On Mon, Oct 28, 2013 at 6:19 PM, Matthew Knepley <[email protected]> wrote:
> On Mon, Oct 28, 2013 at 10:13 AM, Bishesh Khanal <[email protected]>wrote: > >> >> >> >> On Mon, Oct 28, 2013 at 3:49 PM, Matthew Knepley <[email protected]>wrote: >> >>> On Mon, Oct 28, 2013 at 9:06 AM, Bishesh Khanal <[email protected]>wrote: >>> >>>> >>>> On Mon, Oct 28, 2013 at 1:40 PM, Matthew Knepley <[email protected]>wrote: >>>> >>>>> On Mon, Oct 28, 2013 at 5:30 AM, Bishesh Khanal >>>>> <[email protected]>wrote: >>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Oct 25, 2013 at 10:21 PM, Matthew Knepley >>>>>> <[email protected]>wrote: >>>>>> >>>>>>> On Fri, Oct 25, 2013 at 2:55 PM, Bishesh Khanal <[email protected] >>>>>>> > wrote: >>>>>>> >>>>>>>> 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. >>>>>>>> >>>>>>> >>>>>>> Okay, >>>>>>> >>>>>>> 1) clone the repository using Git and build the 'next' branch. >>>>>>> >>>>>>> 2) then we will need to create a PetscSection that puts unknowns >>>>>>> where you want them >>>>>>> >>>>>>> 3) Setup the solver as usual >>>>>>> >>>>>>> You can do 1) an 3) before we do 2). >>>>>>> >>>>>>> I've done 1) and 3). I have one .cxx file that solves the system >>>>>> using DMDA (putting identity into the rows corresponding to the cells >>>>>> that >>>>>> are not used). >>>>>> Please let me know what I should do now. >>>>>> >>>>> >>>>> Okay, now write a loop to setup the PetscSection. I have the DMDA >>>>> partitioning cells, so you would have >>>>> unknowns in cells. The code should look like this: >>>>> >>>>> PetscSectionCreate(comm, &s); >>>>> DMDAGetNumCells(dm, NULL, NULL, NULL, &nC); >>>>> PetscSectionSetChart(s, 0, nC); >>>>> for (k = zs; k < zs+zm; ++k) { >>>>> for (j = ys; j < ys+ym; ++j) { >>>>> for (i = xs; i < xs+xm; ++i) { >>>>> PetscInt point; >>>>> >>>>> DMDAGetCellPoint(dm, i, j, k, &point); >>>>> PetscSectionSetDof(s, point, dof); // You know how many dof are >>>>> on each vertex >>>>> } >>>>> } >>>>> } >>>>> PetscSectionSetUp(s); >>>>> DMSetDefaultSection(dm, s); >>>>> PetscSectionDestroy(&s); >>>>> >>>>> I will merge the necessary stuff into 'next' to make this work. >>>>> >>>> >>>> I have put an example without the PetscSection here: >>>> https://github.com/bishesh/petscPoissonIrregular/blob/master/poissonIrregular.cxx >>>> From the code you have written above, how do we let PetscSection select >>>> only those cells that lie in the computational domain ? Is it that for >>>> every "point" inside the above loop, we check whether it lies in the domain >>>> or not, e.g using the function isPosInDomain(...) in the .cxx file I linked >>>> to? >>>> >>> >>> 1) Give me permission to comment on the source (I am 'knepley') >>> >>> 2) You mask out the (i,j,k) that you do not want in that loop >>> >> >> Done. >> I mask it out using isPosInDomain() function:: >> if(isPosInDomain(&testPoisson,i,j,k)) { >> ierr = DMDAGetCellPoint(dm, i, j, k, &point);CHKERRQ(ierr); >> ierr = PetscSectionSetDof(s, point, testPoisson.mDof); // >> You know how many dof are on each vertex >> } >> >> And please let me know when I can rebuild the 'next' branch of petsc so >> that DMDAGetCellPoint can be used. Currently compiler complains as it >> cannot find it. >> > > Pushed. > Pulled it thanks, but compiler was complaining that it didn't find DMDAGetCellPoint. Doing grep -R 'DMDAGetCellPoint' include/ returned nothing although the implementation is there in dalocal.c So I added the declaration to petscdmda.h file just above the declaration of DMDAGetNumCells. I have also added you as a collaborator in the github project repository so that you can edit and add comments to the file I linked above. My computeMatrix still uses the DMDA instead of the PetscSection, so is it where the changes need to be made ? > Matt > > >> >>> Matt >>> >>> >>>> >>>>> Thanks, >>>>> >>>>> Matt >>>>> >>>>>> >>>>>>> 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 >>>>>>>> >>>>>>> >>>>>>> Jed is talking about a constraint on a the pressure at a point. This >>>>>>> is just decoupling these unknowns from the rest >>>>>>> of the problem. >>>>>>> >>>>>>> >>>>>>>> 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. >>>>>>>> >>>>>>> >>>>>>> It can change the exact iteration, but it does not make the matrix >>>>>>> conditioning worse. >>>>>>> >>>>>>> Matt >>>>>>> >>>>>>> >>>>>>>> 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 >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> 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 >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>>>> >>>> >>>> >>> >>> >>> -- >>> 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 >>> >> >> > > > -- > 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 >
