static PetscErrorCode bfgs_apply(PC pc, Vec xin, Vec xout)
{
TaoLMVMMat *M ;
TaoVecPetsc Xin(xin);
TaoVecPetsc Xout(xout);
TaoTruth info2;
int info;
PetscFunctionBegin;
PetscTruth VerbosePrint = PETSC_FALSE;
PetscOptionsGetTruth(PETSC_NULL,"-verboseapp",&VerbosePrint,PETSC_NULL);
info = PCShellGetContext(pc,(void**)&M); CHKERRQ(info);
PetscScalar solnNorm,solnDot;
info = VecNorm(xin,NORM_2,&solnNorm); CHKERRQ(info)
info=PetscPrintf(PETSC_COMM_WORLD,"bfgs_apply: ||Xin||_2 = %22.15e\n",solnNorm);
if(VerbosePrint) VecView(xin,0);
info = M->Solve(&Xin, &Xout, &info2); CHKERRQ(info);
info = VecNorm(xout,NORM_2,&solnNorm); CHKERRQ(info)
info = VecDot(xin,xout,&solnDot); CHKERRQ(info)
info=PetscPrintf(PETSC_COMM_WORLD,"bfgs_apply: ||Xout||_2 = %22.15e, Xin^T Xout= %22.15e\n",solnNorm,solnDot);
if(VerbosePrint) VecView(xout,0);
PetscFunctionReturn(0);
}
/*
Setup for the custom preconditioner
*/
PetscErrorCode MyPCSetUp(PC pc)
{
AppCtx *app;
PetscErrorCode ierr;
DA da;
PetscFunctionBegin;
ierr = PCShellGetContext(pc,(void**)&app);
CHKERRQ(ierr);
/* create the linear solver for the Neutron diffusion */
ierr = DMMGCreate(app->comm,1,0,&app->fdmmg);
CHKERRQ(ierr);
ierr = DMMGSetOptionsPrefix(app->fdmmg,"phi_");
CHKERRQ(ierr);
ierr = DMMGSetUser(app->fdmmg,0,app);
CHKERRQ(ierr);
ierr = DACreate2d(app->comm,DA_NONPERIODIC,DA_STENCIL_STAR,app->nxv,app->nyvf,PETSC_DETERMINE,1,1,1,0,0,&da);
CHKERRQ(ierr);
ierr = DMMGSetDM(app->fdmmg,(DM)da);
CHKERRQ(ierr);
ierr = DMMGSetKSP(app->fdmmg,PETSC_NULL,MyFormMatrix);
CHKERRQ(ierr);
app->dx = DMMGGetRHS(app->fdmmg);
app->dy = DMMGGetx(app->fdmmg);
ierr = VecDuplicate(app->dy,&app->c);
CHKERRQ(ierr);
ierr = DADestroy(da);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode ourshellsetupctx(PC pc)
{
PetscErrorCode ierr = 0;
void *ctx;
ierr = PCShellGetContext(pc,&ctx);CHKERRQ(ierr);
(*(void (PETSC_STDCALL *)(PC*,void*,PetscErrorCode*))(((PetscObject)pc)->fortran_func_pointers[3]))(&pc,ctx,&ierr);CHKERRQ(ierr);
return 0;
}
PetscErrorCode __feel_petsc_preconditioner_view( PC pc, PetscViewer viewer)
{
void *ctx;
PetscErrorCode ierr = PCShellGetContext( pc,&ctx );
CHKERRQ( ierr );
Preconditioner<double> * preconditioner = static_cast<Preconditioner<double>*>( ctx );
preconditioner->view();
return 0;
}
PetscErrorCode PCShellApply_Matinv(PC pc,Vec xin,Vec xout)
{
PetscErrorCode ierr;
Mat X;
PetscFunctionBeginUser;
ierr = PCShellGetContext(pc,(void**)&X);CHKERRQ(ierr);
ierr = MatMult(X,xin,xout);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode PCDestroy_Noise(PC pc)
{
PetscErrorCode ierr;
PCNoise_Ctx *ctx;
PetscFunctionBeginUser;
ierr = PCShellGetContext(pc,(void**)&ctx);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&ctx->random);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
SampleShellPCApply - This routine demonstrates the use of a
user-provided preconditioner.
Input Parameters:
+ pc - preconditioner object
- x - input vector
Output Parameter:
. y - preconditioned vector
Notes:
This code implements the Jacobi preconditioner, merely as an
example of working with a PCSHELL. Note that the Jacobi method
is already provided within PETSc.
*/
PetscErrorCode SampleShellPCApply(PC pc,Vec x,Vec y)
{
SampleShellPC *shell;
PetscErrorCode ierr;
ierr = PCShellGetContext(pc,(void**)&shell);CHKERRQ(ierr);
ierr = VecPointwiseMult(y,x,shell->diag);CHKERRQ(ierr);
return 0;
}
PetscErrorCode __feel_petsc_preconditioner_setup ( PC pc )
{
void *ctx;
PetscErrorCode ierr = PCShellGetContext( pc,&ctx );
CHKERRQ( ierr );
Preconditioner<double> * preconditioner = static_cast<Preconditioner<double>*>( ctx );
preconditioner->init();
VLOG(2) << "__feel_petsc_preconditioner_setup: init prec\n";
return 0;
}
/*
SampleShellPCDestroy - This routine destroys a user-defined
preconditioner context.
Input Parameter:
. shell - user-defined preconditioner context
*/
PetscErrorCode SampleShellPCDestroy(PC pc)
{
SampleShellPC *shell;
PetscErrorCode ierr;
ierr = PCShellGetContext(pc,(void**)&shell);CHKERRQ(ierr);
ierr = VecDestroy(&shell->diag);CHKERRQ(ierr);
ierr = PetscFree(shell);CHKERRQ(ierr);
return 0;
}
PetscErrorCode PCSetup_Noise(PC pc)
{
PetscErrorCode ierr;
PCNoise_Ctx *ctx;
PetscFunctionBeginUser;
ierr = PCShellGetContext(pc,(void**)&ctx);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&ctx->random);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(ctx->random,-1.0,1.0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode MatLMVMSolveShell(PC pc, Vec b, Vec x)
{
PetscErrorCode ierr;
Mat M;
PetscFunctionBegin;
PetscValidHeaderSpecific(pc,PC_CLASSID,1);
PetscValidHeaderSpecific(b,VEC_CLASSID,2);
PetscValidHeaderSpecific(x,VEC_CLASSID,3);
ierr = PCShellGetContext(pc,(void**)&M);CHKERRQ(ierr);
ierr = MatLMVMSolve(M, b, x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode __feel_petsc_preconditioner_apply( PC pc, Vec x, Vec y )
{
void *ctx;
PetscErrorCode ierr = PCShellGetContext( pc,&ctx );
CHKERRQ( ierr );
Preconditioner<double> * preconditioner = static_cast<Preconditioner<double>*>( ctx );
VectorPetsc<double> x_vec( x );
VectorPetsc<double> y_vec( y );
preconditioner->apply( x_vec,y_vec );
return 0;
}
PetscErrorCode
IBImplicitStaggeredHierarchyIntegrator::compositeIBPCApply_SAMRAI(PC pc, Vec x, Vec y)
{
PetscErrorCode ierr;
void* ctx;
ierr = PCShellGetContext(pc, &ctx);
IBTK_CHKERRQ(ierr);
IBImplicitStaggeredHierarchyIntegrator* ib_integrator =
static_cast<IBImplicitStaggeredHierarchyIntegrator*>(ctx);
ierr = ib_integrator->compositeIBPCApply(x, y);
IBTK_CHKERRQ(ierr);
return ierr;
} // compositeIBPCApply_SAMRAI
PetscErrorCode MyPCDestroy(PC pc)
{
AppCtx *app;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PCShellGetContext(pc,(void**)&app);
CHKERRQ(ierr);
ierr = DMMGDestroy(app->fdmmg);
CHKERRQ(ierr);
ierr = VecDestroy(app->c);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
SampleShellPCSetUp - This routine sets up a user-defined
preconditioner context.
Input Parameters:
. pc - preconditioner object
. pmat - preconditioner matrix
. x - vector
Output Parameter:
. shell - fully set up user-defined preconditioner context
Notes:
In this example, we define the shell preconditioner to be Jacobi's
method. Thus, here we create a work vector for storing the reciprocal
of the diagonal of the preconditioner matrix; this vector is then
used within the routine SampleShellPCApply().
*/
PetscErrorCode SampleShellPCSetUp(PC pc,Mat pmat,Vec x)
{
SampleShellPC *shell;
Vec diag;
PetscErrorCode ierr;
ierr = PCShellGetContext(pc,(void**)&shell);CHKERRQ(ierr);
ierr = VecDuplicate(x,&diag);CHKERRQ(ierr);
ierr = MatGetDiagonal(pmat,diag);CHKERRQ(ierr);
ierr = VecReciprocal(diag);CHKERRQ(ierr);
shell->diag = diag;
return 0;
}
PetscErrorCode PCBDDCDestroyFETIDPPC(PC pc)
{
FETIDPPC_ctx pc_ctx;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PCShellGetContext(pc,(void**)&pc_ctx);CHKERRQ(ierr);
ierr = VecDestroy(&pc_ctx->lambda_local);CHKERRQ(ierr);
ierr = MatDestroy(&pc_ctx->B_Ddelta);CHKERRQ(ierr);
ierr = VecScatterDestroy(&pc_ctx->l2g_lambda);CHKERRQ(ierr);
ierr = MatDestroy(&pc_ctx->S_j);CHKERRQ(ierr);
ierr = PCDestroy(&pc_ctx->pc);CHKERRQ(ierr); /* decrease PCBDDC reference count */
ierr = PetscFree(pc_ctx);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode PCApply_Noise(PC pc,Vec xin,Vec xout)
{
PetscErrorCode ierr;
PCNoise_Ctx *ctx;
PetscReal nrmin, nrmnoise;
PetscFunctionBeginUser;
ierr = PCShellGetContext(pc,(void**)&ctx);CHKERRQ(ierr);
/* xout is ||xin|| * ctx->eta* f, where f is a pseudorandom unit vector
(Note that this should always be combined additively with another PC) */
ierr = VecSetRandom(xout,ctx->random);CHKERRQ(ierr);
ierr = VecNorm(xin,NORM_2,&nrmin);CHKERRQ(ierr);
ierr = VecNorm(xout,NORM_2,&nrmnoise);CHKERRQ(ierr);
ierr = VecScale(xout,ctx->eta*(nrmin/nrmnoise));CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode PCBDDCDestroyNullSpaceCorrectionPC(PC pc)
{
NullSpaceCorrection_ctx pc_ctx;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PCShellGetContext(pc,(void**)&pc_ctx);CHKERRQ(ierr);
ierr = VecDestroy(&pc_ctx->work_small_1);CHKERRQ(ierr);
ierr = VecDestroy(&pc_ctx->work_small_2);CHKERRQ(ierr);
ierr = VecDestroy(&pc_ctx->work_full_1);CHKERRQ(ierr);
ierr = VecDestroy(&pc_ctx->work_full_2);CHKERRQ(ierr);
ierr = MatDestroy(&pc_ctx->basis_mat);CHKERRQ(ierr);
ierr = MatDestroy(&pc_ctx->Lbasis_mat);CHKERRQ(ierr);
ierr = MatDestroy(&pc_ctx->Kbasis_mat);CHKERRQ(ierr);
ierr = PCDestroy(&pc_ctx->local_pc);CHKERRQ(ierr);
ierr = PetscFree(pc_ctx);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode PCBDDCApplyNullSpaceCorrectionPC(PC pc,Vec x,Vec y)
{
NullSpaceCorrection_ctx pc_ctx;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PCShellGetContext(pc,(void**)&pc_ctx);CHKERRQ(ierr);
/* E */
ierr = MatMultTranspose(pc_ctx->Lbasis_mat,x,pc_ctx->work_small_2);CHKERRQ(ierr);
ierr = MatMultAdd(pc_ctx->Kbasis_mat,pc_ctx->work_small_2,x,pc_ctx->work_full_1);CHKERRQ(ierr);
/* P^-1 */
ierr = PCApply(pc_ctx->local_pc,pc_ctx->work_full_1,pc_ctx->work_full_2);CHKERRQ(ierr);
/* E^T */
ierr = MatMultTranspose(pc_ctx->Kbasis_mat,pc_ctx->work_full_2,pc_ctx->work_small_1);CHKERRQ(ierr);
ierr = VecScale(pc_ctx->work_small_1,-1.0);CHKERRQ(ierr);
ierr = MatMultAdd(pc_ctx->Lbasis_mat,pc_ctx->work_small_1,pc_ctx->work_full_2,pc_ctx->work_full_1);CHKERRQ(ierr);
/* Sum contributions */
ierr = MatMultAdd(pc_ctx->basis_mat,pc_ctx->work_small_2,pc_ctx->work_full_1,y);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FETIDPPCApplyTranspose(PC fetipc, Vec x, Vec y)
{
FETIDPPC_ctx pc_ctx;
PC_IS *pcis;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PCShellGetContext(fetipc,(void**)&pc_ctx);
pcis = (PC_IS*)pc_ctx->pc->data;
/* Application of B_Ddelta^T */
ierr = VecScatterBegin(pc_ctx->l2g_lambda,x,pc_ctx->lambda_local,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterEnd(pc_ctx->l2g_lambda,x,pc_ctx->lambda_local,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecSet(pcis->vec2_B,0.0);CHKERRQ(ierr);
ierr = MatMultTranspose(pc_ctx->B_Ddelta,pc_ctx->lambda_local,pcis->vec2_B);CHKERRQ(ierr);
/* Application of local Schur complement */
ierr = MatMultTranspose(pc_ctx->S_j,pcis->vec2_B,pcis->vec1_B);CHKERRQ(ierr);
/* Application of B_Ddelta */
ierr = MatMult(pc_ctx->B_Ddelta,pcis->vec1_B,pc_ctx->lambda_local);CHKERRQ(ierr);
ierr = VecSet(y,0.0);CHKERRQ(ierr);
ierr = VecScatterBegin(pc_ctx->l2g_lambda,pc_ctx->lambda_local,y,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(pc_ctx->l2g_lambda,pc_ctx->lambda_local,y,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode ShellApplyML(PC pc,Vec x,Vec y)
{
PetscErrorCode ierr;
ML_Epetra::MultiLevelPreconditioner *mlp = 0;
void* ctx;
ierr = PCShellGetContext(pc,&ctx); CHKERRQ(ierr);
mlp = (ML_Epetra::MultiLevelPreconditioner*)ctx;
#endif
/* Wrap x and y as Epetra_Vectors. */
PetscScalar *xvals,*yvals;
ierr = VecGetArray(x,&xvals);CHKERRQ(ierr);
Epetra_Vector epx(View,mlp->OperatorDomainMap(),xvals);
ierr = VecGetArray(y,&yvals);CHKERRQ(ierr);
Epetra_Vector epy(View,mlp->OperatorRangeMap(),yvals);
/* Apply ML. */
mlp->ApplyInverse(epx,epy);
/* Clean up and return. */
ierr = VecRestoreArray(x,&xvals);CHKERRQ(ierr);
ierr = VecRestoreArray(y,&yvals);CHKERRQ(ierr);
return 0;
} /*ShellApplyML*/
/*
Here is my custom preconditioner
Capital vectors: X, X1 are global vectors
Small vectors: x, x1 are local ghosted vectors
Prefixed a: ax1, aY1 are arrays that access the vector values (either local (ax1) or global aY1)
*/
PetscErrorCode MyPCApply(PC pc,Vec X,Vec Y)
{
AppCtx *app;
PetscErrorCode ierr;
Vec X1,X2,X3,x1,x2,Y1,Y2,Y3;
DALocalInfo info1,info2,info3;
DA da1,da2,da3;
PetscInt i,j;
FluidField *ax1,*aY1;
PetscScalar **ax2,**aY2;
PetscFunctionBegin;
ierr = PCShellGetContext(pc,(void**)&app);
CHKERRQ(ierr);
/* obtain information about the three meshes */
ierr = DMCompositeGetEntries(app->pack,&da1,&da2,&da3);
CHKERRQ(ierr);
ierr = DAGetLocalInfo(da1,&info1);
CHKERRQ(ierr);
ierr = DAGetLocalInfo(da2,&info2);
CHKERRQ(ierr);
ierr = DAGetLocalInfo(da3,&info3);
CHKERRQ(ierr);
/* get ghosted version of fluid and thermal conduction, global for phi and C */
ierr = DMCompositeGetAccess(app->pack,X,&X1,&X2,&X3);
CHKERRQ(ierr);
ierr = DMCompositeGetLocalVectors(app->pack,&x1,&x2,PETSC_NULL);
CHKERRQ(ierr);
ierr = DAGlobalToLocalBegin(da1,X1,INSERT_VALUES,x1);
CHKERRQ(ierr);
ierr = DAGlobalToLocalEnd(da1,X1,INSERT_VALUES,x1);
CHKERRQ(ierr);
ierr = DAGlobalToLocalBegin(da2,X2,INSERT_VALUES,x2);
CHKERRQ(ierr);
ierr = DAGlobalToLocalEnd(da2,X2,INSERT_VALUES,x2);
CHKERRQ(ierr);
/* get global version of result vector */
ierr = DMCompositeGetAccess(app->pack,Y,&Y1,&Y2,&Y3);
CHKERRQ(ierr);
/* pull out the phi and C values */
ierr = VecStrideGather(X3,0,app->dx,INSERT_VALUES);
CHKERRQ(ierr);
ierr = VecStrideGather(X3,1,app->c,INSERT_VALUES);
CHKERRQ(ierr);
/* update C via formula 38; put back into return vector */
ierr = VecAXPY(app->c,0.0,app->dx);
CHKERRQ(ierr);
ierr = VecScale(app->c,1.0);
CHKERRQ(ierr);
ierr = VecStrideScatter(app->c,1,Y3,INSERT_VALUES);
CHKERRQ(ierr);
/* form the right hand side of the phi equation; solve system; put back into return vector */
ierr = VecAXPBY(app->dx,0.0,1.0,app->c);
CHKERRQ(ierr);
ierr = DMMGSolve(app->fdmmg);
CHKERRQ(ierr);
ierr = VecStrideScatter(app->dy,0,Y3,INSERT_VALUES);
CHKERRQ(ierr);
/* access the ghosted x1 and x2 as arrays */
ierr = DAVecGetArray(da1,x1,&ax1);
CHKERRQ(ierr);
ierr = DAVecGetArray(da2,x2,&ax2);
CHKERRQ(ierr);
/* access global y1 and y2 as arrays */
ierr = DAVecGetArray(da1,Y1,&aY1);
CHKERRQ(ierr);
ierr = DAVecGetArray(da2,Y2,&aY2);
CHKERRQ(ierr);
for (i=info1.xs; i<info1.xs+info1.xm; i++) {
aY1[i].prss = ax1[i].prss;
aY1[i].ergg = ax1[i].ergg;
aY1[i].ergf = ax1[i].ergf;
aY1[i].alfg = ax1[i].alfg;
aY1[i].velg = ax1[i].velg;
aY1[i].velf = ax1[i].velf;
}
for (j=info2.ys; j<info2.ys+info2.ym; j++) {
for (i=info2.xs; i<info2.xs+info2.xm; i++) {
aY2[j][i] = ax2[j][i];
}
}
ierr = DAVecRestoreArray(da1,x1,&ax1);
CHKERRQ(ierr);
ierr = DAVecRestoreArray(da2,x2,&ax2);
CHKERRQ(ierr);
ierr = DAVecRestoreArray(da1,Y1,&aY1);
CHKERRQ(ierr);
ierr = DAVecRestoreArray(da2,Y2,&aY2);
CHKERRQ(ierr);
ierr = DMCompositeRestoreLocalVectors(app->pack,&x1,&x2,PETSC_NULL);
CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(app->pack,X,&X1,&X2,&X3);
CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(app->pack,Y,&Y1,&Y2,&Y3);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PETSC_EXTERN void PETSC_STDCALL pcshellgetcontext_(PC *pc,void **ctx,PetscErrorCode *ierr)
{
*ierr = PCShellGetContext(*pc,ctx);
}