I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. The solution from TSStep is checked for positivity of densities and temperatures.
From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect?
Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd6de787a4fc942f0159708db1127f6c4%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122635595464947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=M7B%2FUuBCftN%2BKwfQYhDocIr5WFpJPn%2BHJVjt%2BmRoU3k%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd6de787a4fc942f0159708db1127f6c4%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122635595464947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=M7B%2FUuBCftN%2BKwfQYhDocIr5WFpJPn%2BHJVjt%2BmRoU3k%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- 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 https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd6de787a4fc942f0159708db1127f6c4%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122635595464947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=S5hErS8YFvtxln1LR%2FdZxBEqNxonH28eUraClfSrx4Q%3D&reserved=0>