[petsc-users] DMSNESSet<Function,Jacobian>

Tue Apr 2 00:18:25 CDT 2013

Hello,
          I should be able to generate petscFEM struct with my code, i have
the required data, I just need to prepare it in the format used by
DMPLexComputeResidualFEM. I will give it a shot.

What is the pStart and pEnd in the call to DMLabelCreateIndex referring to
? Also,my code complains if i use DMLabel :: labelName

This name does not have a type, and must have an explicit type.

For now i can do without DMLabelCreateIndex as fortran interface to DMLabel
doesn't seem to exist.

On Mon, Apr 1, 2013 at 11:02 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Apr 2, 2013 at 1:47 PM, Dharmendar Reddy <dharmareddy84 at gmail.com>wrote:
>
>> 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
>>
>
> The object is just a struct, and has only information you must have for
> FEM, namely
> a quadrature rule, and tabulation of the basis functions are quadrature
> points.
>
>
>> bin/pythonscripts/PetscGenerateFEMQuadrature.py
>>
>> This script just generates a header with the struct information. You can
> make this header
> yourself and obviate the need for the script.
>
>
>> 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.
>>
>
> Can you just use these to create the PetscFEM struct?
>
>
>>
>> So i should be able to get the cell geometry information and cell degree
>> of freedom data via DMPlexVecGet/SetClosure right ?
>>
>
> Yes, although tell me why DMPlexComputeCellGeometry() does not work, and
> if not you can look at the code
> to see me getting the coordinate information.
>
>
>> 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.
>>
>
> Yes.
>
>
>> 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 ?
>>
>
> You use DMLabelGetValue(), and to trade memory for speed
> call DMLabelCreateIndex() first if you want.
>
>
>> 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 ?
>>
>
> Just a pointer.
>
>
>>  I was thinking i could create a section using DMPlexCreateSection and
>> pass that section to DMPlexVecGetClosure when i have to access auxilary
>> data.
>>
>
> This is exactly what I was suggesting, but you have the section be the
> "default section" of the cloned DM. That way
> it interacts with all PETSc functions nicely and you only have the extra
> memory for a DM object which is tiny.
>
>     Matt
>
> 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
>>
>
>
>
> --
> 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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