[petsc-users] Creating a DMNetwork from a DMPlex

[Swarnava Ghosh]

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.

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?

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/>
>
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