PETSC_EXTERN PetscErrorCode MatColoringApply_Power(MatColoring mc,ISColoring *iscoloring)
{
PetscErrorCode ierr;
Mat m = mc->mat,mp,ms;
MatColoring imc;
PetscInt i;
const char *optionsprefix;
PetscFunctionBegin;
/* square the matrix repeatedly if necessary */
if (mc->dist == 1) {
mp = m;
} else {
ierr = MatMatMult(m,m,MAT_INITIAL_MATRIX,2.0,&mp);CHKERRQ(ierr);
for (i=2;i<mc->dist;i++) {
ms = mp;
ierr = MatMatMult(m,ms,MAT_INITIAL_MATRIX,2.0,&mp);CHKERRQ(ierr);
ierr = MatDestroy(&ms);CHKERRQ(ierr);
}
}
ierr = MatColoringCreate(mp,&imc);CHKERRQ(ierr);
ierr = PetscObjectGetOptionsPrefix((PetscObject)mc,&optionsprefix);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject)imc,optionsprefix);CHKERRQ(ierr);
ierr = PetscObjectAppendOptionsPrefix((PetscObject)imc,"power_");CHKERRQ(ierr);
ierr = MatColoringSetType(imc,MATCOLORINGGREEDY);CHKERRQ(ierr);
ierr = MatColoringSetDistance(imc,1);CHKERRQ(ierr);
ierr = MatColoringSetWeightType(imc,mc->weight_type);CHKERRQ(ierr);
ierr = MatColoringSetFromOptions(imc);CHKERRQ(ierr);
ierr = MatColoringApply(imc,iscoloring);CHKERRQ(ierr);
ierr = MatColoringDestroy(&imc);CHKERRQ(ierr);
if (mp != m) {ierr = MatDestroy(&mp);CHKERRQ(ierr);}
PetscFunctionReturn(0);
}
/*@C
TaoGetOptionsPrefix - Gets the prefix used for searching for all
TAO options in the database
Not Collective
Input Parameters:
. tao - the TAO_SOLVER context
Output Parameters:
. prefix - pointer to the prefix string used is returned
Notes: On the fortran side, the user should pass in a string 'prefix' of
sufficient length to hold the prefix.
Level: advanced
.keywords: options
.seealso: TaoSetOptionsPrefix(), TaoAppendOptionsPrefix()
@*/
int TaoGetOptionsPrefix(TAO_SOLVER tao, const char *prefix[])
{
int info;
TaoFunctionBegin;
PetscValidHeaderSpecific(tao,TAO_COOKIE,1);
info = PetscObjectGetOptionsPrefix((PetscObject)tao,prefix); CHKERRQ(info);
TaoFunctionReturn(0);
}
/*@C
KSPGetOptionsPrefix - Gets the prefix used for searching for all
KSP options in the database.
Not Collective
Input Parameters:
. ksp - the Krylov context
Output Parameters:
. prefix - pointer to the prefix string used is returned
Notes: On the fortran side, the user should pass in a string 'prifix' of
sufficient length to hold the prefix.
Level: advanced
.keywords: KSP, set, options, prefix, database
.seealso: KSPSetOptionsPrefix(), KSPAppendOptionsPrefix()
@*/
PetscErrorCode KSPGetOptionsPrefix(KSP ksp,const char *prefix[])
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(ksp,KSP_CLASSID,1);
ierr = PetscObjectGetOptionsPrefix((PetscObject)ksp,prefix);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscViewerGetOptionsPrefix - Sets the prefix used for searching for all
PetscViewer options in the database.
Not Collective
Input Parameter:
. viewer - the PetscViewer context
Output Parameter:
. prefix - pointer to the prefix string used
Notes: On the fortran side, the user should pass in a string 'prefix' of
sufficient length to hold the prefix.
Level: advanced
.keywords: PetscViewer, get, options, prefix, database
.seealso: PetscViewerAppendOptionsPrefix()
@*/
PetscErrorCode PetscViewerGetOptionsPrefix(PetscViewer viewer,const char *prefix[])
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
ierr = PetscObjectGetOptionsPrefix((PetscObject)viewer,prefix);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
MFNGetOptionsPrefix - Gets the prefix used for searching for all
MFN options in the database.
Not Collective
Input Parameters:
. mfn - the matrix function context
Output Parameters:
. prefix - pointer to the prefix string used is returned
Notes: On the fortran side, the user should pass in a string 'prefix' of
sufficient length to hold the prefix.
Level: advanced
.seealso: MFNSetOptionsPrefix(), MFNAppendOptionsPrefix()
@*/
PetscErrorCode MFNGetOptionsPrefix(MFN mfn,const char *prefix[])
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(mfn,MFN_CLASSID,1);
PetscValidPointer(prefix,2);
ierr = PetscObjectGetOptionsPrefix((PetscObject)mfn,prefix);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
EPSGetOptionsPrefix - Gets the prefix used for searching for all
EPS options in the database.
Not Collective
Input Parameters:
. eps - the eigensolver context
Output Parameters:
. prefix - pointer to the prefix string used is returned
Notes: On the fortran side, the user should pass in a string 'prefix' of
sufficient length to hold the prefix.
Level: advanced
.seealso: EPSSetOptionsPrefix(), EPSAppendOptionsPrefix()
@*/
PetscErrorCode EPSGetOptionsPrefix(EPS eps,const char *prefix[])
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(eps,EPS_CLASSID,1);
PetscValidPointer(prefix,2);
ierr = PetscObjectGetOptionsPrefix((PetscObject)eps,prefix);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
NEPGetOptionsPrefix - Gets the prefix used for searching for all
NEP options in the database.
Not Collective
Input Parameters:
. nep - the nonlinear eigensolver context
Output Parameters:
. prefix - pointer to the prefix string used is returned
Notes: On the fortran side, the user should pass in a string 'prefix' of
sufficient length to hold the prefix.
Level: advanced
.seealso: NEPSetOptionsPrefix(), NEPAppendOptionsPrefix()
@*/
PetscErrorCode NEPGetOptionsPrefix(NEP nep,const char *prefix[])
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(nep,NEP_CLASSID,1);
PetscValidPointer(prefix,2);
ierr = PetscObjectGetOptionsPrefix((PetscObject)nep,prefix);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
RGGetOptionsPrefix - Gets the prefix used for searching for all
RG options in the database.
Not Collective
Input Parameters:
. rg - the region context
Output Parameters:
. prefix - pointer to the prefix string used is returned
Notes: On the fortran side, the user should pass in a string 'prefix' of
sufficient length to hold the prefix.
Level: advanced
.seealso: RGSetOptionsPrefix(), RGAppendOptionsPrefix()
@*/
PetscErrorCode RGGetOptionsPrefix(RG rg,const char *prefix[])
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(rg,RG_CLASSID,1);
PetscValidPointer(prefix,2);
ierr = PetscObjectGetOptionsPrefix((PetscObject)rg,prefix);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
MatMFFDView_MFFD - Views matrix-free parameters.
*/
PetscErrorCode MatView_MFFD(Mat J,PetscViewer viewer)
{
PetscErrorCode ierr;
MatMFFD ctx = (MatMFFD)J->data;
PetscBool iascii, viewbase, viewfunction;
const char *prefix;
PetscFunctionBegin;
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
CHKERRQ(ierr);
if (iascii) {
ierr = PetscViewerASCIIPrintf(viewer,"Matrix-free approximation:\n");
CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);
CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"err=%G (relative error in function evaluation)\n",ctx->error_rel);
CHKERRQ(ierr);
if (!((PetscObject)ctx)->type_name) {
ierr = PetscViewerASCIIPrintf(viewer,"The compute h routine has not yet been set\n");
CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer,"Using %s compute h routine\n",((PetscObject)ctx)->type_name);
CHKERRQ(ierr);
}
if (ctx->ops->view) {
ierr = (*ctx->ops->view)(ctx,viewer);
CHKERRQ(ierr);
}
ierr = PetscObjectGetOptionsPrefix((PetscObject)J, &prefix);
CHKERRQ(ierr);
ierr = PetscOptionsHasName(prefix, "-mat_mffd_view_base", &viewbase);
CHKERRQ(ierr);
if (viewbase) {
ierr = PetscViewerASCIIPrintf(viewer, "Base:\n");
CHKERRQ(ierr);
ierr = VecView(ctx->current_u, viewer);
CHKERRQ(ierr);
}
ierr = PetscOptionsHasName(prefix, "-mat_mffd_view_function", &viewfunction);
CHKERRQ(ierr);
if (viewfunction) {
ierr = PetscViewerASCIIPrintf(viewer, "Function:\n");
CHKERRQ(ierr);
ierr = VecView(ctx->current_f, viewer);
CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPopTab(viewer);
CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode MatPartitioningApply_Current(MatPartitioning part,IS *partitioning)
{
PetscErrorCode ierr;
PetscInt m;
PetscMPIInt rank,size;
PetscFunctionBegin;
ierr = MPI_Comm_size(PetscObjectComm((PetscObject)part),&size);CHKERRQ(ierr);
if (part->n != size) {
const char *prefix;
ierr = PetscObjectGetOptionsPrefix((PetscObject)part,&prefix);CHKERRQ(ierr);
SETERRQ1(PetscObjectComm((PetscObject)part),PETSC_ERR_SUP,"This is the DEFAULT NO-OP partitioner, it currently only supports one domain per processor\nuse -%smat_partitioning_type parmetis or chaco or ptscotch for more than one subdomain per processor",prefix ? prefix : "");
}
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)part),&rank);CHKERRQ(ierr);
ierr = MatGetLocalSize(part->adj,&m,NULL);CHKERRQ(ierr);
ierr = ISCreateStride(PetscObjectComm((PetscObject)part),m,rank,0,partitioning);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMCreateFieldIS_Composite(DM dm, PetscInt *numFields,char ***fieldNames, IS **fields)
{
PetscInt nDM;
DM *dms;
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMCompositeGetNumberDM(dm, &nDM);CHKERRQ(ierr);
if (numFields) {*numFields = nDM;}
ierr = DMCompositeGetGlobalISs(dm, fields);CHKERRQ(ierr);
if (fieldNames) {
ierr = PetscMalloc(nDM*sizeof(DM), &dms);CHKERRQ(ierr);
ierr = PetscMalloc(nDM*sizeof(const char *), fieldNames);CHKERRQ(ierr);
ierr = DMCompositeGetEntriesArray(dm, dms);CHKERRQ(ierr);
for (i=0; i<nDM; i++) {
char buf[256];
const char *splitname;
/* Split naming precedence: object name, prefix, number */
splitname = ((PetscObject) dm)->name;
if (!splitname) {
ierr = PetscObjectGetOptionsPrefix((PetscObject)dms[i],&splitname);CHKERRQ(ierr);
if (splitname) {
size_t len;
ierr = PetscStrncpy(buf,splitname,sizeof(buf));CHKERRQ(ierr);
buf[sizeof(buf) - 1] = 0;
ierr = PetscStrlen(buf,&len);CHKERRQ(ierr);
if (buf[len-1] == '_') buf[len-1] = 0; /* Remove trailing underscore if it was used */
splitname = buf;
}
}
if (!splitname) {
ierr = PetscSNPrintf(buf,sizeof(buf),"%D",i);CHKERRQ(ierr);
splitname = buf;
}
ierr = PetscStrallocpy(splitname,&(*fieldNames)[i]);CHKERRQ(ierr);
}
ierr = PetscFree(dms);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*@
KSPGetGuess - Gets the initial guess generator for the KSP.
Not Collective
Input Parameters:
. ksp - the Krylov context
Output Parameters:
. guess - the object
Level: developer
.keywords: KSP, set, options, prefix, database
.seealso: KSPSetOptionsPrefix(), KSPAppendOptionsPrefix(), KSPSetUseFischerGuess(), KSPSetGuess()
@*/
PetscErrorCode KSPGetGuess(KSP ksp,KSPGuess *guess)
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(ksp,KSP_CLASSID,1);
PetscValidPointer(guess,2);
if (!ksp->guess) {
const char* prefix;
ierr = KSPGuessCreate(PetscObjectComm((PetscObject)ksp),&ksp->guess);CHKERRQ(ierr);
ierr = PetscObjectGetOptionsPrefix((PetscObject)ksp,&prefix);CHKERRQ(ierr);
if (prefix) {
ierr = PetscObjectSetOptionsPrefix((PetscObject)ksp->guess,prefix);CHKERRQ(ierr);
}
ksp->guess->ksp = ksp;
}
*guess = ksp->guess;
PetscFunctionReturn(0);
}
/*@
TaoSetOptions - Sets various TAO parameters from user options
Collective on TAO_APPLICATION
Input Parameters:
+ taoapp - the TAO Application (optional)
- tao - the TAO optimization solver (optional)
Level: beginner
Note:
This routine should be called after TaoSetupApplicationSolver()
Note:
This routine must be called if there are multiple processors involved and
the MPI Communicator is different than MPI_COMM_WORLD.
.keywords: options
.seealso: TaoSolveApplication()
@*/
int TaoSetOptions(TAO_APPLICATION taoapp, TAO_SOLVER tao){
int info;
const char *prefix=0;
PetscTruth flg;
MPI_Comm comm=MPI_COMM_WORLD;
PetscFunctionBegin;
if (tao){
PetscValidHeaderSpecific(tao,TAO_COOKIE,2);
info = PetscObjectGetOptionsPrefix((PetscObject)tao,&prefix); CHKERRQ(info);
info = PetscObjectGetComm((PetscObject)tao,&comm);CHKERRQ(info);
info = PetscOptionsBegin(comm,prefix,"TAO PETSC APPLICATIONS ","solver");CHKERRQ(info);
info = TaoSetFromOptions(tao); CHKERRQ(info);
flg=PETSC_FALSE;
info = PetscOptionsName("-tao_xmonitor","Use graphics convergence","TaoPetscXMonitor",&flg);CHKERRQ(info);
if (flg){
info = TaoSetPetscXMonitor(tao); CHKERRQ(info);
}
info = PetscOptionsEnd();CHKERRQ(info);
}
if (taoapp){
info = TaoAppSetFromOptions(taoapp); CHKERRQ(info);
}
if (tao && taoapp){
info = TaoSetupApplicationSolver(taoapp,tao);CHKERRQ(info);
info = PetscOptionsName("-tao_lmvmh","User supplies approximate hessian for LMVM solvers","TaoLMVMSetH0",&flg);
if (flg){
info=TaoBLMVMSetH0(tao,TAO_TRUE);CHKERRQ(info);
info=TaoLMVMSetH0(tao,TAO_TRUE);CHKERRQ(info);
}
}
PetscFunctionReturn(0);
}
/*@C
TaoLineSearchGetOptionsPrefix - Gets the prefix used for searching for all
TaoLineSearch options in the database
Not Collective
Input Parameters:
. ls - the TaoLineSearch context
Output Parameters:
. prefix - pointer to the prefix string used is returned
Notes: On the fortran side, the user should pass in a string 'prefix' of
sufficient length to hold the prefix.
Level: advanced
.seealso: TaoLineSearchSetOptionsPrefix(), TaoLineSearchAppendOptionsPrefix()
@*/
PetscErrorCode TaoLineSearchGetOptionsPrefix(TaoLineSearch ls, const char *p[])
{
return PetscObjectGetOptionsPrefix((PetscObject)ls,p);
}
/*@
KSPSetFromOptions - Sets KSP options from the options database.
This routine must be called before KSPSetUp() if the user is to be
allowed to set the Krylov type.
Collective on KSP
Input Parameters:
. ksp - the Krylov space context
Options Database Keys:
+ -ksp_max_it - maximum number of linear iterations
. -ksp_rtol rtol - relative tolerance used in default determination of convergence, i.e.
if residual norm decreases by this factor than convergence is declared
. -ksp_atol abstol - absolute tolerance used in default convergence test, i.e. if residual
norm is less than this then convergence is declared
. -ksp_divtol tol - if residual norm increases by this factor than divergence is declared
. -ksp_converged_use_initial_residual_norm - see KSPConvergedDefaultSetUIRNorm()
. -ksp_converged_use_min_initial_residual_norm - see KSPConvergedDefaultSetUMIRNorm()
. -ksp_norm_type - none - skip norms used in convergence tests (useful only when not using
convergence test (say you always want to run with 5 iterations) to
save on communication overhead
preconditioned - default for left preconditioning
unpreconditioned - see KSPSetNormType()
natural - see KSPSetNormType()
. -ksp_check_norm_iteration it - do not compute residual norm until iteration number it (does compute at 0th iteration)
works only for PCBCGS, PCIBCGS and and PCCG
. -ksp_lag_norm - compute the norm of the residual for the ith iteration on the i+1 iteration; this means that one can use
the norm of the residual for convergence test WITHOUT an extra MPI_Allreduce() limiting global synchronizations.
This will require 1 more iteration of the solver than usual.
. -ksp_guess_type - Type of initial guess generator for repeated linear solves
. -ksp_fischer_guess <model,size> - uses the Fischer initial guess generator for repeated linear solves
. -ksp_constant_null_space - assume the operator (matrix) has the constant vector in its null space
. -ksp_test_null_space - tests the null space set with MatSetNullSpace() to see if it truly is a null space
. -ksp_knoll - compute initial guess by applying the preconditioner to the right hand side
. -ksp_monitor_cancel - cancel all previous convergene monitor routines set
. -ksp_monitor <optional filename> - print residual norm at each iteration
. -ksp_monitor_lg_residualnorm - plot residual norm at each iteration
. -ksp_monitor_solution [ascii binary or draw][:filename][:format option] - plot solution at each iteration
- -ksp_monitor_singular_value - monitor extreme singular values at each iteration
Notes:
To see all options, run your program with the -help option
or consult Users-Manual: ch_ksp
Level: beginner
.keywords: KSP, set, from, options, database
.seealso: KSPSetOptionsPrefix(), KSPResetFromOptions(), KSPSetUseFischerGuess()
@*/
PetscErrorCode KSPSetFromOptions(KSP ksp)
{
PetscInt indx;
const char *convtests[] = {"default","skip","lsqr"};
char type[256], guesstype[256], monfilename[PETSC_MAX_PATH_LEN];
PetscBool flg,flag,reuse,set;
PetscInt model[2]={0,0},nmax;
KSPNormType normtype;
PCSide pcside;
void *ctx;
MPI_Comm comm;
const char *prefix;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(ksp,KSP_CLASSID,1);
ierr = PetscObjectGetComm((PetscObject) ksp, &comm);CHKERRQ(ierr);
ierr = PetscObjectGetOptionsPrefix((PetscObject) ksp, &prefix);CHKERRQ(ierr);
if (!ksp->skippcsetfromoptions) {
if (!ksp->pc) {ierr = KSPGetPC(ksp,&ksp->pc);CHKERRQ(ierr);}
ierr = PCSetFromOptions(ksp->pc);CHKERRQ(ierr);
}
ierr = KSPRegisterAll();CHKERRQ(ierr);
ierr = PetscObjectOptionsBegin((PetscObject)ksp);CHKERRQ(ierr);
ierr = PetscOptionsFList("-ksp_type","Krylov method","KSPSetType",KSPList,(char*)(((PetscObject)ksp)->type_name ? ((PetscObject)ksp)->type_name : KSPGMRES),type,256,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetType(ksp,type);CHKERRQ(ierr);
}
/*
Set the type if it was never set.
*/
if (!((PetscObject)ksp)->type_name) {
ierr = KSPSetType(ksp,KSPGMRES);CHKERRQ(ierr);
}
ierr = KSPResetViewers(ksp);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)ksp,KSPPREONLY,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PCGetReusePreconditioner(ksp->pc,&reuse);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_error_if_not_converged","Generate error if solver does not converge","KSPSetErrorIfNotConverged",ksp->errorifnotconverged,&ksp->errorifnotconverged,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_reuse_preconditioner","Use initial preconditioner and don't ever compute a new one ","KSPReusePreconditioner",reuse,&reuse,NULL);CHKERRQ(ierr);
ierr = KSPSetReusePreconditioner(ksp,reuse);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view", &ksp->viewer, &ksp->format, &ksp->view);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_converged_reason", &ksp->viewerReason, &ksp->formatReason, &ksp->viewReason);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_mat", &ksp->viewerMat, &ksp->formatMat, &ksp->viewMat);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_pmat", &ksp->viewerPMat, &ksp->formatPMat, &ksp->viewPMat);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_rhs", &ksp->viewerRhs, &ksp->formatRhs, &ksp->viewRhs);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_solution", &ksp->viewerSol, &ksp->formatSol, &ksp->viewSol);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_mat_explicit", &ksp->viewerMatExp, &ksp->formatMatExp, &ksp->viewMatExp);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_final_residual", &ksp->viewerFinalRes,&ksp->formatFinalRes,&ksp->viewFinalRes);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_preconditioned_operator_explicit",&ksp->viewerPOpExp, &ksp->formatPOpExp, &ksp->viewPOpExp);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_diagonal_scale", &ksp->viewerDScale, &ksp->formatDScale, &ksp->viewDScale);CHKERRQ(ierr);
ierr = KSPGetDiagonalScale(ksp,&flag);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_diagonal_scale","Diagonal scale matrix before building preconditioner","KSPSetDiagonalScale",flag,&flag,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetDiagonalScale(ksp,flag);CHKERRQ(ierr);
}
ierr = KSPGetDiagonalScaleFix(ksp,&flag);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_diagonal_scale_fix","Fix diagonally scaled matrix after solve","KSPSetDiagonalScaleFix",flag,&flag,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetDiagonalScaleFix(ksp,flag);CHKERRQ(ierr);
}
goto skipoptions;
}
ierr = PetscOptionsInt("-ksp_max_it","Maximum number of iterations","KSPSetTolerances",ksp->max_it,&ksp->max_it,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-ksp_rtol","Relative decrease in residual norm","KSPSetTolerances",ksp->rtol,&ksp->rtol,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-ksp_atol","Absolute value of residual norm","KSPSetTolerances",ksp->abstol,&ksp->abstol,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-ksp_divtol","Residual norm increase cause divergence","KSPSetTolerances",ksp->divtol,&ksp->divtol,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_converged_use_initial_residual_norm","Use initial residual norm for computing relative convergence","KSPConvergedDefaultSetUIRNorm",PETSC_FALSE,&flag,&set);CHKERRQ(ierr);
if (set && flag) {ierr = KSPConvergedDefaultSetUIRNorm(ksp);CHKERRQ(ierr);}
ierr = PetscOptionsBool("-ksp_converged_use_min_initial_residual_norm","Use minimum of initial residual norm and b for computing relative convergence","KSPConvergedDefaultSetUMIRNorm",PETSC_FALSE,&flag,&set);CHKERRQ(ierr);
if (set && flag) {ierr = KSPConvergedDefaultSetUMIRNorm(ksp);CHKERRQ(ierr);}
ierr = PetscOptionsBool("-ksp_initial_guess_nonzero","Use the contents of the solution vector for initial guess","KSPSetInitialNonzero",ksp->guess_zero ? PETSC_FALSE : PETSC_TRUE,&flag,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetInitialGuessNonzero(ksp,flag);CHKERRQ(ierr);
}
ierr = PCGetReusePreconditioner(ksp->pc,&reuse);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_reuse_preconditioner","Use initial preconditioner and don't ever compute a new one ","KSPReusePreconditioner",reuse,&reuse,NULL);CHKERRQ(ierr);
ierr = KSPSetReusePreconditioner(ksp,reuse);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_knoll","Use preconditioner applied to b for initial guess","KSPSetInitialGuessKnoll",ksp->guess_knoll,&ksp->guess_knoll,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_error_if_not_converged","Generate error if solver does not converge","KSPSetErrorIfNotConverged",ksp->errorifnotconverged,&ksp->errorifnotconverged,NULL);CHKERRQ(ierr);
ierr = PetscOptionsFList("-ksp_guess_type","Initial guess in Krylov method",NULL,KSPGuessList,NULL,guesstype,256,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPGetGuess(ksp,&ksp->guess);CHKERRQ(ierr);
ierr = KSPGuessSetType(ksp->guess,guesstype);CHKERRQ(ierr);
ierr = KSPGuessSetFromOptions(ksp->guess);CHKERRQ(ierr);
} else { /* old option for KSP */
nmax = 2;
ierr = PetscOptionsIntArray("-ksp_fischer_guess","Use Paul Fischer's algorithm for initial guess","KSPSetUseFischerGuess",model,&nmax,&flag);CHKERRQ(ierr);
if (flag) {
if (nmax != 2) SETERRQ(comm,PETSC_ERR_ARG_OUTOFRANGE,"Must pass in model,size as arguments");
ierr = KSPSetUseFischerGuess(ksp,model[0],model[1]);CHKERRQ(ierr);
}
}
ierr = PetscOptionsEList("-ksp_convergence_test","Convergence test","KSPSetConvergenceTest",convtests,3,"default",&indx,&flg);CHKERRQ(ierr);
if (flg) {
switch (indx) {
case 0:
ierr = KSPConvergedDefaultCreate(&ctx);CHKERRQ(ierr);
ierr = KSPSetConvergenceTest(ksp,KSPConvergedDefault,ctx,KSPConvergedDefaultDestroy);CHKERRQ(ierr);
break;
case 1: ierr = KSPSetConvergenceTest(ksp,KSPConvergedSkip,NULL,NULL);CHKERRQ(ierr); break;
case 2:
ierr = KSPConvergedDefaultCreate(&ctx);CHKERRQ(ierr);
ierr = KSPSetConvergenceTest(ksp,KSPLSQRConvergedDefault,ctx,KSPConvergedDefaultDestroy);CHKERRQ(ierr);
break;
}
}
ierr = KSPSetUpNorms_Private(ksp,PETSC_FALSE,&normtype,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnum("-ksp_norm_type","KSP Norm type","KSPSetNormType",KSPNormTypes,(PetscEnum)normtype,(PetscEnum*)&normtype,&flg);CHKERRQ(ierr);
if (flg) { ierr = KSPSetNormType(ksp,normtype);CHKERRQ(ierr); }
ierr = PetscOptionsInt("-ksp_check_norm_iteration","First iteration to compute residual norm","KSPSetCheckNormIteration",ksp->chknorm,&ksp->chknorm,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_lag_norm","Lag the calculation of the residual norm","KSPSetLagNorm",ksp->lagnorm,&flag,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetLagNorm(ksp,flag);CHKERRQ(ierr);
}
ierr = KSPGetDiagonalScale(ksp,&flag);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_diagonal_scale","Diagonal scale matrix before building preconditioner","KSPSetDiagonalScale",flag,&flag,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetDiagonalScale(ksp,flag);CHKERRQ(ierr);
}
ierr = KSPGetDiagonalScaleFix(ksp,&flag);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_diagonal_scale_fix","Fix diagonally scaled matrix after solve","KSPSetDiagonalScaleFix",flag,&flag,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetDiagonalScaleFix(ksp,flag);CHKERRQ(ierr);
}
ierr = PetscOptionsBool("-ksp_constant_null_space","Add constant null space to Krylov solver matrix","MatSetNullSpace",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set && flg) {
MatNullSpace nsp;
Mat Amat;
ierr = MatNullSpaceCreate(comm,PETSC_TRUE,0,NULL,&nsp);CHKERRQ(ierr);
ierr = PCGetOperators(ksp->pc,&Amat,NULL);CHKERRQ(ierr);
if (Amat) {
ierr = MatSetNullSpace(Amat,nsp);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nsp);CHKERRQ(ierr);
} else SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"Cannot set nullspace, matrix has not yet been provided");
}
ierr = PetscOptionsBool("-ksp_monitor_cancel","Remove any hardwired monitor routines","KSPMonitorCancel",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
/* -----------------------------------------------------------------------*/
/*
Cancels all monitors hardwired into code before call to KSPSetFromOptions()
*/
if (set && flg) {
ierr = KSPMonitorCancel(ksp);CHKERRQ(ierr);
}
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor","Monitor the (preconditioned) residual norm","KSPMonitorDefault",KSPMonitorDefault);CHKERRQ(ierr);
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor_range","Monitor the percentage of large entries in the residual","KSPMonitorRange",KSPMonitorRange);CHKERRQ(ierr);
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor_true_residual","Monitor the unprecondiitoned residual norm","KSPMOnitorTrueResidual",KSPMonitorTrueResidualNorm);CHKERRQ(ierr);
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor_max","Monitor the maximum norm of the residual","KSPMonitorTrueResidualMaxNorm",KSPMonitorTrueResidualMaxNorm);CHKERRQ(ierr);
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor_short","Monitor preconditioned residual norm with fewer digits","KSPMonitorDefaultShort",KSPMonitorDefaultShort);CHKERRQ(ierr);
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor_solution","Monitor the solution","KSPMonitorSolution",KSPMonitorSolution);CHKERRQ(ierr);
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor_singular_value","Monitor singular values","KSPMonitorSingularValue",KSPMonitorSingularValue);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,((PetscObject)ksp)->prefix,"-ksp_monitor_singular_value",&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetComputeSingularValues(ksp,PETSC_TRUE);CHKERRQ(ierr);
}
ierr = PetscObjectTypeCompare((PetscObject)ksp->pc,PCKSP,&flg);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)ksp->pc,PCBJACOBI,&flag);CHKERRQ(ierr);
if (flg || flag) {
/* A hack for using dynamic tolerance in preconditioner */
ierr = PetscOptionsString("-sub_ksp_dynamic_tolerance","Use dynamic tolerance for PC if PC is a KSP","KSPMonitorDynamicTolerance","stdout",monfilename,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (flg) {
KSPDynTolCtx *scale;
ierr = PetscMalloc1(1,&scale);CHKERRQ(ierr);
scale->bnrm = -1.0;
scale->coef = 1.0;
ierr = PetscOptionsReal("-sub_ksp_dynamic_tolerance_param","Parameter of dynamic tolerance for inner PCKSP","KSPMonitorDynamicToleranceParam",scale->coef,&scale->coef,&flg);CHKERRQ(ierr);
ierr = KSPMonitorSet(ksp,KSPMonitorDynamicTolerance,scale,KSPMonitorDynamicToleranceDestroy);CHKERRQ(ierr);
}
}
/*
Calls Python function
*/
ierr = PetscOptionsString("-ksp_monitor_python","Use Python function","KSPMonitorSet",0,monfilename,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (flg) {ierr = PetscPythonMonitorSet((PetscObject)ksp,monfilename);CHKERRQ(ierr);}
/*
Graphically plots preconditioned residual norm
*/
ierr = PetscOptionsBool("-ksp_monitor_lg_residualnorm","Monitor graphically preconditioned residual norm","KSPMonitorSet",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set && flg) {
PetscDrawLG ctx;
ierr = KSPMonitorLGResidualNormCreate(comm,NULL,NULL,PETSC_DECIDE,PETSC_DECIDE,400,300,&ctx);CHKERRQ(ierr);
ierr = KSPMonitorSet(ksp,KSPMonitorLGResidualNorm,ctx,(PetscErrorCode (*)(void**))PetscDrawLGDestroy);CHKERRQ(ierr);
}
/*
Graphically plots preconditioned and true residual norm
*/
ierr = PetscOptionsBool("-ksp_monitor_lg_true_residualnorm","Monitor graphically true residual norm","KSPMonitorSet",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set && flg) {
PetscDrawLG ctx;
ierr = KSPMonitorLGTrueResidualNormCreate(comm,NULL,NULL,PETSC_DECIDE,PETSC_DECIDE,400,300,&ctx);CHKERRQ(ierr);
ierr = KSPMonitorSet(ksp,KSPMonitorLGTrueResidualNorm,ctx,(PetscErrorCode (*)(void**))PetscDrawLGDestroy);CHKERRQ(ierr);
}
/*
Graphically plots preconditioned residual norm and range of residual element values
*/
ierr = PetscOptionsBool("-ksp_monitor_lg_range","Monitor graphically range of preconditioned residual norm","KSPMonitorSet",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set && flg) {
PetscViewer ctx;
ierr = PetscViewerDrawOpen(comm,NULL,NULL,PETSC_DECIDE,PETSC_DECIDE,400,300,&ctx);CHKERRQ(ierr);
ierr = KSPMonitorSet(ksp,KSPMonitorLGRange,ctx,(PetscErrorCode (*)(void**))PetscViewerDestroy);CHKERRQ(ierr);
}
/* TODO Do these show up in help? */
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view", &ksp->viewer, &ksp->format, &ksp->view);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_pre", &ksp->viewerPre, &ksp->formatPre, &ksp->viewPre);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_converged_reason", &ksp->viewerReason, &ksp->formatReason, &ksp->viewReason);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_mat", &ksp->viewerMat, &ksp->formatMat, &ksp->viewMat);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_pmat", &ksp->viewerPMat, &ksp->formatPMat, &ksp->viewPMat);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_rhs", &ksp->viewerRhs, &ksp->formatRhs, &ksp->viewRhs);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_solution", &ksp->viewerSol, &ksp->formatSol, &ksp->viewSol);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_mat_explicit", &ksp->viewerMatExp, &ksp->formatMatExp, &ksp->viewMatExp);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_eigenvalues", &ksp->viewerEV, &ksp->formatEV, &ksp->viewEV);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_singularvalues", &ksp->viewerSV, &ksp->formatSV, &ksp->viewSV);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_eigenvalues_explicit", &ksp->viewerEVExp, &ksp->formatEVExp, &ksp->viewEVExp);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_final_residual", &ksp->viewerFinalRes,&ksp->formatFinalRes,&ksp->viewFinalRes);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_preconditioned_operator_explicit",&ksp->viewerPOpExp, &ksp->formatPOpExp, &ksp->viewPOpExp);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_diagonal_scale", &ksp->viewerDScale, &ksp->formatDScale, &ksp->viewDScale);CHKERRQ(ierr);
/* Deprecated options */
if (!ksp->viewEV) {ierr = PetscOptionsGetViewer(comm, ((PetscObject) ksp)->options,prefix, "-ksp_compute_eigenvalues", &ksp->viewerEV, &ksp->formatEV, &ksp->viewEV);CHKERRQ(ierr);}
if (!ksp->viewEV) {
ierr = PetscOptionsName("-ksp_plot_eigenvalues", "[deprecated since PETSc 3.9; use -ksp_view_eigenvalues draw]", "KSPView", &ksp->viewEV);CHKERRQ(ierr);
if (ksp->viewEV) {
ksp->formatEV = PETSC_VIEWER_DEFAULT;
ksp->viewerEV = PETSC_VIEWER_DRAW_(comm);
ierr = PetscObjectReference((PetscObject) ksp->viewerEV);CHKERRQ(ierr);
}
}
if (!ksp->viewEV) {
ierr = PetscOptionsName("-ksp_plot_eigencontours", "[deprecated since PETSc 3.9; use -ksp_view_eigenvalues draw::draw_contour]", "KSPView", &ksp->viewEV);CHKERRQ(ierr);
if (ksp->viewEV) {
ksp->formatEV = PETSC_VIEWER_DRAW_CONTOUR;
ksp->viewerEV = PETSC_VIEWER_DRAW_(comm);
ierr = PetscObjectReference((PetscObject) ksp->viewerEV);CHKERRQ(ierr);
}
}
if (!ksp->viewEVExp) {ierr = PetscOptionsGetViewer(comm, ((PetscObject) ksp)->options,prefix, "-ksp_compute_eigenvalues_explicitly", &ksp->viewerEVExp, &ksp->formatEVExp, &ksp->viewEVExp);CHKERRQ(ierr);}
if (!ksp->viewEVExp) {
ierr = PetscOptionsName("-ksp_plot_eigenvalues_explicitly", "[deprecated since PETSc 3.9; use -ksp_view_eigenvalues_explicit draw]", "KSPView", &ksp->viewEVExp);CHKERRQ(ierr);
if (ksp->viewEVExp) {
ksp->formatEVExp = PETSC_VIEWER_DEFAULT;
ksp->viewerEVExp = PETSC_VIEWER_DRAW_(comm);
ierr = PetscObjectReference((PetscObject) ksp->viewerEVExp);CHKERRQ(ierr);
}
}
if (!ksp->viewSV) {ierr = PetscOptionsGetViewer(comm, ((PetscObject) ksp)->options,prefix, "-ksp_compute_singularvalues", &ksp->viewerSV, &ksp->formatSV, &ksp->viewSV);CHKERRQ(ierr);}
if (!ksp->viewFinalRes) {ierr = PetscOptionsGetViewer(comm, ((PetscObject) ksp)->options,prefix, "-ksp_final_residual", &ksp->viewerFinalRes, &ksp->formatFinalRes, &ksp->viewFinalRes);CHKERRQ(ierr);}
#if defined(PETSC_HAVE_SAWS)
/*
Publish convergence information using AMS
*/
ierr = PetscOptionsBool("-ksp_monitor_saws","Publish KSP progress using SAWs","KSPMonitorSet",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set && flg) {
void *ctx;
ierr = KSPMonitorSAWsCreate(ksp,&ctx);CHKERRQ(ierr);
ierr = KSPMonitorSet(ksp,KSPMonitorSAWs,ctx,KSPMonitorSAWsDestroy);CHKERRQ(ierr);
ierr = KSPSetComputeSingularValues(ksp,PETSC_TRUE);CHKERRQ(ierr);
}
#endif
/* -----------------------------------------------------------------------*/
ierr = KSPSetUpNorms_Private(ksp,PETSC_FALSE,NULL,&pcside);CHKERRQ(ierr);
ierr = PetscOptionsEnum("-ksp_pc_side","KSP preconditioner side","KSPSetPCSide",PCSides,(PetscEnum)pcside,(PetscEnum*)&pcside,&flg);CHKERRQ(ierr);
if (flg) {ierr = KSPSetPCSide(ksp,pcside);CHKERRQ(ierr);}
ierr = PetscOptionsBool("-ksp_compute_singularvalues","Compute singular values of preconditioned operator","KSPSetComputeSingularValues",ksp->calc_sings,&flg,&set);CHKERRQ(ierr);
if (set) { ierr = KSPSetComputeSingularValues(ksp,flg);CHKERRQ(ierr); }
ierr = PetscOptionsBool("-ksp_compute_eigenvalues","Compute eigenvalues of preconditioned operator","KSPSetComputeSingularValues",ksp->calc_sings,&flg,&set);CHKERRQ(ierr);
if (set) { ierr = KSPSetComputeSingularValues(ksp,flg);CHKERRQ(ierr); }
ierr = PetscOptionsBool("-ksp_plot_eigenvalues","Scatter plot extreme eigenvalues","KSPSetComputeSingularValues",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set) { ierr = KSPSetComputeSingularValues(ksp,flg);CHKERRQ(ierr); }
#if defined(PETSC_HAVE_SAWS)
{
PetscBool set;
flg = PETSC_FALSE;
ierr = PetscOptionsBool("-ksp_saws_block","Block for SAWs at end of KSPSolve","PetscObjectSAWsBlock",((PetscObject)ksp)->amspublishblock,&flg,&set);CHKERRQ(ierr);
if (set) {
ierr = PetscObjectSAWsSetBlock((PetscObject)ksp,flg);CHKERRQ(ierr);
}
}
#endif
if (ksp->ops->setfromoptions) {
ierr = (*ksp->ops->setfromoptions)(PetscOptionsObject,ksp);CHKERRQ(ierr);
}
skipoptions:
/* process any options handlers added with PetscObjectAddOptionsHandler() */
ierr = PetscObjectProcessOptionsHandlers(PetscOptionsObject,(PetscObject)ksp);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ksp->setfromoptionscalled++;
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat Amat;
PetscErrorCode ierr;
SNES snes;
KSP ksp;
MPI_Comm comm;
PetscMPIInt npe,rank;
PetscLogStage stage[7];
PetscBool test_nonzero_cols=PETSC_FALSE,use_nearnullspace=PETSC_TRUE;
Vec xx,bb;
PetscInt iter,i,N,dim=3,cells[3]={1,1,1},max_conv_its,local_sizes[7],run_type=1;
DM dm,distdm,basedm;
PetscBool flg;
char convType[256];
PetscReal Lx,mdisp[10],err[10];
const char * const options[10] = {"-ex56_dm_refine 0",
"-ex56_dm_refine 1",
"-ex56_dm_refine 2",
"-ex56_dm_refine 3",
"-ex56_dm_refine 4",
"-ex56_dm_refine 5",
"-ex56_dm_refine 6",
"-ex56_dm_refine 7",
"-ex56_dm_refine 8",
"-ex56_dm_refine 9"};
PetscFunctionBeginUser;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
comm = PETSC_COMM_WORLD;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &npe);CHKERRQ(ierr);
/* options */
ierr = PetscOptionsBegin(comm,NULL,"3D bilinear Q1 elasticity options","");CHKERRQ(ierr);
{
i = 3;
ierr = PetscOptionsIntArray("-cells", "Number of (flux tube) processor in each dimension", "ex56.c", cells, &i, NULL);CHKERRQ(ierr);
Lx = 1.; /* or ne for rod */
max_conv_its = 3;
ierr = PetscOptionsInt("-max_conv_its","Number of iterations in convergence study","",max_conv_its,&max_conv_its,NULL);CHKERRQ(ierr);
if (max_conv_its<=0 || max_conv_its>7) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_USER, "Bad number of iterations for convergence test (%D)",max_conv_its);
ierr = PetscOptionsReal("-lx","Length of domain","",Lx,&Lx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-alpha","material coefficient inside circle","",s_soft_alpha,&s_soft_alpha,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_nonzero_cols","nonzero test","",test_nonzero_cols,&test_nonzero_cols,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-use_mat_nearnullspace","MatNearNullSpace API test","",use_nearnullspace,&use_nearnullspace,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-run_type","0: twisting load on cantalever, 1: 3rd order accurate convergence test","",run_type,&run_type,NULL);CHKERRQ(ierr);
i = 3;
ierr = PetscOptionsInt("-mat_block_size","","",i,&i,&flg);CHKERRQ(ierr);
if (!flg || i!=3) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_USER, "'-mat_block_size 3' must be set (%D) and = 3 (%D)",flg,flg? i : 3);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscLogStageRegister("Mesh Setup", &stage[6]);CHKERRQ(ierr);
ierr = PetscLogStageRegister("1st Setup", &stage[0]);CHKERRQ(ierr);
ierr = PetscLogStageRegister("1st Solve", &stage[1]);CHKERRQ(ierr);
/* create DM, Plex calls DMSetup */
ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr);
ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &dm);CHKERRQ(ierr);
{
DMLabel label;
IS is;
ierr = DMCreateLabel(dm, "boundary");CHKERRQ(ierr);
ierr = DMGetLabel(dm, "boundary", &label);CHKERRQ(ierr);
ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr);
if (run_type==0) {
ierr = DMGetStratumIS(dm, "boundary", 1, &is);CHKERRQ(ierr);
ierr = DMCreateLabel(dm,"Faces");CHKERRQ(ierr);
if (is) {
PetscInt d, f, Nf;
const PetscInt *faces;
PetscInt csize;
PetscSection cs;
Vec coordinates ;
DM cdm;
ierr = ISGetLocalSize(is, &Nf);CHKERRQ(ierr);
ierr = ISGetIndices(is, &faces);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
ierr = DMGetDefaultSection(cdm, &cs);CHKERRQ(ierr);
/* Check for each boundary face if any component of its centroid is either 0.0 or 1.0 */
for (f = 0; f < Nf; ++f) {
PetscReal faceCoord;
PetscInt b,v;
PetscScalar *coords = NULL;
PetscInt Nv;
ierr = DMPlexVecGetClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr);
Nv = csize/dim; /* Calculate mean coordinate vector */
for (d = 0; d < dim; ++d) {
faceCoord = 0.0;
for (v = 0; v < Nv; ++v) faceCoord += PetscRealPart(coords[v*dim+d]);
faceCoord /= Nv;
for (b = 0; b < 2; ++b) {
if (PetscAbs(faceCoord - b) < PETSC_SMALL) { /* domain have not been set yet, still [0,1]^3 */
ierr = DMSetLabelValue(dm, "Faces", faces[f], d*2+b+1);CHKERRQ(ierr);
}
}
}
ierr = DMPlexVecRestoreClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr);
}
ierr = ISRestoreIndices(is, &faces);CHKERRQ(ierr);
}
ierr = ISDestroy(&is);CHKERRQ(ierr);
ierr = DMGetLabel(dm, "Faces", &label);CHKERRQ(ierr);
ierr = DMPlexLabelComplete(dm, label);CHKERRQ(ierr);
}
}
{
PetscInt dimEmbed, i;
PetscInt nCoords;
PetscScalar *coords,bounds[] = {0,Lx,-.5,.5,-.5,.5,}; /* x_min,x_max,y_min,y_max */
Vec coordinates;
if (run_type==1) {
for (i = 0; i < 2*dim; i++) bounds[i] = (i%2) ? 1 : 0;
}
ierr = DMGetCoordinatesLocal(dm,&coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateDim(dm,&dimEmbed);CHKERRQ(ierr);
if (dimEmbed != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"dimEmbed != dim %D",dimEmbed);CHKERRQ(ierr);
ierr = VecGetLocalSize(coordinates,&nCoords);CHKERRQ(ierr);
if (nCoords % dimEmbed) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Coordinate vector the wrong size");CHKERRQ(ierr);
ierr = VecGetArray(coordinates,&coords);CHKERRQ(ierr);
for (i = 0; i < nCoords; i += dimEmbed) {
PetscInt j;
PetscScalar *coord = &coords[i];
for (j = 0; j < dimEmbed; j++) {
coord[j] = bounds[2 * j] + coord[j] * (bounds[2 * j + 1] - bounds[2 * j]);
}
}
ierr = VecRestoreArray(coordinates,&coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm,coordinates);CHKERRQ(ierr);
}
/* convert to p4est, and distribute */
ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsFList("-dm_type","Convert DMPlex to another format (should not be Plex!)","ex56.c",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
if (flg) {
DM newdm;
ierr = DMConvert(dm,convType,&newdm);CHKERRQ(ierr);
if (newdm) {
const char *prefix;
PetscBool isForest;
ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject)newdm,prefix);CHKERRQ(ierr);
ierr = DMIsForest(newdm,&isForest);CHKERRQ(ierr);
if (isForest) {
} else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Converted to non Forest?");
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = newdm;
} else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Convert failed?");
} else {
/* Plex Distribute mesh over processes */
ierr = DMPlexDistribute(dm, 0, NULL, &distdm);CHKERRQ(ierr);
if (distdm) {
const char *prefix;
ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject)distdm,prefix);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = distdm;
}
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
basedm = dm; dm = NULL;
for (iter=0 ; iter<max_conv_its ; iter++) {
ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr);
/* make new DM */
ierr = DMClone(basedm, &dm);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, "ex56_");CHKERRQ(ierr);
ierr = PetscObjectSetName( (PetscObject)dm,"Mesh");CHKERRQ(ierr);
ierr = PetscOptionsClearValue(NULL,"-ex56_dm_refine");CHKERRQ(ierr);
ierr = PetscOptionsInsertString(NULL,options[iter]);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr); /* refinement done here in Plex, p4est */
/* snes */
ierr = SNESCreate(comm, &snes);CHKERRQ(ierr);
ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
/* fem */
{
const PetscInt Ncomp = dim;
const PetscInt components[] = {0,1,2};
const PetscInt Nfid = 1, Npid = 1;
const PetscInt fid[] = {1}; /* The fixed faces (x=0) */
const PetscInt pid[] = {2}; /* The faces with loading (x=L_x) */
PetscFE fe;
PetscDS prob;
DM cdm = dm;
ierr = PetscFECreateDefault(dm, dim, dim, PETSC_FALSE, NULL, PETSC_DECIDE, &fe);CHKERRQ(ierr); /* elasticity */
ierr = PetscObjectSetName((PetscObject) fe, "deformation");CHKERRQ(ierr);
/* FEM prob */
ierr = DMGetDS(dm, &prob);CHKERRQ(ierr);
ierr = PetscDSSetDiscretization(prob, 0, (PetscObject) fe);CHKERRQ(ierr);
/* setup problem */
if (run_type==1) {
ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d);CHKERRQ(ierr);
ierr = PetscDSSetResidual(prob, 0, f0_u_x4, f1_u_3d);CHKERRQ(ierr);
} else {
ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d_alpha);CHKERRQ(ierr);
ierr = PetscDSSetResidual(prob, 0, f0_u, f1_u_3d_alpha);CHKERRQ(ierr);
ierr = PetscDSSetBdResidual(prob, 0, f0_bd_u_3d, f1_bd_u);CHKERRQ(ierr);
}
/* bcs */
if (run_type==1) {
PetscInt id = 1;
ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", "boundary", 0, 0, NULL, (void (*)()) zero, 1, &id, NULL);CHKERRQ(ierr);
} else {
ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "fixed", "Faces", 0, Ncomp, components, (void (*)()) zero, Nfid, fid, NULL);CHKERRQ(ierr);
ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL, "traction", "Faces", 0, Ncomp, components, NULL, Npid, pid, NULL);CHKERRQ(ierr);
}
while (cdm) {
ierr = DMSetDS(cdm,prob);CHKERRQ(ierr);
ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
ierr = PetscFEDestroy(&fe);CHKERRQ(ierr);
}
/* vecs & mat */
ierr = DMCreateGlobalVector(dm,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx, &bb);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) bb, "b");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) xx, "u");CHKERRQ(ierr);
ierr = DMCreateMatrix(dm, &Amat);CHKERRQ(ierr);
ierr = VecGetSize(bb,&N);CHKERRQ(ierr);
local_sizes[iter] = N;
ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d global equations, %d vertices\n",rank,PETSC_FUNCTION_NAME,N,N/dim);CHKERRQ(ierr);
if (use_nearnullspace && N/dim > 1) {
/* Set up the near null space (a.k.a. rigid body modes) that will be used by the multigrid preconditioner */
DM subdm;
MatNullSpace nearNullSpace;
PetscInt fields = 0;
PetscObject deformation;
ierr = DMCreateSubDM(dm, 1, &fields, NULL, &subdm);CHKERRQ(ierr);
ierr = DMPlexCreateRigidBody(subdm, &nearNullSpace);CHKERRQ(ierr);
ierr = DMGetField(dm, 0, &deformation);CHKERRQ(ierr);
ierr = PetscObjectCompose(deformation, "nearnullspace", (PetscObject) nearNullSpace);CHKERRQ(ierr);
ierr = DMDestroy(&subdm);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nearNullSpace);CHKERRQ(ierr); /* created by DM and destroyed by Mat */
}
ierr = DMPlexSetSNESLocalFEM(dm,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, Amat, Amat, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMSetUp(dm);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = PetscLogStagePush(stage[0]);CHKERRQ(ierr);
/* ksp */
ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr);
ierr = KSPSetComputeSingularValues(ksp,PETSC_TRUE);CHKERRQ(ierr);
/* test BCs */
ierr = VecZeroEntries(xx);CHKERRQ(ierr);
if (test_nonzero_cols) {
if (rank==0) ierr = VecSetValue(xx,0,1.0,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(xx);CHKERRQ(ierr);
ierr = VecAssemblyEnd(xx);CHKERRQ(ierr);
}
ierr = VecZeroEntries(bb);CHKERRQ(ierr);
ierr = VecGetSize(bb,&i);CHKERRQ(ierr);
local_sizes[iter] = i;
ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d equations in vector, %d vertices\n",rank,PETSC_FUNCTION_NAME,i,i/dim);CHKERRQ(ierr);
/* setup solver, dummy solve to really setup */
if (0) {
ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,1);CHKERRQ(ierr);
ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr);
ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,50);CHKERRQ(ierr);
ierr = VecZeroEntries(xx);CHKERRQ(ierr);
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
/* solve */
ierr = PetscLogStagePush(stage[1]);CHKERRQ(ierr);
ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = VecNorm(xx,NORM_INFINITY,&mdisp[iter]);CHKERRQ(ierr);
ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
{
PetscViewer viewer = NULL;
PetscViewerFormat fmt;
ierr = PetscOptionsGetViewer(comm,"ex56_","-vec_view",&viewer,&fmt,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscViewerPushFormat(viewer,fmt);CHKERRQ(ierr);
ierr = VecView(xx,viewer);CHKERRQ(ierr);
ierr = VecView(bb,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
/* Free work space */
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = VecDestroy(&xx);CHKERRQ(ierr);
ierr = VecDestroy(&bb);CHKERRQ(ierr);
ierr = MatDestroy(&Amat);CHKERRQ(ierr);
}
ierr = DMDestroy(&basedm);CHKERRQ(ierr);
if (run_type==1) {
err[0] = 59.975208 - mdisp[0]; /* error with what I think is the exact solution */
} else {
err[0] = 171.038 - mdisp[0];
}
for (iter=1 ; iter<max_conv_its ; iter++) {
if (run_type==1) {
err[iter] = 59.975208 - mdisp[iter];
} else {
err[iter] = 171.038 - mdisp[iter];
}
PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %D) N=%12D, max displ=%9.7e, disp diff=%9.2e, error=%4.3e, rate=%3.2g\n",
rank,PETSC_FUNCTION_NAME,iter,local_sizes[iter],mdisp[iter],
mdisp[iter]-mdisp[iter-1],err[iter],log(err[iter-1]/err[iter])/log(2.));
}
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode DMView_AKKT(DM dm, PetscViewer v) {
DM_AKKT* kkt = (DM_AKKT*)(dm->data);
PetscErrorCode ierr;
PetscBool isascii;
PetscInt i, tab, vtab;
const char* name, *prefix;
PetscFunctionBegin;
ierr = PetscObjectTypeCompare((PetscObject)v, PETSCVIEWERASCII, &isascii); CHKERRQ(ierr);
if(!isascii) SETERRQ(((PetscObject)dm)->comm, PETSC_ERR_SUP, "No support for non-ASCII viewers");
ierr = PetscObjectGetTabLevel((PetscObject)dm, &tab); CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)dm, &name); CHKERRQ(ierr);
ierr = PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix); CHKERRQ(ierr);
ierr = PetscViewerASCIIUseTabs(v,PETSC_TRUE); CHKERRQ(ierr);
ierr = PetscViewerASCIIGetTab(v,&vtab); CHKERRQ(ierr);
ierr = PetscViewerASCIISetTab(v,tab); CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(v, "DM Algebraic KKT, name: %s, prefix: %s\n", ((PetscObject)dm)->name, ((PetscObject)dm)->prefix); CHKERRQ(ierr);
if(kkt->dm) {
ierr = PetscViewerASCIIPrintf(v, "DM:\n"); CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(v); CHKERRQ(ierr);
ierr = DMView(kkt->dm,v); CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(v); CHKERRQ(ierr);
}
if(kkt->Aff) {
ierr = PetscViewerASCIIPrintf(v, "Aff:\n"); CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(v); CHKERRQ(ierr);
ierr = MatView(kkt->Aff,v); CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(v); CHKERRQ(ierr);
}
if(kkt->dname) {
ierr = PetscViewerASCIIPrintf(v, "Decomposition, name %s:\n"); CHKERRQ(ierr);
}
for(i = 0; i < 2; ++i) {
const char* label;
if(i == 0) {
label = "Primal";
}
else {
label = "Dual";
}
if(kkt->names[i]) {
ierr = PetscViewerASCIIPrintf(v, "%s, name %s:\n", label, kkt->names[i]); CHKERRQ(ierr);
}
if(kkt->isf[i]){
ierr = PetscViewerASCIIPrintf(v, "%s, IS:\n",label); CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(v); CHKERRQ(ierr);
ierr = ISView(kkt->isf[i],v); CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(v); CHKERRQ(ierr);
}
if(kkt->dmf[i]){
ierr = PetscViewerASCIIPrintf(v, "%s, DM:\n", label); CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(v); CHKERRQ(ierr);
ierr = DMView(kkt->dmf[i],v); CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(v); CHKERRQ(ierr);
}
}
if(kkt->Pfc) {
ierr = PetscViewerASCIIPrintf(v, "Prolongation:\n"); CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(v); CHKERRQ(ierr);
ierr = MatView(kkt->Pfc,v); CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(v); CHKERRQ(ierr);
}
ierr = PetscViewerASCIISetTab(v,vtab); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
