/*@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);
}
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);
}
/*@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);
}
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);
}
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 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);
}
/*
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 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);
}
/*
Evaluates \integral_{-1}^{1} f*v_i where v_i is the ith basis polynomial via the GLL nodes and weights, since the v_i
basis function is zero at all nodes except the ith one the integral is simply the weight_i * f(node_i)
*/
PetscErrorCode ComputeRhs(DM da,PetscGLL *gll,Vec b)
{
PetscErrorCode ierr;
PetscInt i,j,xs,xn,n = gll->n;
PetscScalar *bb,*xx;
PetscReal xd;
Vec blocal,xlocal;
PetscFunctionBegin;
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xn,NULL,NULL);CHKERRQ(ierr);
xs = xs/(n-1);
xn = xn/(n-1);
ierr = DMGetLocalVector(da,&blocal);CHKERRQ(ierr);
ierr = VecZeroEntries(blocal);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,blocal,&bb);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(da,&xlocal);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,xlocal,&xx);CHKERRQ(ierr);
/* loop over local spectral elements */
for (j=xs; j<xs+xn; j++) {
/* loop over GLL points in each element */
for (i=0; i<n; i++) {
xd = xx[j*(n-1) + i];
bb[j*(n-1) + i] += -gll->weights[i]*(-20.*PETSC_PI*xd*PetscSinReal(5.*PETSC_PI*xd) + (2. - (5.*PETSC_PI)*(5.*PETSC_PI)*(xd*xd - 1.))*PetscCosReal(5.*PETSC_PI*xd));
}
}
ierr = DMDAVecRestoreArray(da,xlocal,&xx);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,blocal,&bb);CHKERRQ(ierr);
ierr = VecZeroEntries(b);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da,blocal,ADD_VALUES,b);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,blocal,ADD_VALUES,b);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&blocal);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);
}
/*
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);
}
/*
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);
}
/*
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);
}
/*
We integrate over each cell
(i, j+1)----(i+1, j+1)
| \ |
| \ |
| \ |
| \ |
| \ |
| \ |
| \ |
(i, j)----(i+1, j)
*/
PetscErrorCode ComputeRHS(KSP ksp, Vec b, void *ctx)
{
UserContext *user = (UserContext*)ctx;
PetscScalar phi = user->phi;
PetscScalar *array;
PetscInt ne,nc,i;
const PetscInt *e;
PetscErrorCode ierr;
Vec blocal;
DM da;
PetscFunctionBeginUser;
ierr = KSPGetDM(ksp,&da);CHKERRQ(ierr);
/* access a local vector with room for the ghost points */
ierr = DMGetLocalVector(da,&blocal);CHKERRQ(ierr);
ierr = VecGetArray(blocal, (PetscScalar**) &array);CHKERRQ(ierr);
/* access the list of elements on this processor and loop over them */
ierr = DMDAGetElements(da,&ne,&nc,&e);CHKERRQ(ierr);
for (i=0; i<ne; i++) {
/* this is nonsense, but set each nodal value to phi (will actually do integration over element */
array[e[3*i]] = phi;
array[e[3*i+1]] = phi;
array[e[3*i+2]] = phi;
}
ierr = VecRestoreArray(blocal, (PetscScalar**) &array);CHKERRQ(ierr);
ierr = DMDARestoreElements(da,&ne,&nc,&e);CHKERRQ(ierr);
/* add our partial sums over all processors into b */
ierr = DMLocalToGlobalBegin(da,blocal,ADD_VALUES,b);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,blocal, ADD_VALUES,b);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&blocal);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);
}
/**
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);
}
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 TestFieldProjection(DM dm, DM auxdm, DMLabel label, Vec la, const char name[], AppCtx *user)
{
PetscErrorCode (**afuncs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *);
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[], PetscInt, const PetscScalar[], PetscScalar[]);
Vec lx, lu;
PetscInt Nf, f;
PetscInt val[1] = {1};
char lname[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscFunctionBeginUser;
if (auxdm) {
ierr = PetscObjectCompose((PetscObject) dm, "dmAux", (PetscObject) auxdm);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject) dm, "A", (PetscObject) la);CHKERRQ(ierr);
}
ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr);
ierr = PetscMalloc2(Nf, &funcs, Nf, &afuncs);CHKERRQ(ierr);
for (f = 0; f < Nf; ++f) afuncs[f] = linear;
funcs[0] = linear_vector;
funcs[1] = linear_scalar;
ierr = DMGetLocalVector(dm, &lu);CHKERRQ(ierr);
ierr = PetscStrcpy(lname, "Local Field Input ");CHKERRQ(ierr);
ierr = PetscStrcat(lname, name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) lu, lname);CHKERRQ(ierr);
if (!label) {ierr = DMProjectFunctionLocal(dm, 0.0, afuncs, NULL, INSERT_VALUES, lu);CHKERRQ(ierr);}
else {ierr = DMProjectFunctionLabelLocal(dm, 0.0, label, 1, val, 0, NULL, afuncs, NULL, INSERT_VALUES, lu);CHKERRQ(ierr);}
ierr = VecViewFromOptions(lu, NULL, "-local_input_view");CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &lx);CHKERRQ(ierr);
ierr = PetscStrcpy(lname, "Local Field ");CHKERRQ(ierr);
ierr = PetscStrcat(lname, name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) lx, lname);CHKERRQ(ierr);
if (!label) {ierr = DMProjectFieldLocal(dm, 0.0, lu, funcs, INSERT_VALUES, lx);CHKERRQ(ierr);}
else {ierr = DMProjectFieldLabelLocal(dm, 0.0, label, 1, val, 0, NULL, lu, funcs, INSERT_VALUES, lx);CHKERRQ(ierr);}
ierr = VecViewFromOptions(lx, NULL, "-local_field_view");CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &lx);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &lu);CHKERRQ(ierr);
ierr = PetscFree2(funcs, afuncs);CHKERRQ(ierr);
if (auxdm) {
ierr = PetscObjectCompose((PetscObject) dm, "dmAux", NULL);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject) dm, "A", NULL);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode OpForcing(Op op,DM dm,Vec F) {
PetscErrorCode ierr;
Vec X,Floc;
DM dmx;
const PetscScalar *x;
PetscScalar *f;
const PetscReal *B,*D,*w3;
PetscReal L[3];
PetscInt nelem,ne = op->ne,P,Q,P3,Q3;
PetscFunctionBegin;
ierr = PetscLogEventBegin(OP_Forcing,dm,F,0,0);CHKERRQ(ierr);
ierr = DMFEGetTensorEval(dm,&P,&Q,&B,&D,NULL,NULL,&w3);CHKERRQ(ierr);
P3 = P*P*P;
Q3 = Q*Q*Q;
ierr = DMFEGetUniformCoordinates(dm,L);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&Floc);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm,&dmx);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm,&X);CHKERRQ(ierr);
ierr = DMFEGetNumElements(dm,&nelem);CHKERRQ(ierr);
ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
ierr = VecZeroEntries(Floc);CHKERRQ(ierr);
ierr = VecGetArray(Floc,&f);CHKERRQ(ierr);
for (PetscInt e=0; e<nelem; e+=ne) {
PetscScalar fe[op->dof*P3*ne]_align,fq[op->dof][Q3][ne]_align,xe[3*P3*ne]_align,xq[3][Q3][ne]_align,dx[3][3][Q3][ne]_align,wdxdet[Q3][ne]_align;
ierr = DMFEExtractElements(dmx,x,e,ne,xe);CHKERRQ(ierr);
ierr = PetscMemzero(xq,sizeof xq);CHKERRQ(ierr);
ierr = TensorContract(op->Tensor3,B,B,B,TENSOR_EVAL,xe,xq[0][0]);CHKERRQ(ierr);
ierr = PetscMemzero(dx,sizeof dx);CHKERRQ(ierr);
ierr = TensorContract(op->Tensor3,D,B,B,TENSOR_EVAL,xe,dx[0][0][0]);CHKERRQ(ierr);
ierr = TensorContract(op->Tensor3,B,D,B,TENSOR_EVAL,xe,dx[1][0][0]);CHKERRQ(ierr);
ierr = TensorContract(op->Tensor3,B,B,D,TENSOR_EVAL,xe,dx[2][0][0]);CHKERRQ(ierr);
ierr = PointwiseJacobianInvert(ne,Q*Q*Q,w3,dx,wdxdet);CHKERRQ(ierr);
for (PetscInt i=0; i<Q3; i++) {
for (PetscInt l=0; l<ne; l++) {
PetscReal xx[] = {xq[0][i][l],xq[1][i][l],xq[2][i][l]};
PetscScalar fql[op->dof];
ierr = (op->PointwiseForcing)(op,xx,L,fql);CHKERRQ(ierr);
for (PetscInt d=0; d<op->dof; d++) fq[d][i][l] = wdxdet[i][l] * fql[d];
}
}
ierr = PetscMemzero(fe,sizeof fe);CHKERRQ(ierr);
ierr = TensorContract(op->TensorDOF,B,B,B,TENSOR_TRANSPOSE,fq[0][0],fe);CHKERRQ(ierr);
ierr = DMFESetElements(dm,f,e,ne,ADD_VALUES,DOMAIN_INTERIOR,fe);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
ierr = VecRestoreArray(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);
ierr = PetscLogEventEnd(OP_Forcing,dm,F,0,0);CHKERRQ(ierr);
PetscFunctionReturn(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 FormFunctionMatlab(SNES snes,Vec X,Vec F,void *ptr)
{
AppCtx *user = (AppCtx*)ptr;
PetscErrorCode ierr;
PetscInt Mx,My;
PetscReal lambda,hx,hy;
Vec localX,localF;
MPI_Comm comm;
DM da;
PetscFunctionBeginUser;
ierr = SNESGetDM(snes,&da);CHKERRQ(ierr);
ierr = DMGetLocalVector(da,&localX);CHKERRQ(ierr);
ierr = DMGetLocalVector(da,&localF);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)localX,"localX");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)localF,"localF");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);CHKERRQ(ierr);
lambda = user->param;
hx = 1.0/(PetscReal)(Mx-1);
hy = 1.0/(PetscReal)(My-1);
ierr = PetscObjectGetComm((PetscObject)snes,&comm);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,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = PetscMatlabEnginePut(PETSC_MATLAB_ENGINE_(comm),(PetscObject)localX);CHKERRQ(ierr);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(comm),"localF=ex5m(localX,%18.16e,%18.16e,%18.16e)",hx,hy,lambda);CHKERRQ(ierr);
ierr = PetscMatlabEngineGet(PETSC_MATLAB_ENGINE_(comm),(PetscObject)localF);CHKERRQ(ierr);
/*
Insert values into global vector
*/
ierr = DMLocalToGlobalBegin(da,localF,INSERT_VALUES,F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,localF,INSERT_VALUES,F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&localX);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&localF);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);
}
/* no discretization is given so DMGetNumFields yields 0 */
static PetscErrorCode test0(DM dm, AppCtx *options)
{
Vec locX;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMGetLocalVector(dm, &locX);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locX);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
DM dm, subdm, auxdm;
Vec la;
AppCtx user;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
ierr = ProcessOptions(&user);CHKERRQ(ierr);
ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr);
ierr = SetupDiscretization(dm, user.dim, user.cellSimplex, &user);CHKERRQ(ierr);
/* Volumetric Mesh Projection */
ierr = TestFunctionProjection(dm, NULL, NULL, NULL, "Volumetric Primary", &user);CHKERRQ(ierr);
ierr = TestFieldProjection(dm, NULL, NULL, NULL, "Volumetric Primary", &user);CHKERRQ(ierr);
if (user.auxfield) {
/* Volumetric Mesh Projection with Volumetric Data */
ierr = CreateAuxiliaryData(dm, &auxdm, &la, &user);CHKERRQ(ierr);
ierr = TestFunctionProjection(dm, auxdm, NULL, la, "Volumetric Primary and Volumetric Auxiliary", &user);CHKERRQ(ierr);
ierr = TestFieldProjection(dm, auxdm, NULL, la, "Volumetric Primary and Volumetric Auxiliary", &user);CHKERRQ(ierr);
ierr = VecDestroy(&la);CHKERRQ(ierr);
/* Update of Volumetric Auxiliary Data with primary Volumetric Data */
ierr = DMGetLocalVector(dm, &la);CHKERRQ(ierr);
ierr = VecSet(la, 1.0);CHKERRQ(ierr);
ierr = TestFieldProjection(auxdm, dm, NULL, la, "Volumetric Auxiliary Update with Volumetric Primary", &user);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &la);CHKERRQ(ierr);
ierr = DMDestroy(&auxdm);CHKERRQ(ierr);
}
if (user.submesh) {
DMLabel bdLabel;
/* Boundary Mesh Projection */
ierr = CreateBoundaryMesh(dm, &bdLabel, &subdm, &user);CHKERRQ(ierr);
ierr = TestFunctionProjection(subdm, NULL, NULL, NULL, "Boundary Primary", &user);CHKERRQ(ierr);
ierr = TestFieldProjection(subdm, NULL, NULL, NULL, "Boundary Primary", &user);CHKERRQ(ierr);
if (user.auxfield) {
/* Boundary Mesh Projection with Boundary Data */
ierr = CreateAuxiliaryData(subdm, &auxdm, &la, &user);CHKERRQ(ierr);
ierr = TestFunctionProjection(subdm, auxdm, NULL, la, "Boundary Primary and Boundary Auxiliary", &user);CHKERRQ(ierr);
ierr = TestFieldProjection(subdm, auxdm, NULL, la, "Boundary Primary and Boundary Auxiliary", &user);CHKERRQ(ierr);
ierr = VecDestroy(&la);CHKERRQ(ierr);
ierr = DMDestroy(&auxdm);CHKERRQ(ierr);
/* Volumetric Mesh Projection with Boundary Data */
ierr = CreateAuxiliaryData(subdm, &auxdm, &la, &user);CHKERRQ(ierr);
ierr = TestFunctionProjection(dm, auxdm, bdLabel, la, "Volumetric Primary and Boundary Auxiliary", &user);CHKERRQ(ierr);
ierr = TestFieldProjection(dm, auxdm, bdLabel, la, "Volumetric Primary and Boundary Auxiliary", &user);CHKERRQ(ierr);
ierr = VecDestroy(&la);CHKERRQ(ierr);
ierr = DMDestroy(&auxdm);CHKERRQ(ierr);
}
ierr = DMLabelDestroy(&bdLabel);CHKERRQ(ierr);
ierr = DMDestroy(&subdm);CHKERRQ(ierr);
}
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/* no discretization is given so DMGetNumFields and PetscDSGetTotalDimension yield 0 */
static PetscErrorCode test1(DM dm, AppCtx *options)
{
IS cells;
Vec locX, locX_t, locA;
PetscScalar *u, *u_t, *a;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = ISCreateStride(PETSC_COMM_SELF, 0, 0, 1, &cells);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &locX);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &locX_t);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &locA);CHKERRQ(ierr);
ierr = DMPlexGetCellFields( dm, cells, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr);
ierr = DMPlexRestoreCellFields(dm, cells, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locX);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locX_t);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locA);CHKERRQ(ierr);
ierr = ISDestroy(&cells);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Matrix free operation of 1d Laplacian and Grad for GLL spectral elements
*/
PetscErrorCode MatMult_Laplacian(Mat A,Vec x,Vec y)
{
AppCtx *appctx;
PetscErrorCode ierr;
PetscReal **temp,vv;
PetscInt i,j,xs,xn;
Vec xlocal,ylocal;
const PetscScalar *xl;
PetscScalar *yl;
PetscBLASInt _One = 1,n;
PetscScalar _DOne = 1;
ierr = MatShellGetContext(A,&appctx);CHKERRQ(ierr);
ierr = DMGetLocalVector(appctx->da,&xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(appctx->da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(appctx->da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr);
ierr = DMGetLocalVector(appctx->da,&ylocal);CHKERRQ(ierr);
ierr = VecSet(ylocal,0.0);CHKERRQ(ierr);
ierr = PetscGLLElementLaplacianCreate(&appctx->SEMop.gll,&temp);CHKERRQ(ierr);
for (i=0; i<appctx->param.N; i++) {
vv =-appctx->param.mu*2.0/appctx->param.Le;
for (j=0; j<appctx->param.N; j++) temp[i][j]=temp[i][j]*vv;
}
ierr = DMDAVecGetArrayRead(appctx->da,xlocal,(void*)&xl);CHKERRQ(ierr);
ierr = DMDAVecGetArray(appctx->da,ylocal,&yl);CHKERRQ(ierr);
ierr = DMDAGetCorners(appctx->da,&xs,NULL,NULL,&xn,NULL,NULL);CHKERRQ(ierr);
ierr = PetscBLASIntCast(appctx->param.N,&n);CHKERRQ(ierr);
for (j=xs; j<xs+xn; j += appctx->param.N-1) {
PetscStackCallBLAS("BLASgemv",BLASgemv_("N",&n,&n,&_DOne,&temp[0][0],&n,&xl[j],&_One,&_DOne,&yl[j],&_One));
}
ierr = DMDAVecRestoreArrayRead(appctx->da,xlocal,(void*)&xl);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(appctx->da,ylocal,&yl);CHKERRQ(ierr);
ierr = PetscGLLElementLaplacianDestroy(&appctx->SEMop.gll,&temp);CHKERRQ(ierr);
ierr = VecSet(y,0.0);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(appctx->da,ylocal,ADD_VALUES,y);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(appctx->da,ylocal,ADD_VALUES,y);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(appctx->da,&xlocal);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(appctx->da,&ylocal);CHKERRQ(ierr);
ierr = VecPointwiseDivide(y,y,appctx->SEMop.mass);CHKERRQ(ierr);
return 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 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);
}
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);
}
