Hi Dave,
Thanks a lot for your prompt reply! This is even easier than I thought (and
that is most likely the reason, why I could not think into this direction) :)
And yes, I might/should upgrade our PETSc version used (3.1), but it will take
me some days to check the full code package.
Now, I will create my DA (now in 3.6 called DMDA) for the coupled system via
DACreate3d(PETSC_COMM_WORLD, Periodicity, DA_STENCIL_BOX, Nx, Ny, Nz, Px, Py,
Pz, 4, 1, lx, ly, lz, &MyDA);
instead of
DACreate3d(PETSC_COMM_WORLD, Periodicity, DA_STENCIL_BOX, Nx, Ny, Nz, Px, Py,
Pz, 1, 1, lx, ly, lz, &MyDA);
which I have used for the single equation.
I would like to ask one follow-up question:
Currently, I loop over my matrix (and vectors) via three for-loops over the 3
spatial directions, and set the columns indices in the following way:
for(k){
row.k = k;
col[0].k = k;
col[1].k = k;
col[2].k = k;
col[3].k = k;
col[4].k = k+1;
col[5].k = k-1;
for(j){
row.j = j;
col[0].j = j;
col[1].j = j;
col[2].j = j+1;
col[3].j = j-1;
col[4].j = j;
col[5].j = j;
for(i){
row.i = i;
col[0].i = i+1;
col[1].i = i-1;
col[2].i = i;
col[3].i = i;
col[4].i = i;
col[5].i = i;
Now for the coupled equations, I should overall additionally loop over the
number of DOFs (just 2 in my previous email example). Could you give me an easy
example or pseudo-code for the associated assignment of columns (I have the
same stencil in each of the submatrices, so for the 2 DOFs in 3D, I would get
7+6=13 column entries per row)? Or can you link me to an existing example
within the PETSc help?
Again, Thanks a lot!
Rolf
> Am 24.11.2016 um 22:30 schrieb Dave May <dave.mayhe...@gmail.com>:
>
> When you create the DMDA, set the number of DOFs (degrees of freedom) per
> point to be 2 instead of 1.
>
> You must be using and ancient version of petsc given the function names you
> quoted. Consider upgrading to 3.7
>
> Thanks,
> Dave
>
> On Thu, 24 Nov 2016 at 20:24, Rolf Kuiper <kui...@mpia.de
> <mailto:kui...@mpia.de>> wrote:
> Dear PETSc users,
>
> maybe this is an easy question, but I can’t find the information right away
> in the user’s guide nor online.
>
> What I am currently doing and which works fine:
> To solve a partial differential equation for the quantity q on a parallel
> distributed grid, which is represented by the Distributed Array MyDA, I am
> currently creating the associated sparse matrix for the KSP solver via
> DAGetMatrix(MyDA, MATMPIAIJ, &MyMatrix);
>
> The solution vector and right hand side vector are created via
> DACreateGlobalVector(MyDA, &MyRightHandSideVector);
> VecDuplicate(MyRightHandSideVector, &GlobalSolutionVector);
>
> The DA is constructed using DACreate3d() with the corresponding regular
> structured grid information.
>
> And here is my problem:
> Now, I would like to solve a coupled system of equations for the quantities
> q1 and q2 on the same grid. I.e., the matrix should just get the double
> number of rows and columns, the vectors contain twice the number of entries
> (e.g. first all q1s and then all q2s). And I would like to be sure that the
> entries of q1 and q2, which are associated with the same grid cell are
> located on the same processor.
> Is there already a pre-defined structures available (such as MATMPIAIJ)
> within PETSc to enlarge such a single equation to store the entries of
> coupled equations? Such as
> DACreateTwiceTheGlobalVector()?
>
> The equation is (simplified) of the form
> d/dt q1 + grad q2 = 0
> d/dt q2 + f(q1) = 0
> with an arbitrary function f depending on q1.
>
> Thanks a lot for your help in advance,
> Rolf
