Actual source code: matimpl.h

petsc-3.6.2 2015-10-02
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  2: #ifndef __MATIMPL_H

  5: #include <petscmat.h>
  6: #include <petsc/private/petscimpl.h>

  8: PETSC_EXTERN PetscBool MatRegisterAllCalled;
  9: PETSC_EXTERN PetscBool MatOrderingRegisterAllCalled;
 10: PETSC_EXTERN PetscBool MatColoringRegisterAllCalled;
 11: PETSC_EXTERN PetscBool MatPartitioningRegisterAllCalled;
 12: PETSC_EXTERN PetscBool MatCoarsenRegisterAllCalled;
 13: PETSC_EXTERN PetscErrorCode MatRegisterAll(void);
 14: PETSC_EXTERN PetscErrorCode MatOrderingRegisterAll(void);
 15: PETSC_EXTERN PetscErrorCode MatColoringRegisterAll(void);
 16: PETSC_EXTERN PetscErrorCode MatPartitioningRegisterAll(void);
 17: PETSC_EXTERN PetscErrorCode MatCoarsenRegisterAll(void);

 19: /*
 20:   This file defines the parts of the matrix data structure that are
 21:   shared by all matrix types.
 22: */

 24: /*
 25:     If you add entries here also add them to the MATOP enum
 26:     in include/petscmat.h and include/petsc/finclude/petscmat.h
 27: */
 28: typedef struct _MatOps *MatOps;
 29: struct _MatOps {
 30:   /* 0*/
 31:   PetscErrorCode (*setvalues)(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode);
 32:   PetscErrorCode (*getrow)(Mat,PetscInt,PetscInt *,PetscInt*[],PetscScalar*[]);
 33:   PetscErrorCode (*restorerow)(Mat,PetscInt,PetscInt *,PetscInt *[],PetscScalar *[]);
 34:   PetscErrorCode (*mult)(Mat,Vec,Vec);
 35:   PetscErrorCode (*multadd)(Mat,Vec,Vec,Vec);
 36:   /* 5*/
 37:   PetscErrorCode (*multtranspose)(Mat,Vec,Vec);
 38:   PetscErrorCode (*multtransposeadd)(Mat,Vec,Vec,Vec);
 39:   PetscErrorCode (*solve)(Mat,Vec,Vec);
 40:   PetscErrorCode (*solveadd)(Mat,Vec,Vec,Vec);
 41:   PetscErrorCode (*solvetranspose)(Mat,Vec,Vec);
 42:   /*10*/
 43:   PetscErrorCode (*solvetransposeadd)(Mat,Vec,Vec,Vec);
 44:   PetscErrorCode (*lufactor)(Mat,IS,IS,const MatFactorInfo*);
 45:   PetscErrorCode (*choleskyfactor)(Mat,IS,const MatFactorInfo*);
 46:   PetscErrorCode (*sor)(Mat,Vec,PetscReal,MatSORType,PetscReal,PetscInt,PetscInt,Vec);
 47:   PetscErrorCode (*transpose)(Mat,MatReuse,Mat *);
 48:   /*15*/
 49:   PetscErrorCode (*getinfo)(Mat,MatInfoType,MatInfo*);
 50:   PetscErrorCode (*equal)(Mat,Mat,PetscBool  *);
 51:   PetscErrorCode (*getdiagonal)(Mat,Vec);
 52:   PetscErrorCode (*diagonalscale)(Mat,Vec,Vec);
 53:   PetscErrorCode (*norm)(Mat,NormType,PetscReal*);
 54:   /*20*/
 55:   PetscErrorCode (*assemblybegin)(Mat,MatAssemblyType);
 56:   PetscErrorCode (*assemblyend)(Mat,MatAssemblyType);
 57:   PetscErrorCode (*setoption)(Mat,MatOption,PetscBool );
 58:   PetscErrorCode (*zeroentries)(Mat);
 59:   /*24*/
 60:   PetscErrorCode (*zerorows)(Mat,PetscInt,const PetscInt[],PetscScalar,Vec,Vec);
 61:   PetscErrorCode (*lufactorsymbolic)(Mat,Mat,IS,IS,const MatFactorInfo*);
 62:   PetscErrorCode (*lufactornumeric)(Mat,Mat,const MatFactorInfo*);
 63:   PetscErrorCode (*choleskyfactorsymbolic)(Mat,Mat,IS,const MatFactorInfo*);
 64:   PetscErrorCode (*choleskyfactornumeric)(Mat,Mat,const MatFactorInfo*);
 65:   /*29*/
 66:   PetscErrorCode (*setup)(Mat);
 67:   PetscErrorCode (*ilufactorsymbolic)(Mat,Mat,IS,IS,const MatFactorInfo*);
 68:   PetscErrorCode (*iccfactorsymbolic)(Mat,Mat,IS,const MatFactorInfo*);
 69:   PetscErrorCode (*placeholder_32)(Mat);
 70:   PetscErrorCode (*placeholder_33)(Mat);
 71:   /*34*/
 72:   PetscErrorCode (*duplicate)(Mat,MatDuplicateOption,Mat*);
 73:   PetscErrorCode (*forwardsolve)(Mat,Vec,Vec);
 74:   PetscErrorCode (*backwardsolve)(Mat,Vec,Vec);
 75:   PetscErrorCode (*ilufactor)(Mat,IS,IS,const MatFactorInfo*);
 76:   PetscErrorCode (*iccfactor)(Mat,IS,const MatFactorInfo*);
 77:   /*39*/
 78:   PetscErrorCode (*axpy)(Mat,PetscScalar,Mat,MatStructure);
 79:   PetscErrorCode (*getsubmatrices)(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat *[]);
 80:   PetscErrorCode (*increaseoverlap)(Mat,PetscInt,IS[],PetscInt);
 81:   PetscErrorCode (*getvalues)(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],PetscScalar []);
 82:   PetscErrorCode (*copy)(Mat,Mat,MatStructure);
 83:   /*44*/
 84:   PetscErrorCode (*getrowmax)(Mat,Vec,PetscInt[]);
 85:   PetscErrorCode (*scale)(Mat,PetscScalar);
 86:   PetscErrorCode (*shift)(Mat,PetscScalar);
 87:   PetscErrorCode (*diagonalset)(Mat,Vec,InsertMode);
 88:   PetscErrorCode (*zerorowscolumns)(Mat,PetscInt,const PetscInt[],PetscScalar,Vec,Vec);
 89:   /*49*/
 90:   PetscErrorCode (*setrandom)(Mat,PetscRandom);
 91:   PetscErrorCode (*getrowij)(Mat,PetscInt,PetscBool ,PetscBool ,PetscInt*,const PetscInt *[],const PetscInt *[],PetscBool  *);
 92:   PetscErrorCode (*restorerowij)(Mat,PetscInt,PetscBool ,PetscBool ,PetscInt *,const PetscInt *[],const PetscInt *[],PetscBool  *);
 93:   PetscErrorCode (*getcolumnij)(Mat,PetscInt,PetscBool ,PetscBool ,PetscInt*,const PetscInt *[],const PetscInt *[],PetscBool  *);
 94:   PetscErrorCode (*restorecolumnij)(Mat,PetscInt,PetscBool ,PetscBool ,PetscInt*,const PetscInt *[],const PetscInt *[],PetscBool  *);
 95:   /*54*/
 96:   PetscErrorCode (*fdcoloringcreate)(Mat,ISColoring,MatFDColoring);
 97:   PetscErrorCode (*coloringpatch)(Mat,PetscInt,PetscInt,ISColoringValue[],ISColoring*);
 98:   PetscErrorCode (*setunfactored)(Mat);
 99:   PetscErrorCode (*permute)(Mat,IS,IS,Mat*);
100:   PetscErrorCode (*setvaluesblocked)(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode);
101:   /*59*/
102:   PetscErrorCode (*getsubmatrix)(Mat,IS,IS,MatReuse,Mat*);
103:   PetscErrorCode (*destroy)(Mat);
104:   PetscErrorCode (*view)(Mat,PetscViewer);
105:   PetscErrorCode (*convertfrom)(Mat, MatType,MatReuse,Mat*);
106:   PetscErrorCode (*matmatmult)(Mat,Mat,Mat,MatReuse,PetscReal,Mat*);
107:   /*64*/
108:   PetscErrorCode (*matmatmultsymbolic)(Mat,Mat,Mat,PetscReal,Mat*);
109:   PetscErrorCode (*matmatmultnumeric)(Mat,Mat,Mat,Mat);
110:   PetscErrorCode (*setlocaltoglobalmapping)(Mat,ISLocalToGlobalMapping,ISLocalToGlobalMapping);
111:   PetscErrorCode (*setvalueslocal)(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode);
112:   PetscErrorCode (*zerorowslocal)(Mat,PetscInt,const PetscInt[],PetscScalar,Vec,Vec);
113:   /*69*/
114:   PetscErrorCode (*getrowmaxabs)(Mat,Vec,PetscInt[]);
115:   PetscErrorCode (*getrowminabs)(Mat,Vec,PetscInt[]);
116:   PetscErrorCode (*convert)(Mat, MatType,MatReuse,Mat*);
117:   PetscErrorCode (*setcoloring)(Mat,ISColoring);
118:   PetscErrorCode (*placeholder_73)(Mat,void*);
119:   /*74*/
120:   PetscErrorCode (*setvaluesadifor)(Mat,PetscInt,void*);
121:   PetscErrorCode (*fdcoloringapply)(Mat,MatFDColoring,Vec,void*);
122:   PetscErrorCode (*setfromoptions)(PetscOptions*,Mat);
123:   PetscErrorCode (*multconstrained)(Mat,Vec,Vec);
124:   PetscErrorCode (*multtransposeconstrained)(Mat,Vec,Vec);
125:   /*79*/
126:   PetscErrorCode (*findzerodiagonals)(Mat,IS*);
127:   PetscErrorCode (*mults)(Mat, Vecs, Vecs);
128:   PetscErrorCode (*solves)(Mat, Vecs, Vecs);
129:   PetscErrorCode (*getinertia)(Mat,PetscInt*,PetscInt*,PetscInt*);
130:   PetscErrorCode (*load)(Mat, PetscViewer);
131:   /*84*/
132:   PetscErrorCode (*issymmetric)(Mat,PetscReal,PetscBool *);
133:   PetscErrorCode (*ishermitian)(Mat,PetscReal,PetscBool *);
134:   PetscErrorCode (*isstructurallysymmetric)(Mat,PetscBool *);
135:   PetscErrorCode (*setvaluesblockedlocal)(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode);
136:   PetscErrorCode (*getvecs)(Mat,Vec*,Vec*);
137:   /*89*/
138:   PetscErrorCode (*matmult)(Mat,Mat,MatReuse,PetscReal,Mat*);
139:   PetscErrorCode (*matmultsymbolic)(Mat,Mat,PetscReal,Mat*);
140:   PetscErrorCode (*matmultnumeric)(Mat,Mat,Mat);
141:   PetscErrorCode (*ptap)(Mat,Mat,MatReuse,PetscReal,Mat*);
142:   PetscErrorCode (*ptapsymbolic)(Mat,Mat,PetscReal,Mat*); /* double dispatch wrapper routine */
143:   /*94*/
144:   PetscErrorCode (*ptapnumeric)(Mat,Mat,Mat);             /* double dispatch wrapper routine */
145:   PetscErrorCode (*mattransposemult)(Mat,Mat,MatReuse,PetscReal,Mat*);
146:   PetscErrorCode (*mattransposemultsymbolic)(Mat,Mat,PetscReal,Mat*);
147:   PetscErrorCode (*mattransposemultnumeric)(Mat,Mat,Mat);
148:   PetscErrorCode (*placeholder_98)(Mat);
149:   /*99*/
150:   PetscErrorCode (*placeholder_99)(Mat);
151:   PetscErrorCode (*placeholder_100)(Mat);
152:   PetscErrorCode (*placeholder_101)(Mat);
153:   PetscErrorCode (*conjugate)(Mat);                              /* complex conjugate */
154:   PetscErrorCode (*placeholder_103)(void);
155:   /*104*/
156:   PetscErrorCode (*setvaluesrow)(Mat,PetscInt,const PetscScalar[]);
157:   PetscErrorCode (*realpart)(Mat);
158:   PetscErrorCode (*imaginarypart)(Mat);
159:   PetscErrorCode (*getrowuppertriangular)(Mat);
160:   PetscErrorCode (*restorerowuppertriangular)(Mat);
161:   /*109*/
162:   PetscErrorCode (*matsolve)(Mat,Mat,Mat);
163:   PetscErrorCode (*placeholder_110)(Mat);
164:   PetscErrorCode (*getrowmin)(Mat,Vec,PetscInt[]);
165:   PetscErrorCode (*getcolumnvector)(Mat,Vec,PetscInt);
166:   PetscErrorCode (*missingdiagonal)(Mat,PetscBool *,PetscInt*);
167:   /*114*/
168:   PetscErrorCode (*getseqnonzerostructure)(Mat,Mat *);
169:   PetscErrorCode (*create)(Mat);
170:   PetscErrorCode (*getghosts)(Mat,PetscInt*,const PetscInt *[]);
171:   PetscErrorCode (*getlocalsubmatrix)(Mat,IS,IS,Mat*);
172:   PetscErrorCode (*restorelocalsubmatrix)(Mat,IS,IS,Mat*);
173:   /*119*/
174:   PetscErrorCode (*multdiagonalblock)(Mat,Vec,Vec);
175:   PetscErrorCode (*hermitiantranspose)(Mat,MatReuse,Mat*);
176:   PetscErrorCode (*multhermitiantranspose)(Mat,Vec,Vec);
177:   PetscErrorCode (*multhermitiantransposeadd)(Mat,Vec,Vec,Vec);
178:   PetscErrorCode (*getmultiprocblock)(Mat,MPI_Comm,MatReuse,Mat*);
179:   /*124*/
180:   PetscErrorCode (*findnonzerorows)(Mat,IS*);
181:   PetscErrorCode (*getcolumnnorms)(Mat,NormType,PetscReal*);
182:   PetscErrorCode (*invertblockdiagonal)(Mat,const PetscScalar**);
183:   PetscErrorCode (*placeholder_127)(Mat,Vec,Vec,Vec);
184:   PetscErrorCode (*getsubmatricesmpi)(Mat,PetscInt,const IS[], const IS[], MatReuse, Mat**);
185:   /*129*/
186:   PetscErrorCode (*setvaluesbatch)(Mat,PetscInt,PetscInt,PetscInt*,const PetscScalar*);
187:   PetscErrorCode (*transposematmult)(Mat,Mat,MatReuse,PetscReal,Mat*);
188:   PetscErrorCode (*transposematmultsymbolic)(Mat,Mat,PetscReal,Mat*);
189:   PetscErrorCode (*transposematmultnumeric)(Mat,Mat,Mat);
190:   PetscErrorCode (*transposecoloringcreate)(Mat,ISColoring,MatTransposeColoring);
191:   /*134*/
192:   PetscErrorCode (*transcoloringapplysptoden)(MatTransposeColoring,Mat,Mat);
193:   PetscErrorCode (*transcoloringapplydentosp)(MatTransposeColoring,Mat,Mat);
194:   PetscErrorCode (*rart)(Mat,Mat,MatReuse,PetscReal,Mat*);
195:   PetscErrorCode (*rartsymbolic)(Mat,Mat,PetscReal,Mat*); /* double dispatch wrapper routine */
196:   PetscErrorCode (*rartnumeric)(Mat,Mat,Mat);             /* double dispatch wrapper routine */
197:   /*139*/
198:   PetscErrorCode (*setblocksizes)(Mat,PetscInt,PetscInt);
199:   PetscErrorCode (*aypx)(Mat,PetscScalar,Mat,MatStructure);
200:   PetscErrorCode (*residual)(Mat,Vec,Vec,Vec);
201:   PetscErrorCode (*fdcoloringsetup)(Mat,ISColoring,MatFDColoring);
202:   PetscErrorCode (*findoffblockdiagonalentries)(Mat,IS*);
203:   /*144*/
204:   PetscErrorCode (*creatempimatconcatenateseqmat)(MPI_Comm,Mat,PetscInt,MatReuse,Mat*);

206: };
207: /*
208:     If you add MatOps entries above also add them to the MATOP enum
209:     in include/petscmat.h and include/petsc/finclude/petscmat.h
210: */

212: #include <petscsys.h>
213: PETSC_EXTERN PetscErrorCode MatRegisterOp(MPI_Comm, const char[], PetscVoidFunction, const char[], PetscInt, ...);
214: PETSC_EXTERN PetscErrorCode MatQueryOp(MPI_Comm, PetscVoidFunction*, const char[], PetscInt, ...);

216: typedef struct _p_MatBaseName* MatBaseName;
217: struct _p_MatBaseName {
218:   char        *bname,*sname,*mname;
219:   MatBaseName next;
220: };

222: PETSC_EXTERN MatBaseName MatBaseNameList;

224: /*
225:    Utility private matrix routines
226: */
227: PETSC_INTERN PetscErrorCode MatConvert_Basic(Mat, MatType,MatReuse,Mat*);
228: PETSC_INTERN PetscErrorCode MatCopy_Basic(Mat,Mat,MatStructure);
229: PETSC_INTERN PetscErrorCode MatHeaderMerge(Mat,Mat);
230: PETSC_EXTERN PetscErrorCode MatHeaderReplace(Mat,Mat);
231: PETSC_INTERN PetscErrorCode MatDiagonalSet_Default(Mat,Vec,InsertMode);

233: #if defined(PETSC_USE_DEBUG)
234: #  define MatCheckPreallocated(A,arg) do {                              \
235:     if (PetscUnlikely(!(A)->preallocated)) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call MatXXXSetPreallocation() or MatSetUp() on argument %D \"%s\" before %s()",(arg),#A,PETSC_FUNCTION_NAME); \
236:   } while (0)
237: #else
238: #  define MatCheckPreallocated(A,arg) do {} while (0)
239: #endif

241: /*
242:   The stash is used to temporarily store inserted matrix values that
243:   belong to another processor. During the assembly phase the stashed
244:   values are moved to the correct processor and
245: */

247: typedef struct _MatStashSpace *PetscMatStashSpace;

249: struct _MatStashSpace {
250:   PetscMatStashSpace next;
251:   PetscScalar        *space_head,*val;
252:   PetscInt           *idx,*idy;
253:   PetscInt           total_space_size;
254:   PetscInt           local_used;
255:   PetscInt           local_remaining;
256: };

258: PETSC_EXTERN PetscErrorCode PetscMatStashSpaceGet(PetscInt,PetscInt,PetscMatStashSpace *);
259: PETSC_EXTERN PetscErrorCode PetscMatStashSpaceContiguous(PetscInt,PetscMatStashSpace *,PetscScalar *,PetscInt *,PetscInt *);
260: PETSC_EXTERN PetscErrorCode PetscMatStashSpaceDestroy(PetscMatStashSpace*);

262: typedef struct {
263:   PetscInt      nmax;                   /* maximum stash size */
264:   PetscInt      umax;                   /* user specified max-size */
265:   PetscInt      oldnmax;                /* the nmax value used previously */
266:   PetscInt      n;                      /* stash size */
267:   PetscInt      bs;                     /* block size of the stash */
268:   PetscInt      reallocs;               /* preserve the no of mallocs invoked */
269:   PetscMatStashSpace space_head,space;  /* linked list to hold stashed global row/column numbers and matrix values */
270:   /* The following variables are used for communication */
271:   MPI_Comm      comm;
272:   PetscMPIInt   size,rank;
273:   PetscMPIInt   tag1,tag2;
274:   MPI_Request   *send_waits;            /* array of send requests */
275:   MPI_Request   *recv_waits;            /* array of receive requests */
276:   MPI_Status    *send_status;           /* array of send status */
277:   PetscInt      nsends,nrecvs;          /* numbers of sends and receives */
278:   PetscScalar   *svalues;               /* sending data */
279:   PetscInt      *sindices;
280:   PetscScalar   **rvalues;              /* receiving data (values) */
281:   PetscInt      **rindices;             /* receiving data (indices) */
282:   PetscInt      nprocessed;             /* number of messages already processed */
283:   PetscMPIInt   *flg_v;                 /* indicates what messages have arrived so far and from whom */
284:   PetscBool     reproduce;
285:   PetscInt      reproduce_count;
286: } MatStash;

288: PETSC_INTERN PetscErrorCode MatStashCreate_Private(MPI_Comm,PetscInt,MatStash*);
289: PETSC_INTERN PetscErrorCode MatStashDestroy_Private(MatStash*);
290: PETSC_INTERN PetscErrorCode MatStashScatterEnd_Private(MatStash*);
291: PETSC_INTERN PetscErrorCode MatStashSetInitialSize_Private(MatStash*,PetscInt);
292: PETSC_INTERN PetscErrorCode MatStashGetInfo_Private(MatStash*,PetscInt*,PetscInt*);
293: PETSC_INTERN PetscErrorCode MatStashValuesRow_Private(MatStash*,PetscInt,PetscInt,const PetscInt[],const PetscScalar[],PetscBool );
294: PETSC_INTERN PetscErrorCode MatStashValuesCol_Private(MatStash*,PetscInt,PetscInt,const PetscInt[],const PetscScalar[],PetscInt,PetscBool );
295: PETSC_INTERN PetscErrorCode MatStashValuesRowBlocked_Private(MatStash*,PetscInt,PetscInt,const PetscInt[],const PetscScalar[],PetscInt,PetscInt,PetscInt);
296: PETSC_INTERN PetscErrorCode MatStashValuesColBlocked_Private(MatStash*,PetscInt,PetscInt,const PetscInt[],const PetscScalar[],PetscInt,PetscInt,PetscInt);
297: PETSC_INTERN PetscErrorCode MatStashScatterBegin_Private(Mat,MatStash*,PetscInt*);
298: PETSC_INTERN PetscErrorCode MatStashScatterGetMesg_Private(MatStash*,PetscMPIInt*,PetscInt**,PetscInt**,PetscScalar**,PetscInt*);

300: typedef struct {
301:   PetscInt   dim;
302:   PetscInt   dims[4];
303:   PetscInt   starts[4];
304:   PetscBool  noc;        /* this is a single component problem, hence user will not set MatStencil.c */
305: } MatStencilInfo;

307: /* Info about using compressed row format */
308: typedef struct {
309:   PetscBool  use;                           /* indicates compressed rows have been checked and will be used */
310:   PetscInt   nrows;                         /* number of non-zero rows */
311:   PetscInt   *i;                            /* compressed row pointer  */
312:   PetscInt   *rindex;                       /* compressed row index               */
313: } Mat_CompressedRow;
314: PETSC_EXTERN PetscErrorCode MatCheckCompressedRow(Mat,PetscInt,Mat_CompressedRow*,PetscInt*,PetscInt,PetscReal);

316: typedef struct { /* used by MatCreateRedundantMatrix() for reusing matredundant */
317:   PetscInt     nzlocal,nsends,nrecvs;
318:   PetscMPIInt  *send_rank,*recv_rank;
319:   PetscInt     *sbuf_nz,*rbuf_nz,*sbuf_j,**rbuf_j;
320:   PetscScalar  *sbuf_a,**rbuf_a;
321:   MPI_Comm     subcomm;   /* when user does not provide a subcomm */
322:   IS           isrow,iscol;
323:   Mat          *matseq;
324: } Mat_Redundant;

326: struct _p_Mat {
327:   PETSCHEADER(struct _MatOps);
328:   PetscLayout            rmap,cmap;
329:   void                   *data;            /* implementation-specific data */
330:   MatFactorType          factortype;       /* MAT_FACTOR_LU, ILU, CHOLESKY or ICC */
331:   PetscBool              assembled;        /* is the matrix assembled? */
332:   PetscBool              was_assembled;    /* new values inserted into assembled mat */
333:   PetscInt               num_ass;          /* number of times matrix has been assembled */
334:   PetscObjectState       nonzerostate;     /* each time new nonzeros locations are introduced into the matrix this is updated */
335:   MatInfo                info;             /* matrix information */
336:   InsertMode             insertmode;       /* have values been inserted in matrix or added? */
337:   MatStash               stash,bstash;     /* used for assembling off-proc mat emements */
338:   MatNullSpace           nullsp;           /* null space (operator is singular) */
339:   MatNullSpace           transnullsp;      /* null space of transpose of operator */
340:   MatNullSpace           nearnullsp;       /* near null space to be used by multigrid methods */
341:   PetscBool              preallocated;
342:   MatStencilInfo         stencil;          /* information for structured grid */
343:   PetscBool              symmetric,hermitian,structurally_symmetric,spd;
344:   PetscBool              symmetric_set,hermitian_set,structurally_symmetric_set,spd_set; /* if true, then corresponding flag is correct*/
345:   PetscBool              symmetric_eternal;
346:   PetscBool              nooffprocentries,nooffproczerorows;
347: #if defined(PETSC_HAVE_CUSP)
348:   PetscCUSPFlag          valid_GPU_matrix; /* flag pointing to the matrix on the gpu*/
349: #endif
350: #if defined(PETSC_HAVE_VIENNACL)
351:   PetscViennaCLFlag      valid_GPU_matrix; /* flag pointing to the matrix on the gpu*/
352: #endif
353:   void                   *spptr;          /* pointer for special library like SuperLU */
354:   MatSolverPackage       solvertype;
355:   PetscBool              checksymmetryonassembly,checknullspaceonassembly;
356:   PetscReal              checksymmetrytol;
357:   Mat_Redundant          *redundant;        /* used by MatCreateRedundantMatrix() */
358:   PetscBool              erroriffpe;        /* Generate an error if FPE detected (for example a zero pivot) instead of returning*/
359: };

361: PETSC_INTERN PetscErrorCode MatAXPY_Basic(Mat,PetscScalar,Mat,MatStructure);
362: PETSC_INTERN PetscErrorCode MatAXPY_BasicWithPreallocation(Mat,Mat,PetscScalar,Mat,MatStructure);
363: /*
364:     Object for partitioning graphs
365: */

367: typedef struct _MatPartitioningOps *MatPartitioningOps;
368: struct _MatPartitioningOps {
369:   PetscErrorCode (*apply)(MatPartitioning,IS*);
370:   PetscErrorCode (*setfromoptions)(PetscOptions*,MatPartitioning);
371:   PetscErrorCode (*destroy)(MatPartitioning);
372:   PetscErrorCode (*view)(MatPartitioning,PetscViewer);
373: };

375: struct _p_MatPartitioning {
376:   PETSCHEADER(struct _MatPartitioningOps);
377:   Mat         adj;
378:   PetscInt    *vertex_weights;
379:   PetscReal   *part_weights;
380:   PetscInt    n;                                 /* number of partitions */
381:   void        *data;
382:   PetscInt    setupcalled;
383: };

385: /*
386:     Object for coarsen graphs
387: */
388: typedef struct _MatCoarsenOps *MatCoarsenOps;
389: struct _MatCoarsenOps {
390:   PetscErrorCode (*apply)(MatCoarsen);
391:   PetscErrorCode (*setfromoptions)(PetscOptions*,MatCoarsen);
392:   PetscErrorCode (*destroy)(MatCoarsen);
393:   PetscErrorCode (*view)(MatCoarsen,PetscViewer);
394: };

396: struct _p_MatCoarsen {
397:   PETSCHEADER(struct _MatCoarsenOps);
398:   Mat              graph;
399:   PetscInt         setupcalled;
400:   void             *subctx;
401:   /* */
402:   PetscBool        strict_aggs;
403:   IS               perm;
404:   PetscCoarsenData *agg_lists;
405: };

407: PETSC_EXTERN PetscErrorCode PetscCDCreate(PetscInt,PetscCoarsenData**);
408: PETSC_EXTERN PetscErrorCode PetscCDDestroy(PetscCoarsenData*);
409: PETSC_EXTERN PetscErrorCode PetscLLNSetID(PetscCDIntNd*,PetscInt);
410: PETSC_EXTERN PetscErrorCode PetscLLNGetID(const PetscCDIntNd*,PetscInt*);
411: PETSC_EXTERN PetscErrorCode PetscCDAppendID(PetscCoarsenData*,PetscInt,PetscInt);
412: PETSC_EXTERN PetscErrorCode PetscCDAppendRemove(PetscCoarsenData*,PetscInt,PetscInt);
413: PETSC_EXTERN PetscErrorCode PetscCDAppendNode(PetscCoarsenData*,PetscInt,PetscCDIntNd*);
414: PETSC_EXTERN PetscErrorCode PetscCDRemoveNextNode(PetscCoarsenData*,PetscInt,PetscCDIntNd*);
415: PETSC_EXTERN PetscErrorCode PetscCDRemoveAllAt(PetscCoarsenData*,PetscInt);
416: PETSC_EXTERN PetscErrorCode PetscCDSizeAt(const PetscCoarsenData*,PetscInt,PetscInt*);
417: PETSC_EXTERN PetscErrorCode PetscCDEmptyAt(const PetscCoarsenData*,PetscInt,PetscBool*);
418: PETSC_EXTERN PetscErrorCode PetscCDSetChuckSize(PetscCoarsenData*,PetscInt);
419: PETSC_EXTERN PetscErrorCode PetscCDPrint(const PetscCoarsenData*,MPI_Comm);
420: PETSC_EXTERN PetscErrorCode PetscCDGetMIS(PetscCoarsenData*,IS*);
421: PETSC_EXTERN PetscErrorCode PetscCDGetMat(const PetscCoarsenData*,Mat*);
422: PETSC_EXTERN PetscErrorCode PetscCDSetMat(PetscCoarsenData*,Mat);

424: typedef PetscCDIntNd *PetscCDPos;
425: PETSC_EXTERN PetscErrorCode PetscCDGetHeadPos(const PetscCoarsenData*,PetscInt,PetscCDPos*);
426: PETSC_EXTERN PetscErrorCode PetscCDGetNextPos(const PetscCoarsenData*,PetscInt,PetscCDPos*);
427: PETSC_EXTERN PetscErrorCode PetscCDGetASMBlocks(const PetscCoarsenData*,const PetscInt,PetscInt*,IS**);
428: /* PetscErrorCode PetscCDSetRemovedIS( PetscCoarsenData *ail, MPI_Comm, const PetscInt, PetscInt[] ); */
429: /* PetscErrorCode PetscCDGetRemovedIS( PetscCoarsenData *ail, IS * ); */

431: /*
432:     MatFDColoring is used to compute Jacobian matrices efficiently
433:   via coloring. The data structure is explained below in an example.

435:    Color =   0    1     0    2   |   2      3       0
436:    ---------------------------------------------------
437:             00   01              |          05
438:             10   11              |   14     15               Processor  0
439:                        22    23  |          25
440:                        32    33  |
441:    ===================================================
442:                                  |   44     45     46
443:             50                   |          55               Processor 1
444:                                  |   64            66
445:    ---------------------------------------------------

447:     ncolors = 4;

449:     ncolumns      = {2,1,1,0}
450:     columns       = {{0,2},{1},{3},{}}
451:     nrows         = {4,2,3,3}
452:     rows          = {{0,1,2,3},{0,1},{1,2,3},{0,1,2}}
453:     vwscale       = {dx(0),dx(1),dx(2),dx(3)}               MPI Vec
454:     vscale        = {dx(0),dx(1),dx(2),dx(3),dx(4),dx(5)}   Seq Vec

456:     ncolumns      = {1,0,1,1}
457:     columns       = {{6},{},{4},{5}}
458:     nrows         = {3,0,2,2}
459:     rows          = {{0,1,2},{},{1,2},{1,2}}
460:     vwscale       = {dx(4),dx(5),dx(6)}              MPI Vec
461:     vscale        = {dx(0),dx(4),dx(5),dx(6)}        Seq Vec

463:     See the routine MatFDColoringApply() for how this data is used
464:     to compute the Jacobian.

466: */
467: typedef struct {
468:   PetscInt     row;
469:   PetscInt     col;
470:   PetscScalar  *valaddr;   /* address of value */
471: } MatEntry;

473: typedef struct {
474:   PetscInt     row;
475:   PetscScalar  *valaddr;   /* address of value */
476: } MatEntry2;

478: struct  _p_MatFDColoring{
479:   PETSCHEADER(int);
480:   PetscInt       M,N,m;            /* total rows, columns; local rows */
481:   PetscInt       rstart;           /* first row owned by local processor */
482:   PetscInt       ncolors;          /* number of colors */
483:   PetscInt       *ncolumns;        /* number of local columns for a color */
484:   PetscInt       **columns;        /* lists the local columns of each color (using global column numbering) */
485:   PetscInt       *nrows;           /* number of local rows for each color */
486:   MatEntry       *matentry;        /* holds (row, column, address of value) for Jacobian matrix entry */
487:   MatEntry2      *matentry2;       /* holds (row, address of value) for Jacobian matrix entry */
488:   PetscScalar    *dy;              /* store a block of F(x+dx)-F(x) when J is in BAIJ format */
489:   PetscReal      error_rel;        /* square root of relative error in computing function */
490:   PetscReal      umin;             /* minimum allowable u'dx value */
491:   Vec            w1,w2,w3;         /* work vectors used in computing Jacobian */
492:   PetscBool      fset;             /* indicates that the initial function value F(X) is set */
493:   PetscErrorCode (*f)(void);       /* function that defines Jacobian */
494:   void           *fctx;            /* optional user-defined context for use by the function f */
495:   Vec            vscale;           /* holds FD scaling, i.e. 1/dx for each perturbed column */
496:   PetscInt       currentcolor;     /* color for which function evaluation is being done now */
497:   const char     *htype;           /* "wp" or "ds" */
498:   ISColoringType ctype;            /* IS_COLORING_GLOBAL or IS_COLORING_GHOSTED */
499:   PetscInt       brows,bcols;      /* number of block rows or columns for speedup inserting the dense matrix into sparse Jacobian */
500:   PetscBool      setupcalled;      /* true if setup has been called */
501:   void           (*ftn_func_pointer)(void),*ftn_func_cntx; /* serve the same purpose as *fortran_func_pointers in PETSc objects */
502: };

504: typedef struct _MatColoringOps *MatColoringOps;
505: struct _MatColoringOps {
506:   PetscErrorCode (*destroy)(MatColoring);
507:   PetscErrorCode (*setfromoptions)(PetscOptions*,MatColoring);
508:   PetscErrorCode (*view)(MatColoring,PetscViewer);
509:   PetscErrorCode (*apply)(MatColoring,ISColoring*);
510:   PetscErrorCode (*weights)(MatColoring,PetscReal**,PetscInt**);
511: };

513: struct _p_MatColoring {
514:   PETSCHEADER(struct _MatColoringOps);
515:   Mat                   mat;
516:   PetscInt              dist;             /* distance of the coloring */
517:   PetscInt              maxcolors;        /* the maximum number of colors returned, maxcolors=1 for MIS */
518:   void                  *data;            /* inner context */
519:   PetscBool             valid;            /* check to see if what is produced is a valid coloring */
520:   MatColoringWeightType weight_type;      /* type of weight computation to be performed */
521:   PetscReal             *user_weights;    /* custom weights and permutation */
522:   PetscInt              *user_lperm;
523: };

525: struct  _p_MatTransposeColoring{
526:   PETSCHEADER(int);
527:   PetscInt       M,N,m;            /* total rows, columns; local rows */
528:   PetscInt       rstart;           /* first row owned by local processor */
529:   PetscInt       ncolors;          /* number of colors */
530:   PetscInt       *ncolumns;        /* number of local columns for a color */
531:   PetscInt       *nrows;           /* number of local rows for each color */
532:   PetscInt       currentcolor;     /* color for which function evaluation is being done now */
533:   ISColoringType ctype;            /* IS_COLORING_GLOBAL or IS_COLORING_GHOSTED */

535:   PetscInt       *colorforrow,*colorforcol;  /* pointer to rows and columns */
536:   PetscInt       *rows;                      /* lists the local rows for each color (using the local row numbering) */
537:   PetscInt       *den2sp;                    /* maps (row,color) in the dense matrix to index of sparse matrix array a->a */
538:   PetscInt       *columns;                   /* lists the local columns of each color (using global column numbering) */
539:   PetscInt       brows;                      /* number of rows for efficient implementation of MatTransColoringApplyDenToSp() */
540:   PetscInt       *lstart;                    /* array used for loop over row blocks of Csparse */
541: };

543: /*
544:    Null space context for preconditioner/operators
545: */
546: struct _p_MatNullSpace {
547:   PETSCHEADER(int);
548:   PetscBool      has_cnst;
549:   PetscInt       n;
550:   Vec*           vecs;
551:   PetscScalar*   alpha;                 /* for projections */
552:   PetscErrorCode (*remove)(MatNullSpace,Vec,void*);  /* for user provided removal function */
553:   void*          rmctx;                 /* context for remove() function */
554: };

556: /*
557:    Checking zero pivot for LU, ILU preconditioners.
558: */
559: typedef struct {
560:   PetscInt       nshift,nshift_max;
561:   PetscReal      shift_amount,shift_lo,shift_hi,shift_top,shift_fraction;
562:   PetscBool      newshift;
563:   PetscReal      rs;  /* active row sum of abs(offdiagonals) */
564:   PetscScalar    pv;  /* pivot of the active row */
565: } FactorShiftCtx;

567: PETSC_EXTERN PetscErrorCode MatFactorDumpMatrix(Mat);
568: PETSC_EXTERN PetscErrorCode MatShift_Basic(Mat,PetscScalar);

572: PETSC_STATIC_INLINE PetscErrorCode MatPivotCheck_nz(Mat mat,const MatFactorInfo *info,FactorShiftCtx *sctx,PetscInt row)
573: {
574:   PetscReal _rs   = sctx->rs;
575:   PetscReal _zero = info->zeropivot*_rs;

578:   if (PetscAbsScalar(sctx->pv) <= _zero){
579:     /* force |diag| > zeropivot*rs */
580:     if (!sctx->nshift) sctx->shift_amount = info->shiftamount;
581:     else sctx->shift_amount *= 2.0;
582:     sctx->newshift = PETSC_TRUE;
583:     (sctx->nshift)++;
584:   } else {
585:     sctx->newshift = PETSC_FALSE;
586:   }
587:   return(0);
588: }

592: PETSC_STATIC_INLINE PetscErrorCode MatPivotCheck_pd(Mat mat,const MatFactorInfo *info,FactorShiftCtx *sctx,PetscInt row)
593: {
594:   PetscReal _rs   = sctx->rs;
595:   PetscReal _zero = info->zeropivot*_rs;

598:   if (PetscRealPart(sctx->pv) <= _zero){
599:     /* force matfactor to be diagonally dominant */
600:     if (sctx->nshift == sctx->nshift_max) {
601:       sctx->shift_fraction = sctx->shift_hi;
602:     } else {
603:       sctx->shift_lo = sctx->shift_fraction;
604:       sctx->shift_fraction = (sctx->shift_hi+sctx->shift_lo)/2.;
605:     }
606:     sctx->shift_amount = sctx->shift_fraction * sctx->shift_top;
607:     sctx->nshift++;
608:     sctx->newshift = PETSC_TRUE;
609:   } else {
610:     sctx->newshift = PETSC_FALSE;
611:   }
612:   return(0);
613: }

617: PETSC_STATIC_INLINE PetscErrorCode MatPivotCheck_inblocks(Mat mat,const MatFactorInfo *info,FactorShiftCtx *sctx,PetscInt row)
618: {
619:   PetscReal _zero = info->zeropivot;

622:   if (PetscAbsScalar(sctx->pv) <= _zero){
623:     sctx->pv          += info->shiftamount;
624:     sctx->shift_amount = 0.0;
625:     sctx->nshift++;
626:   }
627:   sctx->newshift = PETSC_FALSE;
628:   return(0);
629: }

633: PETSC_STATIC_INLINE PetscErrorCode MatPivotCheck_none(Mat mat,const MatFactorInfo *info,FactorShiftCtx *sctx,PetscInt row)
634: {
635:   PetscReal      _zero = info->zeropivot;

639:   sctx->newshift = PETSC_FALSE;
640:   if (PetscAbsScalar(sctx->pv) <= _zero) {
641:     if (!mat->erroriffpe) {
642:       PetscInfo3(mat,"Detected zero pivot in factorization in row %D value %g tolerance %g",row,(double)PetscAbsScalar(sctx->pv),(double)_zero);
643:     } else SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_MAT_LU_ZRPVT,"Zero pivot row %D value %g tolerance %g",row,(double)PetscAbsScalar(sctx->pv),(double)_zero);
644:   }
645:   return(0);
646: }

650: PETSC_STATIC_INLINE PetscErrorCode MatPivotCheck(Mat mat,const MatFactorInfo *info,FactorShiftCtx *sctx,PetscInt row)
651: {

655:   if (info->shifttype == (PetscReal) MAT_SHIFT_NONZERO){
656:     MatPivotCheck_nz(mat,info,sctx,row);
657:   } else if (info->shifttype == (PetscReal) MAT_SHIFT_POSITIVE_DEFINITE){
658:     MatPivotCheck_pd(mat,info,sctx,row);
659:   } else if (info->shifttype == (PetscReal) MAT_SHIFT_INBLOCKS){
660:     MatPivotCheck_inblocks(mat,info,sctx,row);
661:   } else {
662:     MatPivotCheck_none(mat,info,sctx,row);
663:   }
664:   return(0);
665: }

667: /*
668:   Create and initialize a linked list
669:   Input Parameters:
670:     idx_start - starting index of the list
671:     lnk_max   - max value of lnk indicating the end of the list
672:     nlnk      - max length of the list
673:   Output Parameters:
674:     lnk       - list initialized
675:     bt        - PetscBT (bitarray) with all bits set to false
676:     lnk_empty - flg indicating the list is empty
677: */
678: #define PetscLLCreate(idx_start,lnk_max,nlnk,lnk,bt) \
679:   (PetscMalloc1(nlnk,&lnk) || PetscBTCreate(nlnk,&(bt)) || (lnk[idx_start] = lnk_max,0))

681: #define PetscLLCreate_new(idx_start,lnk_max,nlnk,lnk,bt,lnk_empty)\
682:   (PetscMalloc1(nlnk,&lnk) || PetscBTCreate(nlnk,&(bt)) || (lnk_empty = PETSC_TRUE,0) ||(lnk[idx_start] = lnk_max,0))

684: /*
685:   Add an index set into a sorted linked list
686:   Input Parameters:
687:     nidx      - number of input indices
688:     indices   - interger array
689:     idx_start - starting index of the list
690:     lnk       - linked list(an integer array) that is created
691:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
692:   output Parameters:
693:     nlnk      - number of newly added indices
694:     lnk       - the sorted(increasing order) linked list containing new and non-redundate entries from indices
695:     bt        - updated PetscBT (bitarray)
696: */
697: #define PetscLLAdd(nidx,indices,idx_start,nlnk,lnk,bt) 0;\
698: {\
699:   PetscInt _k,_entry,_location,_lnkdata;\
700:   nlnk     = 0;\
701:   _lnkdata = idx_start;\
702:   for (_k=0; _k<nidx; _k++){\
703:     _entry = indices[_k];\
704:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
705:       /* search for insertion location */\
706:       /* start from the beginning if _entry < previous _entry */\
707:       if (_k && _entry < _lnkdata) _lnkdata  = idx_start;\
708:       do {\
709:         _location = _lnkdata;\
710:         _lnkdata  = lnk[_location];\
711:       } while (_entry > _lnkdata);\
712:       /* insertion location is found, add entry into lnk */\
713:       lnk[_location] = _entry;\
714:       lnk[_entry]    = _lnkdata;\
715:       nlnk++;\
716:       _lnkdata = _entry; /* next search starts from here if next_entry > _entry */\
717:     }\
718:   }\
719: }

721: /*
722:   Add a permuted index set into a sorted linked list
723:   Input Parameters:
724:     nidx      - number of input indices
725:     indices   - interger array
726:     perm      - permutation of indices
727:     idx_start - starting index of the list
728:     lnk       - linked list(an integer array) that is created
729:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
730:   output Parameters:
731:     nlnk      - number of newly added indices
732:     lnk       - the sorted(increasing order) linked list containing new and non-redundate entries from indices
733:     bt        - updated PetscBT (bitarray)
734: */
735: #define PetscLLAddPerm(nidx,indices,perm,idx_start,nlnk,lnk,bt) 0;\
736: {\
737:   PetscInt _k,_entry,_location,_lnkdata;\
738:   nlnk     = 0;\
739:   _lnkdata = idx_start;\
740:   for (_k=0; _k<nidx; _k++){\
741:     _entry = perm[indices[_k]];\
742:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
743:       /* search for insertion location */\
744:       /* start from the beginning if _entry < previous _entry */\
745:       if (_k && _entry < _lnkdata) _lnkdata  = idx_start;\
746:       do {\
747:         _location = _lnkdata;\
748:         _lnkdata  = lnk[_location];\
749:       } while (_entry > _lnkdata);\
750:       /* insertion location is found, add entry into lnk */\
751:       lnk[_location] = _entry;\
752:       lnk[_entry]    = _lnkdata;\
753:       nlnk++;\
754:       _lnkdata = _entry; /* next search starts from here if next_entry > _entry */\
755:     }\
756:   }\
757: }

759: /*
760:   Add a SORTED ascending index set into a sorted linked list - same as PetscLLAdd() bus skip 'if (_k && _entry < _lnkdata) _lnkdata  = idx_start;'
761:   Input Parameters:
762:     nidx      - number of input indices
763:     indices   - sorted interger array
764:     idx_start - starting index of the list
765:     lnk       - linked list(an integer array) that is created
766:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
767:   output Parameters:
768:     nlnk      - number of newly added indices
769:     lnk       - the sorted(increasing order) linked list containing new and non-redundate entries from indices
770:     bt        - updated PetscBT (bitarray)
771: */
772: #define PetscLLAddSorted(nidx,indices,idx_start,nlnk,lnk,bt) 0;\
773: {\
774:   PetscInt _k,_entry,_location,_lnkdata;\
775:   nlnk      = 0;\
776:   _lnkdata  = idx_start;\
777:   for (_k=0; _k<nidx; _k++){\
778:     _entry = indices[_k];\
779:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
780:       /* search for insertion location */\
781:       do {\
782:         _location = _lnkdata;\
783:         _lnkdata  = lnk[_location];\
784:       } while (_entry > _lnkdata);\
785:       /* insertion location is found, add entry into lnk */\
786:       lnk[_location] = _entry;\
787:       lnk[_entry]    = _lnkdata;\
788:       nlnk++;\
789:       _lnkdata = _entry; /* next search starts from here */\
790:     }\
791:   }\
792: }

794: #define PetscLLAddSorted_new(nidx,indices,idx_start,lnk_empty,nlnk,lnk,bt) 0; \
795: {\
796:   PetscInt _k,_entry,_location,_lnkdata;\
797:   if (lnk_empty){\
798:     _lnkdata  = idx_start;                      \
799:     for (_k=0; _k<nidx; _k++){                  \
800:       _entry = indices[_k];                             \
801:       PetscBTSet(bt,_entry);  /* mark the new entry */          \
802:           _location = _lnkdata;                                 \
803:           _lnkdata  = lnk[_location];                           \
804:         /* insertion location is found, add entry into lnk */   \
805:         lnk[_location] = _entry;                                \
806:         lnk[_entry]    = _lnkdata;                              \
807:         _lnkdata = _entry; /* next search starts from here */   \
808:     }                                                           \
809:     /*\
810:     lnk[indices[nidx-1]] = lnk[idx_start];\
811:     lnk[idx_start]       = indices[0];\
812:     PetscBTSet(bt,indices[0]);  \
813:     for (_k=1; _k<nidx; _k++){                  \
814:       PetscBTSet(bt,indices[_k]);                                          \
815:       lnk[indices[_k-1]] = indices[_k];                                  \
816:     }                                                           \
817:      */\
818:     nlnk      = nidx;\
819:     lnk_empty = PETSC_FALSE;\
820:   } else {\
821:     nlnk      = 0;                              \
822:     _lnkdata  = idx_start;                      \
823:     for (_k=0; _k<nidx; _k++){                  \
824:       _entry = indices[_k];                             \
825:       if (!PetscBTLookupSet(bt,_entry)){  /* new entry */       \
826:         /* search for insertion location */                     \
827:         do {                                                    \
828:           _location = _lnkdata;                                 \
829:           _lnkdata  = lnk[_location];                           \
830:         } while (_entry > _lnkdata);                            \
831:         /* insertion location is found, add entry into lnk */   \
832:         lnk[_location] = _entry;                                \
833:         lnk[_entry]    = _lnkdata;                              \
834:         nlnk++;                                                 \
835:         _lnkdata = _entry; /* next search starts from here */   \
836:       }                                                         \
837:     }                                                           \
838:   }                                                             \
839: }

841: /*
842:   Add a SORTED index set into a sorted linked list used for LUFactorSymbolic()
843:   Same as PetscLLAddSorted() with an additional operation:
844:        count the number of input indices that are no larger than 'diag'
845:   Input Parameters:
846:     indices   - sorted interger array
847:     idx_start - starting index of the list, index of pivot row
848:     lnk       - linked list(an integer array) that is created
849:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
850:     diag      - index of the active row in LUFactorSymbolic
851:     nzbd      - number of input indices with indices <= idx_start
852:     im        - im[idx_start] is initialized as num of nonzero entries in row=idx_start
853:   output Parameters:
854:     nlnk      - number of newly added indices
855:     lnk       - the sorted(increasing order) linked list containing new and non-redundate entries from indices
856:     bt        - updated PetscBT (bitarray)
857:     im        - im[idx_start]: unchanged if diag is not an entry
858:                              : num of entries with indices <= diag if diag is an entry
859: */
860: #define PetscLLAddSortedLU(indices,idx_start,nlnk,lnk,bt,diag,nzbd,im) 0;\
861: {\
862:   PetscInt _k,_entry,_location,_lnkdata,_nidx;\
863:   nlnk     = 0;\
864:   _lnkdata = idx_start;\
865:   _nidx = im[idx_start] - nzbd; /* num of entries with idx_start < index <= diag */\
866:   for (_k=0; _k<_nidx; _k++){\
867:     _entry = indices[_k];\
868:     nzbd++;\
869:     if ( _entry== diag) im[idx_start] = nzbd;\
870:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
871:       /* search for insertion location */\
872:       do {\
873:         _location = _lnkdata;\
874:         _lnkdata  = lnk[_location];\
875:       } while (_entry > _lnkdata);\
876:       /* insertion location is found, add entry into lnk */\
877:       lnk[_location] = _entry;\
878:       lnk[_entry]    = _lnkdata;\
879:       nlnk++;\
880:       _lnkdata = _entry; /* next search starts from here */\
881:     }\
882:   }\
883: }

885: /*
886:   Copy data on the list into an array, then initialize the list
887:   Input Parameters:
888:     idx_start - starting index of the list
889:     lnk_max   - max value of lnk indicating the end of the list
890:     nlnk      - number of data on the list to be copied
891:     lnk       - linked list
892:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
893:   output Parameters:
894:     indices   - array that contains the copied data
895:     lnk       - linked list that is cleaned and initialize
896:     bt        - PetscBT (bitarray) with all bits set to false
897: */
898: #define PetscLLClean(idx_start,lnk_max,nlnk,lnk,indices,bt) 0;\
899: {\
900:   PetscInt _j,_idx=idx_start;\
901:   for (_j=0; _j<nlnk; _j++){\
902:     _idx = lnk[_idx];\
903:     indices[_j] = _idx;\
904:     PetscBTClear(bt,_idx);\
905:   }\
906:   lnk[idx_start] = lnk_max;\
907: }
908: /*
909:   Free memories used by the list
910: */
911: #define PetscLLDestroy(lnk,bt) (PetscFree(lnk) || PetscBTDestroy(&(bt)))

913: /* Routines below are used for incomplete matrix factorization */
914: /*
915:   Create and initialize a linked list and its levels
916:   Input Parameters:
917:     idx_start - starting index of the list
918:     lnk_max   - max value of lnk indicating the end of the list
919:     nlnk      - max length of the list
920:   Output Parameters:
921:     lnk       - list initialized
922:     lnk_lvl   - array of size nlnk for storing levels of lnk
923:     bt        - PetscBT (bitarray) with all bits set to false
924: */
925: #define PetscIncompleteLLCreate(idx_start,lnk_max,nlnk,lnk,lnk_lvl,bt)\
926:   (PetscMalloc1(2*nlnk,&lnk) || PetscBTCreate(nlnk,&(bt)) || (lnk[idx_start] = lnk_max,lnk_lvl = lnk + nlnk,0))

928: /*
929:   Initialize a sorted linked list used for ILU and ICC
930:   Input Parameters:
931:     nidx      - number of input idx
932:     idx       - interger array used for storing column indices
933:     idx_start - starting index of the list
934:     perm      - indices of an IS
935:     lnk       - linked list(an integer array) that is created
936:     lnklvl    - levels of lnk
937:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
938:   output Parameters:
939:     nlnk     - number of newly added idx
940:     lnk      - the sorted(increasing order) linked list containing new and non-redundate entries from idx
941:     lnklvl   - levels of lnk
942:     bt       - updated PetscBT (bitarray)
943: */
944: #define PetscIncompleteLLInit(nidx,idx,idx_start,perm,nlnk,lnk,lnklvl,bt) 0;\
945: {\
946:   PetscInt _k,_entry,_location,_lnkdata;\
947:   nlnk     = 0;\
948:   _lnkdata = idx_start;\
949:   for (_k=0; _k<nidx; _k++){\
950:     _entry = perm[idx[_k]];\
951:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
952:       /* search for insertion location */\
953:       if (_k && _entry < _lnkdata) _lnkdata  = idx_start;\
954:       do {\
955:         _location = _lnkdata;\
956:         _lnkdata  = lnk[_location];\
957:       } while (_entry > _lnkdata);\
958:       /* insertion location is found, add entry into lnk */\
959:       lnk[_location]  = _entry;\
960:       lnk[_entry]     = _lnkdata;\
961:       lnklvl[_entry] = 0;\
962:       nlnk++;\
963:       _lnkdata = _entry; /* next search starts from here if next_entry > _entry */\
964:     }\
965:   }\
966: }

968: /*
969:   Add a SORTED index set into a sorted linked list for ILU
970:   Input Parameters:
971:     nidx      - number of input indices
972:     idx       - sorted interger array used for storing column indices
973:     level     - level of fill, e.g., ICC(level)
974:     idxlvl    - level of idx
975:     idx_start - starting index of the list
976:     lnk       - linked list(an integer array) that is created
977:     lnklvl    - levels of lnk
978:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
979:     prow      - the row number of idx
980:   output Parameters:
981:     nlnk     - number of newly added idx
982:     lnk      - the sorted(increasing order) linked list containing new and non-redundate entries from idx
983:     lnklvl   - levels of lnk
984:     bt       - updated PetscBT (bitarray)

986:   Note: the level of factor(i,j) is set as lvl(i,j) = min{ lvl(i,j), lvl(i,prow)+lvl(prow,j)+1)
987:         where idx = non-zero columns of U(prow,prow+1:n-1), prow<i
988: */
989: #define PetscILULLAddSorted(nidx,idx,level,idxlvl,idx_start,nlnk,lnk,lnklvl,bt,lnklvl_prow) 0;\
990: {\
991:   PetscInt _k,_entry,_location,_lnkdata,_incrlev,_lnklvl_prow=lnklvl[prow];\
992:   nlnk     = 0;\
993:   _lnkdata = idx_start;\
994:   for (_k=0; _k<nidx; _k++){\
995:     _incrlev = idxlvl[_k] + _lnklvl_prow + 1;\
996:     if (_incrlev > level) continue;\
997:     _entry = idx[_k];\
998:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
999:       /* search for insertion location */\
1000:       do {\
1001:         _location = _lnkdata;\
1002:         _lnkdata  = lnk[_location];\
1003:       } while (_entry > _lnkdata);\
1004:       /* insertion location is found, add entry into lnk */\
1005:       lnk[_location]  = _entry;\
1006:       lnk[_entry]     = _lnkdata;\
1007:       lnklvl[_entry] = _incrlev;\
1008:       nlnk++;\
1009:       _lnkdata = _entry; /* next search starts from here if next_entry > _entry */\
1010:     } else { /* existing entry: update lnklvl */\
1011:       if (lnklvl[_entry] > _incrlev) lnklvl[_entry] = _incrlev;\
1012:     }\
1013:   }\
1014: }

1016: /*
1017:   Add a index set into a sorted linked list
1018:   Input Parameters:
1019:     nidx      - number of input idx
1020:     idx   - interger array used for storing column indices
1021:     level     - level of fill, e.g., ICC(level)
1022:     idxlvl - level of idx
1023:     idx_start - starting index of the list
1024:     lnk       - linked list(an integer array) that is created
1025:     lnklvl   - levels of lnk
1026:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
1027:   output Parameters:
1028:     nlnk      - number of newly added idx
1029:     lnk       - the sorted(increasing order) linked list containing new and non-redundate entries from idx
1030:     lnklvl   - levels of lnk
1031:     bt        - updated PetscBT (bitarray)
1032: */
1033: #define PetscIncompleteLLAdd(nidx,idx,level,idxlvl,idx_start,nlnk,lnk,lnklvl,bt) 0;\
1034: {\
1035:   PetscInt _k,_entry,_location,_lnkdata,_incrlev;\
1036:   nlnk     = 0;\
1037:   _lnkdata = idx_start;\
1038:   for (_k=0; _k<nidx; _k++){\
1039:     _incrlev = idxlvl[_k] + 1;\
1040:     if (_incrlev > level) continue;\
1041:     _entry = idx[_k];\
1042:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
1043:       /* search for insertion location */\
1044:       if (_k && _entry < _lnkdata) _lnkdata  = idx_start;\
1045:       do {\
1046:         _location = _lnkdata;\
1047:         _lnkdata  = lnk[_location];\
1048:       } while (_entry > _lnkdata);\
1049:       /* insertion location is found, add entry into lnk */\
1050:       lnk[_location]  = _entry;\
1051:       lnk[_entry]     = _lnkdata;\
1052:       lnklvl[_entry] = _incrlev;\
1053:       nlnk++;\
1054:       _lnkdata = _entry; /* next search starts from here if next_entry > _entry */\
1055:     } else { /* existing entry: update lnklvl */\
1056:       if (lnklvl[_entry] > _incrlev) lnklvl[_entry] = _incrlev;\
1057:     }\
1058:   }\
1059: }

1061: /*
1062:   Add a SORTED index set into a sorted linked list
1063:   Input Parameters:
1064:     nidx      - number of input indices
1065:     idx   - sorted interger array used for storing column indices
1066:     level     - level of fill, e.g., ICC(level)
1067:     idxlvl - level of idx
1068:     idx_start - starting index of the list
1069:     lnk       - linked list(an integer array) that is created
1070:     lnklvl    - levels of lnk
1071:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
1072:   output Parameters:
1073:     nlnk      - number of newly added idx
1074:     lnk       - the sorted(increasing order) linked list containing new and non-redundate entries from idx
1075:     lnklvl    - levels of lnk
1076:     bt        - updated PetscBT (bitarray)
1077: */
1078: #define PetscIncompleteLLAddSorted(nidx,idx,level,idxlvl,idx_start,nlnk,lnk,lnklvl,bt) 0;\
1079: {\
1080:   PetscInt _k,_entry,_location,_lnkdata,_incrlev;\
1081:   nlnk = 0;\
1082:   _lnkdata = idx_start;\
1083:   for (_k=0; _k<nidx; _k++){\
1084:     _incrlev = idxlvl[_k] + 1;\
1085:     if (_incrlev > level) continue;\
1086:     _entry = idx[_k];\
1087:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
1088:       /* search for insertion location */\
1089:       do {\
1090:         _location = _lnkdata;\
1091:         _lnkdata  = lnk[_location];\
1092:       } while (_entry > _lnkdata);\
1093:       /* insertion location is found, add entry into lnk */\
1094:       lnk[_location] = _entry;\
1095:       lnk[_entry]    = _lnkdata;\
1096:       lnklvl[_entry] = _incrlev;\
1097:       nlnk++;\
1098:       _lnkdata = _entry; /* next search starts from here */\
1099:     } else { /* existing entry: update lnklvl */\
1100:       if (lnklvl[_entry] > _incrlev) lnklvl[_entry] = _incrlev;\
1101:     }\
1102:   }\
1103: }

1105: /*
1106:   Add a SORTED index set into a sorted linked list for ICC
1107:   Input Parameters:
1108:     nidx      - number of input indices
1109:     idx       - sorted interger array used for storing column indices
1110:     level     - level of fill, e.g., ICC(level)
1111:     idxlvl    - level of idx
1112:     idx_start - starting index of the list
1113:     lnk       - linked list(an integer array) that is created
1114:     lnklvl    - levels of lnk
1115:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
1116:     idxlvl_prow - idxlvl[prow], where prow is the row number of the idx
1117:   output Parameters:
1118:     nlnk   - number of newly added indices
1119:     lnk    - the sorted(increasing order) linked list containing new and non-redundate entries from idx
1120:     lnklvl - levels of lnk
1121:     bt     - updated PetscBT (bitarray)
1122:   Note: the level of U(i,j) is set as lvl(i,j) = min{ lvl(i,j), lvl(prow,i)+lvl(prow,j)+1)
1123:         where idx = non-zero columns of U(prow,prow+1:n-1), prow<i
1124: */
1125: #define PetscICCLLAddSorted(nidx,idx,level,idxlvl,idx_start,nlnk,lnk,lnklvl,bt,idxlvl_prow) 0;\
1126: {\
1127:   PetscInt _k,_entry,_location,_lnkdata,_incrlev;\
1128:   nlnk = 0;\
1129:   _lnkdata = idx_start;\
1130:   for (_k=0; _k<nidx; _k++){\
1131:     _incrlev = idxlvl[_k] + idxlvl_prow + 1;\
1132:     if (_incrlev > level) continue;\
1133:     _entry = idx[_k];\
1134:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
1135:       /* search for insertion location */\
1136:       do {\
1137:         _location = _lnkdata;\
1138:         _lnkdata  = lnk[_location];\
1139:       } while (_entry > _lnkdata);\
1140:       /* insertion location is found, add entry into lnk */\
1141:       lnk[_location] = _entry;\
1142:       lnk[_entry]    = _lnkdata;\
1143:       lnklvl[_entry] = _incrlev;\
1144:       nlnk++;\
1145:       _lnkdata = _entry; /* next search starts from here */\
1146:     } else { /* existing entry: update lnklvl */\
1147:       if (lnklvl[_entry] > _incrlev) lnklvl[_entry] = _incrlev;\
1148:     }\
1149:   }\
1150: }

1152: /*
1153:   Copy data on the list into an array, then initialize the list
1154:   Input Parameters:
1155:     idx_start - starting index of the list
1156:     lnk_max   - max value of lnk indicating the end of the list
1157:     nlnk      - number of data on the list to be copied
1158:     lnk       - linked list
1159:     lnklvl    - level of lnk
1160:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
1161:   output Parameters:
1162:     indices - array that contains the copied data
1163:     lnk     - linked list that is cleaned and initialize
1164:     lnklvl  - level of lnk that is reinitialized
1165:     bt      - PetscBT (bitarray) with all bits set to false
1166: */
1167: #define PetscIncompleteLLClean(idx_start,lnk_max,nlnk,lnk,lnklvl,indices,indiceslvl,bt) 0;\
1168: {\
1169:   PetscInt _j,_idx=idx_start;\
1170:   for (_j=0; _j<nlnk; _j++){\
1171:     _idx = lnk[_idx];\
1172:     *(indices+_j) = _idx;\
1173:     *(indiceslvl+_j) = lnklvl[_idx];\
1174:     lnklvl[_idx] = -1;\
1175:     PetscBTClear(bt,_idx);\
1176:   }\
1177:   lnk[idx_start] = lnk_max;\
1178: }
1179: /*
1180:   Free memories used by the list
1181: */
1182: #define PetscIncompleteLLDestroy(lnk,bt) (PetscFree(lnk) || PetscBTDestroy(&(bt)))

1184: /* -------------------------------------------------------------------------------------------------------*/
1185: #include <petscbt.h>
1188: /*
1189:   Create and initialize a condensed linked list -
1190:     same as PetscLLCreate(), but uses a scalable array 'lnk' with size of max number of entries, not O(N).
1191:     Barry suggested this approach (Dec. 6, 2011):
1192:       I've thought of an alternative way of representing a linked list that is efficient but doesn't have the O(N) scaling issue
1193:       (it may be faster than the O(N) even sequentially due to less crazy memory access).

1195:       Instead of having some like  a  2  -> 4 -> 11 ->  22  list that uses slot 2  4 11 and 22 in a big array use a small array with two slots
1196:       for each entry for example  [ 2 1 | 4 3 | 22 -1 | 11 2]   so the first number (of the pair) is the value while the second tells you where
1197:       in the list the next entry is. Inserting a new link means just append another pair at the end. For example say we want to insert 13 into the
1198:       list it would then become [2 1 | 4 3 | 22 -1 | 11 4 | 13 2 ] you just add a pair at the end and fix the point for the one that points to it.
1199:       That is 11 use to point to the 2 slot, after the change 11 points to the 4th slot which has the value 13. Note that values are always next
1200:       to each other so memory access is much better than using the big array.

1202:   Example:
1203:      nlnk_max=5, lnk_max=36:
1204:      Initial list: [0, 0 | 36, 2 | 0, 0 | 0, 0 | 0, 0 | 0, 0 | 0, 0]
1205:      here, head_node has index 2 with value lnk[2]=lnk_max=36,
1206:            0-th entry is used to store the number of entries in the list,
1207:      The initial lnk represents head -> tail(marked by 36) with number of entries = lnk[0]=0.

1209:      Now adding a sorted set {2,4}, the list becomes
1210:      [2, 0 | 36, 4 |2, 6 | 4, 2 | 0, 0 | 0, 0 | 0, 0 ]
1211:      represents head -> 2 -> 4 -> tail with number of entries = lnk[0]=2.

1213:      Then adding a sorted set {0,3,35}, the list
1214:      [5, 0 | 36, 8 | 2, 10 | 4, 12 | 0, 4 | 3, 6 | 35, 2 ]
1215:      represents head -> 0 -> 2 -> 3 -> 4 -> 35 -> tail with number of entries = lnk[0]=5.

1217:   Input Parameters:
1218:     nlnk_max  - max length of the list
1219:     lnk_max   - max value of the entries
1220:   Output Parameters:
1221:     lnk       - list created and initialized
1222:     bt        - PetscBT (bitarray) with all bits set to false. Note: bt has size lnk_max, not nln_max!
1223: */
1224: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedCreate(PetscInt nlnk_max,PetscInt lnk_max,PetscInt **lnk,PetscBT *bt)
1225: {
1227:   PetscInt       *llnk;

1230:   PetscMalloc1(2*(nlnk_max+2),lnk);
1231:   PetscBTCreate(lnk_max,bt);
1232:   llnk = *lnk;
1233:   llnk[0] = 0;         /* number of entries on the list */
1234:   llnk[2] = lnk_max;   /* value in the head node */
1235:   llnk[3] = 2;         /* next for the head node */
1236:   return(0);
1237: }

1241: /*
1242:   Add a SORTED ascending index set into a sorted linked list. See PetscLLCondensedCreate() for detailed description.
1243:   Input Parameters:
1244:     nidx      - number of input indices
1245:     indices   - sorted interger array
1246:     lnk       - condensed linked list(an integer array) that is created
1247:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
1248:   output Parameters:
1249:     lnk       - the sorted(increasing order) linked list containing previous and newly added non-redundate indices
1250:     bt        - updated PetscBT (bitarray)
1251: */
1252: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedAddSorted(PetscInt nidx,const PetscInt indices[],PetscInt lnk[],PetscBT bt)
1253: {
1254:   PetscInt _k,_entry,_location,_next,_lnkdata,_nlnk,_newnode;

1257:   _nlnk     = lnk[0]; /* num of entries on the input lnk */
1258:   _location = 2; /* head */
1259:     for (_k=0; _k<nidx; _k++){
1260:       _entry = indices[_k];
1261:       if (!PetscBTLookupSet(bt,_entry)){  /* new entry */
1262:         /* search for insertion location */
1263:         do {
1264:           _next     = _location + 1; /* link from previous node to next node */
1265:           _location = lnk[_next];    /* idx of next node */
1266:           _lnkdata  = lnk[_location];/* value of next node */
1267:         } while (_entry > _lnkdata);
1268:         /* insertion location is found, add entry into lnk */
1269:         _newnode        = 2*(_nlnk+2);   /* index for this new node */
1270:         lnk[_next]      = _newnode;      /* connect previous node to the new node */
1271:         lnk[_newnode]   = _entry;        /* set value of the new node */
1272:         lnk[_newnode+1] = _location;     /* connect new node to next node */
1273:         _location       = _newnode;      /* next search starts from the new node */
1274:         _nlnk++;
1275:       }   \
1276:     }\
1277:   lnk[0]   = _nlnk;   /* number of entries in the list */
1278:   return(0);
1279: }

1283: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedClean(PetscInt lnk_max,PetscInt nidx,PetscInt *indices,PetscInt lnk[],PetscBT bt)
1284: {
1286:   PetscInt       _k,_next,_nlnk;

1289:   _next = lnk[3];       /* head node */
1290:   _nlnk = lnk[0];       /* num of entries on the list */
1291:   for (_k=0; _k<_nlnk; _k++){
1292:     indices[_k] = lnk[_next];
1293:     _next       = lnk[_next + 1];
1294:     PetscBTClear(bt,indices[_k]);
1295:   }
1296:   lnk[0] = 0;          /* num of entries on the list */
1297:   lnk[2] = lnk_max;    /* initialize head node */
1298:   lnk[3] = 2;          /* head node */
1299:   return(0);
1300: }

1304: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedView(PetscInt *lnk)
1305: {
1307:   PetscInt       k;

1310:   PetscPrintf(PETSC_COMM_SELF,"LLCondensed of size %d, (val,  next)\n",lnk[0]);
1311:   for (k=2; k< lnk[0]+2; k++){
1312:     PetscPrintf(PETSC_COMM_SELF," %D: (%D, %D)\n",2*k,lnk[2*k],lnk[2*k+1]);
1313:   }
1314:   return(0);
1315: }

1319: /*
1320:   Free memories used by the list
1321: */
1322: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedDestroy(PetscInt *lnk,PetscBT bt)
1323: {

1327:   PetscFree(lnk);
1328:   PetscBTDestroy(&bt);
1329:   return(0);
1330: }

1332: /* -------------------------------------------------------------------------------------------------------*/
1335: /*
1336:  Same as PetscLLCondensedCreate(), but does not use non-scalable O(lnk_max) bitarray
1337:   Input Parameters:
1338:     nlnk_max  - max length of the list
1339:   Output Parameters:
1340:     lnk       - list created and initialized
1341: */
1342: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedCreate_Scalable(PetscInt nlnk_max,PetscInt **lnk)
1343: {
1345:   PetscInt       *llnk;

1348:   PetscMalloc1(2*(nlnk_max+2),lnk);
1349:   llnk = *lnk;
1350:   llnk[0] = 0;               /* number of entries on the list */
1351:   llnk[2] = PETSC_MAX_INT;   /* value in the head node */
1352:   llnk[3] = 2;               /* next for the head node */
1353:   return(0);
1354: }

1358: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedAddSorted_Scalable(PetscInt nidx,const PetscInt indices[],PetscInt lnk[])
1359: {
1360:   PetscInt _k,_entry,_location,_next,_lnkdata,_nlnk,_newnode;
1361:   _nlnk     = lnk[0]; /* num of entries on the input lnk */
1362:   _location = 2; /* head */ \
1363:     for (_k=0; _k<nidx; _k++){
1364:       _entry = indices[_k];
1365:       /* search for insertion location */
1366:       do {
1367:         _next     = _location + 1; /* link from previous node to next node */
1368:         _location = lnk[_next];    /* idx of next node */
1369:         _lnkdata  = lnk[_location];/* value of next node */
1370:       } while (_entry > _lnkdata);
1371:       if (_entry < _lnkdata) {
1372:         /* insertion location is found, add entry into lnk */
1373:         _newnode        = 2*(_nlnk+2);   /* index for this new node */
1374:         lnk[_next]      = _newnode;      /* connect previous node to the new node */
1375:         lnk[_newnode]   = _entry;        /* set value of the new node */
1376:         lnk[_newnode+1] = _location;     /* connect new node to next node */
1377:         _location       = _newnode;      /* next search starts from the new node */
1378:         _nlnk++;
1379:       }
1380:     }
1381:   lnk[0]   = _nlnk;   /* number of entries in the list */
1382:   return 0;
1383: }

1387: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedClean_Scalable(PetscInt nidx,PetscInt *indices,PetscInt *lnk)
1388: {
1389:   PetscInt _k,_next,_nlnk;
1390:   _next = lnk[3];       /* head node */
1391:   _nlnk = lnk[0];
1392:   for (_k=0; _k<_nlnk; _k++){
1393:     indices[_k] = lnk[_next];
1394:     _next       = lnk[_next + 1];
1395:   }
1396:   lnk[0] = 0;          /* num of entries on the list */
1397:   lnk[3] = 2;          /* head node */
1398:   return 0;
1399: }

1403: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedDestroy_Scalable(PetscInt *lnk)
1404: {
1405:   return PetscFree(lnk);
1406: }

1408: /* -------------------------------------------------------------------------------------------------------*/
1409: /*
1410:       lnk[0]   number of links
1411:       lnk[1]   number of entries
1412:       lnk[3n]  value
1413:       lnk[3n+1] len
1414:       lnk[3n+2] link to next value

1416:       The next three are always the first link

1418:       lnk[3]    PETSC_MIN_INT+1
1419:       lnk[4]    1
1420:       lnk[5]    link to first real entry

1422:       The next three are always the last link

1424:       lnk[6]    PETSC_MAX_INT - 1
1425:       lnk[7]    1
1426:       lnk[8]    next valid link (this is the same as lnk[0] but without the decreases)
1427: */

1431: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedCreate_fast(PetscInt nlnk_max,PetscInt **lnk)
1432: {
1434:   PetscInt       *llnk;

1437:   PetscMalloc1(3*(nlnk_max+3),lnk);
1438:   llnk = *lnk;
1439:   llnk[0] = 0;   /* nlnk: number of entries on the list */
1440:   llnk[1] = 0;          /* number of integer entries represented in list */
1441:   llnk[3] = PETSC_MIN_INT+1;   /* value in the first node */
1442:   llnk[4] = 1;           /* count for the first node */
1443:   llnk[5] = 6;         /* next for the first node */
1444:   llnk[6] = PETSC_MAX_INT-1;   /* value in the last node */
1445:   llnk[7] = 1;           /* count for the last node */
1446:   llnk[8] = 0;         /* next valid node to be used */
1447:   return(0);
1448: }

1450: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedAddSorted_fast(PetscInt nidx,const PetscInt indices[],PetscInt lnk[])
1451: {
1452:   PetscInt k,entry,prev,next;
1453:   prev      = 3;      /* first value */
1454:   next      = lnk[prev+2];
1455:   for (k=0; k<nidx; k++){
1456:     entry = indices[k];
1457:     /* search for insertion location */
1458:     while (entry >= lnk[next]) {
1459:       prev = next;
1460:       next = lnk[next+2];
1461:     }
1462:     /* entry is in range of previous list */
1463:     if (entry < lnk[prev]+lnk[prev+1]) continue;
1464:     lnk[1]++;
1465:     /* entry is right after previous list */
1466:     if (entry == lnk[prev]+lnk[prev+1]) {
1467:       lnk[prev+1]++;
1468:       if (lnk[next] == entry+1) { /* combine two contiquous strings */
1469:         lnk[prev+1] += lnk[next+1];
1470:         lnk[prev+2]  = lnk[next+2];
1471:         next         = lnk[next+2];
1472:         lnk[0]--;
1473:       }
1474:       continue;
1475:     }
1476:     /* entry is right before next list */
1477:     if (entry == lnk[next]-1) {
1478:       lnk[next]--;
1479:       lnk[next+1]++;
1480:       prev = next;
1481:       next = lnk[prev+2];
1482:       continue;
1483:     }
1484:     /*  add entry into lnk */
1485:     lnk[prev+2]    = 3*((lnk[8]++)+3);      /* connect previous node to the new node */
1486:     prev           = lnk[prev+2];
1487:     lnk[prev]      = entry;        /* set value of the new node */
1488:     lnk[prev+1]    = 1;             /* number of values in contiquous string is one to start */
1489:     lnk[prev+2]    = next;          /* connect new node to next node */
1490:     lnk[0]++;
1491:   }
1492:   return 0;
1493: }

1495: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedClean_fast(PetscInt nidx,PetscInt *indices,PetscInt *lnk)
1496: {
1497:   PetscInt _k,_next,_nlnk,cnt,j;
1498:   _next = lnk[5];       /* first node */
1499:   _nlnk = lnk[0];
1500:   cnt   = 0;
1501:   for (_k=0; _k<_nlnk; _k++){
1502:     for (j=0; j<lnk[_next+1]; j++) {
1503:       indices[cnt++] = lnk[_next] + j;
1504:     }
1505:     _next       = lnk[_next + 2];
1506:   }
1507:   lnk[0] = 0;   /* nlnk: number of links */
1508:   lnk[1] = 0;          /* number of integer entries represented in list */
1509:   lnk[3] = PETSC_MIN_INT+1;   /* value in the first node */
1510:   lnk[4] = 1;           /* count for the first node */
1511:   lnk[5] = 6;         /* next for the first node */
1512:   lnk[6] = PETSC_MAX_INT-1;   /* value in the last node */
1513:   lnk[7] = 1;           /* count for the last node */
1514:   lnk[8] = 0;         /* next valid location to make link */
1515:   return 0;
1516: }

1518: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedView_fast(PetscInt *lnk)
1519: {
1520:   PetscInt k,next,nlnk;
1521:   next = lnk[5];       /* first node */
1522:   nlnk = lnk[0];
1523:   for (k=0; k<nlnk; k++){
1524: #if 0                           /* Debugging code */
1525:     printf("%d value %d len %d next %d\n",next,lnk[next],lnk[next+1],lnk[next+2]);
1526: #endif
1527:     next = lnk[next + 2];
1528:   }
1529:   return 0;
1530: }

1532: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedDestroy_fast(PetscInt *lnk)
1533: {
1534:   return PetscFree(lnk);
1535: }

1537: /* alias PetscSortIntWithScalarArray while MatScalar == PetscScalar */
1538: PETSC_STATIC_INLINE PetscErrorCode PetscSortIntWithMatScalarArray(PetscInt n,PetscInt *idx,PetscScalar *val)
1539: {
1540: #if !defined(PETSC_USE_REAL_MAT_SINGLE)
1541:   return PetscSortIntWithScalarArray(n,idx,val);
1542: #else
1543:   {
1544:     MatScalar mtmp;
1545:     return PetscSortIntWithDataArray(n,idx,val,sizeof(MatScalar),&mtmp);
1546:   }
1547: #endif
1548: }

1550: PETSC_EXTERN PetscLogEvent MAT_Mult, MAT_MultMatrixFree, MAT_Mults, MAT_MultConstrained, MAT_MultAdd, MAT_MultTranspose;
1551: PETSC_EXTERN PetscLogEvent MAT_MultTransposeConstrained, MAT_MultTransposeAdd, MAT_Solve, MAT_Solves, MAT_SolveAdd, MAT_SolveTranspose;
1552: PETSC_EXTERN PetscLogEvent MAT_SolveTransposeAdd, MAT_SOR, MAT_ForwardSolve, MAT_BackwardSolve, MAT_LUFactor, MAT_LUFactorSymbolic;
1553: PETSC_EXTERN PetscLogEvent MAT_LUFactorNumeric, MAT_CholeskyFactor, MAT_CholeskyFactorSymbolic, MAT_CholeskyFactorNumeric, MAT_ILUFactor;
1554: PETSC_EXTERN PetscLogEvent MAT_ILUFactorSymbolic, MAT_ICCFactorSymbolic, MAT_Copy, MAT_Convert, MAT_Scale, MAT_AssemblyBegin;
1555: PETSC_EXTERN PetscLogEvent MAT_AssemblyEnd, MAT_SetValues, MAT_GetValues, MAT_GetRow, MAT_GetRowIJ, MAT_GetSubMatrices, MAT_GetColoring, MAT_GetOrdering, MAT_RedundantMat;
1556: PETSC_EXTERN PetscLogEvent MAT_IncreaseOverlap, MAT_Partitioning, MAT_Coarsen, MAT_ZeroEntries, MAT_Load, MAT_View, MAT_AXPY, MAT_FDColoringCreate, MAT_TransposeColoringCreate;
1557: PETSC_EXTERN PetscLogEvent MAT_FDColoringSetUp, MAT_FDColoringApply, MAT_Transpose, MAT_FDColoringFunction,MAT_GetSubMatrix;
1558: PETSC_EXTERN PetscLogEvent MAT_MatMult, MAT_MatSolve,MAT_MatMultSymbolic, MAT_MatMultNumeric,MAT_Getlocalmatcondensed,MAT_GetBrowsOfAcols,MAT_GetBrowsOfAocols;
1559: PETSC_EXTERN PetscLogEvent MAT_PtAP, MAT_PtAPSymbolic, MAT_PtAPNumeric,MAT_Seqstompinum,MAT_Seqstompisym,MAT_Seqstompi,MAT_Getlocalmat;
1560: PETSC_EXTERN PetscLogEvent MAT_RARt, MAT_RARtSymbolic, MAT_RARtNumeric;
1561: PETSC_EXTERN PetscLogEvent MAT_MatTransposeMult, MAT_MatTransposeMultSymbolic, MAT_MatTransposeMultNumeric;
1562: PETSC_EXTERN PetscLogEvent MAT_TransposeMatMult, MAT_TransposeMatMultSymbolic, MAT_TransposeMatMultNumeric;
1563: PETSC_EXTERN PetscLogEvent MAT_MatMatMult, MAT_MatMatMultSymbolic, MAT_MatMatMultNumeric;
1564: PETSC_EXTERN PetscLogEvent MAT_Applypapt, MAT_Applypapt_symbolic, MAT_Applypapt_numeric;
1565: PETSC_EXTERN PetscLogEvent MAT_Getsymtranspose, MAT_Transpose_SeqAIJ, MAT_Getsymtransreduced,MAT_GetSequentialNonzeroStructure;

1567: PETSC_EXTERN PetscLogEvent MATMFFD_Mult;
1568: PETSC_EXTERN PetscLogEvent MAT_GetMultiProcBlock;
1569: PETSC_EXTERN PetscLogEvent MAT_CUSPCopyToGPU, MAT_CUSPARSECopyToGPU, MAT_SetValuesBatch, MAT_SetValuesBatchI, MAT_SetValuesBatchII, MAT_SetValuesBatchIII, MAT_SetValuesBatchIV;
1570: PETSC_EXTERN PetscLogEvent MAT_ViennaCLCopyToGPU;
1571: PETSC_EXTERN PetscLogEvent MAT_Merge,MAT_Residual;
1572: PETSC_EXTERN PetscLogEvent Mat_Coloring_Apply,Mat_Coloring_Comm,Mat_Coloring_Local,Mat_Coloring_ISCreate,Mat_Coloring_SetUp,Mat_Coloring_Weights;

1574: #endif