/*@C
TaoSetJacobianInequalityRoutine - Sets the function to compute the Jacobian
(and its inverse) of the constraint function with respect to the inequality variables.
Used only for pde-constrained optimization.
Logically collective on Tao
Input Parameters:
+ tao - the Tao context
. J - Matrix used for the jacobian
. Jpre - Matrix that will be used operated on by PETSc preconditioner, can be same as J.
. jac - Jacobian evaluation routine
- ctx - [optional] user-defined context for private data for the
Jacobian evaluation routine (may be NULL)
Calling sequence of jac:
$ jac (Tao tao,Vec x,Mat *J,Mat *Jpre,void *ctx);
+ tao - the Tao context
. x - input vector
. J - Jacobian matrix
. Jpre - preconditioner matrix, usually the same as J
- ctx - [optional] user-defined Jacobian context
Level: intermediate
.seealse: TaoComputeJacobianInequality(), TaoSetJacobianDesignRoutine(), TaoSetInequalityDesignIS()
@*/
PetscErrorCode TaoSetJacobianInequalityRoutine(Tao tao, Mat J, Mat Jpre, PetscErrorCode (*func)(Tao, Vec, Mat, Mat,void*), void *ctx)
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(tao,TAO_CLASSID,1);
if (J) {
PetscValidHeaderSpecific(J,MAT_CLASSID,2);
PetscCheckSameComm(tao,1,J,2);
}
if (Jpre) {
PetscValidHeaderSpecific(Jpre,MAT_CLASSID,3);
PetscCheckSameComm(tao,1,Jpre,3);
}
if (ctx) {
tao->user_jac_inequalityP = ctx;
}
if (func) {
tao->ops->computejacobianinequality = func;
}
if (J) {
ierr = PetscObjectReference((PetscObject)J);
CHKERRQ(ierr);
ierr = MatDestroy(&tao->jacobian_inequality);
CHKERRQ(ierr);
tao->jacobian_inequality = J;
}
if (Jpre) {
ierr = PetscObjectReference((PetscObject)Jpre);
CHKERRQ(ierr);
ierr = MatDestroy(&tao->jacobian_inequality_pre);
CHKERRQ(ierr);
tao->jacobian_inequality_pre=Jpre;
}
PetscFunctionReturn(0);
}
/*@
DMDACreateNaturalVector - Creates a parallel PETSc vector that
will hold vector values in the natural numbering, rather than in
the PETSc parallel numbering associated with the DMDA.
Collective
Input Parameter:
. da - the distributed array
Output Parameter:
. g - the distributed global vector
Level: developer
Note:
The output parameter, g, is a regular PETSc vector that should be destroyed
with a call to VecDestroy() when usage is finished.
The number of local entries in the vector on each process is the same
as in a vector created with DMCreateGlobalVector().
.keywords: distributed array, create, global, distributed, vector
.seealso: DMCreateLocalVector(), VecDuplicate(), VecDuplicateVecs(),
DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMGlobalToLocalBegin(),
DMGlobalToLocalEnd(), DMDALocalToGlobalBegin()
@*/
PetscErrorCode DMDACreateNaturalVector(DM da,Vec *g)
{
PetscErrorCode ierr;
PetscInt cnt;
DM_DA *dd = (DM_DA*)da->data;
PetscFunctionBegin;
PetscValidHeaderSpecificType(da,DM_CLASSID,1,DMDA);
PetscValidPointer(g,2);
if (dd->natural) {
ierr = PetscObjectGetReference((PetscObject)dd->natural,&cnt);CHKERRQ(ierr);
if (cnt == 1) { /* object is not currently used by anyone */
ierr = PetscObjectReference((PetscObject)dd->natural);CHKERRQ(ierr);
*g = dd->natural;
} else {
ierr = VecDuplicate(dd->natural,g);CHKERRQ(ierr);
}
} else { /* create the first version of this guy */
ierr = VecCreate(PetscObjectComm((PetscObject)da),g);CHKERRQ(ierr);
ierr = VecSetSizes(*g,dd->Nlocal,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetBlockSize(*g, dd->w);CHKERRQ(ierr);
ierr = VecSetType(*g,da->vectype);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)*g);CHKERRQ(ierr);
dd->natural = *g;
}
PetscFunctionReturn(0);
}
PetscErrorCode SNESVISetVariableBounds_VI(SNES snes,Vec xl,Vec xu)
{
PetscErrorCode ierr;
const PetscScalar *xxl,*xxu;
PetscInt i,n, cnt = 0;
PetscFunctionBegin;
ierr = SNESGetFunction(snes,&snes->vec_func,NULL,NULL);CHKERRQ(ierr);
if (!snes->vec_func) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call SNESSetFunction() or SNESSetDM() first");
{
PetscInt xlN,xuN,N;
ierr = VecGetSize(xl,&xlN);CHKERRQ(ierr);
ierr = VecGetSize(xu,&xuN);CHKERRQ(ierr);
ierr = VecGetSize(snes->vec_func,&N);CHKERRQ(ierr);
if (xlN != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incompatible vector lengths lower bound = %D solution vector = %D",xlN,N);
if (xuN != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incompatible vector lengths: upper bound = %D solution vector = %D",xuN,N);
}
ierr = SNESSetType(snes,SNESVINEWTONRSLS);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)xl);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)xu);CHKERRQ(ierr);
ierr = VecDestroy(&snes->xl);CHKERRQ(ierr);
ierr = VecDestroy(&snes->xu);CHKERRQ(ierr);
snes->xl = xl;
snes->xu = xu;
ierr = VecGetLocalSize(xl,&n);CHKERRQ(ierr);
ierr = VecGetArrayRead(xl,&xxl);CHKERRQ(ierr);
ierr = VecGetArrayRead(xu,&xxu);CHKERRQ(ierr);
for (i=0; i<n; i++) cnt += ((xxl[i] != SNES_VI_NINF) || (xxu[i] != SNES_VI_INF));
ierr = MPI_Allreduce(&cnt,&snes->ntruebounds,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)snes));CHKERRQ(ierr);
ierr = VecRestoreArrayRead(xl,&xxl);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(xu,&xxu);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/** Set rotation for certain nodes in a function space
*
* @param fs the function space
* @param is index set of nodes to rotate, sequential, with respect blocks of local vector
* @param rot Rotation matrices at all nodes in \a is. Should have length \c bs*bs*size(is).
* @param ns number of dofs to enforce strongly at each node (every entry must have 0<=ns[i]<=bs)
* @param v Vector of values for strongly enforced dofs
*
* @example Consider 2D flow over a bed with known melt rates. Suppose the local velocity vector is
*
* [u0x,u0y; u1x,u1y; u2x,u2y; u3x,u3y | u4x,u4y]
*
* (4 owned blocks, one ghosted block) and nodes 1,4 are on the slip boundary with normal and tangent vectors n1,t1,n4,t4
* and melt rates r1,r4. To enforce the melt rate strongly, use
*
* \a is = [1,4]
* \a rot = [n10,n11,t10,t11, n40,n41,t40,t41]
* \a ns = [1,1]
* \a v = [r1,r4]
*
* The rotated vector will become (. = \cdot)
*
* [u0x,u0y; u1.n1,u1.t1; u2x,u2y; u3x,u3y | u4.n4,u4.t4]
*
* and strongly enforcing melt rate produces the global vector
*
* [u0x,u0y; r1,u1.t1; u2x,u2y; u3x,u3y | r4,u4.t4] .
*
* This is what the solver sees, the Jacobian will always have rows and columns of the identity corresponding to the
* strongly enforced components (2,8 of the local vector) and the residual will always be 0 in these components. Hence
* the Newton step v will always be of the form
*
* [v0x,v0y; 0,v1y; v2x,v2y; v3x,v3y | 0,v4y] .
**/
dErr dFSRotationCreate(dFS fs,IS is,dReal rmat[],dInt ns[],Vec v,dFSRotation *inrot)
{
dFSRotation rot;
dInt bs,n;
dErr err;
dFunctionBegin;
dValidHeader(fs,DM_CLASSID,1);
dValidHeader(is,IS_CLASSID,2);
dValidRealPointer(rmat,3);
dValidIntPointer(ns,4);
dValidHeader(v,VEC_CLASSID,5);
dValidPointer(inrot,6);
*inrot = 0;
err = PetscHeaderCreate(rot,_p_dFSRotation,struct _dFSRotationOps,dFSROT_CLASSID,"dFSRotation","Local function space rotation","FS",PETSC_COMM_SELF,dFSRotationDestroy,dFSRotationView);dCHK(err);
err = dFSGetBlockSize(fs,&bs);dCHK(err);
rot->bs = bs;
err = ISGetSize(is,&n);dCHK(err);
rot->n = n;
err = PetscObjectReference((PetscObject)is);dCHK(err);
rot->is = is;
err = PetscObjectReference((PetscObject)v);dCHK(err);
rot->strong = v;
for (dInt i=0; i<n; i++) {
if (ns[i] < 0 || bs < ns[i]) dERROR(PETSC_COMM_SELF,1,"Number of strong dofs must be between 0 and bs=%d (inclusive)",bs);
/* \todo Check that every rmat is orthogonal */
}
err = dMallocA2(n*bs*bs,&rot->rmat,n,&rot->nstrong);dCHK(err);
err = dMemcpy(rot->rmat,rmat,n*bs*bs*sizeof rmat[0]);dCHK(err);
err = dMemcpy(rot->nstrong,ns,n*sizeof ns[0]);dCHK(err);
*inrot = rot;
dFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode TaoLMVMSetH0(Tao tao, Mat H0)
{
TAO_LMVM *lmP;
TAO_BLMVM *blmP;
const TaoType type;
PetscBool is_lmvm, is_blmvm;
PetscErrorCode ierr;
ierr = TaoGetType(tao, &type);CHKERRQ(ierr);
ierr = PetscStrcmp(type, TAOLMVM, &is_lmvm);CHKERRQ(ierr);
ierr = PetscStrcmp(type, TAOBLMVM, &is_blmvm);CHKERRQ(ierr);
if (is_lmvm) {
lmP = (TAO_LMVM *)tao->data;
ierr = PetscObjectReference((PetscObject)H0);CHKERRQ(ierr);
lmP->H0 = H0;
} else if (is_blmvm) {
blmP = (TAO_BLMVM *)tao->data;
ierr = PetscObjectReference((PetscObject)H0);CHKERRQ(ierr);
blmP->H0 = H0;
} else SETERRQ(PetscObjectComm((PetscObject)tao), PETSC_ERR_ARG_WRONGSTATE, "This routine applies to TAO_LMVM and TAO_BLMVM.");
PetscFunctionReturn(0);
}
/*@
ISGetNonlocalIS - Gather all nonlocal indices for this IS and present
them as another sequential index set.
Collective on IS
Input Parameter:
. is - the index set
Output Parameter:
. complement - sequential IS with indices identical to the result of
ISGetNonlocalIndices()
Level: intermediate
Notes: complement represents the result of ISGetNonlocalIndices as an IS.
Therefore scalability issues similar to ISGetNonlocalIndices apply.
The resulting IS must be restored using ISRestoreNonlocalIS().
Concepts: index sets^getting nonlocal indices
.seealso: ISGetNonlocalIndices(), ISRestoreNonlocalIndices(), ISAllGather(), ISGetSize()
@*/
PetscErrorCode ISGetNonlocalIS(IS is, IS *complement)
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(is,IS_CLASSID,1);
PetscValidPointer(complement,2);
/* Check if the complement exists already. */
if (is->complement) {
*complement = is->complement;
ierr = PetscObjectReference((PetscObject)(is->complement));
CHKERRQ(ierr);
} else {
PetscInt N, n;
const PetscInt *idx;
ierr = ISGetSize(is, &N);
CHKERRQ(ierr);
ierr = ISGetLocalSize(is,&n);
CHKERRQ(ierr);
ierr = ISGetNonlocalIndices(is, &idx);
CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF, N-n,idx, PETSC_USE_POINTER, &(is->complement));
CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)is->complement);
CHKERRQ(ierr);
*complement = is->complement;
}
PetscFunctionReturn(0);
}
/*@C
TaoSetHessianRoutine - Sets the function to compute the Hessian as well as the location to store the matrix.
Logically collective on Tao
Input Parameters:
+ tao - the Tao context
. H - Matrix used for the hessian
. Hpre - Matrix that will be used operated on by preconditioner, can be same as H
. hess - Hessian evaluation routine
- ctx - [optional] user-defined context for private data for the
Hessian evaluation routine (may be NULL)
Calling sequence of hess:
$ hess (Tao tao,Vec x,Mat H,Mat Hpre,void *ctx);
+ tao - the Tao context
. x - input vector
. H - Hessian matrix
. Hpre - preconditioner matrix, usually the same as H
- ctx - [optional] user-defined Hessian context
Level: beginner
@*/
PetscErrorCode TaoSetHessianRoutine(Tao tao, Mat H, Mat Hpre, PetscErrorCode (*func)(Tao, Vec, Mat, Mat, void*), void *ctx)
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(tao,TAO_CLASSID,1);
if (H) {
PetscValidHeaderSpecific(H,MAT_CLASSID,2);
PetscCheckSameComm(tao,1,H,2);
}
if (Hpre) {
PetscValidHeaderSpecific(Hpre,MAT_CLASSID,3);
PetscCheckSameComm(tao,1,Hpre,3);
}
if (ctx) {
tao->user_hessP = ctx;
}
if (func) {
tao->ops->computehessian = func;
}
if (H) {
ierr = PetscObjectReference((PetscObject)H);CHKERRQ(ierr);
ierr = MatDestroy(&tao->hessian);CHKERRQ(ierr);
tao->hessian = H;
}
if (Hpre) {
ierr = PetscObjectReference((PetscObject)Hpre);CHKERRQ(ierr);
ierr = MatDestroy(&tao->hessian_pre);CHKERRQ(ierr);
tao->hessian_pre = Hpre;
}
PetscFunctionReturn(0);
}
PetscErrorCode PCBDDCGraphGetDirichletDofsB(PCBDDCGraph graph, IS* dirdofs)
{
PetscErrorCode ierr;
PetscFunctionBegin;
if (graph->dirdofsB) {
ierr = PetscObjectReference((PetscObject)graph->dirdofsB);CHKERRQ(ierr);
} else if (graph->has_dirichlet) {
PetscInt i,size;
PetscInt *dirdofs_idxs;
size = 0;
for (i=0;i<graph->nvtxs;i++) {
if (graph->count[i] && graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) size++;
}
ierr = PetscMalloc1(size,&dirdofs_idxs);CHKERRQ(ierr);
size = 0;
for (i=0;i<graph->nvtxs;i++) {
if (graph->count[i] && graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) dirdofs_idxs[size++] = i;
}
ierr = ISCreateGeneral(PETSC_COMM_SELF,size,dirdofs_idxs,PETSC_OWN_POINTER,&graph->dirdofsB);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)graph->dirdofsB);CHKERRQ(ierr);
}
*dirdofs = graph->dirdofsB;
PetscFunctionReturn(0);
}
static PetscErrorCode PCBDDCScalingSetUp_Deluxe_Private(PC pc)
{
PC_BDDC *pcbddc=(PC_BDDC*)pc->data;
PCBDDCDeluxeScaling deluxe_ctx=pcbddc->deluxe_ctx;
PCBDDCSubSchurs sub_schurs = pcbddc->sub_schurs;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!sub_schurs->n_subs) {
PetscFunctionReturn(0);
}
/* Create work vectors for sequential part of deluxe */
ierr = MatCreateVecs(sub_schurs->S_Ej_all,&deluxe_ctx->seq_work1,&deluxe_ctx->seq_work2);CHKERRQ(ierr);
/* Compute deluxe sequential scatter */
if (sub_schurs->reuse_mumps && !sub_schurs->is_dir) {
PCBDDCReuseMumps reuse_mumps = sub_schurs->reuse_mumps;
ierr = PetscObjectReference((PetscObject)reuse_mumps->correction_scatter_B);CHKERRQ(ierr);
deluxe_ctx->seq_scctx = reuse_mumps->correction_scatter_B;
} else {
ierr = VecScatterCreate(pcbddc->work_scaling,sub_schurs->is_Ej_all,deluxe_ctx->seq_work1,NULL,&deluxe_ctx->seq_scctx);CHKERRQ(ierr);
}
/* Create Mat object for deluxe scaling */
ierr = PetscObjectReference((PetscObject)sub_schurs->S_Ej_all);CHKERRQ(ierr);
deluxe_ctx->seq_mat = sub_schurs->S_Ej_all;
if (sub_schurs->sum_S_Ej_all) { /* if this matrix is present, then we need to create the KSP object to invert it */
PC pc_temp;
MatSolverPackage solver=NULL;
char ksp_prefix[256];
size_t len;
ierr = KSPCreate(PETSC_COMM_SELF,&deluxe_ctx->seq_ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(deluxe_ctx->seq_ksp,sub_schurs->sum_S_Ej_all,sub_schurs->sum_S_Ej_all);CHKERRQ(ierr);
ierr = KSPSetType(deluxe_ctx->seq_ksp,KSPPREONLY);CHKERRQ(ierr);
ierr = KSPGetPC(deluxe_ctx->seq_ksp,&pc_temp);CHKERRQ(ierr);
ierr = PCSetType(pc_temp,PCLU);CHKERRQ(ierr);
ierr = KSPGetPC(pcbddc->ksp_D,&pc_temp);CHKERRQ(ierr);
ierr = PCFactorGetMatSolverPackage(pc_temp,(const MatSolverPackage*)&solver);CHKERRQ(ierr);
if (solver) {
PC new_pc;
PCType type;
ierr = PCGetType(pc_temp,&type);CHKERRQ(ierr);
ierr = KSPGetPC(deluxe_ctx->seq_ksp,&new_pc);CHKERRQ(ierr);
ierr = PCSetType(new_pc,type);CHKERRQ(ierr);
ierr = PCFactorSetMatSolverPackage(new_pc,solver);CHKERRQ(ierr);
}
ierr = PetscStrlen(((PetscObject)(pcbddc->ksp_D))->prefix,&len);CHKERRQ(ierr);
len -= 10; /* remove "dirichlet_" */
ierr = PetscStrncpy(ksp_prefix,((PetscObject)(pcbddc->ksp_D))->prefix,len+1);CHKERRQ(ierr);
ierr = PetscStrcat(ksp_prefix,"deluxe_");CHKERRQ(ierr);
ierr = KSPSetOptionsPrefix(deluxe_ctx->seq_ksp,ksp_prefix);CHKERRQ(ierr);
ierr = KSPSetFromOptions(deluxe_ctx->seq_ksp);CHKERRQ(ierr);
ierr = KSPSetUp(deluxe_ctx->seq_ksp);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode DMAKKTGetFieldDecomposition(DM dm, PetscInt *n, char*** names, IS **iss, DM **dms) {
PetscBool iskkt;
DM_AKKT *kkt = (DM_AKKT*)(dm->data);
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID,1);
PetscValidPointer(names,3);
PetscValidPointer(iss,4);
PetscValidPointer(dms,5);
ierr = PetscObjectTypeCompare((PetscObject)dm, DMAKKT, &iskkt); CHKERRQ(ierr);
if(!iskkt) SETERRQ(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "DM not of type DMAKKT");
if(n) *n = 2;
if(names) {
if(kkt->names) {
ierr = PetscMalloc(sizeof(char*)*2, names); CHKERRQ(ierr);
}
else {
*names = PETSC_NULL;
}
}
if(iss) {
if(kkt->isf) {
ierr = PetscMalloc(sizeof(IS)*2, iss); CHKERRQ(ierr);
}
else {
*iss = PETSC_NULL;
}
}
if(dms) {
if(kkt->dmf) {
ierr = PetscMalloc(sizeof(DM)*2, dms); CHKERRQ(ierr);
}
else {
*dms = PETSC_NULL;
}
}
for(i = 0; i < 2; ++i) {
if(names && kkt->names){
ierr = PetscStrallocpy(kkt->names[i],(*names)+i); CHKERRQ(ierr);
}
if(iss && kkt->isf) {
ierr = PetscObjectReference((PetscObject)kkt->isf[i]); CHKERRQ(ierr);
(*iss)[i] = kkt->isf[i];
}
if(dms && kkt->dmf) {
ierr = PetscObjectReference((PetscObject)kkt->dmf[i]); CHKERRQ(ierr);
(*dms)[i] = kkt->dmf[i];
}
}
PetscFunctionReturn(0);
}
/*@
TaoSetStateDesignIS - Indicate to the Tao which variables in the
solution vector are state variables and which are design. Only applies to
pde-constrained optimization.
Logically Collective on Tao
Input Parameters:
+ tao - The Tao context
. s_is - the index set corresponding to the state variables
- d_is - the index set corresponding to the design variables
Level: intermediate
.seealso: TaoSetJacobianStateRoutine(), TaoSetJacobianDesignRoutine()
@*/
PetscErrorCode TaoSetStateDesignIS(Tao tao, IS s_is, IS d_is)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectReference((PetscObject)s_is);CHKERRQ(ierr);
ierr = ISDestroy(&tao->state_is);CHKERRQ(ierr);
tao->state_is = s_is;
ierr = PetscObjectReference((PetscObject)(d_is));CHKERRQ(ierr);
ierr = ISDestroy(&tao->design_is);CHKERRQ(ierr);
tao->design_is = d_is;
PetscFunctionReturn(0);
}
/*@
MatSchurComplementSet - Sets the matrices that define the Schur complement
Collective on Mat
Input Parameter:
+ N - matrix obtained with MatCreate() and MatSetType(MATSCHURCOMPLEMENT);
- A00,A01,A10,A11 - the four parts of the original matrix (A00 is optional)
Level: intermediate
Notes: The Schur complement is NOT actually formed! Rather this
object performs the matrix-vector product by using the the formula for
the Schur complement and a KSP solver to approximate the action of inv(A)
All four matrices must have the same MPI communicator
A00 and A11 must be square matrices
.seealso: MatCreateNormal(), MatMult(), MatCreate(), MatSchurComplementGetKSP(), MatSchurComplementUpdate(), MatCreateTranspose(), MatGetSchurComplement()
@*/
PetscErrorCode MatSchurComplementSet(Mat N,Mat A00,Mat Ap00,Mat A01,Mat A10,Mat A11)
{
PetscErrorCode ierr;
PetscInt m,n;
Mat_SchurComplement *Na = (Mat_SchurComplement*)N->data;
PetscFunctionBegin;
if (N->assembled) SETERRQ(((PetscObject)N)->comm,PETSC_ERR_ARG_WRONGSTATE,"Use MatSchurComplementUpdate() for already used matrix");
PetscValidHeaderSpecific(A00,MAT_CLASSID,1);
PetscValidHeaderSpecific(Ap00,MAT_CLASSID,2);
PetscValidHeaderSpecific(A01,MAT_CLASSID,3);
PetscValidHeaderSpecific(A10,MAT_CLASSID,4);
PetscCheckSameComm(A00,1,Ap00,2);
PetscCheckSameComm(A00,1,A01,3);
PetscCheckSameComm(A00,1,A10,4);
if (A00->rmap->n != A00->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of A00 %D do not equal local columns %D",A00->rmap->n,A00->cmap->n);
if (A00->rmap->n != Ap00->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of A00 %D do not equal local rows of Ap00 %D",A00->rmap->n,Ap00->rmap->n);
if (Ap00->rmap->n != Ap00->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of Ap00 %D do not equal local columns %D",Ap00->rmap->n,Ap00->cmap->n);
if (A00->cmap->n != A01->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local columns of A00 %D do not equal local rows of A01 %D",A00->cmap->n,A01->rmap->n);
if (A10->cmap->n != A00->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local columns of A10 %D do not equal local rows of A00 %D",A10->cmap->n,A00->rmap->n);
if (A11) {
PetscValidHeaderSpecific(A11,MAT_CLASSID,5);
PetscCheckSameComm(A00,1,A11,5);
if (A11->rmap->n != A11->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of A11 %D do not equal local columns %D",A11->rmap->n,A11->cmap->n);
if (A10->rmap->n != A11->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of A10 %D do not equal local rows A11 %D",A10->rmap->n,A11->rmap->n);
}
ierr = MatGetLocalSize(A01,PETSC_NULL,&n);CHKERRQ(ierr);
ierr = MatGetLocalSize(A10,&m,PETSC_NULL);CHKERRQ(ierr);
ierr = MatSetSizes(N,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)A00);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)Ap00);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)A01);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)A10);CHKERRQ(ierr);
Na->A = A00;
Na->Ap = Ap00;
Na->B = A01;
Na->C = A10;
Na->D = A11;
if (A11) {
ierr = PetscObjectReference((PetscObject)A11);CHKERRQ(ierr);
}
N->assembled = PETSC_TRUE;
N->preallocated = PETSC_TRUE;
ierr = PetscLayoutSetUp((N)->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp((N)->cmap);CHKERRQ(ierr);
ierr = KSPSetOperators(Na->ksp,A00,Ap00,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SNESNASMSetSubdomains_NASM(SNES snes,PetscInt n,SNES subsnes[],VecScatter iscatter[],VecScatter oscatter[],VecScatter gscatter[])
{
PetscInt i;
PetscErrorCode ierr;
SNES_NASM *nasm = (SNES_NASM*)snes->data;
PetscFunctionBegin;
if (snes->setupcalled) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_WRONGSTATE,"SNESNASMSetSubdomains() should be called before calling SNESSetUp().");
/* tear down the previously set things */
ierr = SNESReset(snes);CHKERRQ(ierr);
nasm->n = n;
if (oscatter) {
for (i=0; i<n; i++) {ierr = PetscObjectReference((PetscObject)oscatter[i]);CHKERRQ(ierr);}
}
if (iscatter) {
for (i=0; i<n; i++) {ierr = PetscObjectReference((PetscObject)iscatter[i]);CHKERRQ(ierr);}
}
if (gscatter) {
for (i=0; i<n; i++) {ierr = PetscObjectReference((PetscObject)gscatter[i]);CHKERRQ(ierr);}
}
if (oscatter) {
ierr = PetscMalloc(n*sizeof(IS),&nasm->oscatter);CHKERRQ(ierr);
for (i=0; i<n; i++) {
nasm->oscatter[i] = oscatter[i];
}
}
if (iscatter) {
ierr = PetscMalloc(n*sizeof(IS),&nasm->iscatter);CHKERRQ(ierr);
for (i=0; i<n; i++) {
nasm->iscatter[i] = iscatter[i];
}
}
if (gscatter) {
ierr = PetscMalloc(n*sizeof(IS),&nasm->gscatter);CHKERRQ(ierr);
for (i=0; i<n; i++) {
nasm->gscatter[i] = gscatter[i];
}
}
if (subsnes) {
ierr = PetscMalloc(n*sizeof(SNES),&nasm->subsnes);CHKERRQ(ierr);
for (i=0; i<n; i++) {
nasm->subsnes[i] = subsnes[i];
}
nasm->same_local_solves = PETSC_FALSE;
}
PetscFunctionReturn(0);
}
PetscErrorCode MatSMFResetRowColumn(Mat mat,IS Rows,IS Cols){
MatSubMatFreeCtx ctx;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatShellGetContext(mat,(void **)&ctx);CHKERRQ(ierr);
ierr = ISDestroy(&ctx->Rows);CHKERRQ(ierr);
ierr = ISDestroy(&ctx->Cols);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)Rows);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)Cols);CHKERRQ(ierr);
ctx->Cols=Cols;
ctx->Rows=Rows;
PetscFunctionReturn(0);
}
/*@
MatSchurComplementUpdate - Updates the Schur complement matrix object with new submatrices
Collective on Mat
Input Parameters:
+ N - the matrix obtained with MatCreateSchurComplement()
. A,B,C,D - the four parts of the original matrix (D is optional)
- str - either SAME_NONZERO_PATTERN,DIFFERENT_NONZERO_PATTERN,SAME_PRECONDITIONER
Level: intermediate
Notes: All four matrices must have the same MPI communicator
A and D must be square matrices
All of the matrices provided must have the same sizes as was used with MatCreateSchurComplement() or MatSchurComplementSet()
though they need not be the same matrices
.seealso: MatCreateNormal(), MatMult(), MatCreate(), MatSchurComplementGetKSP(), MatCreateSchurComplement()
@*/
PetscErrorCode MatSchurComplementUpdate(Mat N,Mat A,Mat Ap,Mat B,Mat C,Mat D,MatStructure str)
{
PetscErrorCode ierr;
Mat_SchurComplement *Na = (Mat_SchurComplement*)N->data;
PetscFunctionBegin;
if (!N->assembled) SETERRQ(((PetscObject)N)->comm,PETSC_ERR_ARG_WRONGSTATE,"Use MatSchurComplementSet() for new matrix");
PetscValidHeaderSpecific(A,MAT_CLASSID,1);
PetscValidHeaderSpecific(B,MAT_CLASSID,2);
PetscValidHeaderSpecific(C,MAT_CLASSID,3);
PetscCheckSameComm(A,1,Ap,2);
PetscCheckSameComm(A,1,B,3);
PetscCheckSameComm(A,1,C,4);
if (A->rmap->n != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of A %D do not equal local columns %D",A->rmap->n,A->cmap->n);
if (A->rmap->n != Ap->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of A %D do not equal local rows of Ap %D",A->rmap->n,Ap->rmap->n);
if (Ap->rmap->n != Ap->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of Ap %D do not equal local columns %D",Ap->rmap->n,Ap->cmap->n);
if (A->cmap->n != B->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local columns of A %D do not equal local rows of B %D",A->cmap->n,B->rmap->n);
if (C->cmap->n != A->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local columns of C %D do not equal local rows of A %D",C->cmap->n,A->rmap->n);
if (D) {
PetscValidHeaderSpecific(D,MAT_CLASSID,5);
PetscCheckSameComm(A,1,D,5);
if (D->rmap->n != D->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of D %D do not equal local columns %D",D->rmap->n,D->cmap->n);
if (C->rmap->n != D->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of C %D do not equal local rows D %D",C->rmap->n,D->rmap->n);
}
ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)Ap);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)B);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)C);CHKERRQ(ierr);
if (D) {
ierr = PetscObjectReference((PetscObject)D);CHKERRQ(ierr);
}
ierr = MatDestroy(&Na->A);CHKERRQ(ierr);
ierr = MatDestroy(&Na->Ap);CHKERRQ(ierr);
ierr = MatDestroy(&Na->B);CHKERRQ(ierr);
ierr = MatDestroy(&Na->C);CHKERRQ(ierr);
ierr = MatDestroy(&Na->D);CHKERRQ(ierr);
Na->A = A;
Na->Ap = Ap;
Na->B = B;
Na->C = C;
Na->D = D;
ierr = KSPSetOperators(Na->ksp,A,Ap,str);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
MatCreateSubMatrixFree - Creates a reduced matrix by masking a
full matrix.
Collective on matrix
Input Parameters:
+ mat - matrix of arbitrary type
. Rows - the rows that will be in the submatrix
- Cols - the columns that will be in the submatrix
Output Parameters:
. J - New matrix
Notes:
The user provides the input data and is responsible for destroying
this data after matrix J has been destroyed.
Level: developer
.seealso: MatCreate()
@*/
PetscErrorCode MatCreateSubMatrixFree(Mat mat,IS Rows, IS Cols, Mat *J)
{
MPI_Comm comm=PetscObjectComm((PetscObject)mat);
MatSubMatFreeCtx ctx;
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt mloc,nloc,m,n;
PetscFunctionBegin;
ierr = PetscNew(&ctx);CHKERRQ(ierr);
ctx->A=mat;
ierr = MatGetSize(mat,&m,&n);CHKERRQ(ierr);
ierr = MatGetLocalSize(mat,&mloc,&nloc);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
if (size == 1) {
ierr = VecCreateSeq(comm,n,&ctx->VC);CHKERRQ(ierr);
} else {
ierr = VecCreateMPI(comm,nloc,n,&ctx->VC);CHKERRQ(ierr);
}
ctx->VR=ctx->VC;
ierr = PetscObjectReference((PetscObject)mat);CHKERRQ(ierr);
ctx->Rows = Rows;
ctx->Cols = Cols;
ierr = PetscObjectReference((PetscObject)Rows);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)Cols);CHKERRQ(ierr);
ierr = MatCreateShell(comm,mloc,nloc,m,n,ctx,J);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_MULT,(void(*)(void))MatMult_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_DESTROY,(void(*)(void))MatDestroy_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_VIEW,(void(*)(void))MatView_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_MULT_TRANSPOSE,(void(*)(void))MatMultTranspose_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_DIAGONAL_SET,(void(*)(void))MatDiagonalSet_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_SHIFT,(void(*)(void))MatShift_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_EQUAL,(void(*)(void))MatEqual_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_SCALE,(void(*)(void))MatScale_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_TRANSPOSE,(void(*)(void))MatTranspose_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_GET_DIAGONAL,(void(*)(void))MatGetDiagonal_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_GET_SUBMATRICES,(void(*)(void))MatGetSubMatrices_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_NORM,(void(*)(void))MatNorm_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_DUPLICATE,(void(*)(void))MatDuplicate_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_GET_SUBMATRIX,(void(*)(void))MatGetSubMatrix_SMF);CHKERRQ(ierr);
ierr = MatShellSetOperation(*J,MATOP_GET_ROW_MAX,(void(*)(void))MatDuplicate_SMF);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)(*J));CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
MatCompositeAddMat - add another matrix to a composite matrix
Collective on Mat
Input Parameters:
+ mat - the composite matrix
- smat - the partial matrix
Level: advanced
.seealso: MatCreateComposite()
@*/
PetscErrorCode MatCompositeAddMat(Mat mat,Mat smat)
{
Mat_Composite *shell;
PetscErrorCode ierr;
Mat_CompositeLink ilink,next;
PetscFunctionBegin;
PetscValidHeaderSpecific(mat,MAT_CLASSID,1);
PetscValidHeaderSpecific(smat,MAT_CLASSID,2);
ierr = PetscNewLog(mat,&ilink);CHKERRQ(ierr);
ilink->next = 0;
ierr = PetscObjectReference((PetscObject)smat);CHKERRQ(ierr);
ilink->mat = smat;
shell = (Mat_Composite*)mat->data;
next = shell->head;
if (!next) shell->head = ilink;
else {
while (next->next) {
next = next->next;
}
next->next = ilink;
ilink->prev = next;
}
shell->tail = ilink;
PetscFunctionReturn(0);
}
/*
DMSetVI - Marks a DM as associated with a VI problem. This causes the interpolation/restriction operators to
be restricted to only those variables NOT associated with active constraints.
*/
PetscErrorCode DMSetVI(DM dm,IS inactive)
{
PetscErrorCode ierr;
PetscContainer isnes;
DM_SNESVI *dmsnesvi;
PetscFunctionBegin;
if (!dm) PetscFunctionReturn(0);
ierr = PetscObjectReference((PetscObject)inactive);CHKERRQ(ierr);
ierr = PetscObjectQuery((PetscObject)dm,"VI",(PetscObject *)&isnes);CHKERRQ(ierr);
if (!isnes) {
ierr = PetscContainerCreate(((PetscObject)dm)->comm,&isnes);CHKERRQ(ierr);
ierr = PetscContainerSetUserDestroy(isnes,(PetscErrorCode (*)(void*))DMDestroy_SNESVI);CHKERRQ(ierr);
ierr = PetscNew(DM_SNESVI,&dmsnesvi);CHKERRQ(ierr);
ierr = PetscContainerSetPointer(isnes,(void*)dmsnesvi);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject)dm,"VI",(PetscObject)isnes);CHKERRQ(ierr);
ierr = PetscContainerDestroy(&isnes);CHKERRQ(ierr);
dmsnesvi->createinterpolation = dm->ops->createinterpolation;
dm->ops->createinterpolation = DMCreateInterpolation_SNESVI;
dmsnesvi->coarsen = dm->ops->coarsen;
dm->ops->coarsen = DMCoarsen_SNESVI;
dmsnesvi->createglobalvector = dm->ops->createglobalvector;
dm->ops->createglobalvector = DMCreateGlobalVector_SNESVI;
} else {
ierr = PetscContainerGetPointer(isnes,(void**)&dmsnesvi);CHKERRQ(ierr);
ierr = ISDestroy(&dmsnesvi->inactive);CHKERRQ(ierr);
}
ierr = DMClearGlobalVectors(dm);CHKERRQ(ierr);
ierr = ISGetLocalSize(inactive,&dmsnesvi->n);CHKERRQ(ierr);
dmsnesvi->inactive = inactive;
dmsnesvi->dm = dm;
PetscFunctionReturn(0);
}
/*@
MatCreateTranspose - Creates a new matrix object that behaves like A'
Collective on Mat
Input Parameter:
. A - the (possibly rectangular) matrix
Output Parameter:
. N - the matrix that represents A'
Level: intermediate
Notes:
The transpose A' is NOT actually formed! Rather the new matrix
object performs the matrix-vector product by using the MatMultTranspose() on
the original matrix
.seealso: MatCreateNormal(), MatMult(), MatMultTranspose(), MatCreate()
@*/
PetscErrorCode MatCreateTranspose(Mat A,Mat *N)
{
PetscErrorCode ierr;
PetscInt m,n;
Mat_Transpose *Na;
PetscFunctionBegin;
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
ierr = MatCreate(PetscObjectComm((PetscObject)A),N);CHKERRQ(ierr);
ierr = MatSetSizes(*N,n,m,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = PetscLayoutSetUp((*N)->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp((*N)->cmap);CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)*N,MATTRANSPOSEMAT);CHKERRQ(ierr);
ierr = PetscNewLog(*N,&Na);CHKERRQ(ierr);
(*N)->data = (void*) Na;
ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr);
Na->A = A;
(*N)->ops->destroy = MatDestroy_Transpose;
(*N)->ops->mult = MatMult_Transpose;
(*N)->ops->multadd = MatMultAdd_Transpose;
(*N)->ops->multtranspose = MatMultTranspose_Transpose;
(*N)->ops->multtransposeadd = MatMultTransposeAdd_Transpose;
(*N)->ops->duplicate = MatDuplicate_Transpose;
(*N)->ops->getvecs = MatCreateVecs_Transpose;
(*N)->ops->axpy = MatAXPY_Transpose;
(*N)->assembled = PETSC_TRUE;
ierr = PetscObjectComposeFunction((PetscObject)(*N),"MatTransposeGetMat_C",MatTransposeGetMat_Transpose);CHKERRQ(ierr);
ierr = MatSetBlockSizes(*N,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr);
ierr = MatSetUp(*N);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode VecSetUp_Nest_Private(Vec V,PetscInt nb,Vec x[])
{
Vec_Nest *ctx = (Vec_Nest*)V->data;
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBegin;
if (ctx->setup_called) PetscFunctionReturn(0);
ctx->nb = nb;
if (ctx->nb < 0) SETERRQ(PetscObjectComm((PetscObject)V),PETSC_ERR_ARG_WRONG,"Cannot create VECNEST with < 0 blocks.");
/* Create space */
ierr = PetscMalloc1(ctx->nb,&ctx->v);CHKERRQ(ierr);
for (i=0; i<ctx->nb; i++) {
ctx->v[i] = x[i];
ierr = PetscObjectReference((PetscObject)x[i]);CHKERRQ(ierr);
/* Do not allocate memory for internal sub blocks */
}
ierr = PetscMalloc1(ctx->nb,&ctx->is);CHKERRQ(ierr);
ctx->setup_called = PETSC_TRUE;
PetscFunctionReturn(0);
}
/*@
DMPlexInterpolate - Take in a cell-vertex mesh and return one with all intermediate faces, edges, etc.
Collective on DM
Input Parameter:
. dm - The DMPlex object with only cells and vertices
Output Parameter:
. dmInt - The complete DMPlex object
Level: intermediate
.keywords: mesh
.seealso: DMPlexUninterpolate(), DMPlexCreateFromCellList()
@*/
PetscErrorCode DMPlexInterpolate(DM dm, DM *dmInt)
{
DM idm, odm = dm;
PetscInt depth, dim, d;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLogEventBegin(DMPLEX_Interpolate,dm,0,0,0);CHKERRQ(ierr);
ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
if (dim <= 1) {
ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr);
idm = dm;
}
for (d = 1; d < dim; ++d) {
/* Create interpolated mesh */
ierr = DMCreate(PetscObjectComm((PetscObject)dm), &idm);CHKERRQ(ierr);
ierr = DMSetType(idm, DMPLEX);CHKERRQ(ierr);
ierr = DMPlexSetDimension(idm, dim);CHKERRQ(ierr);
if (depth > 0) {ierr = DMPlexInterpolateFaces_Internal(odm, 1, idm);CHKERRQ(ierr);}
if (odm != dm) {ierr = DMDestroy(&odm);CHKERRQ(ierr);}
odm = idm;
}
*dmInt = idm;
ierr = PetscLogEventEnd(DMPLEX_Interpolate,dm,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscDrawBarCreate - Creates a bar graph data structure.
Collective over PetscDraw
Input Parameters:
. draw - The window where the graph will be made
Output Parameters:
. bar - The bar graph context
Notes: Call PetscDrawBarSetData() to provide the bins to be plotted and then PetscDrawBarDraw() to display the new plot
The difference between a bar chart, PetscDrawBar, and a histogram, PetscDrawHG, is explained here http://stattrek.com/statistics/charts/histogram.aspx?Tutorial=AP
The MPI communicator that owns the PetscDraw owns this PetscDrawBar, but the calls to set options and add data are ignored on all processes except the
zeroth MPI process in the communicator. All MPI processes in the communicator must call PetscDrawBarDraw() to display the updated graph.
Level: intermediate
Concepts: bar graph^creating
.seealso: PetscDrawLGCreate(), PetscDrawLG, PetscDrawSPCreate(), PetscDrawSP, PetscDrawHGCreate(), PetscDrawHG, PetscDrawBarDestroy(), PetscDrawBarSetData(),
PetscDrawBar, PetscDrawBarDraw(), PetscDrawBarSave(), PetscDrawBarSetColor(), PetscDrawBarSort(), PetscDrawBarSetLimits(), PetscDrawBarGetAxis(), PetscDrawAxis,
PetscDrawBarGetDraw(), PetscDrawBarSetFromOptions()
@*/
PetscErrorCode PetscDrawBarCreate(PetscDraw draw,PetscDrawBar *bar)
{
PetscDrawBar h;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(draw,PETSC_DRAW_CLASSID,1);
PetscValidPointer(bar,2);
ierr = PetscHeaderCreate(h,PETSC_DRAWBAR_CLASSID,"DrawBar","Bar Graph","Draw",PetscObjectComm((PetscObject)draw),PetscDrawBarDestroy,NULL);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)draw,(PetscObject)h);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)draw);CHKERRQ(ierr);
h->win = draw;
h->view = NULL;
h->destroy = NULL;
h->color = PETSC_DRAW_GREEN;
h->ymin = 0.; /* if user has not set these then they are determined from the data */
h->ymax = 0.;
h->numBins = 0;
ierr = PetscDrawAxisCreate(draw,&h->axis);CHKERRQ(ierr);
h->axis->xticks = NULL;
*bar = h;
PetscFunctionReturn(0);
}
/*@
VecGhostGetLocalForm - Obtains the local ghosted representation of
a parallel vector (obtained with VecCreateGhost(), VecCreateGhostWithArray()
or VecCreateSeq()). Returns PETSC_NULL if the Vec is not ghosted.
Not Collective
Input Parameter:
. g - the global vector
Output Parameter:
. l - the local (ghosted) representation, PETSC_NULL if g is not ghosted
Notes:
This routine does not actually update the ghost values, but rather it
returns a sequential vector that includes the locations for the ghost
values and their current values. The returned vector and the original
vector passed in share the same array that contains the actual vector data.
To update the ghost values from the locations on the other processes one must call
VecGhostUpdateBegin() and VecGhostUpdateEnd() before accessing the ghost values. Thus normal
usage is
$ VecGhostUpdateBegin(x,INSERT_VALUES,SCATTER_FORWARD);
$ VecGhostUpdateEnd(x,INSERT_VALUES,SCATTER_FORWARD);
$ VecGhostGetLocalForm(x,&xlocal);
$ VecGetArray(xlocal,&xvalues);
$ // access the non-ghost values in locations xvalues[0:n-1] and ghost values in locations xvalues[n:n+nghost];
$ VecRestoreArray(xlocal,&xvalues);
$ VecGhostRestoreLocalForm(x,&xlocal);
One should call VecGhostRestoreLocalForm() or VecDestroy() once one is
finished using the object.
Level: advanced
Concepts: vectors^ghost point access
.seealso: VecCreateGhost(), VecGhostRestoreLocalForm(), VecCreateGhostWithArray()
@*/
PetscErrorCode VecGhostGetLocalForm(Vec g,Vec *l)
{
PetscErrorCode ierr;
PetscBool isseq,ismpi;
PetscFunctionBegin;
PetscValidHeaderSpecific(g,VEC_CLASSID,1);
PetscValidPointer(l,2);
ierr = PetscObjectTypeCompare((PetscObject)g,VECSEQ,&isseq);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)g,VECMPI,&ismpi);CHKERRQ(ierr);
if (ismpi) {
Vec_MPI *v = (Vec_MPI*)g->data;
*l = v->localrep;
} else if (isseq) {
*l = g;
} else {
*l = PETSC_NULL;
}
if (*l) {
ierr = VecGhostStateSync_Private(g,*l);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)*l);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
EXTERN_C_END
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "MatDAADSetDA_AD"
PetscErrorCode MatDAADSetDA_AD(Mat A,DM da)
{
Mat_DAAD *a = (Mat_DAAD*)A->data;
PetscErrorCode ierr;
PetscInt nc,nx,ny,nz,Nx,Ny,Nz;
PetscFunctionBegin;
ierr = PetscObjectReference((PetscObject)da);
CHKERRQ(ierr);
if (a->da) {
ierr = DMDestroy(a->da);
CHKERRQ(ierr);
}
a->da = da;
ierr = DMDAGetInfo(da,0,&Nx,&Ny,&Nz,0,0,0,&nc,0,0,0);
CHKERRQ(ierr);
ierr = DMDAGetCorners(da,0,0,0,&nx,&ny,&nz);
CHKERRQ(ierr);
A->rmap->n = A->cmap->n = nc*nx*ny*nz;
A->rmap->N = A->cmap->N = nc*Nx*Ny*Nz;
ierr = DMCreateLocalVector(da,&a->localu);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode PCRedundantSetScatter_Redundant(PC pc,VecScatter in,VecScatter out)
{
PC_Redundant *red = (PC_Redundant*)pc->data;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectReference((PetscObject)in);CHKERRQ(ierr);
ierr = VecScatterDestroy(&red->scatterin);CHKERRQ(ierr);
red->scatterin = in;
ierr = PetscObjectReference((PetscObject)out);CHKERRQ(ierr);
ierr = VecScatterDestroy(&red->scatterout);CHKERRQ(ierr);
red->scatterout = out;
PetscFunctionReturn(0);
}
/*@
MatSubMatrixUpdate - Updates a submatrix
Collective on Mat
Input Parameters:
+ N - submatrix to update
. A - full matrix in the submatrix
. isrow - rows in the update (same as the first time the submatrix was created)
- iscol - columns in the update (same as the first time the submatrix was created)
Level: developer
Notes:
Most will use MatGetSubMatrix which provides a more efficient representation if it is available.
.seealso: MatGetSubMatrix(), MatCreateSubMatrix()
@*/
PetscErrorCode MatSubMatrixUpdate(Mat N,Mat A,IS isrow,IS iscol)
{
PetscErrorCode ierr;
PetscBool flg;
Mat_SubMatrix *Na;
PetscFunctionBegin;
PetscValidHeaderSpecific(N,MAT_CLASSID,1);
PetscValidHeaderSpecific(A,MAT_CLASSID,2);
PetscValidHeaderSpecific(isrow,IS_CLASSID,3);
PetscValidHeaderSpecific(iscol,IS_CLASSID,4);
ierr = PetscObjectTypeCompare((PetscObject)N,MATSUBMATRIX,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Matrix has wrong type");
Na = (Mat_SubMatrix*)N->data;
ierr = ISEqual(isrow,Na->isrow,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cannot update submatrix with different row indices");
ierr = ISEqual(iscol,Na->iscol,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cannot update submatrix with different column indices");
ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr);
ierr = MatDestroy(&Na->A);CHKERRQ(ierr);
Na->A = A;
Na->scale = 1.0;
ierr = VecDestroy(&Na->left);CHKERRQ(ierr);
ierr = VecDestroy(&Na->right);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
KSPSetDM - Sets the DM that may be used by some preconditioners
Logically Collective on KSP
Input Parameters:
+ ksp - the preconditioner context
- dm - the dm, cannot be NULL
Notes: If this is used then the KSP will attempt to use the DM to create the matrix and use the routine
set with DMKSPSetComputeOperators(). Use KSPSetDMActive(ksp,PETSC_FALSE) to instead use the matrix
you've provided with KSPSetOperators().
Level: intermediate
.seealso: KSPGetDM(), KSPSetDMActive(), KSPSetComputeOperators(), KSPSetComputeRHS(), KSPSetComputeInitialGuess(), DMKSPSetComputeOperators(), DMKSPSetComputeRHS(), DMKSPSetComputeInitialGuess()
@*/
PetscErrorCode KSPSetDM(KSP ksp,DM dm)
{
PetscErrorCode ierr;
PC pc;
PetscFunctionBegin;
PetscValidHeaderSpecific(ksp,KSP_CLASSID,1);
PetscValidHeaderSpecific(dm,DM_CLASSID,2);
ierr = PetscObjectReference((PetscObject)dm);
CHKERRQ(ierr);
if (ksp->dm) { /* Move the DMSNES context over to the new DM unless the new DM already has one */
if (ksp->dm->dmksp && !dm->dmksp) {
DMKSP kdm;
ierr = DMCopyDMKSP(ksp->dm,dm);
CHKERRQ(ierr);
ierr = DMGetDMKSP(ksp->dm,&kdm);
CHKERRQ(ierr);
if (kdm->originaldm == ksp->dm) kdm->originaldm = dm; /* Grant write privileges to the replacement DM */
}
ierr = DMDestroy(&ksp->dm);
CHKERRQ(ierr);
}
ksp->dm = dm;
ksp->dmAuto = PETSC_FALSE;
ierr = KSPGetPC(ksp,&pc);
CHKERRQ(ierr);
ierr = PCSetDM(pc,dm);
CHKERRQ(ierr);
ksp->dmActive = PETSC_TRUE;
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 = ISLocalToGlobalMappingGetBlockSize(rmapping,&bs);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_SELF,&is->A);CHKERRQ(ierr);
if (bs > 1) {
ierr = MatSetType(is->A,MATSEQBAIJ);CHKERRQ(ierr);
} else {
ierr = MatSetType(is->A,MATSEQAIJ);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 = MatCreateVecs(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 PCApply_MG(PC pc,Vec b,Vec x)
{
PC_MG *mg = (PC_MG*)pc->data;
PC_MG_Levels **mglevels = mg->levels;
PetscErrorCode ierr;
PetscInt levels = mglevels[0]->levels,i;
PetscFunctionBegin;
if (mg->stageApply) {ierr = PetscLogStagePush(mg->stageApply);CHKERRQ(ierr);}
/* When the DM is supplying the matrix then it will not exist until here */
for (i=0; i<levels; i++) {
if (!mglevels[i]->A) {
ierr = KSPGetOperators(mglevels[i]->smoothu,&mglevels[i]->A,NULL);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)mglevels[i]->A);CHKERRQ(ierr);
}
}
mglevels[levels-1]->b = b;
mglevels[levels-1]->x = x;
if (mg->am == PC_MG_MULTIPLICATIVE) {
ierr = VecSet(x,0.0);CHKERRQ(ierr);
for (i=0; i<mg->cyclesperpcapply; i++) {
ierr = PCMGMCycle_Private(pc,mglevels+levels-1,NULL);CHKERRQ(ierr);
}
} else if (mg->am == PC_MG_ADDITIVE) {
ierr = PCMGACycle_Private(pc,mglevels);CHKERRQ(ierr);
} else if (mg->am == PC_MG_KASKADE) {
ierr = PCMGKCycle_Private(pc,mglevels);CHKERRQ(ierr);
} else {
ierr = PCMGFCycle_Private(pc,mglevels);CHKERRQ(ierr);
}
if (mg->stageApply) {ierr = PetscLogStagePop();CHKERRQ(ierr);}
PetscFunctionReturn(0);
}
/*@
MatCreateNormalHermitian - Creates a new matrix object that behaves like (A*)'*A.
Collective on Mat
Input Parameter:
. A - the (possibly rectangular complex) matrix
Output Parameter:
. N - the matrix that represents (A*)'*A
Level: intermediate
Notes: The product (A*)'*A is NOT actually formed! Rather the new matrix
object performs the matrix-vector product by first multiplying by
A and then (A*)'
@*/
PetscErrorCode MatCreateNormalHermitian(Mat A,Mat *N)
{
PetscErrorCode ierr;
PetscInt m,n;
Mat_Normal *Na;
PetscFunctionBegin;
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
ierr = MatCreate(PetscObjectComm((PetscObject)A),N);CHKERRQ(ierr);
ierr = MatSetSizes(*N,n,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)*N,MATNORMALHERMITIAN);CHKERRQ(ierr);
ierr = PetscNewLog(*N,&Na);CHKERRQ(ierr);
(*N)->data = (void*) Na;
ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr);
Na->A = A;
Na->scale = 1.0;
ierr = VecCreateMPI(PetscObjectComm((PetscObject)A),m,PETSC_DECIDE,&Na->w);CHKERRQ(ierr);
(*N)->ops->destroy = MatDestroyHermitian_Normal;
(*N)->ops->mult = MatMultHermitian_Normal;
(*N)->ops->multtranspose = MatMultHermitianTranspose_Normal;
(*N)->ops->multtransposeadd = MatMultHermitianTransposeAdd_Normal;
(*N)->ops->multadd = MatMultHermitianAdd_Normal;
(*N)->ops->getdiagonal = MatGetDiagonalHermitian_Normal;
(*N)->ops->scale = MatScaleHermitian_Normal;
(*N)->ops->diagonalscale = MatDiagonalScaleHermitian_Normal;
(*N)->assembled = PETSC_TRUE;
(*N)->cmap->N = A->cmap->N;
(*N)->rmap->N = A->cmap->N;
(*N)->cmap->n = A->cmap->n;
(*N)->rmap->n = A->cmap->n;
PetscFunctionReturn(0);
}