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("Hydrogen", 2, unchecked((int)0xc00A32FF), 0, 50); // neon blue
ParticleStaticObjects.AtomPropertiesDefinition.AddParticleDefinition("Oxygen", 4, unchecked((int)0xc0FF0A32), 1, 49); // red
ParticleStaticObjects.AtomPropertiesDefinition.AddParticleDefinition("Neon", 6, unchecked((int)0xc0320AFF), 2, 45); // purple
ParticleStaticObjects.AtomPropertiesDefinition.AddParticleDefinition("Zinc", 9.2, unchecked((int)0xc026D8FF), 3, 43); // sky blue // 0xc032FF0A, 3, 43); // green
ParticleStaticObjects.AtomPropertiesDefinition.AddParticleDefinition("Iron", 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 override void CalculateEnergyTerms(ParticleEnsemble ensemble)
{
ParticleStaticObjects.AtomPropertiesDefinition.CalculateEnergyTerms();
/*for (int i = 0; i < ensemble.MaxNumberOfParticles; ++i)
{
double radiusi = ensemble.GetParticle(i).Radius;
for (int j = (i + 1); j < ensemble.MaxNumberOfParticles; ++j)
{
double radiusj = ensemble.GetParticle(j).Radius;
double MinDist = 2.0 * (radiusi + radiusj);
MinimumDistance[i, j] = MinDist * MinDist;
MinimumDistance[j, i] = MinimumDistance[i, j];
LJenergyTermA[i, j] = epsilon * Math.Pow(MinDist, 12.0);
LJenergyTermA[j, i] = LJenergyTermA[i, j];
LJenergyTermB[i, j] = -2.0 * epsilon * Math.Pow(MinDist, 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 void ResizeForceArrays(ParticleEnsemble ensemble)
{
DPVector zero = new DPVector(0, 0);
for (int i = 0; i < ensemble.NumberOfParticles; i++)
{
forces[i] = zero;
}
}
public ExternalField(ParticleEnsemble ensemble)
{
GrabberCalls = 0;
CalibrationCalls = 1;
consecutiveZeroThreshold = 3;
BoxHeight = ensemble.BoxHeight;
BoxWidth = ensemble.BoxWidth;
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
forces = new DPVector[ensemble.MaxNumberOfParticles];
// set up the gaussian array with the desired smoothing width parameter
sigma = 10;
nGaussPoints = 2 * (3 * sigma) + 1;
RangeEitherSide = 3 * sigma;
gaussian = 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));
++point;
}
}
public SoftSpheres(ParticleEnsemble pParticleSet)
{
epsilon = 10.0;
// allocate vectors holding positions & forces
LJforces = new DPVector[pParticleSet.MaxNumberOfParticles];
// allocate vector holding cutoff distance for calculating Wall-Particle interactions
WallDistance = new List<double>(new double[pParticleSet.MaxNumberOfParticles]);
// allocate vector holding cutoff distance for calculating particle-particle interaction
//MinimumDistance = new DPMatrix(0, pParticleSet.MaxNumberOfParticles,pParticleSet.MaxNumberOfParticles);
// allocate vectors holding particle-particle LJ energy terms
//LJenergyTermA = new DPMatrix(0, pParticleSet.MaxNumberOfParticles,pParticleSet.MaxNumberOfParticles);
//LJenergyTermB = new DPMatrix(0, pParticleSet.MaxNumberOfParticles, pParticleSet.MaxNumberOfParticles);
//LJgradientTermA = new DPMatrix(0, pParticleSet.MaxNumberOfParticles, pParticleSet.MaxNumberOfParticles);
//LJgradientTermB = new DPMatrix(0, pParticleSet.MaxNumberOfParticles, pParticleSet.MaxNumberOfParticles);
CalculateEnergyTerms(pParticleSet);
// calculate initial forcefield
CalculateForceField(pParticleSet);
}
public override void CalculateForceField(ParticleEnsemble ensemble)
{
// variable declarations
double posXi, posYi;
double posXj, posYj;
double ijSeparation = 0.0, LJforce = 0.0, PotentialEnergy = 0.0;
// variable initializations
int BoxHeight = ensemble.BoxHeight;
int BoxWidth = ensemble.BoxWidth;
double MaxForce = ensemble.MaxForceThreshold;
double MinForce = -1.0 * (ensemble.MaxForceThreshold);
DPVector zero = new DPVector(0, 0);
// initialize vectors holding forces
for (int i = 0; i < ensemble.NumberOfParticles; ++i)
{
LJforces[i] = zero;
}
ensemble.ResetAllParticlesNotWithinRange();
for (int i = 0; i < ensemble.NumberOfParticles; ++i)
{
Particle particlei = ensemble.GetParticle(i);
for (int j = (i + 1); j < ensemble.NumberOfParticles; ++j)
{
Particle particlej = ensemble.GetParticle(j);
// get the interparticle separation distances
ijSeparation = ensemble.GetInterParticleSeparation(i, j);
double LJgradientTermA = particlei.ParticleType.LJgradientTermA[particlej.TypeID];
double LJgradientTermB = particlei.ParticleType.LJgradientTermB[particlej.TypeID];
// update the radial distribution function
double cutoffDistance = particlei.ParticleType.MinimumDistance[particlej.TypeID]; // MinimumDistance[i, j];
if (ijSeparation < cutoffDistance)
{
// for each particle, change the appropriate element of the setWithinRangeOfAnotherParticle vector to true
posXi = particlei.Position.X;
posYi = particlei.Position.Y;
posXj = particlej.Position.X;
posYj = particlej.Position.Y;
LJforce = (posXj - posXi) * (LJgradientTermA / Math.Pow(ijSeparation, 13.0) + LJgradientTermB / Math.Pow(ijSeparation, 7.0)) / ijSeparation;
if (Math.Abs(LJforce) > MaxForce || Math.Abs(LJforce) < MinForce)
{
// error check for real-time stability...
LJforce = 0.0;
}
else if(double.IsNaN(LJforce) || double.IsInfinity(LJforce))
{
// error check for real-time stability...
LJforce = 0.0;
}
LJforces[i].X += LJforce;
LJforces[j].X += -1.0 * LJforce;
LJforce = (posYj - posYi) * (LJgradientTermA / Math.Pow(ijSeparation, 13.0) + LJgradientTermB / Math.Pow(ijSeparation, 7.0)) / ijSeparation;
if (Math.Abs(LJforce) > MaxForce || Math.Abs(LJforce) < MinForce)
{
// error check for real-time stability...
LJforce = 0.0;
}
else if (double.IsNaN(LJforce) || double.IsInfinity(LJforce))
{
// error check for real-time stability...
LJforce = 0.0;
}
LJforces[i].Y += LJforce;
LJforces[j].Y += -1.0 * LJforce;
ensemble.SetParticlesWithinRange(i, j);
ensemble.SetParticlesWithinRange(j, i);
}
//else
//{
// ensemble.SetParticlesNotWithinRange(i, j);
//ensemble.SetParticlesNotWithinRange(j, i);
//}
}
}
// set the forces in the Particle Ensemble Object
ensemble.AddForces(LJforces);
// set the potential energy
ensemble.AddPotentialEnergy(PotentialEnergy);
}
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.BoxHeight;
int BoxWidth = ensemble.BoxWidth;
DPVector zero = new DPVector(0, 0);
// #pragma omp parallel for
for (i = 0; i < ensemble.NumberOfParticles; ++i)
{
// initialize vectors holding forces
forces[i] = zero;
}
//#pragma omp parallel for
for (i = 0; i < ensemble.NumberOfParticles; ++i)
{
Particle particlei = ensemble.GetParticle(i);
posXi = particlei.Position.X;
posYi = particlei.Position.Y;
radius = particlei.Radius;
// 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
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);
forces[i].X = ensemble.GradientScaleFactor * GaussianSmoothedSlope(posXi, m_CalculateForceField_TempArray, count);
GetSubsetOfPixelsAlongY(posXi, posYi, RangeEitherSide + 1, ref m_CalculateForceField_TempArray, out count);
forces[i].Y = ensemble.GradientScaleFactor * GaussianSmoothedSlope(posYi, m_CalculateForceField_TempArray, count);
// get the gradient scale factor, depending on whether the particle is attractive or repulsive
ParticleInfo typeInfo = ParticleStaticObjects.AtomPropertiesDefinition.Lookup[(ensemble.Particles[i]).TypeID];
double attractiveOrRepulsiveFactor = typeInfo.AttractiveOrRepulsive;
forces[i].X *= attractiveOrRepulsiveFactor;
forces[i].Y *= attractiveOrRepulsiveFactor;
}
// set the forces in the Particle Ensemble Object
ensemble.AddForces(forces);
// add in the potential energy
ensemble.AddPotentialEnergy(PotentialEnergy);
}