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Added JJ function #152

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067e3be
Added JJ function
tyh0123 Jul 1, 2026
7372f93
Fix current accumulation bug
tyh0123 Jul 22, 2026
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2 changes: 1 addition & 1 deletion GNUmakefile
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
AMREX_HOME ?= ../amrex
AMREX_HOME = ../../amrex

DEBUG = FALSE
#DEBUG = TRUE
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13 changes: 11 additions & 2 deletions Source/Diagnostics/FlushFormats/FlushFormatCheckpoint.cpp
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Expand Up @@ -115,8 +115,10 @@ FlushFormatCheckpoint::WriteToFile (

if (warpx.getis_synchronized()
|| WarpX::yee_coupled_solver_algo == CoupledYeeSolver::MaxwellLondon
|| warpx.use_lumped_inductor == 1) {
|| warpx.use_lumped_inductor == 1
|| warpx.use_josephson_junction == 1) {
// Need to save j if synchronized because after restart we need j to evolve E by dt/2.
// London / lumped inductor / Josephson junction all treat j as persistent state.
VisMF::Write(warpx.getcurrent_fp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "jx_fp"));
VisMF::Write(warpx.getcurrent_fp(lev, 1),
Expand Down Expand Up @@ -180,7 +182,8 @@ FlushFormatCheckpoint::WriteToFile (

if (warpx.getis_synchronized()
|| WarpX::yee_coupled_solver_algo == CoupledYeeSolver::MaxwellLondon
|| warpx.use_lumped_inductor == 1) {
|| warpx.use_lumped_inductor == 1
|| warpx.use_josephson_junction == 1) {
// Need to save j if synchronized because after restart we need j to evolve E by dt/2.
VisMF::Write(warpx.getcurrent_cp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "jx_cp"));
Expand All @@ -205,6 +208,12 @@ FlushFormatCheckpoint::WriteToFile (
}
}

// Josephson junction state (phi, Js). phi is the junction's only real state and
// is NOT reconstructible from the fields, so without this a restart resets it to 0.
if (warpx.use_josephson_junction == 1) {
warpx.getJosephsonJunction().WriteCheckpoint(checkpointname);
}

CheckpointParticles(checkpointname, particle_diags);

WriteDMaps(checkpointname, nlev);
Expand Down
281 changes: 281 additions & 0 deletions Source/Diagnostics/FlushFormats/FlushFormatCheckpoint.cpp.orig
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@@ -0,0 +1,281 @@
#include "FlushFormatCheckpoint.H"

#include "BoundaryConditions/PML.H"
#if (defined WARPX_DIM_RZ) && (defined WARPX_USE_PSATD)
# include "BoundaryConditions/PML_RZ.H"
#endif
#include "Diagnostics/ParticleDiag/ParticleDiag.H"
#include "Particles/WarpXParticleContainer.H"
#include "Utils/TextMsg.H"
#include "Utils/WarpXProfilerWrapper.H"
#include "WarpX.H"

#include <AMReX_MultiFab.H>
#include <AMReX_ParticleIO.H>
#include <AMReX_PlotFileUtil.H>
#include <AMReX_Print.H>
#include <AMReX_REAL.H>
#include <AMReX_Utility.H>
#include <AMReX_VisMF.H>

using namespace amrex;

namespace
{
const std::string default_level_prefix {"Level_"};
}

void
FlushFormatCheckpoint::WriteToFile (
const amrex::Vector<std::string> /*varnames*/,
const amrex::Vector<amrex::MultiFab>& /*mf*/,
amrex::Vector<amrex::Geometry>& geom,
const amrex::Vector<int> iteration, const double /*time*/,
const amrex::Vector<ParticleDiag>& particle_diags, int nlev,
const std::string prefix, int file_min_digits,
bool /*plot_raw_fields*/,
bool /*plot_raw_fields_guards*/,
const bool /*use_pinned_pc*/,
bool /*isBTD*/, int /*snapshotID*/,
int /*bufferID*/, int /*numBuffers*/,
const amrex::Geometry& /*full_BTD_snapshot*/,
bool /*isLastBTDFlush*/, const amrex::Vector<int>& /* totalParticlesFlushedAlready*/) const
{
WARPX_PROFILE("FlushFormatCheckpoint::WriteToFile()");

auto & warpx = WarpX::GetInstance();

VisMF::Header::Version current_version = VisMF::GetHeaderVersion();
VisMF::SetHeaderVersion(amrex::VisMF::Header::NoFabHeader_v1);

const std::string& checkpointname = amrex::Concatenate(prefix, iteration[0], file_min_digits);

amrex::Print() << Utils::TextMsg::Info(
"Writing checkpoint " + checkpointname);

// const int nlevels = finestLevel()+1;
amrex::PreBuildDirectorHierarchy(checkpointname, default_level_prefix, nlev, true);

WriteWarpXHeader(checkpointname, geom);

WriteJobInfo(checkpointname);

for (int lev = 0; lev < nlev; ++lev)
{
VisMF::Write(warpx.getEfield_fp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Ex_fp"));
VisMF::Write(warpx.getEfield_fp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Ey_fp"));
VisMF::Write(warpx.getEfield_fp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Ez_fp"));
VisMF::Write(warpx.getBfield_fp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Bx_fp"));
VisMF::Write(warpx.getBfield_fp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "By_fp"));
VisMF::Write(warpx.getBfield_fp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Bz_fp"));

#ifdef WARPX_MAG_LLG
VisMF::Write(warpx.getHfield_fp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Hx_fp"));
VisMF::Write(warpx.getHfield_fp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Hy_fp"));
VisMF::Write(warpx.getHfield_fp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Hz_fp"));
VisMF::Write(warpx.getMfield_fp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Mx_fp"));
VisMF::Write(warpx.getMfield_fp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "My_fp"));
VisMF::Write(warpx.getMfield_fp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Mz_fp"));
VisMF::Write(warpx.getH_biasfield_fp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Hxbias_fp"));
VisMF::Write(warpx.getH_biasfield_fp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Hybias_fp"));
VisMF::Write(warpx.getH_biasfield_fp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Hzbias_fp"));
#endif

if (WarpX::fft_do_time_averaging)
{
VisMF::Write(warpx.getEfield_avg_fp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Ex_avg_fp"));
VisMF::Write(warpx.getEfield_avg_fp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Ey_avg_fp"));
VisMF::Write(warpx.getEfield_avg_fp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Ez_avg_fp"));

VisMF::Write(warpx.getBfield_avg_fp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Bx_avg_fp"));
VisMF::Write(warpx.getBfield_avg_fp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "By_avg_fp"));
VisMF::Write(warpx.getBfield_avg_fp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Bz_avg_fp"));
}

if (warpx.getis_synchronized()
|| WarpX::yee_coupled_solver_algo == CoupledYeeSolver::MaxwellLondon
|| warpx.use_lumped_inductor == 1) {
// Need to save j if synchronized because after restart we need j to evolve E by dt/2.
VisMF::Write(warpx.getcurrent_fp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "jx_fp"));
VisMF::Write(warpx.getcurrent_fp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "jy_fp"));
VisMF::Write(warpx.getcurrent_fp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "jz_fp"));
}

if (lev > 0)
{
VisMF::Write(warpx.getEfield_cp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Ex_cp"));
VisMF::Write(warpx.getEfield_cp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Ey_cp"));
VisMF::Write(warpx.getEfield_cp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Ez_cp"));
VisMF::Write(warpx.getBfield_cp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Bx_cp"));
VisMF::Write(warpx.getBfield_cp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "By_cp"));
VisMF::Write(warpx.getBfield_cp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Bz_cp"));

#ifdef WARPX_MAG_LLG
VisMF::Write(warpx.getHfield_cp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Hx_cp"));
VisMF::Write(warpx.getHfield_cp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Hy_cp"));
VisMF::Write(warpx.getHfield_cp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Hz_cp"));
VisMF::Write(warpx.getMfield_cp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Mx_cp"));
VisMF::Write(warpx.getMfield_cp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "My_cp"));
VisMF::Write(warpx.getMfield_cp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Mz_cp"));
VisMF::Write(warpx.getH_biasfield_cp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Hxbias_fp"));
VisMF::Write(warpx.getH_biasfield_cp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Hybias_fp"));
VisMF::Write(warpx.getH_biasfield_cp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Hzbias_fp"));
#endif

if (WarpX::fft_do_time_averaging)
{
VisMF::Write(warpx.getEfield_avg_cp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Ex_avg_cp"));
VisMF::Write(warpx.getEfield_avg_cp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Ey_avg_cp"));
VisMF::Write(warpx.getEfield_avg_cp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Ez_avg_cp"));

VisMF::Write(warpx.getBfield_avg_cp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Bx_avg_cp"));
VisMF::Write(warpx.getBfield_avg_cp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "By_avg_cp"));
VisMF::Write(warpx.getBfield_avg_cp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "Bz_avg_cp"));
}

if (warpx.getis_synchronized()
|| WarpX::yee_coupled_solver_algo == CoupledYeeSolver::MaxwellLondon
|| warpx.use_lumped_inductor == 1) {
// Need to save j if synchronized because after restart we need j to evolve E by dt/2.
VisMF::Write(warpx.getcurrent_cp(lev, 0),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "jx_cp"));
VisMF::Write(warpx.getcurrent_cp(lev, 1),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "jy_cp"));
VisMF::Write(warpx.getcurrent_cp(lev, 2),
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "jz_cp"));
}
}

if (warpx.DoPML()) {
if (warpx.GetPML(lev)) {
warpx.GetPML(lev)->CheckPoint(
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "pml"));
}
#if (defined WARPX_DIM_RZ) && (defined WARPX_USE_PSATD)
if (warpx.GetPML_RZ(lev)) {
warpx.GetPML_RZ(lev)->CheckPoint(
amrex::MultiFabFileFullPrefix(lev, checkpointname, default_level_prefix, "pml_rz"));
}
#endif
}
}

CheckpointParticles(checkpointname, particle_diags);

WriteDMaps(checkpointname, nlev);

VisMF::SetHeaderVersion(current_version);

}

void
FlushFormatCheckpoint::CheckpointParticles (
const std::string& dir,
const amrex::Vector<ParticleDiag>& particle_diags) const
{
for (auto& part_diag: particle_diags) {
WarpXParticleContainer* pc = part_diag.getParticleContainer();

Vector<std::string> real_names;
Vector<std::string> int_names;
Vector<int> int_flags;
Vector<int> real_flags;

real_names.push_back("weight");

real_names.push_back("momentum_x");
real_names.push_back("momentum_y");
real_names.push_back("momentum_z");

#ifdef WARPX_DIM_RZ
real_names.push_back("theta");
#endif

// get the names of the real comps
real_names.resize(pc->NumRealComps());
auto runtime_rnames = pc->getParticleRuntimeComps();
for (auto const& x : runtime_rnames) { real_names[x.second+PIdx::nattribs] = x.first; }

// and the int comps
int_names.resize(pc->NumIntComps());
auto runtime_inames = pc->getParticleRuntimeiComps();
for (auto const& x : runtime_inames) { int_names[x.second+0] = x.first; }

pc->Checkpoint(dir, part_diag.getSpeciesName(), true,
real_names, int_names);
}
}

void
FlushFormatCheckpoint::WriteDMaps (const std::string& dir, int nlev) const
{
if (ParallelDescriptor::IOProcessor()) {
auto & warpx = WarpX::GetInstance();
for (int lev = 0; lev < nlev; ++lev) {
std::string DMFileName = dir;
if (!DMFileName.empty() && DMFileName[DMFileName.size()-1] != '/') {DMFileName += '/';}
DMFileName = amrex::Concatenate(DMFileName + "Level_", lev, 1);
DMFileName += "/DM";

std::ofstream DMFile;
DMFile.open(DMFileName.c_str(), std::ios::out|std::ios::trunc);

if (!DMFile.good()) { amrex::FileOpenFailed(DMFileName); }

DMFile << ParallelDescriptor::NProcs() << "\n";
warpx.DistributionMap(lev).writeOn(DMFile);

DMFile.flush();
DMFile.close();
WARPX_ALWAYS_ASSERT_WITH_MESSAGE(
DMFile.good(),
"FlushFormatCheckpoint::WriteDMaps: problem writing DMFile"
);
}
}
}
12 changes: 12 additions & 0 deletions Source/Diagnostics/FullDiagnostics.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -716,6 +716,18 @@ FullDiagnostics::InitializeFieldFunctors (int lev)
m_all_field_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.getInductor().m_inductor_y_mf.get(), lev, m_crse_ratio);
} else if ( m_varnames[comp] == "inductorz" ){
m_all_field_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.getInductor().m_inductor_z_mf.get(), lev, m_crse_ratio);
} else if ( m_varnames[comp] == "josephson_phi_x" ){
m_all_field_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.getJosephsonJunction().m_phi_x_mf.get(), lev, m_crse_ratio);
} else if ( m_varnames[comp] == "josephson_phi_y" ){
m_all_field_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.getJosephsonJunction().m_phi_y_mf.get(), lev, m_crse_ratio);
} else if ( m_varnames[comp] == "josephson_phi_z" ){
m_all_field_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.getJosephsonJunction().m_phi_z_mf.get(), lev, m_crse_ratio);
} else if ( m_varnames[comp] == "josephson_Ic_x" ){
m_all_field_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.getJosephsonJunction().m_Ic_x_mf.get(), lev, m_crse_ratio);
} else if ( m_varnames[comp] == "josephson_Ic_y" ){
m_all_field_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.getJosephsonJunction().m_Ic_y_mf.get(), lev, m_crse_ratio);
} else if ( m_varnames[comp] == "josephson_Ic_z" ){
m_all_field_functors[lev][comp] = std::make_unique<CellCenterFunctor>(warpx.getJosephsonJunction().m_Ic_z_mf.get(), lev, m_crse_ratio);
}
else {

Expand Down
6 changes: 4 additions & 2 deletions Source/Diagnostics/WarpXIO.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -359,7 +359,8 @@ WarpX::InitFromCheckpoint ()

if (is_synchronized
|| WarpX::yee_coupled_solver_algo == CoupledYeeSolver::MaxwellLondon
|| use_lumped_inductor == 1)
|| use_lumped_inductor == 1
|| use_josephson_junction == 1)
{
VisMF::Read(*current_fp[lev][0],
amrex::MultiFabFileFullPrefix(lev, restart_chkfile, level_prefix, "jx_fp"));
Expand Down Expand Up @@ -426,7 +427,8 @@ WarpX::InitFromCheckpoint ()

if (is_synchronized
|| WarpX::yee_coupled_solver_algo == CoupledYeeSolver::MaxwellLondon
|| use_lumped_inductor == 1) {
|| use_lumped_inductor == 1
|| use_josephson_junction == 1) {
VisMF::Read(*current_cp[lev][0],
amrex::MultiFabFileFullPrefix(lev, restart_chkfile, level_prefix, "jx_cp"));
VisMF::Read(*current_cp[lev][1],
Expand Down
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