ok. I tried. Seems there is no effect. ./my-moose-project -i input.i -snes_type test -mat_mffd_umin 1.e-10 -snes_test_display > out
Also, the webpage says: *-mat_mffd_unim <umin> *I am not quite sure if 'unim' is a typo. I tried both 'umin' and 'unim' anyway. Ling On Tue, Dec 11, 2012 at 3:50 PM, Matthew Knepley <knepley at gmail.com> wrote: > 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 > -------------- next part -------------- An HTML attachment was scrubbed... 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