[Paraview] *****SPAM***** Re: extract surface of multiblock mesh

[Takuya OSHIMA]

I would vote for the ghost points. This is really a cool feature for
datasets that doesn't have overlapping cells.

Takuya OSHIMA, Ph.D.
Faculty of Engineering, Niigata University
8050 Ikarashi-Ninocho, Nishi-ku, Niigata, 950-2181, JAPAN


From: Berk Geveci <berk.geveci at kitware.com>
Subject: Re: [Paraview] extract surface of multiblock mesh
Date: Mon, 6 Apr 2009 19:58:56 -0400

> I did not mean ghost cells. I meant ghost points. If you were to mark
> the points at a shared interface as ghost (more appropriately
> duplicated), we can easily throw away all polygons that contain all
> duplicate points when extracting external surfaces. Even better, if we
> had an array that had values like:
> 
> -1        : point not shared
> n >= 0 : point shared, owned by process n
> 
> we could make bunch of filters work correctly - mainly statistics ones
> and the glyph filter. Is this something that is easy for your
> simulation to write?
> 
> -berk
> 
> On Mon, Apr 6, 2009 at 7:41 PM, Renato Elias <rnelias at gmail.com> wrote:
>> Berk, forgive for delaying my response (I was out of my lab...)
>>
>> Just a silly question:
>>
>> What do you exactly mean by "Ghost cell"? This silly question is justified
>> by the fact that I thought that ghost cells only make sense when we have
>> subdomains _overlapped_. In these cases, the number of overlapped cell
>> layers should (or could) be considered as "ghost level".
>>
>> In my case, the subdomains are not overlapped at all. They are just
>> partitioned by Metis and the solver can deal with the computations without
>> the need to use overlapped elements. Thus, if "ghost cells" can be simply
>> defined by "cells somehow touching the parallel interface (even those not
>> overlapped)" I think I could try tagging my parallel interface cells as
>> "ghost level 0" to see what happens...
>>
>> Renato.
>>
>> On Sun, Apr 5, 2009 at 11:53 PM, Chris Kees
>> <christopher.e.kees at usace.army.mil> wrote:
>>>
>>> Berk,
>>>
>>> Thanks for correcting me. I'll try adding the vtkGhostLevels to the XDMF
>>> and see how that goes.
>>>
>>> Chris
>>> On Apr 4, 2009, at 2:50 PM, Berk Geveci wrote:
>>>
>>>> The right way to deal with this situation is to mark the ghost cells
>>>> as ghost. If you create a cell array called vtkGhostLevels and assign
>>>> 0 to inside cells and 1 to ghost cells, you should not need
>>>> MergeBlocks or CleanToGrid. Note that this array has to be of type
>>>> unsigned char. There are actual benefits to keeping ghost levels since
>>>> some algorithms will produce better results.
>>>>
>>>> -berk
>>>>
>>>> On Thu, Apr 2, 2009 at 6:37 PM, Chris Kees
>>>> <christopher.e.kees at usace.army.mil> wrote:
>>>>>
>>>>> I turned off the overlapping domain decomposition (ghost cells) for a
>>>>> simple
>>>>> problem and the sequence
>>>>>
>>>>> MergeBlocks->CleantoGrid->ExtractSurface->Clip
>>>>>
>>>>> shows just the physical boundary of the problem (clipped open so you can
>>>>> see
>>>>> inside). Also volume visualization and streamline calculation works with
>>>>> no
>>>>> processor boundary artifacts.
>>>>>
>>>>> From what I understand, there are no filters in paraview or abstractions
>>>>> in
>>>>> the XDMF data model  at this time that will allow paraview to read in
>>>>> overlapping blocks and really make use of the ghost cells correctly. For
>>>>> now
>>>>> truncating our output to only "owned" elements will solve our problems.
>>>>> Thanks again for the help.
>>>>>
>>>>> Chris
>>>>>
>>>>> On Mar 30, 2009, at 2:06 PM, Chris Kees wrote:
>>>>>
>>>>>> Thanks for  the help. I also tried suggestions from Paul, Ken, and
>>>>>> Berk,
>>>>>> but it does seem that I'm stuck right now unless I provide ParaView
>>>>>> with
>>>>>> more information. Since streamlines are computed correctly on the
>>>>>> current
>>>>>> multiblock mesh I just generated the mesh on a single processor and
>>>>>> used
>>>>>> ExtractSurface->Clip on that mesh to visualize the geometry around the
>>>>>> streamlines from the multiblock grid.
>>>>>>
>>>>>> On the first method: Each of my UnstructuredGrids in the Multiblock
>>>>>> Grid
>>>>>> is a subdomain in an overlapping decomposition of the domain. Each of
>>>>>> the
>>>>>> subdomains has several elements of overlap (the layer of ghost cells is
>>>>>> more
>>>>>> than one element thick).  Presumably the streamline generation works
>>>>>> now on
>>>>>> the multiblock grid because the overlap is loaded into ParaView. Is
>>>>>> there a
>>>>>> way I can just set a cell-centered attributed to identify the ghost
>>>>>> cells so
>>>>>> that surface extraction and volume visualization will work too?
>>>>>>  Currently
>>>>>> volume visualization of the multiblock grid shows only a single
>>>>>> subdomain
>>>>>> and volume visualization after MergeBlocks shows the whole domain but
>>>>>> with
>>>>>> overlap regions being more opaque.
>>>>>>
>>>>>> On your other method, we have both the external boundary mesh and a
>>>>>> pre-mesh polygonal representation of the boundaries available in the
>>>>>> simulator. You are suggesting that I just dump one of those to a valid
>>>>>> ParaView format as well, is that correct?
>>>>>>
>>>>>> Chris
>>>>>>
>>>>>> On Mar 30, 2009, at 9:14 AM, Jean Favre wrote:
>>>>>>
>>>>>>> Chris Kees wrote:
>>>>>>>>
>>>>>>>> So far I've tried MergeBlocks->ExtractSurface->FeatureEdges->Clip and
>>>>>>>> various permutations that I've seen in previous posts and the wiki,
>>>>>>>> but I always end up with the  surfaces on the interior of the tank as
>>>>>>>> if it still sees each subdomain as a closed surface.
>>>>>>>
>>>>>>> In fact, it seems to me that ParaView does the best it can. Your
>>>>>>> unstructured mesh is partitioned in 512 pieces and [presumably], you
>>>>>>> did
>>>>>>> not specify ghost-cells at the partition boundaries. Without
>>>>>>> ghost-cells, ParaView has no information to help decide whether an
>>>>>>> outside face looks towards the outside world, or to another partition.
>>>>>>> I
>>>>>>> don't think any combination of filters would help you. Removing
>>>>>>> duplicate points may only remove duplicate fake boundaries, but these
>>>>>>> fake boundaries must be removed all together.
>>>>>>>
>>>>>>> I use two methods to achieve what you want. Ghost-cells, or another
>>>>>>> multi-piece object containing the different boundary types (solid,
>>>>>>> symmetries, inflow, outflow, etc) stored as vtkPolyData. These are
>>>>>>> read
>>>>>>> in from the models on disk.
>>>>>>>
>>>>>>> Jean --
>>>>>>> Swiss National Supercomputing Center
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
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