[MOAB-dev] Setting connectivity for single vertex

Mon Feb 2 19:33:34 CST 2015

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

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