No worries. Thanks for your responses. I'm assuming you suggested to use DMNetworkIsGhostVertex() and not modify its value for the case in which I were using the global vectors and not the local vectors, where it is possible, as Matt suggested.
Miguel On Tue, Sep 30, 2014 at 11:22 AM, Abhyankar, Shrirang G. < abhy...@mcs.anl.gov> wrote: > > 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 > > -- *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
