[petsc-users] DMPlexCreateFromCellList and hybrid meshes

[Matthew Knepley]

On Thu, Jan 2, 2014 at 8:08 AM, Cedric Doucet <cedric.doucet at inria.fr>wrote:

>
> Hello,
>
> indeed, I need to have a generalized version of DMPlexCreateFromCellList
> function which can take an hybrid mesh as an input parameter.
>

What interface?


> Modern mesh generators often provide mixed generation functionalities
> (e.g. gmsh which can generate pyramids and prisms).
> As a matter of fact, cells are never numbered independently of vertices in
> hybrid meshes because different generators are used (structured and
> unstructured ones).
> From a practical point of view, it is far much easier to let each
> generator number its own cells without renumbering shared vertices.
> Therefore, cells of hybrid meshes are sorted in a canonical way: cells of
> generator 1, cells of generator 2, etc.
>

I don't understand what you want here. Its imprecise.

   Matt


> I deeply think that this new version is very useful for real-life
> applications.
> Please let me know when this new version will be available.
>
> Thank you very much,
>
> Cédric Doucet
>
>
>
>
>
> ------------------------------
>
> *De: *"Matthew Knepley" <knepley at gmail.com>
> *À: *"Cedric Doucet" <cedric.doucet at inria.fr>
> *Cc: *petsc-users at mcs.anl.gov
> *Envoyé: *Jeudi 31 Octobre 2013 14:13:14
> *Objet: *Re: [petsc-users] DMPlexCreateFromCellList and hybrid meshes
>
> On Thu, Oct 31, 2013 at 5:20 AM, Cedric Doucet <cedric.doucet at inria.fr>wrote:
>
>>
>> Thank you very much for your help.
>> Do you plan to add this code to Petsc?
>> It would be better for us to call an official Petsc function than
>> maintaining a Petsc-style code into our C++ software.
>>
>
> If this is really what you need, then I will put it in. However, I
> intended this to be used primarily for mesh generators, since they
> tend to number cells and vertices independently and have the int and
> double types hardwired.
>
> If you are writing your own code, please consider DMPlexCreateFromDAG()
> which has the flexibility for cell topology that you
> want. The main differences are that it uses PETSc types and a single
> contiguous numbering. Would this work for you?
>
>   Thanks,
>
>      Matt
>
>
>> Best regards,
>>
>> Cédric Doucet
>>
>>
>>
>> ------------------------------
>>
>> *De: *"Matthew Knepley" <knepley at gmail.com>
>> *À: *"Cedric Doucet" <cedric.doucet at inria.fr>
>> *Cc: *petsc-users at mcs.anl.gov
>> *Envoyé: *Mardi 29 Octobre 2013 17:24:03
>> *Objet: *Re: [petsc-users] DMPlexCreateFromCellList and hybrid meshes
>>
>> On Tue, Oct 29, 2013 at 10:24 AM, Cedric Doucet <cedric.doucet at inria.fr>wrote:
>>
>>> Hello,
>>>
>>> I have a short question about the code I need to modify.
>>> As far as I understand, numCorner should be replaced by an array
>>> numCorners[numCells] containing the number of vertices of each cell.
>>> The body of DMPlexBuildFromCellList_Private function becomes
>>>
>>> ---------------------------------------------------------------------------------------------------------------------------------------
>>> ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr);
>>>
>>     maxCorners = 0;
>>
>>>   for (c = 0; c < numCells; ++c) {
>>>     ierr = DMPlexSetConeSize(dm, c, numCorners[c]);CHKERRQ(ierr);
>>>
>>          maxCorners = PetscMax(maxCorners, numCorners[c]);
>>
>>>   }
>>>   ierr = DMSetUp(dm);CHKERRQ(ierr);
>>>
>>
>>     ierr = DMGetWorkArray(dm, maxCorners, PETSC_INT, &cone);CHKERRQ(ierr);
>>
>>
>>>   for (c = 0, off = 0; c < numCells; ++c) {
>>>     for (p = 0; p < numCorners[c]; ++p) {
>>>       cone[p] = cells[off+p]+numCells;
>>>     }
>>>     ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr);
>>>
>>          off += numCorners[c];
>>
>>>    }
>>>
>>     ierr = DMRestoreWorkArray(dm, maxCorners, PETSC_INT,
>> &cone);CHKERRQ(ierr);
>>
>>>
>>
>>>
>>>   ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
>>>   ierr = DMPlexStratify(dm);CHKERRQ(ierr);
>>>
>>
>>    Matt
>>
>>
>>>
>>> ------------------------------------------------------------------------------------------------------------------------------------------
>>> However, I am not quite sure that DMGetWorkArray and DMRestoreWorkArray
>>> should be used like this.
>>> I guess that DMRestoreWorkArray behaves like free function in ansi c but
>>> I am not sure.
>>> Do you think that calling DMGetWorkArray and DMRestoreWorkArray inside a
>>> loop is a good thing from the point of view of computational time and
>>> memory management?
>>>
>>> Note: the best way to do this may be to first sort cells by numCorners
>>> to avoid many calls to DMGetWorkArray and DMRestoreWorkArray. This is
>>> actually what I have in my own code but I would like to maintain Petsc's
>>> philosophy.
>>>
>>> Thanks,
>>>
>>> Cédric
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> *De: *"Matthew Knepley" <knepley at gmail.com>
>>> *À: *"Cedric Doucet" <cedric.doucet at inria.fr>
>>> *Cc: *petsc-users at mcs.anl.gov
>>> *Envoyé: *Vendredi 25 Octobre 2013 16:31:59
>>> *Objet: *Re: [petsc-users] DMPlexCreateFromCellList and hybrid meshes
>>>
>>> On Fri, Oct 25, 2013 at 7:23 AM, Cedric Doucet <cedric.doucet at inria.fr>wrote:
>>>
>>>> Hello,
>>>>
>>>> I've noticed that DMPlexCreateFromCellList assumes that cells have the
>>>> same number of vertices (numcorners argument).
>>>> What should be done when one wants to create a DMPlex from a mesh
>>>> containing different types of cells?
>>>> Does one have to create several DMPlex structures and merge them?
>>>> Does one have to create a unique DMPlex by hand?
>>>>
>>>
>>> The code is very short:
>>>
>>>   ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr);
>>>   for (c = 0; c < numCells; ++c) {
>>>     ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);
>>>   }
>>>   ierr = DMSetUp(dm);CHKERRQ(ierr);
>>>   ierr = DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr);
>>>   for (c = 0; c < numCells; ++c) {
>>>     for (p = 0; p < numCorners; ++p) {
>>>       cone[p] = cells[c*numCorners+p]+numCells;
>>>     }
>>>     ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr);
>>>   }
>>>   ierr = DMRestoreWorkArray(dm, numCorners, PETSC_INT,
>>> &cone);CHKERRQ(ierr);
>>>   ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
>>>   ierr = DMPlexStratify(dm);CHKERRQ(ierr);
>>>
>>> This code is all in plexcreate.c. If you want different cells, you can
>>> change numCorners for each cell.
>>> I could make a convenience form if necessary.
>>>
>>>    Matt
>>>
>>>
>>>>
>>>> Thank you very much for your help.
>>>>
>>>> Cédric
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> What most experimenters take for granted before they begin their
>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead.
>>> -- Norbert Wiener
>>>
>>>
>>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>>
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
>
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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