[petsc-users] DMPlex with spring elements

Fri Sep 26 12:33:05 CDT 2014

I understand. Thanks a lot.

Miguel

On Fri, Sep 26, 2014 at 10:53 AM, Abhyankar, Shrirang G. <
abhyshr at 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 <knepley at gmail.com>
> Date:  Fri, 26 Sep 2014 10:28:26 -0500
> To:  Miguel Angel Salazar de Troya <salazardetroya at gmail.com>
> Cc:  Jed Brown <jed at jedbrown.org>, Shri <abhyshr at mcs.anl.gov>,
> "petsc-users at mcs.anl.gov" <petsc-users at 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
> ><salazardetroya at 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 <knepley at gmail.com>
> >wrote:
> >
> >On Fri, Sep 26, 2014 at 10:06 AM, Miguel Angel Salazar de Troya
> ><salazardetroya at 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/tut
> >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 <knepley at gmail.com>
> >wrote:
> >
> >On Fri, Sep 26, 2014 at 9:31 AM, Miguel Angel Salazar de Troya
> ><salazardetroya at 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 <knepley at gmail.com>
> >wrote:
> >
> >
> >
> >On Thu, Sep 25, 2014 at 5:15 PM, Miguel Angel Salazar de Troya
> ><salazardetroya at 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 <jed at jedbrown.org> wrote:
> >
> >Matthew Knepley <knepley at gmail.com> writes:
> >
> >> On Thu, Sep 25, 2014 at 1:46 PM, Abhyankar, Shrirang G.
> >><abhyshr at 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>
> >
> >
> >salaza11 at 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>
> >salaza11 at 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>
> >salaza11 at 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>
> >salaza11 at 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
salaza11 at illinois.edu
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