[petsc-users] PETSc version 3.9 with Fortran and DMPlex questions

[Matthew Knepley]

On Wed, Apr 11, 2018 at 9:06 AM, Bernardo Rocha <
bernardomartinsrocha at gmail.com> wrote:

> OK Matthew, thanks a lot for your feedback.
>
> Reading the code for the first two faces I noted you used the standard
> numbering for the faces.
> face 0 (bottom) -> nodes 0 1 2 3
> face 1 (top)       -> nodes 4 5 6 7
>

Hi Bernardo,

No, you are misinterpreting the numbering. I want all cell faces to have
outward facing normal, so
the unit cell looks like

      7------6
     /|       /|
    / |      / |
  4------5  |
  |   |     |  |
  |   |     |  |
  |  1------2
  |  /      | /
  | /       |/
  0------3

Does it make more sense now?

  Thanks,

    Matt

When this is defined, all the other faces are fixed.
> Therefore, I noticed some indexes errors in the code:
>
>         //facesTmp[8]  = cone[0]; facesTmp[9]  = cone[3]; facesTmp[10] =
> cone[5]; facesTmp[11] = cone[4]; /* Front */
>         //facesTmp[12] = cone[2]; facesTmp[13] = cone[1]; facesTmp[14] =
> cone[7]; facesTmp[15] = cone[6]; /* Back */
>         //facesTmp[16] = cone[3]; facesTmp[17] = cone[2]; facesTmp[18] =
> cone[6]; facesTmp[19] = cone[5]; /* Right */
>         //facesTmp[20] = cone[0]; facesTmp[21] = cone[4]; facesTmp[22] =
> cone[7]; facesTmp[23] = cone[1]; /* Left */
>
> It should be fixed to (basically swap cone[5] with cone[7]):
>
>         facesTmp[8]  = cone[0]; facesTmp[9]  = cone[3]; facesTmp[10] =
> cone[7]; facesTmp[11] = cone[4]; /* Front */
>         facesTmp[12] = cone[2]; facesTmp[13] = cone[1]; facesTmp[14] =
> cone[5]; facesTmp[15] = cone[6]; /* Back */
>         facesTmp[16] = cone[3]; facesTmp[17] = cone[2]; facesTmp[18] =
> cone[6]; facesTmp[19] = cone[7]; /* Right */
>         facesTmp[20] = cone[0]; facesTmp[21] = cone[4]; facesTmp[22] =
> cone[5]; facesTmp[23] = cone[1]; /* Left */
>
> I did it like this, recompiled the code and at least the number of faces
> and edge are correct for me now
> when using DMPlexCreateFromCellList.
>
> I don't know if this change has some impact in other parts of the code.
> I hope not.
>
> Best regards,
> Bernardo M. Rocha
>
>
>
> On Tue, Apr 10, 2018 at 5:14 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
>
>> On Tue, Apr 10, 2018 at 2:19 PM, Bernardo Rocha <
>> bernardomartinsrocha at gmail.com> wrote:
>>
>>> Hi everyone,
>>>
>>> I have two questions.
>>>
>>> (Q1)
>>> The first one is related to the new PETSc 3.9.
>>> I've been using Fortran and using the "userctx" to wrap some data
>>> for the function calls within my program.
>>>
>>> Just like : call func(...,userctx)
>>> and retrieving data as:
>>> PetscFortranAddr userctx(*)
>>> b = userctx(2)
>>>
>>> With the new version I got the following error:
>>> b = userctx(2)
>>> Error: Can't convert INTEGER(8) to TYPE(tvec) at (1)
>>>
>>> Is there a way to keep using the trick with "userctx", instead of passing
>>> all the arguments to the functions separately?
>>>
>>> (Q2)
>>> The second is related to DMPlex.
>>> When I use the CreateBoxMesh with 2x1x1 cells, I get the expected output:
>>>
>>> DM Object: 1 MPI processes
>>>   type: plex
>>> DM_0x84000000_0 in 3 dimensions:
>>>   0-cells: 12
>>>  * 1-cells: 20*
>>>   *2-cells: 11*
>>>   3-cells: 2
>>> Labels:
>>>   depth: 4 strata with value/size (0 (12), 1 (20), 2 (11), 3 (2))
>>>
>>> However, If I try to create that manually to reproduce the same case
>>> 2x1x1 cells (creating this simple element connectivity by hand) using
>>> DMPlexCreateFromCellList I get the following:
>>>
>>> DM Object: DM_0x84000000_0 1 MPI processes
>>>   type: plex
>>> DM_0x84000000_0 in 3 dimensions:
>>>   0-cells: 12
>>>   *1-cells: 22*
>>> *  2-cells: 12*
>>>   3-cells: 2
>>> Labels:
>>>   depth: 4 strata with value/size (0 (12), 1 (22), 2 (12), 3 (2))
>>>
>>> That is, it seems the shared face between the two cells is counted twice.
>>> Is that right? What am I missing here?
>>>
>>
>> Since the input is cell-vertex, my guess is that the order of the
>> vertices on a cell is not what I expect.
>> I have readers for common formats, but FromCellList() is my own. You can
>> see what vertices I think
>> constitute the faces:
>>
>>   https://bitbucket.org/petsc/petsc/src/05d412bc580c652749a0
>> 91cc13ab756bb8816ec1/src/dm/impls/plex/plexinterpolate.c?
>> at=master&fileviewer=file-view-default#plexinterpolate.c-113
>>
>> Sorry, this was confusing. Most people are using the input formats, mesh
>> generators, or predefined shapes,
>> so I do not get a lot of feedback on this interface.
>>
>>   Thanks,
>>
>>     Matt
>>
>>
>>> Best regards,
>>> Bernardo
>>>
>>
>>
>>
>> --
>> 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
>>
>> https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
>>
>
>


-- 
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

https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20180411/5ec3ebd4/attachment.html>