[petsc-users] how to control snes_mf_operator

[Zou (Non-US), Ling]

Hmm... I have an 'approximated' analytical Jacobian to compare. And I did
this:

./my-moose-project -i input.i -snes_type test -snes_test_display > out

I actually found out that the PETSc provided FD Jacobian gives 'nan'
numbers, while my approximated Jacobian does not give 'nan' at the same
positions.

As we discussed in the previous emails, the perturbation on U0 is too
large, which makes 'nan' appear in the FD Jacobians. So....I am trying to
use a smaller '-mat_mffd_err <number here>', to see if I could get an easy
fix by now, like this,

./my-moose-project -i input.i -snes_type test -md_mffd_err 1.e-10
-snes_test_display > out

seems not working :-(
no matter what number I give to -md_mffd_err, the print out results seem
not changed.

But of course, non-dimensionalization might be the ultimate solution.

Ling

On Tue, Dec 11, 2012 at 3:29 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Dec 11, 2012 at 2:19 PM, Zou (Non-US), Ling <ling.zou at inl.gov>
> wrote:
> > Matt, one more question.
> >
> > Can I combine the options
> > -snes_type test
> > and
> > -mat_mffd_err 1.e-10
> > to see the effect?
>
> I do not understand your question. test does compare the analytic and
> FD Jacobian
> actions, but I thought you did not have an analytic action.
>
>    Matt
>
> > Best,
> >
> > Ling
> >
> >
> >
> > On Tue, Dec 11, 2012 at 2:47 PM, Zou (Non-US), Ling <ling.zou at inl.gov>
> > wrote:
> >>
> >> thank you Matt. I will try to figure it out. Non-dimensionalization is
> >> certainly something worth to try.
> >>
> >> Best,
> >>
> >> Ling
> >>
> >>
> >> On Tue, Dec 11, 2012 at 2:41 PM, Matthew Knepley <knepley at gmail.com>
> >> wrote:
> >>>
> >>> On Tue, Dec 11, 2012 at 1:40 PM, Matthew Knepley <knepley at gmail.com>
> >>> wrote:
> >>> > On Tue, Dec 11, 2012 at 1:34 PM, Zou (Non-US), Ling <
> ling.zou at inl.gov>
> >>> > wrote:
> >>> >> Dear All,
> >>> >>
> >>> >> I have recently had an issue using snes_mf_operator. I've tried to
> >>> >> figure it
> >>> >> out from PETSc manual and PETSc website but didn't get any luck, so
> I
> >>> >> submit
> >>> >> my question here and hope some one could help me out.
> >>> >>
> >>> >> (1)
> >>> >> =================================================================
> >>> >> A little bit background here: my problem has 7 variables, i.e.,
> >>> >>
> >>> >> U = [U0, U1, U2, U3, U4, U5, U6]
> >>> >>
> >>> >> U0 is in the order of 1.
> >>> >> U1, U2, U4 and U5 in the oder of 100.
> >>> >> U3 and U6 are in the order of 1.e8.
> >>> >>
> >>> >> I believe this should be quite common for most PETSc users.
> >>> >>
> >>> >> (2)
> >>> >> =================================================================
> >>> >> My problem here is, U0, by its physical meaning, has to be limited
> >>> >> between 0
> >>> >> and 1. When PETSc starts to perturb the initial solution of U
> (which I
> >>> >> believe properly set) to approximate the operation of J (dU), the U0
> >>> >> get a
> >>> >> perturbation size in the order of 100, which causes problem as U0
> has
> >>> >> to be
> >>> >> smaller than 1.
> >>> >>
> >>> >> From my observation, this same perturbation size, say eps, is
> applied
> >>> >> on all
> >>> >> U0, U1, U2, etc. <=== Is this the default setting?
> >>> >> I also guess that this eps, in the order of 100, is determined from
> my
> >>> >> initial solution vector and other related PETSc parameters.  <=== Is
> >>> >> my
> >>> >> guessing right?
> >>> >>
> >>> >> (3)
> >>> >> =================================================================
> >>> >> My question: I'd like to avoid a perturbation size ~100 on U0,
> i.e., I
> >>> >> have
> >>> >> to limit it to be ~0.01 (or some small number) to avoid the U0 > 1
> >>> >> situation. Is there any way to control that?
> >>> >> Or, is there any advanced option to control the perturbation size on
> >>> >> different variables when using snes_mf_operator?
> >>> >
> >>> > Here is a description of the algorithm for calculating h. It seems to
> >>> > me a better way to do this
> >>> > is to non-dimensionalize first.
> >>>
> >>> I forgot the URL:
> >>>
> >>>
> http://www.mcs.anl.gov/petsc/petsc-dev/docs/manualpages/Mat/MatCreateMFFD.html#MatCreateMFFD
> >>>
> >>>    Matt
> >>>
> >>> >    Matt
> >>> >
> >>> >>
> >>> >> Hope my explanation is clear. Please let me know if it is not.
> >>> >>
> >>> >>
> >>> >> Best Regards,
> >>> >>
> >>> >> Ling
> >>> >>
> >>> >
> >>> >
> >>> >
> >>> > --
> >>> > 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
>
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