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 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 double duration = 10.0;
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 <double>("_rareEventValue", solver);
Assert.AreEqual(0, reExpression.Value);
Assert.AreEqual(30.0, reEventValue);
Assert.AreEqual(1, GetHiddenField <int>("_rareEventType", solver));
}
private static dwSSA InstantiateSolver()
{
const string configString = @"{""solver"":""DWSSA"",""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 dwSSA(modelInfo, 10.0, 1000000, 1);
return(solver);
}
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);
}
public void TestInitialize()
{
const string configString = @"{""solver"":""DWSSA"", ""dwSSA"":{""gamma"":[1.0, 1.0]}}";
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 dwSSA(modelInfo, duration, repeats, samples);
solver.Initialize();
var rareEventValue = GetHiddenField <double>("_rareEventValue", solver);
var reExpression = GetHiddenField <Expression>("_reExpression", solver);
Assert.AreEqual(30.0, rareEventValue);
Assert.AreEqual(0.0, reExpression.Value);
}
private static dwSSA StartStepOnce()
{
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 float duration = 10.0f;
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);
}
public void TestSolve()
{
const string configString = @"{""solver"":""DWSSA"",""prng_seed"":123, ""prng_index"":1,""RNG"":{""type"":""PSEUDODES""},""dwSSA"":{ ""reExpressionName"":""reExpression"", ""reValName"":""reVal"", ""gamma"":[1.3243964798992824, 0.73112035859010072 ]}}";
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 dwSSA(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(1.0419565264447506E-05d, runningMean);
Assert.AreEqual(0.022171169128369424d, runningVariance);
}
public void TestCheckParameters6()
{
const string configString = @"{""solver"":""DWSSA"",""dwSSA"":{""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 dwSSA(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 TestdwSSAConstructor()
{
const string configString = @"{""solver"":""DWSSA"", ""dwSSA"": { ""crossEntropyThreshold"":0.005, ""crossEntropyRuns"":1000000, ""reExpressionName"":""reExpNameCustom"", ""reValName"":""reValNameCustom"", ""outputFileName"":""rever_isom_dwSSA_1e6_Custom.txt"", ""gamma"":[1.0, 1.0]}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
var modelInfo = EmodlLoader.LoadEMODLFile("resources\\rever_isom_custom.emodl");
const double duration = 20.0;
const int repeats = 222;
const int samples = 2;
var solver = new dwSSA(modelInfo, duration, repeats, samples);
Assert.AreEqual(0, GetHiddenField <int>("_trajectoryCounter", solver));
Assert.AreEqual(0.0, GetHiddenField <double>("_runningMean", solver));
Assert.AreEqual(0.0, GetHiddenField <double>("_runningVariance", solver));
Assert.AreEqual(1000000, GetHiddenField <int>("_crossEntropyRuns", solver));
Assert.AreEqual(0.005, GetHiddenField <double>("_crossEntropyThreshold", solver));
Assert.AreEqual(200, GetHiddenField <int>("_crossEntropyMinDataSize", solver));
Assert.AreEqual("reExpNameCustom", GetHiddenField <string>("_reExpressionName", solver));
Assert.AreEqual("reValNameCustom", GetHiddenField <string>("_reValName", solver));
Assert.AreEqual(0.0, GetHiddenField <double>("_rareEventValue", solver));
Assert.AreEqual("rever_isom_dwSSA_1e6_Custom.txt", GetHiddenField <string>("_outputFileName", solver));
var expression = GetHiddenField <Expression>("_reExpression", solver);
Assert.AreEqual("reExpNameCustom", expression.Name);
var equalto = GetHiddenField <EqualTo>("_rareEventTest", solver);
Assert.AreEqual(true, equalto.Value);
var gamma = GetHiddenField <double[]>("_gamma", solver);
Assert.That(gamma, Is.All.EqualTo(1.0));
var reactions = GetHiddenField <ReactionSet>("_reactions", solver);
Assert.AreEqual(gamma.Length, reactions.NumReactions);
}
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);
}
