public static SampleValue Equilibrate(Env env, Symbol outSymbol, SampleValue inSample, Noise noise, double fortime, Netlist netlist, Style style)
{
inSample.CheckConsumed(style); // we will consume it later, but we need to check now
double initialTime = 0.0;
double finalTime = fortime;
string sampleName = (outSymbol.Raw() == "vessel") ? "" : "Sample " + inSample.FormatSymbol(style);
KChartHandler.ChartClear(sampleName, "s", "M", style);
List <SpeciesValue> inSpecies = inSample.stateMap.species;
State initialState = inSample.stateMap.state;
if ((noise == Noise.None) && initialState.lna)
{
initialState = new State(initialState.size, lna: false).InitMeans(initialState.MeanVector());
}
if ((noise != Noise.None) && !initialState.lna)
{
initialState = new State(initialState.size, lna: true).InitMeans(initialState.MeanVector());
}
List <ReactionValue> reactions = inSample.RelevantReactions(netlist, style);
CRN crn = new CRN(inSample, reactions, precomputeLNA: (noise != Noise.None) && KControls.precomputeLNA);
KChartHandler.SetMeanFlowDictionary(crn.MeanFlowDictionary(), style);
// List<ReportEntry> reports = netlist.Reports(inSpecies);
List <ReportEntry> reports = inSample.RelevantReports(style);
Exec.lastExecution.lastCRN = crn; KGui.gui.GuiOutputSetText(crn.FormatNice(style));
Exec.lastExecution.ResetGraphCache();
Func <double, double, Vector, Func <double, Vector, Vector>, IEnumerable <SolPoint> > Solver;
if (KControls.solver == "GearBDF")
{
Solver = Ode.GearBDF;
}
else if (KControls.solver == "RK547M")
{
Solver = Ode.RK547M;
}
else
{
throw new Error("No solver");
}
Func <double, Vector, Vector> Flux;
if (noise != Noise.None)
{
Flux = (t, x) => crn.LNAFlux(t, x, style);
}
else
{
Flux = (t, x) => crn.Flux(t, x, style);
}
bool nonTrivialSolution =
(inSpecies.Count > 0) && // we don't want to run on the empty species list: Oslo crashes
(!crn.Trivial(style)) && // we don't want to run trivial ODEs: some Oslo solvers hang on very small stepping
finalTime > 0; // we don't want to run when fortime==0
// INTEGRATE
(double lastTime, State lastState) =
Integrate(Solver, initialState, initialTime, finalTime, Flux, inSample, reports, noise, nonTrivialSolution, style);
if (lastState == null)
{
lastState = initialState.Clone();
}
lastState = lastState.Positive();
List <SpeciesValue> outSpecies = new List <SpeciesValue> {
}; foreach (SpeciesValue sp in inSpecies)
{
outSpecies.Add(sp); // the species list may be destructively modified (added to) later in the new sample
}
SampleValue outSample = new SampleValue(outSymbol, new StateMap(outSymbol, outSpecies, lastState), new NumberValue(inSample.Volume()), new NumberValue(inSample.Temperature()), produced: true);
outSample.AddReports(inSample.RelevantReports(style));
foreach (ReportEntry report in reports)
{
// an equilibrate may pick up the reports of a previous equilibrate, so we reassign the report even if it has already been assigned
// this does not really affect lexical binding because a second report with the same name will get a new symbol
// P.S. this was changed so that an equilibrate no longer picks up reports of previous equilibrate, so the issue should not arise
if (report.timecourse != null)
{
env.AssignValue(report.timecourse, KChartHandler.ToTimecourse(report.timecourse, report.flow, style), reassign: true);
}
}
inSample.Consume(reactions, lastTime, lastState, netlist, style);
return(outSample);
}