// constructor
public SoftSpheres(ParticleEnsemble pParticleSet)
{
epsilon=10.0;
// allocate vectors holding positions & forces
LJxforces = new List<double>(new double[pParticleSet.GetMaxNumberOfParticles()]);
LJyforces = new List<double>(new double[pParticleSet.GetMaxNumberOfParticles()]);
// allocate vector holding cutoff distance for calculating Wall-Particle interactions
WallDistance = new List<double>(new double[pParticleSet.GetMaxNumberOfParticles()]);
// allocate vector holding cutoff distance for calculating particle-particle interaction
//Mat_DP tmp(0.0,pParticleSet->GetMaxNumberOfParticles(),pParticleSet->GetMaxNumberOfParticles());
MinimumDistance = new DPMatrix(0, pParticleSet.GetMaxNumberOfParticles(),pParticleSet.GetMaxNumberOfParticles());
// allocate vectors holding particle-particle LJ energy terms
LJenergyTermA = new DPMatrix(0, pParticleSet.GetMaxNumberOfParticles(),pParticleSet.GetMaxNumberOfParticles()); // =tmp;
LJenergyTermB = new DPMatrix(0, pParticleSet.GetMaxNumberOfParticles(), pParticleSet.GetMaxNumberOfParticles()); // =tmp;
LJgradientTermA = new DPMatrix(0, pParticleSet.GetMaxNumberOfParticles(), pParticleSet.GetMaxNumberOfParticles()); // =tmp;
LJgradientTermB = new DPMatrix(0, pParticleSet.GetMaxNumberOfParticles(), pParticleSet.GetMaxNumberOfParticles()); // =tmp;
CalculateEnergyTerms(pParticleSet);
// calculate initial forcefield
CalculateForceField(pParticleSet);
}
public void ResizeForceArrays(ParticleEnsemble ensemble)
{
// clear out the forces vectors
xforces.Clear();
yforces.Clear();
// allocate vectors holding positions & forces
xforces.AddRange(new double[ensemble.GetNumberOfParticles()]);
yforces.AddRange(new double[ensemble.GetNumberOfParticles()]);
}
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];
}
}
}
public ExternalField(ParticleEnsemble ensemble)
{
GrabberCalls = 0;
CalibrationCalls = 1;
consecutiveZeroThreshold = 3;
BoxHeight = ensemble.GetBoxHeight();
BoxWidth = ensemble.GetBoxWidth();
Calibrating = false;
// initialize background pixels
BackgroundPixels = new List<double>(new double[BoxHeight * BoxWidth]);
// initialize the calibration count vector
calibrationCountVector = new List<double>(new double[BoxHeight * BoxWidth]);
// initialize timeTpixels
timeTpixels = new List<double>(new double[BoxHeight * BoxWidth]);
// initialize consecutiveZerosCount
consecutiveZerosCount = new List<double>(new double[BoxHeight * BoxWidth]);
// allocate vectors holding positions & forces
xforces = new List<double>(new double[ensemble.GetNumberOfParticles()]);
yforces = new List<double>(new double[ensemble.GetNumberOfParticles()]);
// set up the gaussian array with the desired smoothing width parameter
sigma = 10;
nGaussPoints = 2 * (3 * sigma) + 1;
RangeEitherSide = 3 * sigma;
gaussian = new List<double>(new double[nGaussPoints]);
double point = -1.0 * (3.0 * (double)sigma);
for (int i = 0; i < nGaussPoints; ++i)
{
gaussian[i] = Math.Exp(-0.5 * (Math.Pow(point / (double)sigma, 2.0))) / ((double)sigma * Math.Sqrt(2.0 * Math.PI));
// cout << point << " " << gaussian[i] << endl;
++point;
}
}
public abstract void CalculateForceField(ParticleEnsemble ensemble);
public abstract void UpdateEnergyTerms(ParticleEnsemble ensemble);
public abstract void CalculateEnergyTerms(ParticleEnsemble ensemble);
public override void UpdateEnergyTerms(ParticleEnsemble ensemble)
{
throw new NotImplementedException();
}
/// <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
}
public override void CalculateForceField(ParticleEnsemble ensemble)
{
//variable declarations
double posXi, posYi;
double posXj, posYj;
double LJxf, LJyf;
double ijSeparation = 0.0, LJforce = 0.0, PotentialEnergy = 0.0;
int j, kk, ctr, dimensions = 2;
//variable initializations
int BoxHeight = ensemble.GetBoxHeight();
int BoxWidth = ensemble.GetBoxWidth();
double MaxForce = ensemble.GetMaxForceThreshold();
double MinForce = -1.0 * (ensemble.GetMaxForceThreshold());
// initialize vectors holding forces
for (int i = 0; i < ensemble.GetNumberOfParticles(); ++i)
{
LJxforces[i]=0.0;
LJyforces[i]=0.0;
}
for (int i = 0; i < ensemble.GetNumberOfParticles(); ++i)
{
for (j = (i + 1); j < ensemble.GetNumberOfParticles(); ++j)
{
// get the interparticle separation distances
ijSeparation = ensemble.GetInterParticleSeparation(i, j);
// update the radial distribution function
// pParticleSet->UpdateRadialDistributionFunction((int)(ijSeparation));
double cutoffDistance = MinimumDistance[i, j];
if (ijSeparation < cutoffDistance) {
// for each particle, change the appropriate element of the setWithinRangeOfAnotherParticle vector to true
posXi = ensemble.GetXParticlePosition(i);
posYi = ensemble.GetYParticlePosition(i);
posXj = ensemble.GetXParticlePosition(j);
posYj = ensemble.GetYParticlePosition(j);
// PotentialEnergy += LJenergyTermA[i][j]/(pow(ijSeparation,12.0))+LJenergyTermB[i][j]/pow(ijSeparation,6.0)+epsilon;
LJforce = (posXj - posXi) * (LJgradientTermA[i, j] / Math.Pow(ijSeparation, 13.0) + LJgradientTermB[i, j] / Math.Pow(ijSeparation, 7.0)) / ijSeparation;
if (Math.Abs(LJforce) > MaxForce || Math.Abs(LJforce) < MinForce) { LJforce = 0.0; } // error check for real-time stability...
else if(double.IsNaN(LJforce) || double.IsInfinity(LJforce)){LJforce = 0.0;} // error check for real-time stability...
LJxforces[i] += LJforce;
LJxforces[j] += -1.0*LJforce;
// cout << "x "<< i << " " << j << " " << LJforce << endl;
// cout << "i " << i << " LJxforces[i] " << LJxforces[i] << " j " << j << " LJxforces[j] " << LJxforces[j] << endl;
// cout << "xi:=" << posXi << ";" << "xj:=" << posXj << ";" << "yi:=" << posYi << ";" << "yj:=" << posYj << ";" << LJxforces[i] << endl;
LJforce = (posYj - posYi) * (LJgradientTermA[i, j] / Math.Pow(ijSeparation, 13.0) + LJgradientTermB[i, j] / Math.Pow(ijSeparation, 7.0)) / ijSeparation;
if (Math.Abs(LJforce) > MaxForce || Math.Abs(LJforce) < MinForce) { LJforce = 0.0; } // error check for real-time stability...
else if (double.IsNaN(LJforce) || double.IsInfinity(LJforce)) { LJforce = 0.0; } // error check for real-time stability...
LJyforces[i] += LJforce;
LJyforces[j] += -1.0*LJforce;
ensemble.SetParticlesWithinRange(i, j);
ensemble.SetParticlesWithinRange(j, i);
// cout << i << " " << j << endl;
}
else{
ensemble.SetParticlesNotWithinRange(i, j);
ensemble.SetParticlesNotWithinRange(j, i);
}
}
}
// set the forces in the Particle Ensemble Object
ensemble.AddXForces(LJxforces);
ensemble.AddYForces(LJyforces);
// set the potential energy
ensemble.AddPotentialEnergy(PotentialEnergy);
}
