On Fri, Oct 25, 2013 at 8:18 PM, Matthew Knepley <[email protected]> wrote:
> On Fri, Oct 25, 2013 at 12:09 PM, Bishesh Khanal <[email protected]>wrote: > >> Dear all, >> I would like to know if some of the petsc objects that I have not used so >> far (IS, DMPlex, PetscSection) could be useful in the following case (of >> irregular domains): >> >> Let's say that I have a 3D binary image (a cube). >> The binary information of the image partitions the cube into a >> computational domain and non-computational domain. >> I must solve a pde (say a Poisson equation) only on the computational >> domains (e.g: two isolated spheres within the cube). I'm using finite >> difference and say a dirichlet boundary condition >> >> I know that I can create a dmda that will let me access the information >> from this 3D binary image, get all the coefficients, rhs values etc using >> the natural indexing (i,j,k). >> >> Now, I would like to create a matrix corresponding to the laplace >> operator (e.g. with standard 7 pt. stencil), and the corresponding RHS that >> takes care of the dirchlet values too. >> But in this matrix it should have the rows corresponding to the nodes >> only on the computational domain. It would be nice if I can easily (using >> (i,j,k) indexing) put on the rhs dirichlet values corresponding to the >> boundary points. >> Then, once the system is solved, put the values of the solution back to >> the corresponding positions in the binary image. >> Later, I might have to extend this for the staggered grid case too. >> So is petscsection or dmplex suitable for this so that I can set up the >> matrix with something like DMCreateMatrix ? Or what would you suggest as a >> suitable approach to this problem ? >> >> I have looked at the manual and that led me to search for a simpler >> examples in petsc src directories. But most of the ones I encountered are >> with FEM (and I'm not familiar at all with FEM, so these examples serve >> more as a distraction with FEM jargon!) >> > > It sounds like the right solution for this is to use PetscSection on top > of DMDA. I am working on this, but it is really > alpha code. If you feel comfortable with that level of development, we can > help you. > Thanks, with the (short) experience of using Petsc so far and being familiar with the awesomeness (quick and helpful replies) of this mailing list, I would like to give it a try. Please give me some pointers to get going for the example case I mentioned above. A simple example of using PetscSection along with DMDA for finite volume (No FEM) would be great I think. Just a note: I'm currently using the petsc3.4.3 and have not used the development version before. If not, just put the identity into > the rows you do not use on the full cube. It will not hurt scalability or > convergence. > In the case of Poisson with Dirichlet condition this might be the case. But is it always true that having identity rows in the system matrix will not hurt convergence ? I thought otherwise for the following reasons: 1) Having read Jed's answer here : http://scicomp.stackexchange.com/questions/3426/why-is-pinning-a-point-to-remove-a-null-space-bad/3427#3427 2) Some observation I am getting (but I am still doing more experiments to confirm) while solving my staggered-grid 3D stokes flow with schur complement and using -pc_type gamg for A00 matrix. Putting the identity rows for dirichlet boundaries and for ghost cells seemed to have effects on its convergence. I'm hoping once I know how to use PetscSection, I can get rid of using ghost cells method for the staggered grid and get rid of the identity rows too. Anyway please provide me with some pointers so that I can start trying with petscsection on top of a dmda, in the beginning for non-staggered case. Thanks, Bishesh > > Matt > > >> Thanks, >> Bishesh >> > > > > -- > 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 >
