[MOAB-dev] Setting connectivity for single vertex

Tue Feb 3 08:43:15 CST 2015

On 02/03/2015 03:48 AM, CORTIS M. wrote:
> Vijay/Paul,
>
> As Paul mentioned, the question would be if we always want to write 
> vertices as 1-vertex elements.
>
> I would say that the process of writing a VTK should be
>
> POINTS - are determined from the connectivity of the entities brought 
> up from Range or Meshset (contains entities to be considered as elements)
> CELLS & CELL_TYPES - the connectivity & element type should be created 
> from the entities within the Range/Meshset (hence if Range/Meshset 
> contains vertex entities, their connectivity will be created, 
> otherwise it will be omitted)

MOAB doesn't distinguish from vertices that are used to define other 
elements and vertices that are point elements, they are both of type 
MBVERTEX.  It is easy to detect when they have connectivity to higher 
dimensional elements, and then exclude those from a list of CELLS.

I guess the question is whether or not there is a use case for writing 
both connected mesh and point clouds.

Paul

>
> I am not sure if this change the existing WriteVTK structure, and 
> hence one need to investigate if my proposal make sense or not.
>
> Will consider to create a fork and contribute to moab, but definitely 
> not at this stage, as got all sorts of pressure!
>
> Michael
>
>
>
> On 3 Feb 2015, at 01:33, Paul Wilson <ppwilson at wisc.edu 
> <mailto:ppwilson at wisc.edu>> wrote:
>
>> Hi Vijay,
>>
>> I had the same thought and took a quick look.  Much of the 
>> infrastructure is there, namely, that the VTK writer appears to 
>> already know how to write out nodes as 1-vertex elements.
>>
>> What is missing is to include the list of vertices among the list of 
>> elements to be written.  This happens near lines 144 & 180 in 
>> src/io/WriteVTK.cpp.  I think it would need very few changes to make 
>> it serve Michael's needs, but a little more work and testing to be 
>> implemented as an option.
>>
>> There would also emerge questions about how to implement the option:
>>
>>   * when invoked, always write all vertices as 1-vertex elements, or
>>   * when invoked, only write vertices that lack higher-dimension
>>     connectivity as 1-vertex elements
>>
>> The former is quick and easy, but only serves the special case when a 
>> model has only unconnected vertices.
>>
>> Paul
>>
>> On 02/02/2015 04:49 PM, Vijay S. Mahadevan wrote:
>>> Michael,
>>>
>>> If the intent is just to visualize these point clouds and data on
>>> them, we can certainly add some specific functionality for this when
>>> we output the data to vtk. If you want to contribute some code for
>>> this, we will be happy to take a PR directly on our bitbucket repo.
>>>
>>> Querying connectivity of the point cloud is not currently supported
>>> and unless you do create a higher dimensional element using sets of
>>> vertices, we cannot compute the one ring vertex neighbors (which
>>> involves find the element adjacencies and performing a union on the
>>> connectivity of these entities). Depicting a point as a traditional
>>> element (0-D element) can possibly be done but this is not supported
>>> now and am not sure how easy it will be without few involved changes
>>> in some parts including the I/O writers.
>>>
>>> Vijay
>>>
>>> On Sun, Feb 1, 2015 at 9:39 AM, CORTIS M.<michael.cortis at durham.ac.uk>  wrote:
>>>> Hi,
>>>>
>>>> So if you save points on vtk you have such thing where no connectivity and
>>>> no cell definition.
>>>>
>>>> POINTS 2 double
>>>> 10.0 0 0
>>>> -10.0 0 0
>>>> CELLS 0 0
>>>> CELL_TYPES 0
>>>>
>>>> but if you want to can include connectivities and cel definition as follows
>>>>
>>>> POINTS 2 double
>>>> 10.0 0 0
>>>> -10.0 0 0
>>>> CELLS 2 4
>>>> 1 0
>>>> 1 1
>>>> CELL_TYPES 2
>>>> 1
>>>> 1
>>>>
>>>> This way, Paraview and VisIt can recognise points as elements and
>>>> consequently can visualise them.
>>>>
>>>> Michael
>>>>
>>>>
>>>> On 1 Feb 2015, at 15:34, Paul Wilson<ppwilson at wisc.edu>
>>>>   wrote:
>>>>
>>>> Hello again,
>>>>
>>>> On 02/01/2015 09:31 AM, CORTIS M. wrote:
>>>>
>>>> Hello Paul,
>>>>
>>>> In fact you can create vertices and use them and store data on tag.
>>>> The only problem was that if there is no connectivity,
>>>> ParaView and VisIT does not visualise them unless you plot the points using
>>>> glyphs.
>>>> So I had to create a function which read the points from a mesh file and
>>>> insert their individual connectivities and save them as vtk.
>>>>
>>>> Now I see!  Thanks for the clarification.
>>>>
>>>> So are you connecting the vertices to themselves?  What is the element type
>>>> in VTK for such an element?
>>>>
>>>> Paul
>>>>
>>>>
>>>>
>>>>
>>>> Problem solved. But may be MOAB would consider this problem and do something
>>>> about it.
>>>>
>>>> Thanks for your input,
>>>>
>>>> Michael
>>>>
>>>>
>>>> On 1 Feb 2015, at 15:24, Paul Wilson<ppwilson at wisc.edu>
>>>>   wrote:
>>>>
>>>> Hello Michael,
>>>>
>>>> On 01/29/2015 05:08 PM, CORTIS M. wrote:
>>>>
>>>> Hi Iulian,
>>>>
>>>> Yes I am trying to create an element made from single vertex.
>>>> I want to used these for Material Point Method.
>>>>
>>>> So there is a way of creating the vertices, but not adding connectivity to
>>>> themselves only?
>>>> Or may be another way round?
>>>>
>>>>
>>>> Perhaps, I'm not fully understanding your questions, but it is certainly
>>>> possible to create vertices in MOAB and then use them directly in your
>>>> analysis.  There is no need to create an element if, in fact, all you need
>>>> are the vertices.  Each vertex can be tagged with data in the same way that
>>>> an element can be.
>>>>
>>>> I hope that is helpful,
>>>> Paul
>>>>
>>>> If not, don't worry about. Will create a vtk writer to do this and hopefully
>>>> moab can use the vertices.
>>>>
>>>> Any assistance is really appreciated.
>>>>
>>>> Kind regards
>>>>
>>>> Michael
>>>>
>>>>
>>>>
>>>>
>>>> On 29 Jan 2015, at 17:24, "Grindeanu, Iulian R."<iulian at mcs.anl.gov>  wrote:
>>>>
>>>> Hello,
>>>> Moab does not have elements with a single vertex. Is this what you are
>>>> trying to do?
>>>> A vertex (node) is represented with an entity handle of type MBVERTEX, and
>>>> you can get coordinates for it
>>>>
>>>> I am not sure what are you trying to do.
>>>> Best Regards,
>>>> Iulian
>>>>
>>>> ________________________________
>>>> From:moab-dev-bounces at mcs.anl.gov  [moab-dev-bounces at mcs.anl.gov] on behalf
>>>> of CORTIS M. [michael.cortis at durham.ac.uk]
>>>> Sent: Thursday, January 29, 2015 10:18 AM
>>>> To:moab-dev at mcs.anl.gov
>>>> Cc: Tautges, Timothy J.
>>>> Subject: Re: [MOAB-dev] Setting connectivity for single vertex
>>>>
>>>> Thanks Tim,
>>>>
>>>> I am still having a problem, may be the guys at Argonne can help with this.
>>>>
>>>> I've tried a simpler one and trying to crete the vertex from point.
>>>>
>>>>    double points[9]={0.5,0,0};
>>>>    EntityHandle vertex;
>>>>    rval=moab2.create_vertex(points,vertex);CHKERR_PETSC(rval);
>>>>    EntityHandle dummy;
>>>>    rval = moab2.create_element(MBVERTEX,&vertex,1,dummy); CHKERR_PETSC(rval);
>>>>
>>>> But I am getting Error code 2, MB_TYPE_OUT_OF_RANGE !
>>>> Is it possible to use MBVERTEX here?
>>>>
>>>> Thanks,
>>>>
>>>> Michael
>>>>
>>>> On 29 Jan 2015, at 15:04, Tim Tautges<tautges at mcs.anl.gov>  wrote:
>>>>
>>>> [cc'ng moab-dev list, since I've left Argonne.]
>>>>
>>>> dummy is 0, which is an invalid handle, but should be the handle(s) of the
>>>> entities whose connectivity you're setting; I suspect what you want there is
>>>> *vertices.begin().  And you can't set connectivity until you make an
>>>> element, so you need to call create_element, probably with the number of
>>>> verts per element as 1 and the connectivity just the single vertex defining
>>>> the point element.
>>>>
>>>> - tim
>>>>
>>>> On 01/29/2015 03:34 AM, CORTIS M. wrote:
>>>>
>>>> Dear Tim,
>>>>
>>>> I've got the following problem:
>>>>
>>>> I want to create vertex entities, ie create the points and vertex entities
>>>> using those points.
>>>> So I've create a set of vertices from an array of coordinates.
>>>> And If you try to set the connectivity for every point you get Error code 4
>>>> (MB_ENTITY_NOT_FOUND).
>>>>
>>>> This is my code:
>>>>
>>>> double points[6]={1,0,0, 0,1,0, 0,0,1};
>>>> Range vertices;
>>>> rval = moab.create_vertices(points,2,vertices); CHKERR_PETSC(rval);
>>>> EntityHandle dummy=0;
>>>> rval = moab.set_connectivity(dummy,vertexlist,1); CHKERR_PETSC(rval);
>>>> //Error code 4
>>>>
>>>> Any suggestions how to overcome this problem.
>>>>
>>>> Kind regards,
>>>>
>>>> Michael
>>>>
>>>>
>>>>
>>>> --
>>>> -- ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ --
>>>> Paul Wilson ~ UW-Madison ~ 608-263-0807 ~ cal:http://bit.ly/pphw-cal
>>>> Professor, Engineering Physics. ~http://cnerg.engr.wisc.edu
>>>> Faculty Director, Advanced Computing Infrastructure ~http://aci.wisc.edu
>>>>
>>>>
>>>>
>>>> --
>>>> -- ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ --
>>>> Paul Wilson ~ UW-Madison ~ 608-263-0807 ~ cal:http://bit.ly/pphw-cal
>>>> Professor, Engineering Physics. ~http://cnerg.engr.wisc.edu
>>>> Faculty Director, Advanced Computing Infrastructure ~http://aci.wisc.edu
>>>>
>>>>
>>
>> -- 
>> -- ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ --
>> Paul Wilson ~ UW-Madison ~ 608-263-0807 ~ cal:http://bit.ly/pphw-cal
>> Professor, Engineering Physics. ~http://cnerg.engr.wisc.edu
>> Faculty Director, Advanced Computing Infrastructure ~http://aci.wisc.edu
>

-- 
-- ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ --
Paul Wilson ~ UW-Madison ~ 608-263-0807 ~ cal: http://bit.ly/pphw-cal
Professor, Engineering Physics. ~ http://cnerg.engr.wisc.edu
Faculty Director, Advanced Computing Infrastructure ~ http://aci.wisc.edu

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