[petsc-users] DMPlex with spring elements

[Matthew Knepley]

On Tue, Sep 30, 2014 at 11:22 AM, Abhyankar, Shrirang G. <
abhyshr at mcs.anl.gov> wrote:

>
> From:  Miguel Angel Salazar de Troya <salazardetroya at gmail.com>
> Date:  Mon, 29 Sep 2014 16:55:14 -0500
> To:  Shri <abhyshr at mcs.anl.gov>
> Cc:  "petsc-users at mcs.anl.gov" <petsc-users at 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.
>

This depends on the discretization. In FD, you do not modify ghosts, but in
FEM you do.

   Matt


> Shri
>
> >
> >Thanks
> >Miguel
> >
> >
> >
> >On Fri, Sep 26, 2014 at 12:33 PM, Miguel Angel Salazar de Troya
> ><salazardetroya at gmail.com> wrote:
> >
> >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/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 <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
> >
> >
> >
> >
> >
> >
> >
> >
> >--
> >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
>
>


-- 
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
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