[petsc-users] Finite difference Jacobian in TS context

[Oleksandr Koshkarov]

Hello all,

Sorry for stupid question, but do "SNESComputeJacobianDefault" or 
"SNESComputeJacobianDefaultColor" make Jacobian matrix free? (I was 
thinking so from the start... but now it seems I am totally wrong)

Best regards,

Oleksandr.


On 04/28/2018 07:20 PM, Smith, Barry F. wrote:
> ~/Src/petsc/src/ts/examples/tutorials
> $ grep SNESComputeJacobianDefaultColor *.c
> ex10.c:    ierr = SNESSetJacobian(snes,A,B,SNESComputeJacobianDefaultColor,0);CHKERRQ(ierr);
> ex15.c:      ierr = SNESSetJacobian(snes,Jmf,J,SNESComputeJacobianDefaultColor,0);CHKERRQ(ierr);
> ex17.c:    ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,0);CHKERRQ(ierr);
>
>     I don't think you need to explicitly create the MatFDColoring object.
>
>     Please take a look at ex15.c and see if you can get it working like that example. If that doesn't work let us know and we can take a closer look at it.
>
>
>     Barry
>
>
>> On Apr 28, 2018, at 8:05 PM, Oleksandr Koshkarov <olk548 at mail.usask.ca> wrote:
>>
>> Hello All,
>>
>> I hope someone can help :) I think I am doing something wrong, but cannot understand what. I have a huge time dependent system with 3d DMDA data structure and I am evolving it with explicit Runge-Kutta by using TS and basically only using "TSSetRHSFunction". Now I want to repeat it with implicit time stepper (for now Crank-Nicolson) and I am trying to provide finite difference Jacobian and I am failing miserably. I also cannot find appropriate example in PETSc tutorial (if you can point me to working example, it would be great).
>>
>> Here is my best attempt (what wrong with it?):
>>
>>    DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC,
>>             DMDA_STENCIL_STAR,
>>             NX, NY, NZ,
>>             PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE,
>>             2*3+NC*NS,
>>             1,
>>             NULL,  NULL, NULL,  &da);
>>    DMSetUp(da);
>>    DMCreateGlobalVector(da,&x);
>>    TSCreate(PETSC_COMM_WORLD,&ts);
>>    TSSetProblemType(ts,TS_NONLINEAR);
>>    TSSetRHSFunction(ts,NULL,compute_RHS,NULL);
>>    TSSetMaxTime(ts,T_FINAL);
>>    TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);
>>    TSSetDM(ts,da);
>>    TSSetType(ts,TSCN); //it works with: TSSetType(ts,TSRK);
>>    set_IC(da,x);
>>    TSSetTimeStep(ts,DT);
>>    TSSetSolution(ts,x);
>>
>>    TSGetSNES(ts,&snes);
>>    SNESGetKSP(snes,&ksp);
>>    KSPGetPC(ksp,&pc);
>>    PCSetType(pc,PCNONE);
>>
>>    DMSetMatType(da,MATAIJ);
>>    DMCreateMatrix(da,&J);
>>    ISColoring iscoloring;
>>    MatFDColoring  matfdcoloring;
>>    DMCreateColoring(da,IS_COLORING_GLOBAL,&iscoloring);
>>    MatFDColoringCreate(J,iscoloring,&matfdcoloring);
>>
>>    MatFDColoringSetType(matfdcoloring,MATMFFD_DS);
>>
>> // I think I do something wrong in the following 3 lines
>>
>>    PetscErrorCode (*temp_f)(SNES,Vec,Vec,void*);
>>    SNESGetFunction(snes,NULL,&temp_f,NULL);
>>    MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))temp_f,NULL);
>>
>>    MatFDColoringSetUp(J,iscoloring,matfdcoloring);
>>
>> SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring);
>>    ISColoringDestroy(&iscoloring);
>>
>>    TSSolve(ts,x);
>>
>> Thank you,
>>
>> Oleksandr Koshkarov.
>>