int main(int argc,char **argv)
{
PetscFunctionList plist = NULL;
char pname[256];
TS ts; /* nonlinear solver */
Vec x,r; /* solution, residual vectors */
Mat A; /* Jacobian matrix */
Problem problem;
PetscBool use_monitor;
PetscInt steps,maxsteps = 1000,nonlinits,linits,snesfails,rejects;
PetscReal ftime;
MonitorCtx mon;
PetscErrorCode ierr;
PetscMPIInt size;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize program
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");
/* Register the available problems */
ierr = PetscFunctionListAdd(&plist,"rober",&RoberCreate);CHKERRQ(ierr);
ierr = PetscFunctionListAdd(&plist,"ce",&CECreate);CHKERRQ(ierr);
ierr = PetscFunctionListAdd(&plist,"orego",&OregoCreate);CHKERRQ(ierr);
ierr = PetscStrcpy(pname,"ce");CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set runtime options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Timestepping benchmark options","");CHKERRQ(ierr);
{
ierr = PetscOptionsFList("-problem_type","Name of problem to run","",plist,pname,pname,sizeof(pname),NULL);CHKERRQ(ierr);
use_monitor = PETSC_FALSE;
ierr = PetscOptionsBool("-monitor_error","Display errors relative to exact solutions","",use_monitor,&use_monitor,NULL);CHKERRQ(ierr);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
/* Create the new problem */
ierr = PetscNew(&problem);CHKERRQ(ierr);
problem->comm = MPI_COMM_WORLD;
{
PetscErrorCode (*pcreate)(Problem);
ierr = PetscFunctionListFind(plist,pname,&pcreate);CHKERRQ(ierr);
if (!pcreate) SETERRQ1(PETSC_COMM_SELF,1,"No problem '%s'",pname);
ierr = (*pcreate)(problem);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create necessary matrix and vectors
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,problem->n,problem->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatGetVecs(A,&x,NULL);CHKERRQ(ierr);
ierr = VecDuplicate(x,&r);CHKERRQ(ierr);
mon.comm = PETSC_COMM_WORLD;
mon.problem = problem;
ierr = VecDuplicate(x,&mon.x);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSROSW);CHKERRQ(ierr); /* Rosenbrock-W */
ierr = TSSetIFunction(ts,NULL,problem->function,problem->data);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,A,A,problem->jacobian,problem->data);CHKERRQ(ierr);
ierr = TSSetDuration(ts,maxsteps,problem->final_time);CHKERRQ(ierr);
ierr = TSSetMaxStepRejections(ts,10);CHKERRQ(ierr);
ierr = TSSetMaxSNESFailures(ts,-1);CHKERRQ(ierr); /* unlimited */
if (use_monitor) {
ierr = TSMonitorSet(ts,&MonitorError,&mon,NULL);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = (*problem->solution)(0,x,problem->data);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,.001);CHKERRQ(ierr);
ierr = TSSetSolution(ts,x);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set runtime options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSolve(ts,x);CHKERRQ(ierr);
ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);
ierr = TSGetSNESFailures(ts,&snesfails);CHKERRQ(ierr);
ierr = TSGetStepRejections(ts,&rejects);CHKERRQ(ierr);
ierr = TSGetSNESIterations(ts,&nonlinits);CHKERRQ(ierr);
ierr = TSGetKSPIterations(ts,&linits);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"steps %D (%D rejected, %D SNES fails), ftime %G, nonlinits %D, linits %D\n",steps,rejects,snesfails,ftime,nonlinits,linits);CHKERRQ(ierr);
if (problem->hasexact) {
ierr = MonitorError(ts,steps,ftime,x,&mon);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = VecDestroy(&mon.x);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
if (problem->destroy) {
ierr = (*problem->destroy)(problem);CHKERRQ(ierr);
}
ierr = PetscFree(problem);CHKERRQ(ierr);
ierr = PetscFunctionListDestroy(&plist);CHKERRQ(ierr);
ierr = PetscFinalize();
PetscFunctionReturn(0);
}
void PETSC_STDCALL tssetmaxsteprejections_(TS ts,PetscInt *rejects, int *__ierr ){
*__ierr = TSSetMaxStepRejections(
(TS)PetscToPointer((ts) ),*rejects);
}
int main(int argc,char **argv)
{
TS ts; /* ODE integrator */
Vec U; /* solution */
Mat A; /* Jacobian matrix */
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt n = 4;
AppCtx ctx;
PetscScalar *u;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize program
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create necessary matrix and vectors
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatCreateVecs(A,&U,NULL);CHKERRQ(ierr);
ctx.k1 = 1.0e-5;
ctx.k2 = 1.0e5;
ctx.k3 = 1.0e-16;
ctx.sigma2 = 1.0e6;
ierr = VecDuplicate(U,&ctx.initialsolution);CHKERRQ(ierr);
ierr = VecGetArray(ctx.initialsolution,&u);CHKERRQ(ierr);
u[0] = 0.0;
u[1] = 1.3e8;
u[2] = 5.0e11;
u[3] = 8.0e11;
ierr = VecRestoreArray(ctx.initialsolution,&u);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSROSW);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,(TSIFunction) IFunction,&ctx);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,A,A,(TSIJacobian)IJacobian,&ctx);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = Solution(ts,0,U,&ctx);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,4.0*3600,1.0);CHKERRQ(ierr);
ierr = TSSetSolution(ts,U);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set solver options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetDuration(ts,1000000,518400.0);CHKERRQ(ierr);
ierr = TSSetMaxStepRejections(ts,100);CHKERRQ(ierr);
ierr = TSSetMaxSNESFailures(ts,-1);CHKERRQ(ierr); /* unlimited */
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSolve(ts,U);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecDestroy(&ctx.initialsolution);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&U);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = PetscFinalize();
PetscFunctionReturn(0);
}
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;
}
