void
Dynamics::outputParticleXMLData(magnet::xml::XmlStream& XML, bool applyBC) const
{
XML << magnet::xml::tag("ParticleData");
if (hasOrientationData())
XML << magnet::xml::attr("OrientationData") << "Y";
for (size_t i = 0; i < Sim->N; ++i)
{
Particle tmp(Sim->particles[i]);
if (applyBC)
Sim->BCs->applyBC(tmp.getPosition(), tmp.getVelocity());
tmp.getVelocity() *= (1.0 / Sim->units.unitVelocity());
tmp.getPosition() *= (1.0 / Sim->units.unitLength());
XML << magnet::xml::tag("Pt");
Sim->_properties.outputParticleXMLData(XML, i);
XML << tmp;
if (hasOrientationData())
XML << magnet::xml::tag("O")
<< orientationData[i].angularVelocity
<< magnet::xml::endtag("O")
<< magnet::xml::tag("U")
<< orientationData[i].orientation
<< magnet::xml::endtag("U") ;
XML << magnet::xml::endtag("Pt");
}
XML << magnet::xml::endtag("ParticleData");
}
void
Dynamics::initialise()
{
streamFreq = 10 * Sim->N;
if (hasOrientationData())
{
double sumEnergy(0.0);
for (const Particle& part : Sim->particles)
sumEnergy += Sim->species[part]->getScalarMomentOfInertia(part.getID())
* orientationData[part.getID()].angularVelocity.nrm2();
//Check if any of the species are overridden
bool hasInertia(false);
for (const shared_ptr<Species>& spec : Sim->species)
if (std::dynamic_pointer_cast<SpInertia>(spec))
hasInertia = true;
if (!hasInertia)
M_throw() << "No species have inertia, yet the particles have orientational degrees of freedom set!";
sumEnergy *= 0.5 / Sim->units.unitEnergy();
dout << "System Rotational Energy " << sumEnergy
<< "\nRotational kT " << sumEnergy / Sim->N << std::endl;
}
}
void
Dynamics::rescaleSystemKineticEnergy(const double& scale)
{
double scalefactor(sqrt(scale));
if (std::dynamic_pointer_cast<BCLeesEdwards>(Sim->BCs))
{
const BCLeesEdwards& bc = static_cast<const BCLeesEdwards&>(*Sim->BCs);
for (Particle& part : Sim->particles)
{
const double mass = Sim->species[part]->getMass(part.getID());
if (!std::isinf(mass))
part.getVelocity() = Vector(bc.getPeculiarVelocity(part) * scalefactor + bc.getStreamVelocity(part));
}
}
else
for (Particle& part : Sim->particles)
{
const double mass = Sim->species[part]->getMass(part.getID());
if (!std::isinf(mass))
part.getVelocity() *= scalefactor;
}
if (hasOrientationData())
for (Particle& part : Sim->particles)
{
const double I = Sim->species[part]->getScalarMomentOfInertia(part.getID());
if (!std::isinf(I))
orientationData[part.getID()].angularVelocity *= scalefactor;
}
}
ParticleEventData
DynNewtonian::runAndersenWallCollision(Particle& part, const Vector & vNorm, const double& sqrtT, const double) const
{
updateParticle(part);
if (hasOrientationData())
M_throw() << "Need to implement thermostating of the rotational degrees"
" of freedom";
//This gives a completely new random unit vector with a properly
//distributed Normal component. See Granular Simulation Book
ParticleEventData tmpDat(part, *Sim->species[part], WALL);
double mass = Sim->species[tmpDat.getSpeciesID()]->getMass(part.getID());
for (size_t iDim = 0; iDim < NDIM; iDim++)
part.getVelocity()[iDim] = Sim->normal_sampler() * sqrtT / std::sqrt(mass);
part.getVelocity()
//This first line adds a component in the direction of the normal
+= vNorm * (sqrtT * sqrt(-2.0*log(1.0-Sim->uniform_sampler()) / mass)
//This removes the original normal component
-(part.getVelocity() | vNorm));
tmpDat.setDeltaKE(0.5 * mass * (part.getVelocity().nrm2() - tmpDat.getOldVel().nrm2()));
return tmpDat;
}
ParticleEventData
DynNewtonian::randomGaussianEvent(Particle& part, const double& sqrtT,
const size_t dimensions) const
{
#ifdef DYNAMO_DEBUG
if (dimensions > NDIM)
M_throw() << "Number of dimensions passed larger than NDIM!";
#endif
//See http://mathworld.wolfram.com/SpherePointPicking.html
if (hasOrientationData())
M_throw() << "Need to implement thermostating of the rotational degrees"
" of freedom";
//Ensure the particle is free streamed first
updateParticle(part);
//Collect the precoll data
ParticleEventData tmpDat(part, *Sim->species[part], GAUSSIAN);
double mass = Sim->species[tmpDat.getSpeciesID()]->getMass(part.getID());
double factor = sqrtT / std::sqrt(mass);
//Assign the new velocities
for (size_t iDim = 0; iDim < dimensions; iDim++)
part.getVelocity()[iDim] = Sim->normal_sampler() * factor;
tmpDat.setDeltaKE(0.5 * mass * (part.getVelocity().nrm2() - tmpDat.getOldVel().nrm2()));
return tmpDat;
}
std::pair<bool, double>
DynCompression::getOffcentreSpheresCollision(const double offset1, const double diameter1, const double offset2, const double diameter2, const Particle& p1, const Particle& p2, double t_max, double maxdist) const
{
#ifdef DYNAMO_DEBUG
if (!hasOrientationData())
M_throw() << "Cannot use this function without orientational data";
if (!isUpToDate(p1))
M_throw() << "Particle1 " << p1.getID() << " is not up to date";
if (!isUpToDate(p2))
M_throw() << "Particle2 " << p2.getID() << " is not up to date";
#endif
Vector r12 = p1.getPosition() - p2.getPosition();
Vector v12 = p1.getVelocity() - p2.getVelocity();
Sim->BCs->applyBC(r12, v12);
const double limit_time_window = 1 / growthRate;
std::pair<bool, double> retval = magnet::intersection::offcentre_growing_spheres(r12, v12, orientationData[p1.getID()].angularVelocity, orientationData[p2.getID()].angularVelocity, orientationData[p1.getID()].orientation * Quaternion::initialDirector() * offset1, orientationData[p2.getID()].orientation * Quaternion::initialDirector() * offset2, diameter1, diameter2, maxdist, std::min(limit_time_window, t_max), Sim->systemTime, growthRate);
//Check if there's no collision reported but we've limited the interval
if ((retval.second == HUGE_VAL) && (t_max > limit_time_window))
return std::pair<bool, double>(false, limit_time_window);
//Otherwise return what was calculated
return retval;
}
ParticleEventData
DynCompression::runAndersenWallCollision(Particle& part, const Vector & vNorm, const double& sqrtT, const double d) const
{
updateParticle(part);
if (hasOrientationData())
M_throw() << "Need to implement thermostating of the rotational degrees"
" of freedom";
//This gives a completely new random unit vector with a properly
//distributed Normal component. See Granular Simulation Book
ParticleEventData tmpDat(part, *Sim->species[part], WALL);
double mass = Sim->species[tmpDat.getSpeciesID()]->getMass(part.getID());
std::normal_distribution<> normal_dist;
std::uniform_real_distribution<> uniform_dist;
for (size_t iDim = 0; iDim < NDIM; iDim++)
part.getVelocity()[iDim] = normal_dist(Sim->ranGenerator) * sqrtT / std::sqrt(mass);
part.getVelocity()
//This first line adds a component in the direction of the normal
+= vNorm * (sqrtT * sqrt(-2.0*log(1.0 - uniform_dist(Sim->ranGenerator)) / mass)
//This removes the original normal component
-(part.getVelocity() | vNorm)
//This adds on the velocity of the wall
+ d * growthRate)
;
return tmpDat;
}
void
DynNewtonian::streamParticle(Particle &particle, const double &dt) const
{
particle.getPosition() += particle.getVelocity() * dt;
//The Vector copy is required to make sure that the cached
//orientation doesn't change during calculation
if (hasOrientationData())
orientationData[particle.getID()].orientation
= Rodrigues(orientationData[particle.getID()].angularVelocity * dt)
* Vector(orientationData[particle.getID()].orientation);
}
void
DynGravity::streamParticle(Particle &particle, const double &dt) const
{
bool isDynamic = particle.testState(Particle::DYNAMIC);
particle.getPosition() += dt * (particle.getVelocity() + 0.5 * dt * g * isDynamic);
particle.getVelocity() += dt * g * isDynamic;
if (hasOrientationData())
{
orientationData[particle.getID()].orientation = Quaternion::fromRotationAxis(orientationData[particle.getID()].angularVelocity * dt)
* orientationData[particle.getID()].orientation ;
orientationData[particle.getID()].orientation.normalise();
}
}
double
Liouvillean::getParticleKineticEnergy(const Particle& part) const
{
double energy(0);
if (Sim->dynamics.BCTypeTest<BCLeesEdwards>())
{
const BCLeesEdwards& bc = static_cast<const BCLeesEdwards&>(Sim->dynamics.BCs());
energy += bc.getPeculiarVelocity(part).nrm2()
* Sim->dynamics.getSpecies(part).getMass(part.getID());
}
else
energy += part.getVelocity().nrm2()
* Sim->dynamics.getSpecies(part).getMass(part.getID());
if (hasOrientationData())
energy += orientationData[part.getID()].angularVelocity.nrm2()
* Sim->dynamics.getSpecies(part).getScalarMomentOfInertia(part.getID());
return 0.5 * energy;
}
double
Dynamics::getParticleKineticEnergy(const Particle& part) const
{
double energy(0);
if (std::tr1::dynamic_pointer_cast<BCLeesEdwards>(Sim->BCs))
{
const BCLeesEdwards& bc = static_cast<const BCLeesEdwards&>(*Sim->BCs);
energy += bc.getPeculiarVelocity(part).nrm2()
* Sim->species[part]->getMass(part.getID());
}
else
energy += part.getVelocity().nrm2()
* Sim->species[part]->getMass(part.getID());
if (hasOrientationData())
energy += orientationData[part.getID()].angularVelocity.nrm2()
* Sim->species[part]->getScalarMomentOfInertia(part.getID());
return 0.5 * energy;
}
double
Dynamics::getParticleKineticEnergy(const Particle& part) const
{
const double mass = Sim->species[part]->getMass(part.getID());
double energy(0);
if (!std::isinf(mass))
{
if (std::dynamic_pointer_cast<BCLeesEdwards>(Sim->BCs))
energy += static_cast<const BCLeesEdwards&>(*Sim->BCs).getPeculiarVelocity(part).nrm2() * mass;
else
energy += part.getVelocity().nrm2() * mass;
}
if (hasOrientationData())
{
const double I = Sim->species[part]->getScalarMomentOfInertia(part.getID());
if (!std::isinf(I))
energy += I * orientationData[part.getID()].angularVelocity.nrm2();
}
return 0.5 * energy;
}
/*! \brief Returns the degrees of freedom per particle.
*/
inline size_t getParticleDOF() const { return NDIM + 2 * hasOrientationData(); }