From: Miguel Angel Salazar de Troya <salazardetr...@gmail.com> Date: Mon, 29 Sep 2014 16:55:14 -0500 To: Shri <abhy...@mcs.anl.gov> Cc: "petsc-users@mcs.anl.gov" <petsc-users@mcs.anl.gov> Subject: Re: [petsc-users] DMPlex with spring elements
>Hi all >I'm bumping this post because I have more questions related to the same >problem. > >I am looping over the edges of my DMNetwork, then I obtain the vertices >that make up each edge with DMNetworkGetConnectedNode(). Each of these >vertices have two variables (or actually, two degrees of freedom for my >problem). My intentions are to modify the solution vector entries that >are affected by these variables in each vertex. I would call the function >DMNetworkGetVariableOffset() to do this. What happens if one of the >vertices is a ghost vertex? Can I still modify the solution vector? My >problem is that the edge has information to provide to these nodes. > > Sorry for the delay. I think you would want to use http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMNetworkIsG hostVertex.html and not modify the value for the ghost vertex. Shri > >Thanks >Miguel > > > >On Fri, Sep 26, 2014 at 12:33 PM, Miguel Angel Salazar de Troya ><salazardetr...@gmail.com> wrote: > >I understand. Thanks a lot. >Miguel > > >On Fri, Sep 26, 2014 at 10:53 AM, Abhyankar, Shrirang G. ><abhy...@mcs.anl.gov> wrote: > >What Matt is saying is that there are two interfaces in PETSc for setting >the residual evaluation routine: > >i) SNESSetFunction takes in a function pointer for the residual evaluation >routine that has the prototype > PetscErrorCode xyzroutine(SNES snes, Vec X, Vec F, void* >ctx); > >X and F are the "global" solution and residual vectors. To compute the >global residual evaluation, typically one does -- (a) scattering X and F >onto local vectors localX and localF (DMGlobalToLocal), (b) computing the >local residual, and (c) gathering the localF in the global F >(DMLocalToGlobal). This is what is done in the example. > >ii) DMSNESSetFunctionLocal takes in a function pointer for the residual >evaluation routine that has the prototype > PetscErrorCode xyzlocalroutine(DM, Vec localX, localF, >void* ctx) > >In this case, the localX and localF get passed to the routine. So, you >only have to do the local residual evaluation. PETSc does the >LocalToGlobal gather to form the global residual. > >I chose to use SNESSetFunction in the example. You can use either of them. > >Shri > >From: Matthew Knepley <knep...@gmail.com> >Date: Fri, 26 Sep 2014 10:28:26 -0500 >To: Miguel Angel Salazar de Troya <salazardetr...@gmail.com> >Cc: Jed Brown <j...@jedbrown.org>, Shri <abhy...@mcs.anl.gov>, >"petsc-users@mcs.anl.gov" <petsc-users@mcs.anl.gov> >Subject: Re: [petsc-users] DMPlex with spring elements > > >>On Fri, Sep 26, 2014 at 10:26 AM, Miguel Angel Salazar de Troya >><salazardetr...@gmail.com> wrote: >> >>Yeah, but doesn't it only work with the local vectors localX and localF? >> >> >> >>I am telling you what the interface for the functions is. You can do >>whatever you want inside. >> >> Matt >> >> >>Miguel >> >>On Fri, Sep 26, 2014 at 10:10 AM, Matthew Knepley <knep...@gmail.com> >>wrote: >> >>On Fri, Sep 26, 2014 at 10:06 AM, Miguel Angel Salazar de Troya >><salazardetr...@gmail.com> wrote: >> >>That means that if we call SNESSetFunction() we don't build the residual >>vector in parallel? In the pflow example >>(http://www.mcs.anl.gov/petsc/petsc-as/petsc-current/src/snes/examples/tu >>t >>orials/network/pflow/pf.c.html) the function FormFunction() (Input for >>SNESSetFunction() works with the local vectors. I don't understand this. >> >> >> >>FormFunction() in that link clearly takes in a global vector X and >>returns a global vector F. Inside, it >>converts them to local vectors. This is exactly what you would do for a >>function given to SNESSetFunction(). >> >> Matt >> >> >> >>Thanks >>Miguel >> >> >>On Fri, Sep 26, 2014 at 9:34 AM, Matthew Knepley <knep...@gmail.com> >>wrote: >> >>On Fri, Sep 26, 2014 at 9:31 AM, Miguel Angel Salazar de Troya >><salazardetr...@gmail.com> wrote: >> >>Thanks. I had another question about the DM and SNES and TS. There are >>similar routines to assign the residual and jacobian evaluation to both >>objects. For the SNES case are: >>DMSNESSetFunctionLocal >>DMSNESSetJacobianLocal >> >>What are the differences of these with: >> >>SNESSetFunction >>SNESSetJacobian >> >> >> >> >>SNESSetFunction() expects the user to construct the entire parallel >>residual vector. DMSNESSetFunctionLocal() >>expects the user to construct the local pieces of the residual, and then >>it automatically calls DMLocalToGlobal() >>to assembly the full residual. It also converts the input from global >>vectors to local vectors, and in the case of >>DMDA multidimensional arrays. >> >> Thanks, >> >> Matt >> >> >>and when should we use each? With "Local", it is meant to evaluate the >>function/jacobian for the elements in the local processor? I could get >>the local edges in DMNetwork by calling DMNetworkGetEdgeRange? >> >>Miguel >> >> >>On Thu, Sep 25, 2014 at 5:17 PM, Matthew Knepley <knep...@gmail.com> >>wrote: >> >> >> >>On Thu, Sep 25, 2014 at 5:15 PM, Miguel Angel Salazar de Troya >><salazardetr...@gmail.com> wrote: >> >>> If you need a symmetric Jacobian, you can use the BC facility in >>> PetscSection, which eliminates the >>> variables completely. This is how the FEM examples, like ex12, work. >>Would that be with PetscSectionSetConstraintDof ? For that I will need >>the PetscSection, DofSection, within DMNetwork, how can I obtain it? I >>could cast it to DM_Network from the dm, networkdm, declared in the main >>program, maybe something like this: >>DM_Network *network = (DM_Network*) networkdm->data;Then I would loop >>over the vertices and call PetscSectionSetConstraintDof if it's a >>boundary node (by checking the corresponding component) >> >> >> >> >>I admit to not completely understanding DMNetwork. However, it eventually >>builds a PetscSection for data layout, which >>you could get from DMGetDefaultSection(). The right thing to do is find >>where it builds the Section, and put in your BC >>there, but that sounds like it would entail coding. >> >> Thanks, >> >> Matt >> >> >> >> >>Thanks for your responses.Miguel >> >> >> >> >>On Thu, Sep 25, 2014 at 2:42 PM, Jed Brown <j...@jedbrown.org> wrote: >> >>Matthew Knepley <knep...@gmail.com> writes: >> >>> On Thu, Sep 25, 2014 at 1:46 PM, Abhyankar, Shrirang G. >>><abhy...@mcs.anl.gov >>>> wrote: >>> >>>> You are right. The Jacobian for the power grid application is indeed >>>> non-symmetric. Is that a problem for your application? >>>> >>> >>> If you need a symmetric Jacobian, you can use the BC facility in >>> PetscSection, which eliminates the >>> variables completely. This is how the FEM examples, like ex12, work. >> >>You can also use MatZeroRowsColumns() or do the equivalent >>transformation during assembly (my preference). >> >> >> >> >> >> >> >> >>-- >>Miguel Angel Salazar de Troya >> >> >>Graduate Research Assistant >>Department of Mechanical Science and Engineering >>University of Illinois at Urbana-Champaign > > >>(217) 550-2360 <tel:%28217%29%20550-2360> >> >> >>salaz...@illinois.edu >> >> >> >> >> >> >> >> >> >> >>-- >>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 >> >> >> >> >> >> >> >> >>-- >>Miguel Angel Salazar de Troya >>Graduate Research Assistant >>Department of Mechanical Science and Engineering >>University of Illinois at Urbana-Champaign >>(217) 550-2360 <tel:%28217%29%20550-2360> >>salaz...@illinois.edu >> >> >> >> >> >> >> >> >> >> >>-- >>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 >> >> >> >> >> >> >> >> >> >> >>-- >>Miguel Angel Salazar de Troya >>Graduate Research Assistant >>Department of Mechanical Science and Engineering >>University of Illinois at Urbana-Champaign >>(217) 550-2360 <tel:%28217%29%20550-2360> >>salaz...@illinois.edu >> >> >> >> >> >> >> >> >> >> >>-- >>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 >> >> >> >> >> >> >> >> >> >> >>-- >>Miguel Angel Salazar de Troya >>Graduate Research Assistant >>Department of Mechanical Science and Engineering >>University of Illinois at Urbana-Champaign >>(217) 550-2360 <tel:%28217%29%20550-2360> >>salaz...@illinois.edu >> >> >> >> >> >> >> >> >> >>-- >>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 > > > > > > > > > >-- > > >Miguel Angel Salazar de Troya > > >Graduate Research Assistant >Department of Mechanical Science and Engineering >University of Illinois at Urbana-Champaign >(217) 550-2360 > > >salaz...@illinois.edu > > > > > > > > >-- >Miguel Angel Salazar de Troya >Graduate Research Assistant >Department of Mechanical Science and Engineering >University of Illinois at Urbana-Champaign >(217) 550-2360 >salaz...@illinois.edu
