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)); }
}
}