PetscErrorCode DMSetFromOptions_Mesh(DM dm)
{
PetscBool flg;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
ierr = PetscOptionsHead("DMMesh Options");CHKERRQ(ierr);
/* Handle DMMesh refinement */
/* Handle associated vectors */
/* Handle viewing */
ierr = PetscOptionsBool("-dm_mesh_view_vtk", "Output mesh in VTK format", "DMView", PETSC_FALSE, &flg, PETSC_NULL);CHKERRQ(ierr);
if (flg) {
PetscViewer viewer;
ierr = PetscViewerCreate(((PetscObject) dm)->comm, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "mesh.vtk");CHKERRQ(ierr);
ierr = DMView(dm, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = PetscOptionsBool("-dm_mesh_view", "Exhaustive mesh description", "DMView", PETSC_FALSE, &flg, PETSC_NULL);CHKERRQ(ierr);
if (flg) {
PetscViewer viewer;
ierr = PetscViewerCreate(((PetscObject) dm)->comm, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_INFO_DETAIL);CHKERRQ(ierr);
ierr = DMView(dm, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = PetscOptionsTail();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode PetscViewerFileSetName_VTK(PetscViewer viewer,const char name[])
{
PetscViewer_VTK *vtk = (PetscViewer_VTK*)viewer->data;
PetscErrorCode ierr;
PetscBool isvtk,isvts,isvtu,isvtr;
size_t len;
PetscFunctionBegin;
ierr = PetscViewerFlush(viewer);CHKERRQ(ierr);
ierr = PetscFree(vtk->filename);CHKERRQ(ierr);
ierr = PetscStrlen(name,&len);CHKERRQ(ierr);
ierr = PetscStrcasecmp(name+len-4,".vtk",&isvtk);CHKERRQ(ierr);
ierr = PetscStrcasecmp(name+len-4,".vts",&isvts);CHKERRQ(ierr);
ierr = PetscStrcasecmp(name+len-4,".vtu",&isvtu);CHKERRQ(ierr);
ierr = PetscStrcasecmp(name+len-4,".vtr",&isvtr);CHKERRQ(ierr);
if (isvtk) {
if (viewer->format == PETSC_VIEWER_DEFAULT) {ierr = PetscViewerSetFormat(viewer,PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);}
if (viewer->format != PETSC_VIEWER_ASCII_VTK) SETERRQ2(PetscObjectComm((PetscObject)viewer),PETSC_ERR_ARG_INCOMP,"Cannot use file '%s' with format %s, should have '.vtk' extension",name,PetscViewerFormats[viewer->format]);
} else if (isvts) {
if (viewer->format == PETSC_VIEWER_DEFAULT) {ierr = PetscViewerSetFormat(viewer,PETSC_VIEWER_VTK_VTS);CHKERRQ(ierr);}
if (viewer->format != PETSC_VIEWER_VTK_VTS) SETERRQ2(PetscObjectComm((PetscObject)viewer),PETSC_ERR_ARG_INCOMP,"Cannot use file '%s' with format %s, should have '.vts' extension",name,PetscViewerFormats[viewer->format]);
} else if (isvtu) {
if (viewer->format == PETSC_VIEWER_DEFAULT) {ierr = PetscViewerSetFormat(viewer,PETSC_VIEWER_VTK_VTU);CHKERRQ(ierr);}
if (viewer->format != PETSC_VIEWER_VTK_VTU) SETERRQ2(PetscObjectComm((PetscObject)viewer),PETSC_ERR_ARG_INCOMP,"Cannot use file '%s' with format %s, should have '.vtu' extension",name,PetscViewerFormats[viewer->format]);
} else if (isvtr) {
if (viewer->format == PETSC_VIEWER_DEFAULT) {ierr = PetscViewerSetFormat(viewer,PETSC_VIEWER_VTK_VTR);CHKERRQ(ierr);}
if (viewer->format != PETSC_VIEWER_VTK_VTR) SETERRQ2(PetscObjectComm((PetscObject)viewer),PETSC_ERR_ARG_INCOMP,"Cannot use file '%s' with format %s, should have '.vtr' extension",name,PetscViewerFormats[viewer->format]);
} else SETERRQ1(PetscObjectComm((PetscObject)viewer),PETSC_ERR_ARG_UNKNOWN_TYPE,"File '%s' has unrecognized extension",name);
ierr = PetscStrallocpy(name,&vtk->filename);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
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;
}
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);
}
int main(int argc,char **argv)
{
Mat mat,submat,*submatrices;
PetscInt m = 10,n = 10,i = 4,tmp;
PetscErrorCode ierr;
IS irkeep,ickeep;
PetscScalar value = 1.0;
PetscViewer sviewer;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_SELF,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&mat);CHKERRQ(ierr);
ierr = MatSetSizes(mat,PETSC_DECIDE,PETSC_DECIDE,m,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(mat);CHKERRQ(ierr);
for (i=0; i<m; i++) {
value = (PetscReal)i+1; tmp = i % 5;
ierr = MatSetValues(mat,1,&tmp,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(PETSC_VIEWER_STDOUT_WORLD,"Original matrix\n");CHKERRQ(ierr);
ierr = MatView(mat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* Form submatrix with rows 2-4 and columns 4-8 */
ierr = ISCreateStride(PETSC_COMM_SELF,3,2,1,&irkeep);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,5,4,1,&ickeep);CHKERRQ(ierr);
ierr = MatGetSubMatrices(mat,1,&irkeep,&ickeep,MAT_INITIAL_MATRIX,&submatrices);CHKERRQ(ierr);
submat = *submatrices;
ierr = PetscFree(submatrices);CHKERRQ(ierr);
/*
sviewer will cause the submatrices (one per processor) to be printed in the correct order
*/
ierr = PetscViewerASCIIPrintf(PETSC_VIEWER_STDOUT_WORLD,"Submatrices\n");CHKERRQ(ierr);
ierr = PetscViewerGetSingleton(PETSC_VIEWER_STDOUT_WORLD,&sviewer);CHKERRQ(ierr);
ierr = MatView(submat,sviewer);CHKERRQ(ierr);
ierr = PetscViewerRestoreSingleton(PETSC_VIEWER_STDOUT_WORLD,&sviewer);CHKERRQ(ierr);
ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* Zero the original matrix */
ierr = PetscViewerASCIIPrintf(PETSC_VIEWER_STDOUT_WORLD,"Original zeroed matrix\n");CHKERRQ(ierr);
ierr = MatZeroEntries(mat);CHKERRQ(ierr);
ierr = MatView(mat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISDestroy(&irkeep);CHKERRQ(ierr);
ierr = ISDestroy(&ickeep);CHKERRQ(ierr);
ierr = MatDestroy(&submat);CHKERRQ(ierr);
ierr = MatDestroy(&mat);CHKERRQ(ierr);
ierr = PetscFinalize();
return 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);
}
void PETSc::Print_A(const char *filename)
{
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_MATLAB);
MatView(A, PETSC_VIEWER_STDOUT_WORLD);
}
void PETSc::Print_x(const char *filename)
{
ierr = VecAssemblyBegin(x);
ierr = VecAssemblyEnd(x);
PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_MATLAB);
VecView(x, PETSC_VIEWER_STDOUT_WORLD);
}
int main(int argc,char **argv)
{
Mat A,B;
PetscInt m = 7,n,i,rstart,rend,cols[3];
PetscErrorCode ierr;
PetscScalar v[3];
PetscBool equal;
const char *eq[2];
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr);
n = m;
/* ------- Assemble matrix, --------- */
ierr = MatCreateAIJ(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,m,n,0,0,0,0,&A);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
if (!rstart) {
cols[0] = 0;
cols[1] = 1;
v[0] = 2.0; v[1] = -1.0;
ierr = MatSetValues(A,1,&rstart,2,cols,v,INSERT_VALUES);CHKERRQ(ierr);
rstart++;
}
if (rend == m) {
rend--;
cols[0] = rend-1;
cols[1] = rend;
v[0] = -1.0; v[1] = 2.0;
ierr = MatSetValues(A,1,&rend,2,cols,v,INSERT_VALUES);CHKERRQ(ierr);
}
v[0] = -1.0; v[1] = 2.0; v[2] = -1.0;
for (i=rstart; i<rend; i++) {
cols[0] = i-1;
cols[1] = i;
cols[2] = i+1;
ierr = MatSetValues(A,1,&i,3,cols,v,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr);
ierr = MatEqual(A,B,&equal);
eq[0] = "not equal";
eq[1] = "equal";
ierr = PetscPrintf(PETSC_COMM_WORLD,"Matrices are %s\n",eq[equal]);CHKERRQ(ierr);
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
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);
}
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);
}
void bsscr_writeMat(Mat K, char name[], char message[]){
PetscViewer mat_view_file;
char str[100];
PetscTruth dump=PETSC_FALSE;
PetscOptionsGetTruth( PETSC_NULL ,"-dump_matvec", &dump, 0 );
if(dump){
if( K != NULL ) {
PetscPrintf( PETSC_COMM_WORLD,"%s \n",message);
PetscObjectSetName((PetscObject)K,name);
sprintf(str,"%smatrixBin",name);
PetscViewerBinaryOpen( PETSC_COMM_WORLD, str, FILE_MODE_WRITE, &mat_view_file );
PetscViewerSetFormat( mat_view_file, PETSC_VIEWER_NATIVE );
MatView( K, mat_view_file );
Stg_PetscViewerDestroy(&mat_view_file );
sprintf(str,"%smatrix.m",name);
PetscViewerASCIIOpen( PETSC_COMM_WORLD, str, &mat_view_file );
PetscViewerSetFormat( mat_view_file, PETSC_VIEWER_ASCII_MATLAB );
MatView( K, mat_view_file );
Stg_PetscViewerDestroy(&mat_view_file );
}
}
}
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 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;
}
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);
}
int main(int argc,char **args)
{
PetscErrorCode ierr;
Mat A,AT,B,C;
PetscViewer viewer;
PetscBool flg;
char file[PETSC_MAX_PATH_LEN];
PetscInitialize(&argc,&args,(char *)0,help);
ierr = PetscOptionsGetString(PETSC_NULL,"-fA",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Input fileA not specified");
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATAIJ);CHKERRQ(ierr);
ierr = MatLoad(A,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-fB",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Input fileB not specified");
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetType(B,MATDENSE);CHKERRQ(ierr);
ierr = MatLoad(B,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&AT);CHKERRQ(ierr);
ierr = MatMatMult(AT,B,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&C);
ierr = PetscOptionsHasName(PETSC_NULL,"-view_C",&flg);CHKERRQ(ierr);
if (flg){
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"C.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer,PETSC_VIEWER_NATIVE);CHKERRQ(ierr);
ierr = MatView(C,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&AT);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode test_solve(void)
{
Mat A11, A12,A21,A22, A, tmp[2][2];
KSP ksp;
PC pc;
Vec b,x, f,h, diag, x1,x2;
Vec tmp_x[2],*_tmp_x;
int n, np, i,j;
PetscErrorCode ierr;
PetscFunctionBeginUser;
PetscPrintf(PETSC_COMM_WORLD, "%s \n", PETSC_FUNCTION_NAME);
n = 3;
np = 2;
/* Create matrices */
/* A11 */
ierr = VecCreate(PETSC_COMM_WORLD, &diag);
CHKERRQ(ierr);
ierr = VecSetSizes(diag, PETSC_DECIDE, n);
CHKERRQ(ierr);
ierr = VecSetFromOptions(diag);
CHKERRQ(ierr);
ierr = VecSet(diag, (1.0/10.0));
CHKERRQ(ierr); /* so inverse = diag(10) */
/* As a test, create a diagonal matrix for A11 */
ierr = MatCreate(PETSC_COMM_WORLD, &A11);
CHKERRQ(ierr);
ierr = MatSetSizes(A11, PETSC_DECIDE, PETSC_DECIDE, n, n);
CHKERRQ(ierr);
ierr = MatSetType(A11, MATAIJ);
CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(A11, n, NULL);
CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(A11, np, NULL,np, NULL);
CHKERRQ(ierr);
ierr = MatDiagonalSet(A11, diag, INSERT_VALUES);
CHKERRQ(ierr);
ierr = VecDestroy(&diag);
CHKERRQ(ierr);
/* A12 */
ierr = MatCreate(PETSC_COMM_WORLD, &A12);
CHKERRQ(ierr);
ierr = MatSetSizes(A12, PETSC_DECIDE, PETSC_DECIDE, n, np);
CHKERRQ(ierr);
ierr = MatSetType(A12, MATAIJ);
CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(A12, np, NULL);
CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(A12, np, NULL,np, NULL);
CHKERRQ(ierr);
for (i=0; i<n; i++) {
for (j=0; j<np; j++) {
ierr = MatSetValue(A12, i,j, (PetscScalar)(i+j*n), INSERT_VALUES);
CHKERRQ(ierr);
}
}
ierr = MatSetValue(A12, 2,1, (PetscScalar)(4), INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatAssemblyBegin(A12, MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(A12, MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
/* A21 */
ierr = MatTranspose(A12, MAT_INITIAL_MATRIX, &A21);
CHKERRQ(ierr);
A22 = NULL;
/* Create block matrix */
tmp[0][0] = A11;
tmp[0][1] = A12;
tmp[1][0] = A21;
tmp[1][1] = A22;
ierr = MatCreateNest(PETSC_COMM_WORLD,2,NULL,2,NULL,&tmp[0][0],&A);
CHKERRQ(ierr);
ierr = MatNestSetVecType(A,VECNEST);
CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
/* Create vectors */
ierr = MatCreateVecs(A12, &h, &f);
CHKERRQ(ierr);
ierr = VecSet(f, 1.0);
CHKERRQ(ierr);
ierr = VecSet(h, 0.0);
CHKERRQ(ierr);
/* Create block vector */
tmp_x[0] = f;
tmp_x[1] = h;
ierr = VecCreateNest(PETSC_COMM_WORLD,2,NULL,tmp_x,&b);
CHKERRQ(ierr);
ierr = VecAssemblyBegin(b);
CHKERRQ(ierr);
ierr = VecAssemblyEnd(b);
CHKERRQ(ierr);
ierr = VecDuplicate(b, &x);
CHKERRQ(ierr);
ierr = KSPCreate(PETSC_COMM_WORLD, &ksp);
CHKERRQ(ierr);
ierr = KSPSetOperators(ksp, A, A);
CHKERRQ(ierr);
ierr = KSPSetType(ksp, "gmres");
CHKERRQ(ierr);
ierr = KSPGetPC(ksp, &pc);
CHKERRQ(ierr);
ierr = PCSetType(pc, "none");
CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);
CHKERRQ(ierr);
ierr = KSPSolve(ksp, b, x);
CHKERRQ(ierr);
ierr = VecNestGetSubVecs(x,NULL,&_tmp_x);
CHKERRQ(ierr);
x1 = _tmp_x[0];
x2 = _tmp_x[1];
PetscPrintf(PETSC_COMM_WORLD, "x1 \n");
PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_ASCII_INFO_DETAIL);
ierr = VecView(x1, PETSC_VIEWER_STDOUT_WORLD);
CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD, "x2 \n");
PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_ASCII_INFO_DETAIL);
ierr = VecView(x2, PETSC_VIEWER_STDOUT_WORLD);
CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);
CHKERRQ(ierr);
ierr = VecDestroy(&x);
CHKERRQ(ierr);
ierr = VecDestroy(&b);
CHKERRQ(ierr);
ierr = MatDestroy(&A11);
CHKERRQ(ierr);
ierr = MatDestroy(&A12);
CHKERRQ(ierr);
ierr = MatDestroy(&A21);
CHKERRQ(ierr);
ierr = VecDestroy(&f);
CHKERRQ(ierr);
ierr = VecDestroy(&h);
CHKERRQ(ierr);
ierr = MatDestroy(&A);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* FormTrueJacobianMatrixLocal - Evaluates analytical Jacobian matrix. */
PetscErrorCode FormTrueJacobianMatrixLocal(DMDALocalInfo *info,PetscScalar *u,Mat jacpre,Mat jac,AppCtx *user)
{
PetscErrorCode ierr;
PetscInt i, Mx;
PetscInt col[3],row[1];
PetscScalar v[3];
PetscReal hx, p, duL, duR, omHL, omHR;
PetscScalar *H;
Vec localH;
PetscFunctionBegin;
ierr = DMGetLocalVector(info->da,&localH);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(info->da,user->H,INSERT_VALUES,localH); CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(info->da,user->H,INSERT_VALUES,localH); CHKERRQ(ierr);
p = 1.0 + 1.0 / user->n;
Mx = info->mx;
hx = user->L / ((PetscReal)Mx - 1.0);
ierr = DMDAVecGetArray(info->da,localH,&H);CHKERRQ(ierr);
for (i=info->xs; i<info->xs+info->xm; i++) {
row[0] = i;
if (i == 0) {
col[0] = 0;
v[0] = 1.0;
ierr = MatSetValues(jac,1,row,1,col,v,INSERT_VALUES);CHKERRQ(ierr);
} else {
if (i == 1) {
duL = u[i] - user->ug;
} else {
duL = u[i] - u[i-1];
}
omHL = GetOmega(duL, hx, p, user->epsilon) * H[i-1];
if (i == Mx-1) { /* Neumann: calving front stress boundary condition */
duR = u[Mx-2] + 2.0 * hx * user->gamma - u[Mx-1];
} else {
duR = u[i+1] - u[i];
}
omHR = GetOmega(duR, hx, p, user->epsilon) * H[i];
if (i == 1) {
col[0] = 1; col[1] = 2;
v[0] = - omHL - omHR; v[1] = omHR;
ierr = MatSetValues(jac,1,row,2,col,v,INSERT_VALUES);CHKERRQ(ierr);
} else if (i == Mx-1) {
col[0] = i-1; col[1] = i;
v[0] = omHL + omHR; v[1] = - omHL - omHR;
ierr = MatSetValues(jac,1,row,2,col,v,INSERT_VALUES);CHKERRQ(ierr);
} else {
col[0] = i-1; col[1] = i; col[2] = i+1;
v[0] = omHL; v[1] = - omHL - omHR; v[2] = omHR;
ierr = MatSetValues(jac,1,row,3,col,v,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
ierr = DMDAVecRestoreArray(info->da,localH,&H);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(info->da,&localH);CHKERRQ(ierr);
/* Assemble matrix, using the 2-step process */
ierr = MatAssemblyBegin(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Tell the matrix we will never add a new nonzero location to the
matrix. If we do, it will generate an error. */
ierr = MatSetOption(jac,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
if (user->J != PETSC_NULL) {
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) user->J,"Jacobian_matrix"); CHKERRQ(ierr);
ierr = MatView(user->J, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
SNES snes; /* nonlinear solver */
DM dm; /* problem definition */
Vec u,r; /* solution, residual vectors */
Mat A,J; /* Jacobian matrix */
MatNullSpace nullSpace; /* May be necessary for pressure */
AppCtx user; /* user-defined work context */
JacActionCtx userJ; /* context for Jacobian MF action */
PetscInt its; /* iterations for convergence */
PetscReal error = 0.0; /* L_2 error in the solution */
PetscInt numComponents = 0, f;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr);
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr);
ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr);
ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
ierr = SetupElement(dm, &user);CHKERRQ(ierr);
for (f = 0; f < NUM_FIELDS; ++f) {
PetscInt numComp;
ierr = PetscFEGetNumComponents(user.fe[f], &numComp);CHKERRQ(ierr);
numComponents += numComp;
}
ierr = PetscMalloc(NUM_FIELDS * sizeof(void (*)(const PetscReal[], PetscScalar *)), &user.exactFuncs);CHKERRQ(ierr);
user.fem.bcFuncs = (void (**)(const PetscReal[], PetscScalar *)) user.exactFuncs;
ierr = SetupExactSolution(dm, &user);CHKERRQ(ierr);
ierr = SetupSection(dm, &user);CHKERRQ(ierr);
ierr = DMPlexCreateClosureIndex(dm, NULL);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
ierr = DMSetMatType(dm,MATAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr);
if (user.jacobianMF) {
PetscInt M, m, N, n;
ierr = MatGetSize(J, &M, &N);CHKERRQ(ierr);
ierr = MatGetLocalSize(J, &m, &n);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr);
ierr = MatSetSizes(A, m, n, M, N);CHKERRQ(ierr);
ierr = MatSetType(A, MATSHELL);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))FormJacobianAction);CHKERRQ(ierr);
userJ.dm = dm;
userJ.J = J;
userJ.user = &user;
ierr = DMCreateLocalVector(dm, &userJ.u);CHKERRQ(ierr);
ierr = DMPlexProjectFunctionLocal(dm, user.fe, user.exactFuncs, INSERT_BC_VALUES, userJ.u);CHKERRQ(ierr);
ierr = MatShellSetContext(A, &userJ);CHKERRQ(ierr);
} else {
A = J;
}
ierr = CreatePressureNullSpace(dm, &user, &nullSpace);CHKERRQ(ierr);
ierr = MatSetNullSpace(J, nullSpace);CHKERRQ(ierr);
if (A != J) {
ierr = MatSetNullSpace(A, nullSpace);CHKERRQ(ierr);
}
ierr = DMSNESSetFunctionLocal(dm, (PetscErrorCode (*)(DM,Vec,Vec,void*))DMPlexComputeResidualFEM,&user);CHKERRQ(ierr);
ierr = DMSNESSetJacobianLocal(dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,MatStructure*,void*))DMPlexComputeJacobianFEM,&user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, A, J, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMPlexProjectFunction(dm, user.fe, user.exactFuncs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.runType == RUN_FULL) {
ierr = DMPlexProjectFunction(dm, user.fe, user.initialGuess, INSERT_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.debug) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, u, &error);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %.3g\n", error);CHKERRQ(ierr);
if (user.showSolution) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Solution\n");CHKERRQ(ierr);
ierr = VecChop(u, 3.0e-9);CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
} else {
PetscReal res = 0.0;
/* Check discretization error */
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, u, &error);CHKERRQ(ierr);
if (error >= 1.0e-11) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n", error);CHKERRQ(ierr);
}
/* Check residual */
ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr);
/* Check Jacobian */
{
Vec b;
MatStructure flag;
PetscBool isNull;
ierr = SNESComputeJacobian(snes, u, &A, &A, &flag);CHKERRQ(ierr);
ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr);
if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid.");
ierr = VecDuplicate(u, &b);CHKERRQ(ierr);
ierr = VecSet(r, 0.0);CHKERRQ(ierr);
ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr);
ierr = MatMult(A, u, r);CHKERRQ(ierr);
ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr);
}
}
if (user.runType == RUN_FULL) {
PetscViewer viewer;
Vec uLocal;
const char *name;
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "ex62_sol.vtk");CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &uLocal);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) u, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) uLocal, name);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = VecView(uLocal, viewer);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &uLocal);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr);
ierr = DestroyElement(&user);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
if (user.jacobianMF) {
ierr = VecDestroy(&userJ.u);CHKERRQ(ierr);
}
if (A != J) {
ierr = MatDestroy(&A);CHKERRQ(ierr);
}
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
Mat mat,B;
PetscErrorCode ierr;
PetscInt i,j;
PetscScalar v;
IS isrow,iscol;
PetscViewer viewer;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
/* ------- Assemble matrix, --------- */
ierr = MatCreate(PETSC_COMM_WORLD,&mat);CHKERRQ(ierr);
ierr = MatSetSizes(mat,PETSC_DECIDE,PETSC_DECIDE,4,4);CHKERRQ(ierr);
ierr = MatSetFromOptions(mat);CHKERRQ(ierr);
ierr = MatSetUp(mat);CHKERRQ(ierr);
/* set anti-diagonal of matrix */
v = 1.0;
i = 0; j = 3;
ierr = MatSetValues(mat,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
v = 2.0;
i = 1; j = 2;
ierr = MatSetValues(mat,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
v = 3.0;
i = 2; j = 1;
ierr = MatSetValues(mat,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
v = 4.0;
i = 3; j = 0;
ierr = MatSetValues(mat,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&viewer);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer,PETSC_VIEWER_ASCII_DENSE);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Original matrix\n");CHKERRQ(ierr);
ierr = MatView(mat,viewer);CHKERRQ(ierr);
ierr = MatGetOrdering(mat,MATORDERINGNATURAL,&isrow,&iscol);CHKERRQ(ierr);
ierr = MatPermute(mat,isrow,iscol,&B);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Original matrix permuted by identity\n");CHKERRQ(ierr);
ierr = MatView(B,viewer);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatReorderForNonzeroDiagonal(mat,1.e-8,isrow,iscol);CHKERRQ(ierr);
ierr = MatPermute(mat,isrow,iscol,&B);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Original matrix permuted by identity + NonzeroDiagonal()\n");CHKERRQ(ierr);
ierr = MatView(B,viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Row permutation\n");CHKERRQ(ierr);
ierr = ISView(isrow,viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Column permutation\n");CHKERRQ(ierr);
ierr = ISView(iscol,viewer);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = ISDestroy(&iscol);CHKERRQ(ierr);
ierr = MatGetOrdering(mat,MATORDERINGND,&isrow,&iscol);CHKERRQ(ierr);
ierr = MatPermute(mat,isrow,iscol,&B);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Original matrix permuted by ND\n");CHKERRQ(ierr);
ierr = MatView(B,viewer);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"ND row permutation\n");CHKERRQ(ierr);
ierr = ISView(isrow,viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"ND column permutation\n");CHKERRQ(ierr);
ierr = ISView(iscol,viewer);CHKERRQ(ierr);
ierr = MatReorderForNonzeroDiagonal(mat,1.e-8,isrow,iscol);CHKERRQ(ierr);
ierr = MatPermute(mat,isrow,iscol,&B);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Original matrix permuted by ND + NonzeroDiagonal()\n");CHKERRQ(ierr);
ierr = MatView(B,viewer);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"ND + NonzeroDiagonal() row permutation\n");CHKERRQ(ierr);
ierr = ISView(isrow,viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"ND + NonzeroDiagonal() column permutation\n");CHKERRQ(ierr);
ierr = ISView(iscol,viewer);CHKERRQ(ierr);
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = ISDestroy(&iscol);CHKERRQ(ierr);
ierr = MatGetOrdering(mat,MATORDERINGRCM,&isrow,&iscol);CHKERRQ(ierr);
ierr = MatPermute(mat,isrow,iscol,&B);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Original matrix permuted by RCM\n");CHKERRQ(ierr);
ierr = MatView(B,viewer);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"RCM row permutation\n");CHKERRQ(ierr);
ierr = ISView(isrow,viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"RCM column permutation\n");CHKERRQ(ierr);
ierr = ISView(iscol,viewer);CHKERRQ(ierr);
ierr = MatReorderForNonzeroDiagonal(mat,1.e-8,isrow,iscol);CHKERRQ(ierr);
ierr = MatPermute(mat,isrow,iscol,&B);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Original matrix permuted by RCM + NonzeroDiagonal()\n");CHKERRQ(ierr);
ierr = MatView(B,viewer);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"RCM + NonzeroDiagonal() row permutation\n");CHKERRQ(ierr);
ierr = ISView(isrow,viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"RCM + NonzeroDiagonal() column permutation\n");CHKERRQ(ierr);
ierr = ISView(iscol,viewer);CHKERRQ(ierr);
ierr = MatLUFactor(mat,isrow,iscol,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Factored matrix permuted by RCM + NonzeroDiagonal()\n");CHKERRQ(ierr);
ierr = MatView(mat,viewer);CHKERRQ(ierr);
/* Free data structures */
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = ISDestroy(&iscol);CHKERRQ(ierr);
ierr = MatDestroy(&mat);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode JacMatMultCompare(SNES snes,Vec x,Vec p,double hopt)
{
Vec yy1, yy2; /* work vectors */
PetscViewer view2; /* viewer */
Mat J; /* analytic Jacobian (set as preconditioner matrix) */
Mat Jmf; /* matrix-free Jacobian (set as true system matrix) */
double h; /* differencing parameter */
Vec f;
PetscScalar alpha;
PetscReal yy1n,yy2n,enorm;
PetscErrorCode ierr;
PetscInt i;
PetscBool printv = PETSC_FALSE;
char filename[32];
MPI_Comm comm;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)snes,&comm);CHKERRQ(ierr);
/* Compute function and analytic Jacobian at x */
ierr = SNESGetJacobian(snes,&Jmf,&J,NULL,NULL);CHKERRQ(ierr);
ierr = SNESComputeJacobian(snes,x,Jmf,J);CHKERRQ(ierr);
ierr = SNESGetFunction(snes,&f,NULL,NULL);CHKERRQ(ierr);
ierr = SNESComputeFunction(snes,x,f);CHKERRQ(ierr);
/* Duplicate work vectors */
ierr = VecDuplicate(x,&yy2);CHKERRQ(ierr);
ierr = VecDuplicate(x,&yy1);CHKERRQ(ierr);
/* Compute true matrix-vector product */
ierr = MatMult(J,p,yy1);CHKERRQ(ierr);
ierr = VecNorm(yy1,NORM_2,&yy1n);CHKERRQ(ierr);
/* View product vector if desired */
ierr = PetscOptionsGetBool(NULL,"-print_vecs",&printv,NULL);CHKERRQ(ierr);
if (printv) {
ierr = PetscViewerASCIIOpen(comm,"y1.out",&view2);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(view2,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr);
ierr = VecView(yy1,view2);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view2);CHKERRQ(ierr);
}
/* Test Jacobian-vector product computation */
alpha = -1.0;
h = 0.01 * hopt;
for (i=0; i<5; i++) {
/* Set differencing parameter for matrix-free multiplication */
ierr = SNESDefaultMatrixFreeSetParameters2(Jmf,PETSC_DEFAULT,PETSC_DEFAULT,h);CHKERRQ(ierr);
/* Compute matrix-vector product via differencing approximation */
ierr = MatMult(Jmf,p,yy2);CHKERRQ(ierr);
ierr = VecNorm(yy2,NORM_2,&yy2n);CHKERRQ(ierr);
/* View product vector if desired */
if (printv) {
sprintf(filename,"y2.%d.out",(int)i);
ierr = PetscViewerASCIIOpen(comm,filename,&view2);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(view2,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr);
ierr = VecView(yy2,view2);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view2);CHKERRQ(ierr);
}
/* Compute relative error */
ierr = VecAXPY(yy2,alpha,yy1);CHKERRQ(ierr);
ierr = VecNorm(yy2,NORM_2,&enorm);CHKERRQ(ierr);
enorm = enorm/yy1n;
ierr = PetscFPrintf(comm,stdout,"h = %g: relative error = %g\n",(double)h,(double)enorm);CHKERRQ(ierr);
h *= 10.0;
}
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat C,A;
PetscInt i,j,m = 3,n = 2,rstart,rend;
PetscMPIInt size,rank;
PetscErrorCode ierr;
PetscScalar v;
IS isrow,iscol;
PetscBool flg;
char type[256];
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
n = 2*size;
ierr = PetscStrcpy(type,MATSAME);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-mat_type",type,256,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscStrcmp(type,MATMPIDENSE,&flg);CHKERRQ(ierr);
if (flg) {
ierr = MatCreateDense(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE, m*n,m*n,PETSC_NULL,&C);CHKERRQ(ierr);
} else {
ierr = MatCreateAIJ(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE, m*n,m*n,PETSC_DECIDE,PETSC_NULL,PETSC_DECIDE,PETSC_NULL,&C);CHKERRQ(ierr);
}
/*
This is JUST to generate a nice test matrix, all processors fill up
the entire matrix. This is not something one would ever do in practice.
*/
for (i=0; i<m*n; i++) {
for (j=0; j<m*n; j++) {
v = i + j + 1;
ierr = MatSetValues(C,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr);
ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/*
Generate a new matrix consisting of every second row and column of
the original matrix
*/
ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr);
/* Create parallel IS with the rows we want on THIS processor */
ierr = ISCreateStride(PETSC_COMM_WORLD,(rend-rstart)/2,rstart,2,&isrow);CHKERRQ(ierr);
/* Create parallel IS with the rows we want on THIS processor (same as rows for now) */
ierr = ISCreateStride(PETSC_COMM_WORLD,(rend-rstart)/2,rstart,2,&iscol);CHKERRQ(ierr);
ierr = MatGetSubMatrix(C,isrow,iscol,MAT_INITIAL_MATRIX,&A);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatGetSubMatrix(C,isrow,iscol,MAT_REUSE_MATRIX,&A);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = ISDestroy(&iscol);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
const struct {PetscInt i,j; PetscScalar v;} entries[] = {{0,3,1.},{1,2,2.},{2,1,3.},{2,4,4.},{3,0,5.},{3,3,6.},{4,1,7.},{4,4,8.}};
const PetscInt ixrow[5] = {4,2,1,3,0},ixcol[5] = {3,2,1,4,0};
Mat A,B;
PetscErrorCode ierr;
PetscInt i,rstart,rend,cstart,cend;
IS isrow,iscol;
PetscViewer viewer,sviewer;
PetscBool view_sparse;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
/* ------- Assemble matrix, --------- */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,5,5);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
ierr = MatGetOwnershipRangeColumn(A,&cstart,&cend);CHKERRQ(ierr);
for (i=0; i<(PetscInt)(sizeof(entries)/sizeof(entries[0])); i++) {
ierr = MatSetValue(A,entries[i].i,entries[i].j,entries[i].v,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* ------ Prepare index sets ------ */
ierr = ISCreateGeneral(PETSC_COMM_WORLD,rend-rstart,ixrow+rstart,PETSC_USE_POINTER,&isrow);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,5,ixcol,PETSC_USE_POINTER,&iscol);CHKERRQ(ierr);
ierr = ISSetPermutation(isrow);CHKERRQ(ierr);
ierr = ISSetPermutation(iscol);CHKERRQ(ierr);
ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&viewer);CHKERRQ(ierr);
view_sparse = PETSC_FALSE;
ierr = PetscOptionsGetBool(PETSC_NULL, "-view_sparse", &view_sparse, PETSC_NULL);CHKERRQ(ierr);
if (!view_sparse) {
ierr = PetscViewerSetFormat(viewer,PETSC_VIEWER_ASCII_DENSE);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer,"Original matrix\n");CHKERRQ(ierr);
ierr = MatView(A,viewer);CHKERRQ(ierr);
ierr = MatPermute(A,isrow,iscol,&B);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Permuted matrix\n");CHKERRQ(ierr);
ierr = MatView(B,viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Row permutation\n");CHKERRQ(ierr);
ierr = ISView(isrow,viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Column permutation\n");CHKERRQ(ierr);
ierr = PetscViewerGetSingleton(viewer,&sviewer);CHKERRQ(ierr);
ierr = ISView(iscol,sviewer);CHKERRQ(ierr);
ierr = PetscViewerRestoreSingleton(viewer,&sviewer);CHKERRQ(ierr);
/* Free data structures */
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = ISDestroy(&iscol);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat A;
PetscInt i,j,m = 3,n = 2,rstart,rend;
PetscErrorCode ierr;
PetscScalar v,*array;
PetscViewer view;
PetscInitialize(&argc,&args,(char*)0,help);
/*
Create a parallel dense matrix shared by all processors
*/
ierr = MatCreateDense(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,m,n,NULL,&A);CHKERRQ(ierr);
/*
Set values into the matrix
*/
for (i=0; i<m; i++) {
for (j=0; j<n; j++) {
v = 9.0/(i+j+1); ierr = MatSetValues(A,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/*
Print the matrix to the screen
*/
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/*
Print the local portion of the matrix to the screen
*/
ierr = MatDenseGetArray(A,&array);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
for (j=0; j<n; j++) {
PetscSynchronizedPrintf(PETSC_COMM_WORLD,"%6.4e ",(double)PetscRealPart(array[j*(rend-rstart)+i-rstart]));
}
PetscSynchronizedPrintf(PETSC_COMM_WORLD,"\n");
}
PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
ierr = MatDenseRestoreArray(A,&array);CHKERRQ(ierr);
/*
Store the binary matrix to a file
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, "matrix.dat", FILE_MODE_WRITE, &view);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(view,PETSC_VIEWER_NATIVE);CHKERRQ(ierr);
ierr = MatView(A,view);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
/*
Now reload the matrix and view it
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"matrix.dat",FILE_MODE_READ,&view);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATMPIDENSE);CHKERRQ(ierr);
ierr = MatLoad(A,view);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc, char **argv)
{
SNES snes; /* nonlinear solver */
Vec u,r; /* solution, residual vectors */
Mat A,J; /* Jacobian matrix */
MatNullSpace nullSpace; /* May be necessary for pressure */
AppCtx user; /* user-defined work context */
JacActionCtx userJ; /* context for Jacobian MF action */
PetscInt its; /* iterations for convergence */
PetscReal error = 0.0; /* L_2 error in the solution */
const PetscInt numComponents = NUM_BASIS_COMPONENTS_TOTAL;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr);
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr);
ierr = CreateMesh(PETSC_COMM_WORLD, &user, &user.dm);CHKERRQ(ierr);
ierr = SNESSetDM(snes, user.dm);CHKERRQ(ierr);
ierr = SetupExactSolution(user.dm, &user);CHKERRQ(ierr);
ierr = SetupQuadrature(&user);CHKERRQ(ierr);
ierr = SetupSection(user.dm, &user);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user.dm, &u);CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
ierr = DMCreateMatrix(user.dm, MATAIJ, &J);CHKERRQ(ierr);
if (user.jacobianMF) {
PetscInt M, m, N, n;
ierr = MatGetSize(J, &M, &N);CHKERRQ(ierr);
ierr = MatGetLocalSize(J, &m, &n);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr);
ierr = MatSetSizes(A, m, n, M, N);CHKERRQ(ierr);
ierr = MatSetType(A, MATSHELL);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))FormJacobianAction);CHKERRQ(ierr);
userJ.dm = user.dm;
userJ.J = J;
userJ.user = &user;
ierr = DMCreateLocalVector(user.dm, &userJ.u);CHKERRQ(ierr);
ierr = DMPlexProjectFunctionLocal(user.dm, numComponents, user.exactFuncs, INSERT_BC_VALUES, userJ.u);CHKERRQ(ierr);
ierr = MatShellSetContext(A, &userJ);CHKERRQ(ierr);
} else {
A = J;
}
ierr = CreatePressureNullSpace(user.dm, &user, &nullSpace);CHKERRQ(ierr);
ierr = MatSetNullSpace(J, nullSpace);CHKERRQ(ierr);
if (A != J) {
ierr = MatSetNullSpace(A, nullSpace);CHKERRQ(ierr);
}
ierr = DMSNESSetFunctionLocal(user.dm, (PetscErrorCode (*)(DM,Vec,Vec,void*))DMPlexComputeResidualFEM,&user);CHKERRQ(ierr);
ierr = DMSNESSetJacobianLocal(user.dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,MatStructure*,void*))DMPlexComputeJacobianFEM,&user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, A, J, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMPlexProjectFunction(user.dm, numComponents, user.exactFuncs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(user.dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.runType == RUN_FULL) {
PetscScalar (*initialGuess[numComponents])(const PetscReal x[]);
PetscInt c;
for (c = 0; c < numComponents; ++c) initialGuess[c] = zero;
ierr = DMPlexProjectFunction(user.dm, numComponents, initialGuess, INSERT_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(user.dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.debug) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(user.dm, user.fem.quad, user.exactFuncs, u, &error);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %.3g\n", error);CHKERRQ(ierr);
if (user.showSolution) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Solution\n");CHKERRQ(ierr);
ierr = VecChop(u, 3.0e-9);CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
} else {
PetscReal res = 0.0;
/* Check discretization error */
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(user.dm, user.fem.quad, user.exactFuncs, u, &error);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);
/* Check residual */
ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr);
/* Check Jacobian */
{
Vec b;
MatStructure flag;
PetscBool isNull;
ierr = SNESComputeJacobian(snes, u, &A, &A, &flag);CHKERRQ(ierr);
ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr);
if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid.");
ierr = VecDuplicate(u, &b);CHKERRQ(ierr);
ierr = VecSet(r, 0.0);CHKERRQ(ierr);
ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr);
ierr = MatMult(A, u, r);CHKERRQ(ierr);
ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr);
}
}
if (user.runType == RUN_FULL) {
PetscViewer viewer;
Vec uLocal;
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "ex62_sol.vtk");CHKERRQ(ierr);
ierr = DMGetLocalVector(user.dm, &uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(user.dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user.dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject) user.dm);CHKERRQ(ierr); /* Needed because viewer destroys the DM */
ierr = PetscObjectReference((PetscObject) uLocal);CHKERRQ(ierr); /* Needed because viewer destroys the Vec */
ierr = PetscViewerVTKAddField(viewer, (PetscObject) user.dm, DMPlexVTKWriteAll, PETSC_VTK_POINT_FIELD, (PetscObject) uLocal);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(user.dm, &uLocal);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = DestroyQuadrature(&user);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
if (user.jacobianMF) {
ierr = VecDestroy(&userJ.u);CHKERRQ(ierr);
}
if (A != J) {
ierr = MatDestroy(&A);CHKERRQ(ierr);
}
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&user.dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
/*
GetElasticityMatrix - Forms 3D linear elasticity matrix.
*/
PetscErrorCode GetElasticityMatrix(PetscInt m,Mat *newmat)
{
PetscInt i,j,k,i1,i2,j_1,j2,k1,k2,h1,h2,shiftx,shifty,shiftz;
PetscInt ict,nz,base,r1,r2,N,*rowkeep,nstart;
PetscErrorCode ierr;
IS iskeep;
PetscReal **K,norm;
Mat mat,submat = 0,*submatb;
MatType type = MATSEQBAIJ;
m /= 2; /* This is done just to be consistent with the old example */
N = 3*(2*m+1)*(2*m+1)*(2*m+1);
ierr = PetscPrintf(PETSC_COMM_SELF,"m = %D, N=%D\n",m,N);CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,80,PETSC_NULL,&mat);CHKERRQ(ierr);
/* Form stiffness for element */
ierr = PetscMalloc(81*sizeof(PetscReal *),&K);CHKERRQ(ierr);
for (i=0; i<81; i++) {
ierr = PetscMalloc(81*sizeof(PetscReal),&K[i]);CHKERRQ(ierr);
}
ierr = Elastic20Stiff(K);CHKERRQ(ierr);
/* Loop over elements and add contribution to stiffness */
shiftx = 3; shifty = 3*(2*m+1); shiftz = 3*(2*m+1)*(2*m+1);
for (k=0; k<m; k++) {
for (j=0; j<m; j++) {
for (i=0; i<m; i++) {
h1 = 0;
base = 2*k*shiftz + 2*j*shifty + 2*i*shiftx;
for (k1=0; k1<3; k1++) {
for (j_1=0; j_1<3; j_1++) {
for (i1=0; i1<3; i1++) {
h2 = 0;
r1 = base + i1*shiftx + j_1*shifty + k1*shiftz;
for (k2=0; k2<3; k2++) {
for (j2=0; j2<3; j2++) {
for (i2=0; i2<3; i2++) {
r2 = base + i2*shiftx + j2*shifty + k2*shiftz;
ierr = AddElement(mat,r1,r2,K,h1,h2);CHKERRQ(ierr);
h2 += 3;
}
}
}
h1 += 3;
}
}
}
}
}
}
for (i=0; i<81; i++) {
ierr = PetscFree(K[i]);CHKERRQ(ierr);
}
ierr = PetscFree(K);CHKERRQ(ierr);
ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Exclude any superfluous rows and columns */
nstart = 3*(2*m+1)*(2*m+1);
ict = 0;
ierr = PetscMalloc((N-nstart)*sizeof(PetscInt),&rowkeep);CHKERRQ(ierr);
for (i=nstart; i<N; i++) {
ierr = MatGetRow(mat,i,&nz,0,0);CHKERRQ(ierr);
if (nz) rowkeep[ict++] = i;
ierr = MatRestoreRow(mat,i,&nz,0,0);CHKERRQ(ierr);
}
ierr = ISCreateGeneral(PETSC_COMM_SELF,ict,rowkeep,PETSC_COPY_VALUES,&iskeep);CHKERRQ(ierr);
ierr = MatGetSubMatrices(mat,1,&iskeep,&iskeep,MAT_INITIAL_MATRIX,&submatb);CHKERRQ(ierr);
submat = *submatb;
ierr = PetscFree(submatb);CHKERRQ(ierr);
ierr = PetscFree(rowkeep);CHKERRQ(ierr);
ierr = ISDestroy(&iskeep);CHKERRQ(ierr);
ierr = MatDestroy(&mat);CHKERRQ(ierr);
/* Convert storage formats -- just to demonstrate conversion to various
formats (in particular, block diagonal storage). This is NOT the
recommended means to solve such a problem. */
ierr = MatConvert(submat,type,MAT_INITIAL_MATRIX,newmat);CHKERRQ(ierr);
ierr = MatDestroy(&submat);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr);
ierr = MatView(*newmat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatNorm(*newmat,NORM_1,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"matrix 1 norm = %G\n",norm);CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
Mat mat,tmat = 0;
PetscInt m = 7,n,i,j,rstart,rend,rect = 0;
PetscErrorCode ierr;
PetscMPIInt size,rank;
PetscBool flg;
PetscScalar v, alpha;
PetscReal normf,normi,norm1;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
n = m;
ierr = PetscOptionsHasName(NULL,"-rectA",&flg);CHKERRQ(ierr);
if (flg) {n += 2; rect = 1;}
ierr = PetscOptionsHasName(NULL,"-rectB",&flg);CHKERRQ(ierr);
if (flg) {n -= 2; rect = 1;}
/* ------- Assemble matrix, test MatValid() --------- */
ierr = MatCreate(PETSC_COMM_WORLD,&mat);CHKERRQ(ierr);
ierr = MatSetSizes(mat,PETSC_DECIDE,PETSC_DECIDE,m,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(mat);CHKERRQ(ierr);
ierr = MatSetUp(mat);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(mat,&rstart,&rend);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
for (j=0; j<n; j++) {
v = 10.0*i+j;
ierr = MatSetValues(mat,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* ----------------- Test MatNorm() ----------------- */
ierr = MatNorm(mat,NORM_FROBENIUS,&normf);CHKERRQ(ierr);
ierr = MatNorm(mat,NORM_1,&norm1);CHKERRQ(ierr);
ierr = MatNorm(mat,NORM_INFINITY,&normi);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"original A: Frobenious norm = %G, one norm = %G, infinity norm = %G\n",
normf,norm1,normi);CHKERRQ(ierr);
ierr = MatView(mat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* --------------- Test MatTranspose() -------------- */
ierr = PetscOptionsHasName(NULL,"-in_place",&flg);CHKERRQ(ierr);
if (!rect && flg) {
ierr = MatTranspose(mat,MAT_REUSE_MATRIX,&mat);CHKERRQ(ierr); /* in-place transpose */
tmat = mat; mat = 0;
} else { /* out-of-place transpose */
ierr = MatTranspose(mat,MAT_INITIAL_MATRIX,&tmat);CHKERRQ(ierr);
}
/* ----------------- Test MatNorm() ----------------- */
/* Print info about transpose matrix */
ierr = MatNorm(tmat,NORM_FROBENIUS,&normf);CHKERRQ(ierr);
ierr = MatNorm(tmat,NORM_1,&norm1);CHKERRQ(ierr);
ierr = MatNorm(tmat,NORM_INFINITY,&normi);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"B = A^T: Frobenious norm = %G, one norm = %G, infinity norm = %G\n",
normf,norm1,normi);CHKERRQ(ierr);
ierr = MatView(tmat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* ----------------- Test MatAXPY(), MatAYPX() ----------------- */
if (mat && !rect) {
alpha = 1.0;
ierr = PetscOptionsGetScalar(NULL,"-alpha",&alpha,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"MatAXPY: B = B + alpha * A\n");CHKERRQ(ierr);
ierr = MatAXPY(tmat,alpha,mat,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatView(tmat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"MatAYPX: B = alpha*B + A\n");CHKERRQ(ierr);
ierr = MatAYPX(tmat,alpha,mat,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatView(tmat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
{
Mat C;
alpha = 1.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"MatAXPY: C = C + alpha * A, C=A, SAME_NONZERO_PATTERN\n");CHKERRQ(ierr);
ierr = MatDuplicate(mat,MAT_COPY_VALUES,&C);CHKERRQ(ierr);
ierr = MatAXPY(C,alpha,mat,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
}
{
Mat matB;
/* get matB that has nonzeros of mat in all even numbers of row and col */
ierr = MatCreate(PETSC_COMM_WORLD,&matB);CHKERRQ(ierr);
ierr = MatSetSizes(matB,PETSC_DECIDE,PETSC_DECIDE,m,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(matB);CHKERRQ(ierr);
ierr = MatSetUp(matB);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(matB,&rstart,&rend);CHKERRQ(ierr);
if (rstart % 2 != 0) rstart++;
for (i=rstart; i<rend; i += 2) {
for (j=0; j<n; j += 2) {
v = 10.0*i+j;
ierr = MatSetValues(matB,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(matB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(matB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD," A: original matrix:\n");
ierr = MatView(mat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD," B(a subset of A):\n");
ierr = MatView(matB,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"MatAXPY: B = B + alpha * A, SUBSET_NONZERO_PATTERN\n");CHKERRQ(ierr);
ierr = MatAXPY(mat,alpha,matB,SUBSET_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatView(mat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&matB);CHKERRQ(ierr);
}
/* Free data structures */
if (mat) {ierr = MatDestroy(&mat);CHKERRQ(ierr);}
if (tmat) {ierr = MatDestroy(&tmat);CHKERRQ(ierr);}
ierr = PetscFinalize();
return 0;
}
PetscErrorCode SetupJacobian(DM dm, Vec X, Mat jac, Mat B, void *ctx)
{
User user = (User) ctx;
Physics phys = user->model->physics;
PetscSection section, globalSection;
PetscInt cStart, cEnd, c;
// PetscInt numCells;
PetscInt dof = phys->dof;
PetscErrorCode ierr;
Vec inLocal;
PetscFunctionBegin;
PetscPrintf(PETSC_COMM_WORLD, "dof = %d\n", dof);
ierr = DMGetLocalVector(user->dm, &inLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(user->dm, X, INSERT_VALUES, inLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user->dm, X, INSERT_VALUES, inLocal);CHKERRQ(ierr);
ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);
ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, NULL);CHKERRQ(ierr);
cEnd = user->cEndInterior;
//numCells = cEnd - cStart;
{
PetscInt NumOfIndices;
PetscInt indices[dof];
PetscScalar *values;
for (c = cStart; c < cEnd; ++c) {
ierr = DMPlexGetIndex(dm, section, globalSection, c, &NumOfIndices, indices);CHKERRQ(ierr);
ierr = PetscMalloc1(NumOfIndices*NumOfIndices, &values);CHKERRQ(ierr);
ierr = PetscMemzero(values, NumOfIndices*NumOfIndices* sizeof(PetscScalar));CHKERRQ(ierr);
if (user->second_order){
ierr = ComputeJacobian_LS(dm, inLocal, c, values, user);CHKERRQ(ierr);
}else{
ierr = ComputeJacobian_Upwind(dm, inLocal, c, values, user);CHKERRQ(ierr);
}
ierr = MatSetValues(jac, NumOfIndices, indices, NumOfIndices, indices, values, INSERT_VALUES);
ierr = PetscFree(values);CHKERRQ(ierr);
}
}
ierr = DMLocalToGlobalBegin(user->dm, inLocal, INSERT_VALUES, X);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(user->dm, inLocal, INSERT_VALUES, X);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(user->dm, &inLocal);CHKERRQ(ierr);
ierr = MatAssemblyBegin(jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
{
PetscViewer viewer;
char filename[256];
sprintf(filename,"matJac.m");
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,filename,
&viewer);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_DEFAULT);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "\n% -----------------------------\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "% Matrix Jacobian: \n% -------------------------\n");CHKERRQ(ierr);
ierr = MatView(jac, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat C,A;
PetscInt i, n = 10,midx[3],bs=1;
PetscErrorCode ierr;
PetscScalar v[3];
PetscBool flg,isAIJ;
MatType type;
PetscMPIInt size;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-mat_block_size",&bs,PETSC_NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetType(C,MATAIJ);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatGetType(C,&type);CHKERRQ(ierr);
if (size == 1){
ierr = PetscObjectTypeCompare((PetscObject)C,MATSEQAIJ,&isAIJ);CHKERRQ(ierr);
} else {
ierr = PetscObjectTypeCompare((PetscObject)C,MATMPIAIJ,&isAIJ);CHKERRQ(ierr);
}
ierr = MatSeqAIJSetPreallocation(C,3,PETSC_NULL);
ierr = MatMPIAIJSetPreallocation(C,3,PETSC_NULL,3,PETSC_NULL);CHKERRQ(ierr);
ierr = MatSeqBAIJSetPreallocation(C,bs,3,PETSC_NULL);
ierr = MatMPIBAIJSetPreallocation(C,bs,3,PETSC_NULL,3,PETSC_NULL);CHKERRQ(ierr);
v[0] = -1.; v[1] = 2.; v[2] = -1.;
for (i=1; i<n-1; i++){
midx[2] = i-1; midx[1] = i; midx[0] = i+1;
ierr = MatSetValues(C,1,&i,3,midx,v,INSERT_VALUES);CHKERRQ(ierr);
}
i = 0; midx[0] = 0; midx[1] = 1;
v[0] = 2.0; v[1] = -1.;
ierr = MatSetValues(C,1,&i,2,midx,v,INSERT_VALUES);CHKERRQ(ierr);
i = n-1; midx[0] = n-2; midx[1] = n-1;
v[0] = -1.0; v[1] = 2.;
ierr = MatSetValues(C,1,&i,2,midx,v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* test matrices with different nonzero patterns - Note: A is created with different nonzero pattern of C! */
ierr = MatCopy(C,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatEqual(A,C,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,1,"MatCopy(C,A,DIFFERENT_NONZERO_PATTERN): Matrices are NOT equal");
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"A is obtained with MatCopy(,,DIFFERENT_NONZERO_PATTERN):\n");CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
/* test matrices with same nonzero pattern */
ierr = MatDuplicate(C,MAT_DO_NOT_COPY_VALUES,&A);CHKERRQ(ierr);
ierr = MatCopy(C,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatEqual(A,C,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,1,"MatCopy(C,A,SAME_NONZERO_PATTERN): Matrices are NOT equal");
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nA is obtained with MatCopy(,,SAME_NONZERO_PATTERN):\n");CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"A:\n");CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* test MatStore/RetrieveValues() */
if (isAIJ){
ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);CHKERRQ(ierr);
ierr = MatStoreValues(A);CHKERRQ(ierr);
ierr = MatZeroEntries(A);CHKERRQ(ierr);
ierr = MatRetrieveValues(A);CHKERRQ(ierr);
}
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt time_steps=100,iout,NOUT=1;
PetscMPIInt size;
Vec global;
PetscReal dt,ftime,ftime_original;
TS ts;
PetscViewer viewfile;
Mat J = 0;
Vec x;
Data data;
PetscInt mn;
PetscBool flg;
MatColoring mc;
ISColoring iscoloring;
MatFDColoring matfdcoloring = 0;
PetscBool fd_jacobian_coloring = PETSC_FALSE;
SNES snes;
KSP ksp;
PC pc;
PetscViewer viewer;
char pcinfo[120],tsinfo[120];
TSType tstype;
PetscBool sundials;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
/* set data */
data.m = 9;
data.n = 9;
data.a = 1.0;
data.epsilon = 0.1;
data.dx = 1.0/(data.m+1.0);
data.dy = 1.0/(data.n+1.0);
mn = (data.m)*(data.n);
ierr = PetscOptionsGetInt(NULL,"-time",&time_steps,NULL);CHKERRQ(ierr);
/* set initial conditions */
ierr = VecCreate(PETSC_COMM_WORLD,&global);CHKERRQ(ierr);
ierr = VecSetSizes(global,PETSC_DECIDE,mn);CHKERRQ(ierr);
ierr = VecSetFromOptions(global);CHKERRQ(ierr);
ierr = Initial(global,&data);CHKERRQ(ierr);
ierr = VecDuplicate(global,&x);CHKERRQ(ierr);
/* create timestep context */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,Monitor,&data,NULL);CHKERRQ(ierr);
#if defined(PETSC_HAVE_SUNDIALS)
ierr = TSSetType(ts,TSSUNDIALS);CHKERRQ(ierr);
#else
ierr = TSSetType(ts,TSEULER);CHKERRQ(ierr);
#endif
dt = 0.1;
ftime_original = data.tfinal = 1.0;
ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);
ierr = TSSetDuration(ts,time_steps,ftime_original);CHKERRQ(ierr);
ierr = TSSetSolution(ts,global);CHKERRQ(ierr);
/* set user provided RHSFunction and RHSJacobian */
ierr = TSSetRHSFunction(ts,NULL,RHSFunction,&data);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,mn,mn);CHKERRQ(ierr);
ierr = MatSetFromOptions(J);CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(J,5,NULL);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(J,5,NULL,5,NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-ts_fd",&flg);CHKERRQ(ierr);
if (!flg) {
ierr = TSSetRHSJacobian(ts,J,J,RHSJacobian,&data);CHKERRQ(ierr);
} else {
ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-fd_color",&fd_jacobian_coloring);CHKERRQ(ierr);
if (fd_jacobian_coloring) { /* Use finite differences with coloring */
/* Get data structure of J */
PetscBool pc_diagonal;
ierr = PetscOptionsHasName(NULL,"-pc_diagonal",&pc_diagonal);CHKERRQ(ierr);
if (pc_diagonal) { /* the preconditioner of J is a diagonal matrix */
PetscInt rstart,rend,i;
PetscScalar zero=0.0;
ierr = MatGetOwnershipRange(J,&rstart,&rend);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
ierr = MatSetValues(J,1,&i,1,&i,&zero,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
} else {
/* Fill the structure using the expensive SNESComputeJacobianDefault. Temporarily set up the TS so we can call this function */
ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr);
ierr = TSSetUp(ts);CHKERRQ(ierr);
ierr = SNESComputeJacobianDefault(snes,x,J,J,ts);CHKERRQ(ierr);
}
/* create coloring context */
ierr = MatColoringCreate(J,&mc);CHKERRQ(ierr);
ierr = MatColoringSetType(mc,MATCOLORINGSL);CHKERRQ(ierr);
ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr);
ierr = MatColoringApply(mc,&iscoloring);CHKERRQ(ierr);
ierr = MatColoringDestroy(&mc);CHKERRQ(ierr);
ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))SNESTSFormFunction,ts);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetUp(J,iscoloring,matfdcoloring);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
} else { /* Use finite differences (slow) */
ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefault,NULL);CHKERRQ(ierr);
}
}
/* Pick up a Petsc preconditioner */
/* one can always set method or preconditioner during the run time */
ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCJACOBI);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSetUp(ts);CHKERRQ(ierr);
/* Test TSSetPostStep() */
ierr = PetscOptionsHasName(NULL,"-test_PostStep",&flg);CHKERRQ(ierr);
if (flg) {
ierr = TSSetPostStep(ts,PostStep);CHKERRQ(ierr);
}
ierr = PetscOptionsGetInt(NULL,"-NOUT",&NOUT,NULL);CHKERRQ(ierr);
for (iout=1; iout<=NOUT; iout++) {
ierr = TSSetDuration(ts,time_steps,iout*ftime_original/NOUT);CHKERRQ(ierr);
ierr = TSSolve(ts,global);CHKERRQ(ierr);
ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,ftime,dt);CHKERRQ(ierr);
}
/* Interpolate solution at tfinal */
ierr = TSGetSolution(ts,&global);CHKERRQ(ierr);
ierr = TSInterpolate(ts,ftime_original,global);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-matlab_view",&flg);CHKERRQ(ierr);
if (flg) { /* print solution into a MATLAB file */
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,"out.m",&viewfile);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewfile,PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr);
ierr = VecView(global,viewfile);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewfile);CHKERRQ(ierr);
}
/* display solver info for Sundials */
ierr = TSGetType(ts,&tstype);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)ts,TSSUNDIALS,&sundials);CHKERRQ(ierr);
if (sundials) {
ierr = PetscViewerStringOpen(PETSC_COMM_WORLD,tsinfo,120,&viewer);CHKERRQ(ierr);
ierr = TSView(ts,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscViewerStringOpen(PETSC_COMM_WORLD,pcinfo,120,&viewer);CHKERRQ(ierr);
ierr = PCView(pc,viewer);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"%d Procs,%s TSType, %s Preconditioner\n",size,tsinfo,pcinfo);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
/* free the memories */
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
if (fd_jacobian_coloring) {ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr);}
ierr = PetscFinalize();
return 0;
}
