifndef CT_RXNPATH_H
10#define CT_RXNPATH_H
11
13#include "Group.h"
14#include "Kinetics.h"
15
16namespace Cantera
17{
18enum flow_t { NetFlow, OneWayFlow };
19
20// forward references
21class Path;
22
23/**
24 * Nodes in reaction path graphs.
25 */
27{
28public:
29 //! Default constructor
30 SpeciesNode() = default;
31
32 //! Destructor
33 virtual ~SpeciesNode() = default;
34
35 // public attributes
36 size_t number = npos; //!< Species number
37 string name; //!< Label on graph
38 double value = 0.0; //!< May be used to set node appearance
39 bool visible = false; //!< Visible on graph;
40
41 //! @name References
42 //!
43 //! Return a reference to a path object connecting this node
44 //! to another node.
45 //! @{
46 Path* path(int n) {
47 return m_paths[n];
48 }
49 const Path* path(int n) const {
50 return m_paths[n];
51 }
52 //! @}
53
54 //! Total number of paths to or from this node
55 int nPaths() const {
56 return static_cast<int>(m_paths.size());
57 }
58
59 //! add a path to or from this node
60 void addPath(Path* path);
61
62 double outflow() {
63 return m_out;
64 }
65 double inflow() {
66 return m_in;
67 }
68 double netOutflow() {
69 return m_out - m_in;
70 }
71
72 void printPaths();
73
74protected:
75 double m_in = 0.0;
76 double m_out = 0.0;
77 vector<Path*> m_paths;
78};
79
80
81class Path
82{
83public:
84 typedef map<size_t, double> rxn_path_map;
85
86 /**
87 * Constructor. Construct a one-way path from @c begin to @c end.
88 */
90
91 //! Destructor
92 virtual ~Path() {}
93
94 /**
95 * Add a reaction to the path. Increment the flow from this reaction, the
96 * total flow, and the flow associated with this label.
97 */
98 void addReaction(size_t rxnNumber, double value, const string& label = "");
99
100 //! Upstream node.
101 const SpeciesNode* begin() const {
102 return m_a;
103 }
104 SpeciesNode* begin() {
105 return m_a;
106 }
107
108 //! Downstream node.
109 const SpeciesNode* end() const {
110 return m_b;
111 }
112 SpeciesNode* end() {
113 return m_b;
114 }
115
116 /**
117 * If @c n is one of the nodes this path connects, then
118 * the other node is returned. Otherwise zero is returned.
119 */
121 return (n == m_a ? m_b : (n == m_b ? m_a : 0));
122 }
123
124 //! The total flow in this path
125 double flow() {
126 return m_total;
127 }
128 void setFlow(double v) {
129 m_total = v;
130 }
131
132 //! Number of reactions contributing to this path
134 return static_cast<int>(m_rxn.size());
135 }
136
137 //! Map from reaction number to flow from that reaction in this path.
138 const rxn_path_map& reactionMap() {
139 return m_rxn;
140 }
141
142 /**
143 * Write the label for a path connecting two species, indicating
144 * the percent of the total flow due to each reaction.
145 */
146 void writeLabel(std::ostream& s, double threshold = 0.005);
147
148protected:
149 map<string, double> m_label;
150 SpeciesNode* m_a, *m_b;
151 rxn_path_map m_rxn;
152 double m_total = 0.0;
153};
154
155
156/**
157 * Reaction path diagrams (graphs).
158 */
160{
161public:
162 ReactionPathDiagram() = default;
163
164 /**
165 * Destructor. Deletes all nodes and paths in the diagram.
166 */
167 virtual ~ReactionPathDiagram();
168
169 //! The largest one-way flow value in any path
170 double maxFlow() {
171 return m_flxmax;
172 }
173
174 //! The net flow from node @c k1 to node @c k2
175 double netFlow(size_t k1, size_t k2) {
176 return flow(k1, k2) - flow(k2, k1);
177 }
178
179 //! The one-way flow from node @c k1 to node @c k2
180 double flow(size_t k1, size_t k2) {
181 return (m_paths[k1][k2] ? m_paths[k1][k2]->flow() : 0.0);
182 }
183
184 //! True if a node for species k exists
185 bool hasNode(size_t k) {
186 return (m_nodes[k] != 0);
187 }
188
189 void writeData(std::ostream& s);
190
191 /**
192 * Export the reaction path diagram. This method writes to stream
193 * @c s the commands for the 'dot' program in the @c GraphViz
194 * package from AT&T. (GraphViz may be downloaded from www.graphviz.org.)
195 *
196 * To generate a postscript reaction path diagram from the output of this
197 * method saved in file paths.dot, for example, give the command:
198 * @code
199 * dot -Tps paths.dot > paths.ps
200 * @endcode
201 * To generate a GIF image, replace -Tps with -Tgif
202 */
203 void exportToDot(std::ostream& s);
204
205 void add(ReactionPathDiagram& d);
206 SpeciesNode* node(size_t k) {
207 return m_nodes[k];
208 }
209 Path* path(size_t k1, size_t k2) {
210 return m_paths[k1][k2];
211 }
212 Path* path(size_t n) {
213 return m_pathlist[n];
214 }
215 size_t nPaths() {
216 return m_pathlist.size();
217 }
218 size_t nNodes() {
219 return m_nodes.size();
220 }
221
222 void addNode(size_t k, const string& nm, double x = 0.0);
223
224 void displayOnly(size_t k=npos) {
225 m_local = k;
226 }
227
228 void linkNodes(size_t k1, size_t k2, size_t rxn, double value, string legend = "");
229
230 void include(const string& aaname) {
231 m_include.push_back(aaname);
232 }
233 void exclude(const string& aaname) {
234 m_exclude.push_back(aaname);
235 }
236 void include(vector<string>& names) {
237 for (size_t i = 0; i < names.size(); i++) {
238 m_include.push_back(names[i]);
239 }
240 }
241 void exclude(vector<string>& names) {
242 for (size_t i = 0; i < names.size(); i++) {
243 m_exclude.push_back(names[i]);
244 }
245 }
246 vector<string>& included() {
247 return m_include;
248 }
249 vector<string>& excluded() {
250 return m_exclude;
251 }
252 vector<size_t> species();
253 vector<int> reactions();
254 void findMajorPaths(double threshold, size_t lda, double* a);
255 void setFont(const string& font) {
256 m_font = font;
257 }
258 // public attributes
259
260 string title;
261 string bold_color = "blue";
262 string normal_color = "steelblue";
263 string dashed_color = "gray";
264 string element;
265 string m_font = "Helvetica";
266 double threshold = 0.005;
267 double bold_min = 0.2;
268 double dashed_max = 0.0;
269 double label_min = 0.0;
270 double x_size = -1.0;
271 double y_size = -1.0;
272 string name = "reaction_paths";
273 string dot_options = "center=1;";
274 flow_t flow_type = NetFlow;
275 double scale = -1;
276 double arrow_width = -5.0;
277 bool show_details = false;
278 double arrow_hue = 0.6666;
279
280protected:
281 double m_flxmax = 0.0;
282 map<size_t, map<size_t, Path*>> m_paths;
283
284 //! map of species index to SpeciesNode
285 map<size_t, SpeciesNode*> m_nodes;
286 vector<Path*> m_pathlist;
287 vector<string> m_include;
288 vector<string> m_exclude;
289 vector<size_t> m_speciesNumber;
290
291 //! Indices of reactions that are included in the diagram
292 set<size_t> m_rxns;
293 size_t m_local = npos;
294};
295
296
298{
299public:
300 ReactionPathBuilder() = default;
301 virtual ~ReactionPathBuilder() = default;
302
303 int init(std::ostream& logfile, Kinetics& s);
304
305 int build(Kinetics& s, const string& element, std::ostream& output,
306 ReactionPathDiagram& r, bool quiet=false);
307
308 //! Analyze a reaction to determine which reactants lead to which products.
309 int findGroups(std::ostream& logfile, Kinetics& s);
310
311protected:
312 void findElements(Kinetics& kin);
313
314 size_t m_nr;
315 size_t m_ns;
316 size_t m_nel;
317 vector<double> m_ropf;
318 vector<double> m_ropr;
319 vector<double> m_x;
320 vector<vector<size_t>> m_reac;
321 vector<vector<size_t>> m_prod;
322 DenseMatrix m_elatoms;
323 vector<vector<int>> m_groups;
324 vector<Group> m_sgroup;
325 vector<string> m_elementSymbols;
326
327 //! m_transfer[reaction][reactant number][product number] where "reactant
328 //! number" means the number of the reactant in the reaction equation. For example,
329 //! for "A+B -> C+D", "B" is reactant number 1 and "C" is product number 0.
330 map<size_t, map<size_t, map<size_t, Group>>> m_transfer;
331
332 vector<bool> m_determinate;
333 Array2D m_atoms;
334 map<string, size_t> m_enamemap;
335};
336
337}
338
339#endif
Headers for the DenseMatrix object, which deals with dense rectangular matrices and description of th...
Base class for kinetics managers and also contains the kineticsmgr module documentation (see Kinetics...
A class for 2D arrays stored in column-major (Fortran-compatible) form.
Definition Array.h:32
A class for full (non-sparse) matrices with Fortran-compatible data storage, which adds matrix operat...
Definition DenseMatrix.h:55
Public interface for kinetics managers.
Definition Kinetics.h:125
virtual ~Path()
Destructor.
const SpeciesNode * begin() const
Upstream node.
int nReactions()
Number of reactions contributing to this path.
void addReaction(size_t rxnNumber, double value, const string &label="")
Add a reaction to the path.
void writeLabel(std::ostream &s, double threshold=0.005)
Write the label for a path connecting two species, indicating the percent of the total flow due to ea...
double flow()
The total flow in this path.
SpeciesNode * otherNode(SpeciesNode *n)
If n is one of the nodes this path connects, then the other node is returned.
const rxn_path_map & reactionMap()
Map from reaction number to flow from that reaction in this path.
const SpeciesNode * end() const
Downstream node.
int findGroups(std::ostream &logfile, Kinetics &s)
Analyze a reaction to determine which reactants lead to which products.
map< size_t, map< size_t, map< size_t, Group > > > m_transfer
m_transfer[reaction][reactant number][product number] where "reactant number" means the number of the...
Reaction path diagrams (graphs).
map< size_t, SpeciesNode * > m_nodes
map of species index to SpeciesNode
void exportToDot(std::ostream &s)
Export the reaction path diagram.
bool hasNode(size_t k)
True if a node for species k exists.
set< size_t > m_rxns
Indices of reactions that are included in the diagram.
virtual ~ReactionPathDiagram()
Destructor.
double maxFlow()
The largest one-way flow value in any path.
double flow(size_t k1, size_t k2)
The one-way flow from node k1 to node k2.
double netFlow(size_t k1, size_t k2)
The net flow from node k1 to node k2.
Nodes in reaction path graphs.
virtual ~SpeciesNode()=default
Destructor.
string name
Label on graph.
bool visible
Visible on graph;.
int nPaths() const
Total number of paths to or from this node.
SpeciesNode()=default
Default constructor.
double value
May be used to set node appearance.
size_t number
Species number.
void addPath(Path *path)
add a path to or from this node
Namespace for the Cantera kernel.
Definition AnyMap.cpp:564
const size_t npos
index returned by functions to indicate "no position"
Definition ct_defs.h:180