PetscErrorCode bsscr_DGMiGtD( Mat *_K2, Mat K, Mat G, Mat M){ Mat K2; Vec diag; Vec Mdiag; Mat MinvGt; Mat Gtrans; PetscErrorCode ierr; PetscFunctionBegin; MatGetVecs( K, &diag, PETSC_NULL ); MatGetDiagonal( K, diag ); VecSqrt(diag); //VecReciprocal(diag);/* trying something different here */ MatGetVecs( M, &Mdiag, PETSC_NULL ); MatGetDiagonal( M, Mdiag ); VecReciprocal(Mdiag); #if( PETSC_VERSION_MAJOR <= 2 ) ierr=MatTranspose(G, &Gtrans);CHKERRQ(ierr); #else ierr=MatTranspose(G, MAT_INITIAL_MATRIX,&Gtrans);CHKERRQ(ierr); #endif ierr=MatConvert(Gtrans, MATSAME, MAT_INITIAL_MATRIX, &MinvGt);CHKERRQ(ierr);/* copy Gtrans -> MinvGt */ MatDiagonalScale(MinvGt, Mdiag, PETSC_NULL);/* Minv*Gtrans */ /* MAT_INITIAL_MATRIX -> creates K2 matrix : PETSC_DEFAULT for fill ratio: run with -info to find what it should be*/ ierr=MatMatMult( G, MinvGt, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &K2);CHKERRQ(ierr);/* K2 = G*Minv*Gtrans */ MatDiagonalScale(K2, diag, diag );/* K2 = D*K2*D = D*G*Minv*Gtrans*D */ Stg_MatDestroy(&Gtrans); Stg_MatDestroy(&MinvGt); Stg_VecDestroy(&diag); Stg_VecDestroy(&Mdiag); *_K2=K2; PetscFunctionReturn(0); }
PetscErrorCode KSPBuildPressure_CB_Nullspace_BSSCR(KSP ksp) { KSP_BSSCR *bsscr = (KSP_BSSCR *)ksp->data; FeEquationNumber *eq_num = bsscr->solver->st_sle->pSolnVec->feVariable->eqNum; FeMesh *feMesh = bsscr->solver->st_sle->pSolnVec->feVariable->feMesh; /* is the pressure mesh */ unsigned ijk[3]; Vec t, v; int numLocalNodes, globalNodeNumber, i, j, eq; MatStokesBlockScaling BA = bsscr->BA; PetscErrorCode ierr; Mat Amat,Pmat, G; MatStructure pflag; PetscFunctionBegin; /* get G matrix from Amat matrix operator on ksp */ ierr=Stg_PCGetOperators(ksp->pc,&Amat,&Pmat,&pflag);CHKERRQ(ierr); MatNestGetSubMat( Amat, 0,1, &G );/* G should always exist */ /* now create Vecs t and v to match size of G: i.e. pressure */ /* NOTE: not using "h" vector from ksp->vec_rhs because this part of the block vector doesn't always exist */ MatGetVecs( G, &t, PETSC_NULL );/* t and v are destroyed in KSPDestroy_BSSCR */ MatGetVecs( G, &v, PETSC_NULL );/* t and v such that can do G*t */ numLocalNodes = Mesh_GetLocalSize( feMesh, MT_VERTEX); /* number of nodes on current proc not counting any shadow nodes */ for(j=0;j<numLocalNodes;j++){ i = globalNodeNumber = Mesh_DomainToGlobal( feMesh, MT_VERTEX, j); RegularMeshUtils_Element_1DTo3D(feMesh, i, ijk); eq = eq_num->destinationArray[j][0];/* get global equation number -- 2nd arg is always 0 because pressure has only one dof */ if(eq != -1){ if( (ijk[0]+ijk[1]+ijk[2])%2 ==0 ){ VecSetValue(t,eq,1.0,INSERT_VALUES); } else{ VecSetValue(v,eq,1.0,INSERT_VALUES); }}} VecAssemblyBegin( t ); VecAssemblyEnd( t ); VecAssemblyBegin( v ); VecAssemblyEnd( v ); /* Scaling the null vectors here because it easier at the moment *//* maybe should do this in the original scaling function */ if( BA->scaling_exists == PETSC_TRUE ){ Vec R2; /* Get the scalings out the block mat data */ VecNestGetSubVec( BA->Rz, 1, &R2 ); VecPointwiseDivide( t, t, R2); /* x <- x * 1/R2 */ VecPointwiseDivide( v, v, R2); } bsscr_writeVec( t, "t", "Writing t vector"); bsscr_writeVec( v, "v", "Writing v vector"); bsscr->t=t; bsscr->v=v; PetscFunctionReturn(0); }
/*@C KSPGetVecs - Gets a number of work vectors. Input Parameters: + ksp - iterative context . rightn - number of right work vectors - leftn - number of left work vectors to allocate Output Parameter: + right - the array of vectors created - left - the array of left vectors Note: The right vector has as many elements as the matrix has columns. The left vector has as many elements as the matrix has rows. Level: advanced .seealso: MatGetVecs() @*/ PetscErrorCode KSPGetVecs(KSP ksp,PetscInt rightn, Vec **right,PetscInt leftn,Vec **left) { PetscErrorCode ierr; Vec vecr,vecl; PetscFunctionBegin; if (rightn) { if (!right) SETERRQ(PetscObjectComm((PetscObject)ksp),PETSC_ERR_ARG_INCOMP,"You asked for right vectors but did not pass a pointer to hold them"); if (ksp->vec_sol) vecr = ksp->vec_sol; else { if (ksp->dm) { ierr = DMGetGlobalVector(ksp->dm,&vecr);CHKERRQ(ierr); } else { Mat mat; if (!ksp->pc) {ierr = KSPGetPC(ksp,&ksp->pc);CHKERRQ(ierr);} ierr = PCGetOperators(ksp->pc,&mat,NULL,NULL);CHKERRQ(ierr); ierr = MatGetVecs(mat,&vecr,NULL);CHKERRQ(ierr); } } ierr = VecDuplicateVecs(vecr,rightn,right);CHKERRQ(ierr); if (!ksp->vec_sol) { if (ksp->dm) { ierr = DMRestoreGlobalVector(ksp->dm,&vecr);CHKERRQ(ierr); } else { ierr = VecDestroy(&vecr);CHKERRQ(ierr); } } } if (leftn) { if (!left) SETERRQ(PetscObjectComm((PetscObject)ksp),PETSC_ERR_ARG_INCOMP,"You asked for left vectors but did not pass a pointer to hold them"); if (ksp->vec_rhs) vecl = ksp->vec_rhs; else { if (ksp->dm) { ierr = DMGetGlobalVector(ksp->dm,&vecl);CHKERRQ(ierr); } else { Mat mat; if (!ksp->pc) {ierr = KSPGetPC(ksp,&ksp->pc);CHKERRQ(ierr);} ierr = PCGetOperators(ksp->pc,&mat,NULL,NULL);CHKERRQ(ierr); ierr = MatGetVecs(mat,NULL,&vecl);CHKERRQ(ierr); } } ierr = VecDuplicateVecs(vecl,leftn,left);CHKERRQ(ierr); if (!ksp->vec_rhs) { if (ksp->dm) { ierr = DMRestoreGlobalVector(ksp->dm,&vecl);CHKERRQ(ierr); } else { ierr = VecDestroy(&vecl);CHKERRQ(ierr); } } } PetscFunctionReturn(0); }
static PetscErrorCode PCSetUp_Eisenstat(PC pc) { PetscErrorCode ierr; PetscInt M,N,m,n; PC_Eisenstat *eis = (PC_Eisenstat*)pc->data; PetscFunctionBegin; if (!pc->setupcalled) { ierr = MatGetSize(pc->mat,&M,&N);CHKERRQ(ierr); ierr = MatGetLocalSize(pc->mat,&m,&n);CHKERRQ(ierr); ierr = MatCreate(((PetscObject)pc)->comm,&eis->shell);CHKERRQ(ierr); ierr = MatSetSizes(eis->shell,m,n,M,N);CHKERRQ(ierr); ierr = MatSetType(eis->shell,MATSHELL);CHKERRQ(ierr); ierr = MatSetUp(eis->shell);CHKERRQ(ierr); ierr = MatShellSetContext(eis->shell,(void*)pc);CHKERRQ(ierr); ierr = PetscLogObjectParent(pc,eis->shell);CHKERRQ(ierr); ierr = MatShellSetOperation(eis->shell,MATOP_MULT,(void(*)(void))PCMult_Eisenstat);CHKERRQ(ierr); } if (!eis->usediag) PetscFunctionReturn(0); if (!pc->setupcalled) { ierr = MatGetVecs(pc->pmat,&eis->diag,0);CHKERRQ(ierr); ierr = PetscLogObjectParent(pc,eis->diag);CHKERRQ(ierr); } ierr = MatGetDiagonal(pc->pmat,eis->diag);CHKERRQ(ierr); PetscFunctionReturn(0); }
static void ApplyPCPrecPETSCGen(void *x, PRIMME_INT *ldx, void *y, PRIMME_INT *ldy, int *blockSize, int trans, PC *pc, MPI_Comm comm) { int i; Vec xvec, yvec; Mat matrix; PetscErrorCode ierr; PetscInt mLocal, nLocal; ierr = PCGetOperators(pc[0],&matrix,NULL); CHKERRABORT(comm, ierr); assert(sizeof(PetscScalar) == sizeof(SCALAR)); ierr = MatGetLocalSize(matrix, &mLocal, &nLocal); CHKERRABORT(comm, ierr); assert(mLocal == nLocal && nLocal <= *ldx && mLocal <= *ldy); #if PETSC_VERSION_LT(3,6,0) ierr = MatGetVecs(matrix, &xvec, &yvec); CHKERRABORT(comm, ierr); #else ierr = MatCreateVecs(matrix, &xvec, &yvec); CHKERRABORT(comm, ierr); #endif for (i=0; i<*blockSize; i++) { ierr = VecPlaceArray(xvec, ((SCALAR*)x) + (*ldx)*i); CHKERRABORT(comm, ierr); ierr = VecPlaceArray(yvec, ((SCALAR*)y) + (*ldy)*i); CHKERRABORT(comm, ierr); if (trans == 0) { ierr = PCApply(*pc, xvec, yvec); CHKERRABORT(comm, ierr); } else if (pc[1]) { ierr = PCApply(pc[1], xvec, yvec); CHKERRABORT(comm, ierr); } else { ierr = PCApplyTranspose(pc[0], xvec, yvec); } ierr = VecResetArray(xvec); CHKERRABORT(comm, ierr); ierr = VecResetArray(yvec); CHKERRABORT(comm, ierr); } ierr = VecDestroy(&xvec); CHKERRABORT(comm, ierr); ierr = VecDestroy(&yvec); CHKERRABORT(comm, ierr); }
void createOuterContext(OuterContext* & ctx) { int rank; int npes; MPI_Comm_rank(PETSC_COMM_WORLD, &rank); MPI_Comm_size(PETSC_COMM_WORLD, &npes); ctx = new OuterContext; ctx->data = NULL; ctx->root = NULL; ctx->outerMat = PETSC_NULL; ctx->outerKsp = PETSC_NULL; ctx->outerPC = PETSC_NULL; ctx->outerSol = PETSC_NULL; ctx->outerRhs = PETSC_NULL; createLocalData(ctx->data); createRSDtree(ctx->root, rank, npes); createOuterMat(ctx); createOuterPC(ctx); createOuterKsp(ctx); MatGetVecs(ctx->outerMat, &(ctx->outerSol), &(ctx->outerRhs)); }
// updated PetscErrorCode BSSCR_MatStokesMVBlockDefaultBuildScaling( MatStokesBlockScaling BA, Mat A, Vec b, Vec x, PetscTruth sym ) { Mat K,G,D,C; Vec rG; PetscScalar rg2, rg, ra; PetscInt N; Vec rA, rC; Vec L1,L2, R1,R2; Mat S; VecNestGetSubVec( BA->Lz, 0, &L1 ); VecNestGetSubVec( BA->Lz, 1, &L2 ); VecNestGetSubVec( BA->Rz, 0, &R1 ); VecNestGetSubVec( BA->Rz, 1, &R2 ); rA = L1; rC = L2; MatNestGetSubMat( A, 0,0, &K ); MatNestGetSubMat( A, 0,1, &G ); MatNestGetSubMat( A, 1,0, &D ); MatNestGetSubMat( A, 1,1, &C ); VecDuplicate( rA, &rG ); /* Get magnitude of K */ //px_MatGetAbsRowSum( K, rA ); //MatGetRowMax( K, rA, PETSC_NULL ); MatGetDiagonal( K, rA); VecSqrt( rA ); VecReciprocal( rA ); /* VecDot( rA,rA, &ra ); */ /* VecGetSize( rA, &N ); */ /* ra = PetscSqrtScalar( ra/N ); */ /* Get magnitude of G */ //px_MatGetAbsRowSum( G, rG ); //MatGetRowMax( G, rG, PETSC_NULL ); Mat A21_cpy; Mat Shat; Vec diag; /* same as rA*rA */ MatGetVecs( K, &diag, PETSC_NULL ); MatGetDiagonal( K, diag ); VecReciprocal( diag ); if( sym ) #if( PETSC_VERSION_MAJOR <= 2 ) MatTranspose( G, &A21_cpy ); #else MatTranspose( G, MAT_INITIAL_MATRIX, &A21_cpy ); #endif else {
NonlocalCollection(Mat depends_on, IS interest_set) { find_influences(depends_on, interest_set, &nodes); PetscInt local_size; ISGetLocalSize(nodes, &local_size); VecCreateMPI(PETSC_COMM_WORLD, local_size, PETSC_DECIDE, &vec); IS onto_index_set; describe_partition(vec, &onto_index_set); PetscInt begin; PetscInt end; VecGetOwnershipRange(vec, &begin, &end); PetscInt *indicies; ISGetIndices(nodes, &indicies); assert(local_size == end-begin); for (int ii=0; ii<local_size; ii++) { map[indicies[ii]] = ii+begin; } ISRestoreIndices(nodes, &indicies); Vec w; MatGetVecs(depends_on, PETSC_NULL, &w); VecScatterCreate(w, nodes, vec, onto_index_set, &scatter); VecDestroy(w); ISDestroy(onto_index_set); }
PetscErrorCode MatMultTranspose_Composite_Multiplicative(Mat A,Vec x,Vec y) { Mat_Composite *shell = (Mat_Composite*)A->data; Mat_CompositeLink tail = shell->tail; PetscErrorCode ierr; Vec in,out; PetscFunctionBegin; if (!tail) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must provide at least one matrix with MatCompositeAddMat()"); in = x; if (shell->left) { if (!shell->leftwork) { ierr = VecDuplicate(shell->left,&shell->leftwork);CHKERRQ(ierr); } ierr = VecPointwiseMult(shell->leftwork,shell->left,in);CHKERRQ(ierr); in = shell->leftwork; } while (tail->prev) { if (!tail->prev->work) { /* should reuse previous work if the same size */ ierr = MatGetVecs(tail->mat,NULL,&tail->prev->work);CHKERRQ(ierr); } out = tail->prev->work; ierr = MatMultTranspose(tail->mat,in,out);CHKERRQ(ierr); in = out; tail = tail->prev; } ierr = MatMultTranspose(tail->mat,in,y);CHKERRQ(ierr); if (shell->right) { ierr = VecPointwiseMult(y,shell->right,y);CHKERRQ(ierr); } ierr = VecScale(y,shell->scale);CHKERRQ(ierr); PetscFunctionReturn(0); }
static void PETScMatvecGenNoBlock(void *x, PRIMME_INT ldx, void *y, PRIMME_INT ldy, int blockSize, int trans, Mat matrix, MPI_Comm comm) { int i; Vec xvec, yvec; PetscInt m, n, mLocal, nLocal; PetscErrorCode ierr; assert(sizeof(PetscScalar) == sizeof(SCALAR)); ierr = MatGetSize(matrix, &m, &n); CHKERRABORT(comm, ierr); ierr = MatGetLocalSize(matrix, &mLocal, &nLocal); CHKERRABORT(comm, ierr); #if PETSC_VERSION_LT(3,6,0) ierr = MatGetVecs(matrix, &xvec, &yvec); CHKERRABORT(comm, ierr); #else ierr = MatCreateVecs(matrix, &xvec, &yvec); CHKERRABORT(comm, ierr); #endif if (trans == 1) { Vec aux = xvec; xvec = yvec; yvec = aux; } for (i=0; i<blockSize; i++) { ierr = VecPlaceArray(xvec, ((SCALAR*)x) + ldx*i); CHKERRABORT(comm, ierr); ierr = VecPlaceArray(yvec, ((SCALAR*)y) + ldy*i); CHKERRABORT(comm, ierr); if (trans == 0) { ierr = MatMult(matrix, xvec, yvec); CHKERRABORT(comm, ierr); } else { ierr = MatMultHermitianTranspose(matrix, xvec, yvec); CHKERRABORT(comm, ierr); } ierr = VecResetArray(xvec); CHKERRABORT(comm, ierr); ierr = VecResetArray(yvec); CHKERRABORT(comm, ierr); } ierr = VecDestroy(&xvec); CHKERRABORT(comm, ierr); ierr = VecDestroy(&yvec); CHKERRABORT(comm, ierr); }
PetscErrorCode computeMaxEigVal(Mat A, PetscInt its, PetscScalar *eig) { PetscErrorCode ierr; PetscRandom rctx; /* random number generator context */ Vec x0, x, x_1, tmp; PetscScalar lambda_its, lambda_its_1; PetscInt i; PetscFunctionBeginUser; ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr); ierr = MatGetVecs(A, &x_1, &x);CHKERRQ(ierr); ierr = VecSetRandom(x, rctx);CHKERRQ(ierr); ierr = VecDuplicate(x, &x0);CHKERRQ(ierr); ierr = VecCopy(x, x0);CHKERRQ(ierr); ierr = MatMult(A, x, x_1);CHKERRQ(ierr); for (i=0; i<its; i++) { tmp = x; x = x_1; x_1 = tmp; ierr = MatMult(A, x, x_1);CHKERRQ(ierr); } ierr = VecDot(x0, x, &lambda_its);CHKERRQ(ierr); ierr = VecDot(x0, x_1, &lambda_its_1);CHKERRQ(ierr); *eig = lambda_its_1/lambda_its; ierr = VecDestroy(&x0);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&x_1);CHKERRQ(ierr); PetscFunctionReturn(0); }
/*@ PCMGGetRScale - Gets the pointwise scaling for the restriction operator from level l to l-1. Collective on PC Input Parameters: + pc - the multigrid context . rscale - the scaling - l - the level (0 is coarsest) to supply [Do not supply 0] Level: advanced Notes: When evaluating a function on a coarse level one does not want to do F(R * x) one does F(rscale * R * x) where rscale is 1 over the row sums of R. .keywords: MG, set, multigrid, restriction, level .seealso: PCMGSetInterpolation(), PCMGGetRestriction() @*/ PetscErrorCode PCMGGetRScale(PC pc,PetscInt l,Vec *rscale) { PetscErrorCode ierr; PC_MG *mg = (PC_MG*)pc->data; PC_MG_Levels **mglevels = mg->levels; PetscFunctionBegin; PetscValidHeaderSpecific(pc,PC_CLASSID,1); if (!mglevels) SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_ARG_WRONGSTATE,"Must set MG levels before calling"); if (l <= 0 || mg->nlevels <= l) SETERRQ2(PetscObjectComm((PetscObject)pc),PETSC_ERR_ARG_OUTOFRANGE,"Level %D must be in range {1,...,%D}",l,mg->nlevels-1); if (!mglevels[l]->rscale) { Mat R; Vec X,Y,coarse,fine; PetscInt M,N; ierr = PCMGGetRestriction(pc,l,&R);CHKERRQ(ierr); ierr = MatGetVecs(R,&X,&Y);CHKERRQ(ierr); ierr = MatGetSize(R,&M,&N);CHKERRQ(ierr); if (M < N) { fine = X; coarse = Y; } else if (N < M) { fine = Y; coarse = X; } else SETERRQ(PetscObjectComm((PetscObject)R),PETSC_ERR_SUP,"Restriction matrix is square, cannot determine which Vec is coarser"); ierr = VecSet(fine,1.);CHKERRQ(ierr); ierr = MatRestrict(R,fine,coarse);CHKERRQ(ierr); ierr = VecDestroy(&fine);CHKERRQ(ierr); ierr = VecReciprocal(coarse);CHKERRQ(ierr); mglevels[l]->rscale = coarse; } *rscale = mglevels[l]->rscale; PetscFunctionReturn(0); }
PetscErrorCode MatMult_SchurComplement(Mat N,Vec x,Vec y) { Mat_SchurComplement *Na = (Mat_SchurComplement*)N->data; PetscErrorCode ierr; PetscFunctionBegin; if (!Na->work1) {ierr = MatGetVecs(Na->A,&Na->work1,PETSC_NULL);CHKERRQ(ierr);} if (!Na->work2) {ierr = MatGetVecs(Na->A,&Na->work2,PETSC_NULL);CHKERRQ(ierr);} ierr = MatMult(Na->B,x,Na->work1);CHKERRQ(ierr); ierr = KSPSolve(Na->ksp,Na->work1,Na->work2);CHKERRQ(ierr); ierr = MatMult(Na->C,Na->work2,y);CHKERRQ(ierr); ierr = VecScale(y,-1.0);CHKERRQ(ierr); if (Na->D) { ierr = MatMultAdd(Na->D,x,y,y);CHKERRQ(ierr); } PetscFunctionReturn(0); }
/* PEPLinearExtract_Norm - Auxiliary routine that copies the solution of the linear eigenproblem to the PEP object. The eigenvector of the generalized problem is supposed to be z = [ x ] [ l*x ] If |l|<1.0, the eigenvector is taken from z(1:n), otherwise from z(n+1:2*n). Finally, x is normalized so that ||x||_2 = 1. */ static PetscErrorCode PEPLinearExtract_Norm(PEP pep,EPS eps) { PetscErrorCode ierr; PetscInt i,offset; PetscScalar *px; Vec xr,xi,w,vi; #if !defined(PETSC_USE_COMPLEX) Vec vi1; #endif Mat A; PetscFunctionBegin; ierr = EPSGetOperators(eps,&A,NULL);CHKERRQ(ierr); ierr = MatGetVecs(A,&xr,NULL);CHKERRQ(ierr); ierr = VecDuplicate(xr,&xi);CHKERRQ(ierr); ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)pep),1,pep->nloc,pep->n,NULL,&w);CHKERRQ(ierr); for (i=0;i<pep->nconv;i++) { ierr = EPSGetEigenpair(eps,i,&pep->eigr[i],&pep->eigi[i],xr,xi);CHKERRQ(ierr); pep->eigr[i] *= pep->sfactor; pep->eigi[i] *= pep->sfactor; if (SlepcAbsEigenvalue(pep->eigr[i],pep->eigi[i])>1.0) offset = pep->nloc; else offset = 0; #if !defined(PETSC_USE_COMPLEX) if (pep->eigi[i]>0.0) { /* first eigenvalue of a complex conjugate pair */ ierr = VecGetArray(xr,&px);CHKERRQ(ierr); ierr = VecPlaceArray(w,px+offset);CHKERRQ(ierr); ierr = BVInsertVec(pep->V,i,w);CHKERRQ(ierr); ierr = VecResetArray(w);CHKERRQ(ierr); ierr = VecRestoreArray(xr,&px);CHKERRQ(ierr); ierr = VecGetArray(xi,&px);CHKERRQ(ierr); ierr = VecPlaceArray(w,px+offset);CHKERRQ(ierr); ierr = BVInsertVec(pep->V,i+1,w);CHKERRQ(ierr); ierr = VecResetArray(w);CHKERRQ(ierr); ierr = VecRestoreArray(xi,&px);CHKERRQ(ierr); ierr = BVGetColumn(pep->V,i,&vi);CHKERRQ(ierr); ierr = BVGetColumn(pep->V,i+1,&vi1);CHKERRQ(ierr); ierr = SlepcVecNormalize(vi,vi1,PETSC_TRUE,NULL);CHKERRQ(ierr); ierr = BVRestoreColumn(pep->V,i,&vi);CHKERRQ(ierr); ierr = BVRestoreColumn(pep->V,i+1,&vi1);CHKERRQ(ierr); } else if (pep->eigi[i]==0.0) /* real eigenvalue */ #endif { ierr = VecGetArray(xr,&px);CHKERRQ(ierr); ierr = VecPlaceArray(w,px+offset);CHKERRQ(ierr); ierr = BVInsertVec(pep->V,i,w);CHKERRQ(ierr); ierr = VecResetArray(w);CHKERRQ(ierr); ierr = VecRestoreArray(xr,&px);CHKERRQ(ierr); ierr = BVGetColumn(pep->V,i,&vi);CHKERRQ(ierr); ierr = SlepcVecNormalize(vi,NULL,PETSC_FALSE,NULL);CHKERRQ(ierr); ierr = BVRestoreColumn(pep->V,i,&vi);CHKERRQ(ierr); } } ierr = VecDestroy(&w);CHKERRQ(ierr); ierr = VecDestroy(&xr);CHKERRQ(ierr); ierr = VecDestroy(&xi);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode MatGetVecs_SchurComplement(Mat N,Vec *right,Vec *left) { Mat_SchurComplement *Na = (Mat_SchurComplement*)N->data; PetscErrorCode ierr; PetscFunctionBegin; if (Na->D) { ierr = MatGetVecs(Na->D,right,left);CHKERRQ(ierr); PetscFunctionReturn(0); } if (right) { ierr = MatGetVecs(Na->B,right,PETSC_NULL);CHKERRQ(ierr); } if (left) { ierr = MatGetVecs(Na->C,PETSC_NULL,left);CHKERRQ(ierr); } PetscFunctionReturn(0); }
PetscErrorCode RunTest(void) { PetscInt N = 100; PetscBool draw = PETSC_FALSE; PetscReal rnorm; Mat A; Vec b,x,r; KSP ksp; PC pc; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscOptionsGetInt(0,"-N",&N,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(0,"-draw",&draw,NULL);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr); ierr = MatSetType(A,MATPYTHON);CHKERRQ(ierr); ierr = MatPythonSetType(A,"example1.py:Laplace1D");CHKERRQ(ierr); ierr = MatSetUp(A);CHKERRQ(ierr); ierr = MatGetVecs(A,&x,&b);CHKERRQ(ierr); ierr = VecSet(b,1);CHKERRQ(ierr); ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr); ierr = KSPSetType(ksp,KSPPYTHON);CHKERRQ(ierr); ierr = KSPPythonSetType(ksp,"example1.py:ConjGrad");CHKERRQ(ierr); ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr); ierr = PCSetType(pc,PCPYTHON);CHKERRQ(ierr); ierr = PCPythonSetType(pc,"example1.py:Jacobi");CHKERRQ(ierr); ierr = KSPSetOperators(ksp,A,A);CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr); ierr = VecDuplicate(b,&r);CHKERRQ(ierr); ierr = MatMult(A,x,r);CHKERRQ(ierr); ierr = VecAYPX(r,-1,b);CHKERRQ(ierr); ierr = VecNorm(r,NORM_2,&rnorm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"error norm = %g\n",rnorm);CHKERRQ(ierr); if (draw) { ierr = VecView(x,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr); ierr = PetscSleep(2);CHKERRQ(ierr); } ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = KSPDestroy(&ksp);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode MatSetLocalToGlobalMapping_IS(Mat A,ISLocalToGlobalMapping rmapping,ISLocalToGlobalMapping cmapping) { PetscErrorCode ierr; PetscInt n,bs; Mat_IS *is = (Mat_IS*)A->data; IS from,to; Vec global; PetscFunctionBegin; PetscCheckSameComm(A,1,rmapping,2); if (rmapping != cmapping) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_INCOMP,"MATIS requires the row and column mappings to be identical"); if (is->mapping) { /* Currenly destroys the objects that will be created by this routine. Is there anything else that should be checked? */ ierr = ISLocalToGlobalMappingDestroy(&is->mapping);CHKERRQ(ierr); ierr = VecDestroy(&is->x);CHKERRQ(ierr); ierr = VecDestroy(&is->y);CHKERRQ(ierr); ierr = VecScatterDestroy(&is->ctx);CHKERRQ(ierr); ierr = MatDestroy(&is->A);CHKERRQ(ierr); } ierr = PetscObjectReference((PetscObject)rmapping);CHKERRQ(ierr); ierr = ISLocalToGlobalMappingDestroy(&is->mapping);CHKERRQ(ierr); is->mapping = rmapping; /* ierr = PetscLayoutSetISLocalToGlobalMapping(A->rmap,rmapping);CHKERRQ(ierr); ierr = PetscLayoutSetISLocalToGlobalMapping(A->cmap,cmapping);CHKERRQ(ierr); */ /* Create the local matrix A */ ierr = ISLocalToGlobalMappingGetSize(rmapping,&n);CHKERRQ(ierr); ierr = MatGetBlockSize(A,&bs);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_SELF,&is->A);CHKERRQ(ierr); ierr = MatSetSizes(is->A,n,n,n,n);CHKERRQ(ierr); ierr = MatSetBlockSize(is->A,bs);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(is->A,((PetscObject)A)->prefix);CHKERRQ(ierr); ierr = MatAppendOptionsPrefix(is->A,"is_");CHKERRQ(ierr); ierr = MatSetFromOptions(is->A);CHKERRQ(ierr); /* Create the local work vectors */ ierr = VecCreate(PETSC_COMM_SELF,&is->x);CHKERRQ(ierr); ierr = VecSetBlockSize(is->x,bs);CHKERRQ(ierr); ierr = VecSetSizes(is->x,n,n);CHKERRQ(ierr); ierr = VecSetOptionsPrefix(is->x,((PetscObject)A)->prefix);CHKERRQ(ierr); ierr = VecAppendOptionsPrefix(is->x,"is_");CHKERRQ(ierr); ierr = VecSetFromOptions(is->x);CHKERRQ(ierr); ierr = VecDuplicate(is->x,&is->y);CHKERRQ(ierr); /* setup the global to local scatter */ ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&to);CHKERRQ(ierr); ierr = ISLocalToGlobalMappingApplyIS(rmapping,to,&from);CHKERRQ(ierr); ierr = MatGetVecs(A,&global,NULL);CHKERRQ(ierr); ierr = VecScatterCreate(global,from,is->x,to,&is->ctx);CHKERRQ(ierr); ierr = VecDestroy(&global);CHKERRQ(ierr); ierr = ISDestroy(&to);CHKERRQ(ierr); ierr = ISDestroy(&from);CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode PCSetUp_CP(PC pc) { PC_CP *cp = (PC_CP*)pc->data; PetscInt i,j,*colcnt; PetscErrorCode ierr; PetscTruth flg; Mat_SeqAIJ *aij = (Mat_SeqAIJ*)pc->pmat->data; PetscFunctionBegin; ierr = PetscTypeCompare((PetscObject)pc->pmat,MATSEQAIJ,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_ERR_SUP,"Currently only handles SeqAIJ matrices"); ierr = MatGetLocalSize(pc->pmat,&cp->m,&cp->n);CHKERRQ(ierr); if (cp->m != cp->n) SETERRQ(PETSC_ERR_SUP,"Currently only for square matrices"); if (!cp->work) {ierr = MatGetVecs(pc->pmat,&cp->work,PETSC_NULL);CHKERRQ(ierr);} if (!cp->d) {ierr = PetscMalloc(cp->n*sizeof(PetscScalar),&cp->d);CHKERRQ(ierr);} if (cp->a && pc->flag != SAME_NONZERO_PATTERN) { ierr = PetscFree3(cp->a,cp->i,cp->j);CHKERRQ(ierr); cp->a = 0; } /* convert to column format */ if (!cp->a) { ierr = PetscMalloc3(aij->nz,PetscScalar,&cp->a,cp->n+1,PetscInt,&cp->i,aij->nz,PetscInt,&cp->j);CHKERRQ(ierr); } ierr = PetscMalloc(cp->n*sizeof(PetscInt),&colcnt);CHKERRQ(ierr); ierr = PetscMemzero(colcnt,cp->n*sizeof(PetscInt));CHKERRQ(ierr); for (i=0; i<aij->nz; i++) { colcnt[aij->j[i]]++; } cp->i[0] = 0; for (i=0; i<cp->n; i++) { cp->i[i+1] = cp->i[i] + colcnt[i]; } ierr = PetscMemzero(colcnt,cp->n*sizeof(PetscInt));CHKERRQ(ierr); for (i=0; i<cp->m; i++) { /* over rows */ for (j=aij->i[i]; j<aij->i[i+1]; j++) { /* over columns in row */ cp->j[cp->i[aij->j[j]]+colcnt[aij->j[j]]] = i; cp->a[cp->i[aij->j[j]]+colcnt[aij->j[j]]++] = aij->a[j]; } } ierr = PetscFree(colcnt);CHKERRQ(ierr); /* compute sum of squares of each column d[] */ for (i=0; i<cp->n; i++) { /* over columns */ cp->d[i] = 0.; for (j=cp->i[i]; j<cp->i[i+1]; j++) { /* over rows in column */ cp->d[i] += cp->a[j]*cp->a[j]; } cp->d[i] = 1.0/cp->d[i]; } PetscFunctionReturn(0); }
/*@ MatComputeExplicitOperator - Computes the explicit matrix Collective on Mat Input Parameter: . inmat - the matrix Output Parameter: . mat - the explict preconditioned operator Notes: This computation is done by applying the operators to columns of the identity matrix. Currently, this routine uses a dense matrix format when 1 processor is used and a sparse format otherwise. This routine is costly in general, and is recommended for use only with relatively small systems. Level: advanced .keywords: Mat, compute, explicit, operator @*/ PetscErrorCode MatComputeExplicitOperator(Mat inmat,Mat *mat) { Vec in,out; PetscErrorCode ierr; PetscInt i,m,n,M,N,*rows,start,end; MPI_Comm comm; PetscScalar *array,zero = 0.0,one = 1.0; PetscMPIInt size; PetscFunctionBegin; PetscValidHeaderSpecific(inmat,MAT_CLASSID,1); PetscValidPointer(mat,2); ierr = PetscObjectGetComm((PetscObject)inmat,&comm);CHKERRQ(ierr); ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); ierr = MatGetLocalSize(inmat,&m,&n);CHKERRQ(ierr); ierr = MatGetSize(inmat,&M,&N);CHKERRQ(ierr); ierr = MatGetVecs(inmat,&in,&out);CHKERRQ(ierr); ierr = VecSetOption(in,VEC_IGNORE_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); ierr = VecGetOwnershipRange(out,&start,&end);CHKERRQ(ierr); ierr = PetscMalloc(m*sizeof(PetscInt),&rows);CHKERRQ(ierr); for (i=0; i<m; i++) rows[i] = start + i; ierr = MatCreate(comm,mat);CHKERRQ(ierr); ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); if (size == 1) { ierr = MatSetType(*mat,MATSEQDENSE);CHKERRQ(ierr); ierr = MatSeqDenseSetPreallocation(*mat,NULL);CHKERRQ(ierr); } else { ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); ierr = MatMPIAIJSetPreallocation(*mat,n,NULL,N-n,NULL);CHKERRQ(ierr); } for (i=0; i<N; i++) { ierr = VecSet(in,zero);CHKERRQ(ierr); ierr = VecSetValues(in,1,&i,&one,INSERT_VALUES);CHKERRQ(ierr); ierr = VecAssemblyBegin(in);CHKERRQ(ierr); ierr = VecAssemblyEnd(in);CHKERRQ(ierr); ierr = MatMult(inmat,in,out);CHKERRQ(ierr); ierr = VecGetArray(out,&array);CHKERRQ(ierr); ierr = MatSetValues(*mat,m,rows,1,&i,array,INSERT_VALUES);CHKERRQ(ierr); ierr = VecRestoreArray(out,&array);CHKERRQ(ierr); } ierr = PetscFree(rows);CHKERRQ(ierr); ierr = VecDestroy(&out);CHKERRQ(ierr); ierr = VecDestroy(&in);CHKERRQ(ierr); ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode PCSetUp_Jacobi_NonSymmetric(PC pc) { PetscErrorCode ierr; PC_Jacobi *jac = (PC_Jacobi*)pc->data; PetscFunctionBegin; ierr = MatGetVecs(pc->pmat,&jac->diag,0);CHKERRQ(ierr); ierr = PetscLogObjectParent(pc,jac->diag);CHKERRQ(ierr); ierr = PCSetUp_Jacobi(pc);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode PCGAMGOptProl_Classical_Jacobi(PC pc,const Mat A,Mat *P) { PetscErrorCode ierr; PetscInt f,s,n,cf,cs,i,idx; PetscInt *coarserows; PetscInt ncols; const PetscInt *pcols; const PetscScalar *pvals; Mat Pnew; Vec diag; PC_MG *mg = (PC_MG*)pc->data; PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; PC_GAMG_Classical *cls = (PC_GAMG_Classical*)pc_gamg->subctx; PetscFunctionBegin; if (cls->nsmooths == 0) { ierr = PCGAMGTruncateProlongator_Private(pc,P);CHKERRQ(ierr); PetscFunctionReturn(0); } ierr = MatGetOwnershipRange(*P,&s,&f);CHKERRQ(ierr); n = f-s; ierr = MatGetOwnershipRangeColumn(*P,&cs,&cf);CHKERRQ(ierr); ierr = PetscMalloc(sizeof(PetscInt)*n,&coarserows);CHKERRQ(ierr); /* identify the rows corresponding to coarse unknowns */ idx = 0; for (i=s;i<f;i++) { ierr = MatGetRow(*P,i,&ncols,&pcols,&pvals);CHKERRQ(ierr); /* assume, for now, that it's a coarse unknown if it has a single unit entry */ if (ncols == 1) { if (pvals[0] == 1.) { coarserows[idx] = i; idx++; } } ierr = MatRestoreRow(*P,i,&ncols,&pcols,&pvals);CHKERRQ(ierr); } ierr = MatGetVecs(A,&diag,0);CHKERRQ(ierr); ierr = MatGetDiagonal(A,diag);CHKERRQ(ierr); ierr = VecReciprocal(diag);CHKERRQ(ierr); for (i=0;i<cls->nsmooths;i++) { ierr = MatMatMult(A,*P,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&Pnew);CHKERRQ(ierr); ierr = MatZeroRows(Pnew,idx,coarserows,0.,NULL,NULL);CHKERRQ(ierr); ierr = MatDiagonalScale(Pnew,diag,0);CHKERRQ(ierr); ierr = MatAYPX(Pnew,-1.0,*P,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); ierr = MatDestroy(P);CHKERRQ(ierr); *P = Pnew; Pnew = NULL; } ierr = VecDestroy(&diag);CHKERRQ(ierr); ierr = PetscFree(coarserows);CHKERRQ(ierr); ierr = PCGAMGTruncateProlongator_Private(pc,P);CHKERRQ(ierr); PetscFunctionReturn(0); }
/*@ SNESFASCreateCoarseVec - create Vec corresponding to a state vector on one level coarser than current level Collective Input Arguments: . snes - SNESFAS Output Arguments: . Xcoarse - vector on level one coarser than snes Level: developer .seealso: SNESFASSetRestriction(), SNESFASRestrict() @*/ PetscErrorCode SNESFASCreateCoarseVec(SNES snes,Vec *Xcoarse) { PetscErrorCode ierr; SNES_FAS *fas = (SNES_FAS*)snes->data; PetscFunctionBegin; if (fas->rscale) {ierr = VecDuplicate(fas->rscale,Xcoarse);CHKERRQ(ierr);} else if (fas->inject) {ierr = MatGetVecs(fas->inject,Xcoarse,PETSC_NULL);CHKERRQ(ierr);} else SETERRQ(((PetscObject)snes)->comm,PETSC_ERR_ARG_WRONGSTATE,"Must set restriction or injection");CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode KSPRemovePressureNullspace_BSSCR(KSP ksp, Vec h_hat) { KSP_BSSCR *bsscr = (KSP_BSSCR *)ksp->data; MatStokesBlockScaling BA = bsscr->BA; PetscErrorCode ierr; PetscScalar norm, a, a1, a2, hnorm, pnorm, gnorm; Vec t2, t,v; Mat Amat,Pmat, D; MatStructure pflag; double nstol = bsscr->nstol; /* set in KSPCreate_BSSCR */ PetscFunctionBegin; t=bsscr->t; v=bsscr->v; /* get G matrix from Amat matrix operator on ksp */ ierr=Stg_PCGetOperators(ksp->pc,&Amat,&Pmat,&pflag);CHKERRQ(ierr); //MatNestGetSubMat( Amat, 0,1, &G );/* G should always exist */ MatNestGetSubMat( Amat, 1,0, &D );/* D should always exist */ /* now create Vec t2 to match left hand size of G: i.e. velocity */ MatGetVecs( D, &t2, PETSC_NULL ); MatNorm(D,NORM_INFINITY,&gnorm); /* seems like not a bad estimate of the largest eigenvalue for this matrix */ if(t){/* assumes that v and t are initially set to PETSC_NULL (in KSPCreate_BSSCR ) */ MatMultTranspose( D, t, t2); VecNorm(t2, NORM_2, &norm); VecNorm(t, NORM_2, &a); norm=norm/a;/* so we are using unit null vector */ if(norm < nstol*gnorm){/* then t in NS of G */ VecDot(t,h_hat, &a1); VecDot(t,t, &a2); a=-a1/a2; VecAXPY(h_hat, a, t); VecDot(t,h_hat, &a1); PetscPrintf( PETSC_COMM_WORLD, "\n\t* Found t NS norm= %g : Dot = %g\n\n", norm, a1); } } if(v){ MatMultTranspose( D, v, t2); VecNorm(t2, NORM_2, &norm); VecNorm(v, NORM_2, &a); norm=norm/a;/* so we are using unit null vector */ if(norm < nstol*gnorm){/* then v in NS of G */ VecDot(v,h_hat, &a1); VecDot(v,v, &a2); a=-a1/a2; VecAXPY(h_hat, a, v); VecDot(v,h_hat, &a1); PetscPrintf( PETSC_COMM_WORLD, "\n\t* Found v NS norm= %g : Dot = %g\n\n", norm, a1); } } bsscr_writeVec( h_hat, "h", "Writing h_hat Vector in Solver"); Stg_VecDestroy(&t2); PetscFunctionReturn(0); }
/*@ STComputeExplicitOperator - Computes the explicit operator associated to the eigenvalue problem with the specified spectral transformation. Collective on ST Input Parameter: . st - the spectral transform context Output Parameter: . mat - the explicit operator Notes: This routine builds a matrix containing the explicit operator. For example, in generalized problems with shift-and-invert spectral transformation the result would be matrix (A - s B)^-1 B. This computation is done by applying the operator to columns of the identity matrix. This is analogous to MatComputeExplicitOperator(). Level: advanced .seealso: STApply() @*/ PetscErrorCode STComputeExplicitOperator(ST st,Mat *mat) { PetscErrorCode ierr; Vec in,out; PetscInt i,M,m,*rows,start,end; const PetscScalar *array; PetscScalar one = 1.0; PetscMPIInt size; PetscFunctionBegin; PetscValidHeaderSpecific(st,ST_CLASSID,1); PetscValidPointer(mat,2); STCheckMatrices(st,1); if (st->nmat>2) SETERRQ(PetscObjectComm((PetscObject)st),PETSC_ERR_ARG_WRONGSTATE,"Can only be used with 1 or 2 matrices"); ierr = MPI_Comm_size(PetscObjectComm((PetscObject)st),&size);CHKERRQ(ierr); ierr = MatGetVecs(st->A[0],&in,&out);CHKERRQ(ierr); ierr = VecGetSize(out,&M);CHKERRQ(ierr); ierr = VecGetLocalSize(out,&m);CHKERRQ(ierr); ierr = VecSetOption(in,VEC_IGNORE_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); ierr = VecGetOwnershipRange(out,&start,&end);CHKERRQ(ierr); ierr = PetscMalloc1(m,&rows);CHKERRQ(ierr); for (i=0;i<m;i++) rows[i] = start + i; ierr = MatCreate(PetscObjectComm((PetscObject)st),mat);CHKERRQ(ierr); ierr = MatSetSizes(*mat,m,m,M,M);CHKERRQ(ierr); if (size == 1) { ierr = MatSetType(*mat,MATSEQDENSE);CHKERRQ(ierr); ierr = MatSeqDenseSetPreallocation(*mat,NULL);CHKERRQ(ierr); } else { ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); ierr = MatMPIAIJSetPreallocation(*mat,m,NULL,M-m,NULL);CHKERRQ(ierr); } for (i=0;i<M;i++) { ierr = VecSet(in,0.0);CHKERRQ(ierr); ierr = VecSetValues(in,1,&i,&one,INSERT_VALUES);CHKERRQ(ierr); ierr = VecAssemblyBegin(in);CHKERRQ(ierr); ierr = VecAssemblyEnd(in);CHKERRQ(ierr); ierr = STApply(st,in,out);CHKERRQ(ierr); ierr = VecGetArrayRead(out,&array);CHKERRQ(ierr); ierr = MatSetValues(*mat,m,rows,1,&i,array,INSERT_VALUES);CHKERRQ(ierr); ierr = VecRestoreArrayRead(out,&array);CHKERRQ(ierr); } ierr = PetscFree(rows);CHKERRQ(ierr); ierr = VecDestroy(&in);CHKERRQ(ierr); ierr = VecDestroy(&out);CHKERRQ(ierr); ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode DMCreateGlobalVector_AKKT(DM dm, Vec *v) { PetscBool iskkt; PetscErrorCode ierr; DM_AKKT* kkt = (DM_AKKT*)(dm->data); PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID,1); ierr = PetscObjectTypeCompare((PetscObject)dm, DMAKKT, &iskkt); CHKERRQ(ierr); if(!iskkt) SETERRQ(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "DM not of type DMAKKT"); if(v) { ierr = MatGetVecs(kkt->Aff, v, PETSC_NULL); CHKERRQ(ierr); } PetscFunctionReturn(0); }
static PetscErrorCode PCSetUp_Composite(PC pc) { PetscErrorCode ierr; PC_Composite *jac = (PC_Composite*)pc->data; PC_CompositeLink next = jac->head; PetscFunctionBegin; if (!jac->work1) { ierr = MatGetVecs(pc->pmat,&jac->work1,0);CHKERRQ(ierr); } while (next) { ierr = PCSetOperators(next->pc,pc->mat,pc->pmat);CHKERRQ(ierr); next = next->next; } PetscFunctionReturn(0); }
/*@ SVDComputeResidualNorms - Computes the norms of the residual vectors associated with the i-th computed singular triplet. Collective on SVD Input Parameters: + svd - the singular value solver context - i - the solution index Output Parameters: + norm1 - the norm ||A*v-sigma*u||_2 where sigma is the singular value, u and v are the left and right singular vectors. - norm2 - the norm ||A^T*u-sigma*v||_2 with the same sigma, u and v Note: The index i should be a value between 0 and nconv-1 (see SVDGetConverged()). Both output parameters can be NULL on input if not needed. Level: beginner .seealso: SVDSolve(), SVDGetConverged(), SVDComputeRelativeError() @*/ PetscErrorCode SVDComputeResidualNorms(SVD svd,PetscInt i,PetscReal *norm1,PetscReal *norm2) { PetscErrorCode ierr; Vec u,v,x = NULL,y = NULL; PetscReal sigma; PetscInt M,N; PetscFunctionBegin; PetscValidHeaderSpecific(svd,SVD_CLASSID,1); PetscValidLogicalCollectiveInt(svd,i,2); if (svd->reason == SVD_CONVERGED_ITERATING) SETERRQ(PetscObjectComm((PetscObject)svd),PETSC_ERR_ARG_WRONGSTATE,"SVDSolve must be called first"); if (i<0 || i>=svd->nconv) SETERRQ(PetscObjectComm((PetscObject)svd),PETSC_ERR_ARG_OUTOFRANGE,"Argument 2 out of range"); ierr = MatGetVecs(svd->OP,&v,&u);CHKERRQ(ierr); ierr = SVDGetSingularTriplet(svd,i,&sigma,u,v);CHKERRQ(ierr); if (norm1) { ierr = VecDuplicate(u,&x);CHKERRQ(ierr); ierr = MatMult(svd->OP,v,x);CHKERRQ(ierr); ierr = VecAXPY(x,-sigma,u);CHKERRQ(ierr); ierr = VecNorm(x,NORM_2,norm1);CHKERRQ(ierr); } if (norm2) { ierr = VecDuplicate(v,&y);CHKERRQ(ierr); if (svd->A && svd->AT) { ierr = MatGetSize(svd->OP,&M,&N);CHKERRQ(ierr); if (M<N) { ierr = MatMult(svd->A,u,y);CHKERRQ(ierr); } else { ierr = MatMult(svd->AT,u,y);CHKERRQ(ierr); } } else { #if defined(PETSC_USE_COMPLEX) ierr = MatMultHermitianTranspose(svd->OP,u,y);CHKERRQ(ierr); #else ierr = MatMultTranspose(svd->OP,u,y);CHKERRQ(ierr); #endif } ierr = VecAXPY(y,-sigma,v);CHKERRQ(ierr); ierr = VecNorm(y,NORM_2,norm2);CHKERRQ(ierr); } ierr = VecDestroy(&v);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&y);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode PCGAMGGetDataWithGhosts(const Mat Gmat,const PetscInt data_sz,const PetscReal data_in[],PetscInt *a_stride,PetscReal **a_data_out) { PetscErrorCode ierr; PetscMPIInt rank,size; MPI_Comm comm; Vec tmp_crds; Mat_MPIAIJ *mpimat = (Mat_MPIAIJ*)Gmat->data; PetscInt nnodes,num_ghosts,dir,kk,jj,my0,Iend,nloc; PetscScalar *data_arr; PetscReal *datas; PetscBool isMPIAIJ; PetscFunctionBegin; ierr = PetscObjectGetComm((PetscObject)Gmat,&comm);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)Gmat, MATMPIAIJ, &isMPIAIJ);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); ierr = MatGetOwnershipRange(Gmat, &my0, &Iend);CHKERRQ(ierr); nloc = Iend - my0; ierr = VecGetLocalSize(mpimat->lvec, &num_ghosts);CHKERRQ(ierr); nnodes = num_ghosts + nloc; *a_stride = nnodes; ierr = MatGetVecs(Gmat, &tmp_crds, 0);CHKERRQ(ierr); ierr = PetscMalloc1(data_sz*nnodes, &datas);CHKERRQ(ierr); for (dir=0; dir<data_sz; dir++) { /* set local, and global */ for (kk=0; kk<nloc; kk++) { PetscInt gid = my0 + kk; PetscScalar crd = (PetscScalar)data_in[dir*nloc + kk]; /* col oriented */ datas[dir*nnodes + kk] = PetscRealPart(crd); ierr = VecSetValues(tmp_crds, 1, &gid, &crd, INSERT_VALUES);CHKERRQ(ierr); } ierr = VecAssemblyBegin(tmp_crds);CHKERRQ(ierr); ierr = VecAssemblyEnd(tmp_crds);CHKERRQ(ierr); /* get ghost datas */ ierr = VecScatterBegin(mpimat->Mvctx,tmp_crds,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(mpimat->Mvctx,tmp_crds,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecGetArray(mpimat->lvec, &data_arr);CHKERRQ(ierr); for (kk=nloc,jj=0;jj<num_ghosts;kk++,jj++) datas[dir*nnodes + kk] = PetscRealPart(data_arr[jj]); ierr = VecRestoreArray(mpimat->lvec, &data_arr);CHKERRQ(ierr); } ierr = VecDestroy(&tmp_crds);CHKERRQ(ierr); *a_data_out = datas; PetscFunctionReturn(0); }
PetscErrorCode KSPSetUp_GCR( KSP ksp ) { KSP_GCR *ctx = (KSP_GCR*)ksp->data; PetscErrorCode ierr; Mat A; PetscBool diagonalscale; PetscFunctionBegin; ierr = PCGetDiagonalScale(ksp->pc,&diagonalscale);CHKERRQ(ierr); if (diagonalscale) SETERRQ1(((PetscObject)ksp)->comm,PETSC_ERR_SUP,"Krylov method %s does not support diagonal scaling",((PetscObject)ksp)->type_name); ierr = KSPGetOperators( ksp, &A, 0, 0 );CHKERRQ(ierr); ierr = MatGetVecs( A, &ctx->R, PETSC_NULL );CHKERRQ(ierr); ierr = VecDuplicateVecs( ctx->R, ctx->restart, &ctx->VV );CHKERRQ(ierr); ierr = VecDuplicateVecs( ctx->R, ctx->restart, &ctx->SS );CHKERRQ(ierr); ierr = PetscMalloc( sizeof(PetscScalar)*ctx->restart, &ctx->val );CHKERRQ(ierr); PetscFunctionReturn(0); }
/*@ NEPAllocateSolution - Allocate memory storage for common variables such as eigenvalues and eigenvectors. Collective on NEP Input Parameters: + nep - eigensolver context - extra - number of additional positions, used for methods that require a working basis slightly larger than ncv Developers Note: This is PETSC_EXTERN because it may be required by user plugin NEP implementations. Level: developer @*/ PetscErrorCode NEPAllocateSolution(NEP nep,PetscInt extra) { PetscErrorCode ierr; PetscInt oldsize,newc,requested; PetscLogDouble cnt; Mat T; Vec t; PetscFunctionBegin; requested = nep->ncv + extra; /* oldsize is zero if this is the first time setup is called */ ierr = BVGetSizes(nep->V,NULL,NULL,&oldsize);CHKERRQ(ierr); newc = PetscMax(0,requested-oldsize); /* allocate space for eigenvalues and friends */ if (requested != oldsize) { if (oldsize) { ierr = PetscFree4(nep->eigr,nep->eigi,nep->errest,nep->perm);CHKERRQ(ierr); } ierr = PetscMalloc4(requested,&nep->eigr,requested,&nep->eigi,requested,&nep->errest,requested,&nep->perm);CHKERRQ(ierr); cnt = newc*sizeof(PetscScalar) + newc*sizeof(PetscReal) + newc*sizeof(PetscInt); ierr = PetscLogObjectMemory((PetscObject)nep,cnt);CHKERRQ(ierr); } /* allocate V */ if (!nep->V) { ierr = NEPGetBV(nep,&nep->V);CHKERRQ(ierr); } if (!oldsize) { if (!((PetscObject)(nep->V))->type_name) { ierr = BVSetType(nep->V,BVSVEC);CHKERRQ(ierr); } if (nep->split) T = nep->A[0]; else { ierr = NEPGetFunction(nep,&T,NULL,NULL,NULL);CHKERRQ(ierr); } ierr = MatGetVecs(T,&t,NULL);CHKERRQ(ierr); ierr = BVSetSizesFromVec(nep->V,t,requested);CHKERRQ(ierr); ierr = VecDestroy(&t);CHKERRQ(ierr); } else { ierr = BVResize(nep->V,requested,PETSC_FALSE);CHKERRQ(ierr); } PetscFunctionReturn(0); }