PETSC_EXTERN void PETSC_STDCALL tspseudosettimestepincrement_(TS ts,PetscReal *inc, int *__ierr ){
*__ierr = TSPseudoSetTimeStepIncrement(
(TS)PetscToPointer((ts) ),*inc);
}
int main(int argc, char **argv)
{
TS ts; /* time-stepping context */
Vec x; /* State vector */
Mat J; /* Jacobian matrix */
AppCtx user; /* user-defined context */
PetscErrorCode ierr;
PetscReal ftime;
PetscInt its;
PetscMPIInt size;
PetscInitialize(&argc, &argv, NULL, help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);
if(size != 1) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_SUP, "This is a uniprocessor example only");
/*
* Allow user to set the grid dimensions and the equations parameters
*/
user.nb_cells = 50;
user.alpha = 10.;
user.beta = 1.;
user.rho_a = 1.;
user.rho_h = 2.;
user.mu_a = 2.;
user.mu_h = 3.;
user.D_a = 0.;
user.D_h = 30.;
ierr = PetscOptionsBegin(PETSC_COMM_WORLD, "", "Problem settings", "PROBLEM");
ierr = PetscOptionsInt("-nb_cells", "Number of cells", "ex42.c",user.nb_cells, &user.nb_cells,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-alpha", "Autocatalysis factor", "ex42.c",user.alpha, &user.alpha,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-beta", "Inhibition factor", "ex42.c",user.beta, &user.beta,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-rho_a", "Default production of the activator", "ex42.c",user.rho_a, &user.rho_a,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-mu_a", "Degradation rate of the activator", "ex42.c",user.mu_a, &user.mu_a,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-D_a", "Diffusion rate of the activator", "ex42.c",user.D_a, &user.D_a,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-rho_h", "Default production of the inhibitor", "ex42.c",user.rho_h, &user.rho_h,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-mu_h", "Degradation rate of the inhibitor", "ex42.c",user.mu_h, &user.mu_h,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-D_h", "Diffusion rate of the inhibitor", "ex42.c",user.D_h, &user.D_h,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
ierr = PetscPrintf(PETSC_COMM_WORLD, "nb_cells: %D\n", user.nb_cells);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "alpha: %5.5g\n", user.alpha);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "beta: %5.5g\n", user.beta);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "rho_a: %5.5g\n", user.rho_a);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "mu_a: %5.5g\n", user.mu_a);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "D_a: %5.5g\n", user.D_a);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "rho_h: %5.5g\n", user.rho_h);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "mu_h: %5.5g\n", user.mu_h);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "D_h: %5.5g\n", user.D_h);CHKERRQ(ierr);
/*
* Create vector to hold the solution
*/
ierr = VecCreateSeq(PETSC_COMM_WORLD, 2*user.nb_cells, &x);CHKERRQ(ierr);
/*
* Create time-stepper context
*/
ierr = TSCreate(PETSC_COMM_WORLD, &ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts, TS_NONLINEAR);CHKERRQ(ierr);
/*
* Tell the time-stepper context where to compute the solution
*/
ierr = TSSetSolution(ts, x);CHKERRQ(ierr);
/*
* Allocate the jacobian matrix
*/
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD, 2*user.nb_cells, 2*user.nb_cells, 4, 0, &J);CHKERRQ(ierr);
/*
* Provide the call-back for the non-linear function we are evaluating.
*/
ierr = TSSetRHSFunction(ts, NULL, RHSFunction, &user);CHKERRQ(ierr);
/*
* Set the Jacobian matrix and the function user to compute Jacobians
*/
ierr = TSSetRHSJacobian(ts, J, J, RHSJacobian, &user);CHKERRQ(ierr);
/*
* Set the function checking the domain
*/
ierr = TSSetFunctionDomainError(ts, &DomainErrorFunction);CHKERRQ(ierr);
/*
* Initialize the problem with random values
*/
ierr = FormInitialState(x, &user);CHKERRQ(ierr);
/*
* Read the solver type from options
*/
ierr = TSSetType(ts, TSPSEUDO);CHKERRQ(ierr);
/*
* Set a large number of timesteps and final duration time to insure
* convergenge to steady state
*/
ierr = TSSetDuration(ts, 5000, 1e12);
/*
* Set a larger number of potential errors
*/
ierr = TSSetMaxStepRejections(ts, 50);CHKERRQ(ierr);
/*
* Also start with a very small dt
*/
ierr = TSSetTimeStep(ts, 0.05);CHKERRQ(ierr);
/*
* Set a larger time step increment
*/
ierr = TSPseudoSetTimeStepIncrement(ts, 1.5);CHKERRQ(ierr);
/*
* Let the user personalise TS
*/
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
/*
* Set the context for the time stepper
*/
ierr = TSSetApplicationContext(ts, &user);CHKERRQ(ierr);
/*
* Setup the time stepper, ready for evaluation
*/
ierr = TSSetUp(ts);CHKERRQ(ierr);
/*
* Perform the solve.
*/
ierr = TSSolve(ts, x);CHKERRQ(ierr);
ierr = TSGetSolveTime(ts, &ftime);CHKERRQ(ierr);
ierr = TSGetTimeStepNumber(ts,&its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of time steps = %D, final time: %4.2e\nResult:\n\n", its, (double)ftime);CHKERRQ(ierr);
ierr = PrintSolution(x, &user);CHKERRQ(ierr);
/*
* Free the data structures
*/
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
