private void SetupForTesting(int Nparticles)
{
double gradScaleFactor = 3000.0;
double MinRad = 40.0;
double MaxRad = 50.0;
List<string> FFtype = new List<string>(new string[] { "SoftSpheres", "ExternalField" });
ParticleStaticObjects.AtomPropertiesDefinition.Clear();
ParticleStaticObjects.AtomPropertiesDefinition.addParticleDefinition(2, unchecked((int)0xc00A32FF), 0, 50); // neon blue
ParticleStaticObjects.AtomPropertiesDefinition.addParticleDefinition(4, unchecked((int)0xc0FF0A32), 1, 49); // red
ParticleStaticObjects.AtomPropertiesDefinition.addParticleDefinition(6, unchecked((int)0xc0320AFF), 2, 45); // purple
ParticleStaticObjects.AtomPropertiesDefinition.addParticleDefinition(9.2, unchecked((int)0xc026D8FF), 3, 43); // sky blue // 0xc032FF0A, 3, 43); // green
ParticleStaticObjects.AtomPropertiesDefinition.addParticleDefinition(12.6, unchecked((int)0xc0FF320A), 4, 38); // orange
ParticleStaticObjects.ReSeedRandom(42);
Ensemble1 = new ParticleEnsemble(Nparticles, MinRad, MaxRad, FFtype, m_SizeY, m_SizeX, gradScaleFactor);
Field = new ExternalField(Ensemble1);
double[] background = new double[m_NumberOfPixels];
for (int i = 0; i < m_NumberOfPixels; i++)
{
background[i] = 512;
}
Field.IncrementGrabberCalls(); // increment the number of grabber calls
Field.BackgroundCalibration(m_NumberOfPixels, background); // in order to simply set the background to zero
Field.SetCalibrating(false);
}
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 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;
}
}
/// <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;
List<double> SubsetOfPixelsAlongX = GetSubsetOfPixelsAlongX(posYi, posXi, RangeEitherSide + 1);
// 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, SubsetOfPixelsAlongX);
// 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);
List<double> SubsetOfPixelsAlongY = GetSubsetOfPixelsAlongY(posXi, posYi, RangeEitherSide + 1);
// cout << "Yposition " << endl;
yforces[i] = ensemble.GetGradientScaleFactor() * GaussianSmoothedSlope(posYi, SubsetOfPixelsAlongY);
// 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 UpdateEnergyTerms(ParticleEnsemble ensemble)
{
throw new NotImplementedException();
}
