Data not available (XMF3)

ParaView Support
1

Hello, I am trying to use paraview 5.8.0 to visualize some data sets from a wave model. The models output arrays containing x y z displacements and torsional rotations for each. I save the data within an hdf5 and create an xmf3 descriptor for these files, which I can load into paraview, however some of my arrays are missing.

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image515×802 23.6 KB

Indicates that all of my input arrays have been loaded, however when I look at the spread sheet view I expect to see scalars x,y,z,t but I appear to be missing z and t.

This the relevant piece of code that describes the process I use to create the xmf3 file

 f = open(paraviewFname.split('.')[0]+".xmf", 'w')
# Header for xml file
f.write('''<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="2.0">
<Domain>
<Grid Name="Box" GridType="Collection" CollectionType="Temporal">
''')

# loop over the attributes name written using time
t = 0
for t in range(0,timeSteps,dtStep):
    # Naming datasets 
    dataSetName1 = paraviewFname+":/XparaviewSnaps/"+str(t)
    dataSetName2 = paraviewFname+":/YparaviewSnaps/"+str(t)
    dataSetName3 = paraviewFname+":/ZparaviewSnaps/"+str(t)
    dataSetName4 = paraviewFname+":/TorisonalparaviewSnaps/"+str(t)
    # at individual time write the time independent Box grid. is it overdoing?
    f.write('''
    <!-- time step -->
    <Grid Name="Box %d" GridType="Uniform">  
    <Topology TopologyType="3DCoRectMesh" Dimensions="%d %d %d"/>
    <Geometry GeometryType="ORIGIN_DXDYDZ">
       <DataItem DataType="Float" Dimensions="3" Format="XML">0.0 0.0 0.0</DataItem>
       <DataItem DataType="Float" Dimensions="3" Format="XML">%d %d %d</DataItem>
    </Geometry>
    <Time Value="%d" />
    \n'''%(t, Nx, Ny, Nz,h,h,h, t))

    # First Attribute
    f.write('''\n
    <Attribute Name="X" AttributeType="Scalar" Center="Node">
    <DataItem Dimensions="%d %d %d" NumberType="Float" Precision="4"
    Format="HDF">
    %s
    </DataItem>
    </Attribute>
    \n'''%(Nx, Ny, Nz, dataSetName1))


    # Second Attribute
    f.write('''\n
    <Attribute Name="Y" AttributeType="Scalar" Center="Node">
    <DataItem Dimensions="%d %d %d " NumberType="Float" Precision="4"
    Format="HDF">
    %s
    </DataItem>
    </Attribute>
    </Grid>\n'''%(Nx, Ny, Nz, dataSetName2))
    
    # Third Attribute
    f.write('''\n
    <Attribute Name="Z" AttributeType="Scalar" Center="Node">
    <DataItem Dimensions="%d %d %d" NumberType="Float" Precision="4"
    Format="HDF">
    %s
    </DataItem>
    </Attribute>
    \n'''%(Nx, Ny, Nz, dataSetName3))

    # Fourth Attribute
    f.write('''\n
    <Attribute Name="T" AttributeType="Scalar" Center="Node">
    <DataItem Dimensions="%d %d %d" NumberType="Float" Precision="4"
    Format="HDF">
    %s
    </DataItem>
    </Attribute>
    \n'''%(Nx, Ny, Nz, dataSetName4))


# End the xmf file
f.write('''
   </Grid>
</Domain>
</Xdmf>
''')
f.flush()
f.close()

Here is the first time step within the XMF3 File:

<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="2.0">
<Domain>
<Grid Name="Box" GridType="Collection" CollectionType="Temporal">

    <!-- time step -->
    <Grid Name="Box 0" GridType="Uniform">  
    <Topology TopologyType="3DCoRectMesh" Dimensions="189 189 2"/>
    <Geometry GeometryType="ORIGIN_DXDYDZ">
       <DataItem DataType="Float" Dimensions="3" Format="XML">0.0 0.0 0.0</DataItem>
       <DataItem DataType="Float" Dimensions="3" Format="XML">8 8 8</DataItem>
    </Geometry>
    <Time Value="0" />
    


    <Attribute Name="X" AttributeType="Scalar" Center="Node">
    <DataItem Dimensions="189 189 2" NumberType="Float" Precision="4"
    Format="HDF">
    location54LargeDISP_PARAVIEW.hdf5:/XparaviewSnaps/0
    </DataItem>
    </Attribute>
    


    <Attribute Name="Y" AttributeType="Scalar" Center="Node">
    <DataItem Dimensions="189 189 2 " NumberType="Float" Precision="4"
    Format="HDF">
    location54LargeDISP_PARAVIEW.hdf5:/YparaviewSnaps/0
    </DataItem>
    </Attribute>
    </Grid>


    <Attribute Name="Z" AttributeType="Scalar" Center="Node">
    <DataItem Dimensions="189 189 2" NumberType="Float" Precision="4"
    Format="HDF">
    location54LargeDISP_PARAVIEW.hdf5:/ZparaviewSnaps/0
    </DataItem>
    </Attribute>
    


    <Attribute Name="T" AttributeType="Scalar" Center="Node">
    <DataItem Dimensions="189 189 2" NumberType="Float" Precision="4"
    Format="HDF">
    location54LargeDISP_PARAVIEW.hdf5:/TorisonalparaviewSnaps/0
    </DataItem>
    </Attribute>

I would greatly appreciate any assistance in correcting this problem. Just to clarify I want to to have my scalar arrays for x,y,z displacement and torsional motion associated with there corresponding points in the 3d mesh.