static PetscErrorCode FormFunction_All(SNES snes,Vec X,Vec F,void *ctx)
{
User user = (User)ctx;
DM dau,dak;
DMDALocalInfo infou,infok;
PetscScalar *u,*k;
PetscScalar *fu,*fk;
PetscErrorCode ierr;
Vec Uloc,Kloc,Fu,Fk;
PetscFunctionBeginUser;
ierr = DMCompositeGetEntries(user->pack,&dau,&dak);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dau,&infou);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dak,&infok);CHKERRQ(ierr);
ierr = DMCompositeGetLocalVectors(user->pack,&Uloc,&Kloc);CHKERRQ(ierr);
switch (user->ptype) {
case 0:
ierr = DMGlobalToLocalBegin(dau,X,INSERT_VALUES,Uloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd (dau,X,INSERT_VALUES,Uloc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dau,Uloc,&u);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dak,user->Kloc,&k);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dau,F,&fu);CHKERRQ(ierr);
ierr = FormFunctionLocal_U(user,&infou,u,k,fu);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dau,F,&fu);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dau,Uloc,&u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dak,user->Kloc,&k);CHKERRQ(ierr);
break;
case 1:
ierr = DMGlobalToLocalBegin(dak,X,INSERT_VALUES,Kloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd (dak,X,INSERT_VALUES,Kloc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dau,user->Uloc,&u);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dak,Kloc,&k);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dak,F,&fk);CHKERRQ(ierr);
ierr = FormFunctionLocal_K(user,&infok,u,k,fk);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dak,F,&fk);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dau,user->Uloc,&u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dak,Kloc,&k);CHKERRQ(ierr);
break;
case 2:
ierr = DMCompositeScatter(user->pack,X,Uloc,Kloc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dau,Uloc,&u);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dak,Kloc,&k);CHKERRQ(ierr);
ierr = DMCompositeGetAccess(user->pack,F,&Fu,&Fk);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dau,Fu,&fu);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dak,Fk,&fk);CHKERRQ(ierr);
ierr = FormFunctionLocal_U(user,&infou,u,k,fu);CHKERRQ(ierr);
ierr = FormFunctionLocal_K(user,&infok,u,k,fk);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dau,Fu,&fu);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dak,Fk,&fk);CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(user->pack,F,&Fu,&Fk);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dau,Uloc,&u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dak,Kloc,&k);CHKERRQ(ierr);
break;
}
ierr = DMCompositeRestoreLocalVectors(user->pack,&Uloc,&Kloc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode IFunction(TS ts,PetscReal t,Vec X,Vec Xdot,Vec F,void *ctx)
{
PetscErrorCode ierr;
AppCtx *user=(AppCtx*)ctx;
DM cda;
DMDACoor2d **coors;
PetscScalar **p,**f,**pdot;
PetscInt i,j;
PetscInt xs,ys,xm,ym,M,N;
Vec localX,gc,localXdot;
PetscScalar p_adv1,p_adv2,p_diff;
PetscFunctionBeginUser;
ierr = DMDAGetInfo(user->da,NULL,&M,&N,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
ierr = DMGetCoordinateDM(user->da,&cda);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&xs,&ys,0,&xm,&ym,0);CHKERRQ(ierr);
ierr = DMGetLocalVector(user->da,&localX);CHKERRQ(ierr);
ierr = DMGetLocalVector(user->da,&localXdot);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(user->da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user->da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(user->da,Xdot,INSERT_VALUES,localXdot);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user->da,Xdot,INSERT_VALUES,localXdot);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(user->da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(user->da,localX,&p);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(user->da,localXdot,&pdot);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,F,&f);CHKERRQ(ierr);
PetscScalar diffuse1,gamma;
gamma = user->D*user->ws/(2*user->H);
diffuse1 = user->lambda*user->lambda*user->q/(user->lambda*gamma+1)*(1.0 - PetscExpScalar(-t*(gamma+1.0)/user->lambda));
user->disper_coe = user->ws*user->ws/(4*user->H*user->H)*diffuse1;
for (i=xs; i < xs+xm; i++) {
for (j=ys; j < ys+ym; j++) {
ierr = adv1(p,coors[j][i].y,i,j,M,&p_adv1,user);CHKERRQ(ierr);
ierr = adv2(p,coors[j][i].x,coors[j][i].y,i,j,N,&p_adv2,user);CHKERRQ(ierr);
ierr = diffuse(p,i,j,t,&p_diff,user);CHKERRQ(ierr);
f[j][i] = -p_adv1 - p_adv2 + p_diff - pdot[j][i];
}
}
ierr = DMDAVecRestoreArrayRead(user->da,localX,&p);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(user->da,localX,&pdot);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(user->da,&localX);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(user->da,&localXdot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->da,F,&f);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(cda,gc,&coors);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormResidual(TS ts,PetscReal t,Vec U,Vec Udot,Vec R,void *user)
{
PetscFunctionBegin;
PetscErrorCode ierr;
DMDALocalInfo info;
DM dm;
Vec localU,localUdot,localR; // local versions
Field **h,**hdot,**r;
/* get the da from the snes */
ierr = TSGetDM(ts, &dm);CHKERRQ(ierr);
/* handle the vec U */
ierr = DMGetLocalVector(dm,&localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,U,INSERT_VALUES,localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,U,INSERT_VALUES,localU);CHKERRQ(ierr);
/* handle the vec Udot */
ierr = DMGetLocalVector(dm,&localUdot);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,Udot,INSERT_VALUES,localUdot);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,Udot,INSERT_VALUES,localUdot);CHKERRQ(ierr);
/* handle the vec R */
ierr = DMGetLocalVector(dm,&localR);CHKERRQ(ierr);
ierr = VecZeroEntries(localR);CHKERRQ(ierr);
/* Get the arrays from the vectors */
ierr = DMIGAVecGetArray(dm,localU,&h);CHKERRQ(ierr);
ierr = DMIGAVecGetArray(dm,localUdot,&hdot);CHKERRQ(ierr);
ierr = DMIGAVecGetArray(dm,localR,&r);CHKERRQ(ierr);
/* Grab the local info and call the local residual routine */
ierr = DMIGAGetLocalInfo(dm,&info);CHKERRQ(ierr);CHKERRQ(ierr);
ierr = FormResidualLocal(&info,t,h,hdot,r,(AppCtx *) user);CHKERRQ(ierr);
/* Restore the arrays */
ierr = DMIGAVecRestoreArray(dm,localR,&r);CHKERRQ(ierr);
ierr = DMIGAVecRestoreArray(dm,localUdot,&hdot);CHKERRQ(ierr);
ierr = DMIGAVecRestoreArray(dm,localU,&h);CHKERRQ(ierr);
/* Add contributions back to global R */
ierr = VecZeroEntries(R);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm,localR,ADD_VALUES,R);CHKERRQ(ierr); // this one adds the values
ierr = DMLocalToGlobalEnd(dm,localR,ADD_VALUES,R);CHKERRQ(ierr);
/* Restore the local vectors */
ierr = DMRestoreLocalVector(dm,&localU);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&localUdot);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&localR);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormTangent(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal shift,Mat *A,Mat *B,MatStructure *flag,void *ctx)
{
PetscFunctionBegin;
PetscErrorCode ierr;
SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "FormTangent not implemented, use -snes_mf");
DMDALocalInfo info;
DM da_dof;
Vec localU,localUdot; // local versions
Field **h,**hdot;
/* get the da from the snes */
ierr = TSGetDM(ts,(DM*)&da_dof);CHKERRQ(ierr);
/* handle the vec U */
ierr = DMGetLocalVector(da_dof,&localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da_dof,U,INSERT_VALUES,localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da_dof,U,INSERT_VALUES,localU);CHKERRQ(ierr);
/* handle the vec Udot */
ierr = DMGetLocalVector(da_dof,&localUdot);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da_dof,Udot,INSERT_VALUES,localUdot);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da_dof,Udot,INSERT_VALUES,localUdot);CHKERRQ(ierr);
/* Get the arrays from the vectors */
ierr = DMDAVecGetArray(da_dof,localU,&h);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da_dof,localUdot,&hdot);CHKERRQ(ierr);
/* Grab the local info and call the local tangent routine */
ierr = DMDAGetLocalInfo(da_dof,&info);CHKERRQ(ierr);CHKERRQ(ierr);
ierr = MatZeroEntries(*B);CHKERRQ(ierr); // pre-zero the matrix
ierr = FormTangentLocal(&info,t,h,hdot,shift,B,(AppCtx *) ctx);CHKERRQ(ierr);
ierr = MatAssemblyBegin(*B,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(*B,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
if (*A != *B) { // then we could be matrix free
ierr = MatAssemblyBegin(*A,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(*A,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
}
*flag = SAME_NONZERO_PATTERN; /* the sparsity pattern does not change */
ierr = DMDAVecRestoreArray(da_dof,localUdot,&hdot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da_dof,localU,&h);CHKERRQ(ierr);
/* Restore the arrays and local vectors */
ierr = DMRestoreLocalVector(da_dof,&localU);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da_dof,&localUdot);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
DMPlexProjectField - This projects the given function of the fields into the function space provided.
Input Parameters:
+ dm - The DM
. U - The input field vector
. funcs - The functions to evaluate, one per field
- mode - The insertion mode for values
Output Parameter:
. X - The output vector
Level: developer
.seealso: DMPlexProjectFunction(), DMPlexComputeL2Diff()
@*/
PetscErrorCode DMPlexProjectField(DM dm, Vec U, void (**funcs)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal [], PetscScalar []), InsertMode mode, Vec X)
{
Vec localX, localU;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, U, INSERT_VALUES, localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, U, INSERT_VALUES, localU);CHKERRQ(ierr);
ierr = DMPlexProjectFieldLocal(dm, localU, funcs, mode, localX);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm, localX, mode, X);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm, localX, mode, X);CHKERRQ(ierr);
if (mode == INSERT_VALUES || mode == INSERT_ALL_VALUES || mode == INSERT_BC_VALUES) {
Mat cMat;
ierr = DMGetDefaultConstraints(dm, NULL, &cMat);CHKERRQ(ierr);
if (cMat) {
ierr = DMGlobalToLocalSolve(dm, localX, X);CHKERRQ(ierr);
}
}
ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &localU);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/**
Form the time step function for the mass term
@param Vec in: (y^(n+1))
out @param Vec out: My^(n+1) - M y^(n) if timestep = 1, backward euler
will do the BDF2
**/
PetscErrorCode FormMassTimeStepFunction(User user, Algebra algebra, Vec in, Vec out, PetscBool rebuild)
{
PetscErrorCode ierr;
PetscMPIInt rank;
Vec inLocal;
PetscFunctionBegin;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = VecSet(out, 0.0);CHKERRQ(ierr);
ierr = DMGetLocalVector(user->dm, &inLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(user->dm, in, INSERT_VALUES, inLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user->dm, in, INSERT_VALUES, inLocal);CHKERRQ(ierr);
ierr = ApplyBC(user->dm, user->current_time, inLocal, user);CHKERRQ(ierr);
ierr = CaculateLocalMassFunction(user->dm, inLocal, out, user);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(user->dm, inLocal, INSERT_VALUES, in);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(user->dm, inLocal, INSERT_VALUES, in);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(user->dm, &inLocal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
This function should eventually replace:
DMDAComputeFunction() and DMDAComputeFunction1()
*/
static PetscErrorCode SNESComputeObjective_DMDA(SNES snes,Vec X,PetscReal *ob,void *ctx)
{
PetscErrorCode ierr;
DM dm;
DMSNES_DA *dmdasnes = (DMSNES_DA*)ctx;
DMDALocalInfo info;
Vec Xloc;
void *x;
PetscFunctionBegin;
PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
PetscValidHeaderSpecific(X,VEC_CLASSID,2);
PetscValidPointer(ob,3);
if (!dmdasnes->objectivelocal) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_PLIB,"Corrupt context");
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Xloc,&x);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdasnes->objectivelocal)(&info,x,ob,dmdasnes->objectivelocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = DMDAVecRestoreArray(dm,Xloc,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode SNESComputeFunction_DMLocal(SNES snes,Vec X,Vec F,void *ctx)
{
PetscErrorCode ierr;
DM dm;
DMSNES_Local *dmlocalsnes = (DMSNES_Local*)ctx;
Vec Xloc,Floc;
PetscFunctionBegin;
PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
PetscValidHeaderSpecific(X,VEC_CLASSID,2);
PetscValidHeaderSpecific(F,VEC_CLASSID,3);
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&Floc);CHKERRQ(ierr);
ierr = VecZeroEntries(Xloc);CHKERRQ(ierr);
ierr = VecZeroEntries(Floc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmlocalsnes->residuallocal)(dm,Xloc,Floc,dmlocalsnes->residuallocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = VecZeroEntries(F);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm,Floc,ADD_VALUES,F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm,Floc,ADD_VALUES,F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Floc);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xloc);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);
}
PetscErrorCode FormFunction(SNES snes, Vec X, Vec F, void *user)
{
DMDALocalInfo info;
Field **u,**fu;
PetscErrorCode ierr;
Vec localX;
DM da;
PetscFunctionBegin;
ierr = SNESGetDM(snes,(DM*)&da);CHKERRQ(ierr);
ierr = DMGetLocalVector(da,&localX);CHKERRQ(ierr);
/*
Scatter ghost points to local vector, using the 2-step process
DMGlobalToLocalBegin(), DMGlobalToLocalEnd().
*/
ierr = DMGlobalToLocalBegin(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,localX,&u);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,F,&fu);CHKERRQ(ierr);
ierr = FormFunctionLocal(&info,u,fu,user);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,localX,&u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&fu);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&localX);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode SNESComputePicardJacobian_DMDA(SNES snes,Vec X,Mat *A,Mat *B,MatStructure *mstr,void *ctx)
{
PetscErrorCode ierr;
DM dm;
DMSNES_DA *dmdasnes = (DMSNES_DA*)ctx;
DMDALocalInfo info;
Vec Xloc;
void *x;
PetscFunctionBegin;
if (!dmdasnes->jacobianplocal) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_PLIB,"Corrupt context");
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Xloc,&x);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdasnes->jacobianplocal)(&info,x,*A,*B,mstr,dmdasnes->picardlocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = DMDAVecRestoreArray(dm,Xloc,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
*mstr = SAME_NONZERO_PATTERN;
if (*A != *B) {
ierr = MatAssemblyBegin(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*
Caculate the source term of the equations, which includes all
terms except convetion term, diffusion term, and timedependent term.
*/
PetscErrorCode CaculateLocalSourceTerm(DM dm, Vec locX, Vec F, User user)
{
PetscErrorCode ierr;
DM dmGrad = user->dmGrad;
const PetscScalar *x;
PetscScalar *f;
PetscInt cStart, cell;
const PetscScalar *cellgeom;
const CellGeom *cg;
Vec locGrad, Grad;
const PetscScalar *grad;
DM dmCell;
PetscFunctionBeginUser;
ierr = VecGetDM(user->cellgeom,&dmCell);CHKERRQ(ierr);
ierr = VecGetArrayRead(locX,&x);CHKERRQ(ierr);
ierr = VecGetArray(F,&f);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, NULL);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = DMGetGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = DMGetLocalVector(dmGrad,&locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmGrad,Grad,INSERT_VALUES,locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dmGrad,Grad,INSERT_VALUES,locGrad);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = VecGetArrayRead(locGrad,&grad);CHKERRQ(ierr);
for (cell = cStart; cell < user->cEndInterior; cell++) {
PetscScalar *fref;
const PetscScalar *xref;
PetscScalar *cgrad;
ierr = DMPlexPointLocalRead(dmCell,cell,cellgeom,&cg);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm,cell,x,&xref);CHKERRQ(ierr); /*For the unkown variables*/
ierr = DMPlexPointGlobalRef(dm,cell,f,&fref);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmGrad,cell,grad,&cgrad);CHKERRQ(ierr);
// if (!fref){ PetscPrintf(PETSC_COMM_WORLD,"%d, %d\n", cell, user->cEndInterior);}
if (fref){
fref[0] += SourceRho(user, cgrad, xref, cg->centroid);/*the continuity equation*/
fref[1] += SourceU(user, cgrad, xref, cg->centroid); /*Momentum U*/
fref[2] += SourceV(user, cgrad, xref, cg->centroid); /*Momentum V*/
fref[3] += SourceW(user, cgrad, xref, cg->centroid); /*Momentum W*/
fref[4] += SourceE(user, cgrad, xref, cg->centroid);/*Energy*/
}
}
ierr = VecRestoreArrayRead(locX,&x);CHKERRQ(ierr);
ierr = VecRestoreArray(F,&f);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(locGrad,&grad);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmGrad,&locGrad);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetCoordinates1d(DM da)
{
PetscErrorCode ierr;
PetscInt i,start,m;
Vec local,global;
PetscScalar *coors,*coorslocal;
DM cda;
PetscFunctionBeginUser;
ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&global);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(da,&local);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,global,&coors);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(cda,local,&coorslocal);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&start,0,0,&m,0,0);CHKERRQ(ierr);
for (i=start; i<start+m; i++) {
if (i % 2) {
coors[i] = coorslocal[i-1] + .1*(coorslocal[i+1] - coorslocal[i-1]);
}
}
ierr = DMDAVecRestoreArray(cda,global,&coors);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(cda,local,&coorslocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(cda,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(cda,global,INSERT_VALUES,local);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
DMProjectField - This projects the given function of the fields into the function space provided.
Input Parameters:
+ dm - The DM
. time - The time
. U - The input field vector
. funcs - The functions to evaluate, one per field
- mode - The insertion mode for values
Output Parameter:
. X - The output vector
Level: developer
.seealso: DMProjectFunction(), DMComputeL2Diff()
@*/
PetscErrorCode DMProjectField(DM dm, PetscReal time, Vec U,
void (**funcs)(PetscInt, PetscInt, PetscInt,
const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
PetscReal, const PetscReal[], PetscScalar[]),
InsertMode mode, Vec X)
{
Vec localX, localU;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr);
/* We currently check whether locU == locX to see if we need to apply BC */
if (U != X) {ierr = DMGetLocalVector(dm, &localU);CHKERRQ(ierr);}
else {localU = localX;}
ierr = DMGlobalToLocalBegin(dm, U, INSERT_VALUES, localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, U, INSERT_VALUES, localU);CHKERRQ(ierr);
ierr = DMProjectFieldLocal(dm, time, localU, funcs, mode, localX);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm, localX, mode, X);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm, localX, mode, X);CHKERRQ(ierr);
if (mode == INSERT_VALUES || mode == INSERT_ALL_VALUES || mode == INSERT_BC_VALUES) {
Mat cMat;
ierr = DMGetDefaultConstraints(dm, NULL, &cMat);CHKERRQ(ierr);
if (cMat) {
ierr = DMGlobalToLocalSolve(dm, localX, X);CHKERRQ(ierr);
}
}
ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr);
if (U != X) {ierr = DMRestoreLocalVector(dm, &localU);CHKERRQ(ierr);}
PetscFunctionReturn(0);
}
PetscErrorCode SetCoordinates2d(DM da)
{
PetscErrorCode ierr;
PetscInt i,j,mstart,m,nstart,n;
Vec local,global;
DMDACoor2d **coors,**coorslocal;
DM cda;
PetscFunctionBeginUser;
ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&global);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(da,&local);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,global,&coors);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(cda,local,&coorslocal);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&mstart,&nstart,0,&m,&n,0);CHKERRQ(ierr);
for (i=mstart; i<mstart+m; i++) {
for (j=nstart; j<nstart+n; j++) {
if (i % 2) {
coors[j][i].x = coorslocal[j][i-1].x + .1*(coorslocal[j][i+1].x - coorslocal[j][i-1].x);
}
if (j % 2) {
coors[j][i].y = coorslocal[j-1][i].y + .3*(coorslocal[j+1][i].y - coorslocal[j-1][i].y);
}
}
}
ierr = DMDAVecRestoreArray(cda,global,&coors);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(cda,local,&coorslocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(cda,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(cda,global,INSERT_VALUES,local);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode TSComputeRHSJacobian_DMDA(TS ts,PetscReal ptime,Vec X,Mat *A,Mat *B,MatStructure *mstr,void *ctx)
{
PetscErrorCode ierr;
DM dm;
DMTS_DA *dmdats = (DMTS_DA*)ctx;
DMDALocalInfo info;
Vec Xloc;
void *x;
PetscFunctionBegin;
if (!dmdats->rhsfunctionlocal) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_PLIB,"Corrupt context");
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
if (dmdats->rhsjacobianlocal) {
ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Xloc,&x);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdats->rhsjacobianlocal)(&info,ptime,x,*A,*B,mstr,dmdats->rhsjacobianlocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = DMDAVecRestoreArray(dm,Xloc,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
} else SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_PLIB,"TSComputeRHSJacobian_DMDA() called without calling DMDATSSetRHSJacobian()");
/* This will be redundant if the user called both, but it's too common to forget. */
if (*A != *B) {
ierr = MatAssemblyBegin(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*
ComputeFunction - Evaluates nonlinear function, F(x).
Input Parameters:
. X - input vector
. user - user-defined application context
Output Parameter:
. F - function vector
*/
PetscErrorCode ComputeFunction(AppCtx *user,Vec X,Vec F)
{
PetscErrorCode ierr;
PetscInt i,j,row,mx,my,xs,ys,xm,ym,gxs,gys,gxm,gym;
PetscReal two = 2.0,one = 1.0,lambda,hx,hy,hxdhy,hydhx,sc;
PetscScalar u,uxx,uyy,*x,*f;
Vec localX = user->localX;
mx = user->mx; my = user->my; lambda = user->param;
hx = one/(PetscReal)(mx-1); hy = one/(PetscReal)(my-1);
sc = hx*hy*lambda; hxdhy = hx/hy; hydhx = hy/hx;
/*
Scatter ghost points to local vector, using the 2-step process
DMGlobalToLocalBegin(), DMGlobalToLocalEnd().
By placing code between these two statements, computations can be
done while messages are in transition.
*/
ierr = DMGlobalToLocalBegin(user->da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user->da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
/*
Get pointers to vector data
*/
ierr = VecGetArray(localX,&x);CHKERRQ(ierr);
ierr = VecGetArray(F,&f);CHKERRQ(ierr);
/*
Get local grid boundaries
*/
ierr = DMDAGetCorners(user->da,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);
ierr = DMDAGetGhostCorners(user->da,&gxs,&gys,NULL,&gxm,&gym,NULL);CHKERRQ(ierr);
/*
Compute function over the locally owned part of the grid
*/
for (j=ys; j<ys+ym; j++) {
row = (j - gys)*gxm + xs - gxs - 1;
for (i=xs; i<xs+xm; i++) {
row++;
if (i == 0 || j == 0 || i == mx-1 || j == my-1) {
f[row] = x[row];
continue;
}
u = x[row];
uxx = (two*u - x[row-1] - x[row+1])*hydhx;
uyy = (two*u - x[row-gxm] - x[row+gxm])*hxdhy;
f[row] = uxx + uyy - sc*PetscExpScalar(u);
}
}
/*
Restore vectors
*/
ierr = VecRestoreArray(localX,&x);CHKERRQ(ierr);
ierr = VecRestoreArray(F,&f);CHKERRQ(ierr);
ierr = PetscLogFlops(11.0*ym*xm);CHKERRQ(ierr);
return 0;
}
static PetscErrorCode SNESComputeJacobian_DMLocal(SNES snes,Vec X,Mat A,Mat B,void *ctx)
{
PetscErrorCode ierr;
DM dm;
DMSNES_Local *dmlocalsnes = (DMSNES_Local*)ctx;
Vec Xloc;
PetscFunctionBegin;
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
if (dmlocalsnes->jacobianlocal) {
ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = VecZeroEntries(Xloc);CHKERRQ(ierr);
if (dmlocalsnes->boundarylocal) {ierr = (*dmlocalsnes->boundarylocal)(dm,Xloc,dmlocalsnes->boundarylocalctx);CHKERRQ(ierr);}
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmlocalsnes->jacobianlocal)(dm,Xloc,A,B,dmlocalsnes->jacobianlocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
} else {
MatFDColoring fdcoloring;
ierr = PetscObjectQuery((PetscObject)dm,"DMDASNES_FDCOLORING",(PetscObject*)&fdcoloring);CHKERRQ(ierr);
if (!fdcoloring) {
ISColoring coloring;
ierr = DMCreateColoring(dm,dm->coloringtype,&coloring);CHKERRQ(ierr);
ierr = MatFDColoringCreate(B,coloring,&fdcoloring);CHKERRQ(ierr);
ierr = ISColoringDestroy(&coloring);CHKERRQ(ierr);
switch (dm->coloringtype) {
case IS_COLORING_GLOBAL:
ierr = MatFDColoringSetFunction(fdcoloring,(PetscErrorCode (*)(void))SNESComputeFunction_DMLocal,dmlocalsnes);CHKERRQ(ierr);
break;
default: SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_SUP,"No support for coloring type '%s'",ISColoringTypes[dm->coloringtype]);
}
ierr = PetscObjectSetOptionsPrefix((PetscObject)fdcoloring,((PetscObject)dm)->prefix);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(fdcoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetUp(B,coloring,fdcoloring);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject)dm,"DMDASNES_FDCOLORING",(PetscObject)fdcoloring);CHKERRQ(ierr);
ierr = PetscObjectDereference((PetscObject)fdcoloring);CHKERRQ(ierr);
/* The following breaks an ugly reference counting loop that deserves a paragraph. MatFDColoringApply() will call
* VecDuplicate() with the state Vec and store inside the MatFDColoring. This Vec will duplicate the Vec, but the
* MatFDColoring is composed with the DM. We dereference the DM here so that the reference count will eventually
* drop to 0. Note the code in DMDestroy() that exits early for a negative reference count. That code path will be
* taken when the PetscObjectList for the Vec inside MatFDColoring is destroyed.
*/
ierr = PetscObjectDereference((PetscObject)dm);CHKERRQ(ierr);
}
ierr = MatFDColoringApply(B,fdcoloring,X,snes);CHKERRQ(ierr);
}
/* This will be redundant if the user called both, but it's too common to forget. */
if (A != B) {
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode DMGlobalToLocalBegin_Network(DM dm, Vec g, InsertMode mode, Vec l)
{
PetscErrorCode ierr;
DM_Network *network = (DM_Network*) dm->data;
PetscFunctionBegin;
ierr = DMGlobalToLocalBegin(network->plex,g,mode,l);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
RHSFunction - Evaluates nonlinear function, F(u).
Input Parameters:
. ts - the TS context
. U - input vector
. ptr - optional user-defined context, as set by TSSetFunction()
Output Parameter:
. F - function vector
*/
PetscErrorCode RHSFunction(TS ts,PetscReal ftime,Vec U,Vec F,void *ptr)
{
/* PETSC_UNUSED AppCtx *user=(AppCtx*)ptr; */
DM da;
PetscErrorCode ierr;
PetscInt i,j,Mx,My,xs,ys,xm,ym;
PetscReal two = 2.0,hx,hy,sx,sy;
PetscScalar u,uxx,uyy,**uarray,**f;
Vec localU;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMGetLocalVector(da,&localU);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,&My,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,
PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);
hx = 1.0/(PetscReal)(Mx-1); sx = 1.0/(hx*hx);
hy = 1.0/(PetscReal)(My-1); sy = 1.0/(hy*hy);
/*
Scatter ghost points to local vector,using the 2-step process
DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
By placing code between these two statements, computations can be
done while messages are in transition.
*/
ierr = DMGlobalToLocalBegin(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);
/* Get pointers to vector data */
ierr = DMDAVecGetArray(da,localU,&uarray);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,F,&f);CHKERRQ(ierr);
/* Get local grid boundaries */
ierr = DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);
/* Compute function over the locally owned part of the grid */
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
if (i == 0 || j == 0 || i == Mx-1 || j == My-1) {
f[j][i] = uarray[j][i];
continue;
}
u = uarray[j][i];
uxx = (-two*u + uarray[j][i-1] + uarray[j][i+1])*sx;
uyy = (-two*u + uarray[j-1][i] + uarray[j+1][i])*sy;
f[j][i] = uxx + uyy;
}
}
/* Restore vectors */
ierr = DMDAVecRestoreArray(da,localU,&uarray);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&localU);CHKERRQ(ierr);
ierr = PetscLogFlops(11.0*ym*xm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode SNESComputeFunction_DMDA(SNES snes,Vec X,Vec F,void *ctx)
{
PetscErrorCode ierr;
DM dm;
DMSNES_DA *dmdasnes = (DMSNES_DA*)ctx;
DMDALocalInfo info;
Vec Xloc;
void *x,*f;
PetscFunctionBegin;
PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
PetscValidHeaderSpecific(X,VEC_CLASSID,2);
PetscValidHeaderSpecific(F,VEC_CLASSID,3);
if (!dmdasnes->residuallocal) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_PLIB,"Corrupt context");
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Xloc,&x);CHKERRQ(ierr);
switch (dmdasnes->residuallocalimode) {
case INSERT_VALUES: {
ierr = DMDAVecGetArray(dm,F,&f);CHKERRQ(ierr);
ierr = PetscLogEventBegin(SNES_FunctionEval,snes,X,F,0);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdasnes->residuallocal)(&info,x,f,dmdasnes->residuallocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = PetscLogEventEnd(SNES_FunctionEval,snes,X,F,0);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dm,F,&f);CHKERRQ(ierr);
} break;
case ADD_VALUES: {
Vec Floc;
ierr = DMGetLocalVector(dm,&Floc);CHKERRQ(ierr);
ierr = VecZeroEntries(Floc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Floc,&f);CHKERRQ(ierr);
ierr = PetscLogEventBegin(SNES_FunctionEval,snes,X,F,0);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdasnes->residuallocal)(&info,x,f,dmdasnes->residuallocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = PetscLogEventEnd(SNES_FunctionEval,snes,X,F,0);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dm,Floc,&f);CHKERRQ(ierr);
ierr = VecZeroEntries(F);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm,Floc,ADD_VALUES,F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm,Floc,ADD_VALUES,F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Floc);CHKERRQ(ierr);
} break;
default: SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_INCOMP,"Cannot use imode=%d",(int)dmdasnes->residuallocalimode);
}
ierr = DMDAVecRestoreArray(dm,Xloc,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
if (snes->domainerror) {
ierr = VecSetInf(F);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*
FormFunction - Evaluates nonlinear function, F(x).
Input Parameters:
. snes - the SNES context
. x - input vector
. ctx - optional user-defined context, as set by SNESSetFunction()
Output Parameter:
. f - function vector
Note:
The user-defined context can contain any application-specific
data needed for the function evaluation.
*/
PetscErrorCode FormFunction(SNES snes,Vec x,Vec f,void *ctx)
{
DM da = (DM) ctx;
PetscScalar *xx,*ff;
PetscReal h;
PetscErrorCode ierr;
PetscInt i,M,xs,xm;
Vec xlocal;
PetscFunctionBeginUser;
/* Get local work vector */
ierr = DMGetLocalVector(da,&xlocal);CHKERRQ(ierr);
/*
Scatter ghost points to local vector, using the 2-step process
DMGlobalToLocalBegin(), DMGlobalToLocalEnd().
By placing code between these two statements, computations can
be done while messages are in transition.
*/
ierr = DMGlobalToLocalBegin(da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr);
/*
Get pointers to vector data.
- The vector xlocal includes ghost point; the vectors x and f do
NOT include ghost points.
- Using DMDAVecGetArray() allows accessing the values using global ordering
*/
ierr = DMDAVecGetArray(da,xlocal,&xx);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,f,&ff);CHKERRQ(ierr);
/*
Get local grid boundaries (for 1-dimensional DMDA):
xs, xm - starting grid index, width of local grid (no ghost points)
*/
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,NULL,&M,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
/*
Compute function over locally owned part of the grid
Note the [i-1] and [i+1] will automatically access the ghost points from other processes or the periodic points.
*/
h = 1.0/M;
for (i=xs; i<xs+xm; i++) ff[i] = (xx[i-1] - 2.0*xx[i] + xx[i+1])/(h*h) - PetscSinReal(2.0*PETSC_PI*i*h);
/*
Restore vectors
*/
ierr = DMDAVecRestoreArray(da,xlocal,&xx);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,f,&ff);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&xlocal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
FormFunction - Evaluates nonlinear function, F(x).
Input Parameters:
. ts - the TS context
. X - input vector
. ptr - optional user-defined context, as set by SNESSetFunction()
Output Parameter:
. F - function vector
*/
PetscErrorCode FormFunction(TS ts,PetscReal ftime,Vec X,Vec F,void *ptr)
{
DM da;
PetscErrorCode ierr;
PetscInt i,Mx,xs,xm;
PetscReal hx,sx;
PetscScalar *x,*f;
Vec localX;
UserCtx *ctx = (UserCtx*)ptr;
PetscFunctionBegin;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMGetLocalVector(da,&localX);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);
hx = 1.0/(PetscReal)Mx; sx = 1.0/(hx*hx);
/*
Scatter ghost points to local vector,using the 2-step process
DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
By placing code between these two statements, computations can be
done while messages are in transition.
*/
ierr = DMGlobalToLocalBegin(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
/*
Get pointers to vector data
*/
ierr = DMDAVecGetArrayRead(da,localX,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,F,&f);CHKERRQ(ierr);
/*
Get local grid boundaries
*/
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
/*
Compute function over the locally owned part of the grid
*/
for (i=xs; i<xs+xm; i++) {
f[i] = ctx->kappa*(x[i-1] + x[i+1] - 2.0*x[i])*sx;
if (ctx->allencahn) f[i] += (x[i] - x[i]*x[i]*x[i]);
}
/*
Restore vectors
*/
ierr = DMDAVecRestoreArrayRead(da,localX,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&localX);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode FormIFunction(TS ts,PetscReal t,Vec X,Vec Xdot,Vec F,void *ptr)
{
User user = (User)ptr;
DM da;
DMDALocalInfo info;
PetscInt i;
Field *x,*xdot,*f;
PetscReal hx;
Vec Xloc;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
hx = 1.0/(PetscReal)(info.mx-1);
/*
Scatter ghost points to local vector,using the 2-step process
DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
By placing code between these two statements, computations can be
done while messages are in transition.
*/
ierr = DMGetLocalVector(da,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
/* Get pointers to vector data */
ierr = DMDAVecGetArray(da,Xloc,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,Xdot,&xdot);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,F,&f);CHKERRQ(ierr);
/* Compute function over the locally owned part of the grid */
for (i=info.xs; i<info.xs+info.xm; i++) {
if (i == 0) {
f[i].u = hx * (x[i].u - user->uleft);
f[i].v = hx * (x[i].v - user->vleft);
} else if (i == info.mx-1) {
f[i].u = hx * (x[i].u - user->uright);
f[i].v = hx * (x[i].v - user->vright);
} else {
f[i].u = hx * xdot[i].u - user->alpha * (x[i-1].u - 2.*x[i].u + x[i+1].u) / hx;
f[i].v = hx * xdot[i].v - user->alpha * (x[i-1].v - 2.*x[i].v + x[i+1].v) / hx;
}
}
/* Restore vectors */
ierr = DMDAVecRestoreArray(da,Xloc,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,Xdot,&xdot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&Xloc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode FormRHSFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
{
User user = (User)ptr;
DM da;
Vec Xloc;
DMDALocalInfo info;
PetscInt i,j;
PetscReal hx;
Field *f;
const Field *x;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
hx = 1.0/(PetscReal)info.mx;
/*
Scatter ghost points to local vector,using the 2-step process
DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
By placing code between these two statements, computations can be
done while messages are in transition.
*/
ierr = DMGetLocalVector(da,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
/* Get pointers to vector data */
ierr = DMDAVecGetArrayRead(da,Xloc,(void*)&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,F,&f);CHKERRQ(ierr);
/* Compute function over the locally owned part of the grid */
for (i=info.xs; i<info.xs+info.xm; i++) {
const PetscReal *a = user->a;
PetscReal u0t[2];
u0t[0] = 1.0 - PetscPowRealInt(PetscSinReal(12*t),4);
u0t[1] = 0.0;
for (j=0; j<2; j++) {
if (i == 0) f[i][j] = a[j]/hx*(1./3*u0t[j] + 0.5*x[i][j] - x[i+1][j] + 1./6*x[i+2][j]);
else if (i == 1) f[i][j] = a[j]/hx*(-1./12*u0t[j] + 2./3*x[i-1][j] - 2./3*x[i+1][j] + 1./12*x[i+2][j]);
else if (i == info.mx-2) f[i][j] = a[j]/hx*(-1./6*x[i-2][j] + x[i-1][j] - 0.5*x[i][j] - 1./3*x[i+1][j]);
else if (i == info.mx-1) f[i][j] = a[j]/hx*(-x[i][j] + x[i-1][j]);
else f[i][j] = a[j]/hx*(-1./12*x[i-2][j] + 2./3*x[i-1][j] - 2./3*x[i+1][j] + 1./12*x[i+2][j]);
}
}
/* Restore vectors */
ierr = DMDAVecRestoreArrayRead(da,Xloc,(void*)&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&Xloc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
This function should eventually replace:
DMDAComputeFunction() and DMDAComputeFunction1()
*/
static PetscErrorCode TSComputeIFunction_DMDA(TS ts,PetscReal ptime,Vec X,Vec Xdot,Vec F,void *ctx)
{
PetscErrorCode ierr;
DM dm;
DMTS_DA *dmdats = (DMTS_DA*)ctx;
DMDALocalInfo info;
Vec Xloc;
void *x,*f,*xdot;
PetscFunctionBegin;
PetscValidHeaderSpecific(ts,TS_CLASSID,1);
PetscValidHeaderSpecific(X,VEC_CLASSID,2);
PetscValidHeaderSpecific(F,VEC_CLASSID,3);
if (!dmdats->ifunctionlocal) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_PLIB,"Corrupt context");
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Xloc,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Xdot,&xdot);CHKERRQ(ierr);
switch (dmdats->ifunctionlocalimode) {
case INSERT_VALUES: {
ierr = DMDAVecGetArray(dm,F,&f);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdats->ifunctionlocal)(&info,ptime,x,xdot,f,dmdats->ifunctionlocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = DMDAVecRestoreArray(dm,F,&f);CHKERRQ(ierr);
} break;
case ADD_VALUES: {
Vec Floc;
ierr = DMGetLocalVector(dm,&Floc);CHKERRQ(ierr);
ierr = VecZeroEntries(Floc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Floc,&f);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdats->ifunctionlocal)(&info,ptime,x,xdot,f,dmdats->ifunctionlocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = DMDAVecRestoreArray(dm,Floc,&f);CHKERRQ(ierr);
ierr = VecZeroEntries(F);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm,Floc,ADD_VALUES,F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm,Floc,ADD_VALUES,F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Floc);CHKERRQ(ierr);
} break;
default: SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_INCOMP,"Cannot use imode=%d",(int)dmdats->ifunctionlocalimode);
}
ierr = DMDAVecRestoreArray(dm,Xloc,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dm,Xdot,&xdot);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetInitialValues(DM networkdm,Vec X,void* appctx)
{
PetscErrorCode ierr;
VERTEXDATA bus;
GEN gen;
PetscInt v, vStart, vEnd, offset;
PetscBool ghostvtex;
Vec localX;
PetscScalar *xarr;
PetscInt key,numComps,j,offsetd;
DMNetworkComponentGenericDataType *arr;
PetscFunctionBegin;
ierr = DMNetworkGetVertexRange(networkdm,&vStart, &vEnd);CHKERRQ(ierr);
ierr = DMGetLocalVector(networkdm,&localX);CHKERRQ(ierr);
ierr = VecSet(X,0.0);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(networkdm,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(networkdm,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = VecGetArray(localX,&xarr);CHKERRQ(ierr);
ierr = DMNetworkGetComponentDataArray(networkdm,&arr);CHKERRQ(ierr);
for (v = vStart; v < vEnd; v++) {
ierr = DMNetworkIsGhostVertex(networkdm,v,&ghostvtex);CHKERRQ(ierr);
if (ghostvtex) continue;
ierr = DMNetworkGetVariableOffset(networkdm,v,&offset);CHKERRQ(ierr);
ierr = DMNetworkGetNumComponents(networkdm,v,&numComps);CHKERRQ(ierr);
for (j=0; j < numComps; j++) {
ierr = DMNetworkGetComponentTypeOffset(networkdm,v,j,&key,&offsetd);CHKERRQ(ierr);
if (key == 1) {
bus = (VERTEXDATA)(arr+offsetd);
xarr[offset] = bus->va*PETSC_PI/180.0;
xarr[offset+1] = bus->vm;
} else if(key == 2) {
gen = (GEN)(arr+offsetd);
if (!gen->status) continue;
xarr[offset+1] = gen->vs;
break;
}
}
}
ierr = VecRestoreArray(localX,&xarr);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(networkdm,localX,ADD_VALUES,X);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(networkdm,localX,ADD_VALUES,X);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(networkdm,&localX);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscMPIInt rank;
PetscInt M = 10,N = 8,m = PETSC_DECIDE,n = PETSC_DECIDE;
PetscErrorCode ierr;
DM da;
PetscViewer viewer;
Vec local,global;
PetscScalar value;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"",300,0,300,300,&viewer);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,"-m",&m,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
/* Create distributed array and get vectors */
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,m,n,1,1,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
value = -3.0;
ierr = VecSet(global,value);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
value = rank+1;
ierr = VecScale(local,value);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da,local,ADD_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,local,ADD_VALUES,global);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMView(da,viewer);CHKERRQ(ierr);
/* Free memory */
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode FormJacobian_Grid(AppCtx *user,GridCtx *grid,Vec X, Mat *J,Mat *B)
{
Mat jac = *J;
PetscErrorCode ierr;
PetscInt i, j, row, mx, my, xs, ys, xm, ym, Xs, Ys, Xm, Ym, col[5], nloc, *ltog, grow;
PetscScalar two = 2.0, one = 1.0, lambda, v[5], hx, hy, hxdhy, hydhx, sc, *x, value;
Vec localX = grid->localX;
mx = grid->mx; my = grid->my; lambda = user->param;
hx = one/(double)(mx-1); hy = one/(double)(my-1);
sc = hx*hy; hxdhy = hx/hy; hydhx = hy/hx;
/* Get ghost points */
ierr = DMGlobalToLocalBegin(grid->da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(grid->da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMDAGetCorners(grid->da,&xs,&ys,0,&xm,&ym,0);CHKERRQ(ierr);
ierr = DMDAGetGhostCorners(grid->da,&Xs,&Ys,0,&Xm,&Ym,0);CHKERRQ(ierr);
ierr = DMDAGetGlobalIndices(grid->da,&nloc,<og);CHKERRQ(ierr);
ierr = VecGetArray(localX,&x);CHKERRQ(ierr);
/* Evaluate Jacobian of function */
for (j=ys; j<ys+ym; j++) {
row = (j - Ys)*Xm + xs - Xs - 1;
for (i=xs; i<xs+xm; i++) {
row++;
grow = ltog[row];
if (i > 0 && i < mx-1 && j > 0 && j < my-1) {
v[0] = -hxdhy; col[0] = ltog[row - Xm];
v[1] = -hydhx; col[1] = ltog[row - 1];
v[2] = two*(hydhx + hxdhy) - sc*lambda*exp(x[row]); col[2] = grow;
v[3] = -hydhx; col[3] = ltog[row + 1];
v[4] = -hxdhy; col[4] = ltog[row + Xm];
ierr = MatSetValues(jac,1,&grow,5,col,v,INSERT_VALUES);CHKERRQ(ierr);
} else if ((i > 0 && i < mx-1) || (j > 0 && j < my-1)){
value = .5*two*(hydhx + hxdhy);
ierr = MatSetValues(jac,1,&grow,1,&grow,&value,INSERT_VALUES);CHKERRQ(ierr);
} else {
value = .25*two*(hydhx + hxdhy);
ierr = MatSetValues(jac,1,&grow,1,&grow,&value,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
ierr = MatAssemblyBegin(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecRestoreArray(localX,&x);CHKERRQ(ierr);
ierr = MatAssemblyEnd(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
return 0;
}
static PetscErrorCode FormIFunction(TS ts, PetscReal t, Vec U, Vec Udot, Vec F, void *ctx)
{
User user = (User) ctx;
DM dm, cdm;
DMDALocalInfo info;
Vec Uloc, C;
Field *u, *udot, *f;
PetscScalar *x;
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = TSGetDM(ts, &dm);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm, &info);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &C);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &Uloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, U, INSERT_VALUES, Uloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, U, INSERT_VALUES, Uloc);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(dm, Uloc, &u);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(dm, Udot, &udot);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm, F, &f);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(cdm, C, &x);CHKERRQ(ierr);
for (i = info.xs; i < info.xs+info.xm; ++i) {
if (i == 0) {
const PetscScalar hx = x[i+1] - x[i];
f[i].u = hx * udot[i].u;
f[i].v = hx * udot[i].v - PetscSqr(user->c) * (u[i+1].u - u[i].u) / hx;
f[i].th = hx * udot[i].th;
} else if (i == info.mx-1) {
const PetscScalar hx = x[i] - x[i-1];
f[i].u = hx * udot[i].u;
f[i].v = hx * udot[i].v - PetscSqr(user->c) * (u[i-1].u - u[i].u) / hx;
f[i].th = hx * udot[i].th;
} else {
const PetscScalar hx = x[i+1] - x[i];
f[i].u = hx * udot[i].u;
f[i].v = hx * udot[i].v - PetscSqr(user->c) * (u[i-1].u - 2.*u[i].u + u[i+1].u) / hx;
f[i].th = hx * udot[i].th;
}
}
ierr = DMDAVecRestoreArrayRead(dm, Uloc, &u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(dm, Udot, &udot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dm, F, &f);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(cdm, C, &x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &Uloc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
