/// <summary>
/// Creates a new instance of the <see cref="BiasingBehavior"/> class.
/// </summary>
/// <param name="name">The name of the behavior.</param>
public BiasingBehavior(string name, ComponentBindingContext context) : base(name)
{
if (context == null)
{
throw new ArgumentNullException(nameof(context));
}
// Get our resistor parameters (we want our A and B parameter values)
_bp = context.GetParameterSet <BaseParameters>();
// Get the simulation parameters (we want to use Gmin)
_baseConfig = context.GetSimulationParameterSet <BiasingParameters>();
// Request the node variables
var state = context.GetState <IBiasingSimulationState>();
_nodeA = state.GetSharedVariable(context.Nodes[0]);
_nodeB = state.GetSharedVariable(context.Nodes[1]);
// We need 4 matrix elements and 2 RHS vector elements
var indexA = state.Map[_nodeA];
var indexB = state.Map[_nodeB];
_elements = new ElementSet <double>(state.Solver, new[] {
new MatrixLocation(indexA, indexA),
new MatrixLocation(indexA, indexB),
new MatrixLocation(indexB, indexA),
new MatrixLocation(indexB, indexB)
}, new[] { indexA, indexB });
}
public sdwSSA(ModelInfo modelinfo, double duration, int repeats, int samples)
: base(modelinfo, duration, repeats, samples)
{
Configuration config = Configuration.CurrentConfiguration;
_reactions = new StateDependentReactionSet(model.Reactions, _gammaSize);
_trajectoryCounter = 0;
_runningMean = 0.0;
_runningVariance = 0.0;
_crossEntropyRuns = config.GetParameterWithDefault("sdwSSA.crossEntropyRuns", 100000);
_crossEntropyThreshold = config.GetParameterWithDefault("sdwSSA.crossEntropyThreshold", 0.01);
_crossEntropyMinDataSize = config.GetParameterWithDefault("sdwSSA.crossEntropyMinDataSize", 200);
_reExpressionName = config.GetParameterWithDefault("sdwSSA.reExpressionName", "reExpression");
_reValName = config.GetParameterWithDefault("sdwSSA.reValName", "reVal");
_gammaSize = config.GetParameterWithDefault("sdwSSA.gammaSize", 15);
_binCountThreshold = config.GetParameterWithDefault("sdwSSA.binCount", 20);
_reExpression = model.Expressions.FirstOrDefault(e => e.Name == _reExpressionName);
_rareEventValue = 0.0;
_rareEventTest = new EqualTo(_reExpression, new ConstantValue(_rareEventValue));
_gamma = new List <double[]>();
_propensityCutoff = new List <double[]>();
_gammaIndex = new int[_reactions.NumReactions];
_binIndex = new int[_reactions.NumReactions];
_biasingParametersFileName = config.GetParameterWithDefault("sdwSSA.biasingParametersFileName", modelinfo.Name + "_biasingParameters.json");
_biasingParametersFlag = (String.CompareOrdinal(_biasingParametersFileName, modelinfo.Name + "_biasingParameters.json") == 0);
_biasingParameters = _biasingParametersFlag ? new BiasingParameters() : BiasingParametersDeserializer.ReadParametersFromJsonFile(_biasingParametersFileName);
_outputFileName = config.GetParameterWithDefault("sdwSSA.outputFileName", modelInfo.Name + "_sdwSSA_1e" + Math.Log(SamplingParams.RealizationCount, 10) + ".txt");
}
public void BiasingParametersLoadParametersFromNull()
{
// ReSharper disable UnusedVariable
var parameters = BiasingParameters.LoadParametersFromJson(null);
// ReSharper restore UnusedVariable
Assert.Fail("LoadParametersFromJson(null) should throw an ArgumentNullException.");
}
public void BiasingParametersJsonFileBinCountNotCutoffSize()
{
const string inputFile = "resources\\biasing_sample_BIN_COUNT_not_CUTOFF_array_size.json";
// ReSharper disable UnusedVariable
var parameters = BiasingParameters.LoadParametersFromJson(inputFile);
// ReSharper restore UnusedVariable
Assert.Fail("BiasingParametersJsonFileBinCountNotCutoffSize() should throw a System.ArgumentException.");
}
public void BiasingParametersJsonFileIreCountNotRareEventInfoSize()
{
const string inputFile = "resources\\biasing_sample_IRE_COUNT_not_RARE_EVENT_INFO_array_size.json";
// ReSharper disable UnusedVariable
var parameters = BiasingParameters.LoadParametersFromJson(inputFile);
// ReSharper restore UnusedVariable
Assert.Fail("BiasingParametersJsonFileIreCountNotRareEventInfoSize() should throw a System.ArgumentException.");
}
public void BiasingParametersJsonFileReactionCountLessThanReactionArraySize()
{
const string inputFile = "resources\\biasing_sample_REACTION_COUNT_less_than_REACTION_array_size.json";
// ReSharper disable UnusedVariable
var parameters = BiasingParameters.LoadParametersFromJson(inputFile);
// ReSharper restore UnusedVariable
Assert.Fail("BiasingParametersJsonFileReactionCountLessThanReactionArraySize() should throw a System.ArgumentException.");
}
public void BiasingParametersJsonFileMissingIreCountParameter()
{
const string inputFile = "resources\\biasing_sample_IRE_COUNT_missing.json";
// ReSharper disable UnusedVariable
var parameters = BiasingParameters.LoadParametersFromJson(inputFile);
// ReSharper restore UnusedVariable
Assert.Fail("BiasingParametersJsonFileMissingIreCountParameter() should throw a System.ArgumentException.");
}
public void BiasingParametersLoadParametersFromInvalidJson()
{
const string jsonFilename = "resources\\invalid.json";
// ReSharper disable UnusedVariable
var parameters = BiasingParameters.LoadParametersFromJson(jsonFilename);
// ReSharper restore UnusedVariable
Assert.Fail("LoadParametersFromInvalidJson({0}) should throw an ArgumentException.", jsonFilename);
}
public void BiasingParametersConstructor()
{
var parameters = new BiasingParameters();
Assert.AreEqual(string.Empty, parameters.RareEvent.ExpressionLocale);
Assert.AreEqual(string.Empty, parameters.RareEvent.ExpressionName);
Assert.AreEqual(0, parameters.RareEvent.IntermediateRareEventCount);
Assert.IsEmpty(parameters.RareEvent.Thresholds);
Assert.IsEmpty(parameters.Locales);
}
public void BiasingParametersLoadParametersFromMissingFile()
{
string tempFileName = Path.GetTempFileName();
File.Delete(tempFileName);
// ReSharper disable UnusedVariable
var parameters = BiasingParameters.LoadParametersFromJson(tempFileName);
// ReSharper restore UnusedVariable
Assert.Fail("LoadParametersFromMissingFile(tempFileName) should throw an IO.FileNotFoundException.");
}
/// <summary>
/// Initializes a new instance of the <see cref="Biasing"/> class.
/// </summary>
/// <param name="context">The binding context.</param>
/// <exception cref="ArgumentNullException">Thrown if <paramref name="context"/> is <c>null</c>.</exception>
public Biasing(IComponentBindingContext context)
: base(context)
{
var state = context.GetState <IBiasingSimulationState>();
_config = context.GetSimulationParameterSet <BiasingParameters>();
_iteration = context.GetState <IIterationSimulationState>();
_args = new MosfetContributionEventArgs(_contributions);
context.TryGetState(out _time);
context.TryGetState(out _method);
_variables = new MosfetVariables <double>(context, state);
// Get matrix pointers
_elements = new ElementSet <double>(state.Solver,
_variables.GetMatrixLocations(state.Map),
_variables.GetRhsIndices(state.Map));
}
public void BiasingParametersLoadParametersFromJson()
{
const string filename = "resources\\biasing_sample.json";
var parameters = BiasingParameters.LoadParametersFromJson(filename);
// Verify rare event spec
Assert.AreEqual("site_1", parameters.RareEvent.ExpressionLocale);
Assert.AreEqual("reExpression", parameters.RareEvent.ExpressionName);
Assert.AreEqual(2, parameters.RareEvent.IntermediateRareEventCount);
Assert.AreEqual(24, parameters.RareEvent.Thresholds[0]);
Assert.AreEqual(32, parameters.RareEvent.Thresholds[1]);
// Verify locale[s]
Assert.AreEqual(1, parameters.Locales.Count);
var localeInfo = parameters.Locales[0];
Assert.AreEqual("site_1", localeInfo.Name);
Assert.AreEqual(8, localeInfo.ReactionCount);
Assert.AreEqual(8, localeInfo.Reactions.Count);
// Verify first reaction
var reactionInfo = localeInfo.Reactions[0];
Assert.AreEqual("R1", reactionInfo.Name);
Assert.AreEqual(2, reactionInfo.RareEvents.Count);
var rareEventInfo = reactionInfo.RareEvents[0];
Assert.AreEqual(2, rareEventInfo.BinCount);
Assert.AreEqual(2, rareEventInfo.Gammas.Length);
Assert.AreEqual(1, rareEventInfo.Thresholds.Length);
Assert.AreEqual(1.06863, rareEventInfo.Gammas[0]);
Assert.AreEqual(1.56882, rareEventInfo.Gammas[1]);
Assert.AreEqual(0.00031386, rareEventInfo.Thresholds[0]);
// Verify last reaction
reactionInfo = localeInfo.Reactions[localeInfo.ReactionCount - 1];
Assert.AreEqual("R8", reactionInfo.Name);
Assert.AreEqual(2, reactionInfo.RareEvents.Count);
rareEventInfo = reactionInfo.RareEvents[1];
Assert.AreEqual(7, rareEventInfo.BinCount);
Assert.AreEqual(7, rareEventInfo.Gammas.Length);
Assert.AreEqual(6, rareEventInfo.Thresholds.Length);
Assert.AreEqual(2.37130, rareEventInfo.Gammas[0]);
Assert.AreEqual(2.191004, rareEventInfo.Gammas[6]);
Assert.AreEqual(0.3935499, rareEventInfo.Thresholds[5]);
}
/// <summary>
/// Initializes a new instance of the <see cref="Biasing"/> class.
/// </summary>
/// <param name="context">The binding context.</param>
/// <exception cref="ArgumentNullException">Thrown if <paramref name="context"/> is <c>null</c>.</exception>
public Biasing(IComponentBindingContext context)
: base(context)
{
var state = context.GetState <IBiasingSimulationState>();
_config = context.GetSimulationParameterSet <BiasingParameters>();
_iteration = context.GetState <IIterationSimulationState>();
_args = new MosfetContributionEventArgs(_contributions);
context.TryGetState(out _time);
context.TryGetState(out _method);
_variables = new MosfetVariables <double>(Name, state, context.Nodes,
!ModelParameters.DrainResistance.Equals(0.0) || !ModelParameters.SheetResistance.Equals(0.0) && Parameters.DrainSquares > 0,
!ModelParameters.SourceResistance.Equals(0.0) || !ModelParameters.SheetResistance.Equals(0.0) && Parameters.SourceSquares > 0);
// Get matrix pointers
_elements = new ElementSet <double>(state.Solver,
_variables.GetMatrixLocations(state.Map),
_variables.GetRhsIndices(state.Map));
}
public void BiasingParametersWriteParametersToJson()
{
const string inputFile = "resources\\biasing_sample.json";
var parameters = BiasingParameters.LoadParametersFromJson(inputFile);
string outputFile = Path.GetTempFileName();
bool areSame = false;
try
{
Console.WriteLine("Writing biasing parameters to '{0}'...", outputFile);
parameters.WriteParametersToJsonFile(outputFile);
FileAssert.AreEqual(inputFile, outputFile);
areSame = true;
}
finally
{
if (areSame)
{
File.Delete(outputFile);
}
}
}
