[petsc-users] petsc_gen_xdmf.py errors

[Fande Kong]

Thanks, Justin,

I can get a correct xml file now.


Thanks,

Fande Kong,

On Wed, Aug 12, 2015 at 2:39 PM, Justin Chang <jychang48 at gmail.com> wrote:

> Sorry there was a typo. Here's the correct run:
>
> ./src/snes/examples/tutorials/ex12 -run_type test -refinement_limit 0.0
> -bc_type dirichlet -interpolate 1 -petscspace_order 1 -dm_view hdf5:sol.h5
> -vec_view hdf5:sol.h5::append
>
> On Wed, Aug 12, 2015 at 2:22 PM, Justin Chang <jychang48 at gmail.com> wrote:
>
>> Fande,
>>
>> Your sol.h5 is old and outdated. If you generate a more recent sol.h5
>> with the following SNES example inside your PETSC_DIR:
>>
>> ./src/snes/examples/tutorial/ex12 -run_type test -refinement_limit 0.0
>> -bc_type dirichlet -interpolate 1 -petscspace_order 1 -dm_view hdf5:sol.h5
>> -vec_view hdf5:sol.h5::append
>> ./bin/petsc_gen_xdmf.py sol.h5
>>
>> the resulting sol.xmf is compatible with Paraview
>>
>> Thanks,
>> Justin
>>
>>
>> On Tue, Aug 11, 2015 at 8:53 PM, Fande Kong <fdkong.jd at gmail.com> wrote:
>>
>>> Hi all,
>>>
>>> I tried to use petsc_gen_xdmf.py to generate a xml file for visulaztion
>>> using paraview. I got the following errors:
>>>
>>> ./petsc_gen_xdmf.py sol.h5
>>> Traceback (most recent call last):
>>>   File "./petsc_gen_xdmf.py", line 236, in <module>
>>>     generateXdmf(sys.argv[1])
>>>   File "./petsc_gen_xdmf.py", line 231, in generateXdmf
>>>     Xdmf(xdmfFilename).write(hdfFilename, topoPath, numCells,
>>> numCorners, cellDim, geomPath, numVertices, spaceDim, time, vfields,
>>> cfields)
>>>   File "./petsc_gen_xdmf.py", line 190, in write
>>>     for vf in vfields: self.writeField(fp, len(time), t, cellDim,
>>> spaceDim, '/vertex_fields/'+vf[0], vf, 'Node')
>>>   File "./petsc_gen_xdmf.py", line 164, in writeField
>>>     self.writeFieldComponents(fp, numSteps, timestep, spaceDim, name, f,
>>> domain)
>>>   File "./petsc_gen_xdmf.py", line 120, in writeFieldComponents
>>>     dims   = '1 %d 1' % (numSteps, dof, bs)
>>> TypeError: not all arguments converted during string formatting
>>>
>>>
>>> The hdf5 file is attached. Originally from Matthew. Configuration and
>>> make log files are also attached.
>>>
>>> Fande Kong,
>>>
>>> Thanks,
>>>
>>
>>
>
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