// constructor
public SoftSpheres(ParticleEnsemble pParticleSet)
{
epsilon=10.0;
// allocate vectors holding positions & forces
LJforces = new DPVector[pParticleSet.GetMaxNumberOfParticles()];
// allocate vector holding cutoff distance for calculating Wall-Particle interactions
WallDistance = 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 ParticleEnsemble(int nparticles, double MinRad, double MaxRad, List<string> FFtype, int Height, int Width, double scaleFactor)
{
int i;
maxNumberOfParticles = 1000; // set the maximum number of particles to 1000
kb = 8.314; // value of the boltzmann constant - we dont really care about units now...
BerendsenCoupling = 1.0; // value of the berendsen coupling constant - set this to be controlled by the artist...
Tequilibrium = 20000;
BerendsenThermostat = true;
// BerendsenThermostat=false;
EnsembleReinitializationFlag = false;
NumberOfParticlesChangedFlag = false;
NumberOfParticlesIsGreaterFlag = false;
radiiScaleFactor = 1.0;
InitialKE = 0.0;
gradientScaleFactor = scaleFactor;
step = 0;
NumberOfParticles = nparticles;
BoxHeight = Height;
BoxWidth = Width;
MaxForceThreshold = 1.0e6;
initialMaxForceThreshold = MaxForceThreshold;
AverageVelocityAutoCorrelationFunction = new List<double>(new double[1024]);
InitialMinVel = 100.0;
InitialMaxVel = 200.0;
for (int ii = 0; ii < maxNumberOfParticles; ++ii)
{
initializeOneNewParticle();
}
if (!EliminateParticleOverlap(Height, Width))
{
// adjust particle positions to eliminate overlap
do
{
//cout << "Can't fit " << NumberOfParticles << " particles into the simulation box " << endl;
NumberOfParticles -= 1; // if there's too many particles to fit in the simulation box
//cout << "Decrementing the number of particles to " << NumberOfParticles << endl;
EliminateParticleOverlap(Height, Width); // decrement the particles till it's ok
}
while (!EliminateParticleOverlap(Height, Width));
}
//DPMatrix tmp1 = new DPMatrix(0.0, maxNumberOfParticles, maxNumberOfParticles); // assign tmp1 matrix to distanceMatrix & distanceMatrixLastTime
distanceMatrix = new DPMatrix(0.0, maxNumberOfParticles, maxNumberOfParticles);
distanceMatrixLastTime = new DPMatrix(0.0, maxNumberOfParticles, maxNumberOfParticles);
distanceMatrixLastLastTime = new DPMatrix(0.0, maxNumberOfParticles, maxNumberOfParticles);
particlesWithinRange = new BoolMatrix(false, maxNumberOfParticles, maxNumberOfParticles); // update the particlesWithinRange matrix
UpdateInterParticleSeparations(); // update the interparticle separation matrix
PotentialEnergy = 0.0;
//initialize forcefield Object
// cout << FFtype[0] << endl;
//if(FFtype[0]=="HardSpheres"){
// pForceFieldVector.push_back(new HardSpheres(this));
//}
//else{
// push back forceField objects onto pForceFieldVector - at present, we only have LJ forces, but this can be
// easily expanded
for (i = 0; i < FFtype.Count; ++i)
{
if (FFtype[i] == "SoftSpheres") { pForceFieldVector.Add(new SoftSpheres(this)); }
// if(FFtype[i]=="ExternalField"){ pForceFieldVector.push_back(new ExternalField(this));}
}
//}
// test of the matrix class implementation
/*
Mat_DP AA(1.0,3,3), BB(2.0,3,3), CC(0.0,3,3);
NR::matadd(AA, BB, CC); // matrix addition
for(int i=0; i<3; ++i){ // print out
for(int j=0; j<3; ++j){
cout << CC[i][j] << endl;
}
}
*/
}
// this stuff is for the FFT - move this stuff to a ParticleMath class
//void four1(std::vector<double> &data, const int isign);
//void realft(std::vector<double> &data, const int isign);
// update the interparticle distanceMatrix
public void UpdateInterParticleSeparations()
{
double ijSeparation = 0;
DPMatrix temp = distanceMatrixLastLastTime;
distanceMatrixLastLastTime = distanceMatrixLastTime;
distanceMatrixLastTime = distanceMatrix;
distanceMatrix = temp;
for (int i = 0; i < NumberOfParticles; ++i)
{
for (int j = (i + 1); j < NumberOfParticles; ++j)
{
//distanceMatrixLastLastTime[i, j] = distanceMatrixLastTime[i, j];
//distanceMatrixLastLastTime[j, i] = distanceMatrixLastTime[j, i];
//distanceMatrixLastTime[i, j] = distanceMatrix[i, j]; // move the present distances to the last
//distanceMatrixLastTime[j, i] = distanceMatrix[j, i];
//ijSeparation = Math.Sqrt(Math.Pow(pParticleVector[i].getpx() - pParticleVector[j].getpx(), 2.0) + Math.Pow(pParticleVector[i].getpy() - pParticleVector[j].getpy(), 2.0));
ijSeparation = Math.Pow(pParticleVector[i].getpx() - pParticleVector[j].getpx(), 2.0) + Math.Pow(pParticleVector[i].getpy() - pParticleVector[j].getpy(), 2.0);
distanceMatrix[i, j] = ijSeparation;
distanceMatrix[j, i] = ijSeparation; // assign the present distances
}
}
}
/// <summary>
/// update the interparticle distanceMatrix
/// </summary>
public void UpdateInterParticleSeparations()
{
double ijSeparation = 0;
DPMatrix temp = m_DistanceMatrixLastLastTime;
m_DistanceMatrixLastLastTime = m_DistanceMatrixLastTime;
m_DistanceMatrixLastTime = m_DistanceMatrix;
m_DistanceMatrix = temp;
for (int i = 0; i < m_NumberOfParticles; ++i)
{
for (int j = (i + 1); j < m_NumberOfParticles; ++j)
{
//distanceMatrixLastLastTime[i, j] = distanceMatrixLastTime[i, j];
//distanceMatrixLastLastTime[j, i] = distanceMatrixLastTime[j, i];
//distanceMatrixLastTime[i, j] = distanceMatrix[i, j]; // move the present distances to the last
//distanceMatrixLastTime[j, i] = distanceMatrix[j, i];
//ijSeparation = Math.Sqrt(Math.Pow(pParticleVector[i].getpx() - pParticleVector[j].getpx(), 2.0) + Math.Pow(pParticleVector[i].getpy() - pParticleVector[j].getpy(), 2.0));
DPVector posi = Particles[i].Position;
DPVector posj = Particles[j].Position;
ijSeparation = Math.Sqrt(Math.Pow(posi.X - posj.X, 2.0) + Math.Pow(posi.Y - posj.Y, 2.0));
m_DistanceMatrix[i, j] = ijSeparation;
m_DistanceMatrix[j, i] = ijSeparation; // assign the present distances
}
}
}
public ParticleEnsemble(int nparticles, double MinRad, double MaxRad, List<string> FFtype, int Height, int Width, double scaleFactor)
{
int i;
// set the maximum number of particles to 1000
m_MaxNumberOfParticles = 1000;
// value of the boltzmann constant - we dont really care about units now...
m_KB = 8.314;
// value of the berendsen coupling constant - set this to be controlled by the artist...
m_BerendsenCoupling = 1.0;
m_Tequilibrium = 20000;
m_BerendsenThermostat = true;
// BerendsenThermostat=false;
m_EnsembleReinitializationFlag = false;
m_NumberOfParticlesChangedFlag = false;
m_NumberOfParticlesIsGreaterFlag = false;
m_RadiiScaleFactor = 1.0;
m_InitialKE = 0.0;
m_GradientScaleFactor = scaleFactor;
m_Step = 0;
m_NumberOfParticles = nparticles;
m_BoxHeight = Height;
m_BoxWidth = Width;
m_MaxForceThreshold = 1.0e6;
m_InitialMaxForceThreshold = m_MaxForceThreshold;
m_AverageVelocityAutoCorrelationFunction = new List<double>(new double[1024]);
m_InitialMinVel = 100.0;
m_InitialMaxVel = 200.0;
for (int ii = 0; ii < m_MaxNumberOfParticles; ++ii)
{
InitializeOneNewParticle();
}
if (!EliminateParticleOverlap(Height, Width))
{
// adjust particle positions to eliminate overlap
do
{
//cout << "Can't fit " << NumberOfParticles << " particles into the simulation box " << endl;
// if there's too many particles to fit in the simulation box
m_NumberOfParticles -= 1;
//cout << "Decrementing the number of particles to " << NumberOfParticles << endl;
// decrement the particles till it's ok
EliminateParticleOverlap(Height, Width);
}
while (!EliminateParticleOverlap(Height, Width));
}
// assign tmp1 matrix to distanceMatrix & distanceMatrixLastTime
m_DistanceMatrix = new DPMatrix(0.0, m_MaxNumberOfParticles, m_MaxNumberOfParticles);
m_DistanceMatrixLastTime = new DPMatrix(0.0, m_MaxNumberOfParticles, m_MaxNumberOfParticles);
m_DistanceMatrixLastLastTime = new DPMatrix(0.0, m_MaxNumberOfParticles, m_MaxNumberOfParticles);
// update the particlesWithinRange matrix
m_ParticlesWithinRange = new BoolMatrix(false, m_MaxNumberOfParticles, m_MaxNumberOfParticles);
// update the interparticle separation matrix
UpdateInterParticleSeparations();
m_PotentialEnergy = 0.0;
// push back forceField objects onto pForceFieldVector - at present, we only have LJ forces, but this can be easily expanded
for (i = 0; i < FFtype.Count; ++i)
{
if (FFtype[i] == "SoftSpheres")
{
m_ForceFields.Add(new SoftSpheres(this));
}
}
}
public ParticleEnsemble(int nparticles, double MinRad, double MaxRad, List<string> FFtype, int Height, int Width, double scaleFactor)
{
int i;
// set the maximum number of particles to 1000
m_MaxNumberOfParticles = 1000;
Particles = new ParticleCollection(this, m_MaxNumberOfParticles);
// value of the boltzmann constant - we dont really care about units now...
kb = 8.314;
// value of the berendsen coupling constant - set this to be controlled by the artist...
m_BerendsenThermostatCoupling = 1.0;
m_EquilibriumTemperature = 20000;
BerendsenThermostat = true;
// BerendsenThermostat=false;
EnsembleReinitializationFlag = false;
NumberOfParticlesChangedFlag = false;
NumberOfParticlesIsGreaterFlag = false;
m_RadiiScaleFactor = 1.0;
InitialKE = 0.0;
m_GradientScaleFactor = scaleFactor;
step = 0;
//NumberOfParticles = nparticles;
m_BoxHeight = Height;
m_BoxWidth = Width;
m_MaxForceThreshold = 1.0e6;
m_InitialMaxForceThreshold = m_MaxForceThreshold;
// allocate maximum space for and initialize the velocity autocorrelation & FFT vectors
m_FFTenabled = true;
m_FFTofCorrelationFunction = new List<double>(new double[MAX_CORR_FTN_SIZE]);
m_VelocityAutoCorrelationFunction = new double[MAX_CORR_FTN_SIZE];
for (int ii = 0; ii < MAX_CORR_FTN_SIZE; ++ii)
{
m_VelocityAutoCorrelationFunction[ii] = 0.0;
m_FFTofCorrelationFunction[ii] = 0.0;
}
for (int ii = 0; ii < FFTmatrixForMovingAverage.Count(); ++ii)
{
FFTmatrixForMovingAverage[ii]= new List<double>(new double[m_NumberOfFFTAverages]);
for(int kk=0; kk < m_NumberOfFFTAverages; ++kk){
FFTmatrixForMovingAverage[ii][kk] = 0.0;
}
}
InitialMinVel = 100.0;
InitialMaxVel = 200.0;
for (int ii = 0; ii < m_MaxNumberOfParticles; ++ii)
{
InitializeOneNewParticle();
}
for (int ii = nparticles; ii < m_MaxNumberOfParticles; ++ii)
{
Particles.Pop();
}
if (!EliminateParticleOverlap(Height, Width))
{
// adjust particle positions to eliminate overlap
do
{
// if there's too many particles to fit in the simulation box
//NumberOfParticles -= 1;
Particles.Pop();
// decrement the particles till it's ok
EliminateParticleOverlap(Height, Width);
}
while (!EliminateParticleOverlap(Height, Width));
}
// create matrix to distanceMatrix & distanceMatrixLastTime
distanceMatrix = new DPMatrix(0.0, MaxNumberOfParticles, MaxNumberOfParticles);
distanceMatrixLastTime = new DPMatrix(0.0, MaxNumberOfParticles, MaxNumberOfParticles);
distanceMatrixLastLastTime = new DPMatrix(0.0, MaxNumberOfParticles, MaxNumberOfParticles);
// update the particlesWithinRange matrix
particlesWithinRange = new BoolMatrix(false, MaxNumberOfParticles, MaxNumberOfParticles);
// update the interparticle separation matrix
UpdateInterParticleSeparations();
m_PotentialEnergy = 0.0;
// push back forceField objects onto pForceFieldVector - at present, we only have LJ forces, but this can be
// easily expanded
for (i = 0; i < FFtype.Count; ++i)
{
if (FFtype[i] == "SoftSpheres") { ForceFields.Add(new SoftSpheres(this)); }
}
}
/// <summary>
/// update the interparticle distanceMatrix
/// </summary>
public void UpdateInterParticleSeparations()
{
double ijSeparation = 0;
DPMatrix temp = distanceMatrixLastLastTime;
distanceMatrixLastLastTime = distanceMatrixLastTime;
distanceMatrixLastTime = distanceMatrix;
distanceMatrix = temp;
int numberOfParticles = NumberOfParticles;
for (int i = 0; i < numberOfParticles; ++i)
{
Particle particlei = Particles[i];
for (int j = (i + 1); j < numberOfParticles; ++j)
{
Particle particlej = Particles[j];
if (particlei.GridSector.IsInJoiningSectors(particlej.GridSector) == false)
{
continue;
}
// THIS ONE !UsePOW`
#if !UsePOW
// SQRT MOD
//ijSeparation = Math.Sqrt(Math.Pow(Particles[i].Position.X - Particles[j].Position.X, 2.0) + Math.Pow(Particles[i].Position.Y - Particles[j].Position.Y, 2.0));
ijSeparation = Math.Pow(Particles[i].Position.X - Particles[j].Position.X, 2.0) + Math.Pow(Particles[i].Position.Y - Particles[j].Position.Y, 2.0);
#else
// SQRT MOD
//ijSeparation = Math.Sqrt(MathHelper.Pow2(Particles[i].Position.X - Particles[j].Position.X) + MathHelper.Pow2(Particles[i].Position.Y - Particles[j].Position.Y));
ijSeparation = MathHelper.Pow2(Particles[i].Position.X - Particles[j].Position.X) + MathHelper.Pow2(Particles[i].Position.Y - Particles[j].Position.Y);
#endif
// assign the present distances
distanceMatrix[i, j] = ijSeparation;
distanceMatrix[j, i] = ijSeparation;
}
}
}
