[petsc-users] DMSNESSet<Function,Jacobian>

[Dharmendar Reddy]

Hello,
         I looked at the source code of SNESSetFunction after i sent the
email. From what i understood, SNESSetFunction calls DMSNESSetFunction
internally. I was like, why not just use SNESSetFunction with out passing
DM. But i get it now, not all problems have to use DM. If i am using DM i
should rather use DMSNESSetFunction. A better way is DMSNESSetFunctionLocal
right ? DMSNesSetFunction i called inside DMSNESSetFunctionLocal.


I did look at DMPlexComputeResidualFEM but that requires userContext to
have PetscFEM object. Is PetscFEM object accisable from Fortran or is it
genrated using

bin/pythonscripts/PetscGenerateFEMQuadrature.py


I structured my code such that, user provides the Linear and bilinear form
subroutines:

subroutine biLinearFrom(u,v,cell,Kelm,eqnCtx)
type(FunctionSpace) :: u,v
type(FEMCell) :: cell
PetscScalar :: Kelm
class(*),pointer :: eqnCtx
end subroutine

Function space object provide the routines for evaluation of basis
functions and gradients, given cell coordinates, and cell degrees of
freedom.
So i should be able to get the cell geometry information and cell degree of
freedom data via DMPlexVecGet/SetClosure right ?

At this point i was able to create a DMPlex object from a mesh created by
gmsh. I used DMPLexCreateLabel to add the physical region labels i created
in GMSh . So no i have a mapping from given a region label, list of cells
in that region.

If i am doing a physical region wise assemble of the problem, i could use
the DMPlexgetStratumIS for each regionlabel.

since i am doing a cell wise assemble, i would be interested in a mapping
from cell id to  regionId (i can have a local array of labels indexed by
region Id) so that i can pass the material information to FEMCell.  Right
now i have a integer array which holds the map from cellId to regionId.

I was wondering if i could add a integer section to DM object ?

I also need to have some other auxiliary scalar data associated with the
DM. You suggested in one of the earlier email  that i created another DM
using DMplexClone ? If i clone a object is it creating another copy of the
mesh in memory or is it just storing pointers ?
I was thinking i could create a section using DMPlexCreateSection and pass
that section to DMPlexVecGetClosure when i have to access auxilary data.

Basically the problem is to solve Poisson equation with current continuity
equation for a semiconductor. I solve the problem by solving each equation
until the solutions of both are consistent. For Poisson problem, the degree
freedom is potential and takes charge density as input. For continuation
equation degree of freedom is charge density and take potential as input.

Do you have alternative approaches to what i am thinking ?

On Mon, Apr 1, 2013 at 8:24 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Apr 2, 2013 at 10:16 AM, Dharmendar Reddy <dharmareddy84 at gmail.com
> > wrote:
>
>> Hello,
>>         I am confused about the usage of SNESSetFunction,
>> DMSNESSetFunction, DMSNESSetFunctionLocal and the corresponding Jacobin
>> routines.
>>
>> At present my code is set up as follows.
>>
>> I initiate SNES with getFunction and getJacobain routines required as per
>> SNESSet<Function,Jacobian>. I pass a user context  which has the mesh  and
>> field layout information. I assemble the residual function and Jacobin
>> element wise using the information from user context. My code at this point
>> is serial, so i run the element loop from 1 to numberofTotalElements.
>>
>> Now i want to switch to using DMPlex. How should i change the interface
>> to my code.
>>
>
> You can always look at SNES ex62
> http://www.mcs.anl.gov/petsc/petsc-dev/src/snes/examples/tutorials/ex62.c.html
>
>
>> If i set the dm for snes using SNESSetDM, i can see that the DM can be
>> accessed via SNESGetDM inside getFunction and getJacobian, then i get the
>> elementStartID and elementEndID to run the loop for assmbler. But now i
>> will have to assemble to local vector into global vector right ?
>>
>
> No, here is the sequence:
>
>   1) SNESSetDM(snes, dm)
>
>   2) DMSNESSetFunctionLocal(dm, userResidual, userCtx)
>
> where we have
>
>   userResidual(DM dm, Vec X, Vec F, void *userCtx)
>
> Both X and F are local vectors which I normally interact with using
> DMPlexVecGet/SetClosure(). If you
> are using FEM, you can DMPlexComputeResidualFEM() here and
> use DMPlexSetFEMIntegration() to
> input point-wise physics functions as is done in ex62.
>
>
>> Looks like the DMSNESSetFunctionLocal will assemble the local
>> vector into global vector. The function provided to this should just
>> evaluate the local vector. Did i understand this right ?
>>
>> I am confused about passing the DM in DMSNESSet<Function,Jacobian>. When
>> the DM can be accessed via SNESGetDM, why do we pass it again explicitly ?
>>
>
> You are not passing the SNES, so where would it come from in this call?
>





>
>    Matt
>
>
>>
>> --
>> -----------------------------------------------------
>> Dharmendar Reddy Palle
>> Graduate Student
>> Microelectronics Research center,
>> University of Texas at Austin,
>> 10100 Burnet Road, Bldg. 160
>> MER 2.608F, TX 78758-4445
>> e-mail: dharmareddy84 at gmail.com
>> Phone: +1-512-350-9082
>> United States of America.
>> Homepage: https://webspace.utexas.edu/~dpr342
>>
>
>
>
> --
> 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
>



-- 
-----------------------------------------------------
Dharmendar Reddy Palle
Graduate Student
Microelectronics Research center,
University of Texas at Austin,
10100 Burnet Road, Bldg. 160
MER 2.608F, TX 78758-4445
e-mail: dharmareddy84 at gmail.com
Phone: +1-512-350-9082
United States of America.
Homepage: https://webspace.utexas.edu/~dpr342
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