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PhysicalParticleContainer.cpp
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/* Copyright 2019-2020 Andrew Myers, Aurore Blelly, Axel Huebl
* David Grote, Glenn Richardson, Jean-Luc Vay
* Ligia Diana Amorim, Luca Fedeli, Maxence Thevenet
* Michael Rowan, Remi Lehe, Revathi Jambunathan
* Weiqun Zhang, Yinjian Zhao
*
* This file is part of WarpX.
*
* License: BSD-3-Clause-LBNL
*/
#include "PhysicalParticleContainer.H"
#include "Filter/NCIGodfreyFilter.H"
#include "Initialization/InjectorDensity.H"
#include "Initialization/InjectorMomentum.H"
#include "Initialization/InjectorPosition.H"
#include "MultiParticleContainer.H"
#ifdef WARPX_QED
# include "Particles/ElementaryProcess/QEDInternals/BreitWheelerEngineWrapper.H"
# include "Particles/ElementaryProcess/QEDInternals/QuantumSyncEngineWrapper.H"
#endif
#include "Particles/Gather/FieldGather.H"
#include "Particles/Gather/GetExternalFields.H"
#include "Particles/ParticleCreation/DefaultInitialization.H"
#include "Particles/Pusher/CopyParticleAttribs.H"
#include "Particles/Pusher/GetAndSetPosition.H"
#include "Particles/Pusher/PushSelector.H"
#include "Particles/Pusher/UpdateMomentumBoris.H"
#include "Particles/Pusher/UpdateMomentumBorisWithRadiationReaction.H"
#include "Particles/Pusher/UpdateMomentumHigueraCary.H"
#include "Particles/Pusher/UpdateMomentumVay.H"
#include "Particles/Pusher/UpdatePosition.H"
#include "Particles/SpeciesPhysicalProperties.H"
#include "Particles/WarpXParticleContainer.H"
#include "Utils/Parser/ParserUtils.H"
#include "Utils/ParticleUtils.H"
#include "Utils/Physics/IonizationEnergiesTable.H"
#include "Utils/TextMsg.H"
#include "Utils/WarpXAlgorithmSelection.H"
#include "Utils/WarpXConst.H"
#include "Utils/WarpXProfilerWrapper.H"
#ifdef AMREX_USE_EB
# include "EmbeddedBoundary/ParticleBoundaryProcess.H"
# include "EmbeddedBoundary/ParticleScraper.H"
#endif
#include "WarpX.H"
#include <ablastr/warn_manager/WarnManager.H>
#include <AMReX.H>
#include <AMReX_Algorithm.H>
#include <AMReX_Array.H>
#include <AMReX_Array4.H>
#include <AMReX_ArrayOfStructs.H>
#include <AMReX_BLassert.H>
#include <AMReX_Box.H>
#include <AMReX_BoxArray.H>
#include <AMReX_Config.H>
#include <AMReX_Dim3.H>
#include <AMReX_Extension.H>
#include <AMReX_FArrayBox.H>
#include <AMReX_FabArray.H>
#include <AMReX_Geometry.H>
#include <AMReX_GpuAtomic.H>
#include <AMReX_GpuControl.H>
#include <AMReX_GpuDevice.H>
#include <AMReX_GpuElixir.H>
#include <AMReX_GpuLaunch.H>
#include <AMReX_GpuQualifiers.H>
#include <AMReX_INT.H>
#include <AMReX_IndexType.H>
#include <AMReX_IntVect.H>
#include <AMReX_LayoutData.H>
#include <AMReX_MFIter.H>
#include <AMReX_Math.H>
#include <AMReX_MultiFab.H>
#include <AMReX_PODVector.H>
#include <AMReX_ParGDB.H>
#include <AMReX_ParIter.H>
#include <AMReX_ParallelDescriptor.H>
#include <AMReX_ParmParse.H>
#include <AMReX_Particle.H>
#include <AMReX_ParticleContainerBase.H>
#include <AMReX_AmrParticles.H>
#include <AMReX_ParticleTile.H>
#include <AMReX_Print.H>
#include <AMReX_Random.H>
#include <AMReX_SPACE.H>
#include <AMReX_Scan.H>
#include <AMReX_StructOfArrays.H>
#include <AMReX_Utility.H>
#include <AMReX_Vector.H>
#include <AMReX_Parser.H>
#ifdef AMREX_USE_OMP
# include <omp.h>
#endif
#ifdef WARPX_USE_OPENPMD
# include <openPMD/openPMD.hpp>
#endif
#include <algorithm>
#include <array>
#include <cmath>
#include <cstdlib>
#include <limits>
#include <map>
#include <random>
#include <string>
#include <utility>
#include <vector>
#include <sstream>
using namespace amrex;
namespace
{
using ParticleType = WarpXParticleContainer::ParticleType;
// Since the user provides the density distribution
// at t_lab=0 and in the lab-frame coordinates,
// we need to find the lab-frame position of this
// particle at t_lab=0, from its boosted-frame coordinates
// Assuming ballistic motion, this is given by:
// z0_lab = gamma*( z_boost*(1-beta*betaz_lab) - ct_boost*(betaz_lab-beta) )
// where betaz_lab is the speed of the particle in the lab frame
//
// In order for this equation to be solvable, betaz_lab
// is explicitly assumed to have no dependency on z0_lab
//
// Note that we use the bulk momentum to perform the ballistic correction
// Assume no z0_lab dependency
AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE
Real applyBallisticCorrection(const XDim3& pos, const InjectorMomentum* inj_mom,
Real gamma_boost, Real beta_boost, Real t) noexcept
{
const XDim3 u_bulk = inj_mom->getBulkMomentum(pos.x, pos.y, pos.z);
const Real gamma_bulk = std::sqrt(1._rt +
(u_bulk.x*u_bulk.x+u_bulk.y*u_bulk.y+u_bulk.z*u_bulk.z));
const Real betaz_bulk = u_bulk.z/gamma_bulk;
const Real z0 = gamma_boost * ( pos.z*(1.0_rt-beta_boost*betaz_bulk)
- PhysConst::c*t*(betaz_bulk-beta_boost) );
return z0;
}
struct PDim3 {
ParticleReal x, y, z;
AMREX_GPU_HOST_DEVICE
PDim3(const amrex::XDim3& a):
x{a.x}, y{a.y}, z{a.z}
{}
AMREX_GPU_HOST_DEVICE
~PDim3() = default;
AMREX_GPU_HOST_DEVICE
PDim3(PDim3 const &) = default;
AMREX_GPU_HOST_DEVICE
PDim3& operator=(PDim3 const &) = default;
AMREX_GPU_HOST_DEVICE
PDim3(PDim3&&) = default;
AMREX_GPU_HOST_DEVICE
PDim3& operator=(PDim3&&) = default;
};
AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE
XDim3 getCellCoords (const GpuArray<Real, AMREX_SPACEDIM>& lo_corner,
const GpuArray<Real, AMREX_SPACEDIM>& dx,
const XDim3& r, const IntVect& iv) noexcept
{
XDim3 pos;
#if defined(WARPX_DIM_3D)
pos.x = lo_corner[0] + (iv[0]+r.x)*dx[0];
pos.y = lo_corner[1] + (iv[1]+r.y)*dx[1];
pos.z = lo_corner[2] + (iv[2]+r.z)*dx[2];
#elif defined(WARPX_DIM_XZ) || defined(WARPX_DIM_RZ)
pos.x = lo_corner[0] + (iv[0]+r.x)*dx[0];
pos.y = 0.0_rt;
#if defined WARPX_DIM_XZ
pos.z = lo_corner[1] + (iv[1]+r.y)*dx[1];
#elif defined WARPX_DIM_RZ
// Note that for RZ, r.y will be theta
pos.z = lo_corner[1] + (iv[1]+r.z)*dx[1];
#endif
#else
pos.x = 0.0_rt;
pos.y = 0.0_rt;
pos.z = lo_corner[0] + (iv[0]+r.x)*dx[0];
#endif
return pos;
}
/**
* \brief This function is called in AddPlasma when we want a particle to be removed at the
* next call to redistribute. It initializes all the particle properties to zero (to be safe
* and avoid any possible undefined behavior before the next call to redistribute) and sets
* the particle id to -1 so that it can be effectively deleted.
*
* \param idcpu particle id soa data
* \param pa particle real soa data
* \param ip index for soa data
* \param do_field_ionization whether species has ionization
* \param pi ionization level data
* \param has_quantum_sync whether species has quantum synchrotron
* \param p_optical_depth_QSR quantum synchrotron optical depth data
* \param has_breit_wheeler whether species has Breit-Wheeler
* \param p_optical_depth_BW Breit-Wheeler optical depth data
*/
AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE
void ZeroInitializeAndSetNegativeID (
uint64_t * AMREX_RESTRICT idcpu,
const GpuArray<ParticleReal*,PIdx::nattribs>& pa, long& ip,
const bool& do_field_ionization, int* pi
#ifdef WARPX_QED
,const bool& has_quantum_sync, amrex::ParticleReal* AMREX_RESTRICT p_optical_depth_QSR
,const bool& has_breit_wheeler, amrex::ParticleReal* AMREX_RESTRICT p_optical_depth_BW
#endif
) noexcept
{
pa[PIdx::z][ip] = 0._rt;
#if (AMREX_SPACEDIM >= 2)
pa[PIdx::x][ip] = 0._rt;
#endif
#if defined(WARPX_DIM_3D)
pa[PIdx::y][ip] = 0._rt;
#endif
pa[PIdx::w ][ip] = 0._rt;
pa[PIdx::ux][ip] = 0._rt;
pa[PIdx::uy][ip] = 0._rt;
pa[PIdx::uz][ip] = 0._rt;
#ifdef WARPX_DIM_RZ
pa[PIdx::theta][ip] = 0._rt;
#endif
if (do_field_ionization) {pi[ip] = 0;}
#ifdef WARPX_QED
if (has_quantum_sync) {p_optical_depth_QSR[ip] = 0._rt;}
if (has_breit_wheeler) {p_optical_depth_BW[ip] = 0._rt;}
#endif
idcpu[ip] = amrex::ParticleIdCpus::Invalid;
}
}
PhysicalParticleContainer::PhysicalParticleContainer (AmrCore* amr_core, int ispecies,
const std::string& name)
: WarpXParticleContainer(amr_core, ispecies),
species_name(name)
{
BackwardCompatibility();
const ParmParse pp_species_name(species_name);
std::string injection_style = "none";
pp_species_name.query("injection_style", injection_style);
if (injection_style != "none") {
// The base plasma injector, whose input parameters have no source prefix.
// Only created if needed
plasma_injectors.push_back(std::make_unique<PlasmaInjector>(species_id, species_name, amr_core->Geom(0)));
}
std::vector<std::string> injection_sources;
pp_species_name.queryarr("injection_sources", injection_sources);
for (auto &source_name : injection_sources) {
plasma_injectors.push_back(std::make_unique<PlasmaInjector>(species_id, species_name, amr_core->Geom(0),
source_name));
}
// Setup the charge and mass. There are multiple ways that they can be specified, so checks are needed to
// ensure that a value is specified and warnings given if multiple values are specified.
// The ordering is that species.charge and species.mass take precedence over all other values.
// Next is charge and mass determined from species_type.
// Last is charge and mass from the plasma injector setup
bool charge_from_source = false;
bool mass_from_source = false;
for (auto const& plasma_injector : plasma_injectors) {
// For now, use the last value for charge and mass that is found.
// A check could be added for consistency of multiple values, but it'll probably never be needed
charge_from_source |= plasma_injector->queryCharge(charge);
mass_from_source |= plasma_injector->queryMass(mass);
}
std::string physical_species_s;
const bool species_is_specified = pp_species_name.query("species_type", physical_species_s);
if (species_is_specified) {
const auto physical_species_from_string = species::from_string( physical_species_s );
WARPX_ALWAYS_ASSERT_WITH_MESSAGE(physical_species_from_string,
physical_species_s + " does not exist!");
physical_species = physical_species_from_string.value();
charge = species::get_charge( physical_species );
mass = species::get_mass( physical_species );
}
// parse charge and mass (overriding values above)
const bool charge_is_specified = utils::parser::queryWithParser(pp_species_name, "charge", charge);
const bool mass_is_specified = utils::parser::queryWithParser(pp_species_name, "mass", mass);
if (charge_is_specified && species_is_specified) {
ablastr::warn_manager::WMRecordWarning("Species",
"Both '" + species_name + ".charge' and " +
species_name + ".species_type' are specified.\n" +
species_name + ".charge' will take precedence.\n");
}
if (mass_is_specified && species_is_specified) {
ablastr::warn_manager::WMRecordWarning("Species",
"Both '" + species_name + ".mass' and " +
species_name + ".species_type' are specified.\n" +
species_name + ".mass' will take precedence.\n");
}
WARPX_ALWAYS_ASSERT_WITH_MESSAGE(
charge_from_source ||
charge_is_specified ||
species_is_specified,
"Need to specify at least one of species_type or charge for species '" +
species_name + "'."
);
WARPX_ALWAYS_ASSERT_WITH_MESSAGE(
mass_from_source ||
mass_is_specified ||
species_is_specified,
"Need to specify at least one of species_type or mass for species '" +
species_name + "'."
);
pp_species_name.query("boost_adjust_transverse_positions", boost_adjust_transverse_positions);
pp_species_name.query("do_backward_propagation", do_backward_propagation);
pp_species_name.query("random_theta", m_rz_random_theta);
// Initialize splitting
pp_species_name.query("do_splitting", do_splitting);
pp_species_name.query("split_type", split_type);
pp_species_name.query("do_not_deposit", do_not_deposit);
pp_species_name.query("do_not_gather", do_not_gather);
pp_species_name.query("do_not_push", do_not_push);
pp_species_name.query("do_continuous_injection", do_continuous_injection);
pp_species_name.query("initialize_self_fields", initialize_self_fields);
utils::parser::queryWithParser(
pp_species_name, "self_fields_required_precision", self_fields_required_precision);
utils::parser::queryWithParser(
pp_species_name, "self_fields_absolute_tolerance", self_fields_absolute_tolerance);
utils::parser::queryWithParser(
pp_species_name, "self_fields_max_iters", self_fields_max_iters);
pp_species_name.query("self_fields_verbosity", self_fields_verbosity);
pp_species_name.query("do_field_ionization", do_field_ionization);
pp_species_name.query("do_resampling", do_resampling);
if (do_resampling) { m_resampler = Resampling(species_name); }
//check if Radiation Reaction is enabled and do consistency checks
pp_species_name.query("do_classical_radiation_reaction", do_classical_radiation_reaction);
//if the species is not a lepton, do_classical_radiation_reaction
//should be false
WARPX_ALWAYS_ASSERT_WITH_MESSAGE(
!(do_classical_radiation_reaction &&
!(AmIA<PhysicalSpecies::electron>() ||
AmIA<PhysicalSpecies::positron>() )),
"can't enable classical radiation reaction for non lepton species '"
+ species_name + "'.");
//Only Boris pusher is compatible with radiation reaction
WARPX_ALWAYS_ASSERT_WITH_MESSAGE(
!(do_classical_radiation_reaction &&
WarpX::particle_pusher_algo != ParticlePusherAlgo::Boris),
"Radiation reaction can be enabled only if Boris pusher is used");
//_____________________________
#ifdef WARPX_QED
pp_species_name.query("do_qed_quantum_sync", m_do_qed_quantum_sync);
if (m_do_qed_quantum_sync) {
AddRealComp("opticalDepthQSR");
}
pp_species_name.query("do_qed_breit_wheeler", m_do_qed_breit_wheeler);
if (m_do_qed_breit_wheeler) {
AddRealComp("opticalDepthBW");
}
if(m_do_qed_quantum_sync){
pp_species_name.get("qed_quantum_sync_phot_product_species",
m_qed_quantum_sync_phot_product_name);
}
#endif
// User-defined integer attributes
pp_species_name.queryarr("addIntegerAttributes", m_user_int_attribs);
const auto n_user_int_attribs = static_cast<int>(m_user_int_attribs.size());
std::vector< std::string > str_int_attrib_function;
str_int_attrib_function.resize(n_user_int_attribs);
m_user_int_attrib_parser.resize(n_user_int_attribs);
for (int i = 0; i < n_user_int_attribs; ++i) {
utils::parser::Store_parserString(
pp_species_name, "attribute."+m_user_int_attribs.at(i)+"(x,y,z,ux,uy,uz,t)",
str_int_attrib_function.at(i));
m_user_int_attrib_parser.at(i) = std::make_unique<amrex::Parser>(
utils::parser::makeParser(str_int_attrib_function.at(i),{"x","y","z","ux","uy","uz","t"}));
AddIntComp(m_user_int_attribs.at(i));
}
// User-defined real attributes
pp_species_name.queryarr("addRealAttributes", m_user_real_attribs);
const auto n_user_real_attribs = static_cast<int>(m_user_real_attribs.size());
std::vector< std::string > str_real_attrib_function;
str_real_attrib_function.resize(n_user_real_attribs);
m_user_real_attrib_parser.resize(n_user_real_attribs);
for (int i = 0; i < n_user_real_attribs; ++i) {
utils::parser::Store_parserString(
pp_species_name, "attribute."+m_user_real_attribs.at(i)+"(x,y,z,ux,uy,uz,t)",
str_real_attrib_function.at(i));
m_user_real_attrib_parser.at(i) = std::make_unique<amrex::Parser>(
utils::parser::makeParser(str_real_attrib_function.at(i),{"x","y","z","ux","uy","uz","t"}));
AddRealComp(m_user_real_attribs.at(i));
}
// If old particle positions should be saved add the needed components
pp_species_name.query("save_previous_position", m_save_previous_position);
if (m_save_previous_position) {
#if (AMREX_SPACEDIM >= 2)
AddRealComp("prev_x");
#endif
#if defined(WARPX_DIM_3D)
AddRealComp("prev_y");
#endif
AddRealComp("prev_z");
#ifdef WARPX_DIM_RZ
amrex::Abort("Saving previous particle positions not yet implemented in RZ");
#endif
}
// Read reflection models for absorbing boundaries; defaults to a zero
pp_species_name.query("reflection_model_xlo(E)", m_boundary_conditions.reflection_model_xlo_str);
pp_species_name.query("reflection_model_xhi(E)", m_boundary_conditions.reflection_model_xhi_str);
pp_species_name.query("reflection_model_ylo(E)", m_boundary_conditions.reflection_model_ylo_str);
pp_species_name.query("reflection_model_yhi(E)", m_boundary_conditions.reflection_model_yhi_str);
pp_species_name.query("reflection_model_zlo(E)", m_boundary_conditions.reflection_model_zlo_str);
pp_species_name.query("reflection_model_zhi(E)", m_boundary_conditions.reflection_model_zhi_str);
m_boundary_conditions.BuildReflectionModelParsers();
const ParmParse pp_boundary("boundary");
bool flag = false;
pp_boundary.query("reflect_all_velocities", flag);
m_boundary_conditions.Set_reflect_all_velocities(flag);
}
PhysicalParticleContainer::PhysicalParticleContainer (AmrCore* amr_core)
: WarpXParticleContainer(amr_core, 0)
{
}
void
PhysicalParticleContainer::BackwardCompatibility ()
{
const ParmParse pp_species_name(species_name);
std::vector<std::string> backward_strings;
if (pp_species_name.queryarr("plot_vars", backward_strings)){
WARPX_ABORT_WITH_MESSAGE("<species>.plot_vars is not supported anymore. "
"Please use the new syntax for diagnostics, see documentation.");
}
int backward_int;
if (pp_species_name.query("plot_species", backward_int)){
WARPX_ABORT_WITH_MESSAGE("<species>.plot_species is not supported anymore. "
"Please use the new syntax for diagnostics, see documentation.");
}
}
void PhysicalParticleContainer::InitData ()
{
AddParticles(0); // Note - add on level 0
Redistribute(); // We then redistribute
}
void PhysicalParticleContainer::MapParticletoBoostedFrame (
ParticleReal& x, ParticleReal& y, ParticleReal& z, ParticleReal& ux, ParticleReal& uy, ParticleReal& uz, Real t_lab) const
{
// Map the particles from the lab frame to the boosted frame.
// This boosts the particle to the lab frame and calculates
// the particle time in the boosted frame. It then maps
// the position to the time in the boosted frame.
// For now, start with the assumption that this will only happen
// at the start of the simulation.
const ParticleReal uz_boost = WarpX::gamma_boost*WarpX::beta_boost*PhysConst::c;
// tpr is the particle's time in the boosted frame
const ParticleReal tpr = WarpX::gamma_boost*t_lab - uz_boost*z/(PhysConst::c*PhysConst::c);
// The particle's transformed location in the boosted frame
const ParticleReal xpr = x;
const ParticleReal ypr = y;
const ParticleReal zpr = WarpX::gamma_boost*z - uz_boost*t_lab;
// transform u and gamma to the boosted frame
const ParticleReal gamma_lab = std::sqrt(1._rt + (ux*ux + uy*uy + uz*uz)/(PhysConst::c*PhysConst::c));
// ux = ux;
// uy = uy;
uz = WarpX::gamma_boost*uz - uz_boost*gamma_lab;
const ParticleReal gammapr = std::sqrt(1._rt + (ux*ux + uy*uy + uz*uz)/(PhysConst::c*PhysConst::c));
const ParticleReal vxpr = ux/gammapr;
const ParticleReal vypr = uy/gammapr;
const ParticleReal vzpr = uz/gammapr;
if (do_backward_propagation){
uz = -uz;
}
//Move the particles to where they will be at t = t0, the current simulation time in the boosted frame
constexpr int lev = 0;
const amrex::Real t0 = WarpX::GetInstance().gett_new(lev);
if (boost_adjust_transverse_positions) {
x = xpr - (tpr-t0)*vxpr;
y = ypr - (tpr-t0)*vypr;
}
z = zpr - (tpr-t0)*vzpr;
}
void
PhysicalParticleContainer::AddGaussianBeam (
PlasmaInjector const& plasma_injector,
const Real x_m, const Real y_m, const Real z_m,
const Real x_rms, const Real y_rms, const Real z_rms,
const Real x_cut, const Real y_cut, const Real z_cut,
const Real q_tot, long npart,
const int do_symmetrize,
const int symmetrization_order) {
// Declare temporary vectors on the CPU
Gpu::HostVector<ParticleReal> particle_x;
Gpu::HostVector<ParticleReal> particle_y;
Gpu::HostVector<ParticleReal> particle_z;
Gpu::HostVector<ParticleReal> particle_ux;
Gpu::HostVector<ParticleReal> particle_uy;
Gpu::HostVector<ParticleReal> particle_uz;
Gpu::HostVector<ParticleReal> particle_w;
if (ParallelDescriptor::IOProcessor()) {
// If do_symmetrize, create either 4x or 8x fewer particles, and
// Replicate each particle either 4 times (x,y) (-x,y) (x,-y) (-x,-y)
// or 8 times, additionally (y,x), (-y,x), (y,-x), (-y,-x)
if (do_symmetrize){
npart /= symmetrization_order;
}
for (long i = 0; i < npart; ++i) {
#if defined(WARPX_DIM_3D) || defined(WARPX_DIM_RZ)
const Real weight = q_tot/(npart*charge);
const Real x = amrex::RandomNormal(x_m, x_rms);
const Real y = amrex::RandomNormal(y_m, y_rms);
const Real z = amrex::RandomNormal(z_m, z_rms);
#elif defined(WARPX_DIM_XZ)
const Real weight = q_tot/(npart*charge*y_rms);
const Real x = amrex::RandomNormal(x_m, x_rms);
constexpr Real y = 0._prt;
const Real z = amrex::RandomNormal(z_m, z_rms);
#elif defined(WARPX_DIM_1D_Z)
const Real weight = q_tot/(npart*charge*x_rms*y_rms);
constexpr Real x = 0._prt;
constexpr Real y = 0._prt;
const Real z = amrex::RandomNormal(z_m, z_rms);
#endif
if (plasma_injector.insideBounds(x, y, z) &&
std::abs( x - x_m ) <= x_cut * x_rms &&
std::abs( y - y_m ) <= y_cut * y_rms &&
std::abs( z - z_m ) <= z_cut * z_rms ) {
XDim3 u = plasma_injector.getMomentum(x, y, z);
u.x *= PhysConst::c;
u.y *= PhysConst::c;
u.z *= PhysConst::c;
if (do_symmetrize && symmetrization_order == 8){
// Add eight particles to the beam:
CheckAndAddParticle(x, y, z, u.x, u.y, u.z, weight/8._rt,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
CheckAndAddParticle(x, -y, z, u.x, -u.y, u.z, weight/8._rt,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
CheckAndAddParticle(-x, y, z, -u.x, u.y, u.z, weight/8._rt,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
CheckAndAddParticle(-x, -y, z, -u.x, -u.y, u.z, weight/8._rt,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
CheckAndAddParticle(y, x, z, u.y, u.x, u.z, weight/8._rt,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
CheckAndAddParticle(-y, x, z, -u.y, u.x, u.z, weight/8._rt,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
CheckAndAddParticle(y, -x, z, u.y, -u.x, u.z, weight/8._rt,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
CheckAndAddParticle(-y, -x, z, -u.y, -u.x, u.z, weight/8._rt,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
} else if (do_symmetrize && symmetrization_order == 4){
// Add four particles to the beam:
CheckAndAddParticle(x, y, z, u.x, u.y, u.z, weight/4._rt,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
CheckAndAddParticle(x, -y, z, u.x, -u.y, u.z, weight/4._rt,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
CheckAndAddParticle(-x, y, z, -u.x, u.y, u.z, weight/4._rt,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
CheckAndAddParticle(-x, -y, z, -u.x, -u.y, u.z, weight/4._rt,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
} else {
CheckAndAddParticle(x, y, z, u.x, u.y, u.z, weight,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w);
}
}
}
}
// Add the temporary CPU vectors to the particle structure
auto const np = static_cast<long>(particle_z.size());
amrex::Vector<ParticleReal> xp(particle_x.data(), particle_x.data() + np);
amrex::Vector<ParticleReal> yp(particle_y.data(), particle_y.data() + np);
amrex::Vector<ParticleReal> zp(particle_z.data(), particle_z.data() + np);
amrex::Vector<ParticleReal> uxp(particle_ux.data(), particle_ux.data() + np);
amrex::Vector<ParticleReal> uyp(particle_uy.data(), particle_uy.data() + np);
amrex::Vector<ParticleReal> uzp(particle_uz.data(), particle_uz.data() + np);
amrex::Vector<amrex::Vector<ParticleReal>> attr;
amrex::Vector<ParticleReal> wp(particle_w.data(), particle_w.data() + np);
attr.push_back(wp);
amrex::Vector<amrex::Vector<int>> attr_int;
AddNParticles(0, np, xp, yp, zp, uxp, uyp, uzp,
1, attr, 0, attr_int, 1);
}
void
PhysicalParticleContainer::AddPlasmaFromFile(PlasmaInjector & plasma_injector,
ParticleReal q_tot,
ParticleReal z_shift)
{
// Declare temporary vectors on the CPU
Gpu::HostVector<ParticleReal> particle_x;
Gpu::HostVector<ParticleReal> particle_z;
Gpu::HostVector<ParticleReal> particle_ux;
Gpu::HostVector<ParticleReal> particle_uz;
Gpu::HostVector<ParticleReal> particle_w;
Gpu::HostVector<ParticleReal> particle_y;
Gpu::HostVector<ParticleReal> particle_uy;
#ifdef WARPX_USE_OPENPMD
//TODO: Make changes for read/write in multiple MPI ranks
if (ParallelDescriptor::IOProcessor()) {
// take ownership of the series and close it when done
auto series = std::move(plasma_injector.m_openpmd_input_series);
// assumption asserts: see PlasmaInjector
openPMD::Iteration it = series->iterations.begin()->second;
const ParmParse pp_species_name(species_name);
pp_species_name.query("impose_t_lab_from_file", impose_t_lab_from_file);
double t_lab = 0._prt;
if (impose_t_lab_from_file) {
// Impose t_lab as being the time stored in the openPMD file
t_lab = it.time<double>() * it.timeUnitSI();
}
std::string const ps_name = it.particles.begin()->first;
openPMD::ParticleSpecies ps = it.particles.begin()->second;
auto const npart = ps["position"]["x"].getExtent()[0];
#if !defined(WARPX_DIM_1D_Z) // 2D, 3D, and RZ
const std::shared_ptr<ParticleReal> ptr_x = ps["position"]["x"].loadChunk<ParticleReal>();
const std::shared_ptr<ParticleReal> ptr_offset_x = ps["positionOffset"]["x"].loadChunk<ParticleReal>();
auto const position_unit_x = static_cast<ParticleReal>(ps["position"]["x"].unitSI());
auto const position_offset_unit_x = static_cast<ParticleReal>(ps["positionOffset"]["x"].unitSI());
#endif
#if !(defined(WARPX_DIM_XZ) || defined(WARPX_DIM_1D_Z))
const std::shared_ptr<ParticleReal> ptr_y = ps["position"]["y"].loadChunk<ParticleReal>();
const std::shared_ptr<ParticleReal> ptr_offset_y = ps["positionOffset"]["y"].loadChunk<ParticleReal>();
auto const position_unit_y = static_cast<ParticleReal>(ps["position"]["y"].unitSI());
auto const position_offset_unit_y = static_cast<ParticleReal>(ps["positionOffset"]["y"].unitSI());
#endif
const std::shared_ptr<ParticleReal> ptr_z = ps["position"]["z"].loadChunk<ParticleReal>();
const std::shared_ptr<ParticleReal> ptr_offset_z = ps["positionOffset"]["z"].loadChunk<ParticleReal>();
auto const position_unit_z = static_cast<ParticleReal>(ps["position"]["z"].unitSI());
auto const position_offset_unit_z = static_cast<ParticleReal>(ps["positionOffset"]["z"].unitSI());
const std::shared_ptr<ParticleReal> ptr_ux = ps["momentum"]["x"].loadChunk<ParticleReal>();
auto const momentum_unit_x = static_cast<ParticleReal>(ps["momentum"]["x"].unitSI());
const std::shared_ptr<ParticleReal> ptr_uz = ps["momentum"]["z"].loadChunk<ParticleReal>();
auto const momentum_unit_z = static_cast<ParticleReal>(ps["momentum"]["z"].unitSI());
const std::shared_ptr<ParticleReal> ptr_w = ps["weighting"][openPMD::RecordComponent::SCALAR].loadChunk<ParticleReal>();
auto const w_unit = static_cast<ParticleReal>(ps["weighting"][openPMD::RecordComponent::SCALAR].unitSI());
std::shared_ptr<ParticleReal> ptr_uy = nullptr;
auto momentum_unit_y = 1.0_prt;
if (ps["momentum"].contains("y")) {
ptr_uy = ps["momentum"]["y"].loadChunk<ParticleReal>();
momentum_unit_y = static_cast<ParticleReal>(ps["momentum"]["y"].unitSI());
}
series->flush(); // shared_ptr data can be read now
if (q_tot != 0.0) {
std::stringstream warnMsg;
warnMsg << " Loading particle species from file. " << ps_name << ".q_tot is ignored.";
ablastr::warn_manager::WMRecordWarning("AddPlasmaFromFile",
warnMsg.str(), ablastr::warn_manager::WarnPriority::high);
}
for (auto i = decltype(npart){0}; i<npart; ++i){
ParticleReal const weight = ptr_w.get()[i]*w_unit;
#if !defined(WARPX_DIM_1D_Z)
ParticleReal const x = ptr_x.get()[i]*position_unit_x + ptr_offset_x.get()[i]*position_offset_unit_x;
#else
ParticleReal const x = 0.0_prt;
#endif
#if defined(WARPX_DIM_3D) || defined(WARPX_DIM_RZ)
ParticleReal const y = ptr_y.get()[i]*position_unit_y + ptr_offset_y.get()[i]*position_offset_unit_y;
#else
ParticleReal const y = 0.0_prt;
#endif
ParticleReal const z = ptr_z.get()[i]*position_unit_z + ptr_offset_z.get()[i]*position_offset_unit_z + z_shift;
if (plasma_injector.insideBounds(x, y, z)) {
ParticleReal const ux = ptr_ux.get()[i]*momentum_unit_x/mass;
ParticleReal const uz = ptr_uz.get()[i]*momentum_unit_z/mass;
ParticleReal uy = 0.0_prt;
if (ps["momentum"].contains("y")) {
uy = ptr_uy.get()[i]*momentum_unit_y/mass;
}
CheckAndAddParticle(x, y, z, ux, uy, uz, weight,
particle_x, particle_y, particle_z,
particle_ux, particle_uy, particle_uz,
particle_w, static_cast<amrex::Real>(t_lab));
}
}
auto const np = particle_z.size();
if (np < npart) {
ablastr::warn_manager::WMRecordWarning("Species",
"Simulation box doesn't cover all particles",
ablastr::warn_manager::WarnPriority::high);
}
} // IO Processor
auto const np = static_cast<long>(particle_z.size());
amrex::Vector<ParticleReal> xp(particle_x.data(), particle_x.data() + np);
amrex::Vector<ParticleReal> yp(particle_y.data(), particle_y.data() + np);
amrex::Vector<ParticleReal> zp(particle_z.data(), particle_z.data() + np);
amrex::Vector<ParticleReal> uxp(particle_ux.data(), particle_ux.data() + np);
amrex::Vector<ParticleReal> uyp(particle_uy.data(), particle_uy.data() + np);
amrex::Vector<ParticleReal> uzp(particle_uz.data(), particle_uz.data() + np);
amrex::Vector<amrex::Vector<ParticleReal>> attr;
amrex::Vector<ParticleReal> wp(particle_w.data(), particle_w.data() + np);
attr.push_back(wp);
amrex::Vector<amrex::Vector<int>> attr_int;
AddNParticles(0, np, xp, yp, zp, uxp, uyp, uzp,
1, attr, 0, attr_int, 1);
#endif // WARPX_USE_OPENPMD
ignore_unused(plasma_injector, q_tot, z_shift);
}
void
PhysicalParticleContainer::DefaultInitializeRuntimeAttributes (
typename ContainerLike<amrex::PinnedArenaAllocator>::ParticleTileType& pinned_tile,
int n_external_attr_real,
int n_external_attr_int)
{
ParticleCreation::DefaultInitializeRuntimeAttributes(pinned_tile,
n_external_attr_real, n_external_attr_int,
m_user_real_attribs, m_user_int_attribs,
particle_comps, particle_icomps,
amrex::GetVecOfPtrs(m_user_real_attrib_parser),
amrex::GetVecOfPtrs(m_user_int_attrib_parser),
#ifdef WARPX_QED
true,
m_shr_p_bw_engine.get(),
m_shr_p_qs_engine.get(),
#endif
ionization_initial_level,
0,pinned_tile.numParticles());
}
void
PhysicalParticleContainer::CheckAndAddParticle (
ParticleReal x, ParticleReal y, ParticleReal z,
ParticleReal ux, ParticleReal uy, ParticleReal uz,
ParticleReal weight,
Gpu::HostVector<ParticleReal>& particle_x,
Gpu::HostVector<ParticleReal>& particle_y,
Gpu::HostVector<ParticleReal>& particle_z,
Gpu::HostVector<ParticleReal>& particle_ux,
Gpu::HostVector<ParticleReal>& particle_uy,
Gpu::HostVector<ParticleReal>& particle_uz,
Gpu::HostVector<ParticleReal>& particle_w,
Real t_lab) const
{
if (WarpX::gamma_boost > 1.) {
MapParticletoBoostedFrame(x, y, z, ux, uy, uz, t_lab);
}
particle_x.push_back(x);
particle_y.push_back(y);
particle_z.push_back(z);
particle_ux.push_back(ux);
particle_uy.push_back(uy);
particle_uz.push_back(uz);
particle_w.push_back(weight);
}
void
PhysicalParticleContainer::AddParticles (int lev)
{
WARPX_PROFILE("PhysicalParticleContainer::AddParticles()");
for (auto const& plasma_injector : plasma_injectors) {
if (plasma_injector->add_single_particle) {
if (WarpX::gamma_boost > 1.) {
MapParticletoBoostedFrame(plasma_injector->single_particle_pos[0],
plasma_injector->single_particle_pos[1],
plasma_injector->single_particle_pos[2],
plasma_injector->single_particle_u[0],
plasma_injector->single_particle_u[1],
plasma_injector->single_particle_u[2]);
}
amrex::Vector<ParticleReal> xp = {plasma_injector->single_particle_pos[0]};
amrex::Vector<ParticleReal> yp = {plasma_injector->single_particle_pos[1]};
amrex::Vector<ParticleReal> zp = {plasma_injector->single_particle_pos[2]};
amrex::Vector<ParticleReal> uxp = {plasma_injector->single_particle_u[0]};
amrex::Vector<ParticleReal> uyp = {plasma_injector->single_particle_u[1]};
amrex::Vector<ParticleReal> uzp = {plasma_injector->single_particle_u[2]};
amrex::Vector<amrex::Vector<ParticleReal>> attr = {{plasma_injector->single_particle_weight}};
amrex::Vector<amrex::Vector<int>> attr_int;
AddNParticles(lev, 1, xp, yp, zp, uxp, uyp, uzp,
1, attr, 0, attr_int, 0);
return;
}
if (plasma_injector->add_multiple_particles) {
if (WarpX::gamma_boost > 1.) {
for (int i=0 ; i < plasma_injector->multiple_particles_pos_x.size() ; i++) {
MapParticletoBoostedFrame(plasma_injector->multiple_particles_pos_x[i],
plasma_injector->multiple_particles_pos_y[i],
plasma_injector->multiple_particles_pos_z[i],
plasma_injector->multiple_particles_ux[i],
plasma_injector->multiple_particles_uy[i],
plasma_injector->multiple_particles_uz[i]);
}
}
amrex::Vector<amrex::Vector<ParticleReal>> attr;
attr.push_back(plasma_injector->multiple_particles_weight);
amrex::Vector<amrex::Vector<int>> attr_int;
AddNParticles(lev, static_cast<int>(plasma_injector->multiple_particles_pos_x.size()),
plasma_injector->multiple_particles_pos_x,
plasma_injector->multiple_particles_pos_y,
plasma_injector->multiple_particles_pos_z,
plasma_injector->multiple_particles_ux,
plasma_injector->multiple_particles_uy,
plasma_injector->multiple_particles_uz,
1, attr, 0, attr_int, 0);
}
if (plasma_injector->gaussian_beam) {
AddGaussianBeam(*plasma_injector,
plasma_injector->x_m,
plasma_injector->y_m,
plasma_injector->z_m,
plasma_injector->x_rms,
plasma_injector->y_rms,
plasma_injector->z_rms,
plasma_injector->x_cut,
plasma_injector->y_cut,
plasma_injector->z_cut,
plasma_injector->q_tot,
plasma_injector->npart,
plasma_injector->do_symmetrize,
plasma_injector->symmetrization_order);
}
if (plasma_injector->external_file) {
AddPlasmaFromFile(*plasma_injector,
plasma_injector->q_tot,
plasma_injector->z_shift);
}
if ( plasma_injector->doInjection() ) {
AddPlasma(*plasma_injector, lev);
}
}
}
void
PhysicalParticleContainer::AddPlasma (PlasmaInjector const& plasma_injector, int lev, RealBox part_realbox)
{
WARPX_PROFILE("PhysicalParticleContainer::AddPlasma()");
// If no part_realbox is provided, initialize particles in the whole domain
const Geometry& geom = Geom(lev);
if (!part_realbox.ok()) { part_realbox = geom.ProbDomain(); }
const int num_ppc = plasma_injector.num_particles_per_cell;
#ifdef WARPX_DIM_RZ
Real rmax = std::min(plasma_injector.xmax, part_realbox.hi(0));
#endif
const auto dx = geom.CellSizeArray();
const auto problo = geom.ProbLoArray();
defineAllParticleTiles();
amrex::LayoutData<amrex::Real>* cost = WarpX::getCosts(lev);
const int nlevs = numLevels();
static bool refine_injection = false;
static Box fine_injection_box;
static amrex::IntVect rrfac(AMREX_D_DECL(1,1,1));
// This does not work if the mesh is dynamic. But in that case, we should
// not use refined injected either. We also assume there is only one fine level.
if (WarpX::moving_window_active(WarpX::GetInstance().getistep(0)+1) and WarpX::refine_plasma
and do_continuous_injection and nlevs == 2)
{
refine_injection = true;
fine_injection_box = ParticleBoxArray(1).minimalBox();
fine_injection_box.setSmall(WarpX::moving_window_dir, std::numeric_limits<int>::lowest()/2);
fine_injection_box.setBig(WarpX::moving_window_dir, std::numeric_limits<int>::max()/2);
rrfac = m_gdb->refRatio(0);
fine_injection_box.coarsen(rrfac);
}
InjectorPosition* inj_pos = plasma_injector.getInjectorPosition();
InjectorDensity* inj_rho = plasma_injector.getInjectorDensity();
InjectorMomentum* inj_mom = plasma_injector.getInjectorMomentumDevice();
const Real gamma_boost = WarpX::gamma_boost;
const Real beta_boost = WarpX::beta_boost;
const Real t = WarpX::GetInstance().gett_new(lev);
const Real density_min = plasma_injector.density_min;
const Real density_max = plasma_injector.density_max;
#ifdef WARPX_DIM_RZ
const int nmodes = WarpX::n_rz_azimuthal_modes;
bool radially_weighted = plasma_injector.radially_weighted;
#endif
MFItInfo info;
if (do_tiling && Gpu::notInLaunchRegion()) {
info.EnableTiling(tile_size);
}
#ifdef AMREX_USE_OMP
info.SetDynamic(true);
#pragma omp parallel if (not WarpX::serialize_initial_conditions)
#endif
for (MFIter mfi = MakeMFIter(lev, info); mfi.isValid(); ++mfi)
{
if (cost && WarpX::load_balance_costs_update_algo == LoadBalanceCostsUpdateAlgo::Timers)
{
amrex::Gpu::synchronize();
}
auto wt = static_cast<amrex::Real>(amrex::second());
const Box& tile_box = mfi.tilebox();
const RealBox tile_realbox = WarpX::getRealBox(tile_box, lev);
// Find the cells of part_box that overlap with tile_realbox
// If there is no overlap, just go to the next tile in the loop
RealBox overlap_realbox;
Box overlap_box;
IntVect shifted;
bool no_overlap = false;
for (int dir=0; dir<AMREX_SPACEDIM; dir++) {
if ( tile_realbox.lo(dir) <= part_realbox.hi(dir) ) {
const Real ncells_adjust = std::floor( (tile_realbox.lo(dir) - part_realbox.lo(dir))/dx[dir] );
overlap_realbox.setLo( dir, part_realbox.lo(dir) + std::max(ncells_adjust, 0._rt) * dx[dir]);
} else {
no_overlap = true; break;
}
if ( tile_realbox.hi(dir) >= part_realbox.lo(dir) ) {
const Real ncells_adjust = std::floor( (part_realbox.hi(dir) - tile_realbox.hi(dir))/dx[dir] );
overlap_realbox.setHi( dir, part_realbox.hi(dir) - std::max(ncells_adjust, 0._rt) * dx[dir]);
} else {