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fix transverse size of IO for level 1 #569

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Jul 28, 2021
Merged

fix transverse size of IO for level 1 #569

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319d9f3
fix transverse size for MR IO
SeverinDiederichs Jul 21, 2021
2bed7a2
Update src/diagnostics/OpenPMDWriter.cpp
SeverinDiederichs Jul 28, 2021
e9e1234
Apply suggestions from code review
SeverinDiederichs Jul 28, 2021
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2 changes: 1 addition & 1 deletion src/diagnostics/OpenPMDWriter.H
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,7 @@ private:
* \param[in] output_step current time step to dump
* \param[in] lev MR level
*/
void WriteFieldData (amrex::FArrayBox const& fab, amrex::Geometry const& geom,
void WriteFieldData (amrex::FArrayBox const& fab, amrex::Vector<amrex::Geometry> const& geom,
const int slice_dir, const amrex::Vector< std::string > varnames,
openPMD::Iteration iteration, const int output_step, const int lev);

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31 changes: 23 additions & 8 deletions src/diagnostics/OpenPMDWriter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
#include "utils/HipaceProfilerWrapper.H"
#include "utils/Constants.H"
#include "utils/IOUtil.H"
#include "particles/pusher/GetDomainLev.H"

#ifdef HIPACE_USE_OPENPMD

Expand Down Expand Up @@ -83,7 +84,7 @@ OpenPMDWriter::WriteDiagnostics (
m_outputSeries[lev]->flush();

} else if (call_type == OpenPMDWriterCallType::fields ) {
WriteFieldData(a_mf[lev], geom[lev], slice_dir, varnames, iteration, output_step, lev);
WriteFieldData(a_mf[lev], geom, slice_dir, varnames, iteration, output_step, lev);
m_outputSeries[lev]->flush();
m_last_output_dumped[lev] = output_step;
}
Expand All @@ -92,7 +93,7 @@ OpenPMDWriter::WriteDiagnostics (

void
OpenPMDWriter::WriteFieldData (
amrex::FArrayBox const& fab, amrex::Geometry const& geom,
amrex::FArrayBox const& fab, amrex::Vector<amrex::Geometry> const& geom,
const int slice_dir, const amrex::Vector< std::string > varnames,
openPMD::Iteration iteration, const int output_step, const int lev)
{
Expand All @@ -113,10 +114,19 @@ OpenPMDWriter::WriteFieldData (
// node staggering
auto relative_cell_pos = utils::getRelativeCellPosition(fab); // AMReX Fortran index order
std::reverse(relative_cell_pos.begin(), relative_cell_pos.end()); // now in C order

amrex::Box const data_box = fab.box();

// labels, spacing and offsets
std::vector< std::string > axisLabels {"z", "y", "x"};
auto dCells = utils::getReversedVec(geom.CellSize()); // dx, dy, dz
auto offWindow = utils::getReversedVec(geom.ProbLo()); // start of moving window
auto dCells = utils::getReversedVec(geom[lev].CellSize()); // dx, dy, dz
amrex::GpuArray<amrex::Real,AMREX_SPACEDIM> correct_problo = GetDomainLev(geom[lev], data_box, 1, lev);
amrex::Vector<double> finalproblo = {AMREX_D_DECL(
static_cast<double>(geom[lev].ProbLo()[2]),
static_cast<double>(correct_problo[1]),
static_cast<double>(correct_problo[0])
)};
auto offWindow = finalproblo;
if (slice_dir >= 0) {
// User requested slice IO
// remove the slicing direction in position, label, resolution, offset
Expand All @@ -132,7 +142,14 @@ OpenPMDWriter::WriteFieldData (

// data type and global size of the simulation
openPMD::Datatype datatype = openPMD::determineDatatype< amrex::Real >();
openPMD::Extent global_size = utils::getReversedVec(geom.Domain().size());
amrex::IntVect prob_size = data_box.bigEnd() - data_box.smallEnd()
+ amrex::IntVect::TheUnitVector();
amrex::Vector<long unsigned int> probsize_reformat = {AMREX_D_DECL(
static_cast<long unsigned int>(geom[lev].Domain().size()[2]),
static_cast<long unsigned int>(prob_size[1]),
static_cast<long unsigned int>(prob_size[0])
)};
openPMD::Extent global_size = probsize_reformat; //geom[lev].Domain().size());
// If slicing requested, remove number of points for the slicing direction
if (slice_dir >= 0) global_size.erase(global_size.begin() + 2-slice_dir);

Expand All @@ -142,13 +159,11 @@ OpenPMDWriter::WriteFieldData (
}

// Store the provided box as a chunk with openpmd
amrex::Box const data_box = fab.box();
std::shared_ptr< amrex::Real const > data;

data = openPMD::shareRaw( fab.dataPtr( icomp ) ); // non-owning view until flush()

// Determine the offset and size of this data chunk in the global output
amrex::IntVect const box_offset = data_box.smallEnd();
amrex::IntVect const box_offset = {0, 0, data_box.smallEnd(2)};
openPMD::Offset chunk_offset = utils::getReversedVec(box_offset);
openPMD::Extent chunk_size = utils::getReversedVec(data_box.size());
if (slice_dir >= 0) { // remove Ny components
Expand Down