[petsc-users] Creating a DMNetwork from a DMPlex

[Matthew Knepley]

On Mon, May 20, 2019 at 12:51 PM Swarnava Ghosh <swarnava89 at gmail.com>
wrote:

> Hi Barry and Matt,
>
> Maybe try building by hand in a DMNetwork using a handrawn mesh with just
> a few vertices and endless and see if what you want to do makes sense
> > Okay, will try to do that. Do you have any DMNetwork example which I
> could follow.
>
> I think DMNetwork is not buying you anything here. It seems to make more
> sense to do it directly in Plex.
> You can easily lay down a P1 element for each field so that you can
> interpolate wherever you want.
> > Okay, then will it be possible to do vertex partitioning with plex?
> Essentially two processes can share an element but not vertex.
>

We can worry about that when everything works. Some things are easy but
that breaks a lot of the model, so it
unclear what all would have to change in order to do what you want. The
partitioning of vertices, however, is trivial.


> I would start from a clean example, such as SNES ex17. That solves
> elasticity, so it has multiple fields and FEM.
> The change is that you don't want to use any of the assembly functions, so
> you keep the code that does data layout
> and FEM discretization, but it ignore the residual/Jacobian stuff. Feel
> free to ask about using the lower-level
> interpolation stuff which is not as documented.
> >Thanks for pointing out the reference. Could you please share the
> functions for interpolation?
>

There are at least two ways to do it:

  1) Locally: DMPlexEvaluateFieldJets_Internal() or DMFieldEvaluate() which
is newer

  2) Globally:
https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/SNES/DMInterpolationEvaluate.html

  Thanks,

    Matt


> Sincerely,
> SG
>
>
> On Mon, May 20, 2019 at 4:02 AM Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Mon, May 20, 2019 at 3:05 AM Swarnava Ghosh via petsc-users <
>> petsc-users at mcs.anl.gov> wrote:
>>
>>> Hi Barry,
>>>
>>> Thank you for your email. My planned discretization is based on the fact
>>> that I need a distributed unstructured mesh, where at each vertex point I
>>> perform local calculations. For these calculations, I do NOT need need to
>>> assemble any global matrix. I will have fields defined at the vertices, and
>>> using linear interpolation, I am planing to find the values of these fields
>>> at some spatial points with are within a ball around each vertex. Once the
>>> values of these fields are known within the compact support around each
>>> vertex, I do local computations to calculate my unknown field. My reason
>>> for having the a mesh is essentially to 1) define fields at the vertices
>>> and 2) perform linear interpolation (using finite elements) at some spatial
>>> points. Also the local computations around at each vertex is
>>> computationally the most expensive step. In that case, having a cell
>>> partitioning will result in vertices being shared among processes, which
>>> will result in redundant computations.
>>>
>>> My idea is therefore to have DMNetwork to distribute vertices across
>>> processes and use finite elements for the linear interpolation part.
>>>
>>
>> I think DMNetwork is not buying you anything here. It seems to make more
>> sense to do it directly in Plex.
>> You can easily lay down a P1 element for each field so that you can
>> interpolate wherever you want.
>>
>> I would start from a clean example, such as SNES ex17. That solves
>> elasticity, so it has multiple fields and FEM.
>> The change is that you don't want to use any of the assembly functions,
>> so you keep the code that does data layout
>> and FEM discretization, but it ignore the residual/Jacobian stuff. Feel
>> free to ask about using the lower-level
>> interpolation stuff which is not as documented.
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Thanks,
>>> SG
>>>
>>>
>>>
>>> On Sun, May 19, 2019 at 6:54 PM Smith, Barry F. <bsmith at mcs.anl.gov>
>>> wrote:
>>>
>>>>
>>>>   I am not sure you want DMNetwork, DMNetwork has no geometry; it only
>>>> has vertices and edges. Vertices are connected to other vertices through
>>>> the edges. For example I can't see how one would do vertex centered finite
>>>> volume methods with DMNetwork. Maybe if you said something more about your
>>>> planned discretization we could figure something out.
>>>>
>>>> > On May 19, 2019, at 8:32 PM, Swarnava Ghosh <swarnava89 at gmail.com>
>>>> wrote:
>>>> >
>>>> > Hi Barry,
>>>> >
>>>> > No, the gmesh file contains a mesh and not a graph/network.
>>>> > In that case, is it possible to create a DMNetwork first from the
>>>> DMPlex and then distribute the DMNetwork.
>>>> >
>>>> > I have this case, because I want a vertex partitioning of my mesh.
>>>> Domain decomposition of DMPlex gives me cell partitioning. Essentially what
>>>> I want is that no two processes can share a vertex BUT that can share an
>>>> edge. Similar to how a DMDA is distributed.
>>>> >
>>>> > Thanks,
>>>> > Swarnava
>>>> >
>>>> > On Sun, May 19, 2019 at 4:50 PM Smith, Barry F. <bsmith at mcs.anl.gov>
>>>> wrote:
>>>> >
>>>> >    This use case never occurred to us. Is the gmesh file containing a
>>>> graph/network (as opposed to a mesh)? There seem two choices
>>>> >
>>>> > 1) if the gmesh file contains a graph/network one could write a gmesh
>>>> reader for that case that reads directly for and constructs a DMNetwork or
>>>> >
>>>> > 2) write a converter for a DMPlex to DMNetwork.
>>>> >
>>>> >    I lean toward the first
>>>> >
>>>> >    Either way you need to understand the documentation for DMNetwork
>>>> and how to build one up.
>>>> >
>>>> >
>>>> >    Barry
>>>> >
>>>> >
>>>> > > On May 19, 2019, at 6:34 PM, Swarnava Ghosh via petsc-users <
>>>> petsc-users at mcs.anl.gov> wrote:
>>>> > >
>>>> > > Hi Petsc users and developers,
>>>> > >
>>>> > > I am trying to find a way of creating a DMNetwork from a DMPlex. I
>>>> have read the DMPlex from a gmesh file and have it distributed.
>>>> > >
>>>> > > Thanks,
>>>> > > SG
>>>> >
>>>>
>>>>
>>
>> --
>> 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.cse.buffalo.edu/~knepley/>
>>
>

-- 
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.cse.buffalo.edu/~knepley/>
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