private static void Execute_Worker(bool doParse, bool doAST, bool doScope, bool autoContinue, bool chartOutput)
{
KGui.gui.GuiBeginningExecution();
lastExecution = null;
KGui.gui.GuiSaveInput();
KGui.gui.GuiOutputClear();
DateTime startTime = DateTime.Now;
if (TheParser.Parser().Parse(KGui.gui.GuiInputGetText(), out IReduction root))
{
if (doParse)
{
root.DrawReductionTree();
}
else
{
Netlist netlist = new Netlist(autoContinue);
try
{
Statements statements = Parser.ParseTop(root);
if (doAST)
{
KGui.gui.GuiOutputAppendText(statements.Format());
}
else
{
SampleValue vessel = Vessel(KControls.SelectNoiseSelectedItem != Noise.None);
Env initialEnv = new ValueEnv("vessel", Type.Sample, vessel, new BuiltinEnv(new NullEnv()));
Scope initialScope = initialEnv.ToScope();
Scope scope = statements.Scope(initialScope);
if (doScope)
{
KGui.gui.GuiOutputAppendText(scope.Format());
}
else
{
Style style = new Style(varchar: scopeVariants ? defaultVarchar : null, new SwapMap(),
map: remapVariants ? new AlphaMap() : null, numberFormat: "G4", dataFormat: "full", // we want it full for samples, but maybe only headers for functions/networks?
exportTarget: ExportTarget.Standard, traceFull: false, chartOutput: chartOutput);
KChartHandler.ChartClear("", "s", "M", style);
KChartHandler.LegendUpdate(style);
KScoreHandler.ScoreClear();
KControls.ParametersClear(style);
KDeviceHandler.Clear(style);
KDeviceHandler.Sample(vessel, style);
netlist.Emit(new SampleEntry(vessel));
DateTime evalTime = DateTime.Now;
lastExecution = new ExecutionInstance(vessel, netlist, style, startTime, evalTime);
lastExecution.environment = statements.EvalReject(initialEnv, netlist, style, 0);
if (lastExecution.environment == null)
{
throw new Error("Top level reject");
}
lastExecution.EndTime();
if (style.chartOutput)
{
foreach (ParameterEntry parameter in netlist.Parameters())
{
KControls.AddParameter(parameter.symbol.Format(style), (parameter.value as NumberValue).value, parameter.distribution, style);
}
KGui.gui.GuiParametersUpdate(); // calls back KControls.ParametersUpdate, but only on Win/Mac
}
KGui.gui.GuiProcessOutput();
}
}
}
catch (ExecutionEnded) { lastExecution.EndTime(); KGui.gui.GuiOutputAppendText(lastExecution.ElapsedTime()); }
catch (ConstantEvaluation ex) { string cat = "Does not have a value: "; netlist.Emit(new CommentEntry(cat + ": " + ex.Message)); KGui.gui.GuiInputSetErrorSelection(-1, -1, 0, cat, ex.Message); }
catch (Error ex) { netlist.Emit(new CommentEntry(ex.Message)); KGui.gui.GuiInputSetErrorSelection(-1, -1, 0, "Error", ex.Message); try { KGui.gui.GuiProcessOutput(); } catch { }; }
catch (StackOverflowException ex) { netlist.Emit(new CommentEntry(ex.Message)); KGui.gui.GuiInputSetErrorSelection(-1, -1, 0, "Stack Overflow", ex.Message); }
catch (Exception ex) { string cat = "Something happened"; netlist.Emit(new CommentEntry(cat + ": " + ex.Message)); KGui.gui.GuiInputSetErrorSelection(-1, -1, 0, cat, ex.Message); }
}
}
else
{
KGui.gui.GuiInputSetErrorSelection(TheParser.Parser().FailLineNumber(), TheParser.Parser().FailColumnNumber(), TheParser.Parser().FailLength(), TheParser.Parser().FailCategory(), TheParser.Parser().FailMessage());
}
EndingExecution();
}
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);
}