OPRGyration::molGyrationDat
OPRGyration::getGyrationEigenSystem(const shared_ptr<IDRange>& range, const dynamo::Simulation* Sim)
{
//Determine the centre of mass. Watch for periodic images
Vector tmpVec;
molGyrationDat retVal;
retVal.MassCentre = Vector{0,0,0};
double totmass = Sim->species[Sim->particles[*(range->begin())]]->getMass(*(range->begin()));
std::vector<Vector> relVecs;
relVecs.reserve(range->size());
relVecs.push_back(Vector{0,0,0});
//Walk along the chain
for (IDRange::iterator iPtr = range->begin()+1; iPtr != range->end(); iPtr++)
{
Vector currRelPos = Sim->particles[*iPtr].getPosition()
- Sim->particles[*(iPtr - 1)].getPosition();
Sim->BCs->applyBC(currRelPos);
relVecs.push_back(currRelPos + relVecs.back());
double mass = Sim->species[Sim->particles[*iPtr]]->getMass(*iPtr);
retVal.MassCentre += relVecs.back() * mass;
totmass += mass;
}
retVal.MassCentre /= totmass;
//Now determine the inertia tensor
Matrix inertiaTensor;
for (Vector& vec : relVecs)
{
vec -= retVal.MassCentre;
inertiaTensor += Dyadic(vec, vec);
}
std::pair<std::array<Vector, 3>, std::array<double, 3> > result
= magnet::math::symmetric_eigen_decomposition(inertiaTensor);
for (size_t i = 0; i < NDIM; i++)
{
retVal.EigenVal[i] = result.second[i] / range->size();
//EigenVec Components
for (size_t j = 0; j < NDIM; j++)
retVal.EigenVec[i][j] = result.first[i][j];
}
retVal.MassCentre += Sim->particles[*(range->begin())].getPosition();
return retVal;
}
OPRGyration::molGyrationDat
OPRGyration::getGyrationEigenSystem(const shared_ptr<IDRange>& range, const dynamo::Simulation* Sim)
{
//Determine the centre of mass. Watch for periodic images
Vector tmpVec;
molGyrationDat retVal;
retVal.MassCentre = Vector{0,0,0};
double totmass = Sim->species(Sim->particles[*(range->begin())])->getMass(*(range->begin()));
//Walk along the chain
Vector origin_position = Vector{0,0,0};
Matrix inertiaTensor;
for (IDRange::iterator iPtr = range->begin()+1; iPtr != range->end(); iPtr++)
{
Vector currRelPos = Sim->particles[*iPtr].getPosition() - Sim->particles[*(iPtr - 1)].getPosition();
Sim->BCs->applyBC(currRelPos);
const Vector unfolded_pos = currRelPos + origin_position;
const double mass = Sim->species(Sim->particles[*iPtr])->getMass(*iPtr);
retVal.MassCentre += origin_position * mass;
inertiaTensor += mass * ((unfolded_pos * unfolded_pos) * Matrix::identity() - Dyadic(unfolded_pos, unfolded_pos));
totmass += mass;
origin_position = unfolded_pos;
}
retVal.MassCentre /= totmass;
retVal.MassCentre += Sim->particles[*(range->begin())].getPosition();
std::pair<std::array<Vector, 3>, std::array<double, 3> > result
= magnet::math::symmetric_eigen_decomposition(inertiaTensor / totmass);
for (size_t i = 0; i < NDIM; i++)
{
retVal.EigenVal[i] = result.second[i] / range->size();
//EigenVec Components
for (size_t j = 0; j < NDIM; j++)
retVal.EigenVec[i][j] = result.first[i][j];
}
return retVal;
}
OPRGyration::molGyrationDat
OPRGyration::getGyrationEigenSystem(const shared_ptr<IDRange>& range, const dynamo::Simulation* Sim)
{
//Determine the centre of mass. Watch for periodic images
Vector tmpVec;
molGyrationDat retVal;
retVal.MassCentre = Vector (0,0,0);
double totmass = Sim->species[Sim->particles[*(range->begin())]]->getMass(*(range->begin()));
std::vector<Vector> relVecs;
relVecs.reserve(range->size());
relVecs.push_back(Vector(0,0,0));
//Walk along the chain
for (IDRange::iterator iPtr = range->begin()+1; iPtr != range->end(); iPtr++)
{
Vector currRelPos = Sim->particles[*iPtr].getPosition()
- Sim->particles[*(iPtr - 1)].getPosition();
Sim->BCs->applyBC(currRelPos);
relVecs.push_back(currRelPos + relVecs.back());
double mass = Sim->species[Sim->particles[*iPtr]]->getMass(*iPtr);
retVal.MassCentre += relVecs.back() * mass;
totmass += mass;
}
retVal.MassCentre /= totmass;
//Now determine the inertia tensor
Matrix inertiaTensor;
inertiaTensor.zero();
BOOST_FOREACH(Vector & vec, relVecs)
{
vec -= retVal.MassCentre;
inertiaTensor += Dyadic(vec, vec);
}
void
OPMisc::initialise()
{
_KE.init(Sim->dynamics->getSystemKineticEnergy());
_internalE.init(Sim->calcInternalEnergy());
dout << "Particle Count " << Sim->N
<< "\nSim Unit Length " << Sim->units.unitLength()
<< "\nSim Unit Time " << Sim->units.unitTime()
<< "\nDensity " << Sim->getNumberDensity()
* Sim->units.unitVolume()
<< "\nPacking Fraction " << Sim->getPackingFraction()
<< "\nTemperature " << getCurrentkT() / Sim->units.unitEnergy()
<< "\nNo. of Species " << Sim->species.size()
<< "\nSimulation box length <x y z> < ";
for (size_t iDim = 0; iDim < NDIM; iDim++)
dout << Sim->primaryCellSize[iDim] / Sim->units.unitLength() << " ";
dout << ">\n";
Matrix kineticP;
Vector thermalConductivityFS(0,0,0);
_speciesMomenta.clear();
_speciesMomenta.resize(Sim->species.size());
_speciesMasses.clear();
_speciesMasses.resize(Sim->species.size());
BOOST_FOREACH(const Particle& part, Sim->particles)
{
const Species& sp = *(Sim->species[part]);
const double mass = sp.getMass(part.getID());
kineticP += mass * Dyadic(part.getVelocity(), part.getVelocity());
_speciesMasses[sp.getID()] += mass;
_speciesMomenta[sp.getID()] += mass * part.getVelocity();
thermalConductivityFS
+= part.getVelocity() * Sim->dynamics->getParticleKineticEnergy(part);
}
Vector sysMomentum(0,0,0);
_systemMass = 0;
for (size_t i(0); i < Sim->species.size(); ++i)
{
sysMomentum += _speciesMomenta[i];
_systemMass += _speciesMasses[i];
}
_kineticP.init(kineticP);
_sysMomentum.init(sysMomentum);
//Set up the correlators
double correlator_dt = Sim->lastRunMFT / 8;
if (correlator_dt == 0.0)
correlator_dt = 1.0 / sqrt(getCurrentkT());
_thermalConductivity.resize(correlator_dt, 10);
_thermalConductivity.setFreeStreamValue(thermalConductivityFS);
_viscosity.resize(correlator_dt, 10);
_viscosity.setFreeStreamValue(kineticP);
_thermalDiffusion.resize(Sim->species.size());
_mutualDiffusion.resize(Sim->species.size() * Sim->species.size());
for (size_t spid1(0); spid1 < Sim->species.size(); ++spid1)
{
_thermalDiffusion[spid1].resize(correlator_dt, 10);
_thermalDiffusion[spid1]
.setFreeStreamValue(thermalConductivityFS,
_speciesMomenta[spid1]
- (_speciesMasses[spid1] / _systemMass)
* _sysMomentum.current());
for (size_t spid2(spid1); spid2 < Sim->species.size(); ++spid2)
{
_mutualDiffusion[spid1 * Sim->species.size() + spid2].resize(correlator_dt, 10);
_mutualDiffusion[spid1 * Sim->species.size() + spid2].setFreeStreamValue
(_speciesMomenta[spid1] - (_speciesMasses[spid1] / _systemMass) * _sysMomentum.current(),
_speciesMomenta[spid2] - (_speciesMasses[spid2] / _systemMass) * _sysMomentum.current());
}
}
dout << "Total momentum < ";
for (size_t iDim = 0; iDim < NDIM; iDim++)
dout << _sysMomentum.current()[iDim] / Sim->units.unitMomentum() << " ";
dout << ">\n";
std::time(&tstartTime);
clock_gettime(CLOCK_MONOTONIC, &acc_tstartTime);
std::string sTime(std::ctime(&tstartTime));
sTime[sTime.size()-1] = ' ';
dout << "Started on " << sTime << std::endl;
}
void OPMisc::eventUpdate(const NEventData& NDat)
{
Vector thermalDel(0,0,0);
BOOST_FOREACH(const ParticleEventData& PDat, NDat.L1partChanges)
{
const Particle& part = Sim->particles[PDat.getParticleID()];
const double p1E = Sim->dynamics->getParticleKineticEnergy(Sim->particles[PDat.getParticleID()]);
const Species& species = *Sim->species[PDat.getSpeciesID()];
double mass = species.getMass(part.getID());
Vector delP1 = mass * (part.getVelocity() - PDat.getOldVel());
_singleEvents += (PDat.getType() != VIRTUAL);
_virtualEvents += (PDat.getType() == VIRTUAL);
_KE += PDat.getDeltaKE();
_internalE += PDat.getDeltaU();
_kineticP += mass * (Dyadic(part.getVelocity(), part.getVelocity())
- Dyadic(PDat.getOldVel(), PDat.getOldVel()));
_sysMomentum += delP1;
_speciesMomenta[species.getID()] += delP1;
thermalDel += part.getVelocity() * p1E
- PDat.getOldVel() * (p1E - PDat.getDeltaKE());
}
BOOST_FOREACH(const PairEventData& PDat, NDat.L2partChanges)
{
_KE += PDat.particle1_.getDeltaKE() + PDat.particle2_.getDeltaKE();
_internalE += PDat.particle1_.getDeltaU() + PDat.particle2_.getDeltaU();
_dualEvents += (PDat.getType() != VIRTUAL);
_virtualEvents += (PDat.getType() == VIRTUAL);
const Particle& part1 = Sim->particles[PDat.particle1_.getParticleID()];
const Particle& part2 = Sim->particles[PDat.particle2_.getParticleID()];
const Species& sp1 = *Sim->species[PDat.particle1_.getSpeciesID()];
const Species& sp2 = *Sim->species[PDat.particle2_.getSpeciesID()];
const double p1E = Sim->dynamics->getParticleKineticEnergy(part1);
const double p2E = Sim->dynamics->getParticleKineticEnergy(part2);
const double mass1 = sp1.getMass(part1.getID());
const double mass2 = sp2.getMass(part2.getID());
Vector delP = mass1 * (part1.getVelocity() - PDat.particle1_.getOldVel());
collisionalP += magnet::math::Dyadic(PDat.rij, delP);
_kineticP
+= mass1 * (Dyadic(part1.getVelocity(), part1.getVelocity())
- Dyadic(PDat.particle1_.getOldVel(), PDat.particle1_.getOldVel()))
+ mass2 * (Dyadic(part2.getVelocity(), part2.getVelocity())
- Dyadic(PDat.particle2_.getOldVel(), PDat.particle2_.getOldVel()));
_viscosity.addImpulse(magnet::math::Dyadic(PDat.rij, delP));
_speciesMomenta[sp1.getID()] += delP;
_speciesMomenta[sp2.getID()] -= delP;
Vector thermalImpulse = PDat.rij * PDat.particle1_.getDeltaKE();
_thermalConductivity.addImpulse(thermalImpulse);
for (size_t spid1(0); spid1 < Sim->species.size(); ++spid1)
_thermalDiffusion[spid1].addImpulse(thermalImpulse, Vector(0,0,0));
thermalDel += part1.getVelocity() * p1E + part2.getVelocity() * p2E
- PDat.particle1_.getOldVel() * (p1E - PDat.particle1_.getDeltaKE())
- PDat.particle2_.getOldVel() * (p2E - PDat.particle2_.getDeltaKE());
}
_thermalConductivity.setFreeStreamValue
(_thermalConductivity.getFreeStreamValue() + thermalDel);
_viscosity.setFreeStreamValue(_kineticP.current());
for (size_t spid1(0); spid1 < Sim->species.size(); ++spid1)
{
_thermalDiffusion[spid1]
.setFreeStreamValue(_thermalConductivity.getFreeStreamValue(),
_speciesMomenta[spid1] - _sysMomentum.current() * (_speciesMasses[spid1] / _systemMass));
for (size_t spid2(spid1); spid2 < Sim->species.size(); ++spid2)
_mutualDiffusion[spid1 * Sim->species.size() + spid2].setFreeStreamValue
(_speciesMomenta[spid1] - (_speciesMasses[spid1] / _systemMass) * _sysMomentum.current(),
_speciesMomenta[spid2] - (_speciesMasses[spid2] / _systemMass) * _sysMomentum.current());
}
}
