PETSC_EXTERN void PETSC_STDCALL dmdasetblockfills_(DM da, PetscInt *dfill, PetscInt *ofill, int *__ierr ){
*__ierr = DMDASetBlockFills(
(DM)PetscToPointer((da) ),dfill,ofill);
}
int main(int argc,char **argv)
{
TS ts; /* nonlinear solver */
Vec C; /* solution */
PetscErrorCode ierr;
DM da; /* manages the grid data */
AppCtx ctx; /* holds problem specific paramters */
PetscInt He,dof = 3*N+N*N,*ofill;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize program
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
PetscInitialize(&argc,&argv,(char *)0,help);
PetscFunctionBeginUser;
ctx.noreactions = PETSC_FALSE;
ctx.nodissociations = PETSC_FALSE;
ierr = PetscOptionsHasName(PETSC_NULL,"-noreactions",&ctx.noreactions);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-nodissociations",&ctx.nodissociations);CHKERRQ(ierr);
ctx.HeDiffusion[1] = 1000*2.95e-4; /* From Tibo's notes times 1,000 */
ctx.HeDiffusion[2] = 1000*3.24e-4;
ctx.HeDiffusion[3] = 1000*2.26e-4;
ctx.HeDiffusion[4] = 1000*1.68e-4;
ctx.HeDiffusion[5] = 1000*5.20e-5;
ctx.VDiffusion[1] = 1000*2.71e-3;
ctx.IDiffusion[1] = 1000*2.13e-4;
ctx.forcingScale = 100.; /* made up numbers */
ctx.reactionScale = .001;
ctx.dissociationScale = .0001;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create distributed array (DMDA) to manage parallel grid and vectors
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMDACreate1d(PETSC_COMM_WORLD, DMDA_BOUNDARY_MIRROR,-8,dof,1,PETSC_NULL,&da);CHKERRQ(ierr);
/* The only spatial coupling in the Jacobian (diffusion) is for the first 5 He, the first V, and the first I.
The ofill (thought of as a dof by dof 2d (row-oriented) array represents the nonzero coupling between degrees
of freedom at one point with degrees of freedom on the adjacent point to the left or right. A 1 at i,j in the
ofill array indicates that the degree of freedom i at a point is coupled to degree of freedom j at the
adjacent point. In this case ofill has only a few diagonal entries since the only spatial coupling is regular diffusion. */
ierr = PetscMalloc(dof*dof*sizeof(PetscInt),&ofill);CHKERRQ(ierr);
ierr = PetscMemzero(ofill,dof*dof*sizeof(PetscInt));CHKERRQ(ierr);
for (He=0; He<PetscMin(N,5); He++) ofill[He*dof + He] = 1; ofill[N*dof + N] = ofill[2*N*dof + 2*N] = 1;
ierr = DMDASetBlockFills(da,PETSC_NULL,ofill);CHKERRQ(ierr);
ierr = PetscFree(ofill);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Extract global vector from DMDA to hold solution
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMCreateGlobalVector(da,&C);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr);
ierr = TSSetDM(ts,da);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,PETSC_NULL,IFunction,&ctx);CHKERRQ(ierr);
ierr = TSSetSolution(ts,C);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set solver options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetInitialTimeStep(ts,0.0,.001);CHKERRQ(ierr);
ierr = TSSetDuration(ts,100,50.0);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = MyMonitorSetUp(ts);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = InitialConditions(da,C);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the ODE system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSolve(ts,C);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecDestroy(&C);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
PetscFunctionReturn(0);
}
