int main(int argc, char **argv)
{
PetscErrorCode ierr;
Vec U,cv,eta;
DM da,da2;
PetscViewer viewer,view_vtk_cv,view_vtk_eta;
char filename[PETSC_MAX_PATH_LEN],cv_filename[PETSC_MAX_PATH_LEN],eta_filename[PETSC_MAX_PATH_LEN];
PetscBool flg,sflg = PETSC_FALSE;
PetscInt i,n=10000;
PetscInt seed;
PetscInitialize(&argc,&argv, (char*)0, help);
ierr = PetscOptionsSetValue("-viewer_binary_skip_info","true");CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-f",filename,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) {
ierr = PetscOptionsGetInt(PETSC_NULL,"-random_seed",&seed,&sflg);CHKERRQ(ierr);
if (!sflg) {
ierr = PetscStrcpy(filename,"ex61.data");CHKERRQ(ierr);
} else {
sprintf(filename,"ex61.data.%d",seed);
}
}
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
/* Get physics and time parameters */
ierr = DMCreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr);
ierr = DMLoad(da,viewer);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&U);CHKERRQ(ierr);
ierr = DMDAGetReducedDA(da,1,&da2);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da2,&cv);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da2,&eta);CHKERRQ(ierr);
for (i=0; i<n; i++) {
/* when this fails it simply means the file is finished */
ierr = VecLoad(U,viewer);CHKERRQ(ierr);
ierr = VecStrideGather(U,1,cv,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecStrideGather(U,4,eta,INSERT_VALUES);CHKERRQ(ierr);
sprintf(cv_filename,"%s_cv_%d.vtk",filename,i);
sprintf(eta_filename,"%s_eta_%d.vtk",filename,i);
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,cv_filename,&view_vtk_cv);CHKERRQ(ierr);
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,eta_filename,&view_vtk_eta);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(view_vtk_cv, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(view_vtk_eta, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = DMView(da2,view_vtk_cv);CHKERRQ(ierr);
ierr = DMView(da2,view_vtk_eta);CHKERRQ(ierr);
ierr = VecView(cv,view_vtk_cv);CHKERRQ(ierr);
ierr = VecView(eta,view_vtk_eta);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view_vtk_cv);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view_vtk_eta);CHKERRQ(ierr);
}
ierr = VecDestroy(&U);CHKERRQ(ierr);
ierr = VecDestroy(&cv);CHKERRQ(ierr);
ierr = VecDestroy(&eta);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = DMDestroy(&da2);CHKERRQ(ierr);
PetscFinalize();
return 0;
}
int BSSCR_create_execute_script( void )
{
int argc;
char **args;
int i;
PetscViewer viewer, viewer_dated;
time_t currTime;
struct tm* timeInfo;
int adjustedYear;
int adjustedMonth;
char *filename;
/* get file name with date */
currTime = time( NULL );
timeInfo = localtime( &currTime );
/* See man localtime() for why to adjust these */
adjustedYear = 1900 + timeInfo->tm_year;
adjustedMonth = 1 + timeInfo->tm_mon;
/* Format; name-YYYY.MM.DD-HH.MM.SS.sh */
asprintf( &filename, "%s-%.4d.%.2d.%.2d-%.2d.%.2d.%.2d.%s",
"execute-job",
adjustedYear, adjustedMonth, timeInfo->tm_mday,
timeInfo->tm_hour, timeInfo->tm_min, timeInfo->tm_sec ,
"sh" );
PetscViewerASCIIOpen( PETSC_COMM_SELF, filename, &viewer_dated );
/* get file name without */
PetscViewerASCIIOpen( PETSC_COMM_SELF, "execute-job.sh", &viewer );
/* ouput what the command line arguments were */
PetscGetArgs( &argc, &args );
for( i=0; i<argc; i++ ) {
PetscViewerASCIIPrintf( viewer, "%s ", args[i] );
PetscViewerASCIIPrintf( viewer_dated, "%s ", args[i] );
}
Stg_PetscViewerDestroy(&viewer);
Stg_PetscViewerDestroy(&viewer_dated);
free( filename );
return 0;
}
static PetscErrorCode TSSetFromOptions_Pseudo(TS ts)
{
TS_Pseudo *pseudo = (TS_Pseudo*)ts->data;
PetscErrorCode ierr;
PetscBool flg = PETSC_FALSE;
PetscViewer viewer;
PetscFunctionBegin;
ierr = PetscOptionsHead("Pseudo-timestepping options");CHKERRQ(ierr);
ierr = PetscOptionsBool("-ts_monitor_pseudo","Monitor convergence","TSPseudoMonitorDefault",flg,&flg,NULL);CHKERRQ(ierr);
if (flg) {
ierr = PetscViewerASCIIOpen(PetscObjectComm((PetscObject)ts),"stdout",&viewer);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,TSPseudoMonitorDefault,viewer,(PetscErrorCode (*)(void**))PetscViewerDestroy);CHKERRQ(ierr);
}
flg = PETSC_FALSE;
ierr = PetscOptionsBool("-ts_pseudo_increment_dt_from_initial_dt","Increase dt as a ratio from original dt","TSPseudoIncrementDtFromInitialDt",flg,&flg,NULL);CHKERRQ(ierr);
if (flg) {
ierr = TSPseudoIncrementDtFromInitialDt(ts);CHKERRQ(ierr);
}
ierr = PetscOptionsReal("-ts_pseudo_increment","Ratio to increase dt","TSPseudoSetTimeStepIncrement",pseudo->dt_increment,&pseudo->dt_increment,0);CHKERRQ(ierr);
ierr = PetscOptionsReal("-ts_pseudo_max_dt","Maximum value for dt","TSPseudoSetMaxTimeStep",pseudo->dt_max,&pseudo->dt_max,0);CHKERRQ(ierr);
ierr = SNESSetFromOptions(ts->snes);CHKERRQ(ierr);
ierr = PetscOptionsTail();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode StokesWriteSolution(Stokes *s)
{
PetscMPIInt size;
PetscInt n,i,j;
const PetscScalar *array;
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* write data (*warning* only works sequential) */
MPI_Comm_size(MPI_COMM_WORLD,&size);
/*ierr = PetscPrintf(PETSC_COMM_WORLD," number of processors = %D\n",size);CHKERRQ(ierr);*/
if (size == 1) {
PetscViewer viewer;
ierr = VecGetArrayRead(s->x, &array);CHKERRQ(ierr);
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD, "solution.dat", &viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "# x, y, u, v, p\n");CHKERRQ(ierr);
for (j = 0; j < s->ny; j++) {
for (i = 0; i < s->nx; i++) {
n = j*s->nx+i;
ierr = PetscViewerASCIIPrintf(viewer, "%.12g %.12g %.12g %.12g %.12g\n", (double)(i*s->hx+s->hx/2),(double)(j*s->hy+s->hy/2), (double)PetscRealPart(array[n]), (double)PetscRealPart(array[n+s->nx*s->ny]),(double)PetscRealPart(array[n+2*s->nx*s->ny]));CHKERRQ(ierr);
}
}
ierr = VecRestoreArrayRead(s->x, &array);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int printVectorToFile(Vec& v,const char* filename){
PetscViewer viewer;
PetscViewerASCIIOpen(PETSC_COMM_WORLD,filename,&viewer);
VecView(v,viewer);
PetscViewerDestroy(&viewer);
return 0;
}
PetscErrorCode PetscViewerGetSubcomm_ASCII(PetscViewer viewer,MPI_Comm subcomm,PetscViewer *outviewer)
{
PetscErrorCode ierr;
PetscViewer_ASCII *vascii = (PetscViewer_ASCII *)viewer->data,*ovascii;
const char *name;
PetscFunctionBegin;
if (vascii->sviewer) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Subcomm viewer already obtained from PetscViewer and not restored");
/* Note that we need to open vascii->filename for the subcomm:
we can't count on reusing viewer's fd since the root in comm and subcomm may differ.
Further, if the subcomm happens to be the same as comm, PetscViewerASCIIOpen() will
will return the current viewer, having increfed it.
*/
ierr = PetscViewerASCIIOpen(subcomm,vascii->filename, outviewer);CHKERRQ(ierr);
if(*outviewer == viewer) PetscFunctionReturn(0);
ovascii = (PetscViewer_ASCII*)(*outviewer)->data;
ovascii->tab = vascii->tab;
vascii->sviewer = *outviewer;
(*outviewer)->format = viewer->format;
(*outviewer)->iformat = viewer->iformat;
ierr = PetscObjectGetName((PetscObject)viewer,&name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)(*outviewer),name);CHKERRQ(ierr);
((PetscViewer_ASCII*)((*outviewer)->data))->bviewer = viewer;
(*outviewer)->ops->destroy = PetscViewerDestroy_ASCII_Subcomm;
PetscFunctionReturn(0);
}
END_TEST
START_TEST( Generate2DLapacian_test )
{
PetscErrorCode ierr;
PetscInt d = 50, len = d*d;
Mat m;
PetscViewer view;
Generate2DLapacian( d, d, &m);
PetscViewerASCIIOpen(PETSC_COMM_SELF, "mat.dat", &view);
MatView(m, view);
KSP ksp;
PC pc;
ierr = KSPCreate(PETSC_COMM_SELF, &ksp); CHKERRQ(ierr);
KSPSetType(ksp, KSPPREONLY);
KSPGetPC(ksp, &pc);
PCSetType(pc, PCCHOLESKY);
KSPSetOperators(ksp, m, m, SAME_PRECONDITIONER);
Vec v, s;
VecCreateSeq(PETSC_COMM_SELF,len,&v);
VecDuplicate(v, &s);
VecSet(v, 1);
ierr = KSPSolve(ksp, v, s); CHKERRQ(ierr);
}
int printMatrixToFile(Mat& m,const char* filename){
PetscViewer viewer;
PetscViewerASCIIOpen(PETSC_COMM_WORLD,filename,&viewer);
MatView(m,viewer);
PetscViewerDestroy(&viewer);
return 0;
}
void
PetscSparseMtrx :: writeToFile(const char* fname) const
{
PetscViewer viewer;
PetscViewerASCIIOpen(PETSC_COMM_WORLD, fname, &viewer);
MatView(this->mtrx, viewer);
PetscViewerDestroy(&viewer);
}
void PetscMatrix<T>::print_matlab (const std::string name) const
{
libmesh_assert (this->initialized());
semiparallel_only();
// libmesh_assert (this->closed());
this->close();
PetscErrorCode ierr=0;
PetscViewer petsc_viewer;
ierr = PetscViewerCreate (this->comm().get(),
&petsc_viewer);
LIBMESH_CHKERRABORT(ierr);
/**
* Create an ASCII file containing the matrix
* if a filename was provided.
*/
if (name != "NULL")
{
ierr = PetscViewerASCIIOpen( this->comm().get(),
name.c_str(),
&petsc_viewer);
LIBMESH_CHKERRABORT(ierr);
ierr = PetscViewerSetFormat (petsc_viewer,
PETSC_VIEWER_ASCII_MATLAB);
LIBMESH_CHKERRABORT(ierr);
ierr = MatView (_mat, petsc_viewer);
LIBMESH_CHKERRABORT(ierr);
}
/**
* Otherwise the matrix will be dumped to the screen.
*/
else
{
ierr = PetscViewerSetFormat (PETSC_VIEWER_STDOUT_WORLD,
PETSC_VIEWER_ASCII_MATLAB);
LIBMESH_CHKERRABORT(ierr);
ierr = MatView (_mat, PETSC_VIEWER_STDOUT_WORLD);
LIBMESH_CHKERRABORT(ierr);
}
/**
* Destroy the viewer.
*/
ierr = LibMeshPetscViewerDestroy (&petsc_viewer);
LIBMESH_CHKERRABORT(ierr);
}
void
output_data(Pointer<PatchHierarchy<NDIM> > patch_hierarchy,
Pointer<INSHierarchyIntegrator> navier_stokes_integrator,
LDataManager* l_data_manager,
const int iteration_num,
const double loop_time,
const int output_level,
const string& data_dump_dirname)
{
if (output_level >= 0)
{
pout << "\nWriting output files at timestep # " << iteration_num << " t=" << loop_time << "\n";
}
string file_name = data_dump_dirname + "/" + "hier_data.";
char temp_buf[128];
sprintf(temp_buf, "%05d.samrai.%05d", iteration_num, SAMRAI_MPI::getRank());
file_name += temp_buf;
// Write Cartesian data.
if (output_level >= 3)
{
Pointer<HDFDatabase> hier_db = new HDFDatabase("hier_db");
hier_db->create(file_name);
VariableDatabase<NDIM>* var_db = VariableDatabase<NDIM>::getDatabase();
ComponentSelector hier_data;
hier_data.setFlag(var_db->mapVariableAndContextToIndex(navier_stokes_integrator->getVelocityVariable(),
navier_stokes_integrator->getCurrentContext()));
hier_data.setFlag(var_db->mapVariableAndContextToIndex(navier_stokes_integrator->getPressureVariable(),
navier_stokes_integrator->getCurrentContext()));
patch_hierarchy->putToDatabase(hier_db->putDatabase("PatchHierarchy"), hier_data);
hier_db->putDouble("loop_time", loop_time);
hier_db->putInteger("iteration_num", iteration_num);
hier_db->close();
}
// Write Lagrangian data.
if (output_level >= 0)
{
const int finest_hier_level = patch_hierarchy->getFinestLevelNumber();
Pointer<LData> X_data = l_data_manager->getLData("X", finest_hier_level);
Vec X_petsc_vec = X_data->getVec();
Vec X_lag_vec;
VecDuplicate(X_petsc_vec, &X_lag_vec);
l_data_manager->scatterPETScToLagrangian(X_petsc_vec, X_lag_vec, finest_hier_level);
file_name = data_dump_dirname + "/" + "X.";
sprintf(temp_buf, "%05d", iteration_num);
file_name += temp_buf;
PetscViewer viewer;
PetscViewerASCIIOpen(PETSC_COMM_WORLD, file_name.c_str(), &viewer);
VecView(X_lag_vec, viewer);
PetscViewerDestroy(&viewer);
VecDestroy(&X_lag_vec);
}
return;
} // output_data
PetscErrorCode OutputVec(MPI_Comm comm, Vec x, const char *filenameComm, const char *filenameProperty)
{
PetscErrorCode ierr;
PetscViewer viewer;
char filename[100]="";
strcat(strcat(filename,filenameComm),filenameProperty);
ierr = PetscViewerASCIIOpen(comm, filename, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_MATLAB); CHKERRQ(ierr);
ierr = VecView(x,viewer); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void PetscVector<T>::print_matlab (const std::string name) const
{
this->_restore_array();
libmesh_assert (this->closed());
PetscErrorCode ierr=0;
PetscViewer petsc_viewer;
ierr = PetscViewerCreate (libMesh::COMM_WORLD,
&petsc_viewer);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
/**
* Create an ASCII file containing the matrix
* if a filename was provided.
*/
if (name != "NULL")
{
ierr = PetscViewerASCIIOpen( libMesh::COMM_WORLD,
name.c_str(),
&petsc_viewer);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
ierr = PetscViewerSetFormat (petsc_viewer,
PETSC_VIEWER_ASCII_MATLAB);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
ierr = VecView (_vec, petsc_viewer);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
}
/**
* Otherwise the matrix will be dumped to the screen.
*/
else
{
ierr = PetscViewerSetFormat (PETSC_VIEWER_STDOUT_WORLD,
PETSC_VIEWER_ASCII_MATLAB);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
ierr = VecView (_vec, PETSC_VIEWER_STDOUT_WORLD);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
}
/**
* Destroy the viewer.
*/
ierr = LibMeshPetscViewerDestroy (&petsc_viewer);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
}
PetscErrorCode OutputMat(MPI_Comm comm, Mat A, const char *filenameComm, const char *filenameProperty)
{
PetscErrorCode ierr;
PetscViewer viewer;
char filename[100]="";
strcat(strcat(filename,filenameComm),filenameProperty);
ierr = PetscViewerASCIIOpen(comm, filename, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr);
ierr = MatView(A,viewer); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
// When runing parallely, it may need -mat_ascii_output_large
PetscFunctionReturn(0);
}
/*@
TSTrajectorySetMonitor - Monitor the schedules generated by the checkpointing controller
Collective on TSTrajectory
Input Arguments:
+ tj - the TSTrajectory context
- flg - PETSC_TRUE to active a monitor, PETSC_FALSE to disable
Options Database Keys:
. -ts_trajectory_monitor - print TSTrajectory information
Level: intermediate
.keywords: TS, trajectory, set, monitor
.seealso: TSTrajectoryCreate(), TSTrajectoryDestroy(), TSTrajectorySetUp()
@*/
PetscErrorCode TSTrajectorySetMonitor(TSTrajectory tj,PetscBool flg)
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(tj,TSTRAJECTORY_CLASSID,1);
PetscValidLogicalCollectiveBool(tj,flg,2);
if (flg) {
if (!tj->monitor) {ierr = PetscViewerASCIIOpen(PetscObjectComm((PetscObject)tj),"stdout",&tj->monitor);CHKERRQ(ierr);}
} else {
ierr = PetscViewerDestroy(&tj->monitor);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*@
TSAdaptSetMonitor - Monitor the choices made by the adaptive controller
Collective on TSAdapt
Input Arguments:
+ adapt - adaptive controller context
- flg - PETSC_TRUE to active a monitor, PETSC_FALSE to disable
Options Database Keys:
. -ts_adapt_monitor - to turn on monitoring
Level: intermediate
.seealso: TSAdaptChoose()
@*/
PetscErrorCode TSAdaptSetMonitor(TSAdapt adapt,PetscBool flg)
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(adapt,TSADAPT_CLASSID,1);
PetscValidLogicalCollectiveBool(adapt,flg,2);
if (flg) {
if (!adapt->monitor) {ierr = PetscViewerASCIIOpen(PetscObjectComm((PetscObject)adapt),"stdout",&adapt->monitor);CHKERRQ(ierr);}
} else {
ierr = PetscViewerDestroy(&adapt->monitor);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
void linearSystemPETSc<scalar>::printMatlab(const char *filename) const
{
_try(MatAssemblyBegin(_a, MAT_FINAL_ASSEMBLY));
_try(MatAssemblyEnd(_a, MAT_FINAL_ASSEMBLY));
_try(VecAssemblyBegin(_b));
_try(VecAssemblyEnd(_b));
PetscViewer viewer;
PetscViewerASCIIOpen(PETSC_COMM_WORLD, filename, &viewer);
PetscViewerSetFormat(viewer,PETSC_VIEWER_ASCII_MATLAB);
MatView(_a, viewer);
PetscViewerDestroy(&viewer);
return;
}
END_TEST
START_TEST( GenerateLaplacian2DNoBC_test )
{
PetscInt d1, d2;
Mat m;
PetscViewer view;
d1 = d2 = 1e2;
GenerateLaplacian2DNoBC(d1, d2, &m);
PetscViewerASCIIOpen(PETSC_COMM_SELF, "mat.dat", &view);
MatView(m, view);
}
int main(int argc,char **args)
{
PetscErrorCode ierr;
PetscViewer viewer;
ierr = PetscInitialize(&argc,&args,(char *)0,help);CHKERRQ(ierr);
ierr = PetscViewerCreate(PETSC_COMM_WORLD,&viewer);CHKERRQ(ierr);
ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,"stdout",&viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode PreCheckSetFromOptions(PreCheck precheck)
{
PetscErrorCode ierr;
PetscBool flg;
PetscFunctionBegin;
ierr = PetscOptionsBegin(precheck->comm,PETSC_NULL,"PreCheck Options","none");CHKERRQ(ierr);
ierr = PetscOptionsReal("-precheck_angle","Angle in degrees between successive search directions necessary to activate step correction","",precheck->angle,&precheck->angle,PETSC_NULL);CHKERRQ(ierr);
flg = PETSC_FALSE;
ierr = PetscOptionsBool("-precheck_monitor","Monitor choices made by precheck routine","",flg,&flg,PETSC_NULL);CHKERRQ(ierr);
if (flg) {
ierr = PetscViewerASCIIOpen(precheck->comm,"stdout",&precheck->monitor);CHKERRQ(ierr);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DataSave(Vec x, char *filename)
{
PetscErrorCode ierr;
PetscViewer dataviewer;
PetscFunctionBegin;
ierr = PetscPrintf(PETSC_COMM_WORLD, "\n Save %s", filename); CHKERRQ(ierr);
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,filename,&dataviewer); CHKERRQ(ierr);
ierr = PetscViewerSetFormat(dataviewer,PETSC_VIEWER_ASCII_SYMMODU); CHKERRQ(ierr);
ierr = VecView(x,dataviewer); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "\n Done with %s", filename); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&dataviewer); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode BSSCR_StokesCreateOperatorSummary( Mat K, Mat G, Mat C, Vec f, Vec h, const char filename[] )
{
MPI_Comm comm;
PetscViewer v;
char op_name[PETSC_MAX_PATH_LEN];
PetscTruth flg;
PetscObjectGetComm( (PetscObject)K, &comm );
PetscViewerASCIIOpen( comm, filename, &v );
BSSCR_GeneratePetscHeader_for_viewer( v );
PetscViewerASCIIPrintf( v, "\nInput matrices:\n");
PetscViewerASCIIPushTab(v);
PetscOptionsGetString( PETSC_NULL,"-stokes_A11",op_name,PETSC_MAX_PATH_LEN-1,&flg );
if (flg) { PetscViewerASCIIPrintf( v, "A11: %s\n", op_name ); }
PetscOptionsGetString( PETSC_NULL,"-stokes_A12",op_name,PETSC_MAX_PATH_LEN-1,&flg );
if (flg) { PetscViewerASCIIPrintf( v, "A12: %s\n", op_name ); }
PetscOptionsGetString( PETSC_NULL,"-stokes_A22",op_name,PETSC_MAX_PATH_LEN-1,&flg );
if (flg) { PetscViewerASCIIPrintf( v, "A22: %s\n", op_name ); }
PetscOptionsGetString( PETSC_NULL,"-stokes_Smat",op_name,PETSC_MAX_PATH_LEN-1,&flg );
if (flg) { PetscViewerASCIIPrintf( v, "Smat: %s\n", op_name ); }
PetscOptionsGetString( PETSC_NULL,"-stokes_b1",op_name,PETSC_MAX_PATH_LEN-1,&flg );
if (flg) { PetscViewerASCIIPrintf( v, "b1: %s\n", op_name ); }
PetscOptionsGetString( PETSC_NULL,"-stokes_b2",op_name,PETSC_MAX_PATH_LEN-1,&flg );
if (flg) { PetscViewerASCIIPrintf( v, "b2: %s\n", op_name ); }
PetscViewerASCIIPopTab(v);
PetscViewerASCIIPrintf( v, "\n");
BSSCR_MatInfoLog(v,K,"stokes_A11"); PetscViewerASCIIPrintf( v, "\n");
BSSCR_MatInfoLog(v,G,"stokes_A12"); PetscViewerASCIIPrintf( v, "\n");
if (C) { BSSCR_MatInfoLog(v,C,"stokes_A22"); PetscViewerASCIIPrintf( v, "\n"); }
BSSCR_VecInfoLog(v,f,"stokes_b1"); PetscViewerASCIIPrintf( v, "\n");
BSSCR_VecInfoLog(v,h,"stokes_b2"); PetscViewerASCIIPrintf( v, "\n");
Stg_PetscViewerDestroy(&v );
PetscFunctionReturn(0);
}
void PETScVector::viewer(const std::string &file_name, const PetscViewerFormat vw_format) const
{
PetscViewer viewer;
PetscViewerASCIIOpen(PETSC_COMM_WORLD, file_name.c_str(), &viewer);
PetscViewerPushFormat(viewer, vw_format);
PetscObjectSetName((PetscObject)_v, file_name.c_str());
VecView(_v, viewer);
#define nEXIT_TEST
#ifdef EXIT_TEST
VecDestroy(_v);
PetscFinalize();
exit(0);
#endif
}
END_TEST
START_TEST( test_PeriodicBC )
{
PetscErrorCode ierr;
PetscInt d1 = 7, d2 = d1;
Mat m;
PetscViewer view;
Generate2DLaplacianPeriodicBC( d1, d2, &m);
ierr = MatView( m, PETSC_VIEWER_STDOUT_SELF); CHKERRQ(ierr);
PetscViewerASCIIOpen(PETSC_COMM_SELF, "mat.dat", &view);
MatView(m, view);
MatDestroy(m);
}
PetscErrorCode KSPSetFromOptions_LSQR(KSP ksp)
{
PetscErrorCode ierr;
KSP_LSQR *lsqr = (KSP_LSQR*)ksp->data;
char monfilename[PETSC_MAX_PATH_LEN];
PetscViewer monviewer;
PetscBool flg;
PetscFunctionBegin;
ierr = PetscOptionsHead("KSP LSQR Options");CHKERRQ(ierr);
ierr = PetscOptionsName("-ksp_lsqr_set_standard_error","Set Standard Error Estimates of Solution","KSPLSQRSetStandardErrorVec",&lsqr->se_flg);CHKERRQ(ierr);
ierr = PetscOptionsString("-ksp_lsqr_monitor","Monitor residual norm and norm of residual of normal equations","KSPMonitorSet","stdout",monfilename,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscViewerASCIIOpen(PetscObjectComm((PetscObject)ksp),monfilename,&monviewer);CHKERRQ(ierr);
ierr = KSPMonitorSet(ksp,KSPLSQRMonitorDefault,monviewer,(PetscErrorCode (*)(void**))PetscViewerDestroy);CHKERRQ(ierr);
}
ierr = PetscOptionsTail();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscViewerASCIIGetStdout - Creates a ASCII PetscViewer shared by all processors
in a communicator. Error returning version of PETSC_VIEWER_STDOUT_()
Collective on MPI_Comm
Input Parameter:
. comm - the MPI communicator to share the PetscViewer
Level: beginner
Notes:
This should be used in all PETSc source code instead of PETSC_VIEWER_STDOUT_()
.seealso: PETSC_VIEWER_DRAW_(), PetscViewerASCIIOpen(), PETSC_VIEWER_STDERR_, PETSC_VIEWER_STDOUT_WORLD,
PETSC_VIEWER_STDOUT_SELF
@*/
PetscErrorCode PetscViewerASCIIGetStdout(MPI_Comm comm,PetscViewer *viewer)
{
PetscErrorCode ierr;
PetscBool flg;
MPI_Comm ncomm;
PetscFunctionBegin;
ierr = PetscCommDuplicate(comm,&ncomm,NULL);CHKERRQ(ierr);
if (Petsc_Viewer_Stdout_keyval == MPI_KEYVAL_INVALID) {
ierr = MPI_Keyval_create(MPI_NULL_COPY_FN,MPI_NULL_DELETE_FN,&Petsc_Viewer_Stdout_keyval,0);CHKERRQ(ierr);
}
ierr = MPI_Attr_get(ncomm,Petsc_Viewer_Stdout_keyval,(void**)viewer,(PetscMPIInt*)&flg);CHKERRQ(ierr);
if (!flg) { /* PetscViewer not yet created */
ierr = PetscViewerASCIIOpen(ncomm,"stdout",viewer);CHKERRQ(ierr);
ierr = PetscObjectRegisterDestroy((PetscObject)*viewer);CHKERRQ(ierr);
ierr = MPI_Attr_put(ncomm,Petsc_Viewer_Stdout_keyval,(void*)*viewer);CHKERRQ(ierr);
}
ierr = PetscCommDestroy(&ncomm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
SNESMonitorSetRatio - Sets SNES to use a monitor that prints the
ratio of the function norm at each iteration.
Collective on SNES
Input Parameters:
+ snes - the SNES context
- viewer - ASCII viewer to print output
Level: intermediate
.keywords: SNES, nonlinear, monitor, norm
.seealso: SNESMonitorSet(), SNESMonitorSolution(), SNESMonitorDefault()
@*/
PetscErrorCode SNESMonitorSetRatio(SNES snes,PetscViewer viewer)
{
PetscErrorCode ierr;
SNESMonitorRatioContext *ctx;
PetscReal *history;
PetscFunctionBegin;
if (!viewer) {
ierr = PetscViewerASCIIOpen(((PetscObject)snes)->comm,"stdout",&viewer);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)viewer);CHKERRQ(ierr);
}
ierr = PetscNewLog(snes,SNESMonitorRatioContext,&ctx);CHKERRQ(ierr);
ierr = SNESGetConvergenceHistory(snes,&history,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
if (!history) {
ierr = PetscMalloc(100*sizeof(PetscReal),&ctx->history);CHKERRQ(ierr);
ierr = SNESSetConvergenceHistory(snes,ctx->history,0,100,PETSC_TRUE);CHKERRQ(ierr);
}
ctx->viewer = viewer;
ierr = SNESMonitorSet(snes,SNESMonitorRatio,ctx,SNESMonitorRatioDestroy);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode PCSetFromOptions_SVD(PC pc)
{
PetscErrorCode ierr;
PC_SVD *jac = (PC_SVD*)pc->data;
PetscBool flg,set;
PetscFunctionBegin;
ierr = PetscOptionsHead("SVD options");CHKERRQ(ierr);
ierr = PetscOptionsReal("-pc_svd_zero_sing","Singular values smaller than this treated as zero","None",jac->zerosing,&jac->zerosing,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-pc_svd_ess_rank","Essential rank of operator (0 to use entire operator)","None",jac->essrank,&jac->essrank,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-pc_svd_monitor","Monitor the conditioning, and extremal singular values","None",jac->monitor ? PETSC_TRUE : PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set) { /* Should make PCSVDSetMonitor() */
if (flg && !jac->monitor) {
ierr = PetscViewerASCIIOpen(PetscObjectComm((PetscObject)pc),"stdout",&jac->monitor);CHKERRQ(ierr);
} else if (!flg) {
ierr = PetscViewerDestroy(&jac->monitor);CHKERRQ(ierr);
}
}
ierr = PetscOptionsTail();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void bsscr_dirwriteVec(Vec V, char name[], char dir[], char message[]){
PetscViewer vec_view_file;
char str[100];
PetscTruth dump=PETSC_FALSE;
PetscOptionsGetTruth( PETSC_NULL ,"-dump_matvec", &dump, 0 );
if(dump){
if( V != NULL ) {
PetscPrintf( PETSC_COMM_WORLD,"%s \n",message);
PetscObjectSetName((PetscObject)V,name);
sprintf(str,"%s%svectorBin",dir,name);
PetscViewerBinaryOpen( PETSC_COMM_WORLD, str, FILE_MODE_WRITE, &vec_view_file );
PetscViewerSetFormat( vec_view_file, PETSC_VIEWER_NATIVE );
VecView( V, vec_view_file );
Stg_PetscViewerDestroy(&vec_view_file );
sprintf(str,"%s%svector.m",dir,name);
PetscViewerASCIIOpen( PETSC_COMM_WORLD, str, &vec_view_file );
PetscViewerSetFormat( vec_view_file, PETSC_VIEWER_ASCII_MATLAB );
VecView( V, vec_view_file );
Stg_PetscViewerDestroy(&vec_view_file );
}
}
}
void _UnderworldContext_GenerateOptionsFile( UnderworldContext* context ) {
char* optionsFilename;
#if ((PETSC_VERSION_MAJOR==3) && (PETSC_VERSION_MINOR>=2))
PetscViewer options;
#else
FILE* options;
#endif
Stg_asprintf( &optionsFilename, "%s/options-%s.txt", context->outputPath, context->timeStamp );
/* Generate PETSc options file. */
#if ((PETSC_VERSION_MAJOR==3) && (PETSC_VERSION_MINOR>=2))
PetscViewerASCIIOpen( context->communicator, optionsFilename, &options );
PetscOptionsView( options );
PetscViewerDestroy( &options );
#else
options = fopen( optionsFilename, "w" );
PetscOptionsPrint( options );
fclose( options );
#endif
Memory_Free( optionsFilename );
}
