[Paraview] Error reading timeseries with spatial grid collection with XDMF

Nikolaos Beratlis nikos.beratlis at gmail.com
Sat Nov 11 13:31:51 EST 2017


Hi,

I have a cartesian structured grid made of two sub-domains and a two snap
shots in a time that I would like to read in Paraview. The data and grid
files are stored in HDF5 file and I use a XDMF file to read them in a
Paraview. The XDMF files looks like this:

<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="2.2">
<Domain Name="Bump">
<Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">

<Grid Name="0" GridType="Collection" CollectionType="Spatial">
<Time TimeType="Single" Value="0.0"/>

<Grid GridType="Uniform" Name="GridZone0001">
<Topology TopologyType="3DRectMesh" Dimensions="    2  202  267"/>
<Geometry GeometryType="VXVYVZ">
<DataItem Dimensions="  267" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
</DataItem>
<DataItem Dimensions="  202" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/YC
</DataItem>
<DataItem Dimensions="    2" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
</DataItem>
</Geometry>
<Attribute Name="Q" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="    2  202  267" NumberType="Float" Precision="4"
Format="HDF">
../Q_VPreg.h5sp.0001:/zone0001
</DataItem>
</Attribute>
</Grid>

<Grid GridType="Uniform" Name="GridZone0002">
<Topology TopologyType="3DRectMesh" Dimensions="    2  202  268"/>
<Geometry GeometryType="VXVYVZ">
<DataItem Dimensions="  268" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
</DataItem>
<DataItem Dimensions="  202" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/YC
</DataItem>
<DataItem Dimensions="    2" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
</DataItem>
</Geometry>
<Attribute Name="Q" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="    2  202  268" NumberType="Float" Precision="4"
Format="HDF">
../Q_VPreg.h5sp.0001:/zone0002
</DataItem>
</Attribute>
</Grid>
</Grid>

<Grid Name="0" GridType="Collection" CollectionType="Spatial">
<Time TimeType="Single" Value="0.0"/>

<Grid GridType="Uniform" Name="GridZone0001">
<Topology TopologyType="3DRectMesh" Dimensions="    2  202  267"/>
<Geometry GeometryType="VXVYVZ">
<DataItem Dimensions="  267" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
</DataItem>
<DataItem Dimensions="  202" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/YC
</DataItem>
<DataItem Dimensions="    2" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
</DataItem>
</Geometry>
<Attribute Name="Q" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="    2  202  267" NumberType="Float" Precision="4"
Format="HDF">
../Q_VPreg.h5sp.0001:/zone0001
</DataItem>
</Attribute>
</Grid>

<Grid GridType="Uniform" Name="GridZone0002">
<Topology TopologyType="3DRectMesh" Dimensions="    2  202  268"/>
<Geometry GeometryType="VXVYVZ">
<DataItem Dimensions="  268" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
</DataItem>
<DataItem Dimensions="  202" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/YC
</DataItem>
<DataItem Dimensions="    2" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
</DataItem>
</Geometry>
<Attribute Name="Q" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="    2  202  268" NumberType="Float" Precision="4"
Format="HDF">
../Q_VPreg.h5sp.0002:/zone0002
</DataItem>
</Attribute>
</Grid>

</Grid>

</Grid>
</Domain>
</Xdmf>

The file is read in Paraview. When I advance in to the second instant in
time I get the following error:

Failed to read attribute data.

Paraview shows data from the first subset (zone0001), it can't read the
data from the second subset (zone0002).


When I read only on instant in time like this:

<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="2.2">
<Domain Name="Bump">
<Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">

<Grid Name="0" GridType="Collection" CollectionType="Spatial">
<Time TimeType="Single" Value="0.0"/>

<Grid GridType="Uniform" Name="GridZone0001">
<Topology TopologyType="3DRectMesh" Dimensions="    2  202  267"/>
<Geometry GeometryType="VXVYVZ">
<DataItem Dimensions="  267" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
</DataItem>
<DataItem Dimensions="  202" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/YC
</DataItem>
<DataItem Dimensions="    2" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
</DataItem>
</Geometry>
<Attribute Name="Q" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="    2  202  267" NumberType="Float" Precision="4"
Format="HDF">
../Q_VPreg.h5sp.0001:/zone0001
</DataItem>
</Attribute>
</Grid>

<Grid GridType="Uniform" Name="GridZone0002">
<Topology TopologyType="3DRectMesh" Dimensions="    2  202  268"/>
<Geometry GeometryType="VXVYVZ">
<DataItem Dimensions="  268" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
</DataItem>
<DataItem Dimensions="  202" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/YC
</DataItem>
<DataItem Dimensions="    2" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
</DataItem>
</Geometry>
<Attribute Name="Q" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="    2  202  268" NumberType="Float" Precision="4"
Format="HDF">
../Q_VPreg.h5sp.0001:/zone0002
</DataItem>
</Attribute>
</Grid>
</Grid>

</Grid>
</Domain>
</Xdmf>

the file is read successfully and no errors show up.

Also when I read two time instants but with only one subset (zone0001)
Paraview doesn't throw any errors.

<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="2.2">
<Domain Name="Bump">
<Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">

<Grid Name="0" GridType="Collection" CollectionType="Spatial">
<Time TimeType="Single" Value="0.0"/>

<Grid GridType="Uniform" Name="GridZone0001">
<Topology TopologyType="3DRectMesh" Dimensions="    2  202  267"/>
<Geometry GeometryType="VXVYVZ">
<DataItem Dimensions="  267" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
</DataItem>
<DataItem Dimensions="  202" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/YC
</DataItem>
<DataItem Dimensions="    2" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
</DataItem>
</Geometry>
<Attribute Name="Q" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="    2  202  267" NumberType="Float" Precision="4"
Format="HDF">
../Q_VPreg.h5sp.0001:/zone0001
</DataItem>
</Attribute>
</Grid>

<Grid Name="0" GridType="Collection" CollectionType="Spatial">
<Time TimeType="Single" Value="0.0"/>

<Grid GridType="Uniform" Name="GridZone0001">
<Topology TopologyType="3DRectMesh" Dimensions="    2  202  267"/>
<Geometry GeometryType="VXVYVZ">
<DataItem Dimensions="  267" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
</DataItem>
<DataItem Dimensions="  202" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/YC
</DataItem>
<DataItem Dimensions="    2" NumberType="Float" Precision="4" Format="HDF">
../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
</DataItem>
</Geometry>
<Attribute Name="Q" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="    2  202  267" NumberType="Float" Precision="4"
Format="HDF">
../Q_VPreg.h5sp.0001:/zone0001
</DataItem>
</Attribute>
</Grid>

</Grid>

</Grid>
</Domain>
</Xdmf>


Does anyone see the problem in the code?

Kind regards,

Nikos
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