Cleaned up Doxygen docs for Reaction path related classes
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Ray Speth
parent
c43b02e130
commit
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4 changed files with 36 additions and 69 deletions
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@ -101,6 +101,12 @@ public:
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// }
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}
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/*!
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* A group is 'valid' if all of its nonzero atom numbers have
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* the same sign, either positive or negative. This method
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* checks for this, and if the group is not valid it sets
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* m_sign to -999, and sets all atom numbers to zero.
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*/
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void validate();
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/**
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@ -17,7 +17,6 @@
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namespace Cantera
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{
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enum flow_t { NetFlow, OneWayFlow };
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// forward references
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@ -42,9 +41,6 @@ public:
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doublereal value; ///< May be used to set node appearance
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bool visible; ///< Visible on graph;
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// public methods
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/**
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* @name References.
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* Return a reference to a path object connecting this node
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@ -59,7 +55,6 @@ public:
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}
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//@}
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/// Total number of paths to or from this node
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int nPaths() const {
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return static_cast<int>(m_paths.size());
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@ -80,7 +75,6 @@ public:
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void printPaths();
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protected:
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doublereal m_in;
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doublereal m_out;
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@ -88,12 +82,9 @@ protected:
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};
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class Path
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{
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public:
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typedef std::map<size_t, doublereal> rxn_path_map;
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/**
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@ -105,6 +96,11 @@ public:
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/// Destructor
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virtual ~Path() {}
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/**
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* Add a reaction to the path. Increment the flow from this
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* reaction, the total flow, and the flow associated with this
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* label.
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*/
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void addReaction(size_t rxnNumber, doublereal value,
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const std::string& label = "");
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@ -150,10 +146,13 @@ public:
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return m_rxn;
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}
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/**
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* Write the label for a path connecting two species, indicating
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* the percent of the total flow due to each reaction.
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*/
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void writeLabel(std::ostream& s, doublereal threshold = 0.005);
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protected:
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std::map<std::string, doublereal> m_label;
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SpeciesNode* m_a, *m_b;
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rxn_path_map m_rxn;
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@ -166,11 +165,12 @@ protected:
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*/
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class ReactionPathDiagram
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{
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public:
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ReactionPathDiagram();
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/**
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* Destructor. Deletes all nodes and paths in the diagram.
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*/
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virtual ~ReactionPathDiagram();
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/// The largest one-way flow value in any path
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@ -194,7 +194,23 @@ public:
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}
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void writeData(std::ostream& s);
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/**
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* Export the reaction path diagram. This method writes to stream
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* \c s the commands for the 'dot' program in the \c GraphViz
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* package from AT&T. (GraphViz may be downloaded from
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* www.graphviz.org.)
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*
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* To generate a postscript reaction path diagram from the
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* output of this method saved in file paths.dot, for example, give
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* the command:
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* \code
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* dot -Tps paths.dot > paths.ps
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* \endcode
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* To generate a GIF image, replace -Tps with -Tgif
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*/
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void exportToDot(std::ostream& s);
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void add(ReactionPathDiagram& d);
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SpeciesNode* node(size_t k) {
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return m_nodes[k];
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@ -268,7 +284,6 @@ public:
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doublereal arrow_hue;
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protected:
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doublereal m_flxmax;
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std::map<size_t, std::map<size_t, Path*> > m_paths;
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std::map<size_t, SpeciesNode*> m_nodes;
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@ -281,10 +296,8 @@ protected:
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};
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class ReactionPathBuilder
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{
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public:
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ReactionPathBuilder() {}
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virtual ~ReactionPathBuilder() {}
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@ -294,6 +307,8 @@ public:
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int build(Kinetics& s, const std::string& element, std::ostream& output,
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ReactionPathDiagram& r, bool quiet=false);
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//! Analyze a reaction to determine which reactants lead to which
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//! products.
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int findGroups(std::ostream& logfile, Kinetics& s);
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void writeGroup(std::ostream& out, const Group& g);
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@ -16,12 +16,6 @@
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namespace Cantera
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{
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/**
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* A group is 'valid' if all of its nonzero atom numbers have
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* the same sign, either positive or negative. This method
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* checks for this, and if the group is not valid it sets
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* m_sign to -999, and sets all atom numbers to zero.
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*/
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void Group::validate()
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{
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@ -14,7 +14,6 @@ using namespace std;
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namespace Cantera
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{
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/// add a path to or from this node
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void SpeciesNode::addPath(Path* path)
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{
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m_paths.push_back(path);
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@ -36,10 +35,6 @@ void SpeciesNode::printPaths()
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}
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}
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/**
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* Construct a path connecting two species nodes.
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*/
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Path::Path(SpeciesNode* begin, SpeciesNode* end)
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: m_a(begin), m_b(end), m_total(0.0)
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{
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@ -47,12 +42,6 @@ Path::Path(SpeciesNode* begin, SpeciesNode* end)
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end->addPath(this);
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}
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/**
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* add a reaction to the path. Increment the flow from this
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* reaction, the total flow, and the flow associated with this
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* label.
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*/
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void Path::addReaction(size_t rxnNumber, doublereal value,
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const string& label)
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{
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@ -63,11 +52,6 @@ void Path::addReaction(size_t rxnNumber, doublereal value,
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}
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}
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/**
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* Write the label for a path connecting two species, indicating
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* the percent of the total flow due to each reaction.
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*/
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void Path::writeLabel(ostream& s, doublereal threshold)
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{
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size_t nn = m_label.size();
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@ -92,10 +76,6 @@ void Path::writeLabel(ostream& s, doublereal threshold)
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}
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}
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/**
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* Default constructor.
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*/
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ReactionPathDiagram::ReactionPathDiagram()
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{
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name = "reaction_paths";
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@ -120,10 +100,6 @@ ReactionPathDiagram::ReactionPathDiagram()
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m_local = npos;
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}
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/**
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* Destructor. Deletes all nodes and paths in the diagram.
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*/
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ReactionPathDiagram::~ReactionPathDiagram()
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{
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// delete the nodes
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@ -139,7 +115,6 @@ ReactionPathDiagram::~ReactionPathDiagram()
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}
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}
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vector_int ReactionPathDiagram::reactions()
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{
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size_t i, npaths = nPaths();
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@ -243,21 +218,6 @@ void ReactionPathDiagram::writeData(ostream& s)
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}
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}
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/**
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* Export the reaction path diagram. This method writes to stream
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* \c s the commands for the 'dot' program in the \c GraphViz
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* package from AT&T. (GraphViz may be downloaded from
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* www.graphviz.org.)
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*
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* To generate a postscript reaction path diagram from the
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* output of this method saved in file paths.dot, for example, give
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* the command:
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* \code
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* dot -Tps paths.dot > paths.ps
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* \endcode
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* To generate a GIF image, replace -Tps with -Tgif
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*/
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void ReactionPathDiagram::exportToDot(ostream& s)
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{
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doublereal flxratio, flmax = 0.0, lwidth;
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@ -497,10 +457,6 @@ std::vector<size_t> ReactionPathDiagram::species()
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return m_speciesNumber;
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}
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/**
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* analyze a reaction to determine which reactants lead to which products.
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*/
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int ReactionPathBuilder::findGroups(ostream& logfile, Kinetics& s)
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{
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m_groups.resize(m_nr);
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@ -718,8 +674,6 @@ void ReactionPathBuilder::findElements(Kinetics& kin)
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}
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}
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int ReactionPathBuilder::init(ostream& logfile, Kinetics& kin)
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{
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//m_warn.clear();
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@ -879,7 +833,6 @@ string reactionLabel(size_t i, size_t kr, size_t nr,
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return label;
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}
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int ReactionPathBuilder::build(Kinetics& s, const string& element,
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ostream& output, ReactionPathDiagram& r, bool quiet)
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{
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@ -1033,5 +986,4 @@ int ReactionPathBuilder::build(Kinetics& s, const string& element,
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return 1;
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}
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}
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