[petsc-users] how to control snes_mf_operator

[Matthew Knepley]

On Tue, Dec 11, 2012 at 2:40 PM, Zou (Non-US), Ling <ling.zou at inl.gov> wrote:
> 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,

I don't think 'err' has anything to do with it. If you read the page I
mailed you, I
believe umin can be made very small.

   Matt

> ./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
>
>



--
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