public void TestSelectAndFireReaction()
{
const string configString = @"{""solver"":""DWSSA"", ""prng_seed"":123, ""prng_index"":1, ""RNG"":{""type"":""PSEUDODES""}, ""dwSSA"":{""crossEntropyThreshold"":0.005, ""crossEntropyRuns"":100000, ""reExpressionName"":""reExpression"", ""reValName"":""reVal"", ""gamma"":[2.0, 0.5]}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
RunResetRNGFactory();
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 1;
const int samples = 1;
var solver = new dwSSA(modelInfo, duration, repeats, samples);
solver.Initialize();
var startRealization = GetHiddenMethod("StartRealization", solver);
startRealization.Invoke(solver, null);
var method = solver.GetType().GetMethod("SelectAndFireReaction", BindingFlags.NonPublic | BindingFlags.Instance, Type.DefaultBinder, new[] { typeof(double) }, null);
var inputArray1 = new object[] { 1.5 };
method.Invoke(solver, inputArray1);
var reactions = GetHiddenField <ReactionSet>("_reactions", solver);
Assert.AreEqual(reactions.Reactions[0].Reactants[0].Value, 99);
}
public void TestSetRareEventType()
{
const string configString = @"{""solver"":""DWSSA"",""dwSSA"":{""gamma"": [1, 1]}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const float duration = 10.0f;
const int repeats = 100000;
const int samples = 1;
var solver = new dwSSA(modelInfo, duration, repeats, samples);
solver.Initialize();
var method = FindMethod("SetRareEventType", typeof(dwSSA));
method.Invoke(solver, null);
var reExpression = GetHiddenField <Expression>("_reExpression", solver);
var reEventValue = GetHiddenField <float>("_rareEventValue", solver);
Assert.AreEqual(0, reExpression.Value);
Assert.AreEqual(30.0f, reEventValue);
Assert.AreEqual(1, GetHiddenField <int>("_rareEventType", solver));
}
public void CheckParametersTest()
{
var configString = @"{""solver"":""Tau"",""tau-leaping"":{""epsilon"": -1}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
var modelInfo = EmodlLoader.LoadEMODLFile("resources//testmodelTau.emodl");
const double duration = 6.28318531;
const int repeats = 42;
const int samples = 100;
try
{
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
Assert.Fail();
}
catch (ApplicationException ex)
{
Assert.That(ex.GetBaseException().ToString(), Is.StringContaining("Epsilon was set to less than or equal to zero."));
}
configString = @"{""solver"":""Tau"",""tau-leaping"":{""Nc"": -1}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
try
{
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
Assert.Fail();
}
catch (ApplicationException ex)
{
Assert.That(ex.GetBaseException().ToString(), Is.StringContaining("Nc was et to less than zero or equal to zero."));
}
configString = @"{""solver"":""Tau"",""tau-leaping"":{""Multiple"": -1}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
try
{
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
Assert.Fail();
}
catch (ApplicationException ex)
{
Assert.That(ex.GetBaseException().ToString(), Is.StringContaining("Multiple was set to less than or equal to zero."));
}
configString = @"{""solver"":""Tau"",""tau-leaping"":{""SSARuns"": 0}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
try
{
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
Assert.Fail();
}
catch (ApplicationException ex)
{
Assert.That(ex.GetBaseException().ToString(), Is.StringContaining("SSAruns was set to less than one."));
}
}
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 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 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 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 });
}
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 TestSolveOnce()
{
const string configString = @"{""solver"":""DWSSA"",""prng_seed"":123, ""prng_index"":1,""RNG"":{""type"":""PSEUDODES""},""dwSSA"":{""reExpressionName"":""reExpression"", ""reValName"":""reVal"", ""gamma"":[1, 1]}}";
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 dwSSA(modelInfo, duration, repeats, samples);
solver.Initialize();
var method = solver.GetType().GetMethod("SolveOnce", BindingFlags.NonPublic | BindingFlags.Instance, Type.DefaultBinder, new Type[] { }, null);
method.Invoke(solver, null);
var trajectoryCounter = GetHiddenField <int>("_trajectoryCounter", solver);
var runningMean = GetHiddenField <double>("_runningMean", solver);
var currentTime = GetHiddenField <double>("_currentTime", solver);
Assert.AreEqual(1, trajectoryCounter);
Assert.AreEqual(0.0, runningMean);
Assert.GreaterOrEqual(currentTime, duration);
}
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 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 static ModelInfo LoadModel(String modelFileName)
{
ModelInfo model;
var modelFileInfo = new FileInfo(modelFileName);
switch (modelFileInfo.Extension.ToUpper().Substring(1))
{
case "CMDL":
throw new NotSupportedException("CMDL support not present.");
case "EMODL":
model = EmodlLoader.LoadEMODLFile(modelFileName);
break;
case "SBML":
case "XML":
throw new NotSupportedException("SBML [XML] support not yet present.");
case "BNGL":
throw new NotSupportedException("BNGL support not yet present.");
default:
Console.Error.WriteLine("Unknown model description language for '{0}'", modelFileName);
throw new ArgumentException($"Unknown model description language for '{modelFileName}'", nameof(modelFileName));
}
return(model);
}
private static TauLeaping DefaultSetupForCalculateProposedTauTests(out Model model,
out MethodInfo calculateProposedTauMethod, out MethodInfo resetModelStateMethod)
{
////// /Setup the test /////////
const string configString = @"{""solver"":""Tau"",""prng_seed"":123, ""prng_index"":1,""RNG"":{""type"":""PSEUDODES""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources//testmodelTau.emodl");
const double duration = 6.28318531;
const int repeats = 42;
const int samples = 100;
ReflectionUtility.RunResetRngFactory();
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
//Find Hidden Method to in order to initialize the population of each of the species
resetModelStateMethod = ReflectionUtility.GetHiddenMethod("ResetModelState", solver);
resetModelStateMethod.Invoke(solver, null);
//Find the model object
model = ReflectionUtility.GetHiddenField <Model>("model", solver);
//Find the method
calculateProposedTauMethod = ReflectionUtility.GetHiddenMethod("CalculateProposedTau", solver);
return(solver);
}
private static MidPoint InstantiateSolver()
{
const string configString = @"{""solver"":""MID""}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources//testmodel.emodl");
var solver = new MidPoint(modelInfo, 6.28318531f, 42, 100);
return(solver);
}
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 TestToString()
{
const string configString = @"{""solver"":""Tau""}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources\\testmodel.emodl");
const double duration = 6.28318531;
const int repeats = 42;
const int samples = 100;
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
Assert.AreEqual("Tau-Leaping", solver.ToString());
}
public void TestToString()
{
const string configString = @"{""solver"":""MID""}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources\\testmodel.emodl");
const float duration = 6.28318531f;
const int repeats = 42;
const int samples = 100;
var solver = new MidPoint(modelInfo, duration, repeats, samples);
Assert.AreEqual("Mid-Point", solver.ToString());
}
public void GillespieTauTest()
{
////// /Setup the test /////////
const string configString = @"{""solver"":""Tau"",""prng_seed"":123, ""prng_index"":1,""RNG"":{""type"":""PSEUDODES""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources//testmodelTau.emodl");
const double duration = 6.28318531;
const int repeats = 42;
const int samples = 100;
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
//Find the method
MethodInfo gillespieTauMethod = ReflectionUtility.GetHiddenMethod("GillespieTau", solver);
//No need to test a0 = 0, since the method is only called when a0 != 0.
// a0 != 0
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("rng", solver, RNGFactory.GetRNG());
var inputArray = new object[1];
inputArray[0] = 1;
var tauOut1 = gillespieTauMethod.Invoke(solver, inputArray);
Assert.That(tauOut1, Is.EqualTo(0.21309720500123394));
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("rng", solver, RNGFactory.GetRNG());
inputArray[0] = 100;
var tauOut2 = gillespieTauMethod.Invoke(solver, inputArray);
Assert.That(tauOut2, Is.EqualTo(0.0021309720500123394));
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("rng", solver, RNGFactory.GetRNG());
inputArray[0] = 0.001;
var tauOut3 = gillespieTauMethod.Invoke(solver, inputArray);
Assert.That(tauOut3, Is.EqualTo(213.09720500123393));
}
public void TestCatchNaNPropensityTauLeaping()
{
const string configString = @"{""solver"":""TauLeaping""}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources\\nanpropensity.emodl");
const double duration = 6.28318531;
const int repeats = 42;
const int samples = 100;
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
solver.Solve();
Assert.Fail("Execution should fail on reaction propensity evaluates to NaN.");
}
public void TestCatchInfinitePropensityNextReaction()
{
const string configString = @"{""solver"":""NextReaction""}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources\\infinitepropensity.emodl");
const double duration = 6.28318531;
const int repeats = 42;
const int samples = 100;
var solver = new GibsonBruck(modelInfo, duration, repeats, samples);
solver.Solve();
Assert.Fail("Execution should fail on reaction propensity evaluates to infinity.");
}
public void TestCatchNegativePropensityHybridSsa()
{
const string configString = @"{""solver"":""Hybrid""}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources\\negativepropensity.emodl");
const double duration = 6.28318531;
const int repeats = 42;
const int samples = 100;
var solver = new HybridSSA(modelInfo, duration, repeats, samples);
solver.Solve();
Assert.Fail("Execution should fail on negative reaction propensity.");
}
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 ComputeLMoreThanOneReactantTest()
{
// Need to access the RHS of the or boolean (tempmin > tempminproposed))
// In order to do that I need more than one species in the reactants list
////// /Setup the test /////////
const string configString = @"{""solver"":""TAU""}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
var modelInfo = EmodlLoader.LoadEMODLFile("resources//testmodelTau3.emodl");
const double duration = 6.28318531;
const int repeats = 42;
const int samples = 100;
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
//Find Hidden Method to in order to initialize the population of each of the species
var resetModelStateMethod = ReflectionUtility.GetHiddenMethod("ResetModelState", solver);
resetModelStateMethod.Invoke(solver, null);
//Find the model object
var model = ReflectionUtility.GetHiddenField <Model>("model", solver);
//Find the method
var computeLMethod = ReflectionUtility.GetHiddenMethod("ComputeL", solver);
var criticalReactions = new List <Reaction>();
var nonCriticalReactions = new List <Reaction>();
//ComputeL(out List<Reaction> criticalReactions, out List<Reaction> nonCriticalReactions, int nc)
// All noncritical
var inputArray = new object[3];
inputArray[0] = criticalReactions;
inputArray[1] = nonCriticalReactions;
inputArray[2] = 2;
computeLMethod.Invoke(solver, inputArray);
Assert.AreEqual(criticalReactions, inputArray[0]);
Assert.AreEqual(model.Reactions, inputArray[1]);
}
public void SolverFactoryTest()
{
var model = EmodlLoader.LoadEMODLModel(_sirModel);
ISolver solver = SolverFactory.CreateSolver("SSA", model, 1, 2.0, 3);
Assert.IsTrue(solver is Gillespie);
solver = SolverFactory.CreateSolver("FIRST", model, 1, 2.0, 3);
Assert.IsTrue(solver is GillespieFirstReaction);
solver = SolverFactory.CreateSolver("NEXT", model, 1, 2.0, 3);
Assert.IsTrue(solver is GibsonBruck);
solver = SolverFactory.CreateSolver("HYBRID", model, 1, 2.0, 3);
Assert.IsTrue(solver is HybridSSA);
solver = SolverFactory.CreateSolver("TAU", model, 1, 2.0, 3);
Assert.IsTrue(solver is TauLeaping);
solver = SolverFactory.CreateSolver("MID", model, 1, 2.0, 3);
Assert.IsTrue(solver is MidPoint);
solver = SolverFactory.CreateSolver("R", model, 1, 2.0, 3);
Assert.IsTrue(solver is RLeaping);
solver = SolverFactory.CreateSolver("RFAST", model, 1, 2.0, 3);
Assert.IsTrue(solver is RLeapingFast);
solver = SolverFactory.CreateSolver("BLEAP", model, 1, 2.0, 3);
Assert.IsTrue(solver is BLeaping);
solver = SolverFactory.CreateSolver("TSSA", model, 1, 2.0, 3);
Assert.IsTrue(solver is TransportSSA);
solver = SolverFactory.CreateSolver("DFSP", model, 1, 2.0, 3);
Assert.IsTrue(solver is DFSP);
solver = SolverFactory.CreateSolver("OTSSA", model, 1, 2.0, 3);
Assert.IsTrue(solver is OptimalTransportSSA);
/* Fractional diffusion solver doesn't handle single node models gracefully.
* solver = SolverFactory.CreateSolver("LEVY", model, 1, 2.0, 3);
* Assert.IsTrue(solver is FractionalDiffusion);
*/
/* Exit times solver doesn't handle missing target condition gracefully.
* solver = SolverFactory.CreateSolver("EXITTIMES", model, 1, 2.0, 3);
* Assert.IsTrue(solver is ExitTimes);
*/
/* dwSSA solver automatically starts solving
* Configuration.CurrentConfiguration = Configuration.ConfigurationFromString("{\"dwSSA\":{\"re_name\":\"I\",\"re_val\":500}}");
* solver = SolverFactory.CreateSolver("DWSSA", model, 1, 2.0, 3);
* Assert.IsTrue(solver is dwSSA);
*/
}
public void TestMidPointConstructorWithDefaults()
{
const string configString = @"{""solver"":""MID""}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources\\testmodel.emodl");
const double duration = 6.28318531;
const int repeats = 42;
const int samples = 100;
var solver = new MidPoint(modelInfo, duration, repeats, samples);
Assert.AreEqual(0.01, ReflectionUtility.GetHiddenField <double>("epsilon", solver));
Assert.AreEqual(2, ReflectionUtility.GetHiddenField <int>("nc", solver));
Assert.AreEqual(10, ReflectionUtility.GetHiddenField <int>("multiple", solver));
Assert.AreEqual(100, ReflectionUtility.GetHiddenField <int>("SSAruns", solver));
string regimeName = ReflectionUtility.GetSolverRegimeName(solver);
Assert.AreEqual("Leaping", regimeName);
}
public void TestMidPointConstructor()
{
const string configString = @"{""solver"":""MID"",""midpoint"":{""epsilon"":0.02,""Nc"":3,""Multiple"":8,""SSARuns"":50}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources\\testmodel.emodl");
const float duration = 6.28318531f;
const int repeats = 42;
const int samples = 100;
var solver = new MidPoint(modelInfo, duration, repeats, samples);
Assert.AreEqual(0.02f, ReflectionUtility.GetHiddenField <float>("epsilon", solver));
Assert.AreEqual(3, ReflectionUtility.GetHiddenField <int>("nc", solver));
Assert.AreEqual(8, ReflectionUtility.GetHiddenField <int>("multiple", solver));
Assert.AreEqual(50, ReflectionUtility.GetHiddenField <int>("SSAruns", solver));
string regimeName = ReflectionUtility.GetSolverRegimeName(solver);
Assert.AreEqual("Leaping", regimeName);
}
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 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 ComputeNonlinearModelJacobianTest()
{
//0. Setup
const string configString = @"{""solver"":""TAU""}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources//testmodelTau2.emodl");
const double duration = 6.28318531;
const int repeats = 42;
const int samples = 100;
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
//Find Hidden Method to in order to initialize the population of each of the species
MethodInfo resetModelStateMethod = ReflectionUtility.GetHiddenMethod("ResetModelState", solver);
resetModelStateMethod.Invoke(solver, null);
//Find the model object
var model = ReflectionUtility.GetHiddenField <Model>("model", solver);
//Find methods
MethodInfo computeJacobianMethod = ReflectionUtility.GetHiddenMethod("ComputeJacobian", solver);
//Set currentRates
double[] currentRates = new double[2];
currentRates[0] = model.Reactions[0].Rate;
currentRates[1] = model.Reactions[1].Rate;
ReflectionUtility.SetHiddenField("_currentRates", solver, currentRates);
//Test Function
var jacobian = computeJacobianMethod.Invoke(solver, null);
double[,] check = new double[2, 2];
check[0, 0] = 4.0;
check[0, 1] = 10.0;
check[1, 0] = 2.0;
check[1, 1] = 5.0;
Assert.AreEqual(check, jacobian);
}
private static dwSSA SetupCrossEntropy()
{
const string configString =
@"{""solver"":""DWSSA"", ""prng_seed"":123, ""prng_index"":1, ""RNG"":{""type"":""PSEUDODES""}, ""dwSSA"":{""gamma"":[1, 1]}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
RunResetRNGFactory();
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom.emodl");
const double duration = 10.0;
const int repeats = 1;
const int samples = 1;
var solver = new dwSSA(modelInfo, duration, repeats, samples);
solver.Initialize();
var startRealization = GetHiddenMethod("StartRealization", solver);
startRealization.Invoke(solver, null);
return(solver);
}
