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. > > 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 >
