Don't forget to reply to the list --
Without seeing errors or images of what was wrong about it, there isn't much we
can do to help. The file I sent does work and PV reads it just fine. The
coordinate axes in this case is Y-Z, but ultimately those are just names since
it's 2D right? It doesn't matter if I call it X-Y, Y-Z, or X-Z so long as I
have 2 orthogonal coordinates.
The axes are specified in reverse order when you list them the way it is done
there. So the first dataitem is always Z, the second is always Y and the third,
if you have one, is always X. This also comes up when you specify the
multi-dimensional data items in the attribute section because you have to
remember it uses C memory layout (row major), which is different from the
Fortran layout (column major) .
We use XDMF for massive multiblock structured simulations and we store our
coordinates in hdf5 files in full 3D arrays (so what something like the
meshgrid function returns in Matlab/Numpy) and I've put an example at the end
of my email here. In this case, we have a grid which in Fortran would have
coordinates X(I,J,K) where I = 1, 83; J = 1, 83; K = 1, 4. Note that the
indexing is flipped when we specify it in the XDMF file. It is also flipped
from what one would expect coming from Fortran when you look at the h5dump
(after the XDMF example). Our strategy is to specify our grid points as an
array of vectors and we create that array of vectors using the JOIN function.
The XDMF documentation isn't always as helpful as I'd like sometimes. It took a
lot of trial and error on our part to get this working (and it's made more
complicated because we use hyperslabs a lot to only display portions of our
data). The PV release binaries are also not helpful in understanding the
problems sometimes -- very often, it will just segfault or crash with a glibc
double-linked list error or something. Building PV yourself with debug options
may help if you are really stuck.
But what you seem to be trying to do is fully supported and you just need to
keep working at it to understand why it doesn't work. And if you are having
problems, posting images of what it looks like when you import the data would
really help if the issue is just that it doesn't seem to be what you think it
should be.
Tim
<Topology TopologyType="3DSMesh" Dimensions="4 83 83 3"/>
<Geometry GeometryType="XYZ" Units="m">
<DataItem ItemType="Function" Function="JOIN($0, $1, $2)" Dimensions="4 83 83
3">
<DataItem Dimensions="6 85 85" NumberType="Float" Precision="8"
Format="HDF">&gridpath;/grid.h5:/Domain_00001/x</DataItem>
<DataItem Dimensions="6 85 85" NumberType="Float" Precision="8"
Format="HDF">&gridpath;/grid.h5:/Domain_00001/y</DataItem>
<DataItem Dimensions="6 85 85" NumberType="Float" Precision="8"
Format="HDF">&gridpath;/grid.h5:/Domain_00001/z</DataItem>
</DataItem>
</DataItem>
</Geometry>
<Attribute AttributeType="Scalar" Center="Cell" Name="Temperature [K]">
<DataItem NumberType="Float" Dimensions="3 82 82" Precision="8"
Format="HDF">&outputpath;/RESTS/REST_00000.h5:/FlowData/temperature</DataItem>
GROUP "/" {
GROUP "Domain_00001" {
DATASET "x" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 6, 85, 85 ) / ( 6, 85, 85 ) }
}
DATASET "y" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 6, 85, 85 ) / ( 6, 85, 85 ) }
}
DATASET "z" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 6, 85, 85 ) / ( 6, 85, 85 ) }
}
}
----- Original Message -----
From: "Canis Major" <canismajorw...@gmail.com>
To: "tim gallagher" <tim.gallag...@gatech.edu>
Sent: Friday, March 6, 2015 6:05:43 PM
Subject: Re: [Paraview] Import of XDMF/HDF5:Cell centered attribute of 2D
Rectangular grid
Tim, thank you for your concerns. But of course I tried the configuration like
this, it is most intuitive way of description. But unfortunately, it does not
work with paraview. In this case the wrong geometry is being created, I do not
know how to more clearly describe what is wrong with it. First of all, there is
nothing in X direction anymore, but in Y-Z plane, and the geometry shape is
wrong, I do not know.
Also I think there is no such geometry type as VXVY. I have not seen it in Xmdf
specification.
I suppose Armin tried it too and, as he said, failed.
With Best Regards,
Slava
On Fri, Mar 6, 2015 at 11:54 PM, Tim Gallagher < tim.gallag...@gatech.edu >
wrote:
Hi guys,
So the problems you're having are due to specifying inconsistent data here. You
are specifying a 2DRectMesh grid but then giving it 3 vectors for the points. I
don't have your HDF5 files so I made a light data XMF file that works for me on
all versions going back to 3.14. I have attached it here for you to test.
This all works fine. I've also created a 3DRectMesh. For that, you need to give
it 2 points in the 3rd direction for the grid because you are specifying cell
centered data. If you only give it 1 point in the 3rd direction, there is no
"cell" anymore in which to specify the data.
I'll leave adding the 3rd dimension as an exercise for you to work with. Once
you figure out how it needs to work using the light data format, then switch
over to using the heavy data format and get it working again.
Hope that helps,
Tim
----- Original Message -----
From: dkxl...@gmail.com
To: canismajorw...@gmail.com
Cc: paraview@paraview.org
Sent: Friday, March 6, 2015 4:55:37 PM
Subject: Re: [Paraview] Import of XDMF/HDF5:Cell centered attribute of 2D
Rectangular grid
I have had similar problems with 2D structured grids and XDMF in the past.
I never got them to work in ParaView.
I solved the problem by using 3D grids and set the first dimension (i.e. the
slowest varying) one to 1, the same way as you have done it with VXVYVZ.
You just have to adjust your data arrays accordingly, i.e. dimensions 1 82 221
in your example.
I can send you a working xdmf file when back in the office.
I believe the computational overhead from 2D to 3D grids with effectively 2
dimensions is rather small.
Maybe the next-generation XDMF reader in ParaView works better for 2D structued
grids or somebody with the knowledge explains us how to write them correctly.
:)
-Armin
On Fri Mar 6 23:17:52 2015 GMT+0200, Canis Major wrote:
> I have troubles importing xdmf output to paraview.
>
> This is an example of xdmf of 0th iteration.
>
> <?xml version="1.0" ?>
> <Xdmf>
> <Domain>
> <Grid Name="Grid" GridType="Uniform">
> <Topology TopologyType="2DRectMesh" Dimensions="1 82 221"/>
> <Geometry GeometryType="VXVYVZ">
>
> <DataItem Dimensions="1" NumberType="Float" Precision="4" Format="HDF">
> xdmf2d.h5:/Z
> </DataItem>
>
> <DataItem Dimensions="83" NumberType="Float" Precision="4" Format="HDF">
> xdmf2d.h5:/Y </DataItem>
>
> <DataItem Dimensions="221" NumberType="Float" Precision="4" Format="HDF">
> xdmf2d.h5:/X </DataItem> </Geometry>
>
> <Attribute Name="pressure" AttributeType="Scalar" Center="Cell">
> <DataItem Dimensions="82 220" NumberType="Float" Precision="4"
> Format="HDF">
> xdmf2d.0.h5:/pressure
> </DataItem>
> </Attribute>
>
> </Grid>
> </Domain>
> </Xdmf>
>
>
> I have an error that paraview failed to import attribute. What could
> be wrong? I have played around the parameters nothing helps.
>
--
Sent from my Jolla
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