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Allow flushing before defining position and positionOffset components of particle species #518

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Merged
ax3l merged 2 commits into from
Jun 6, 2019
Merged

Allow flushing before defining position and positionOffset components of particle species #518

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6b31e79
Adapt tests to allowing delayed write of position and positionOffset
franzpoeschel Jun 5, 2019
4bdd73f
Allow flushes before defining position and positionOffset records
franzpoeschel Jun 5, 2019
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3 changes: 0 additions & 3 deletions include/openPMD/ParticleSpecies.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -55,9 +55,6 @@ namespace traits
template< typename T >
void operator()(T & ret)
{
/* enforce these two RecordComponents as required by the standard */
ret["position"].setUnitDimension({{UnitDimension::L, 1}});
ret["positionOffset"].setUnitDimension({{UnitDimension::L, 1}});
ret.particlePatches.linkHierarchy(ret.m_writable);

auto& np = ret.particlePatches["numParticles"];
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11 changes: 11 additions & 0 deletions src/ParticleSpecies.cpp
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Expand Up @@ -122,6 +122,17 @@ ParticleSpecies::flush(std::string const& path)
for( auto& patch : particlePatches )
patch.second.flush(patch.first);
}

iterator it = find("position");
if ( it != end() )
{
it->second.setUnitDimension({{UnitDimension::L, 1}});
}
it = find("positionOffset");
if ( it != end() )
{
it->second.setUnitDimension({{UnitDimension::L, 1}});
}
}
}
} // openPMD
4 changes: 0 additions & 4 deletions test/CoreTest.cpp
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Expand Up @@ -234,8 +234,6 @@ TEST_CASE( "particleSpecies_modification_test", "[core]" )
REQUIRE(1 == particles.size());
REQUIRE(1 == particles.count("species"));
REQUIRE(0 == species.numAttributes());
REQUIRE(2 == species.size()); //position, positionOffset
REQUIRE(1 == species.count("position"));
auto dset = Dataset(Datatype::DOUBLE, {1});
species["position"][RecordComponent::SCALAR].resetDataset(dset);
species["positionOffset"][RecordComponent::SCALAR].resetDataset(dset);
Expand Down Expand Up @@ -451,8 +449,6 @@ TEST_CASE( "structure_test", "[core]" )
REQUIRE(o.iterations[1].particles["P"].particlePatches.IOHandler);
REQUIRE(o.iterations[1].particles["P"].particlePatches.parent == getWritable(&o.iterations[1].particles["P"]));

REQUIRE(1 == o.iterations[1].particles["P"].count("position"));
REQUIRE(1 == o.iterations[1].particles["P"].count("positionOffset"));
auto dset = Dataset(Datatype::DOUBLE, {1});
o.iterations[1].particles["P"]["position"][RecordComponent::SCALAR].resetDataset(dset);
o.iterations[1].particles["P"]["positionOffset"][RecordComponent::SCALAR].resetDataset(dset);
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35 changes: 35 additions & 0 deletions test/SerialIOTest.cpp
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Expand Up @@ -171,6 +171,41 @@ TEST_CASE( "constant_scalar", "[serial]" )
}
}

TEST_CASE( "flush_without_position_positionOffset", "[serial]" )
{
for( auto const & t : backends )
{
const std::string & file_ending = std::get< 0 >( t );
Series s = Series(
"../samples/flush_without_position_positionOffset." + file_ending,
AccessType::CREATE );
ParticleSpecies e = s.iterations[ 0 ].particles[ "e" ];
RecordComponent weighting = e[ "weighting" ][ RecordComponent::SCALAR ];
weighting.resetDataset( Dataset( Datatype::FLOAT, Extent{ 2, 2 } ) );
weighting.storeChunk( std::shared_ptr< float >(
new float[ 4 ]{},
[]( float * ptr ) { delete[] ptr; } ),
{ 0, 0 },
{ 2, 2 } );

s.flush();

for( auto const & key : { "position", "positionOffset" } )
{
for( auto const & dim : { "x", "y", "z" } )
{
RecordComponent rc = e[ key ][ dim ];
rc.resetDataset( Dataset( Datatype::FLOAT , Extent{ 2, 2 } ) );
rc.storeChunk( std::shared_ptr< float >(
new float[ 4 ]{},
[]( float * ptr ) { delete[] ptr; } ),
{ 0, 0 },
{ 2, 2 } );
}
}
}
}


inline
void particle_patches( std::string file_ending )
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