Date: 2015-10-02T22:12:12+00:00

Actual source code: gcreate.c
petsc-3.6.2 2015-10-02
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      2: #include <petsc/private/matimpl.h>       /*I "petscmat.h"  I*/

      6: PetscErrorCode MatShift_Basic(Mat Y,PetscScalar a)
      7: {
      9:   PetscInt       i,start,end;
     10:   PetscScalar    alpha = a;
     11:   PetscBool      prevoption;

     14:   MatGetOption(Y,MAT_NO_OFF_PROC_ENTRIES,&prevoption);
     15:   MatSetOption(Y,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);
     16:   MatGetOwnershipRange(Y,&start,&end);
     17:   for (i=start; i<end; i++) {
     18:     MatSetValues(Y,1,&i,1,&i,&alpha,ADD_VALUES);
     19:   }
     20:   MatAssemblyBegin(Y,MAT_FINAL_ASSEMBLY);
     21:   MatAssemblyEnd(Y,MAT_FINAL_ASSEMBLY);
     22:   MatSetOption(Y,MAT_NO_OFF_PROC_ENTRIES,prevoption);
     23:   return(0);
     24: }

     28: /*@
     29:    MatCreate - Creates a matrix where the type is determined
     30:    from either a call to MatSetType() or from the options database
     31:    with a call to MatSetFromOptions(). The default matrix type is
     32:    AIJ, using the routines MatCreateSeqAIJ() or MatCreateAIJ()
     33:    if you do not set a type in the options database. If you never
     34:    call MatSetType() or MatSetFromOptions() it will generate an
     35:    error when you try to use the matrix.

     37:    Collective on MPI_Comm

     39:    Input Parameter:
     40: .  comm - MPI communicator

     42:    Output Parameter:
     43: .  A - the matrix

     45:    Options Database Keys:
     46: +    -mat_type seqaij   - AIJ type, uses MatCreateSeqAIJ()
     47: .    -mat_type mpiaij   - AIJ type, uses MatCreateAIJ()
     48: .    -mat_type seqdense - dense type, uses MatCreateSeqDense()
     49: .    -mat_type mpidense - dense type, uses MatCreateDense()
     50: .    -mat_type seqbaij  - block AIJ type, uses MatCreateSeqBAIJ()
     51: -    -mat_type mpibaij  - block AIJ type, uses MatCreateBAIJ()

     53:    Even More Options Database Keys:
     54:    See the manpages for particular formats (e.g., MatCreateSeqAIJ())
     55:    for additional format-specific options.

     57:    Notes:

     59:    Level: beginner

     61:    User manual sections:
     62: +   Section 3.1 Creating and Assembling Matrices
     63: -   Chapter 3 Matrices

     65: .keywords: matrix, create

     67: .seealso: MatCreateSeqAIJ(), MatCreateAIJ(),
     68:           MatCreateSeqDense(), MatCreateDense(),
     69:           MatCreateSeqBAIJ(), MatCreateBAIJ(),
     70:           MatCreateSeqSBAIJ(), MatCreateSBAIJ(),
     71:           MatConvert()
     72: @*/
     73: PetscErrorCode  MatCreate(MPI_Comm comm,Mat *A)
     74: {
     75:   Mat            B;

     81:   *A = NULL;
     82:   MatInitializePackage();

     84:   PetscHeaderCreate(B,MAT_CLASSID,"Mat","Matrix","Mat",comm,MatDestroy,MatView);
     85:   PetscLayoutCreate(comm,&B->rmap);
     86:   PetscLayoutCreate(comm,&B->cmap);

     88:   B->preallocated = PETSC_FALSE;
     89:   *A              = B;
     90:   return(0);
     91: }

     95: /*@
     96:    MatSetErrorIfFPE - Causes Mat to generate an error if a FPE, for example a zero pivot, is detected.

     98:    Logically Collective on Mat

    100:    Input Parameters:
    101: +  mat -  matrix obtained from MatCreate()
    102: -  flg - PETSC_TRUE indicates you want the error generated

    104:    Level: advanced

    106: .keywords: Mat, set, initial guess, nonzero

    108: .seealso: PCSetErrorIfFailure()
    109: @*/
    110: PetscErrorCode  MatSetErrorIfFPE(Mat mat,PetscBool flg)
    111: {
    115:   mat->erroriffpe = flg;
    116:   return(0);
    117: }

    121: /*@
    122:   MatSetSizes - Sets the local and global sizes, and checks to determine compatibility

    124:   Collective on Mat

    126:   Input Parameters:
    127: +  A - the matrix
    128: .  m - number of local rows (or PETSC_DECIDE)
    129: .  n - number of local columns (or PETSC_DECIDE)
    130: .  M - number of global rows (or PETSC_DETERMINE)
    131: -  N - number of global columns (or PETSC_DETERMINE)

    133:    Notes:
    134:    m (n) and M (N) cannot be both PETSC_DECIDE
    135:    If one processor calls this with M (N) of PETSC_DECIDE then all processors must, otherwise the program will hang.

    137:    If PETSC_DECIDE is not used for the arguments 'm' and 'n', then the
    138:    user must ensure that they are chosen to be compatible with the
    139:    vectors. To do this, one first considers the matrix-vector product
    140:    'y = A x'. The 'm' that is used in the above routine must match the
    141:    local size used in the vector creation routine VecCreateMPI() for 'y'.
    142:    Likewise, the 'n' used must match that used as the local size in
    143:    VecCreateMPI() for 'x'.

    145:    You cannot change the sizes once they have been set.

    147:    The sizes must be set before MatSetUp() or MatXXXSetPreallocation() is called.

    149:   Level: beginner

    151: .seealso: MatGetSize(), PetscSplitOwnership()
    152: @*/
    153: PetscErrorCode  MatSetSizes(Mat A, PetscInt m, PetscInt n, PetscInt M, PetscInt N)
    154: {
    159:   if (M > 0 && m > M) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Local column size %D cannot be larger than global column size %D",m,M);
    160:   if (N > 0 && n > N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Local row size %D cannot be larger than global row size %D",n,N);
    161:   if ((A->rmap->n >= 0 && A->rmap->N >= 0) && (A->rmap->n != m || A->rmap->N != M)) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot change/reset row sizes to %D local %D global after previously setting them to %D local %D global",m,M,A->rmap->n,A->rmap->N);
    162:   if ((A->cmap->n >= 0 && A->cmap->N >= 0) && (A->cmap->n != n || A->cmap->N != N)) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot change/reset column sizes to %D local %D global after previously setting them to %D local %D global",n,N,A->cmap->n,A->cmap->N);
    163:   A->rmap->n = m;
    164:   A->cmap->n = n;
    165:   A->rmap->N = M;
    166:   A->cmap->N = N;
    167:   return(0);
    168: }

    172: /*@
    173:    MatSetFromOptions - Creates a matrix where the type is determined
    174:    from the options database. Generates a parallel MPI matrix if the
    175:    communicator has more than one processor.  The default matrix type is
    176:    AIJ, using the routines MatCreateSeqAIJ() and MatCreateAIJ() if
    177:    you do not select a type in the options database.

    179:    Collective on Mat

    181:    Input Parameter:
    182: .  A - the matrix

    184:    Options Database Keys:
    185: +    -mat_type seqaij   - AIJ type, uses MatCreateSeqAIJ()
    186: .    -mat_type mpiaij   - AIJ type, uses MatCreateAIJ()
    187: .    -mat_type seqdense - dense type, uses MatCreateSeqDense()
    188: .    -mat_type mpidense - dense type, uses MatCreateDense()
    189: .    -mat_type seqbaij  - block AIJ type, uses MatCreateSeqBAIJ()
    190: -    -mat_type mpibaij  - block AIJ type, uses MatCreateBAIJ()

    192:    Even More Options Database Keys:
    193:    See the manpages for particular formats (e.g., MatCreateSeqAIJ())
    194:    for additional format-specific options.

    196:    Level: beginner

    198: .keywords: matrix, create

    200: .seealso: MatCreateSeqAIJ((), MatCreateAIJ(),
    201:           MatCreateSeqDense(), MatCreateDense(),
    202:           MatCreateSeqBAIJ(), MatCreateBAIJ(),
    203:           MatCreateSeqSBAIJ(), MatCreateSBAIJ(),
    204:           MatConvert()
    205: @*/
    206: PetscErrorCode  MatSetFromOptions(Mat B)
    207: {
    209:   const char     *deft = MATAIJ;
    210:   char           type[256];
    211:   PetscBool      flg,set;

    216:   PetscObjectOptionsBegin((PetscObject)B);

    218:   if (B->rmap->bs < 0) {
    219:     PetscInt newbs = -1;
    220:     PetscOptionsInt("-mat_block_size","Set the blocksize used to store the matrix","MatSetBlockSize",newbs,&newbs,&flg);
    221:     if (flg) {
    222:       PetscLayoutSetBlockSize(B->rmap,newbs);
    223:       PetscLayoutSetBlockSize(B->cmap,newbs);
    224:     }
    225:   }

    227:   PetscOptionsFList("-mat_type","Matrix type","MatSetType",MatList,deft,type,256,&flg);
    228:   if (flg) {
    229:     MatSetType(B,type);
    230:   } else if (!((PetscObject)B)->type_name) {
    231:     MatSetType(B,deft);
    232:   }

    234:   PetscOptionsName("-mat_is_symmetric","Checks if mat is symmetric on MatAssemblyEnd()","MatIsSymmetric",&B->checksymmetryonassembly);
    235:   PetscOptionsReal("-mat_is_symmetric","Checks if mat is symmetric on MatAssemblyEnd()","MatIsSymmetric",B->checksymmetrytol,&B->checksymmetrytol,NULL);
    236:   PetscOptionsBool("-mat_null_space_test","Checks if provided null space is correct in MatAssemblyEnd()","MatSetNullSpaceTest",B->checknullspaceonassembly,&B->checknullspaceonassembly,NULL);

    238:   if (B->ops->setfromoptions) {
    239:     (*B->ops->setfromoptions)(PetscOptionsObject,B);
    240:   }

    242:   flg  = PETSC_FALSE;
    243:   PetscOptionsBool("-mat_new_nonzero_location_err","Generate an error if new nonzeros are created in the matrix structure (useful to test preallocation)","MatSetOption",flg,&flg,&set);
    244:   if (set) {MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,flg);}
    245:   flg  = PETSC_FALSE;
    246:   PetscOptionsBool("-mat_new_nonzero_allocation_err","Generate an error if new nonzeros are allocated in the matrix structure (useful to test preallocation)","MatSetOption",flg,&flg,&set);
    247:   if (set) {MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,flg);}

    249:   /* process any options handlers added with PetscObjectAddOptionsHandler() */
    250:   PetscObjectProcessOptionsHandlers((PetscObject)B);
    251:   PetscOptionsEnd();
    252:   return(0);
    253: }

    257: /*@
    258:    MatXAIJSetPreallocation - set preallocation for serial and parallel AIJ, BAIJ, and SBAIJ matrices

    260:    Collective on Mat

    262:    Input Arguments:
    263: +  A - matrix being preallocated
    264: .  bs - block size
    265: .  dnnz - number of nonzero blocks per block row of diagonal part of parallel matrix
    266: .  onnz - number of nonzero blocks per block row of off-diagonal part of parallel matrix
    267: .  dnnzu - number of nonzero blocks per block row of upper-triangular part of diagonal part of parallel matrix
    268: -  onnzu - number of nonzero blocks per block row of upper-triangular part of off-diagonal part of parallel matrix

    270:    Level: beginner

    272: .seealso: MatSeqAIJSetPreallocation(), MatMPIAIJSetPreallocation(), MatSeqBAIJSetPreallocation(), MatMPIBAIJSetPreallocation(), MatSeqSBAIJSetPreallocation(), MatMPISBAIJSetPreallocation(),
    273:           PetscSplitOwnership()
    274: @*/
    275: PetscErrorCode MatXAIJSetPreallocation(Mat A,PetscInt bs,const PetscInt dnnz[],const PetscInt onnz[],const PetscInt dnnzu[],const PetscInt onnzu[])
    276: {
    278:   void           (*aij)(void);

    281:   MatSetBlockSize(A,bs);
    282:   MatGetBlockSize(A,&bs);
    283:   PetscLayoutSetUp(A->rmap);
    284:   PetscLayoutSetUp(A->cmap);
    285:   MatSeqBAIJSetPreallocation(A,bs,0,dnnz);
    286:   MatMPIBAIJSetPreallocation(A,bs,0,dnnz,0,onnz);
    287:   MatSeqSBAIJSetPreallocation(A,bs,0,dnnzu);
    288:   MatMPISBAIJSetPreallocation(A,bs,0,dnnzu,0,onnzu);
    289:   /*
    290:     In general, we have to do extra work to preallocate for scalar (AIJ) matrices so we check whether it will do any
    291:     good before going on with it.
    292:   */
    293:   PetscObjectQueryFunction((PetscObject)A,"MatMPIAIJSetPreallocation_C",&aij);
    294:   if (!aij) {
    295:     PetscObjectQueryFunction((PetscObject)A,"MatSeqAIJSetPreallocation_C",&aij);
    296:   }
    297:   if (aij) {
    298:     if (bs == 1) {
    299:       MatSeqAIJSetPreallocation(A,0,dnnz);
    300:       MatMPIAIJSetPreallocation(A,0,dnnz,0,onnz);
    301:     } else {                    /* Convert block-row precallocation to scalar-row */
    302:       PetscInt i,m,*sdnnz,*sonnz;
    303:       MatGetLocalSize(A,&m,NULL);
    304:       PetscMalloc2((!!dnnz)*m,&sdnnz,(!!onnz)*m,&sonnz);
    305:       for (i=0; i<m; i++) {
    306:         if (dnnz) sdnnz[i] = dnnz[i/bs] * bs;
    307:         if (onnz) sonnz[i] = onnz[i/bs] * bs;
    308:       }
    309:       MatSeqAIJSetPreallocation(A,0,dnnz ? sdnnz : NULL);
    310:       MatMPIAIJSetPreallocation(A,0,dnnz ? sdnnz : NULL,0,onnz ? sonnz : NULL);
    311:       PetscFree2(sdnnz,sonnz);
    312:     }
    313:   }
    314:   return(0);
    315: }

    317: /*
    318:         Merges some information from Cs header to A; the C object is then destroyed

    320:         This is somewhat different from MatHeaderReplace() it would be nice to merge the code
    321: */
    324: PetscErrorCode MatHeaderMerge(Mat A,Mat C)
    325: {
    327:   PetscInt       refct;
    328:   PetscOps       Abops;
    329:   struct _MatOps Aops;
    330:   char           *mtype,*mname;
    331:   void           *spptr;

    334:   /* save the parts of A we need */
    335:   Abops = ((PetscObject)A)->bops[0];
    336:   Aops  = A->ops[0];
    337:   refct = ((PetscObject)A)->refct;
    338:   mtype = ((PetscObject)A)->type_name;
    339:   mname = ((PetscObject)A)->name;
    340:   spptr = A->spptr;

    342:   /* zero these so the destroy below does not free them */
    343:   ((PetscObject)A)->type_name = 0;
    344:   ((PetscObject)A)->name      = 0;

    346:   /* free all the interior data structures from mat */
    347:   (*A->ops->destroy)(A);

    349:   PetscFree(C->spptr);

    351:   PetscLayoutDestroy(&A->rmap);
    352:   PetscLayoutDestroy(&A->cmap);
    353:   PetscFunctionListDestroy(&((PetscObject)A)->qlist);
    354:   PetscObjectListDestroy(&((PetscObject)A)->olist);

    356:   /* copy C over to A */
    357:   PetscMemcpy(A,C,sizeof(struct _p_Mat));

    359:   /* return the parts of A we saved */
    360:   ((PetscObject)A)->bops[0]   = Abops;
    361:   A->ops[0]                   = Aops;
    362:   ((PetscObject)A)->refct     = refct;
    363:   ((PetscObject)A)->type_name = mtype;
    364:   ((PetscObject)A)->name      = mname;
    365:   A->spptr                    = spptr;

    367:   /* since these two are copied into A we do not want them destroyed in C */
    368:   ((PetscObject)C)->qlist = 0;
    369:   ((PetscObject)C)->olist = 0;

    371:   PetscHeaderDestroy(&C);
    372:   return(0);
    373: }
    374: /*
    375:         Replace A's header with that of C; the C object is then destroyed

    377:         This is essentially code moved from MatDestroy()

    379:         This is somewhat different from MatHeaderMerge() it would be nice to merge the code

    381:         Used in DM hence is declared PETSC_EXTERN
    382: */
    385: PETSC_EXTERN PetscErrorCode MatHeaderReplace(Mat A,Mat C)
    386: {
    387:   PetscErrorCode   ierr;
    388:   PetscInt         refct;
    389:   PetscObjectState state;

    394:   if (A == C) return(0);
    396:   if (((PetscObject)C)->refct != 1) SETERRQ1(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"Object C has refct %D > 1, would leave hanging reference",((PetscObject)C)->refct);

    398:   /* free all the interior data structures from mat */
    399:   (*A->ops->destroy)(A);
    400:   PetscHeaderDestroy_Private((PetscObject)A);
    401:   PetscLayoutDestroy(&A->rmap);
    402:   PetscLayoutDestroy(&A->cmap);
    403:   PetscFree(A->spptr);

    405:   /* copy C over to A */
    406:   refct = ((PetscObject)A)->refct;
    407:   state = ((PetscObject)A)->state;
    408:   PetscMemcpy(A,C,sizeof(struct _p_Mat));

    410:   ((PetscObject)A)->refct = refct;
    411:   ((PetscObject)A)->state = state + 1;

    413:   PetscFree(C);
    414:   return(0);
    415: }