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WarpXInitData.cpp
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/* Copyright 2019-2020 Andrew Myers, Ann Almgren, Aurore Blelly
* Axel Huebl, Burlen Loring, Maxence Thevenet
* Michael Rowan, Remi Lehe, Revathi Jambunathan
* Weiqun Zhang
*
*
* This file is part of WarpX.
*
* License: BSD-3-Clause-LBNL
*/
#include "WarpX.H"
#include "BoundaryConditions/PML.H"
#if (defined WARPX_DIM_RZ) && (defined WARPX_USE_FFT)
# include "BoundaryConditions/PML_RZ.H"
#endif
#include "Diagnostics/MultiDiagnostics.H"
#include "Diagnostics/ReducedDiags/MultiReducedDiags.H"
#include "EmbeddedBoundary/Enabled.H"
#ifdef AMREX_USE_EB
# include "EmbeddedBoundary/EmbeddedBoundaryInit.H"
#endif
#include "Fields.H"
#include "FieldSolver/ElectrostaticSolvers/ElectrostaticSolver.H"
#include "FieldSolver/FiniteDifferenceSolver/MacroscopicProperties/MacroscopicProperties.H"
#include "FieldSolver/FiniteDifferenceSolver/HybridPICModel/HybridPICModel.H"
#include "Filter/BilinearFilter.H"
#include "Filter/NCIGodfreyFilter.H"
#include "Initialization/ExternalField.H"
#include "Initialization/DivCleaner/ProjectionDivCleaner.H"
#include "Particles/MultiParticleContainer.H"
#include "Utils/Logo/GetLogo.H"
#include "Utils/Parser/ParserUtils.H"
#include "Utils/TextMsg.H"
#include "Utils/WarpXAlgorithmSelection.H"
#include "Utils/WarpXConst.H"
#include "Utils/WarpXProfilerWrapper.H"
#include "Utils/WarpXUtil.H"
#include "Python/callbacks.H"
#include <ablastr/fields/MultiFabRegister.H>
#include <ablastr/math/LinearInterpolation.H>
#include <ablastr/parallelization/MPIInitHelpers.H>
#include <ablastr/utils/Communication.H>
#include <ablastr/utils/UsedInputsFile.H>
#include <ablastr/warn_manager/WarnManager.H>
#include <AMReX.H>
#include <AMReX_AmrCore.H>
#ifdef AMREX_USE_SENSEI_INSITU
# include <AMReX_AmrMeshInSituBridge.H>
#endif
#include <AMReX_Array.H>
#include <AMReX_Array4.H>
#include <AMReX_BLassert.H>
#include <AMReX_Box.H>
#include <AMReX_BoxArray.H>
#include <AMReX_BoxList.H>
#include <AMReX_Config.H>
#include <AMReX_Geometry.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_MultiFab.H>
#include <AMReX_ParallelDescriptor.H>
#include <AMReX_ParmParse.H>
#include <AMReX_Parser.H>
#include <AMReX_Print.H>
#include <AMReX_REAL.H>
#include <AMReX_RealBox.H>
#include <AMReX_SPACE.H>
#include <AMReX_Vector.H>
#include <algorithm>
#include <array>
#include <cctype>
#include <iostream>
#include <memory>
#include <string>
#include <utility>
#ifdef WARPX_USE_OPENPMD
# include <openPMD/openPMD.hpp>
#endif
#include "FieldSolver/FiniteDifferenceSolver/FiniteDifferenceSolver.H"
using namespace amrex;
namespace
{
/** Print dt and dx,dy,dz */
void PrintDtDxDyDz (
int max_level, const amrex::Vector<Geometry>& geom, const amrex::Vector<amrex::Real>& dt)
{
for (int lev=0; lev <= max_level; lev++) {
const amrex::Real* dx_lev = geom[lev].CellSize();
amrex::Print() << "Level " << lev << ": dt = " << dt[lev]
#if defined(WARPX_DIM_1D_Z)
<< " ; dz = " << dx_lev[0] << '\n';
#elif defined(WARPX_DIM_XZ) || defined(WARPX_DIM_RZ)
<< " ; dx = " << dx_lev[0]
<< " ; dz = " << dx_lev[1] << '\n';
#elif defined(WARPX_DIM_3D)
<< " ; dx = " << dx_lev[0]
<< " ; dy = " << dx_lev[1]
<< " ; dz = " << dx_lev[2] << '\n';
#endif
}
}
/**
* \brief Check that the number of guard cells is smaller than the number of valid cells,
* for a given MultiFab, and abort otherwise.
*/
void CheckGuardCells (
ablastr::fields::MultiFabRegister& fields,
const std::string& mf_name,
int lev
)
{
if (!fields.has(mf_name, lev)) { return; }
auto & mf = *fields.get(mf_name, lev);
for (amrex::MFIter mfi(mf); mfi.isValid(); ++mfi)
{
const amrex::IntVect vc = mfi.validbox().enclosedCells().size();
const amrex::IntVect gc = mf.nGrowVect();
std::stringstream ss_msg;
ss_msg << "MultiFab " << mf.tags()[1].c_str() << ":" <<
" the number of guard cells " << gc <<
" is larger than or equal to the number of valid cells "
<< vc << ", please reduce the number of guard cells" <<
" or increase the grid size by changing domain decomposition.";
WARPX_ALWAYS_ASSERT_WITH_MESSAGE(vc.allGT(gc), ss_msg.str());
}
}
/**
* \brief Check the requested resources and write performance hints
*
* @param[in] total_nboxes total number of boxes in the simulation
* @param[in] nprocs number of MPI processes
*/
void PerformanceHints (const amrex::Long total_nboxes, const amrex::Long nprocs)
{
// Check: are there more MPI ranks than Boxes?
if (nprocs > total_nboxes) {
std::stringstream warnMsg;
warnMsg << "Too many resources / too little work!\n"
<< " It looks like you requested more compute resources than "
<< "there are total number of boxes of cells available ("
<< total_nboxes << "). "
<< "You started with (" << nprocs
<< ") MPI ranks, so (" << nprocs - total_nboxes
<< ") rank(s) will have no work.\n"
#ifdef AMREX_USE_GPU
<< " On GPUs, consider using 1-8 boxes per GPU that together fill "
<< "each GPU's memory sufficiently. If you do not rely on dynamic "
<< "load-balancing, then one large box per GPU is ideal.\n"
#endif
<< "Consider decreasing the amr.blocking_factor and "
<< "amr.max_grid_size parameters and/or using fewer MPI ranks.\n"
<< " More information:\n"
<< " https://warpx.readthedocs.io/en/latest/usage/workflows/parallelization.html\n";
ablastr::warn_manager::WMRecordWarning(
"Performance", warnMsg.str(), ablastr::warn_manager::WarnPriority::high);
}
#ifdef AMREX_USE_GPU
// Check: Are there more than 12 boxes per GPU?
if (total_nboxes > nprocs * 12) {
std::stringstream warnMsg;
warnMsg << "Too many boxes per GPU!\n"
<< " It looks like you split your simulation domain "
<< "in too many boxes (" << total_nboxes << "), which "
<< "results in an average number of ("
<< amrex::Long(total_nboxes/nprocs) << ") per GPU. "
<< "This causes severe overhead in the communication of "
<< "border/guard regions.\n"
<< " On GPUs, consider using 1-8 boxes per GPU that together fill "
<< "each GPU's memory sufficiently. If you do not rely on dynamic "
<< "load-balancing, then one large box per GPU is ideal.\n"
<< "Consider increasing the amr.blocking_factor and "
<< "amr.max_grid_size parameters and/or using more MPI ranks.\n"
<< " More information:\n"
<< " https://warpx.readthedocs.io/en/latest/usage/workflows/parallelization.html\n";
ablastr::warn_manager::WMRecordWarning(
"Performance", warnMsg.str(), ablastr::warn_manager::WarnPriority::high);
}
#endif
// TODO: warn if some ranks have disproportionally more work than all others
// tricky: it can be ok to assign "vacuum" boxes to some ranks w/o slowing down
// all other ranks; we need to measure this with our load-balancing
// routines and issue a warning only of some ranks stall all other ranks
// TODO: check MPI-rank to GPU ratio (should be 1:1)
// TODO: check memory per MPI rank, especially if GPUs are underutilized
// TODO: CPU tiling hints with OpenMP
}
}
void
WarpX::PostProcessBaseGrids (BoxArray& ba0) const
{
if (numprocs != 0) {
const Box& dom = Geom(0).Domain();
const IntVect& domlo = dom.smallEnd();
const IntVect& domlen = dom.size();
const IntVect sz = domlen / numprocs;
const IntVect extra = domlen - sz*numprocs;
BoxList bl;
#if defined(WARPX_DIM_3D)
for (int k = 0; k < numprocs[2]; ++k) {
// The first extra[2] blocks get one extra cell with a total of
// sz[2]+1. The rest get sz[2] cells. The decomposition in y
// and x directions are similar.
int klo = (k < extra[2]) ? k*(sz[2]+1) : (k*sz[2]+extra[2]);
int khi = (k < extra[2]) ? klo+(sz[2]+1)-1 : klo+sz[2]-1;
klo += domlo[2];
khi += domlo[2];
#endif
#if (AMREX_SPACEDIM >= 2)
for (int j = 0; j < numprocs[1]; ++j) {
int jlo = (j < extra[1]) ? j*(sz[1]+1) : (j*sz[1]+extra[1]);
int jhi = (j < extra[1]) ? jlo+(sz[1]+1)-1 : jlo+sz[1]-1;
jlo += domlo[1];
jhi += domlo[1];
#endif
for (int i = 0; i < numprocs[0]; ++i) {
int ilo = (i < extra[0]) ? i*(sz[0]+1) : (i*sz[0]+extra[0]);
int ihi = (i < extra[0]) ? ilo+(sz[0]+1)-1 : ilo+sz[0]-1;
ilo += domlo[0];
ihi += domlo[0];
bl.push_back(Box(IntVect(AMREX_D_DECL(ilo,jlo,klo)),
IntVect(AMREX_D_DECL(ihi,jhi,khi))));
AMREX_D_TERM(},},})
ba0 = BoxArray(std::move(bl));
}
}
void
WarpX::PrintMainPICparameters ()
{
amrex::Print() << "-------------------------------------------------------------------------------\n";
amrex::Print() << "--------------------------- MAIN EM PIC PARAMETERS ----------------------------\n";
amrex::Print() << "-------------------------------------------------------------------------------\n";
// print warpx build information
if constexpr (std::is_same_v<Real, float>) {
amrex::Print() << "Precision: | SINGLE" << "\n";
}
else {
amrex::Print() << "Precision: | DOUBLE" << "\n";
}
if constexpr (std::is_same_v<ParticleReal, float>) {
amrex::Print() << "Particle precision: | SINGLE" << "\n";
}
else {
amrex::Print() << "Particle precision: | DOUBLE" << "\n";
}
// Print geometry dimensionality
const amrex::ParmParse pp_geometry("geometry");
std::string dims;
pp_geometry.query( "dims", dims );
if (dims=="1") {
amrex::Print() << "Geometry: | 1D (Z)" << "\n";
}
else if (dims=="2") {
amrex::Print() << "Geometry: | 2D (XZ)" << "\n";
}
else if (dims=="3") {
amrex::Print() << "Geometry: | 3D (XYZ)" << "\n";
}
else if (dims=="RZ") {
amrex::Print() << "Geometry: | 2D (RZ)" << "\n";
}
#ifdef WARPX_DIM_RZ
amrex::Print() << " | - n_rz_azimuthal_modes = " <<
WarpX::n_rz_azimuthal_modes << "\n";
#endif // WARPX_USE_RZ
//Print solver's operation mode (e.g., EM or electrostatic)
if (electrostatic_solver_id == ElectrostaticSolverAlgo::LabFrame) {
amrex::Print() << "Operation mode: | Electrostatic" << "\n";
amrex::Print() << " | - laboratory frame" << "\n";
}
else if (electrostatic_solver_id == ElectrostaticSolverAlgo::Relativistic){
amrex::Print() << "Operation mode: | Electrostatic" << "\n";
amrex::Print() << " | - relativistic" << "\n";
}
else if (electrostatic_solver_id == ElectrostaticSolverAlgo::LabFrameElectroMagnetostatic){
amrex::Print() << "Operation mode: | Electrostatic" << "\n";
amrex::Print() << " | - laboratory frame, electrostatic + magnetostatic" << "\n";
}
else if (electrostatic_solver_id == ElectrostaticSolverAlgo::LabFrameEffectivePotential){
amrex::Print() << "Operation mode: | Electrostatic" << "\n";
amrex::Print() << " | - laboratory frame, effective potential scheme" << "\n";
}
else{
amrex::Print() << "Operation mode: | Electromagnetic" << "\n";
}
if (m_em_solver_medium == MediumForEM::Vacuum ){
amrex::Print() << " | - vacuum" << "\n";
}
else if (m_em_solver_medium == MediumForEM::Macroscopic ){
amrex::Print() << " | - macroscopic" << "\n";
}
if ( (m_em_solver_medium == MediumForEM::Macroscopic) &&
(WarpX::macroscopic_solver_algo == MacroscopicSolverAlgo::LaxWendroff)){
amrex::Print() << " | - Lax-Wendroff algorithm\n";
}
else if ((m_em_solver_medium == MediumForEM::Macroscopic) &&
(WarpX::macroscopic_solver_algo == MacroscopicSolverAlgo::BackwardEuler)){
amrex::Print() << " | - Backward Euler algorithm\n";
}
if(electrostatic_solver_id != ElectrostaticSolverAlgo::None){
if(poisson_solver_id == PoissonSolverAlgo::IntegratedGreenFunction){
amrex::Print() << "Poisson solver: | FFT-based" << "\n";
}
else if(poisson_solver_id == PoissonSolverAlgo::Multigrid){
amrex::Print() << "Poisson solver: | multigrid" << "\n";
}
}
amrex::Print() << "-------------------------------------------------------------------------------\n";
// Print type of current deposition
if (current_deposition_algo == CurrentDepositionAlgo::Direct){
amrex::Print() << "Current Deposition: | direct \n";
}
else if (current_deposition_algo == CurrentDepositionAlgo::Vay){
amrex::Print() << "Current Deposition: | Vay \n";
}
else if (current_deposition_algo == CurrentDepositionAlgo::Esirkepov){
amrex::Print() << "Current Deposition: | Esirkepov \n";
}
else if (current_deposition_algo == CurrentDepositionAlgo::Villasenor){
amrex::Print() << "Current Deposition: | Villasenor \n";
}
// Print type of particle pusher
if (particle_pusher_algo == ParticlePusherAlgo::Vay){
amrex::Print() << "Particle Pusher: | Vay \n";
}
else if (particle_pusher_algo == ParticlePusherAlgo::HigueraCary){
amrex::Print() << "Particle Pusher: | Higuera-Cary \n";
}
else if (particle_pusher_algo == ParticlePusherAlgo::Boris){
amrex::Print() << "Particle Pusher: | Boris \n";
}
// Print type of charge deposition
if (charge_deposition_algo == ChargeDepositionAlgo::Standard){
amrex::Print() << "Charge Deposition: | standard \n";
}
// Print field gathering algorithm
if (field_gathering_algo == GatheringAlgo::MomentumConserving){
amrex::Print() << "Field Gathering: | momentum-conserving \n";
}
else{
amrex::Print() << "Field Gathering: | energy-conserving \n";
}
// Print particle's shape factors
amrex::Print() << "Particle Shape Factor:| " << WarpX::nox << "\n";
amrex::Print() << "-------------------------------------------------------------------------------\n";
// Print solver's type: Yee, CKC, ECT
if (WarpX::electromagnetic_solver_id == ElectromagneticSolverAlgo::Yee){
amrex::Print() << "Maxwell Solver: | Yee \n";
}
else if (WarpX::electromagnetic_solver_id == ElectromagneticSolverAlgo::CKC){
amrex::Print() << "Maxwell Solver: | CKC \n";
}
else if (WarpX::electromagnetic_solver_id == ElectromagneticSolverAlgo::ECT){
amrex::Print() << "Maxwell Solver: | ECT \n";
}
else if (WarpX::electromagnetic_solver_id == ElectromagneticSolverAlgo::HybridPIC){
amrex::Print() << "Maxwell Solver: | Hybrid-PIC (Ohm's law) \n";
}
#ifdef WARPX_USE_FFT
// Print PSATD solver's configuration
if (WarpX::electromagnetic_solver_id == ElectromagneticSolverAlgo::PSATD){
amrex::Print() << "Maxwell Solver: | PSATD \n";
}
if ((m_v_galilean[0]!=0) or (m_v_galilean[1]!=0) or (m_v_galilean[2]!=0)) {
amrex::Print() << " | - Galilean \n" <<
" | - v_galilean = (" << m_v_galilean[0] << "," <<
m_v_galilean[1] << "," << m_v_galilean[2] << ")\n";
}
if ((m_v_comoving[0]!=0) or (m_v_comoving[1]!=0) or (m_v_comoving[2]!=0)) {
amrex::Print() << " | - comoving \n" <<
" | - v_comoving = (" << m_v_comoving[0] << "," <<
m_v_comoving[1] << "," << m_v_comoving[2] << ")\n";
}
if (WarpX::update_with_rho) {
amrex::Print() << " | - update with rho is ON \n";
}
if (current_correction) {
amrex::Print() << " | - current correction is ON \n";
}
if (WarpX::do_dive_cleaning) {
amrex::Print() << " | - div(E) cleaning is ON \n";
}
if (WarpX::do_divb_cleaning) {
amrex::Print() << " | - div(B) cleaning is ON \n";
}
if (do_multi_J){
amrex::Print() << " | - multi-J deposition is ON \n";
amrex::Print() << " | - do_multi_J_n_depositions = "
<< WarpX::do_multi_J_n_depositions << "\n";
if (J_in_time == JInTime::Linear){
amrex::Print() << " | - J_in_time = linear \n";
}
if (J_in_time == JInTime::Constant){
amrex::Print() << " | - J_in_time = constant \n";
}
if (rho_in_time == RhoInTime::Linear){
amrex::Print() << " | - rho_in_time = linear \n";
}
if (rho_in_time == RhoInTime::Constant){
amrex::Print() << " | - rho_in_time = constant \n";
}
}
if (fft_do_time_averaging){
amrex::Print()<<" | - time-averaged is ON \n";
}
#endif // WARPX_USE_FFT
if (grid_type == GridType::Collocated){
amrex::Print() << " | - collocated grid \n";
}
#ifdef WARPX_USE_FFT
if ( (grid_type == GridType::Staggered) && (field_gathering_algo == GatheringAlgo::EnergyConserving) ){
amrex::Print()<<" | - staggered grid " << "\n";
}
else if ( (grid_type == GridType::Hybrid) && (field_gathering_algo == GatheringAlgo::MomentumConserving) ){
amrex::Print()<<" | - hybrid grid " << "\n";
if (dims=="3"){
amrex::Print() << " | - field_centering_nox = " << WarpX::field_centering_nox << "\n";
amrex::Print() << " | - field_centering_noy = " << WarpX::field_centering_noy << "\n";
amrex::Print() << " | - field_centering_noz = " << WarpX::field_centering_noz << "\n";
amrex::Print() << " | - current_centering_nox = " << WarpX::current_centering_nox << "\n";
amrex::Print() << " | - current_centering_noy = " << WarpX::current_centering_noy << "\n";
amrex::Print() << " | - current_centering_noz = " << WarpX::current_centering_noz << "\n";
}
else if (dims=="2"){
amrex::Print() << " | - field_centering_nox = " << WarpX::field_centering_nox << "\n";
amrex::Print() << " | - field_centering_noz = " << WarpX::field_centering_noz << "\n";
amrex::Print() << " | - current_centering_nox = " << WarpX::current_centering_nox << "\n";
amrex::Print() << " | - current_centering_noz = " << WarpX::current_centering_noz << "\n";
}
else if (dims=="1"){
amrex::Print() << " | - field_centering_noz = " << WarpX::field_centering_noz << "\n";
amrex::Print() << " | - current_centering_noz = " << WarpX::current_centering_noz << "\n";
}
}
if (WarpX::use_hybrid_QED){
amrex::Print() << " | - use_hybrid_QED = true \n";
}
if (WarpX::electromagnetic_solver_id == ElectromagneticSolverAlgo::PSATD){
// Print solver's order
std::string psatd_nox_fft, psatd_noy_fft, psatd_noz_fft;
psatd_nox_fft = (nox_fft == -1) ? "inf" : std::to_string(nox_fft);
psatd_noy_fft = (noy_fft == -1) ? "inf" : std::to_string(noy_fft);
psatd_noz_fft = (noz_fft == -1) ? "inf" : std::to_string(noz_fft);
if (dims=="3" ){
amrex::Print() << "Spectral order: | - psatd.nox = " << psatd_nox_fft << "\n";
amrex::Print() << " | - psatd.noy = " << psatd_noy_fft << "\n";
amrex::Print() << " | - psatd.noz = " << psatd_noz_fft << "\n";
}
else if (dims=="2" and WarpX::electromagnetic_solver_id == ElectromagneticSolverAlgo::PSATD){
amrex::Print() << "Spectral order: | - psatd.nox = " << psatd_nox_fft << "\n";
amrex::Print() << " | - psatd.noz = " << psatd_noz_fft << "\n";
}
else if (dims=="1" and WarpX::electromagnetic_solver_id == ElectromagneticSolverAlgo::PSATD){
amrex::Print() << "Spectral order: | - psatd.noz = " << psatd_noz_fft << "\n";
}
}
// Print guard cells number
amrex::Print() << "Guard cells | - ng_alloc_EB = " << guard_cells.ng_alloc_EB << "\n";
amrex::Print() << " (allocated for E/B) | \n";
#endif // WARPX_USE_FFT
amrex::Print() << "-------------------------------------------------------------------------------" << "\n";
//Print main boosted frame algorithm's parameters
if (WarpX::gamma_boost!=1){
amrex::Print() << "Boosted Frame: | ON \n";
amrex::Print() << " | - gamma_boost = " << WarpX::gamma_boost << "\n";
amrex::Print() << " | - boost_direction = (" << WarpX::boost_direction[0] <<
"," << WarpX::boost_direction[1] << "," << WarpX::boost_direction[2] << ")\n";
amrex::Print() << "------------------------------------------------------------------------------- \n";
}
//Print moving window details
if (WarpX::do_moving_window == 1){
amrex::Print() << "Moving window: | ON \n";
if (WarpX::moving_window_dir == 0){
amrex::Print() << " | - moving_window_dir = x \n";
}
#if defined(WARPX_DIM_3D)
else if (WarpX::moving_window_dir == 1){
amrex::Print() << " | - moving_window_dir = y \n";
}
#endif
else if (WarpX::moving_window_dir == WARPX_ZINDEX) {
amrex::Print() << " | - moving_window_dir = z \n";
}
amrex::Print() << " | - moving_window_v = " << WarpX::moving_window_v << "\n";
amrex::Print() << "------------------------------------------------------------------------------- \n";
}
}
void
WarpX::WriteUsedInputsFile () const
{
std::string filename = "warpx_used_inputs";
ParmParse pp_warpx("warpx");
pp_warpx.queryAdd("used_inputs_file", filename);
ablastr::utils::write_used_inputs_file(filename);
}
void
WarpX::InitData ()
{
WARPX_PROFILE("WarpX::InitData()");
using ablastr::fields::Direction;
using warpx::fields::FieldType;
ablastr::parallelization::check_mpi_thread_level();
#ifdef WARPX_QED
Print() << "PICSAR (" << WarpX::PicsarVersion() << ")\n";
#endif
Print() << "WarpX (" << WarpX::Version() << ")\n";
Print() << utils::logo::get_logo();
// Diagnostics
multi_diags = std::make_unique<MultiDiagnostics>();
/** create object for reduced diagnostics */
reduced_diags = std::make_unique<MultiReducedDiags>();
// WarpX::computeMaxStepBoostAccelerator
// needs to start from the initial zmin_domain_boost,
// even if restarting from a checkpoint file
if (m_zmax_plasma_to_compute_max_step.has_value()) {
zmin_domain_boost_step_0 = geom[0].ProbLo(WARPX_ZINDEX);
}
if (restart_chkfile.empty())
{
ComputeDt();
::PrintDtDxDyDz(max_level, geom, dt);
InitFromScratch();
InitDiagnostics();
}
else
{
InitFromCheckpoint();
::PrintDtDxDyDz(max_level, geom, dt);
PostRestart();
reduced_diags->InitData();
}
ComputeMaxStep();
ComputePMLFactors();
if (WarpX::use_fdtd_nci_corr) {
WarpX::InitNCICorrector();
}
BuildBufferMasks();
if (m_em_solver_medium == MediumForEM::Macroscopic) {
const int lev_zero = 0;
m_macroscopic_properties->InitData(
Geom(lev_zero),
m_fields.get(FieldType::Efield_fp, Direction{0}, lev_zero)->ixType().toIntVect(),
m_fields.get(FieldType::Efield_fp, Direction{1}, lev_zero)->ixType().toIntVect(),
m_fields.get(FieldType::Efield_fp, Direction{2}, lev_zero)->ixType().toIntVect()
);
}
m_electrostatic_solver->InitData();
if (WarpX::electromagnetic_solver_id == ElectromagneticSolverAlgo::HybridPIC) {
m_hybrid_pic_model->InitData();
}
if (ParallelDescriptor::IOProcessor()) {
std::cout << "\nGrids Summary:\n";
printGridSummary(std::cout, 0, finestLevel());
}
// Check that the number of guard cells is smaller than the number of valid cells for all MultiFabs
// (example: a box with 16 valid cells and 32 guard cells in z will not be considered valid)
CheckGuardCells();
PrintMainPICparameters();
if (m_implicit_solver) {
m_implicit_solver->PrintParameters();
}
WriteUsedInputsFile();
// Run div cleaner here on loaded external fields
if (m_do_divb_cleaning_external) {
WarpX::ProjectionCleanDivB();
}
if (restart_chkfile.empty())
{
// Loop through species and calculate their space-charge field
bool const reset_fields = false; // Do not erase previous user-specified values on the grid
ExecutePythonCallback("beforeInitEsolve");
ComputeSpaceChargeField(reset_fields);
ExecutePythonCallback("afterInitEsolve");
if (electrostatic_solver_id == ElectrostaticSolverAlgo::LabFrameElectroMagnetostatic) {
ComputeMagnetostaticField();
}
// Add external fields to the fine patch fields. This makes it so that the
// net fields are the sum of the field solutions and any external fields.
for (int lev = 0; lev <= max_level; ++lev) {
AddExternalFields(lev);
}
}
else {
ExecutePythonCallback("afterInitatRestart");
}
if (restart_chkfile.empty() || write_diagnostics_on_restart) {
// Write full diagnostics before the first iteration.
multi_diags->FilterComputePackFlush(istep[0] - 1);
// Write reduced diagnostics before the first iteration.
if (reduced_diags->m_plot_rd != 0)
{
reduced_diags->ComputeDiags(istep[0] - 1);
reduced_diags->WriteToFile(istep[0] - 1);
}
}
// Computes available boxes on all levels.
amrex::Long total_nboxes = 0;
for (int ilev = 0; ilev <= finestLevel(); ++ilev) {
total_nboxes += boxArray(ilev).size();
}
auto const nprocs = ParallelDescriptor::NProcs();
::PerformanceHints(total_nboxes, nprocs);
CheckKnownIssues();
}
void
WarpX::AddExternalFields (int const lev)
{
using ablastr::fields::Direction;
using warpx::fields::FieldType;
// FIXME: RZ multimode has more than one component for all these
if (m_p_ext_field_params->E_ext_grid_type != ExternalFieldType::default_zero) {
ablastr::fields::MultiLevelVectorField Efield_fp = m_fields.get_mr_levels_alldirs(FieldType::Efield_fp, max_level);
if (m_p_ext_field_params->E_ext_grid_type == ExternalFieldType::constant) {
Efield_fp[lev][0]->plus(m_p_ext_field_params->E_external_grid[0], guard_cells.ng_alloc_EB.min());
Efield_fp[lev][1]->plus(m_p_ext_field_params->E_external_grid[1], guard_cells.ng_alloc_EB.min());
Efield_fp[lev][2]->plus(m_p_ext_field_params->E_external_grid[2], guard_cells.ng_alloc_EB.min());
}
else {
amrex::MultiFab::Add(*Efield_fp[lev][0], *m_fields.get(FieldType::Efield_fp_external, Direction{0}, lev), 0, 0, 1, guard_cells.ng_alloc_EB);
amrex::MultiFab::Add(*Efield_fp[lev][1], *m_fields.get(FieldType::Efield_fp_external, Direction{1}, lev), 0, 0, 1, guard_cells.ng_alloc_EB);
amrex::MultiFab::Add(*Efield_fp[lev][2], *m_fields.get(FieldType::Efield_fp_external, Direction{2}, lev), 0, 0, 1, guard_cells.ng_alloc_EB);
}
}
if (m_p_ext_field_params->B_ext_grid_type != ExternalFieldType::default_zero) {
ablastr::fields::MultiLevelVectorField const& Bfield_fp = m_fields.get_mr_levels_alldirs(FieldType::Bfield_fp, max_level);
if (m_p_ext_field_params->B_ext_grid_type == ExternalFieldType::constant) {
Bfield_fp[lev][0]->plus(m_p_ext_field_params->B_external_grid[0], guard_cells.ng_alloc_EB.min());
Bfield_fp[lev][1]->plus(m_p_ext_field_params->B_external_grid[1], guard_cells.ng_alloc_EB.min());
Bfield_fp[lev][2]->plus(m_p_ext_field_params->B_external_grid[2], guard_cells.ng_alloc_EB.min());
}
else {
amrex::MultiFab::Add(*Bfield_fp[lev][0], *m_fields.get(FieldType::Bfield_fp_external, Direction{0}, lev), 0, 0, 1, guard_cells.ng_alloc_EB);
amrex::MultiFab::Add(*Bfield_fp[lev][1], *m_fields.get(FieldType::Bfield_fp_external, Direction{1}, lev), 0, 0, 1, guard_cells.ng_alloc_EB);
amrex::MultiFab::Add(*Bfield_fp[lev][2], *m_fields.get(FieldType::Bfield_fp_external, Direction{2}, lev), 0, 0, 1, guard_cells.ng_alloc_EB);
}
}
}
void
WarpX::InitDiagnostics () {
multi_diags->InitData();
reduced_diags->InitData();
}
void
WarpX::InitFromScratch ()
{
const Real time = 0.0;
AmrCore::InitFromScratch(time); // This will call MakeNewLevelFromScratch
if (m_implicit_solver) {
m_implicit_solver->Define(this);
m_implicit_solver->GetParticleSolverParams( max_particle_its_in_implicit_scheme,
particle_tol_in_implicit_scheme );
m_implicit_solver->CreateParticleAttributes();
}
mypc->AllocData();
mypc->InitData();
InitPML();
}
void
WarpX::InitPML ()
{
for (int idim = 0; idim < AMREX_SPACEDIM; ++idim) {
if (WarpX::field_boundary_lo[idim] == FieldBoundaryType::PML) {
do_pml = 1;
do_pml_Lo[0][idim] = 1; // on level 0
}
if (WarpX::field_boundary_hi[idim] == FieldBoundaryType::PML) {
do_pml = 1;
do_pml_Hi[0][idim] = 1; // on level 0
}
}
if (max_level > 0) { do_pml = 1; }
if (do_pml)
{
bool const eb_enabled = EB::enabled();
#if (defined WARPX_DIM_RZ) && (defined WARPX_USE_FFT)
do_pml_Lo[0][0] = 0; // no PML at r=0, in cylindrical geometry
pml_rz[0] = std::make_unique<PML_RZ>(0, boxArray(0), DistributionMap(0), &Geom(0), pml_ncell, do_pml_in_domain);
#else
// Note: fill_guards_fields and fill_guards_current are both set to
// zero (amrex::IntVect(0)) (what we do with damping BCs does not apply
// to the PML, for example in the presence of mesh refinement patches)
pml[0] = std::make_unique<PML>(
0, boxArray(0), DistributionMap(0), do_similar_dm_pml, &Geom(0), nullptr,
pml_ncell, pml_delta, amrex::IntVect::TheZeroVector(),
dt[0], nox_fft, noy_fft, noz_fft, grid_type,
do_moving_window, pml_has_particles, do_pml_in_domain,
m_psatd_solution_type, J_in_time, rho_in_time,
do_pml_dive_cleaning, do_pml_divb_cleaning,
amrex::IntVect(0), amrex::IntVect(0),
eb_enabled,
guard_cells.ng_FieldSolver.max(),
v_particle_pml,
m_fields,
do_pml_Lo[0], do_pml_Hi[0]);
#endif
for (int lev = 1; lev <= max_level; ++lev)
{
do_pml_Lo[lev] = amrex::IntVect::TheUnitVector();
do_pml_Hi[lev] = amrex::IntVect::TheUnitVector();
// check if fine patch edges co-incide with domain boundary
const amrex::Box levelBox = boxArray(lev).minimalBox();
// Domain box at level, lev
const amrex::Box DomainBox = Geom(lev).Domain();
for (int idim = 0; idim < AMREX_SPACEDIM; ++idim) {
if (levelBox.smallEnd(idim) == DomainBox.smallEnd(idim)) {
do_pml_Lo[lev][idim] = do_pml_Lo[0][idim];
}
if (levelBox.bigEnd(idim) == DomainBox.bigEnd(idim)) {
do_pml_Hi[lev][idim] = do_pml_Hi[0][idim];
}
}
#ifdef WARPX_DIM_RZ
//In cylindrical geometry, if the edge of the patch is at r=0, do not add PML
if ((max_level > 0) && (fine_tag_lo[0]==0.)) {
do_pml_Lo[lev][0] = 0;
}
#endif
// Note: fill_guards_fields and fill_guards_current are both set to
// zero (amrex::IntVect(0)) (what we do with damping BCs does not apply
// to the PML, for example in the presence of mesh refinement patches)
pml[lev] = std::make_unique<PML>(
lev, boxArray(lev), DistributionMap(lev), do_similar_dm_pml,
&Geom(lev), &Geom(lev-1),
pml_ncell, pml_delta, refRatio(lev-1),
dt[lev], nox_fft, noy_fft, noz_fft, grid_type,
do_moving_window, pml_has_particles, do_pml_in_domain,
m_psatd_solution_type, J_in_time, rho_in_time, do_pml_dive_cleaning, do_pml_divb_cleaning,
amrex::IntVect(0), amrex::IntVect(0),
eb_enabled,
guard_cells.ng_FieldSolver.max(),
v_particle_pml,
m_fields,
do_pml_Lo[lev], do_pml_Hi[lev]);
}
}
}
void
WarpX::ComputePMLFactors ()
{
if (do_pml)
{
for (int lev = 0; lev <= max_level; ++lev)
{
if (pml[lev]) {
pml[lev]->ComputePMLFactors(dt[lev]);
}
}
}
}
void
WarpX::ComputeMaxStep ()
{
if (m_zmax_plasma_to_compute_max_step.has_value()) {
computeMaxStepBoostAccelerator();
}
}
/* \brief computes max_step for wakefield simulation in boosted frame.
* \param geom: Geometry object that contains simulation domain.
*
* max_step is set so that the simulation stop when the lower corner of the
* simulation box passes input parameter zmax_plasma_to_compute_max_step.
*/
void
WarpX::computeMaxStepBoostAccelerator() {
// Sanity checks: can use zmax_plasma_to_compute_max_step only if
// the moving window and the boost are all in z direction.
WARPX_ALWAYS_ASSERT_WITH_MESSAGE(
WarpX::moving_window_dir == WARPX_ZINDEX,
"Can use zmax_plasma_to_compute_max_step only if "
"moving window along z. TODO: all directions.");
if (gamma_boost > 1){
WARPX_ALWAYS_ASSERT_WITH_MESSAGE(
(WarpX::boost_direction[0]-0)*(WarpX::boost_direction[0]-0) +
(WarpX::boost_direction[1]-0)*(WarpX::boost_direction[1]-0) +
(WarpX::boost_direction[2]-1)*(WarpX::boost_direction[2]-1) < 1.e-12,
"Can use zmax_plasma_to_compute_max_step in boosted frame only if "
"warpx.boost_direction = z. TODO: all directions.");
}
// Lower end of the simulation domain. All quantities are given in boosted
// frame except zmax_plasma_to_compute_max_step.
// End of the plasma: Transform input argument
// zmax_plasma_to_compute_max_step to boosted frame.
const Real len_plasma_boost = m_zmax_plasma_to_compute_max_step.value()/gamma_boost;
// Plasma velocity
const Real v_plasma_boost = -beta_boost * PhysConst::c;
// Get time at which the lower end of the simulation domain passes the
// upper end of the plasma (in the z direction).
const Real interaction_time_boost = (len_plasma_boost-zmin_domain_boost_step_0)/
(moving_window_v-v_plasma_boost);
// Divide by dt, and update value of max_step.
const auto computed_max_step = (m_do_subcycling)?
static_cast<int>(interaction_time_boost/dt[0]):
static_cast<int>(interaction_time_boost/dt[maxLevel()]);
max_step = computed_max_step;
Print()<<"max_step computed in computeMaxStepBoostAccelerator: "
<<max_step<<"\n";
}
void
WarpX::InitNCICorrector ()
{
#if !(defined WARPX_DIM_1D_Z)
if (WarpX::use_fdtd_nci_corr)
{
for (int lev = 0; lev <= max_level; ++lev)
{
const Geometry& gm = Geom(lev);
const Real* dx = gm.CellSize();
#if defined(WARPX_DIM_3D)
const auto dz = dx[2];
#elif defined(WARPX_DIM_XZ) || defined(WARPX_DIM_RZ)
const auto dz = dx[1];
#else
const auto dz = dx[0];
#endif
const auto cdtodz = PhysConst::c * dt[lev] / dz;
// Initialize Godfrey filters
// Same filter for fields Ex, Ey and Bz
const bool nodal_gather = !galerkin_interpolation;
nci_godfrey_filter_exeybz[lev] = std::make_unique<NCIGodfreyFilter>(
godfrey_coeff_set::Ex_Ey_Bz, cdtodz, nodal_gather);
// Same filter for fields Bx, By and Ez
nci_godfrey_filter_bxbyez[lev] = std::make_unique<NCIGodfreyFilter>(
godfrey_coeff_set::Bx_By_Ez, cdtodz, nodal_gather);
// Compute Godfrey filters stencils
nci_godfrey_filter_exeybz[lev]->ComputeStencils();
nci_godfrey_filter_bxbyez[lev]->ComputeStencils();
}
}
#endif
}
void
WarpX::InitFilter (){
if (WarpX::use_filter){
WarpX::bilinear_filter.npass_each_dir = WarpX::filter_npass_each_dir.toArray<unsigned int>();
WarpX::bilinear_filter.ComputeStencils();
}
}
void
WarpX::PostRestart ()
{
mypc->PostRestart();
for (int lev = 0; lev <= maxLevel(); ++lev) {
LoadExternalFields(lev);
}
}
void
WarpX::InitLevelData (int lev, Real /*time*/)
{
using ablastr::fields::Direction;
using warpx::fields::FieldType;
// initialize the averaged fields only if the averaged algorithm
// is activated ('psatd.do_time_averaging=1')
const ParmParse pp_psatd("psatd");
pp_psatd.query("do_time_averaging", fft_do_time_averaging );
for (int i = 0; i < 3; ++i) {
// Externally imposed fields are only initialized until the user-defined maxlevel_extEMfield_init.
// The default maxlevel_extEMfield_init value is the total number of levels in the simulation
const auto is_B_ext_const =
m_p_ext_field_params->B_ext_grid_type == ExternalFieldType::constant ||
m_p_ext_field_params->B_ext_grid_type == ExternalFieldType::default_zero;
if ( is_B_ext_const && (lev <= maxlevel_extEMfield_init) )
{
if (fft_do_time_averaging) {
m_fields.get(FieldType::Bfield_avg_fp, Direction{i}, lev)->setVal(m_p_ext_field_params->B_external_grid[i]);
}
if (lev > 0) {
m_fields.get(FieldType::Bfield_aux, Direction{i}, lev)->setVal(m_p_ext_field_params->B_external_grid[i]);
m_fields.get(FieldType::Bfield_cp, Direction{i}, lev)->setVal(m_p_ext_field_params->B_external_grid[i]);
if (fft_do_time_averaging) {
m_fields.get(FieldType::Bfield_avg_cp, Direction{i}, lev)->setVal(m_p_ext_field_params->B_external_grid[i]);
}
}
}
// Externally imposed fields are only initialized until the user-defined maxlevel_extEMfield_init.
// The default maxlevel_extEMfield_init value is the total number of levels in the simulation
const auto is_E_ext_const =
m_p_ext_field_params->E_ext_grid_type == ExternalFieldType::constant ||
m_p_ext_field_params->E_ext_grid_type == ExternalFieldType::default_zero;
if ( is_E_ext_const && (lev <= maxlevel_extEMfield_init) )
{
if (fft_do_time_averaging) {
m_fields.get(FieldType::Efield_avg_fp, Direction{i}, lev)->setVal(m_p_ext_field_params->E_external_grid[i]);
}
if (lev > 0) {
m_fields.get(FieldType::Efield_aux, Direction{i}, lev)->setVal(m_p_ext_field_params->E_external_grid[i]);
m_fields.get(FieldType::Efield_cp, Direction{i}, lev)->setVal(m_p_ext_field_params->E_external_grid[i]);
if (fft_do_time_averaging) {
m_fields.get(FieldType::Efield_avg_cp, Direction{i}, lev)->setVal(m_p_ext_field_params->E_external_grid[i]);
}
}
}
}
#ifdef AMREX_USE_EB
bool const eb_enabled = EB::enabled();
if (eb_enabled) { InitializeEBGridData(lev); }
#endif
// if the input string for the B-field is "parse_b_ext_grid_function",
// then the analytical expression or function must be
// provided in the input file.
// Externally imposed fields are only initialized until the user-defined maxlevel_extEMfield_init.
// The default maxlevel_extEMfield_init value is the total number of levels in the simulation
if ((m_p_ext_field_params->B_ext_grid_type == ExternalFieldType::parse_ext_grid_function)
&& (lev > 0) && (lev <= maxlevel_extEMfield_init)) {
ComputeExternalFieldOnGridUsingParser(
FieldType::Bfield_aux,
m_p_ext_field_params->Bxfield_parser->compile<4>(),
m_p_ext_field_params->Byfield_parser->compile<4>(),
m_p_ext_field_params->Bzfield_parser->compile<4>(),
lev, PatchType::fine, m_eb_update_B);