Reading a point mesh with xdmf

[Mreichert91]

Hey,
I'm new to VisIt and I have a very basic question regarding reading in data. I have point cloud consisting of e.g.,100 points. I managed to read the points as an ASCII file via the points3d read option in VisIt, using the following file:

 x y z value
 #coordflag xyzv
 -8.8619e+04 -4.1008e+03 3.3974e+06 5.2105e-01
 -5.5636e+03 -2.4487e+01 3.4601e+06 5.3843e-01
 -1.6453e+05 -5.4838e+03 3.5672e+06 5.4867e-01
 -1.3573e+05 -1.4542e+03 3.6964e+06 5.6051e-01
 ......

Now, I want to read in the same thing in hdf5 format using a xdmf file as described in the manual of visit. The hdf5 file is structured in a way that it has x, y, and z-coordinates in separate entries. Furthermore it contains some values in an additional entry. My problem is that there does not really seem to exist a TopologyType for this (or at least I don't understand which one I should take for a simple point mesh). The file that I used (which does not work properly) is:

<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="2.0">
 <Domain>
    <Grid Name="Mesh" GridType="Uniform">
     <Topology TopologyType="3DRectMesh" NumberOfElements="100"/>
     <Geometry GeometryType="X_Y_Z">
       <DataItem Dimensions="100" NumberType="Float" Precision="8" Format="HDF">
         h5file.h5:/x
       </DataItem>
       <DataItem Dimensions="100" NumberType="Float" Precision="8" Format="HDF">
         h5file.h5:/y
       </DataItem>
       <DataItem Dimensions="100" NumberType="Float" Precision="8" Format="HDF">
         h5file.h5:/z
       </DataItem>
     </Geometry>
     <Attribute Name="value" AttributeType="Vector" Center="Node">
       <DataItem Dimensions="100" NumberType="Float" Precision="8" Format="HDF">
         h5file.h5:/value
       </DataItem>
     </Attribute>
     <Time Value="    1.0E+00" />
    </Grid>
 </Domain>
</Xdmf>

Originally, I wanted to read a file which has the coordinates in a shape of (time_dim,coord_dim), where time_dim is the time dimension and coord_dim the number of points. However, I already failed with the simple example outlined above. I'm sorry about this rather stupid question...

I would be really happy about any answer!

[brugger1]

You would need to use the "Polyvertex" topology type. Here is an example file.

<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="2.0">
 <Domain>
   <Grid Name="points" GridType="Uniform">
     <Topology TopologyType="Polyvertex" Dimensions="7161" NodesPerElement="1">
       <DataItem Format="HDF" Dimensions="7161" NumberType="Int">
        mesh.h5:/Indexes
       </DataItem>
     </Topology>
     <Geometry Type="XYZ">
       <DataItem Format="HDF" Dimensions="7161 3" NumberType="Float">
        mesh.h5:/XYZ
       </DataItem>
     </Geometry>
     <Attribute Name="VelocityZ" AttributeType="Scalar" Center="Node">
       <DataItem Format="HDF" Dimensions="7161" NumberType="Int">
        mesh.h5:/VelocityZ
       </DataItem>
     </Attribute>
   </Grid>
 </Domain>
</Xdmf>

The "Indexes" array in the HDF5 file would be an array of 7161 integers going from 0 to 7160.

Note that I am using interleaved coordinates in my example. I am not 100% sure that having them in separate arrays will work. You can give it a try and if it doesn't work, switch to the interleaved version.

[Mreichert91]

This worked out perfectly!! Thank you so much!

[brugger1]

Awesome! Thanks for closing the loop.

[CsatiZoltan]

Thank you, it helped me a lot in my project!