| _bulkValue | simulator.geometry.Bulk | |
| _D | simulator.geometry.Bulk | |
| _isConstant | simulator.geometry.Bulk | |
| _sIn | simulator.geometry.Bulk | |
| Bulk(Simulator aSim, XMLParser aBulkRoot) | simulator.geometry.Bulk | |
| computeFlow(SoluteGrid aSG, DiscreteVector aDC, ContinuousVector flow) | simulator.geometry.Bulk | |
| contains(int soluteIndex) | simulator.geometry.Bulk | |
| counter | simulator.geometry.FluctEnv | static |
| cumProb | simulator.geometry.FluctEnv | static |
| envCumProb | simulator.geometry.FluctEnv | static |
| envCumProb() | simulator.geometry.FluctEnv | |
| envDic() | simulator.geometry.FluctEnv | |
| envIter | simulator.geometry.FluctEnv | static |
| envListTime | simulator.geometry.FluctEnv | static |
| envName | simulator.geometry.FluctEnv | static |
| envNameList | simulator.geometry.FluctEnv | static |
| envProb() | simulator.geometry.FluctEnv | |
| envStatus | simulator.geometry.FluctEnv | static |
| envTrans | simulator.geometry.FluctEnv | static |
| envTransName() | simulator.geometry.FluctEnv | |
| FluctEnv(Simulator aSim, XMLParser aBulkRoot) | simulator.geometry.FluctEnv | |
| getName() | simulator.geometry.Bulk | |
| getTimeConstraint() | simulator.geometry.Bulk | |
| getValue(int soluteIndex) | simulator.geometry.Bulk | |
| indexCalc() | simulator.geometry.FluctEnv | |
| indices | simulator.geometry.FluctEnv | static |
| mySim | simulator.geometry.Bulk | |
| setEnv() | simulator.geometry.FluctEnv | |
| setEnvCycle(int index) | simulator.geometry.FluctEnv | static |
| setValue(int soluteIndex, double value) | simulator.geometry.Bulk | |
| transitions | simulator.geometry.FluctEnv | static |
| transMatrix() | simulator.geometry.FluctEnv | |
| transProb | simulator.geometry.FluctEnv | static |
| transProbVal() | simulator.geometry.FluctEnv | |
| updateBulk(SoluteGrid[] soluteGrid, SoluteGrid[] reacGrid, double timeStep) | simulator.geometry.Bulk | |
| updateBulkByGradient(SoluteGrid[] soluteGrid, double timeStep) | simulator.geometry.Bulk | |
| updateBulkByReaction(SoluteGrid[] reacGrid, double timeStep) | simulator.geometry.Bulk | |
| updateChemostatBulk(SoluteGrid[] allSol, SoluteGrid[] reacGrid) | simulator.geometry.Bulk | |
| writeReport(ResultFile buffer) | simulator.geometry.Bulk | |