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. 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
