[petsc-users] Insert values into matrix using MatSetValuesStencil or MatSetValuesLocal

Timothée Nicolas timothee.nicolas at gmail.com
Mon Aug 24 04:54:54 CDT 2015


ex5 of snes can give you an example of the two routines.

The C version ex5.c uses MatSetValuesStencil whereas the Fortran90 version
ex5f90.F uses MatSetValuesLocal.

However, I use MatSetValuesStencil also in Fortran, there is no problem,
and no need to mess around with DMDAGetAO, I think.

To input values in the matrix, you need to do the following :

! Declare the matstencils for matrix columns and rows
MatStencil  :: row(4,1),col(4,n)
! Declare the quantity which will store the actual matrix elements
PetscScalar :: v(8)

The first dimension in row and col is 4 to allow for 3 spatial dimensions
(even if you use only 2) plus one degree of freedom if you have several
fields in your DMDA. The second dimension is 1 for row (you input one row
at a time) and n for col, where n is the number of columns that you input.
For instance, if at node (1,i,j)  (1 is the index of the degree of
freedom), you have, say, 6 couplings, with nodes (1,i,j), (1,i+1,j),
(1,i-1,j), (1,i,j-1), (1,i,j+1), (2,i,j) for example, then you need to set

Then you define the row number by naturally doing the following, inside a
local loop :

row(MatStencil_i,1) = i          -1
row(MatStencil_j,1) = j          -1
row(MatStencil_c,1) = 1          -1

the -1 are here because FORTRAN indexing is different from the native C
indexing. I put them on the right to make this more apparent.

Then the column information. For instance to declare the coupling with node
(1,i,j), (1,i-1,j) and (2,i,j) (you can make up for the rest) you will have
to write (still within the same local loop on i and j)

col(MatStencil_i,1) = i         -1
col(MatStencil_j,1) = j         -1
col(MatStencil_c,1) = 1         -1
v(1) = whatever_it_is

col(MatStencil_i,2) = i-1       -1
col(MatStencil_j,2) = j         -1
col(MatStencil_c,2) = 1         -1
v(2) = whatever_it_is

col(MatStencil_i,3) = i       -1
col(MatStencil_j,3) = j         -1
col(MatStencil_c,3) = 2         -1
v(3) = whatever_it_is



Note that the index of the degree of freedom (or what field you are
coupling to), is indicated by MatStencil_c

Finally use MatSetValuesStencil

ione = 1
isix = 6
call MatSetValuesStencil(Matrix,ione,row,isix,col,v,INSERT_VALUES,ierr)

If it is not clear don't hesitate to ask more details. For me it worked
that way, I succesfully computed a Jacobian that way. It is very sensitive.
If you slightly depart from the right jacobian, you will see a huge
difference compared to using  matrix free with -snes_mf, so you can hardly
make a mistake because you would see it. That's how I finally got it to



2015-08-24 18:09 GMT+09:00 Wee-Beng Tay <zonexo at gmail.com>:

> Hi,
> I'm modifying my 3d fortran code from MPI along 1 direction (z) to MPI
> along 2 directions (y,z)
> Previously I was using MatSetValues with global indices. However, now I'm
> using DM and global indices is much more difficult.
> I come across MatSetValuesStencil or MatSetValuesLocal.
> So what's the difference bet the one since they both seem to work locally?
> Which is a simpler/better option?
> Is there an example in Fortran for MatSetValuesStencil?
> Do I also need to use DMDAGetAO together with MatSetValuesStencil or
> MatSetValuesLocal?
> Thanks!
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