public MoleculeDynamicsSimulator(Molecule molecule,
List <CustomAtomForce> customAtomForces,
MoleculeDynamicsSimulationSettings simulationSettings)
{
this.customAtomForces = customAtomForces;
this.simulationSettings = simulationSettings;
Molecule = molecule;
}
private static void ApplyAtomForces(Molecule molecule,
UnitValue elapsedTime,
ForceCalculatorResult forces,
MoleculeDynamicsSimulationSettings settings)
{
var maxVelocity = 1e2;
var dT = settings.TimeStep.In(Unit.Second);
foreach (var vertexForce in forces.ForceLookup)
{
var atom = molecule.GetAtom(vertexForce.Key);
var force = vertexForce.Value;
if (settings.ForceRampUp && elapsedTime < settings.ForceRampUpPeriod)
{
var quotient = elapsedTime.Value / settings.ForceRampUpPeriod.Value;
force *= quotient;//Math.Pow(10, (int)(-100*quotient));
}
if (force.Magnitude() < ForceLowerCutoff)
{
continue;
}
atom.Velocity += settings.TimeStep * (force.To(Unit.Newton) / atom.Mass);
if (atom.Velocity.Magnitude().In(Unit.MetersPerSecond) > maxVelocity)
{
atom.Velocity *= maxVelocity / atom.Velocity.Magnitude().In(Unit.MetersPerSecond);
}
atom.Position += dT * atom.Velocity;
if (settings.ResetAtomVelocityAfterEachTimestep)
{
atom.Velocity = new UnitVector3D(Unit.MetersPerSecond, 0, 0, 0);
}
else
{
atom.Velocity *= 1.0; // TODO: Scale velocity to maintain a specific total energy, matching the environement's temperature
}
}
}