CD_TracerParticleStepperImplem.H

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/* chombo-discharge
 * Copyright © 2022 SINTEF Energy Research.
 * Please refer to Copyright.txt and LICENSE in the chombo-discharge root directory.
 */
 
#ifndef CD_TracerParticleStepperImplem_H
#define CD_TracerParticleStepperImplem_H
 
// Chombo includes
#include <CH_Timer.H>
 
// Our includes
#include <CD_ParticleManagement.H>
#include <CD_Random.H>
#include <CD_TracerParticleStepper.H>
#include <CD_NamespaceHeader.H>
 
using namespace Physics::TracerParticle;
 
template <typename P>
inline TracerParticleStepper<P>::TracerParticleStepper()
{
  CH_TIME("TracerParticleStepper::TracerParticleStepper");
 
  m_realm = Realm::Primal;
  m_phase = phase::gas;
 
  this->parseOptions();
}
 
template <typename P>
inline TracerParticleStepper<P>::~TracerParticleStepper()
{
  CH_TIME("TracerParticleStepper::~TracerParticleStepper");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::~TracerParticleStepper" << endl;
  }
}
 
template <typename P>
inline void
TracerParticleStepper<P>::setupSolvers()
{
  CH_TIME("TracerParticleStepper::setupSolvers()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::setupSolvers()" << endl;
  }
 
  m_solver = RefCountedPtr<TracerParticleSolver<P>>(new TracerParticleSolver<P>(m_amr, m_computationalGeometry));
 
  m_solver->setPhase(m_phase);
  m_solver->setRealm(m_realm);
  m_solver->parseOptions();
}
 
template <typename P>
inline void
TracerParticleStepper<P>::allocate()
{
  CH_TIME("TracerParticleStepper::allocate()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::allocate()" << endl;
  }
 
  m_amr->allocate(m_velocity, m_realm, m_phase, SpaceDim);
  m_solver->allocate();
}
 
template <typename P>
inline void
TracerParticleStepper<P>::initialData()
{
  CH_TIME("TracerParticleStepper::initialData()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::initialData()" << endl;
  }
 
  this->setVelocity();
  this->initialParticles();
 
  m_solver->setVelocity(m_velocity);
  m_solver->interpolateVelocities();
}
 
template <typename P>
inline void
TracerParticleStepper<P>::registerRealms()
{
  CH_TIME("TracerParticleStepper::registerRealms()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::registerRealms()" << endl;
  }
 
  m_amr->registerRealm(m_realm);
}
 
template <typename P>
inline void
TracerParticleStepper<P>::registerOperators()
{
  CH_TIME("TracerParticleStepper::registerOperators()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::registerOperators()" << endl;
  }
 
  m_solver->registerOperators();
}
 
template <typename P>
inline void
TracerParticleStepper<P>::parseOptions()
{
  CH_TIME("TracerParticleStepper::parseOptions()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::parseOptions()" << endl;
  }
 
  this->parseIntegrator();
  this->parseVelocityField();
  this->parseInitialConditions();
}
 
template <typename P>
inline void
TracerParticleStepper<P>::parseRuntimeOptions()
{
  CH_TIME("TracerParticleStepper::parseRuntimeOptions()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::parseRuntimeOptions()" << endl;
  }
 
  this->parseIntegrator();
 
  m_solver->parseRuntimeOptions();
}
 
template <typename P>
inline void
TracerParticleStepper<P>::parseIntegrator()
{
  CH_TIME("TracerParticleStepper::parseIntegrator()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::parseIntegrator()" << endl;
  }
 
  ParmParse pp("TracerParticleStepper");
 
  std::string str;
 
  pp.get("verbosity", m_verbosity);
  pp.get("cfl", m_cfl);
  pp.get("integration", str);
  if (str == "euler") {
    m_algorithm = IntegrationAlgorithm::Euler;
  }
  else if (str == "rk2") {
    m_algorithm = IntegrationAlgorithm::RK2;
  }
  else if (str == "rk4") {
    m_algorithm = IntegrationAlgorithm::RK4;
  }
  else {
    MayDay::Error("TracerParticleStepper::parseIntegrator -- logic bust");
  }
}
 
template <typename P>
inline void
TracerParticleStepper<P>::parseVelocityField()
{
  CH_TIME("TracerParticleStepper::parseVelocityField()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::parseVelocityField()" << endl;
  }
 
  ParmParse pp("TracerParticleStepper");
 
  int v;
  pp.get("velocity_field", v);
 
  if (v == 0) {
    m_velocityField = VelocityField::Diagonal;
  }
  else if (v == 1) {
    m_velocityField = VelocityField::Rotational;
  }
  else {
    MayDay::Error("TracerParticleStepper::parseVelocityField -- logic bust");
  }
}
 
template <typename P>
inline void
TracerParticleStepper<P>::parseInitialConditions()
{
  CH_TIME("TracerParticleStepper::parseInitialConditions()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::parseInitialConditions()" << endl;
  }
 
  ParmParse pp("TracerParticleStepper");
 
  Real numParticles;
  pp.get("initial_particles", numParticles);
 
  m_numInitialParticles = size_t(std::max(0.0, numParticles));
}
 
#ifdef CH_USE_HDF5
template <typename P>
inline void
TracerParticleStepper<P>::writeCheckpointData(HDF5Handle& a_handle, const int a_lvl) const
{
  CH_TIME("TracerParticleStepper::writeCheckpointData(HDF5Handle, int)");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::writeCheckpointData(HDF5Handle, int)" << endl;
  }
 
  m_solver->writeCheckpointLevel(a_handle, a_lvl);
}
#endif
 
#ifdef CH_USE_HDF5
template <typename P>
inline void
TracerParticleStepper<P>::readCheckpointData(HDF5Handle& a_handle, const int a_lvl)
{
  CH_TIME("TracerParticleStepper::readCheckpointData(HDF5Handle, int)");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::readCheckpointData(HDF5Handle, int)" << endl;
  }
 
  m_solver->readCheckpointLevel(a_handle, a_lvl);
}
#endif
 
template <typename P>
inline int
TracerParticleStepper<P>::getNumberOfPlotVariables() const
{
  CH_TIME("TracerParticleStepper::getNumberOfPlotVariables()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::getNumberOfPlotVariables()" << endl;
  }
 
  return m_solver->getNumberOfPlotVariables();
}
 
template <typename P>
inline Vector<std::string>
TracerParticleStepper<P>::getPlotVariableNames() const
{
  CH_TIME("TracerParticleStepper::getPlotVariableNames()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::getPlotVariableNames()" << endl;
  }
 
  return m_solver->getPlotVariableNames();
}
 
template <typename P>
inline void
TracerParticleStepper<P>::writePlotData(LevelData<EBCellFAB>& a_output,
                                        int&                  a_icomp,
                                        const std::string     a_outputRealm,
                                        const int             a_level) const
{
  CH_TIME("TracerParticleStepper::writePlotData(EBAMRCellData, Vector<std::string>, int)");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::writePlotData(EBAMRCellData, Vector<std::string>, int)" << endl;
  }
 
  CH_assert(a_level >= 0);
  CH_assert(a_level <= m_amr->getFinestLevel());
 
  m_solver->writePlotData(a_output, a_icomp, a_outputRealm, a_level);
}
 
template <typename P>
inline Real
TracerParticleStepper<P>::computeDt()
{
  CH_TIME("TracerParticleStepper::computeDt()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::computeDt()" << endl;
  }
 
  return m_cfl * m_solver->computeDt();
}
 
template <typename P>
inline Real
TracerParticleStepper<P>::advance(const Real a_dt)
{
  CH_TIME("TracerParticleStepper::advance(Real)");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::advance(Real)" << endl;
  }
 
  switch (m_algorithm) {
  case IntegrationAlgorithm::Euler: {
    this->advanceParticlesEuler(a_dt);
 
    break;
  }
  case IntegrationAlgorithm::RK2: {
    this->advanceParticlesRK2(a_dt);
 
    break;
  }
  case IntegrationAlgorithm::RK4: {
    this->advanceParticlesRK4(a_dt);
 
    break;
  }
  default: {
    MayDay::Error("TracerParticleStepper::advance -- logic bust");
  }
  }
 
  return a_dt;
}
 
template <typename P>
inline void
TracerParticleStepper<P>::synchronizeSolverTimes(const int a_step, const Real a_time, const Real a_dt)
{
  CH_TIME("TracerParticleStepper::synchronizeSolverTimes");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::synchronizeSolverTimes" << endl;
  }
 
  m_timeStep = a_step;
  m_time     = a_time;
  m_dt       = a_dt;
 
  m_solver->setTime(a_step, a_time, a_dt);
}
 
template <typename P>
inline void
TracerParticleStepper<P>::preRegrid(const int a_lmin, const int a_oldFinestLevel)
{
  CH_TIME("TracerParticleStepper::preRegrid(int, int)");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::preRegrid(int, int)" << endl;
  }
 
  m_solver->preRegrid(a_lmin, a_oldFinestLevel);
}
 
template <typename P>
inline void
TracerParticleStepper<P>::regrid(const int a_lmin, const int a_oldFinestLevel, const int a_newFinestLevel)
{
  CH_TIME("TracerParticleStepper::regrid(int, int, int)");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::regrid(int, int, int)" << endl;
  }
 
  // Define velocity field on the new mesh.
  m_amr->reallocate(m_velocity, m_phase, a_lmin);
  DataOps::setValue(m_velocity, 0.0);
 
  // Regrid tracer particles.
  m_solver->regrid(a_lmin, a_oldFinestLevel, a_newFinestLevel);
}
 
template <typename P>
inline void
TracerParticleStepper<P>::postRegrid()
{
  CH_TIME("TracerParticleStepper::postRegrid()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::postRegrid()" << endl;
  }
 
  // Update particle velocities.
  this->setVelocity();
  m_solver->interpolateVelocities();
}
 
template <typename P>
inline void
TracerParticleStepper<P>::setVelocity()
{
  CH_TIME("TracerParticleStepper::setVelocity()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::setVelocity()" << endl;
  }
 
  std::function<RealVect(const RealVect a_position)> velFunc;
 
  switch (m_velocityField) {
  case VelocityField::Diagonal: {
    velFunc = [](const RealVect& a_position) -> RealVect {
      return RealVect::Unit;
    };
 
    break;
  }
  case VelocityField::Rotational: {
    velFunc = [](const RealVect pos) -> RealVect {
      const Real r     = pos.vectorLength();
      const Real theta = atan2(pos[1], pos[0]);
 
      return RealVect(D_DECL(-r * sin(theta), r * cos(theta), 0.));
    };
 
    break;
  }
  }
 
  DataOps::setValue(m_velocity, velFunc, m_amr->getProbLo(), m_amr->getDx());
 
  m_amr->conservativeAverage(m_velocity, m_realm, m_phase);
  m_amr->interpGhost(m_velocity, m_realm, m_phase);
}
 
template <typename P>
inline void
TracerParticleStepper<P>::initialParticles()
{
  CH_TIME("TracerParticleStepper::initialParticles()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::initialParticles()" << endl;
  }
 
  // TLDR: This code draws distributed particles. Thanks to our nifty ParticleManagement and Random static classes this is just
  //       a matter of defining a distribution function. We define this as a lambda that draws particles uniformly distributed
  //       inside a box.
  //
  //       After creating the distribution we draw the particles (MPI rank distribution being taken care of under the hood) and
  //       set their weight to one. Finally, we add these particles to the ParticleContainer and remove the particles that lie inside
  //       the EB.
 
  // Create a random distribution which draw particles uniformly distributed in the domain.
  const RealVect probLo = m_amr->getProbLo();
  const RealVect probHi = m_amr->getProbHi();
 
  auto uniformDistribution = [probLo, probHi]() -> RealVect {
    RealVect ret = probLo;
 
    for (int dir = 0; dir < SpaceDim; dir++) {
      ret[dir] += (probHi - probLo)[dir] * Random::getUniformReal01();
    }
 
    return ret;
  };
 
  // Draw particles using the distribution above. Set their weight to one.
  List<P> initialParticles;
 
  ParticleManagement::drawRandomParticles(initialParticles, m_numInitialParticles, uniformDistribution);
  for (ListIterator<P> lit(initialParticles); lit.ok(); ++lit) {
    lit().weight() = 1.0;
  }
 
  // Put the particles in the solver particle data holder.
  ParticleContainer<P>& solverParticles = m_solver->getParticles();
  solverParticles.clearParticles();
  solverParticles.addParticlesDestructive(initialParticles);
 
  // Remove particles inside the EB.
  pout() << "removing particles" << endl;
  m_amr->removeCoveredParticlesIF(solverParticles, m_phase);
  pout() << "done initial particles" << endl;
}
 
template <typename P>
inline void
TracerParticleStepper<P>::advanceParticlesEuler(const Real a_dt)
{
  CH_TIME("TracerParticleStepper::advanceParticlesEuler()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::advanceParticlesEuler()" << endl;
  }
 
  // TLDR: The new position is just x^(k+1) = x^k + dt*v^k
 
  ParticleContainer<P>& amrParticles = m_solver->getParticles();
 
  for (int lvl = 0; lvl <= m_amr->getFinestLevel(); lvl++) {
    const DisjointBoxLayout& dbl = m_amr->getGrids(m_realm)[lvl];
    const DataIterator&      dit = dbl.dataIterator();
 
    const int nbox = dit.size();
 
#pragma omp parallel for schedule(runtime)
    for (int mybox = 0; mybox < nbox; mybox++) {
      const DataIndex& din = dit[mybox];
 
      List<P>& particles = amrParticles[lvl][din].listItems();
 
      for (ListIterator<P> lit(particles); lit.ok(); ++lit) {
        P& p = lit();
 
        p.position() += p.velocity() * a_dt;
      }
    }
  }
 
  amrParticles.remap();
  m_amr->removeCoveredParticlesIF(amrParticles, m_phase);
 
  m_solver->interpolateVelocities();
}
 
template <typename P>
inline void
TracerParticleStepper<P>::advanceParticlesRK2(const Real a_dt)
{
  CH_TIME("TracerParticleStepper::advanceParticlesRK2()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::advanceParticlesRK2()" << endl;
  }
 
  // TLDR: The new positions are x^(k+1) = x^k + 0.5*dt*[ v(x^k) + v(x^*) ] where x^* = x^k + dt*v^k.
 
  ParticleContainer<P>& amrParticles = m_solver->getParticles();
 
  // First step. Store old position and velocity and do the Euler advance.
  for (int lvl = 0; lvl <= m_amr->getFinestLevel(); lvl++) {
    const DisjointBoxLayout& dbl = m_amr->getGrids(m_realm)[lvl];
    const DataIterator&      dit = dbl.dataIterator();
 
    const int nbox = dit.size();
 
#pragma omp parallel for schedule(runtime)
    for (int mybox = 0; mybox < nbox; mybox++) {
      const DataIndex& din = dit[mybox];
 
      List<P>& particles = amrParticles[lvl][din].listItems();
 
      for (ListIterator<P> lit(particles); lit.ok(); ++lit) {
        P& p = lit();
 
        p.template vect<0>() = p.position();
        p.template vect<1>() = p.velocity();
 
        p.position() += p.velocity() * a_dt;
      }
    }
  }
 
  // Remap and interpolate the velocities again. This puts the velocity v = v(x^*) into the particles
  amrParticles.remap();
  m_amr->removeCoveredParticlesIF(amrParticles, m_phase);
  m_solver->interpolateVelocities();
 
  // Do the second RK2 stage.
  for (int lvl = 0; lvl <= m_amr->getFinestLevel(); lvl++) {
    const DisjointBoxLayout& dbl = m_amr->getGrids(m_realm)[lvl];
    const DataIterator&      dit = dbl.dataIterator();
 
    const int nbox = dit.size();
 
#pragma omp parallel for schedule(runtime)
    for (int mybox = 0; mybox < nbox; mybox++) {
      const DataIndex& din = dit[mybox];
 
      List<P>& particles = amrParticles[lvl][din].listItems();
 
      for (ListIterator<P> lit(particles); lit.ok(); ++lit) {
        P& p = lit();
 
        // x^k+1     = x^k                  + dt/2     * [v(x^k)               + v(x^*)      ]
        p.position() = p.template vect<0>() + 0.5 * a_dt * (p.template vect<1>() + p.velocity());
      }
    }
  }
 
  // Remap and interpolate the velocities again
  amrParticles.remap();
  m_amr->removeCoveredParticlesIF(amrParticles, m_phase);
  m_solver->interpolateVelocities();
}
 
template <typename P>
inline void
TracerParticleStepper<P>::advanceParticlesRK4(const Real a_dt)
{
  CH_TIME("TracerParticleStepper::advanceParticlesRK4()");
  if (m_verbosity > 5) {
    pout() << "TracerParticleStepper::advanceParticlesRK4()" << endl;
  }
 
  // TLDR: Just the standard RK4 method.
 
  ParticleContainer<P>& amrParticles = m_solver->getParticles();
 
  const Real dtHalf  = a_dt / 2.0;
  const Real dtThird = a_dt / 3.0;
  const Real dtSixth = a_dt / 6.0;
 
  // k1 step.
  {
    for (int lvl = 0; lvl <= m_amr->getFinestLevel(); lvl++) {
      const DisjointBoxLayout& dbl = m_amr->getGrids(m_realm)[lvl];
      const DataIterator&      dit = dbl.dataIterator();
 
      const int nbox = dit.size();
 
#pragma omp parallel for schedule(runtime)
      for (int mybox = 0; mybox < nbox; mybox++) {
        const DataIndex& din = dit[mybox];
 
        for (ListIterator<P> lit(amrParticles[lvl][din].listItems()); lit.ok(); ++lit) {
          P& p = lit();
 
          // Store old position.
          p.template vect<0>() = p.position();
 
          p.template vect<1>() = p.velocity();                                 // k1 = v(x^k)
          p.position()         = p.template vect<0>() + dtHalf * p.velocity(); // x = x^k + 0.5*dt*k1
        }
      }
    }
 
    // Remap and compute v = v(x)
    amrParticles.remap();
    m_solver->interpolateVelocities();
  }
 
  // k2 step.
  {
    for (int lvl = 0; lvl <= m_amr->getFinestLevel(); lvl++) {
      const DisjointBoxLayout& dbl = m_amr->getGrids(m_realm)[lvl];
      const DataIterator&      dit = dbl.dataIterator();
 
      const int nbox = dit.size();
 
#pragma omp parallel for schedule(runtime)
      for (int mybox = 0; mybox < nbox; mybox++) {
        const DataIndex& din = dit[mybox];
 
        for (ListIterator<P> lit(amrParticles[lvl][din].listItems()); lit.ok(); ++lit) {
          P& p = lit();
 
          p.template vect<2>() = p.velocity();                                 // k2 = v(x^k + 0.5 * k1 * dt)
          p.position()         = p.template vect<0>() + dtHalf * p.velocity(); // x = x^k + 0.5*dt*k2
        }
      }
    }
 
    // Remap and compute v = v(x)
    amrParticles.remap();
    m_solver->interpolateVelocities();
  }
 
  // k3 step.
  {
    for (int lvl = 0; lvl <= m_amr->getFinestLevel(); lvl++) {
      const DisjointBoxLayout& dbl = m_amr->getGrids(m_realm)[lvl];
      const DataIterator&      dit = dbl.dataIterator();
 
      const int nbox = dit.size();
 
#pragma omp parallel for schedule(runtime)
      for (int mybox = 0; mybox < nbox; mybox++) {
        const DataIndex& din = dit[mybox];
 
        for (ListIterator<P> lit(amrParticles[lvl][din].listItems()); lit.ok(); ++lit) {
          P& p = lit();
 
          p.template vect<3>() = p.velocity();                               // k3 = v(x^k + 0.5 * k2 * dt)
          p.position()         = p.template vect<0>() + a_dt * p.velocity(); // x^k + k3*a_dt
        }
      }
    }
 
    // Remap and compute v = v(x)
    amrParticles.remap();
    m_solver->interpolateVelocities();
  }
 
  // Final step.
  {
    for (int lvl = 0; lvl <= m_amr->getFinestLevel(); lvl++) {
      const DisjointBoxLayout& dbl = m_amr->getGrids(m_realm)[lvl];
      const DataIterator&      dit = dbl.dataIterator();
 
      const int nbox = dit.size();
 
#pragma omp parallel for schedule(runtime)
      for (int mybox = 0; mybox < nbox; mybox++) {
        const DataIndex& din = dit[mybox];
 
        for (ListIterator<P> lit(amrParticles[lvl][din].listItems()); lit.ok(); ++lit) {
          P& p = lit();
 
          p.position() = p.template vect<0>() + dtSixth * p.template vect<1>() + dtHalf * p.template vect<2>() +
                         dtHalf * p.template vect<3>() + dtSixth * p.velocity();
        }
      }
    }
 
    // Remap and compute v = v(x)
    amrParticles.remap();
    m_solver->interpolateVelocities();
  }
 
  m_amr->removeCoveredParticlesIF(amrParticles, m_phase);
}
 
#include <CD_NamespaceFooter.H>
 
#endif