[petsc-dev] Inquiry about contributing to MMG interface

Matthew Knepley knepley at gmail.com
Wed Feb 5 12:15:58 CST 2025 

On Wed, Feb 5, 2025 at 1:06 PM neil liu <liufield at gmail.com> wrote:

> Hi, Matt,
>
> It is not enough to only turn on -the open boundary.
> For the above example,  the 4 physical corner vertices (0D) for this
> internal quadrilateral surface have to be set, otherwise the shape can not
> be kept.
> In addition, for my present case, the boundary edges (1D) consisting of
> this quadrilateral surface need to be tagged.
> The present bdLabel seems to only work for 2D shapes for 3D cases.
> Please correct me if I am wrong.
>

Are you saying that this is the interface published by MMG? Can you point
me toward the piece of MMG documentation? I just want to understand the
interface requirements before we make any changes to PETSc.

  Thanks,

     Matt


>
> Thanks,
>
> Xiaodong
>
> On Wed, Feb 5, 2025 at 12:05 PM Matthew Knepley <knepley at gmail.com> wrote:
>
>> This is a really poor name. The boundary is not open in any sense. It
>> should be called an internal boundary, and what they call internal
>> boundaries should be called interdomain boundaries, but it seems too late
>> to fix this.
>>
>> Turning on open boundaries is just a flag, so that is easy, and one can
>> see the usefulness of this mode.
>>
>> My understanding from the documentation link below is that MMG does not
>> change anything about parts of the mesh marked
>> as internal boundaries, so we can read them right back out from the
>> boundary label. Why would we need a new label for this?
>>
>>   Thanks,
>>
>>      Matt
>>
>> On Wed, Feb 5, 2025 at 11:22 AM Pierre Jolivet <pierre at joliv.et> wrote:
>>
>>> See also:
>>> https://urldefense.us/v3/__https://www.mmgtools.org/mmg-remesher-try-mmg/mmg-remesher-tutorials/mmg-remesher-mmg3d/open-boundary-remeshing__;!!G_uCfscf7eWS!cb6ykLnRPMmL6lTuOwFvgRD8WX26biEjG4dzzYxzmbImFrhzFngp3qz8__PbBICIwsOWs-MrYKjLnusRx3Vq$ 
>>> .
>>>
>>> Thanks,
>>> Pierre
>>>
>>> On 5 Feb 2025, at 4:39 PM, neil liu <liufield at gmail.com> wrote:
>>>
>>> It seems the figures were  broken. Please see the following attached.
>>>
>>> On Wed, Feb 5, 2025 at 10:36 AM neil liu <liufield at gmail.com> wrote:
>>>
>>>> Hi, Mark,
>>>>
>>>> For example, in the left figure, the yellow rectangular face needs to
>>>> be preserved during mesh refinement. However, without specifying its four
>>>> corner points, the rectangle cannot be maintained, as shown in the right
>>>> figure. Additionally, the four edges of this face must be recorded and
>>>> retrieved for post-processing.
>>>>
>>>> This yellow face is an *open boundary*, meaning it is not an interface
>>>> between different materials. To ensure its preservation during mesh
>>>> refinement, MMG must be run in *opnbdy* (open boundary) mode.
>>>>
>>>> Thanks a lot,
>>>>
>>>> Xiaodong
>>>> [image: image.png] [image: image.png]
>>>>
>>>>
>>>> On Wed, Feb 5, 2025 at 10:05 AM Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Wed, Feb 5, 2025 at 9:52 AM neil liu <liufield at gmail.com> wrote:
>>>>>
>>>>>> Dear developers,
>>>>>>
>>>>>> I am currently working with MMG in the context of PETSc and have
>>>>>> identified a need to modify the existing MMG interface,
>>>>>> DMAdaptMetric_Mmg_Plex(), for our use case. Given these
>>>>>> requirements, I would like to explore the feasibility of contributing to
>>>>>> PETSc to enhance this interface, which has been verified and validated in
>>>>>> our research code.
>>>>>> *Proposed Modifications:*
>>>>>>
>>>>>>    1.
>>>>>>
>>>>>>    *Additional Labels for Physical Entities:*
>>>>>>    - In addition to the existing bdLabel and rgLabel, our case
>>>>>>       requires two additional labels to represent physical vertices and edges
>>>>>>       within the computational domain (3D).
>>>>>>
>>>>>> I am open to this. Can you be more specific about what it means?
>>>>>
>>>>>>
>>>>>>    1.
>>>>>>       - One approach is to introduce two new parameters in the
>>>>>>       subroutine’s input list. However, this may require modifications across
>>>>>>       related components, such as Pragmatic.
>>>>>>
>>>>>> This is not a problem. I can modify those.
>>>>>
>>>>>>
>>>>>>    1.
>>>>>>
>>>>>>    *Support for Open Boundaries:*
>>>>>>    - The current interface does not support open boundaries, a
>>>>>>       feature available in MMG.
>>>>>>       - As a result, several MMG benchmark cases involving open
>>>>>>       boundary remeshing cannot be executed within PETSc.
>>>>>>
>>>>>> Can you explain what this means? What is an open boundary exactly?
>>>>>
>>>>>
>>>>>> Would this be a viable contribution to PETSc? If so, I would
>>>>>> appreciate any guidance on the best approach to implementing these changes
>>>>>> while maintaining compatibility with existing features.
>>>>>>
>>>>> Yes. Please make a fork of the petsc repo, make a branch with the
>>>>> proposed changes, make an MR for that branch, and add me to your fork (I am
>>>>> knepley on GitLab). I can help you get it going.
>>>>>
>>>>>   Thanks,
>>>>>
>>>>>     Matt
>>>>>
>>>>>
>>>>>> Looking forward to your thoughts.
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Thanks,
>>>>>> Xiaodong
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cb6ykLnRPMmL6lTuOwFvgRD8WX26biEjG4dzzYxzmbImFrhzFngp3qz8__PbBICIwsOWs-MrYKjLnmg87pa0$ 
>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!anvbtQDqn57whvgg2qc1Dix0Izm9kxNlvUkeyYkcfknnt6VmqbCE0mlGSj6O1DLJx6qR7-7UsHv48zbaqVDECw$>
>>>>>
>>>> <The right figure.png><The left figure.png>
>>>
>>>
>>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>> https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cb6ykLnRPMmL6lTuOwFvgRD8WX26biEjG4dzzYxzmbImFrhzFngp3qz8__PbBICIwsOWs-MrYKjLnmg87pa0$ 
>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cb6ykLnRPMmL6lTuOwFvgRD8WX26biEjG4dzzYxzmbImFrhzFngp3qz8__PbBICIwsOWs-MrYKjLnuBX3RLl$ >
>>
>

-- 
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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cb6ykLnRPMmL6lTuOwFvgRD8WX26biEjG4dzzYxzmbImFrhzFngp3qz8__PbBICIwsOWs-MrYKjLnmg87pa0$  <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cb6ykLnRPMmL6lTuOwFvgRD8WX26biEjG4dzzYxzmbImFrhzFngp3qz8__PbBICIwsOWs-MrYKjLnuBX3RLl$ >
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