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-rw-r--r--Source/Diagnostics/BTDiagnostics.cpp101
1 files changed, 69 insertions, 32 deletions
diff --git a/Source/Diagnostics/BTDiagnostics.cpp b/Source/Diagnostics/BTDiagnostics.cpp
index 204b28b07..a5b85c6b6 100644
--- a/Source/Diagnostics/BTDiagnostics.cpp
+++ b/Source/Diagnostics/BTDiagnostics.cpp
@@ -88,10 +88,17 @@ void BTDiagnostics::DerivedInitData ()
m_snapshot_full.resize( m_num_buffers );
m_lastValidZSlice.resize( m_num_buffers );
m_buffer_k_index_hi.resize(m_num_buffers);
+ m_first_flush_after_restart.resize(m_num_buffers);
+ m_snapshot_geometry_defined.resize(m_num_buffers);
+ m_field_buffer_multifab_defined.resize(m_num_buffers);
for (int i = 0; i < m_num_buffers; ++i) {
m_geom_snapshot[i].resize(nmax_lev);
m_snapshot_full[i] = 0;
m_lastValidZSlice[i] = 0;
+ m_buffer_flush_counter[i] = 0;
+ m_first_flush_after_restart[i] = 1;
+ m_snapshot_geometry_defined[i] = 0;
+ m_field_buffer_multifab_defined[i] = 0;
}
for (int lev = 0; lev < nmax_lev; ++lev) {
// Define cell-centered multifab over the whole domain with
@@ -329,13 +336,21 @@ BTDiagnostics::DoComputeAndPack (int step, bool force_flush)
}
void
-BTDiagnostics::InitializeBufferData ( int i_buffer , int lev)
+BTDiagnostics::InitializeBufferData ( int i_buffer , int lev, bool restart)
{
auto & warpx = WarpX::GetInstance();
+
+ // When restarting boosted simulations, the code below needs to take
+ // into account the fact that the position of the box at the beginning
+ // of the simulation, is not the one that we had at t=0 (because of the moving window)
+ amrex::Real boosted_moving_window_v = (warpx.moving_window_v - m_beta_boost*PhysConst::c)
+ / (1._rt - m_beta_boost * warpx.moving_window_v/PhysConst::c);
// Lab-frame time for the i^th snapshot
- amrex::Real zmax_0 = warpx.Geom(lev).ProbHi(m_moving_window_dir);
- m_t_lab.at(i_buffer) = m_intervals.GetBTDIteration(i_buffer) * m_dt_snapshots_lab
- + m_gamma_boost*m_beta_boost*zmax_0/PhysConst::c;
+ if (restart == false) {
+ amrex::Real zmax_0 = warpx.Geom(lev).ProbHi(m_moving_window_dir);
+ m_t_lab.at(i_buffer) = m_intervals.GetBTDIteration(i_buffer) * m_dt_snapshots_lab
+ + m_gamma_boost*m_beta_boost*zmax_0/PhysConst::c;
+ }
// Define buffer domain in boosted frame at level, lev, with user-defined lo and hi
amrex::RealBox diag_dom;
@@ -392,15 +407,13 @@ BTDiagnostics::InitializeBufferData ( int i_buffer , int lev)
// Define buffer_domain in lab-frame for the i^th snapshot.
// Replace z-dimension with lab-frame co-ordinates.
- amrex::Real zmin_buffer_lab = diag_dom.lo(m_moving_window_dir)
- / ( (1.0_rt + m_beta_boost) * m_gamma_boost);
- amrex::Real zmax_buffer_lab = diag_dom.hi(m_moving_window_dir)
- / ( (1.0_rt + m_beta_boost) * m_gamma_boost);
-
+ amrex::Real zmin_buffer_lab = ( diag_dom.lo(m_moving_window_dir) - boosted_moving_window_v * warpx.gett_new(0) )
+ / ( (1.0_rt + m_beta_boost) * m_gamma_boost);
+ amrex::Real zmax_buffer_lab = ( diag_dom.hi(m_moving_window_dir) - boosted_moving_window_v * warpx.gett_new(0) )
+ / ( (1.0_rt + m_beta_boost) * m_gamma_boost);
// Initialize buffer counter and z-positions of the i^th snapshot in
// boosted-frame and lab-frame
- m_buffer_flush_counter[i_buffer] = 0;
m_buffer_counter[i_buffer] = 0;
m_current_z_lab[i_buffer] = 0._rt;
m_current_z_boost[i_buffer] = 0._rt;
@@ -450,7 +463,6 @@ BTDiagnostics::InitializeBufferData ( int i_buffer , int lev)
m_snapshot_ncells_lab[i_buffer] = amrex::IntVect(Nz_lab);
#endif
-
// Box covering the extent of the user-defined diag in the back-transformed frame
// for the ith snapshot
// estimating the maximum number of buffer multifabs needed to obtain the
@@ -461,20 +473,23 @@ BTDiagnostics::InitializeBufferData ( int i_buffer , int lev)
// number of cells in z is modified since each buffer multifab always
// contains a minimum m_buffer_size=256 cells
int num_z_cells_in_snapshot = m_max_buffer_multifabs[i_buffer] * m_buffer_size;
- m_snapshot_domain_lab[i_buffer] = diag_dom;
- m_snapshot_domain_lab[i_buffer].setLo(m_moving_window_dir,
- zmin_buffer_lab + warpx.moving_window_v * m_t_lab[i_buffer]);
- m_snapshot_domain_lab[i_buffer].setHi(m_moving_window_dir,
- zmax_buffer_lab + warpx.moving_window_v * m_t_lab[i_buffer]);
- // To prevent round off errors, moving the snapshot domain by half a cell so that all the slices
- // lie close to the cell-centers in the lab-frame grid instead of on the edge of cell.
- amrex::Real new_hi = m_snapshot_domain_lab[i_buffer].hi(m_moving_window_dir)
- + 0.5_rt * dz_lab(warpx.getdt(lev), ref_ratio[m_moving_window_dir]);
- m_snapshot_domain_lab[i_buffer].setHi(m_moving_window_dir,new_hi);
- amrex::Real new_lo = m_snapshot_domain_lab[i_buffer].hi(m_moving_window_dir) -
- num_z_cells_in_snapshot *
- dz_lab(warpx.getdt(lev), ref_ratio[m_moving_window_dir]);
- m_snapshot_domain_lab[i_buffer].setLo(m_moving_window_dir, new_lo);
+ if (restart == false) {
+ m_snapshot_domain_lab[i_buffer] = diag_dom;
+ m_snapshot_domain_lab[i_buffer].setLo(m_moving_window_dir,
+ zmin_buffer_lab + warpx.moving_window_v * m_t_lab[i_buffer]);
+ m_snapshot_domain_lab[i_buffer].setHi(m_moving_window_dir,
+ zmax_buffer_lab + warpx.moving_window_v * m_t_lab[i_buffer]);
+ // To prevent round off errors, moving the snapshot domain by half a cell so that all the slices
+ // lie close to the cell-centers in the lab-frame grid instead of on the edge of cell.
+ amrex::Real new_hi = m_snapshot_domain_lab[i_buffer].hi(m_moving_window_dir)
+ + 0.5_rt * dz_lab(warpx.getdt(lev), ref_ratio[m_moving_window_dir]);
+ m_snapshot_domain_lab[i_buffer].setHi(m_moving_window_dir,new_hi);
+ amrex::Real new_lo = m_snapshot_domain_lab[i_buffer].hi(m_moving_window_dir) -
+ num_z_cells_in_snapshot *
+ dz_lab(warpx.getdt(lev), ref_ratio[m_moving_window_dir]);
+ m_snapshot_domain_lab[i_buffer].setLo(m_moving_window_dir, new_lo);
+ }
+
// cell-centered index that corresponds to the hi-end of the lab-frame in the z-direction
// Adding 0.5 dz_lab so that we obtain the cell-centered index consistent to the hi-end
int snapshot_kindex_hi = static_cast<int>(floor(
@@ -487,8 +502,9 @@ BTDiagnostics::InitializeBufferData ( int i_buffer , int lev)
m_snapshot_box[i_buffer].setSmall( m_moving_window_dir,
snapshot_kindex_hi - (num_z_cells_in_snapshot-1) );
// Setting hi k-index for the first buffer
- m_buffer_k_index_hi[i_buffer] = m_snapshot_box[i_buffer].bigEnd(m_moving_window_dir);
-
+ if (restart == false) {
+ m_buffer_k_index_hi[i_buffer] = m_snapshot_box[i_buffer].bigEnd(m_moving_window_dir);
+ }
}
void
@@ -809,15 +825,18 @@ BTDiagnostics::PrepareFieldDataForOutput ()
// Check if the zslice is in domain
bool ZSliceInDomain = GetZSliceInDomainFlag (i_buffer, lev);
// Initialize and define field buffer multifab if buffer is empty
- if (ZSliceInDomain) {
+ bool kindexInSnapshotBox = GetKIndexInSnapshotBoxFlag (i_buffer, lev);
+ if (kindexInSnapshotBox) {
if ( buffer_empty(i_buffer) ) {
- if ( m_buffer_flush_counter[i_buffer] == 0) {
+ if ( m_buffer_flush_counter[i_buffer] == 0 || m_first_flush_after_restart[i_buffer] == 1) {
// Compute the geometry, snapshot lab-domain extent
// and box-indices
DefineSnapshotGeometry(i_buffer, lev);
}
DefineFieldBufferMultiFab(i_buffer, lev);
}
+ }
+ if (ZSliceInDomain) {
WARPX_ALWAYS_ASSERT_WITH_MESSAGE(
m_current_z_lab[i_buffer] >= m_buffer_domain_lab[i_buffer].lo(m_moving_window_dir) and
m_current_z_lab[i_buffer] <= m_buffer_domain_lab[i_buffer].hi(m_moving_window_dir),
@@ -877,6 +896,7 @@ BTDiagnostics::SetSnapshotFullStatus (const int i_buffer)
void
BTDiagnostics::DefineFieldBufferMultiFab (const int i_buffer, const int lev)
{
+ if (m_field_buffer_multifab_defined[i_buffer] == 1) return;
auto & warpx = WarpX::GetInstance();
const int hi_k_lab = m_buffer_k_index_hi[i_buffer];
@@ -931,12 +951,14 @@ BTDiagnostics::DefineFieldBufferMultiFab (const int i_buffer, const int lev)
m_geom_output[i_buffer][lev] = amrex::refine( m_geom_output[i_buffer][lev-1],
warpx.RefRatio(lev-1) );
}
+ m_field_buffer_multifab_defined[i_buffer] = 1;
}
void
BTDiagnostics::DefineSnapshotGeometry (const int i_buffer, const int lev)
{
+ if (m_snapshot_geometry_defined[i_buffer] == 1) return;
auto & warpx = WarpX::GetInstance();
if (lev == 0) {
@@ -954,6 +976,7 @@ BTDiagnostics::DefineSnapshotGeometry (const int i_buffer, const int lev)
m_geom_snapshot[i_buffer][lev] = amrex::refine( m_geom_snapshot[i_buffer][lev-1],
warpx.RefRatio(lev-1) );
}
+ m_snapshot_geometry_defined[i_buffer] = 1;
}
bool
@@ -975,6 +998,18 @@ BTDiagnostics::GetZSliceInDomainFlag (const int i_buffer, const int lev)
return true;
}
+
+bool
+BTDiagnostics::GetKIndexInSnapshotBoxFlag (const int i_buffer, const int lev)
+{
+ if (k_index_zlab(i_buffer, lev) >= m_snapshot_box[i_buffer].smallEnd(m_moving_window_dir) and
+ k_index_zlab(i_buffer, lev) <= m_snapshot_box[i_buffer].bigEnd(m_moving_window_dir)) {
+ return true;
+ }
+
+ return false;
+}
+
void
BTDiagnostics::Flush (int i_buffer)
{
@@ -1070,7 +1105,9 @@ BTDiagnostics::Flush (int i_buffer)
// Reset the buffer counter to zero after flushing out data stored in the buffer.
ResetBufferCounter(i_buffer);
+ m_field_buffer_multifab_defined[i_buffer] = 0;
IncrementBufferFlushCounter(i_buffer);
+ NullifyFirstFlush(i_buffer);
// if particles are selected for output then update and reset counters
if (m_output_species_names.size() > 0) {
UpdateTotalParticlesFlushed(i_buffer);
@@ -1120,7 +1157,7 @@ void BTDiagnostics::MergeBuffersForPlotfile (int i_snapshot)
std::string recent_Buffer_Level0_path = recent_Buffer_filepath + "/Level_0";
std::string recent_Buffer_FabHeaderFilename = recent_Buffer_Level0_path + "/Cell_H";
// Create directory only when the first buffer is flushed out.
- if (m_buffer_flush_counter[i_snapshot] == 0 ) {
+ if (m_buffer_flush_counter[i_snapshot] == 0 || m_first_flush_after_restart[i_snapshot] == 1) {
// Create Level_0 directory to store all Cell_D and Cell_H files
if (!amrex::UtilCreateDirectory(snapshot_Level0_path, permission_flag_rwxrxrx) )
amrex::CreateDirectoryFailed(snapshot_Level0_path);
@@ -1162,7 +1199,7 @@ void BTDiagnostics::MergeBuffersForPlotfile (int i_snapshot)
// Cell_D_<number> is padded with 5 zeros as that is the default AMReX output
std::string new_snapshotFabFilename = amrex::Concatenate("Cell_D_", m_buffer_flush_counter[i_snapshot], amrex_fabfile_digits);
- if ( m_buffer_flush_counter[i_snapshot] == 0) {
+ if (m_buffer_flush_counter[i_snapshot] == 0 || m_first_flush_after_restart[i_snapshot] == 1) {
std::rename(recent_Header_filename.c_str(), snapshot_Header_filename.c_str());
Buffer_FabHeader.SetFabName(0, Buffer_FabHeader.fodPrefix(0),
new_snapshotFabFilename,
@@ -1208,7 +1245,7 @@ void BTDiagnostics::MergeBuffersForPlotfile (int i_snapshot)
m_buffer_flush_counter[i_snapshot],
amrex_partfile_digits);
- if (m_buffer_flush_counter[i_snapshot] == 0) {
+ if (m_buffer_flush_counter[i_snapshot] == 0 || m_first_flush_after_restart[i_snapshot] == 1) {
BufferSpeciesHeader.set_DataIndex(0,0,m_buffer_flush_counter[i_snapshot]);
BufferSpeciesHeader.WriteHeader();
generated by cgit v1.2.3 (git 2.39.1) at 2025-08-09 12:30:12 +0000