[petsc-users] MatSetValuesStencil for cols not in the dmda stencil width

[Xiangdong]

Thanks, Matt.  For a cell in DMDA 3d with global id (ix,iy,iz), what is the
global row id of that cell corresponding to the matrix generated by
DMCreateMatrix? It is not always ix + iy*Nx + iz*Ny*Nx for
different da_processors_xyz, is it? How can I obtain that global row id?

Thanks.

Xiangdong



On Wed, Jan 25, 2017 at 10:53 AM, Matthew Knepley <knepley at gmail.com> wrote:

> On Wed, Jan 25, 2017 at 9:17 AM, Xiangdong <epscodes at gmail.com> wrote:
>
>> Hello everyone,
>>
>> I have a question on setting matrix entries which are not in the stencil
>> width. Take ksp ex45.c as an example,
>> http://www.mcs.anl.gov/petsc/petsc-current/src/ksp/ksp/examp
>> les/tutorials/ex45.c.html
>>
>> Instead of setting up the standard 7-point stencil, now for each cell,
>> the matrix also has a additional dependency on the cell (Mx, My, Mz).
>> Namely, for each row, the col corresponding to (Mx, My, Mz) is always
>> nonzero. I modify the example code to add this entries:
>>
>> +  MatSetOption(B,MAT_NEW_NONZERO_LOCATIONS,PETSC_TRUE);
>> +  MatSetOption(jac,MAT_NEW_NONZERO_LOCATIONS,PETSC_TRUE);
>>
>> +  v[7] = 100; col[7].i = mx-1; col[7].j = my-1; col[7].k = mz-1;
>> +  ierr = MatSetValuesStencil(B,1,&row,8,col,v,INSERT_VALUES);CHKERRQ(
>> ierr);
>>
>> It is okay to for np=1, but crash for np>=2 with the error message:
>>
>
> You can do this, but
>
> 1) You cannot use MatSetStencil, since your entry is not actually in your
> stencil. You will have to make a separate call to MatSetValues() using the
> global index.
>
> 2) The nonzero pattern we have allocated will be wrong. You will have to
> set the MatOption which gives an error on new nonzeros to PETSC_FALSE.
>
> 3) You will have a dense row in your Jacobian, which is hard to make
> perform well, and also stymies most preconditioners.
>
>   Thanks,
>
>     Matt
>
>
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [0]PETSC ERROR: Argument out of range
>> [0]PETSC ERROR: Local index 342 too large 244 (max) at 7
>>
>> [0]PETSC ERROR: #1 ISLocalToGlobalMappingApply() line 423 in
>> petsc-3.7.4/src/vec/is/utils/isltog.c
>> [0]PETSC ERROR: #2 MatSetValuesLocal() line 2052 in
>> petsc-3.7.4/src/mat/interface/matrix.c
>> [0]PETSC ERROR: #3 MatSetValuesStencil() line 1447 in
>> petsc-3.7.4/src/mat/interface/matrix.c
>> [0]PETSC ERROR: #4 ComputeMatrix() line 151 in extest.c
>>
>> Can I add new entries to the cols not in the stencil width into the dmda
>> matrix or Jacobian?
>>
>> Attached please find the modifed ex45 example, the diff file as well as
>> the run log.
>>
>> Thanks for your help.
>>
>> Best,
>> Xiangdong
>>
>>
>
>
> --
> 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
>
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