public void TestStepOnceWithWeight()
{
const string configString = @"{""solver"":""SDWSSA"",""prng_seed"":123, ""prng_index"":1,""RNG"":{""type"":""PSEUDODES""},""sdwSSA"":{""biasingParametersFileName"":""resources\\rever_isom_CEinfo.json""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
RunResetRNGFactory();
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 100000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
solver.Initialize();
var startRealization = GetHiddenMethod("StartRealization", solver);
startRealization.Invoke(solver, null);
var stepOnce = solver.GetType().GetMethod("StepOnce", BindingFlags.NonPublic | BindingFlags.Instance, Type.DefaultBinder, new[] { typeof(double).MakeByRefType() }, null);
var inputArray1 = new object[] { 1.5 };
stepOnce.Invoke(solver, inputArray1);
var currentTime = GetHiddenField <double>("_currentTime", solver);
Assert.AreEqual(0.0075434142087234968, currentTime);
}
public void TestLocaleAndReactionIndex()
{
const string configString = @"{""solver"":""SDWSSA"", ""sdwSSA"":{""crossEntropyThreshold"":0.005, ""crossEntropyRuns"":1000000, ""biasingParametersFileName"":""resources\\rever_isom_CEinfo.json""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
RunResetRNGFactory();
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 1000000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
var reactionSet = GetHiddenField <StateDependentReactionSet>("_reactions", solver);
var reaction1 = reactionSet.Reactions[0];
var inputObject = new object[2];
inputObject[0] = reaction1;
inputObject[1] = 0;
Assert.AreEqual(0, GetHiddenMethod("ReactionIndex", solver).Invoke(solver, inputObject));
var inputObject2 = new object[1];
inputObject2[0] = reaction1;
Assert.AreEqual(0, GetHiddenMethod("LocaleIndex", solver).Invoke(solver, inputObject2));
}
public void TestRunCrossEntropy()
{
const string configString = @"{""solver"":""SDWSSA"",""prng_seed"":123, ""prng_index"":1,""RNG"":{""type"":""PSEUDODES""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
RunResetRNGFactory();
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 100000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
solver.Initialize();
var startRealization = GetHiddenMethod("StartRealization", solver);
startRealization.Invoke(solver, null);
GetHiddenMethod("RunCrossEntropy", solver).Invoke(solver, null);
var biasingParameters = GetHiddenField <BiasingParameters>("_biasingParameters", solver);
Console.Error.WriteLine("** TestRunCrossEntropy gammas **");
foreach (double value in biasingParameters.Locales[0].Reactions[0].RareEvents[0].Gammas)
{
Console.Error.WriteLine(value);
}
Assert.AreEqual(new[] { 2.0273575170009774, 1.6011280886463515, 1.2909305036960836, 1.1580792074159503, 1.1014233907817004, 1.0495114005076731, 1.0308762479433711, 1.01949884022247545, 1.0123811789981323, 1.013972793156378, 1.0147858262235918, 0.97835339270352839, 1.025712153478078 },
biasingParameters.Locales[0].Reactions[0].RareEvents[0].Gammas);
}
public void TestSetRareEventType()
{
const string configString = @"{""solver"":""SDWSSA"",""sdwSSA"":{""biasingParametersFileName"":""resources\\rever_isom_CEinfo.json""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 100000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
solver.Initialize();
var method = FindMethod("SetRareEventType", typeof(sdwSSA));
method.Invoke(solver, null);
var reExpression = GetHiddenField <Expression>("_reExpression", solver);
var reEventValue = GetHiddenField <double>("_rareEventValue", solver);
Assert.AreEqual(0, reExpression.Value);
Assert.AreEqual(30.0, reEventValue);
Assert.AreEqual(1, GetHiddenField <int>("_rareEventType", solver));
}
public void TestUpdateBinEdges()
{
const string configString = @"{""solver"":""SDWSSA""}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 1000000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
var startPC = new[] { 0.012, 0.432 };
var endPC = new[] { 0.899, 0.2134 };
const double a0 = 2.0;
const int mu = 0;
var inputObjectArray = new object[4];
inputObjectArray[0] = startPC;
inputObjectArray[1] = endPC;
inputObjectArray[2] = a0;
inputObjectArray[3] = mu;
GetHiddenMethod("UpdateBinEdges", solver).Invoke(solver, inputObjectArray);
Assert.AreEqual(startPC[mu], 0.0);
}
public void TestInitialize()
{
const string configString = @"{""solver"":""SDWSSA"",""sdwSSA"":{""biasingParametersFileName"":""resources\\rever_isom_CEinfo.json""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 1000000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
solver.Initialize();
Assert.AreEqual(30.0, GetHiddenField <double>("_rareEventValue", solver));
Assert.AreEqual(0.0, GetHiddenField <Expression>("_reExpression", solver).Value);
Assert.AreEqual(1, GetHiddenField <int>("_rareEventType", solver));
var biasingParameters = GetHiddenField <BiasingParameters>("_biasingParameters", solver);
var reaction1 = biasingParameters.Locales[0].Reactions[0];
var reaction2 = biasingParameters.Locales[0].Reactions[1];
var gammas = GetHiddenField <List <double[]> >("_gamma", solver);
var pcs = GetHiddenField <List <double[]> >("_propensityCutoff", solver);
Assert.AreEqual(reaction1.RareEvents[1].Gammas, gammas[0]);
Assert.AreEqual(reaction2.RareEvents[1].Gammas, gammas[1]);
Assert.AreEqual(reaction1.RareEvents[1].Thresholds, pcs[0]);
Assert.AreEqual(reaction2.RareEvents[1].Thresholds, pcs[1]);
}
public void TestRunCrossEntropy()
{
const string configString = @"{""solver"":""SDWSSA"",""prng_seed"":123, ""prng_index"":1,""RNG"":{""type"":""PSEUDODES""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
RunResetRNGFactory();
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const float duration = 10.0f;
const int repeats = 100000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
solver.Initialize();
var startRealization = GetHiddenMethod("StartRealization", solver);
startRealization.Invoke(solver, null);
GetHiddenMethod("RunCrossEntropy", solver).Invoke(solver, null);
var biasingParameters = GetHiddenField <BiasingParameters>("_biasingParameters", solver);
Assert.AreEqual(biasingParameters.Locales[0].Reactions[0].RareEvents[0].Gammas, new[]
{ 2.0631374260651874, 1.6275260813957282, 1.2852465989965649, 1.1551778002545692, 1.0896852429443773, 1.0597861285148038, 1.0521305608249278, 1.0491667590772435, 1.0058609338670563, 1.0114445292874816, 1.0208331777734598, 1.01513053565442, 1.0298844136066307 });
}
private static sdwSSA InstantiateSolver()
{
const string configString = @"{""solver"":""SDWSSA"",""prng_seed"":123, ""prng_index"":1,""RNG"":{""type"":""PSEUDODES""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
RunResetRNGFactory();
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
var solver = new sdwSSA(modelInfo, 10.0, 1000000, 1);
return(solver);
}
public void TestsdwSSAConstructorWithBiasingParameters()
{
const string configString = @"{""solver"":""SDWSSA"",""prng_seed"":123, ""prng_index"":1,""RNG"":{""type"":""PSEUDODES""}, ""sdwSSA"":{""crossEntropyThreshold"":0.005, ""crossEntropyRuns"":1000000, ""biasingParametersFileName"":""resources\\rever_isom_sdwSSA_CEinfo.json""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
RunResetRNGFactory();
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 1000000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
Assert.AreEqual(1000000, GetHiddenField <int>("_crossEntropyRuns", solver));
Assert.AreEqual(0.005, GetHiddenField <double>("_crossEntropyThreshold", solver));
Assert.AreEqual("resources\\rever_isom_sdwSSA_CEinfo.json", GetHiddenField <string>("_biasingParametersFileName", solver));
Assert.AreEqual(false, GetHiddenField <Boolean>("_biasingParametersFlag", solver));
var biasingParameters = GetHiddenField <BiasingParameters>("_biasingParameters", solver);
Assert.AreEqual("global", biasingParameters.Locales[0].Name);
Assert.AreEqual(2, biasingParameters.Locales[0].ReactionCount);
Assert.AreEqual("reExpression", biasingParameters.RareEvent.ExpressionName);
Assert.AreEqual("global", biasingParameters.RareEvent.ExpressionLocale);
Assert.AreEqual(2, biasingParameters.RareEvent.IntermediateRareEventCount);
Assert.That(new float[] { 23, 30 }, Is.EquivalentTo(biasingParameters.RareEvent.Thresholds));
var reaction1 = biasingParameters.Locales[0].Reactions[0];
Assert.AreEqual("interconvert1", reaction1.Name);
Assert.AreEqual(13, reaction1.RareEvents[0].BinCount);
Assert.AreEqual(new[] { 2.06313742606519, 1.62752608139573, 1.28524659899656, 1.1551778002545701, 1.08968524294438, 1.05978612851480, 1.05213056082493, 1.04916675907724, 1.00586093386706, 1.01144452928748, 1.02083317777346, 1.01513053565442, 1.02988441360663 }, reaction1.RareEvents[0].Gammas);
Assert.AreEqual(new[] { 0.330135030236500, 0.381663104833693, 0.433191179430885, 0.484719254028077, 0.536247328625270, 0.587775403222462, 0.639303477819654, 0.690831552416846, 0.742359627014039, 0.845415776208423, 0.896943850805615, 0.948471925402808 }, reaction1.RareEvents[0].Thresholds);
Assert.AreEqual(13, reaction1.RareEvents[1].BinCount);
Assert.AreEqual(new[] { 2.476968001615, 1.64117464971143, 1.30252163933866, 1.16127755928718, 1.10320326699327, 1.06106835822293, 1.04512721554582, 1.03240567633747, 1.01985869635349, 1.01823044314009, 1.02103023510684, 1.01935203218744, 1.01472718645925 }, reaction1.RareEvents[1].Gammas);
Assert.AreEqual(new[] { 0.3301350302365, 0.381663104833693, 0.433191179430885, 0.484719254028077, 0.53624732862527, 0.587775403222462, 0.639303477819654, 0.690831552416846, 0.742359627014039, 0.845415776208423, 0.896943850805615, 0.948471925402808 }, reaction1.RareEvents[1].Thresholds);
var reaction2 = biasingParameters.Locales[0].Reactions[1];
Assert.AreEqual("interconvert2", reaction2.Name);
Assert.AreEqual(14, reaction2.RareEvents[0].BinCount);
Assert.AreEqual(new[] { 0.98850417047106398, 0.917309756657961, 1.03395184011107, 0.975731835263174, 1.00611856107535, 0.984970326735658, 0.94726738124926602, 0.96614763699818795, 0.93530750400835505, 0.910799215582815, 0.86803893648544395, 0.77448007324552304, 0.613574832946266, 0.499713830449480 }, reaction2.RareEvents[0].Gammas);
Assert.AreEqual(new[] { 0.123991842069282, 0.170343933275611, 0.216696024481939, 0.263048115688268, 0.309400206894597, 0.355752298100925, 0.402104389307254, 0.448456480513583, 0.494808571719912, 0.541160662926240, 0.587512754132569, 0.633864845338898, 0.680216936545227 }, reaction2.RareEvents[0].Thresholds);
Assert.AreEqual(14, reaction2.RareEvents[1].BinCount);
Assert.AreEqual(new[] { 0.98423158970711, 1.01498329340952, 0.990253088665499, 0.975106365160516, 0.986861478077715, 0.978625997732093, 0.962392697806862, 0.949116411528197, 0.936334221304811, 0.909940261969898, 0.85882305727793, 0.76550824189768, 0.611330117387254, 0.413838468692494 }, reaction2.RareEvents[1].Gammas);
Assert.AreEqual(new[] { 0.123991842069282, 0.170343933275611, 0.216696024481939, 0.263048115688268, 0.309400206894597, 0.355752298100925, 0.402104389307254, 0.448456480513583, 0.494808571719912, 0.54116066292624, 0.587512754132569, 0.633864845338898, 0.680216936545227 }, reaction2.RareEvents[1].Thresholds);
}
public void TestSelectAndFireReaction()
{
const string configString = @"{""solver"":""SDWSSA"",""sdwSSA"":{""biasingParametersFileName"":""resources\\rever_isom_CEinfo.json""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 100000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
solver.Initialize();
var method = FindMethod("SelectAndFireReaction", typeof(sdwSSA));
var inputArray = new object[] { 0.1 };
var mu = (int)method.Invoke(solver, inputArray);
Assert.AreEqual(0, mu);
}
public void TestUpdateReactionInfo()
{
const string configString = @"{""solver"":""SDWSSA"", ""sdwSSA"":{""crossEntropyThreshold"":0.005, ""crossEntropyRuns"":1000000, ""biasingParametersFileName"":""resources\\rever_isom_CEinfo.json""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 1000000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
var biasingParameters = GetHiddenField <BiasingParameters>("_biasingParameters", solver);
var tempREInfo = biasingParameters.Locales[0].Reactions[0].RareEvents[0];
var inputArray = new object[] { tempREInfo, 0 };
GetHiddenMethod("UpdateReactionInfo", solver).Invoke(solver, inputArray);
Assert.AreEqual(tempREInfo.Thresholds, biasingParameters.Locales[0].Reactions[0].RareEvents[2].Thresholds);
}
public void TestSolve()
{
const string configString = @"{""solver"":""SDWSSA"",""prng_seed"":123, ""prng_index"":1,""RNG"":{""type"":""PSEUDODES""},""sdwSSA"":{""biasingParametersFileName"":""resources\\rever_isom_CEinfo.json""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
RunResetRNGFactory();
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 100000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
solver.Solve();
var trajectoryCounter = GetHiddenField <int>("_trajectoryCounter", solver);
var runningMean = GetHiddenField <double>("_runningMean", solver);
var runningVariance = GetHiddenField <double>("_runningVariance", solver);
Assert.AreEqual(100000, trajectoryCounter);
Assert.AreEqual(0.000011777283310510327, runningMean);
Assert.AreEqual(0.00017388263350241653, runningVariance);
}
public void TestCheckParameters7()
{
const string configString = @"{""solver"":""SDWSSA"",""sdwSSA"":{""reExpressionName"":""reExpNameCustom""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 1000000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
var method = GetHiddenMethod("CheckParameters", solver);
try
{
method.Invoke(solver, null);
Assert.Fail("CheckParameters should have thrown an Error");
}
catch (TargetInvocationException ex)
{
Assert.That(ex.GetBaseException().ToString(), Is.StringContaining("rare event expression field"));
}
}
public void TestUpdateBiasingParameters()
{
const string configString = @"{""solver"":""SDWSSA"", ""sdwSSA"":{""crossEntropyThreshold"":0.005, ""crossEntropyRuns"":1000000, ""biasingParametersFileName"":""resources\\rever_isom_CEinfo.json""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 1000000;
const int samples = 1;
var solver = new sdwSSA(modelInfo, duration, repeats, samples);
var gammaInfo = new StateDependentGammaInfo(2, 10, 20);
var method = GetHiddenMethod("UpdateBiasingParameters", solver);
var inputObjectArray = new object[2];
inputObjectArray[0] = gammaInfo;
inputObjectArray[1] = 35;
method.Invoke(solver, inputObjectArray);
var biasingParameters = GetHiddenField <BiasingParameters>("_biasingParameters", solver);
Assert.AreEqual(35, biasingParameters.RareEvent.Thresholds[2]);
}
public static ISolver CreateSolver(string solverName, ModelInfo model, int repeats, double duration, int samples)
{
ISolver solver;
switch (solverName.ToUpper())
{
/*
* SSA and variants
*/
case "SSA":
case "GILLESPIE":
case "GILLESPIEDIRECT":
solver = new Gillespie(model, duration, repeats, samples);
break;
case "FIRST":
case "FIRSTREACTION":
case "GILLESPIEFIRSTREACTION":
solver = new GillespieFirstReaction(model, duration, repeats, samples);
break;
case "NEXT":
case "NEXTREACTION":
case "GIBSONBRUCK":
solver = new GibsonBruck(model, duration, repeats, samples);
break;
case "HYBRID":
solver = new HybridSSA(model, duration, repeats, samples);
break;
/*
* Leaping solvers
*/
case "TAU":
case "TAULEAPING":
solver = new TauLeaping(model, duration, repeats, samples);
break;
case "MID":
case "MP":
case "MIDPOINT":
solver = new MidPoint(model, duration, repeats, samples);
break;
case "R":
case "RLEAPING":
solver = new RLeaping(model, duration, repeats, samples);
break;
case "RF":
case "RFAST":
case "RLEAPINGFAST":
solver = new RLeapingFast(model, duration, repeats, samples);
break;
case "BLEAP":
case "BLEAPING":
case "B":
solver = new BLeaping(model, duration, repeats, samples);
break;
/*
* Diffusion/migration solvers
*/
case "TSSA":
case "TRANSPORTSSA":
case "DIFFUSIONSSA":
case "ISSA":
solver = new TransportSSA(model, duration, repeats, samples);
break;
case "DFSP":
case "DIFFUSIONFSP":
case "TRANSPORTFSP":
solver = new DFSP(model, duration, repeats, samples);
break;
case "DFSPPRIME":
case "OTSSA":
case "OPTIMALTRANSPORTSSA":
solver = new OptimalTransportSSA(model, duration, repeats, samples);
break;
case "LEVY":
case "LEVYFLIGHT":
case "FRACTIONAL":
case "FRACTIONALDIFFUSION":
case "FD":
solver = new FractionalDiffusion(model, duration, repeats, samples);
break;
/*
* Specialty solvers
*/
case "ET":
case "EXITTIME":
case "EXITTIMES":
case "TS":
case "TIMESTRETCHING":
solver = new ExitTimes(model, duration, repeats, samples);
break;
case "DWSSA":
solver = new dwSSA(model, duration, repeats, samples);
break;
case "SDWSSA":
solver = new sdwSSA(model, duration, repeats, samples);
break;
default:
Console.Error.WriteLine("Unknown solver selection '{0}'.", solverName);
throw new ArgumentException(string.Format("Unknown solver '{0}'", solverName), "solverName");
}
return(solver);
}
