From 6b31e7944145fcfef05bdc8885f14c1e9ce130fd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Franz=20P=C3=B6schel?= <franz.poeschel@gmail.com>
Date: Wed, 5 Jun 2019 16:56:38 +0200
Subject: [PATCH 1/2] Adapt tests to allowing delayed write of position and
 positionOffset

---
 test/CoreTest.cpp     |  2 --
 test/SerialIOTest.cpp | 35 +++++++++++++++++++++++++++++++++++
 2 files changed, 35 insertions(+), 2 deletions(-)

diff --git a/test/CoreTest.cpp b/test/CoreTest.cpp
index dc647b6265..e0358e8f00 100644
--- a/test/CoreTest.cpp
+++ b/test/CoreTest.cpp
@@ -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);
diff --git a/test/SerialIOTest.cpp b/test/SerialIOTest.cpp
index 82e6a4890b..efbb81fead 100644
--- a/test/SerialIOTest.cpp
+++ b/test/SerialIOTest.cpp
@@ -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 )

From 4bdd73fbed07023e9b4b8718c432b049e8492b19 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Franz=20P=C3=B6schel?= <franz.poeschel@gmail.com>
Date: Wed, 5 Jun 2019 16:57:22 +0200
Subject: [PATCH 2/2] Allow flushes before defining position and positionOffset
 records

This will ensure openPMD specific requirements for those records at flush time as soon as those records are present -- rather than at creation time of the particle species object.
Currently missing is any kind of check that those records are present before closing the series.
---
 include/openPMD/ParticleSpecies.hpp |  3 ---
 src/ParticleSpecies.cpp             | 11 +++++++++++
 test/CoreTest.cpp                   |  2 --
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/include/openPMD/ParticleSpecies.hpp b/include/openPMD/ParticleSpecies.hpp
index 288d0d28e0..6c11a715a8 100644
--- a/include/openPMD/ParticleSpecies.hpp
+++ b/include/openPMD/ParticleSpecies.hpp
@@ -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"];
diff --git a/src/ParticleSpecies.cpp b/src/ParticleSpecies.cpp
index 91fe4ea429..be653bf246 100644
--- a/src/ParticleSpecies.cpp
+++ b/src/ParticleSpecies.cpp
@@ -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
diff --git a/test/CoreTest.cpp b/test/CoreTest.cpp
index e0358e8f00..ed9a17959b 100644
--- a/test/CoreTest.cpp
+++ b/test/CoreTest.cpp
@@ -449,8 +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);