[petsc-users] Insert values into matrix using MatSetValuesStencil
Timothée Nicolas
timothee.nicolas at gmail.com
Wed Sep 23 03:45:58 CDT 2015
Yes, I had understood that, I am doing the same, but with 8 dof. This does
not change the declaration for row and col.
Can you send (i) the commands you use to create the DMDA, (ii) the commands
to create the matrix and (iii) those for the definitions of
ksta2,kend2,jsta2,jend2,size_x ?
Timothée
2015-09-23 17:37 GMT+09:00 TAY wee-beng <zonexo at gmail.com>:
> Hi Timothée,
>
> The matrix is created with 3 dof - u,v,w. So for each i,j,k, there are 3
> values. Actually I got 3 eqns from the u,v,w momentum eqns. They are not
> coupled together so I can also solve them individually. But I was told it's
> faster to group them together. The global indices is something like this:
>
> i, j, k, ijk global indices, dof
> 1 1 1 1 u
> 1 1 1 2 v
> 1 1 1 3 w
> 2 1 1 4 u
>
> ...
>
> Hope it's clearer now.
>
> Ok, I changed the stencil, it's now working.
>
> Thank you
>
> Yours sincerely,
>
> TAY wee-beng
>
> On 23/9/2015 4:22 PM, Timothée Nicolas wrote:
>
> Can you also tell how you created the matrix ? Just in case you created it
> with the 1 dof DMDA, it would not work if you try to input values at places
> where it is not allocated (which could explain the error message)
>
> 2015-09-23 17:18 GMT+09:00 Timothée Nicolas <timothee.nicolas at gmail.com>:
>
>> The first thing that strikes me is your definition of the stencils
>>
>> *MatStencil :: row(6,1),col(6,7)*
>>
>> Why is it not defined with
>>
>> *MatStencil :: row(4,1),col(4,7)*
>>
>> instead ?
>>
>> Where does the 6 come from ?
>>
>> Timothée
>>
>>
>> 2015-09-23 17:14 GMT+09:00 TAY wee-beng < <zonexo at gmail.com>
>> zonexo at gmail.com>:
>>
>>> Hi,
>>>
>>> I have successfully used MatSetValuesStencil to insert values into a
>>> Poisson eqn matrix which has 1 DOF (pressure). Now I'm trying to insert
>>> values in a momentum eqn matrix which has 3 DOF (u,v,w)
>>>
>>> However, I got the error:
>>>
>>> *[0]PETSC ERROR: --------------------- Error Message
>>> ----------------------------*
>>> *----------------------------------*
>>> *[0]PETSC ERROR: Argument out of range*
>>> *[0]PETSC ERROR: Inserting a new nonzero at (111,5) in the matrix*
>>> *[0]PETSC ERROR: See
>>> <http://www.mcs.anl.gov/petsc/documentation/faq.html>http://www.mcs.anl.gov/petsc/documentation/faq.html
>>> <http://www.mcs.anl.gov/petsc/documentation/faq.html> for trou*
>>> *ble shooting.*
>>>
>>> I wonder what's wrong. For the momentum eqn, for each DOF, at at node
>>> (dof,i,j,k), I have coupling i +/- 1, j +/- 1 and k +/- 1.
>>>
>>> The error happens at 111,5, which corresponds to i = 2, j = 2, k = 2,
>>> which is an internal node.
>>>
>>> Here's part of my code below. Hope someone can help. Thanks!
>>>
>>> *PetscScalar :: value_insert(7)*
>>>
>>> *MatStencil :: row(6,1),col(6,7)*
>>>
>>> *ione = 1; iseven = 7*
>>>
>>> *if (cell_type == 'u') then*
>>>
>>> * offset = 1*
>>>
>>> *else if (cell_type == 'v') then*
>>>
>>> * offset = 2*
>>>
>>> *else if (cell_type == 'w') then*
>>>
>>> * offset = 3*
>>>
>>> *end if*
>>>
>>> *do k=ksta2,kend2*
>>>
>>> * do j = jsta2,jend2*
>>>
>>> * do i=2,size_x-1*
>>>
>>> * row(MatStencil_i,1) = i - 1*
>>>
>>> * row(MatStencil_j,1) = j - 1*
>>>
>>> * row(MatStencil_k,1) = k - 1*
>>>
>>> * row(MatStencil_c,1) = offset - 1*
>>>
>>> * value_insert = 0.d0*
>>>
>>> * col(MatStencil_i,3) = i + 1 - 1 !east*
>>>
>>> * col(MatStencil_j,3) = j - 1*
>>>
>>> * col(MatStencil_k,3) = k - 1*
>>>
>>> * col(MatStencil_c,3) = offset - 1*
>>>
>>> * value_insert(3) = -(
>>> 1./(cell_x(i)%pd_E+cell_x(i+1)%pd_W))*(c_yz(j,k)%fc_E)*inv_Re*
>>>
>>> * col(MatStencil_i,5) = i - 1 - 1 !west*
>>>
>>> * col(MatStencil_j,5) = j - 1*
>>>
>>> * col(MatStencil_k,5) = k - 1*
>>>
>>> * col(MatStencil_c,5) = offset - 1*
>>>
>>> * value_insert(5) = -(
>>> 1./(cell_x(i)%pd_W+cell_x(i-1)%pd_E))*(c_yz(j,k)%fc_E)*inv_Re*
>>>
>>> * col(MatStencil_i,2) = i - 1 !north*
>>>
>>> * col(MatStencil_j,2) = j + 1 - 1*
>>>
>>> * col(MatStencil_k,2) = k - 1*
>>>
>>> * col(MatStencil_c,2) = offset - 1*
>>>
>>> * value_insert(2) = -(
>>> 1./(cell_y(j)%pd_N+cell_y(j+1)%pd_S))*(c_zx(i,k)%fc_N)*inv_Re*
>>>
>>> * col(MatStencil_i,4) = i - 1 !south*
>>>
>>> * col(MatStencil_j,4) = j - 1 - 1*
>>>
>>> * col(MatStencil_k,4) = k - 1*
>>>
>>> * col(MatStencil_c,4) = offset - 1*
>>>
>>> * value_insert(4) = -(
>>> 1./(cell_y(j)%pd_S+cell_y(j-1)%pd_N))*(c_zx(i,k)%fc_N)*inv_Re*
>>>
>>> * col(MatStencil_i,6) = i - 1 !front*
>>>
>>> * col(MatStencil_j,6) = j - 1*
>>>
>>> * col(MatStencil_k,6) = k + 1 - 1*
>>>
>>> * col(MatStencil_c,6) = offset - 1*
>>>
>>> * value_insert(6) = -(
>>> 1./(cell_z(k)%pd_F+cell_z(k+1)%pd_B))*(c_xy(i,j)%fc_F)*inv_Re*
>>>
>>> * col(MatStencil_i,7) = i - 1 !back*
>>>
>>> * col(MatStencil_j,7) = j - 1*
>>>
>>> * col(MatStencil_k,7) = k - 1 - 1*
>>>
>>> * col(MatStencil_c,7) = offset - 1*
>>>
>>> * value_insert(7) = -(
>>> 1./(cell_z(k)%pd_B+cell_z(k-1)%pd_F))*(c_xy(i,j)%fc_F)*inv_Re*
>>>
>>> * col(MatStencil_i,1) = i - 1*
>>>
>>> * col(MatStencil_j,1) = j - 1*
>>>
>>> * col(MatStencil_k,1) = k - 1*
>>>
>>> * col(MatStencil_c,1) = offset - 1*
>>>
>>> * value_insert(1) = 2.*c(i,j,k)%vol/del_t -
>>> (value_insert(2)+value_insert(3)+value_insert(4)+value_insert(5)+value_insert(6)+value_insert(7))*
>>>
>>> * call
>>> MatSetValuesStencil(A_semi_xyz,ione,row,iseven,col,value_insert,INSERT_VALUES,ierr)*
>>>
>>> * end do*
>>>
>>> * end do*
>>>
>>> *end do *
>>>
>>> Thank you
>>>
>>> Yours sincerely,
>>>
>>> TAY wee-beng
>>>
>>>
>>>
>>
>
>
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