public override SimulationResult Simulate()
{
// initial energy
Elast = ForceAndTorque();
CheckForClashes(true);
Elast += Eclash;
int ntotal = 0; // current number of iterations
int nsuccessfull = 0; // number of successfull iterations
//const int nsuccessfull_max = 2000; // required number of successfull iterations between snapshots
// simulate: main loop
do
{
nsuccessfull += this.Iterate() ? 1 : 0;
ntotal++;
} while (nsuccessfull < this.SimulationParameters.MaxIterations);//while (ntotal < this.SimulationParameters.MaxIterations && nsuccessfull < nsuccessfull_max);
// save result
SimulationResult sr = new SimulationResult();
for (int i = 0; i < translation.Length; i++)
{
this.rotation[i] = Matrix3.RepairRotation(rotation[i]);
}
sr.E = ForceAndTorque();
CheckForClashes(true);
sr.E += Eclash;
sr.ParentStructure = _originalstate.InternalNumber;
sr.Eclash = Eclash;
sr.Ebond = Ebond;
sr.Converged = (ntotal < this.SimulationParameters.MaxIterations);
sr.SimulationMethod = _originalstate.SimulationMethod | SimulationMethods.MetropolisSampling;
sr.Translation = new Vector3[translation.Length];
sr.Rotation = new Matrix3[translation.Length];
for (int i = 0; i < translation.Length; i++)
{
sr.Translation[i] = Matrix3.Transpose(rotation[0]) * (translation[i] - translation[0])
- _molecules[i].CM + _molecules[0].CM;
this.rotation[i] = Matrix3.RepairRotation(rotation[i]);
sr.Rotation[i] = Matrix3.RepairRotation(Matrix3.Transpose(rotation[0]) * rotation[i]);
}
sr.Molecules = _molecules;
sr.CalculateBestFitTranslation(false);
return(sr);
}
public override SimulationResult Simulate()
{
double E, K, Etot, theta, abst, normF, normT;
Molecule m;
Vector3 tnorm;
// select dt and do the first time step
E = ForceAndTorque();
CheckForClashes(true);
E = E + Eclash;
dt = dr4dt / Math.Sqrt(2.0 * Math.Max(E, Nmolecules) / minmass) * SimulationParameters.TimeStepFactor;
rdt = 1.0 / dt;
Etot_last = E;
double Mtot = 0.0, ktot = 0.0;
for (int i = 0; i < Nmolecules; i++)
{
Mtot += _molecules[i].Mass;
}
for (int i = 0; i < kplus.Length; i++)
{
ktot += Math.Max(kplus[i], kminus[i]);
}
viscosity_per_dt = SimulationParameters.ViscosityFactor * 2.0 * dt * Math.Sqrt(ktot / Mtot);
viscosity = viscosity_per_dt * dt;
viscosity = Math.Max(minviscosity, viscosity);
viscosity = Math.Min(maxviscosity, viscosity);
for (int i = 0; i < Nmolecules; i++)
{
m = _molecules[i];
translationm1[i] = translation[i];
rotationm1[i] = rotation[i];
translation[i] += force[i] * (0.5 / m.Mass) * dt * dt;
abst = Vector3.Abs(torque[i]);
tnorm = torque[i] * (1.0 / abst);
theta = 0.5 * dt * dt * abst / m.SimpleI;
rotation[i] *= Matrix3.Rotation(tnorm, theta);
}
// main loop
int niter = 0, maxniter;
optimize_selected_now = (SimulationParameters.OptimizeSelected == OptimizeSelected.Selected ||
SimulationParameters.OptimizeSelected == OptimizeSelected.SelectedThenAll);
if (SimulationParameters.OptimizeSelected == OptimizeSelected.SelectedThenAll)
{
maxniter = SimulationParameters.MaxIterations / 2;
}
else
{
maxniter = SimulationParameters.MaxIterations;
}
do
{
E = Iterate(out normF, out normT, out K);
Etot = E + K;
niter++;
if ((niter << 28) == 0 || Eclash > 10.0 || Etot > Etot_last + maxdE)
{
Cleanup(ref Etot);
}
Etot_last = Etot;
}while (((normF > SimulationParameters.FTolerance) || (normT > SimulationParameters.TTolerance) ||
(K > SimulationParameters.KTolerance * Nmolecules)) && (niter < maxniter));
// repeat if selected then all
if (SimulationParameters.OptimizeSelected == OptimizeSelected.SelectedThenAll)
{
dt = dr4dt / Math.Sqrt(2.0 * Math.Max(E, Nmolecules) / minmass) * SimulationParameters.TimeStepFactor;
rdt = 1.0 / dt;
viscosity = SimulationParameters.ViscosityFactor * 2.0 * dt * Math.Sqrt(ktot / Mtot);
viscosity = Math.Max(minviscosity, viscosity);
viscosity = Math.Min(maxviscosity, viscosity);
niter = 0;
optimize_selected_now = false;
do
{
E = Iterate(out normF, out normT, out K);
Etot = E + K;
niter++;
if ((niter << 28) == 0 || Eclash > 10.0 || Etot > Etot_last + maxdE)
{
Cleanup(ref Etot);
}
Etot_last = Etot;
}while (((normF > SimulationParameters.FTolerance) || (normT > SimulationParameters.TTolerance) ||
(K > SimulationParameters.KTolerance * Nmolecules)) && (niter < maxniter));
}
SimulationResult sr = new SimulationResult();
sr.E = E;
sr.Eclash = Eclash;
sr.Ebond = Ebond;
sr.Converged = (niter < SimulationParameters.MaxIterations);
sr.Translation = new Vector3[Nmolecules];
sr.Rotation = new Matrix3[Nmolecules];
sr.ParentStructure = _originalstate.InternalNumber;
sr.SimulationMethod = _originalstate.SimulationMethod | SimulationMethods.Docking;
for (int i = 0; i < Nmolecules; i++)
{
sr.Translation[i] = Matrix3.Transpose(rotation[0]) * (translation[i] - translation[0])
- _molecules[i].CM + _molecules[0].CM;
sr.Rotation[i] = Matrix3.RepairRotation(Matrix3.Transpose(rotation[0]) * rotation[i]);
}
sr.Molecules = _molecules;
sr.CalculateBestFitTranslation(false);
return(sr);
}
