Actual source code: gcreate.c

petsc-master 2015-06-29
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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: }