static PetscErrorCode FormMoleFraction(UserLGCtx *ctx,Vec massf,Vec *molef)
{
User user = ctx->user;
PetscErrorCode ierr;
PetscReal *M,tM=0;
PetscInt i,n = user->Nspec+1;
PetscScalar *mof;
const PetscScalar **maf;
PetscFunctionBegin;
ierr = VecCreateSeq(PETSC_COMM_SELF,n,molef);CHKERRQ(ierr);
ierr = PetscMalloc1(user->Nspec,&M);CHKERRQ(ierr);
TC_getSmass(user->Nspec, M);
ierr = DMDAVecGetArrayDOFRead(user->dm,massf,&maf);CHKERRQ(ierr);
ierr = VecGetArray(*molef,&mof);CHKERRQ(ierr);
mof[0] = maf[ctx->cell][0]; /* copy over temperature */
for (i=1; i<n; i++) tM += maf[ctx->cell][i]/M[i-1];
for (i=1; i<n; i++) {
mof[i] = maf[ctx->cell][i]/(M[i-1]*tM);
}
ierr = DMDAVecRestoreArrayDOFRead(user->dm,massf,&maf);CHKERRQ(ierr);
ierr = VecRestoreArray(*molef,&mof);CHKERRQ(ierr);
ierr = PetscFree(M);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Applies the second order centered difference diffusion operator on a one dimensional periodic domain
*/
static PetscErrorCode FormDiffusionFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
{
User user = (User)ptr;
PetscErrorCode ierr;
PetscScalar **f;
const PetscScalar **x;
DM dm;
PetscInt i,xs,xm,j,dof;
Vec Xlocal;
PetscReal idx;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = DMDAGetInfo(dm,NULL,NULL,NULL,NULL,NULL,NULL,NULL,&dof,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&Xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xlocal);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOFRead(dm,Xlocal,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(dm,F,&f);CHKERRQ(ierr);
ierr = DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
idx = 1.0*user->diffus/user->dx;
for (i=xs; i<xs+xm; i++) {
for (j=0; j<dof; j++) {
f[i][j] += idx*(x[i+1][j] - 2.0*x[i][j] + x[i-1][j]);
}
}
ierr = DMDAVecRestoreArrayDOFRead(dm,Xlocal,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(dm,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xlocal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode FormRHSFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
{
User user = (User)ptr;
PetscErrorCode ierr;
PetscScalar **f;
const PetscScalar **x;
DM dm;
PetscInt i,xs,xm;
PetscFunctionBeginUser;
if (user->reactions) {
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOFRead(dm,X,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(dm,F,&f);CHKERRQ(ierr);
ierr = DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
for (i=xs; i<xs+xm; i++) {
ierr = PetscMemcpy(user->tchemwork,x[i],(user->Nspec+1)*sizeof(x[xs][0]));CHKERRQ(ierr);
user->tchemwork[0] *= user->Tini; /* Dimensionalize */
ierr = TC_getSrc(user->tchemwork,user->Nspec+1,f[i]);TCCHKERRQ(ierr);
f[i][0] /= user->Tini; /* Non-dimensionalize */
}
ierr = DMDAVecRestoreArrayDOFRead(dm,X,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(dm,F,&f);CHKERRQ(ierr);
} else {
ierr = VecZeroEntries(F);CHKERRQ(ierr);
}
if (user->diffusion) {
ierr = FormDiffusionFunction(ts,t,X,F,ptr);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode FormRHSJacobian(TS ts,PetscReal t,Vec X,Mat Amat,Mat Pmat,void *ptr)
{
User user = (User)ptr;
PetscErrorCode ierr;
const PetscScalar **x;
PetscInt M = user->Nspec+1,i,j,xs,xm;;
DM dm;
PetscFunctionBeginUser;
if (user->reactions) {
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = MatZeroEntries(Pmat);CHKERRQ(ierr);
ierr = MatSetOption(Pmat,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr);
ierr = MatSetOption(Pmat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOFRead(dm,X,&x);CHKERRQ(ierr);
ierr = DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
for (i=xs; i<xs+xm; i++) {
ierr = PetscMemcpy(user->tchemwork,x[i],(user->Nspec+1)*sizeof(x[xs][0]));CHKERRQ(ierr);
user->tchemwork[0] *= user->Tini; /* Dimensionalize temperature (first row) because that is what Tchem wants */
ierr = TC_getJacTYN(user->tchemwork,user->Nspec,user->Jdense,1);CHKERRQ(ierr);
for (j=0; j<M; j++) user->Jdense[j + 0*M] /= user->Tini; /* Non-dimensionalize first column */
for (j=0; j<M; j++) user->Jdense[0 + j*M] /= user->Tini; /* Non-dimensionalize first row */
for (j=0; j<M; j++) user->rows[j] = i*M+j;
ierr = MatSetValues(Pmat,M,user->rows,M,user->rows,user->Jdense,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = DMDAVecRestoreArrayDOFRead(dm,X,&x);CHKERRQ(ierr);
ierr = MatAssemblyBegin(Pmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Pmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
} else {
ierr = MatZeroEntries(Pmat);CHKERRQ(ierr);
}
if (user->diffusion) {
ierr = FormDiffusionJacobian(ts,t,X,Amat,Pmat,ptr);CHKERRQ(ierr);
}
if (Amat != Pmat) {
ierr = MatAssemblyBegin(Amat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Amat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscInt M = 10,N = 8,dof=1,s=1,bx=0,by=0,i,n,j,k,m,wrap,xs,ys;
PetscErrorCode ierr;
DM da,dac;
PetscViewer viewer;
Vec local,global,coors;
PetscScalar ***xy,***aglobal;
PetscDraw draw;
char fname[16];
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
/* Create viewers */
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"",PETSC_DECIDE,PETSC_DECIDE,600,200,&viewer);CHKERRQ(ierr);
ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
ierr = PetscDrawSetDoubleBuffer(draw);CHKERRQ(ierr);
/* Read options */
ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-dof",&dof,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-s",&s,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-periodic_x",&wrap,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-periodic_y",&wrap,NULL);CHKERRQ(ierr);
/* Create distributed array and get vectors */
ierr = DMDACreate2d(PETSC_COMM_WORLD,(DMBoundaryType)bx,(DMBoundaryType)by,DMDA_STENCIL_BOX,M,N,PETSC_DECIDE,PETSC_DECIDE,dof,s,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,0.0);CHKERRQ(ierr);
for (i=0; i<dof; i++) {
sprintf(fname,"Field %d",(int)i);
ierr = DMDASetFieldName(da,i,fname);CHKERRQ(ierr);
}
ierr = DMView(da,viewer);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&coors);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da,&dac);CHKERRQ(ierr);
/* Set values into global vectors */
ierr = DMDAVecGetArrayDOFRead(dac,coors,&xy);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,global,&aglobal);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,&ys,0,&m,&n,0);CHKERRQ(ierr);
for (k=0; k<dof; k++) {
for (j=ys; j<ys+n; j++) {
for (i=xs; i<xs+m; i++) {
aglobal[j][i][k] = PetscSinScalar(2.0*PETSC_PI*(k+1)*xy[j][i][0]);
}
}
}
ierr = DMDAVecRestoreArrayDOF(da,global,&aglobal);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOFRead(dac,coors,&xy);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = VecSet(global,0.0);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da,local,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,local,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecView(global,viewer);CHKERRQ(ierr);
/* Free memory */
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}