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."));
}
}
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);
}
public static string GetSolverRegimeName(TauLeaping solver)
{
var regimeType = typeof(TauLeaping).GetNestedType("Regime", BindingFlags.NonPublic);
var regime = GetHiddenField <int>("_regime", solver);
var regimeName = regimeType.GetEnumName(regime);
return(regimeName);
}
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 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 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 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);
}
public void TauLeapingConstructorDefaultTest()
{
const string configString = @"{""solver"":""Tau"",""prng_seed"":123, ""prng_index"":1,""RNG"":{""type"":""PSEUDODES""}}";
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(0.001, 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);
double[] currentRates = ReflectionUtility.GetHiddenField <double[]>("_currentRates", solver);
Assert.AreEqual(15, currentRates.Length);
}
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);
}
public void FireCriticalReactionTest()
{
////// /Setup the test /////////
const string configString = @"{""solver"":""TAU""}";
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;
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
//Find the model object
var model = ReflectionUtility.GetHiddenField <Model>("model", solver);
//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);
var updateAndSumRatesMethod = ReflectionUtility.GetHiddenMethod("UpdateAndSumRates", solver);
var currentRates = ReflectionUtility.GetHiddenField <double[]>("_currentRates", solver);
//Find the method
var fireCriticalReactionMethod = ReflectionUtility.GetHiddenMethod("FireCriticalReaction", solver);
//Find a0 update currentRates.
var inputArrayForUpdate = new object[2];
inputArrayForUpdate[0] = model.Reactions;
inputArrayForUpdate[1] = currentRates;
var a0 = updateAndSumRatesMethod.Invoke(solver, inputArrayForUpdate);
currentRates = ReflectionUtility.GetHiddenField <double[]>("_currentRates", solver);
//Define inputs for method Here there is one reaction
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("rng", solver, RNGFactory.GetRNG());
var inputArray = new object[3];
var criticalReactions = new List <Reaction>();
criticalReactions.Add(model.Reactions[0]);
var criticalRates = new double[1];
criticalRates[0] = currentRates[0];
inputArray[0] = criticalReactions;
inputArray[1] = criticalRates;
inputArray[2] = criticalRates[0];
fireCriticalReactionMethod.Invoke(solver, inputArray);
Assert.AreEqual(6, model.Species[0].Count);
Assert.AreEqual(1, model.Species[1].Count);
//Define inputs for method Here there is for two reactions
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("rng", solver, RNGFactory.GetRNG());
resetModelStateMethod.Invoke(solver, null);
inputArray = new object[3];
criticalReactions = new List <Reaction>();
criticalReactions.Add(model.Reactions[0]);
criticalReactions.Add(model.Reactions[1]);
criticalRates = new double[2];
criticalRates[0] = currentRates[0];
criticalRates[1] = currentRates[1];
inputArray[0] = criticalReactions;
inputArray[1] = criticalRates;
inputArray[2] = a0;
fireCriticalReactionMethod.Invoke(solver, inputArray);
Assert.AreEqual(6, model.Species[0].Count);
Assert.AreEqual(1, model.Species[1].Count);
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("rng", solver, RNGFactory.GetRNG());
resetModelStateMethod.Invoke(solver, null);
inputArray = new object[3];
criticalReactions = new List <Reaction>();
criticalReactions.Add(model.Reactions[0]);
criticalReactions.Add(model.Reactions[1]);
criticalRates = new double[2];
criticalRates[0] = currentRates[0];
criticalRates[1] = currentRates[1];
inputArray[0] = criticalReactions;
inputArray[1] = criticalRates;
inputArray[2] = a0;
fireCriticalReactionMethod.Invoke(solver, inputArray);
Assert.AreEqual(6, model.Species[0].Count);
Assert.AreEqual(1, model.Species[1].Count);
}
public void GillespieReactionTest()
{
////// /Setup the test /////////
const string configString = @"{""solver"":""TAU""}";
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;
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
//Find the model object
var model = ReflectionUtility.GetHiddenField <Model>("model", solver);
//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);
var updateAndSumRatesMethod = ReflectionUtility.GetHiddenMethod("UpdateAndSumRates", solver);
var currentRates = ReflectionUtility.GetHiddenField <double[]>("_currentRates", solver);
//Find the method
var gillespieReactionMethod = ReflectionUtility.GetHiddenMethod("GillespieReaction", solver);
//Test for one value of a0
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("rng", solver, RNGFactory.GetRNG());
var inputArray = new object[1];
inputArray[0] = 0.01;
var reactionOut = gillespieReactionMethod.Invoke(solver, inputArray);
Assert.That(reactionOut, Is.EqualTo(model.Reactions[0]));
//Test for an actual a0 from the model file.
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("rng", solver, RNGFactory.GetRNG());
var inputArrayForUpdate = new object[2];
inputArrayForUpdate[0] = model.Reactions;
inputArrayForUpdate[1] = currentRates;
var a0 = updateAndSumRatesMethod.Invoke(solver, inputArrayForUpdate);
inputArray[0] = a0;
var reactionOut2 = gillespieReactionMethod.Invoke(solver, inputArray);
Assert.That(reactionOut2, Is.EqualTo(model.Reactions[0]));
//Test for a changed a0 and rate parameter
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("rng", solver, RNGFactory.GetRNG());
model.Parameters[3].Value = 10.0;
currentRates = ReflectionUtility.GetHiddenField <double[]>("_currentRates", solver);
inputArrayForUpdate[1] = currentRates;
a0 = updateAndSumRatesMethod.Invoke(solver, inputArrayForUpdate);
inputArray[0] = a0;
var reactionOut3 = gillespieReactionMethod.Invoke(solver, inputArray);
Assert.That(reactionOut3, Is.EqualTo(model.Reactions[1]));
}
public void ComputeLTest()
{
////// /Setup the test /////////
const string configString = @"{""solver"":""TAU""}";
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;
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]);
//Please note the above assertions. Since the method has "out" properties the object[] inputArray is
// modified by ComputeLMethod.Invoke. This is used below as well.
//3. Both critical
resetModelStateMethod.Invoke(solver, null);
model.Species[0].Count = 3;
model.Species[1].Count = 2;
criticalReactions = new List <Reaction>();
nonCriticalReactions = new List <Reaction>();
inputArray[0] = criticalReactions;
inputArray[1] = nonCriticalReactions;
inputArray[2] = 10;
computeLMethod.Invoke(solver, inputArray);
Assert.AreEqual(nonCriticalReactions, inputArray[1]);
Assert.AreEqual(model.Reactions, inputArray[0]);
// One critical, one noncritical.
resetModelStateMethod.Invoke(solver, null);
model.Species[0].Count = 200;
model.Species[1].Count = 2;
criticalReactions = new List <Reaction>();
nonCriticalReactions = new List <Reaction>();
inputArray[0] = criticalReactions;
inputArray[1] = nonCriticalReactions;
inputArray[2] = 10;
computeLMethod.Invoke(solver, inputArray);
var singleReactionList1 = new List <Reaction>();
var singleReactionList2 = new List <Reaction>();
singleReactionList1.Add(model.Reactions[0]);
singleReactionList2.Add(model.Reactions[1]);
Assert.AreEqual(singleReactionList1, inputArray[0]);
Assert.AreEqual(singleReactionList2, inputArray[1]);
}
public void FireNonCriticalReactionsTest()
{
const string configString = @"{""solver"":""Tau"",""prng_seed"":123, ""prng_index"":1,""RNG"":{""type"":""PSEUDODES""}}";
Configuration.CurrentConfiguration = Configuration.ConfigurationFromString(configString);
ModelInfo modelInfo = EmodlLoader.LoadEMODLFile("resources\\testmodelMidPoint.emodl");
const double duration = 6.28318531;
const int repeats = 42;
const int samples = 100;
var solver = new TauLeaping(modelInfo, duration, repeats, samples);
//Inputs for the method
// Tau Step
double tau1 = 0.0;
var tau2 = (1.0 / 200.0);
//Need a list of reactions
var currentRates = new double[1];
var nonCriticalReaction = new List <Reaction>();
//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);
MethodInfo updateAndSumRatesMethod = ReflectionUtility.GetHiddenMethod("UpdateAndSumRates", solver);
//Find the model object
var model = ReflectionUtility.GetHiddenField <Model>("model", solver);
currentRates[0] = model.Reactions[0].Rate;
nonCriticalReaction.Add(model.Reactions[0]);
object[] inputArray1 = new object[3];
inputArray1[0] = tau1; inputArray1[1] = nonCriticalReaction; inputArray1[2] = currentRates;
object[] inputArray2 = new object[3];
inputArray2[0] = tau2; inputArray2[1] = nonCriticalReaction; inputArray2[2] = currentRates;
//Find Hidden Method.
MethodInfo fireNonCriticalReactionsMethod = ReflectionUtility.GetHiddenMethod("FireNonCriticalReactions", solver);
// First Test if Tau = 0;
fireNonCriticalReactionsMethod.Invoke(solver, inputArray1);
Assert.AreEqual(400, model.Species[0].Value);
Assert.AreEqual(200, model.Species[1].Value);
Assert.AreEqual(900, model.Species[2].Value);
//Second Test if Tau = = 0.05. Set the RNG to a known seed number, in order to exactly know what is generated
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("_distributionSampler", solver, RandLibSampler.CreateRandLibSampler(RNGFactory.GetRNG()));
fireNonCriticalReactionsMethod.Invoke(solver, inputArray2);
Assert.AreEqual(384.0, model.Species[0].Value);
Assert.AreEqual(184.0, model.Species[1].Value);
Assert.AreEqual(916.0, model.Species[2].Value);
resetModelStateMethod.Invoke(solver, null);
object[] inputArray3 = new object[2];
inputArray3[0] = model.Reactions; inputArray3[1] = currentRates;
updateAndSumRatesMethod.Invoke(solver, inputArray3);
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("_distributionSampler", solver, RandLibSampler.CreateRandLibSampler(RNGFactory.GetRNG()));
fireNonCriticalReactionsMethod.Invoke(solver, inputArray2);
Assert.AreEqual(384.0, model.Species[0].Value);
Assert.AreEqual(184.0, model.Species[1].Value);
Assert.AreEqual(916.0, model.Species[2].Value);
}
public void ComputeTauTest()
{
//0. Setup
const string configString = @"{""solver"":""TAU""}";
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 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 computeTauMethod = ReflectionUtility.GetHiddenMethod("ComputeTau", solver);
MethodInfo updateAndSumRatesMethod = ReflectionUtility.GetHiddenMethod("UpdateAndSumRates", solver);
var jacobian = new double[2, 2];
var subreactions = new List <Reaction>();
double epsilon;
epsilon = 0.1;
subreactions.Add(model.Reactions[0]);
subreactions.Add(model.Reactions[1]);
var currentRates = new double[2];
currentRates[0] = model.Reactions[0].Rate;
currentRates[1] = model.Reactions[1].Rate;
object[] inputArray = new object[2];
inputArray[0] = subreactions; inputArray[1] = currentRates;
var a0 = updateAndSumRatesMethod.Invoke(solver, inputArray);
jacobian[0, 0] = 2.0;
jacobian[0, 1] = 0.0;
jacobian[1, 0] = 0.0;
jacobian[1, 1] = 1.0;
object[] inputArray2 = new object[4];
inputArray2[0] = jacobian;
inputArray2[1] = epsilon;
inputArray2[2] = a0;
inputArray2[3] = subreactions;
//Test of one model file with two reactions.
var tauOut = computeTauMethod.Invoke(solver, inputArray2);
Assert.AreEqual(0.030000000000000009, tauOut);
//Test of one model file with zero in some input components.
a0 = 0.0;
inputArray2[2] = a0;
tauOut = computeTauMethod.Invoke(solver, inputArray2);
Assert.AreEqual(0.0, tauOut);
updateAndSumRatesMethod.Invoke(solver, inputArray);
inputArray2[1] = 0.0;
tauOut = computeTauMethod.Invoke(solver, inputArray2);
Assert.AreEqual(0.0, tauOut);
}
public void ExecuteReactionsTest()
{
//0. Setup
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 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 the method
MethodInfo executeReactionsMethod = ReflectionUtility.GetHiddenMethod("ExecuteReactions", solver);
//1. ==Regime.SSA
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("_distributionSampler", solver, RandLibSampler.CreateRandLibSampler(RNGFactory.GetRNG()));
ReflectionUtility.SetHiddenField("_regime", solver, 0);
ReflectionUtility.GetHiddenField <Reaction>("_ssaReaction", solver);
//a. _ssaReaction == null;
executeReactionsMethod.Invoke(solver, null);
var regime = ReflectionUtility.GetHiddenField <int>("_regime", solver);
Assert.AreEqual(0, regime);
//b. _ssaReaction != null;
ReflectionUtility.SetHiddenField("_remainingSSAsteps", solver, 1);
ReflectionUtility.SetHiddenField("_ssaReaction", solver, model.Reactions[0]);
ReflectionUtility.RunResetRngFactory();
ReflectionUtility.SetHiddenField("_distributionSampler", solver, RandLibSampler.CreateRandLibSampler(RNGFactory.GetRNG()));
executeReactionsMethod.Invoke(solver, null);
regime = ReflectionUtility.GetHiddenField <int>("_regime", solver);
Assert.AreEqual(3, regime);
Assert.AreEqual(6.0, model.Species[0].Count);
Assert.AreEqual(1.0, model.Species[1].Count);
//2. == Regime.NonCritical
ReflectionUtility.SetHiddenField("_regime", solver, 1);
ReflectionUtility.RunResetRngFactory();
resetModelStateMethod.Invoke(solver, null);
model.Species[0].Count = 100;
model.Species[1].Count = 50;
var nonCriticalReactionsList = new List <Reaction>();
nonCriticalReactionsList.Add(model.Reactions[0]);
nonCriticalReactionsList.Add(model.Reactions[1]);
var nonCriticalRates = new double[2];
nonCriticalRates[0] = model.Reactions[0].Rate;
nonCriticalRates[1] = model.Reactions[1].Rate;
ReflectionUtility.SetHiddenField("_distributionSampler", solver, RandLibSampler.CreateRandLibSampler(RNGFactory.GetRNG()));
ReflectionUtility.SetHiddenField("_leapTau", solver, 0.01);
ReflectionUtility.SetHiddenField("_nonCriticalReactions", solver, nonCriticalReactionsList);
ReflectionUtility.SetHiddenField("_noncriticalRates", solver, nonCriticalRates);
executeReactionsMethod.Invoke(solver, null);
regime = ReflectionUtility.GetHiddenField <int>("_regime", solver);
Assert.AreEqual(3, regime);
Assert.AreEqual(103, model.Species[0].Count);
Assert.AreEqual(47, model.Species[1].Count);
//3. == Regime.Critical ) no noncriticalreactions
ReflectionUtility.SetHiddenField("_regime", solver, 2);
ReflectionUtility.RunResetRngFactory();
resetModelStateMethod.Invoke(solver, null);
model.Species[0].Count = 100;
model.Species[1].Count = 50;
var criticalReactionsList = new List <Reaction>();
criticalReactionsList.Add(model.Reactions[0]);
criticalReactionsList.Add(model.Reactions[1]);
var criticalRates = new double[2];
criticalRates[0] = model.Reactions[0].Rate;
criticalRates[1] = model.Reactions[1].Rate;
MethodInfo updateAndSumRatesMethod = ReflectionUtility.GetHiddenMethod("UpdateAndSumRates", solver);
object[] inputArray1 = new object[2];
inputArray1[0] = criticalReactionsList; inputArray1[1] = criticalRates;
var a0Critical = updateAndSumRatesMethod.Invoke(solver, inputArray1);
ReflectionUtility.SetHiddenField("_distributionSampler", solver, RandLibSampler.CreateRandLibSampler(RNGFactory.GetRNG()));
ReflectionUtility.SetHiddenField("_a0Critical", solver, a0Critical);
ReflectionUtility.SetHiddenField("_criticalReactions", solver, criticalReactionsList);
ReflectionUtility.SetHiddenField("_criticalRates", solver, criticalRates);
ReflectionUtility.SetHiddenField("_nonCriticalReactions", solver, null);
ReflectionUtility.SetHiddenField("_noncriticalRates", solver, null);
executeReactionsMethod.Invoke(solver, null);
regime = ReflectionUtility.GetHiddenField <int>("_regime", solver);
Assert.AreEqual(3, regime);
Assert.AreEqual(101, model.Species[0].Count);
Assert.AreEqual(49, model.Species[1].Count);
//3. == Regime.Critical b) noncriticalreactions and critical reactions
ReflectionUtility.SetHiddenField("_regime", solver, 2);
ReflectionUtility.RunResetRngFactory();
resetModelStateMethod.Invoke(solver, null);
model.Species[0].Count = 100;
model.Species[1].Count = 50;
criticalReactionsList = new List <Reaction>();
nonCriticalReactionsList = new List <Reaction>();
criticalReactionsList.Add(model.Reactions[0]);
nonCriticalReactionsList.Add(model.Reactions[1]);
criticalRates = new double[1];
nonCriticalRates = new double[1];
criticalRates[0] = model.Reactions[0].Rate;
nonCriticalRates[0] = model.Reactions[1].Rate;
inputArray1[0] = criticalReactionsList; inputArray1[1] = criticalRates;
a0Critical = updateAndSumRatesMethod.Invoke(solver, inputArray1);
ReflectionUtility.SetHiddenField("_distributionSampler", solver, RandLibSampler.CreateRandLibSampler(RNGFactory.GetRNG()));
ReflectionUtility.SetHiddenField("_a0Critical", solver, a0Critical);
ReflectionUtility.SetHiddenField("_leapTau", solver, 0.01);
ReflectionUtility.SetHiddenField("_criticalReactions", solver, criticalReactionsList);
ReflectionUtility.SetHiddenField("_criticalRates", solver, criticalRates);
ReflectionUtility.SetHiddenField("_nonCriticalReactions", solver, nonCriticalReactionsList);
ReflectionUtility.SetHiddenField("_noncriticalRates", solver, nonCriticalRates);
executeReactionsMethod.Invoke(solver, null);
regime = ReflectionUtility.GetHiddenField <int>("_regime", solver);
Assert.AreEqual(3, regime);
Assert.AreEqual(100, model.Species[0].Count);
Assert.AreEqual(50, model.Species[1].Count);
//4. == Regime.AnythingElse
ReflectionUtility.SetHiddenField("_regime", solver, 4);
try
{
executeReactionsMethod.Invoke(solver, null);
Assert.Fail();
}
catch (ApplicationException ex)
{
Assert.That(ex.GetBaseException().ToString(), Is.StringContaining("Bad solver mode."));
}
}