Beispiel #1
0
        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);
        }