[petsc-users] using '-snes_type test' to test my coded Jacobian

[Zou (Non-US), Ling]

Thank you Matt. I am working under MOOSE framework, so I am afraid I am not
able to do it alone. I will seek help from them.

Thanks

Ling

On Wed, Sep 19, 2012 at 2:35 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Wed, Sep 19, 2012 at 3:34 PM, Zou (Non-US), Ling <ling.zou at inl.gov>wrote:
>
>> ==================================================
>> Framework Information:
>> SVN Revision:            13656
>> PETSc Version:           3.1.0
>> Current Time:            Wed Sep 19 14:17:01 2012
>> Executable Timestamp:    Wed Sep 19 14:14:46 2012
>> ==================================================
>>
>> I believe my version is 3.1.0.
>>
>
> If you upgrade to the latest release, it will work.
>
>    Matt
>
>
>> Ling
>>
>>
>>
>> On Wed, Sep 19, 2012 at 2:31 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:
>>
>>> Are you using an older version of PETSc?
>>>
>>>
>>> On Wed, Sep 19, 2012 at 2:56 PM, Zou (Non-US), Ling <ling.zou at inl.gov>wrote:
>>>
>>>> No Jacobian output showed when I did this,
>>>>
>>>> ./my-project-opt -i input.i -snes_compare_explicit
>>>>
>>>> Any suggestion?
>>>>
>>>> Ling
>>>>
>>>>
>>>>
>>>> On Wed, Sep 19, 2012 at 1:12 PM, Zou (Non-US), Ling <ling.zou at inl.gov>wrote:
>>>>
>>>>>
>>>>>
>>>>> On Wed, Sep 19, 2012 at 1:03 PM, Jed Brown <jedbrown at mcs.anl.gov>wrote:
>>>>>
>>>>>> On Wed, Sep 19, 2012 at 1:54 PM, Zou (Non-US), Ling <ling.zou at inl.gov
>>>>>> > wrote:
>>>>>>
>>>>>>> Dear Matt,
>>>>>>>
>>>>>>> Thanks again for helping me on the '-snes_type test' issue. This is
>>>>>>> a great tool which helped us make really good progress recently.
>>>>>>>
>>>>>>> I have couple of more questions about the '-snes_type test'. From my
>>>>>>> understanding, this finite difference method is based on a tiny
>>>>>>> perturbation from a base solution vector. This base solution vector, from
>>>>>>> my observation, seems to be [1, 1, 1, ....].  However, this solution vector
>>>>>>> sometimes is very far from real physics, which causes issue, for example a
>>>>>>> dependent pressure variable get negative value.
>>>>>>>
>>>>>>> I wonder,
>>>>>>> 1), if this [1, 1, 1, ...] base solution vector is always used
>>>>>>> during the real simulation, for example when using the finite difference
>>>>>>> preconditioner. Or this base solution vector will change as solution gets
>>>>>>> updated?
>>>>>>>
>>>>>>
>>>>>> -snes_type test tries three different states: your user-defined
>>>>>> state, then constant -1.0, then constant +1.0. It does not solve the system
>>>>>> so you can't continue stepping, but you can just look at the result from
>>>>>> the first test.
>>>>>>
>>>>>
>>>>> Ahhh....... I see, that's why I always see three comparisons there.
>>>>> The first one should help me better when dealing with real simulation case.
>>>>>
>>>>>>
>>>>>>
>>>>>>> 2), is it possible to choose a different base solution, for example,
>>>>>>> [1000, 1000, 1000, 10, 10, 10, 1.e9, 1.e9, 1.e9] as the base solution
>>>>>>> vector when using the '-snes_type test'  option to test my hand-coded
>>>>>>> Jacobian.
>>>>>>>
>>>>>>
>>>>>> You can also use -snes_compare_explicit which shows the matrix (only
>>>>>> linearized around your actual state) and actually solves the system. There
>>>>>> is also -snes_compare_explicit_draw. If you know that you preallocated
>>>>>> correctly, -snes_compare_coloring is better. Details here.
>>>>>>
>>>>>>
>>>>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/SNES/SNESComputeJacobian.html
>>>>>>
>>>>>
>>>>> This is something new to me. I'd take a look at the link. Thanks a
>>>>> lot, Jed.
>>>>>
>>>>> Best,
>>>>>
>>>>> 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
>
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