| _catalystIndex | simulator.reaction.Reaction | |
| _diffUptakeRate | simulator.reaction.Reaction | protected |
| _guild | simulator.reaction.Reaction | protected |
| _guildGrid | simulator.reaction.Reaction | protected |
| _kineticParam | simulator.reaction.Reaction | protected |
| _mySoluteIndex | simulator.reaction.Reaction | |
| _particleNameYield | simulator.reaction.Reaction | protected |
| _particleYield | simulator.reaction.Reaction | protected |
| _reacGrid | simulator.reaction.Reaction | protected |
| _soluteList | simulator.reaction.Reaction | protected |
| _soluteYield | simulator.reaction.Reaction | protected |
| _specRate | simulator.reaction.Reaction | protected |
| _uptakeRate | simulator.reaction.Reaction | protected |
| addAgent(ActiveAgent anAgent) | simulator.reaction.Reaction | |
| applyReaction(SpatialGrid[] concGrid, SpatialGrid[] reacGrid, SpatialGrid[] diffReacGrid, SpatialGrid biomassGrid) | simulator.reaction.Reaction | |
| autocatalytic | simulator.reaction.Reaction | |
| calcdMUdS(Matrix S, double biomass) | simulator.reaction.FirstOrder | virtual |
| calcdMUdT(Matrix S, double biomass) | simulator.reaction.FirstOrder | virtual |
| computeMarginalDiffMu(double[] s) | simulator.reaction.FirstOrder | virtual |
| computeMassGrowthRate(ActiveAgent anAgent) | simulator.reaction.FirstOrder | virtual |
| computeSpecGrowthRate(ActiveAgent anAgent) | simulator.reaction.FirstOrder | virtual |
| computeSpecificGrowthRate(ActiveAgent anAgent) | simulator.reaction.FirstOrder | virtual |
| computeSpecificGrowthRate(double[] s) | simulator.reaction.FirstOrder | virtual |
| computeSpecificGrowthRate(double[] s, ActiveAgent anAgent) | simulator.reaction.FirstOrder | virtual |
| computeSpecRate(double[] s) | simulator.reaction.FirstOrder | virtual |
| computeUptakeRate(double[] s, ActiveAgent anAgent) | simulator.reaction.FirstOrder | |
| computeUptakeRate(double[] s, double mass) | simulator.reaction.FirstOrder | |
| computeUptakeRate(double[] s, double conc, double h) | simulator.reaction.FirstOrder | virtual |
| declareSolutes() | simulator.reaction.Reaction | |
| Dil | simulator.reaction.Reaction | |
| fillParameters(Simulator aSim, XMLParser xmlRoot) | simulator.reaction.Reaction | |
| fitAgentMassOnGrid(SpatialGrid aSpG) | simulator.reaction.Reaction | |
| fitGuildOnGrid() | simulator.reaction.Reaction | |
| getGuild() | simulator.reaction.Reaction | |
| getKinetic() | simulator.reaction.Reaction | |
| getParticulateYield() | simulator.reaction.Reaction | |
| getSoluteIndex() | simulator.reaction.Reaction | |
| getSoluteYield() | simulator.reaction.Reaction | |
| init(Simulator aSim, XMLParser aReactionRoot) | simulator.reaction.FirstOrder | |
| initFromAgent(ActiveAgent anAgent, Simulator aSim, XMLParser aReactionRoot) | simulator.reaction.FirstOrder | |
| reactionIndex | simulator.reaction.Reaction | |
| reactionName | simulator.reaction.Reaction | |
| readConcentrationSeen(ActiveAgent anAgent, SoluteGrid[] concGrid) | simulator.reaction.Reaction | |
| register(String aReactionName, Simulator aSimulator) | simulator.reaction.Reaction | |
| removeAgent(ActiveAgent anAgent) | simulator.reaction.Reaction | |
| totalUptake | simulator.reaction.Reaction | |
| updateMarginalMu(double[] s) | simulator.reaction.FirstOrder | virtual |
| writeReport(ResultFile bufferState, ResultFile bufferSum) | simulator.reaction.Reaction | |
1.8.3.1
