public override void UpdateEnergyTerms(ParticleEnsemble ensemble)
{
for (int i = 0; i < ensemble.GetNumberOfParticles(); ++i)
{
for (int j = (i + 1); j < ensemble.GetNumberOfParticles(); ++j)
{
double MinDistance = 2.0 * (ensemble.GetParticleRadius(i) + ensemble.GetParticleRadius(j));
MinimumDistance[i, j] = MinDistance * MinDistance;
MinimumDistance[j, i] = MinimumDistance[i, j];
LJenergyTermA[i, j] = epsilon * Math.Pow(MinDistance, 12.0);
LJenergyTermA[j, i] = LJenergyTermA[i, j];
LJenergyTermB[i, j] = -2.0 * epsilon * Math.Pow(MinDistance, 6.0);
LJenergyTermB[j, i] = LJenergyTermB[i, j];
LJgradientTermA[i, j] = -12.0 * LJenergyTermA[i, j];
LJgradientTermA[j, i] = LJgradientTermA[i, j];
LJgradientTermB[i, j] = -6.0 * LJenergyTermB[i, j];
LJgradientTermB[j, i] = LJgradientTermB[i, j];
}
}
}
/// <summary>
/// function to calculate Soft Spheres forcefield
/// </summary>
/// <param name="ensemble"></param>
public override void CalculateForceField(ParticleEnsemble ensemble)
{
// variable declarations
int i;
double posXi, posYi, radius;
double PotentialEnergy = 0.0;
// variable initializations
int BoxHeight = ensemble.GetBoxHeight();
int BoxWidth = ensemble.GetBoxWidth();
// #pragma omp parallel for
for (i = 0; i < ensemble.GetNumberOfParticles(); ++i)
{
// initialize vectors holding forces
xforces[i] = 0.0; // HERE'S THE PROBLEM - THE INDEX WILL OVERRUN THE VECTOR SIZE!!!
yforces[i] = 0.0;
}
//#pragma omp parallel for
for (i = 0; i < ensemble.GetNumberOfParticles(); ++i)
{
posXi = ensemble.GetXParticlePosition(i);
posYi = ensemble.GetYParticlePosition(i);
radius = ensemble.GetParticleRadius(i);
// get pixel vectors along the particle's X & Y axes for getting gradient of image field
// there are 2 steps to this process:
// (1) do some gaussian smoothing with a user defined width parameter (this determines how
// many pixels we need
// (2) determine the gradient from linear regression of the 3 surrounding points...
// cout << "particle " << i << " Xpos " << posXi << " Ypos " << posYi << endl;
// first get the vectors that we need - the length of the vectors depend on the width of the gaussian
// if the pixels are near the edge, the pixels beyond them (which arent in the image) are simply returned as zeros
// vector < double > AllThePixelsAlongX = pParticleSet->GetAllThePixelsAlongX(posYi,posXi,RangeEitherSide);
// xforces[i] = pParticleSet->GetGradientScaleFactor()*GaussianSmoothedSlope(posXi,AllThePixelsAlongX);
// cout << "Xposition " << posXi << endl;
if (m_CalculateForceField_TempArray.Length < RangeEitherSide + 1)
{
m_CalculateForceField_TempArray = new double[RangeEitherSide + 1];
}
int count;
GetSubsetOfPixelsAlongX(posYi, posXi, RangeEitherSide + 1, ref m_CalculateForceField_TempArray, out count);
// for(int kk=0; kk<SubsetOfPixelsAlongX.size(); ++kk){
// cout << kk << " " << SubsetOfPixelsAlongX[kk] << endl;
// }
// cout << "Xposition " << posXi << endl;
// for(int kk=1;kk<SubsetOfPixelsAlongX.size();++kk){cout << kk << " " << SubsetOfPixelsAlongX[kk] << endl;}
xforces[i] = ensemble.GetGradientScaleFactor() * GaussianSmoothedSlope(posXi, m_CalculateForceField_TempArray, count);
// vector < double > AllThePixelsAlongY = pParticleSet->GetAllThePixelsAlongY(posXi,posYi,RangeEitherSide);
// cout << "Yposition " << posYi << endl;
// for(int kk=0;kk<AllThePixelsAlongY.size();++kk){cout << kk << " " << AllThePixelsAlongY[kk] << endl;}
// yforces[i] = pParticleSet->GetGradientScaleFactor()*GaussianSmoothedSlope(posYi,AllThePixelsAlongY);
GetSubsetOfPixelsAlongY(posXi, posYi, RangeEitherSide + 1, ref m_CalculateForceField_TempArray, out count);
//List<double> SubsetOfPixelsAlongY = GetSubsetOfPixelsAlongY(posXi, posYi, RangeEitherSide + 1);
// cout << "Yposition " << endl;
yforces[i] = ensemble.GetGradientScaleFactor() * GaussianSmoothedSlope(posYi, m_CalculateForceField_TempArray, count);
// cout << "yforces[i] " << i << " " << yforces[i] << endl;
// get the gradient scale factor, depending on whether the particle is attractive or repulsive
ParticleInfo typeInfo = ParticleStaticObjects.AtomPropertiesDefinition.Lookup[(ensemble.pParticleVector[i]).TypeID];
double attractiveOrRepulsiveFactor = typeInfo.AttractiveOrRepulsive;
xforces[i] *= attractiveOrRepulsiveFactor;
yforces[i] *= attractiveOrRepulsiveFactor;
}
ensemble.AddXForces(xforces); // set the forces in the Particle Ensemble Object
ensemble.AddYForces(yforces); // set the potential energy
ensemble.AddPotentialEnergy(PotentialEnergy); // add in the potential energy
}