[petsc-users] Finite difference Jacobian in TS context

[Smith, Barry F.]

~/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.
>