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

Wed Apr 11 08:28:59 CDT 2018

Uhmmm. Indeed. Sorry for the mistake.
Just fixed my ordering before sending them to DMPlexCreateFromCellList and
it worked fine.
Thanks.

On Wed, Apr 11, 2018 at 10:15 AM, Matthew Knepley <knepley at gmail.com> wrote:

> 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/>
>
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