private void RunSimulation(CancellationToken cancellationToken)
{
var simulationTime = simulationSettings.SimulationTime;
var dT = simulationSettings.TimeStep;
for (CurrentTime = 0.To(Unit.Second); CurrentTime < simulationTime; CurrentTime += dT)
{
cancellationToken.ThrowIfCancellationRequested();
var compactnessForces = simulationSettings.UseCompactingForce
? compactnessForceCalculator.Calculate(CompactnessMeasurer.Measure(Peptide))
: new Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces>();
var ramachandranForces = simulationSettings.UseRamachandranForce
? ramachandranForceCalculator.Calculate(Peptide)
: new Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces>();
var bondForces = bondForceCalculator.Calculate(Peptide);
foreach (var aminoAcid in Peptide.AminoAcids)
{
var resultingForce = new ApproximateAminoAcidForces();
if (compactnessForces.ContainsKey(aminoAcid))
{
var compactnessForce = compactnessForces[aminoAcid];
resultingForce += compactnessForce;
}
if (ramachandranForces.ContainsKey(aminoAcid))
{
var ramachandranForce = ramachandranForces[aminoAcid];
resultingForce += ramachandranForce;
}
if (bondForces.ContainsKey(aminoAcid))
{
var bondForce = bondForces[aminoAcid];
resultingForce += bondForce;
}
ApplyForce(aminoAcid, resultingForce, dT, simulationSettings.ReservoirTemperature);
}
OnSimulationTimestepComplete(new SimulationTimestepCompleteEventArgs(CurrentTime, Peptide));
}
SimulationCompleted?.Invoke(this, EventArgs.Empty);
IsSimulating = false;
}
/// <summary>
/// Measured time, invokes simulation completed event and logs simulation completed event.
/// Simulation completed message: "Calculated *simulation name* simulation in *measured time*ms".
/// </summary>
/// <param name="schematic">Schematic for which to perform the simulation</param>
/// <param name="simulationLogic">Action that is responsible for performing and saving simulation results</param>
/// <param name="simulationName">Name to use in simulation ended message</param>
/// <param name="simulationType">Type of the simulation, for simulation ended event purposes</param>
private void SimulationRunWrapper(ISchematic schematic, Action <AdmittanceMatrixFactory> simulationLogic, string simulationName,
SimulationType simulationType)
{
// Create a stopwatch to measure the duration of simulation
Stopwatch watch = new Stopwatch();
// Start measuring time
watch.Start();
// Create an admittance matrix factory and use it to invoke passed simulation logic
simulationLogic(new AdmittanceMatrixFactory(schematic));
// Stop time measurement
watch.Stop();
// Invoke simulation completed event
SimulationCompleted?.Invoke(this, new SimulationCompletedEventArgs(simulationType));
// Log the simulation time
IoC.Log("Completed " + simulationName + $" in {watch.ElapsedMilliseconds}ms",
InfoLoggerMessageDuration.Short);
}
/// <summary>
/// Invoked when a job is completed.
/// </summary>
/// <param name="sender">The sender of the event.</param>
/// <param name="e">The event arguments.</param>
private void OnJobCompleted(object sender, JobCompleteArguments e)
{
AddException(e.ExceptionThrowByJob);
SimulationCompleted?.Invoke(this, e);
}
private void OnSimulationFinished()
{
SimulationCompleted?.Invoke(this, EventArgs.Empty);
}
