[Paraview] Particle trajectories with Paraview - How to to use an existing dataset (xml / hdf5) - error messages with "Particle Pathlines"

Thu Oct 7 02:52:02 EDT 2010

Oliver,

I received your files (off list) and gave them a try. I see now what the problem is.

You've got a temporal collection, and inside this, is a multi-block set of particles. What is happening is that the pathline filter is being called once per block by the executive, but the DATA_TIME_STEPS key is stamped on the multi-block wrapper, and each time the pathline filter is executed on a sub-block, the sub-block is extracted from the collection and passed in - without - the DATA_TIME_STEPS key stamped on it.

Now this is fixable in two ways.
1) Have the executive stamp the sub-blocks with the wrapper's TIME key as they are extracted and passed in.
2) Have the Xdmf reader stamp the sub-blocks as they are generated (easier to do IMHO).

BUT. 

Even if we make one of these fixes, I suspect the pathline filter will fail. This is because the pathline filter caches particle positions (w.r.t time) each time it is executed and builds a trail for each particle ID. If it is looped over a multiblock dataset - the executive reuses the same copy of the pathline filter for each block - so the pathline filter will get highly confused as it receives 5 executions for each time step - and the ID's present will be also occur 5 times (assuming you have Ids from 0-N for each block, if you have 0-5N and they are not duplicated, then it might just be OK).

Anyway. This is a serious problem as the pathline filter won't operate on the multiblock data. I'll add this to my list of 'one day I must fix this' - actually, I will soon need to use the pathline filter on multiblock data myself, so this is a good heads-up that I need to do something.

Here are ideas - 

Solution 1: Doesn't work. If you use Extract-Block filter in ParaView, it just creates a new multiblock dataset with the unwanted blocks removed - it doesn't solve the problem of the sub-block stamping, you'd still need to fix 2) above in the reader. I have my own vtkFlattenDataset Filter (similar to extract blocks but removes the multiblock hierarchy) which I tried and it does work (for one block, but I didn't check for multiple to see if Ids are reused across blocks as my filter appends the datasets if >1 are taken). Unfortunately, this filter is not very well tested so not safe for public consumption.

Solution 2: If you can you split your blocks into separate Xdmf files so that you load 5 files instead of 1 (sorry, this is painful), then all will be ok. _This will at least work_

Solution 3: I could add multiblock support for the pathline filter, but this would take a spare afternoon/day which I don't have right now.

If I think of a solution 4, I'll post again.

JB

-----Original Message-----
From: paraview-bounces at paraview.org [mailto:paraview-bounces at paraview.org] On Behalf Of Biddiscombe, John A.
Sent: 06 October 2010 15:30
To: Oliver Fochler; paraview at paraview.org
Subject: Re: [Paraview] Particle trajectories with Paraview - How to to use an existing dataset (xml / hdf5) - error messages with "Particle Pathlines"

Oliver

The Xdmf file (or reader) must be not handling the time properly, can you send (or ftp if big) me xdmf and hdf files and I'll have a look at it. I use the pathline filter extensively and know it works ok.

JB

-----Original Message-----
From: paraview-bounces at paraview.org [mailto:paraview-bounces at paraview.org] On Behalf Of Oliver Fochler
Sent: 06 October 2010 14:36
To: paraview at paraview.org
Subject: [Paraview] Particle trajectories with Paraview - How to to use an existing dataset (xml / hdf5) - error messages with "Particle Pathlines"

Dear Paraview users,

I know that this topic has probably been discussed a couple of times.
But so far I haven't been able to get find any real solutions from the
discussion threads to my specific problem. I'm afraid I will need a
detailed dummy / newbie explanation..

What I would like to do:
----------------------------------------

Plot the trajectory of a moving particle, i.e. trace its path with some
sort of line. The position of the particle is given as x,y,z coordinates
(euclidean position) at certain distinct time steps.
The ability to fade out the track after n time steps would be nice. And
of course I need more than one particle, but that doesn't really matter.

The data format I have:
----------------------------------------

I'm using a converter written by someone else to convert the output of
my simulations to a format that is understood by paraview. In principle
I do have the source code of this converter, but I haven't really
bothered to look into it yet (and don't really have the time to do so now).
The output I get from this converter is hdf5, i.e. a xml file and a .h5
file. The data is organized in frames, one frame per time step. See
below for an excerpt from my xml file.

In principle this dataset just holds the positions and momenta of point
like particles (plus some more scalar values) at given time steps.

What I've done so far / Error messages:
--------------------------------------

Loading this dataset (the xml file) into paraview works fine. It
displays all the points and animating is no problem. Each frame is
correctly associated with the actual time (as denoted in the xml file)
and I can loop through the time steps to see the particles evolve,
inspect scalar properties with glyphs and so on.

But how can I get the trajectory of a particle? Or rather the polyline
connecting the coordinate points the particle has passed at the given
time steps.

I've tried using the "Particle Pathlines" filter but it gives me error
messages like

 "vtkCompositeDataPipeline (0x5c93630): Algorithm
vtkTemporalPathLineFilter(0x54ff590) returned failure for request:
vtkInformation (0x55b9160)"

for Paraview 3.6.2 or

"vtkTemporalPathLineFilter (0x4b7a680): The input dataset did not have a
valid DATA_TIME_STEPS information key"
and
"vtkCompositeDataPipeline (0x4b7c0c0): Algorithm
vtkTemporalPathLineFilter(0x4b7a680) returned failure for request:
vtkInformation"

for Paraview 3.8.0

I would be very glad if you had some suggestions!

Cheers,
Oliver

Here's the beginning of my xml file:

<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2"
Name="Case: BAMPS_test">
  <Domain Name="myDomain">
    <Grid Name="euclidean position" GridType="Collection"
CollectionType="Unset">
      <Grid Name="Event 1" GridType="Collection" CollectionType="Temporal">
        <Grid Name="Frame 1" GridType="Uniform">
          <Topology Name="Topology" TopologyType="Polyvertex"
Dimensions="1019"/>
          <Geometry Name="Geometry" GeometryType="XYZ">
            <DataItem NumberType="Float" Precision="4" Dimensions="1019
3" Format="HDF">BAMPS_test.h5:/Case/Event 1/Frame 1/euclidean
position</DataItem>
          </Geometry>
          <Time TimeType="Single" Value="0.2"/>
          <Attribute Name="azimuthal angle" AttributeType="Scalar"
Center="Node">
            <DataItem NumberType="Float" Precision="4" Dimensions="1019"
Format="HDF">BAMPS_test.h5:/Case/Event 1/Frame 1/azimuthal angle</DataItem>
          </Attribute>
          <Attribute Name="electric charge" AttributeType="Scalar"
Center="Node">
            <DataItem NumberType="Float" Precision="4" Dimensions="1019"
Format="HDF">BAMPS_test.h5:/Case/Event 1/Frame 1/electric charge</DataItem>
          </Attribute>
          <Attribute Name="energy" AttributeType="Scalar" Center="Node">
            <DataItem NumberType="Float" Precision="4" Dimensions="1019"
Format="HDF">BAMPS_test.h5:/Case/Event 1/Frame 1/energy</DataItem>
          </Attribute>

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