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Removing namespace io = openPMD #311

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merged 1 commit into from
Jan 12, 2021
Merged

Removing namespace io = openPMD #311

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1 change: 0 additions & 1 deletion src/Hipace.H
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,6 @@
#ifdef HIPACE_USE_OPENPMD
#include <openPMD/openPMD.hpp>
#include "diagnostics/OpenPMDWriter.H"
namespace io = openPMD;
#endif

#include <memory>
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30 changes: 15 additions & 15 deletions src/diagnostics/OpenPMDWriter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -20,15 +20,15 @@ OpenPMDWriter::InitDiagnostics ()

std::string filename = "diags/h5/openpmd.h5"; // bp or h5
#ifdef AMREX_USE_MPI
m_outputSeries = std::make_unique< io::Series >(
filename, io::Access::CREATE, amrex::ParallelDescriptor::Communicator());
m_outputSeries = std::make_unique< openPMD::Series >(
filename, openPMD::Access::CREATE, amrex::ParallelDescriptor::Communicator());
#else
m_outputSeries = std::make_unique< io::Series >(
filename, io::Access::CREATE);
m_outputSeries = std::make_unique< openPMD::Series >(
filename, openPMD::Access::CREATE);
#endif

// open files early and collectively, so later flush calls are non-collective
m_outputSeries->setIterationEncoding( io::IterationEncoding::groupBased );
m_outputSeries->setIterationEncoding( openPMD::IterationEncoding::groupBased );
m_outputSeries->flush();

// TODO: meta-data: author, mesh path, extensions, software
Expand All @@ -41,7 +41,7 @@ OpenPMDWriter::WriteDiagnostics (
const amrex::Real physical_time, const int output_step, const int lev,
const int slice_dir, const amrex::Vector< std::string > varnames)
{
io::Iteration iteration = m_outputSeries->iterations[output_step];
openPMD::Iteration iteration = m_outputSeries->iterations[output_step];
iteration.setTime(physical_time);

WriteFieldData(a_mf[lev], geom[lev], slice_dir, varnames, iteration);
Expand Down Expand Up @@ -70,11 +70,11 @@ OpenPMDWriter::WriteFieldData (
std::string fieldname = varnames[icomp];
// "B" "x" (todo)
// "Bx" "" (just for now)
io::Mesh field = meshes[fieldname];
io::MeshRecordComponent field_comp = field[io::MeshRecordComponent::SCALAR];
openPMD::Mesh field = meshes[fieldname];
openPMD::MeshRecordComponent field_comp = field[openPMD::MeshRecordComponent::SCALAR];

// meta-data
field.setDataOrder(io::Mesh::DataOrder::C);
field.setDataOrder(openPMD::Mesh::DataOrder::C);
// node staggering
auto relative_cell_pos = utils::getRelativeCellPosition(mf); // AMReX Fortran index order
std::reverse(relative_cell_pos.begin(), relative_cell_pos.end()); // now in C order
Expand All @@ -96,12 +96,12 @@ OpenPMDWriter::WriteFieldData (
field.setGridGlobalOffset(offWindow);

// data type and global size of the simulation
io::Datatype datatype = io::determineDatatype< amrex::Real >();
io::Extent global_size = utils::getReversedVec(geom.Domain().size());
openPMD::Datatype datatype = openPMD::determineDatatype< amrex::Real >();
openPMD::Extent global_size = utils::getReversedVec(geom.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);

io::Dataset dataset(datatype, global_size);
openPMD::Dataset dataset(datatype, global_size);
field_comp.resetDataset(dataset);

// Loop over longitudinal boxes on this rank, from head to tail:
Expand All @@ -112,7 +112,7 @@ OpenPMDWriter::WriteFieldData (
amrex::Box const data_box = mfi.validbox(); // w/o guards in all cases
std::shared_ptr< amrex::Real const > data;
if (mfi.validbox() == fab.box() ) {
data = io::shareRaw( fab.dataPtr( icomp ) ); // non-owning view until flush()
data = openPMD::shareRaw( fab.dataPtr( icomp ) ); // non-owning view until flush()
} else {
// copy data to cut away guards
amrex::FArrayBox io_fab(mfi.validbox(), 1, amrex::The_Pinned_Arena());
Expand All @@ -123,8 +123,8 @@ OpenPMDWriter::WriteFieldData (

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