_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 | |