/**
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);
}
/*@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 SetCoordinates3d(DM da)
{
PetscErrorCode ierr;
PetscInt i,j,mstart,m,nstart,n,pstart,p,k;
Vec gc,global;
DMDACoor3d ***coors;
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 = DMGetCoordinatesLocal(da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&mstart,&nstart,&pstart,&m,&n,&p);CHKERRQ(ierr);
for (i=mstart; i<mstart+m; i++) {
for (j=nstart; j<nstart+n; j++) {
for (k=pstart; k<pstart+p; k++) {
if (i % 2) {
coors[k][j][i].x = coors[k][j][i-1].x + .1*(coors[k][j][i+1].x - coors[k][j][i-1].x);
}
if (j % 2) {
coors[k][j][i].y = coors[k][j-1][i].y + .3*(coors[k][j+1][i].y - coors[k][j-1][i].y);
}
if (k % 2) {
coors[k][j][i].z = coors[k-1][j][i].z + .4*(coors[k+1][j][i].z - coors[k-1][j][i].z);
}
}
}
}
ierr = DMDAVecRestoreArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&global);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(cda,gc,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(cda,gc,INSERT_VALUES,global);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetCoordinates1d(DM da)
{
PetscErrorCode ierr;
PetscInt i,start,m;
Vec gc,global;
PetscScalar *coors;
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 = DMGetCoordinatesLocal(da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,gc,&coors);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] = coors[i-1] + .1*(coors[i+1] - coors[i-1]);
}
}
ierr = DMDAVecRestoreArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&global);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(cda,gc,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(cda,gc,INSERT_VALUES,global);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);
}
/*@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);
}
/*
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 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);
}
/*
FormInitialGuess - Forms initial approximation.
Input Parameters:
user - user-defined application context
X - vector
Output Parameter:
X - vector
*/
PetscErrorCode FormInitialGuess(AppCtx *user,Vec X)
{
PetscInt i,j,row,mx,my,xs,ys,xm,ym,gxm,gym,gxs,gys;
PetscErrorCode ierr;
PetscReal one = 1.0,lambda,temp1,temp,hx,hy,hxdhy,hydhx,sc;
PetscScalar *x;
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;
temp1 = lambda/(lambda + one);
/*
Get a pointer to vector data.
- For default PETSc vectors,VecGetArray() returns a pointer to
the data array. Otherwise, the routine is implementation dependent.
- You MUST call VecRestoreArray() when you no longer need access to
the array.
*/
ierr = VecGetArray(localX,&x);CHKERRQ(ierr);
/*
Get local grid boundaries (for 2-dimensional DMDA):
xs, ys - starting grid indices (no ghost points)
xm, ym - widths of local grid (no ghost points)
gxs, gys - starting grid indices (including ghost points)
gxm, gym - widths of local grid (including ghost points)
*/
ierr = DMDAGetCorners(user->da,&xs,&ys,PETSC_NULL,&xm,&ym,PETSC_NULL);CHKERRQ(ierr);
ierr = DMDAGetGhostCorners(user->da,&gxs,&gys,PETSC_NULL,&gxm,&gym,PETSC_NULL);CHKERRQ(ierr);
/*
Compute initial guess over the locally owned part of the grid
*/
for (j=ys; j<ys+ym; j++) {
temp = (PetscReal)(PetscMin(j,my-j-1))*hy;
for (i=xs; i<xs+xm; i++) {
row = i - gxs + (j - gys)*gxm;
if (i == 0 || j == 0 || i == mx-1 || j == my-1) {
x[row] = 0.0;
continue;
}
x[row] = temp1*PetscSqrtReal(PetscMin((PetscReal)(PetscMin(i,mx-i-1))*hx,temp));
}
}
/*
Restore vector
*/
ierr = VecRestoreArray(localX,&x);CHKERRQ(ierr);
/*
Insert values into global vector
*/
ierr = DMLocalToGlobalBegin(user->da,localX,INSERT_VALUES,X);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(user->da,localX,INSERT_VALUES,X);CHKERRQ(ierr);
return 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);
}
PetscErrorCode DMLocalToGlobalBegin_Network(DM dm, Vec l, InsertMode mode, Vec g)
{
PetscErrorCode ierr;
DM_Network *network = (DM_Network*) dm->data;
PetscFunctionBegin;
ierr = DMLocalToGlobalBegin(network->plex,l,mode,g);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);
}
PETSC_INTERN PetscErrorCode DMStagSetUniformCoordinatesExplicit_1d(DM dm,PetscReal xmin,PetscReal xmax)
{
PetscErrorCode ierr;
DM_Stag *stagCoord;
DM dmCoord;
Vec coordLocal,coord;
PetscReal h,min;
PetscScalar **arr;
PetscInt ind,start,n,nExtra,s;
PetscInt ileft,ielement;
PetscFunctionBegin;
ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr);
stagCoord = (DM_Stag*) dmCoord->data;
for (s=0; s<2; ++s) {
if (stagCoord->dof[s] !=0 && stagCoord->dof[s] != 1) SETERRQ2(PetscObjectComm((PetscObject)dm),PETSC_ERR_PLIB,"Coordinate DM in 1 dimensions must have 0 or 1 dof on each stratum, but stratum %d has %d dof",s,stagCoord->dof[s]);
}
ierr = DMGetLocalVector(dmCoord,&coordLocal);CHKERRQ(ierr);
ierr = DMStagVecGetArrayDOF(dmCoord,coordLocal,&arr);CHKERRQ(ierr);
if (stagCoord->dof[0]) {
ierr = DMStagGetLocationSlot(dmCoord,DMSTAG_LEFT,0,&ileft);CHKERRQ(ierr);
}
if (stagCoord->dof[1]) {
ierr = DMStagGetLocationSlot(dmCoord,DMSTAG_ELEMENT,0,&ielement);CHKERRQ(ierr);
}
ierr = DMStagGetCorners(dmCoord,&start,NULL,NULL,&n,NULL,NULL,&nExtra,NULL,NULL);CHKERRQ(ierr);
min = xmin;
h = (xmax-xmin)/stagCoord->N[0];
for(ind=start; ind<start + n + nExtra; ++ind) {
if (stagCoord->dof[0]) {
const PetscReal off = 0.0;
arr[ind][ileft] = min + ((PetscReal)ind + off) * h;
}
if (stagCoord->dof[1]) {
const PetscReal off = 0.5;
arr[ind][ielement] = min + ((PetscReal)ind + off) * h;
}
}
ierr = DMStagVecRestoreArrayDOF(dmCoord,coordLocal,&arr);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dmCoord,&coord);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dmCoord,coordLocal,INSERT_VALUES,coord);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dmCoord,coordLocal,INSERT_VALUES,coord);CHKERRQ(ierr);
ierr = DMSetCoordinates(dm,coord);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)dm,(PetscObject)coord);CHKERRQ(ierr);
ierr = VecDestroy(&coord);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmCoord,&coordLocal);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 SNESNASMComputeFinalJacobian_Private(SNES snes, Vec Xfinal)
{
Vec X = Xfinal;
SNES_NASM *nasm = (SNES_NASM*)snes->data;
SNES subsnes;
PetscInt i,lag = 1;
PetscErrorCode ierr;
Vec Xlloc,Xl,Fl,F;
VecScatter oscat,gscat;
DM dm,subdm;
MatStructure flg = DIFFERENT_NONZERO_PATTERN;
PetscFunctionBegin;
if (nasm->fjtype == 2) X = nasm->xinit;
F = snes->vec_func;
if (snes->normschedule == SNES_NORM_NONE) {ierr = SNESComputeFunction(snes,X,F);CHKERRQ(ierr);}
ierr = SNESComputeJacobian(snes,X,&snes->jacobian,&snes->jacobian_pre,&flg);CHKERRQ(ierr);
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
if (nasm->eventrestrictinterp) {ierr = PetscLogEventBegin(nasm->eventrestrictinterp,snes,0,0,0);CHKERRQ(ierr);}
if (nasm->fjtype != 1) {
for (i=0; i<nasm->n; i++) {
Xlloc = nasm->xl[i];
gscat = nasm->gscatter[i];
oscat = nasm->oscatter[i];
ierr = VecScatterBegin(gscat,X,Xlloc,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
}
}
if (nasm->eventrestrictinterp) {ierr = PetscLogEventEnd(nasm->eventrestrictinterp,snes,0,0,0);CHKERRQ(ierr);}
for (i=0; i<nasm->n; i++) {
Fl = nasm->subsnes[i]->vec_func;
Xl = nasm->x[i];
Xlloc = nasm->xl[i];
subsnes = nasm->subsnes[i];
oscat = nasm->oscatter[i];
gscat = nasm->gscatter[i];
if (nasm->fjtype != 1) {ierr = VecScatterEnd(gscat,X,Xlloc,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);}
ierr = SNESGetDM(subsnes,&subdm);CHKERRQ(ierr);
ierr = DMSubDomainRestrict(dm,oscat,gscat,subdm);CHKERRQ(ierr);
if (nasm->fjtype != 1) {
ierr = DMLocalToGlobalBegin(subdm,Xlloc,INSERT_VALUES,Xl);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(subdm,Xlloc,INSERT_VALUES,Xl);CHKERRQ(ierr);
}
if (subsnes->lagjacobian == -1) subsnes->lagjacobian = -2;
else if (subsnes->lagjacobian > 1) lag = subsnes->lagjacobian;
ierr = SNESComputeFunction(subsnes,Xl,Fl);CHKERRQ(ierr);
ierr = SNESComputeJacobian(subsnes,Xl,&subsnes->jacobian,&subsnes->jacobian_pre,&flg);CHKERRQ(ierr);
if (lag > 1) subsnes->lagjacobian = lag;
ierr = KSPSetOperators(subsnes->ksp,subsnes->jacobian,subsnes->jacobian_pre,flg);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode CreatePressureNullSpace(DM dm, AppCtx *user, MatNullSpace *nullSpace)
{
Vec vec, localVec;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMGetGlobalVector(dm, &vec);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &localVec);CHKERRQ(ierr);
ierr = VecSet(vec, 0.0);CHKERRQ(ierr);
/* Put a constant in for all pressures
Could change this to project the constant function onto the pressure space (when that is finished) */
{
PetscSection section;
PetscInt pStart, pEnd, p;
PetscScalar *a;
ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);
ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr);
ierr = VecGetArray(localVec, &a);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt fDim, off, d;
ierr = PetscSectionGetFieldDof(section, p, 1, &fDim);CHKERRQ(ierr);
ierr = PetscSectionGetFieldOffset(section, p, 1, &off);CHKERRQ(ierr);
for (d = 0; d < fDim; ++d) a[off+d] = 1.0;
}
ierr = VecRestoreArray(localVec, &a);CHKERRQ(ierr);
}
ierr = DMLocalToGlobalBegin(dm, localVec, INSERT_VALUES, vec);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm, localVec, INSERT_VALUES, vec);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &localVec);CHKERRQ(ierr);
ierr = VecNormalize(vec, NULL);CHKERRQ(ierr);
if (user->debug) {
ierr = PetscPrintf(PetscObjectComm((PetscObject)dm), "Pressure Null Space\n");CHKERRQ(ierr);
ierr = VecView(vec, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = MatNullSpaceCreate(PetscObjectComm((PetscObject)dm), PETSC_FALSE, 1, &vec, nullSpace);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dm, &vec);CHKERRQ(ierr);
/* New style for field null spaces */
{
PetscObject pressure;
MatNullSpace nullSpacePres;
ierr = DMGetField(dm, 1, &pressure);CHKERRQ(ierr);
ierr = MatNullSpaceCreate(PetscObjectComm(pressure), PETSC_TRUE, 0, NULL, &nullSpacePres);CHKERRQ(ierr);
ierr = PetscObjectCompose(pressure, "nullspace", (PetscObject) nullSpacePres);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpacePres);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 FormFunction(SNES snes,Vec X,Vec F,void *ptr)
{
AppCtx *user = (AppCtx *) ptr;
PetscInt i, j, row, mx, my, xs, ys, xm, ym, Xs, Ys, Xm, Ym;
PetscErrorCode ierr;
double two = 2.0, one = 1.0, lambda,hx, hy, hxdhy, hydhx,sc;
PetscScalar u, uxx, uyy, *x,*f;
Vec localX = user->fine.localX, localF = user->fine.localF;
mx = user->fine.mx; my = user->fine.my; lambda = user->param;
hx = one/(double)(mx-1); hy = one/(double)(my-1);
sc = hx*hy*lambda; hxdhy = hx/hy; hydhx = hy/hx;
/* Get ghost points */
ierr = DMGlobalToLocalBegin(user->fine.da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user->fine.da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMDAGetCorners(user->fine.da,&xs,&ys,0,&xm,&ym,0);CHKERRQ(ierr);
ierr = DMDAGetGhostCorners(user->fine.da,&Xs,&Ys,0,&Xm,&Ym,0);CHKERRQ(ierr);
ierr = VecGetArray(localX,&x);CHKERRQ(ierr);
ierr = VecGetArray(localF,&f);CHKERRQ(ierr);
/* Evaluate function */
for (j=ys; j<ys+ym; j++) {
row = (j - Ys)*Xm + xs - Xs - 1;
for (i=xs; i<xs+xm; i++) {
row++;
if (i > 0 && i < mx-1 && j > 0 && j < my-1) {
u = x[row];
uxx = (two*u - x[row-1] - x[row+1])*hydhx;
uyy = (two*u - x[row-Xm] - x[row+Xm])*hxdhy;
f[row] = uxx + uyy - sc*exp(u);
} else if ((i > 0 && i < mx-1) || (j > 0 && j < my-1)){
f[row] = .5*two*(hydhx + hxdhy)*x[row];
} else {
f[row] = .25*two*(hydhx + hxdhy)*x[row];
}
}
}
ierr = VecRestoreArray(localX,&x);CHKERRQ(ierr);
ierr = VecRestoreArray(localF,&f);CHKERRQ(ierr);
/* Insert values into global vector */
ierr = DMLocalToGlobalBegin(user->fine.da,localF,INSERT_VALUES,F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(user->fine.da,localF,INSERT_VALUES,F);CHKERRQ(ierr);
ierr = PetscLogFlops(11.0*ym*xm);CHKERRQ(ierr);
return 0;
}
/*@
DMPlexTSComputeRHSFunctionFVM - Form the local forcing F from the local input X using pointwise functions specified by the user
Input Parameters:
+ dm - The mesh
. t - The time
. locX - Local solution
- user - The user context
Output Parameter:
. F - Global output vector
Level: developer
.seealso: DMPlexComputeJacobianActionFEM()
@*/
PetscErrorCode DMPlexTSComputeRHSFunctionFVM(DM dm, PetscReal time, Vec locX, Vec F, void *user)
{
Vec locF;
PetscInt cStart, cEnd, cEndInterior;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
ierr = DMGetLocalVector(dm, &locF);CHKERRQ(ierr);
ierr = VecZeroEntries(locF);CHKERRQ(ierr);
ierr = DMPlexComputeResidual_Internal(dm, cStart, cEnd, time, locX, NULL, locF, user);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm, locF, INSERT_VALUES, F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm, locF, INSERT_VALUES, F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locF);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);
}
static PetscErrorCode TestFields(DM dmstag)
{
PetscErrorCode ierr;
Vec vecLocal,vecGlobal;
PetscReal norm2;
PetscFunctionBeginUser;
ierr = DMCreateLocalVector(dmstag,&vecLocal);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dmstag,&vecGlobal);CHKERRQ(ierr);
ierr = VecSet(vecLocal,1.0);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dmstag,vecLocal,INSERT_VALUES,vecGlobal);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd (dmstag,vecLocal,INSERT_VALUES,vecGlobal);CHKERRQ(ierr);
ierr = VecSet(vecGlobal,2.0);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmstag,vecGlobal,INSERT_VALUES,vecLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd (dmstag,vecGlobal,INSERT_VALUES,vecLocal);CHKERRQ(ierr);
ierr = VecNorm(vecGlobal,NORM_2,&norm2);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"2 Norm of test vector: %g\n",(double)norm2);CHKERRQ(ierr);
ierr = VecDestroy(&vecLocal);CHKERRQ(ierr);
ierr = VecDestroy(&vecGlobal);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;
}
PetscErrorCode MatMult_GlobalToLocalNormal(Mat CtC, Vec x, Vec y)
{
DM dm;
Vec local, mask;
projectConstraintsCtx *ctx;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatShellGetContext(CtC,&ctx);CHKERRQ(ierr);
dm = ctx->dm;
mask = ctx->mask;
ierr = DMGetLocalVector(dm,&local);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,x,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,x,INSERT_VALUES,local);CHKERRQ(ierr);
if (mask) {ierr = VecPointwiseMult(local,mask,local);CHKERRQ(ierr);}
ierr = VecSet(y,0.);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm,local,ADD_VALUES,y);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm,local,ADD_VALUES,y);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&local);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexTSComputeRHSFunctionFVM - Form the local forcing F from the local input X using pointwise functions specified by the user
Input Parameters:
+ dm - The mesh
. t - The time
. locX - Local solution
- user - The user context
Output Parameter:
. F - Global output vector
Level: developer
.seealso: DMPlexComputeJacobianActionFEM()
@*/
PetscErrorCode DMPlexTSComputeRHSFunctionFVM(DM dm, PetscReal time, Vec locX, Vec F, void *user)
{
Vec locF;
PetscInt cStart, cEnd, cEndInterior;
DM plex;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMTSConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
ierr = DMGetLocalVector(plex, &locF);CHKERRQ(ierr);
ierr = VecZeroEntries(locF);CHKERRQ(ierr);
ierr = DMPlexComputeResidual_Internal(plex, cStart, cEnd, time, locX, NULL, time, locF, user);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(plex, locF, ADD_VALUES, F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(plex, locF, ADD_VALUES, F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(plex, &locF);CHKERRQ(ierr);
ierr = DMDestroy(&plex);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetInitialCondition(DM dm, Vec X, User user)
{
DM dmCell;
const PetscScalar *cellgeom;
PetscScalar *x;
PetscInt cStart, cEnd, cEndInterior = user->cEndInterior, c;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = VecGetDM(user->cellgeom, &dmCell);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->cellgeom, &cellgeom);CHKERRQ(ierr);
ierr = VecGetArray(X, &x);CHKERRQ(ierr);
for (c = cStart; c < cEndInterior; ++c) {
const CellGeom *cg;
PetscScalar *xc;
ierr = DMPlexPointLocalRead(dmCell,c,cellgeom,&cg);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dm,c,x,&xc);CHKERRQ(ierr);
if (xc) {
ierr = InitialCondition(0.0, cg->centroid, xc, user);CHKERRQ(ierr);
}
}
ierr = VecRestoreArrayRead(user->cellgeom, &cellgeom);CHKERRQ(ierr);
ierr = VecRestoreArray(X, &x);CHKERRQ(ierr);
{ //Apply the Boundary condition for the intial condition
Vec XLocal;
ierr = DMGetLocalVector(user->dm, &XLocal);CHKERRQ(ierr);
ierr = VecSet(XLocal, 0);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(user->dm, X, INSERT_VALUES, XLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user->dm, X, INSERT_VALUES, XLocal);CHKERRQ(ierr);
ierr = ApplyBC(user->dm, user->current_time, XLocal, user);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(user->dm, XLocal, INSERT_VALUES, X);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(user->dm, XLocal, INSERT_VALUES, X);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode FormInitialGuess1(AppCtx *user,Vec X)
{
PetscInt i, j, row, mx, my, xs, ys, xm, ym, Xm, Ym, Xs, Ys;
PetscErrorCode ierr;
double one = 1.0, lambda, temp1, temp, hx, hy;
/* double hxdhy, hydhx,sc; */
PetscScalar *x;
Vec localX = user->fine.localX;
mx = user->fine.mx; my = user->fine.my; lambda = user->param;
hx = one/(double)(mx-1); hy = one/(double)(my-1);
/* sc = hx*hy*lambda; hxdhy = hx/hy; hydhx = hy/hx; */
temp1 = lambda/(lambda + one);
/* Get ghost points */
ierr = DMDAGetCorners(user->fine.da,&xs,&ys,0,&xm,&ym,0);CHKERRQ(ierr);
ierr = DMDAGetGhostCorners(user->fine.da,&Xs,&Ys,0,&Xm,&Ym,0);CHKERRQ(ierr);
ierr = VecGetArray(localX,&x);CHKERRQ(ierr);
/* Compute initial guess */
for (j=ys; j<ys+ym; j++) {
temp = (double)(PetscMin(j,my-j-1))*hy;
for (i=xs; i<xs+xm; i++) {
row = i - Xs + (j - Ys)*Xm;
if (i == 0 || j == 0 || i == mx-1 || j == my-1 ) {
x[row] = 0.0;
continue;
}
x[row] = temp1*PetscSqrtReal( PetscMin( (double)(PetscMin(i,mx-i-1))*hx,temp) );
}
}
ierr = VecRestoreArray(localX,&x);CHKERRQ(ierr);
/* Insert values into global vector */
ierr = DMLocalToGlobalBegin(user->fine.da,localX,INSERT_VALUES,X);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(user->fine.da,localX,INSERT_VALUES,X);CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
PetscInt M = 6,N = 5,P = 4, m = PETSC_DECIDE,n = PETSC_DECIDE,p = PETSC_DECIDE,i,j,k,is,js,ks,in,jen,kn;
PetscErrorCode ierr;
DM da;
Vec local,global;
PetscScalar ****l;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
/* Create distributed array and get vectors */
ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,P,m,n,p,2,1,NULL,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);
ierr = DMDAGetCorners(da,&is,&js,&ks,&in,&jen,&kn);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(da,local,&l);CHKERRQ(ierr);
for (i=is; i<is+in; i++) {
for (j=js; j<js+jen; j++) {
for (k=ks; k<ks+kn; k++) {
l[k][j][i][0] = 2*(i + j*M + k*M*N);
l[k][j][i][1] = 2*(i + j*M + k*M*N) + 1;
}
}
}
ierr = DMDAVecRestoreArrayDOF(da,local,&l);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);
/* Free memory */
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode ComputePredictor(DM da, UserContext *user)
{
Vec uOldLocal, uLocal,uOld;
PetscScalar *pOld;
PetscScalar *p;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMGetGlobalVector(da, &uOld);CHKERRQ(ierr);
ierr = DMGetLocalVector(da, &uOldLocal);CHKERRQ(ierr);
ierr = DMGetLocalVector(da, &uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da, uOld, INSERT_VALUES, uOldLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da, uOld, INSERT_VALUES, uOldLocal);CHKERRQ(ierr);
ierr = VecGetArray(uOldLocal, &pOld);CHKERRQ(ierr);
ierr = VecGetArray(uLocal, &p);CHKERRQ(ierr);
/* Source terms are all zero right now */
ierr = CalculateElementVelocity(da, user);CHKERRQ(ierr);
ierr = TaylorGalerkinStepI(da, user);CHKERRQ(ierr);
ierr = TaylorGalerkinStepIIMomentum(da, user);CHKERRQ(ierr);
ierr = TaylorGalerkinStepIIMassEnergy(da, user);CHKERRQ(ierr);
/* Solve equation (9) for \delta(\rho\vu) and (\rho\vu)^* */
/* Solve equation (13) for \delta\rho and \rho^* */
/* Solve equation (15) for \delta(\rho e_t) and (\rho e_t)^* */
/* Apply artifical dissipation */
/* Determine the smoothed explicit pressure, \tilde P and temperature \tilde T using the equation of state */
ierr = VecRestoreArray(uOldLocal, &pOld);CHKERRQ(ierr);
ierr = VecRestoreArray(uLocal, &p);CHKERRQ(ierr);
#if 0
ierr = DMLocalToGlobalBegin(da, uLocal, ADD_VALUES,u);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da, uLocal, ADD_VALUES,u);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da, &uOldLocal);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da, &uLocal);CHKERRQ(ierr);
#endif
PetscFunctionReturn(0);
}
