Actual source code: petsc-matimpl.h
petsc-3.4.2 2013-07-02

      2: #ifndef __MATIMPL_H

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

      8: /*
      9:   This file defines the parts of the matrix data structure that are
     10:   shared by all matrix types.
     11: */

     13: /*
     14:     If you add entries here also add them to the MATOP enum
     15:     in include/petscmat.h and include/finclude/petscmat.h
     16: */
     17: typedef struct _MatOps *MatOps;
     18: struct _MatOps {
     19:   /* 0*/
     20:   PetscErrorCode (*setvalues)(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode);
     21:   PetscErrorCode (*getrow)(Mat,PetscInt,PetscInt *,PetscInt*[],PetscScalar*[]);
     22:   PetscErrorCode (*restorerow)(Mat,PetscInt,PetscInt *,PetscInt *[],PetscScalar *[]);
     23:   PetscErrorCode (*mult)(Mat,Vec,Vec);
     24:   PetscErrorCode (*multadd)(Mat,Vec,Vec,Vec);
     25:   /* 5*/
     26:   PetscErrorCode (*multtranspose)(Mat,Vec,Vec);
     27:   PetscErrorCode (*multtransposeadd)(Mat,Vec,Vec,Vec);
     28:   PetscErrorCode (*solve)(Mat,Vec,Vec);
     29:   PetscErrorCode (*solveadd)(Mat,Vec,Vec,Vec);
     30:   PetscErrorCode (*solvetranspose)(Mat,Vec,Vec);
     31:   /*10*/
     32:   PetscErrorCode (*solvetransposeadd)(Mat,Vec,Vec,Vec);
     33:   PetscErrorCode (*lufactor)(Mat,IS,IS,const MatFactorInfo*);
     34:   PetscErrorCode (*choleskyfactor)(Mat,IS,const MatFactorInfo*);
     35:   PetscErrorCode (*sor)(Mat,Vec,PetscReal,MatSORType,PetscReal,PetscInt,PetscInt,Vec);
     36:   PetscErrorCode (*transpose)(Mat,MatReuse,Mat *);
     37:   /*15*/
     38:   PetscErrorCode (*getinfo)(Mat,MatInfoType,MatInfo*);
     39:   PetscErrorCode (*equal)(Mat,Mat,PetscBool  *);
     40:   PetscErrorCode (*getdiagonal)(Mat,Vec);
     41:   PetscErrorCode (*diagonalscale)(Mat,Vec,Vec);
     42:   PetscErrorCode (*norm)(Mat,NormType,PetscReal*);
     43:   /*20*/
     44:   PetscErrorCode (*assemblybegin)(Mat,MatAssemblyType);
     45:   PetscErrorCode (*assemblyend)(Mat,MatAssemblyType);
     46:   PetscErrorCode (*setoption)(Mat,MatOption,PetscBool );
     47:   PetscErrorCode (*zeroentries)(Mat);
     48:   /*24*/
     49:   PetscErrorCode (*zerorows)(Mat,PetscInt,const PetscInt[],PetscScalar,Vec,Vec);
     50:   PetscErrorCode (*lufactorsymbolic)(Mat,Mat,IS,IS,const MatFactorInfo*);
     51:   PetscErrorCode (*lufactornumeric)(Mat,Mat,const MatFactorInfo*);
     52:   PetscErrorCode (*choleskyfactorsymbolic)(Mat,Mat,IS,const MatFactorInfo*);
     53:   PetscErrorCode (*choleskyfactornumeric)(Mat,Mat,const MatFactorInfo*);
     54:   /*29*/
     55:   PetscErrorCode (*setup)(Mat);
     56:   PetscErrorCode (*ilufactorsymbolic)(Mat,Mat,IS,IS,const MatFactorInfo*);
     57:   PetscErrorCode (*iccfactorsymbolic)(Mat,Mat,IS,const MatFactorInfo*);
     58:   PetscErrorCode (*dummy29)(Mat);
     59:   PetscErrorCode (*dummy210)(Mat);
     60:   /*34*/
     61:   PetscErrorCode (*duplicate)(Mat,MatDuplicateOption,Mat*);
     62:   PetscErrorCode (*forwardsolve)(Mat,Vec,Vec);
     63:   PetscErrorCode (*backwardsolve)(Mat,Vec,Vec);
     64:   PetscErrorCode (*ilufactor)(Mat,IS,IS,const MatFactorInfo*);
     65:   PetscErrorCode (*iccfactor)(Mat,IS,const MatFactorInfo*);
     66:   /*39*/
     67:   PetscErrorCode (*axpy)(Mat,PetscScalar,Mat,MatStructure);
     68:   PetscErrorCode (*getsubmatrices)(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat *[]);
     69:   PetscErrorCode (*increaseoverlap)(Mat,PetscInt,IS[],PetscInt);
     70:   PetscErrorCode (*getvalues)(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],PetscScalar []);
     71:   PetscErrorCode (*copy)(Mat,Mat,MatStructure);
     72:   /*44*/
     73:   PetscErrorCode (*getrowmax)(Mat,Vec,PetscInt[]);
     74:   PetscErrorCode (*scale)(Mat,PetscScalar);
     75:   PetscErrorCode (*shift)(Mat,PetscScalar);
     76:   PetscErrorCode (*diagonalset)(Mat,Vec,InsertMode);
     77:   PetscErrorCode (*zerorowscolumns)(Mat,PetscInt,const PetscInt[],PetscScalar,Vec,Vec);
     78:   /*49*/
     79:   PetscErrorCode (*setrandom)(Mat,PetscRandom);
     80:   PetscErrorCode (*getrowij)(Mat,PetscInt,PetscBool ,PetscBool ,PetscInt*,const PetscInt *[],const PetscInt *[],PetscBool  *);
     81:   PetscErrorCode (*restorerowij)(Mat,PetscInt,PetscBool ,PetscBool ,PetscInt *,const PetscInt *[],const PetscInt *[],PetscBool  *);
     82:   PetscErrorCode (*getcolumnij)(Mat,PetscInt,PetscBool ,PetscBool ,PetscInt*,const PetscInt *[],const PetscInt *[],PetscBool  *);
     83:   PetscErrorCode (*restorecolumnij)(Mat,PetscInt,PetscBool ,PetscBool ,PetscInt*,const PetscInt *[],const PetscInt *[],PetscBool  *);
     84:   /*54*/
     85:   PetscErrorCode (*fdcoloringcreate)(Mat,ISColoring,MatFDColoring);
     86:   PetscErrorCode (*coloringpatch)(Mat,PetscInt,PetscInt,ISColoringValue[],ISColoring*);
     87:   PetscErrorCode (*setunfactored)(Mat);
     88:   PetscErrorCode (*permute)(Mat,IS,IS,Mat*);
     89:   PetscErrorCode (*setvaluesblocked)(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode);
     90:   /*59*/
     91:   PetscErrorCode (*getsubmatrix)(Mat,IS,IS,MatReuse,Mat*);
     92:   PetscErrorCode (*destroy)(Mat);
     93:   PetscErrorCode (*view)(Mat,PetscViewer);
     94:   PetscErrorCode (*convertfrom)(Mat, MatType,MatReuse,Mat*);
     95:   PetscErrorCode (*matmatmult)(Mat,Mat,Mat,MatReuse,PetscReal,Mat*);
     96:   /*64*/
     97:   PetscErrorCode (*matmatmultsymbolic)(Mat,Mat,Mat,PetscReal,Mat*);
     98:   PetscErrorCode (*matmatmultnumeric)(Mat,Mat,Mat,Mat);
     99:   PetscErrorCode (*setlocaltoglobalmapping)(Mat,ISLocalToGlobalMapping,ISLocalToGlobalMapping);
    100:   PetscErrorCode (*setvalueslocal)(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode);
    101:   PetscErrorCode (*zerorowslocal)(Mat,PetscInt,const PetscInt[],PetscScalar,Vec,Vec);
    102:   /*69*/
    103:   PetscErrorCode (*getrowmaxabs)(Mat,Vec,PetscInt[]);
    104:   PetscErrorCode (*getrowminabs)(Mat,Vec,PetscInt[]);
    105:   PetscErrorCode (*convert)(Mat, MatType,MatReuse,Mat*);
    106:   PetscErrorCode (*setcoloring)(Mat,ISColoring);
    107:   PetscErrorCode (*dummy3)(Mat,void*);
    108:   /*74*/
    109:   PetscErrorCode (*setvaluesadifor)(Mat,PetscInt,void*);
    110:   PetscErrorCode (*fdcoloringapply)(Mat,MatFDColoring,Vec,MatStructure*,void*);
    111:   PetscErrorCode (*setfromoptions)(Mat);
    112:   PetscErrorCode (*multconstrained)(Mat,Vec,Vec);
    113:   PetscErrorCode (*multtransposeconstrained)(Mat,Vec,Vec);
    114:   /*79*/
    115:   PetscErrorCode (*findzerodiagonals)(Mat,IS*);
    116:   PetscErrorCode (*mults)(Mat, Vecs, Vecs);
    117:   PetscErrorCode (*solves)(Mat, Vecs, Vecs);
    118:   PetscErrorCode (*getinertia)(Mat,PetscInt*,PetscInt*,PetscInt*);
    119:   PetscErrorCode (*load)(Mat, PetscViewer);
    120:   /*84*/
    121:   PetscErrorCode (*issymmetric)(Mat,PetscReal,PetscBool *);
    122:   PetscErrorCode (*ishermitian)(Mat,PetscReal,PetscBool *);
    123:   PetscErrorCode (*isstructurallysymmetric)(Mat,PetscBool *);
    124:   PetscErrorCode (*setvaluesblockedlocal)(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode);
    125:   PetscErrorCode (*getvecs)(Mat,Vec*,Vec*);
    126:   /*89*/
    127:   PetscErrorCode (*matmult)(Mat,Mat,MatReuse,PetscReal,Mat*);
    128:   PetscErrorCode (*matmultsymbolic)(Mat,Mat,PetscReal,Mat*);
    129:   PetscErrorCode (*matmultnumeric)(Mat,Mat,Mat);
    130:   PetscErrorCode (*ptap)(Mat,Mat,MatReuse,PetscReal,Mat*);
    131:   PetscErrorCode (*ptapsymbolic)(Mat,Mat,PetscReal,Mat*); /* double dispatch wrapper routine */
    132:   /*94*/
    133:   PetscErrorCode (*ptapnumeric)(Mat,Mat,Mat);             /* double dispatch wrapper routine */
    134:   PetscErrorCode (*mattransposemult)(Mat,Mat,MatReuse,PetscReal,Mat*);
    135:   PetscErrorCode (*mattransposemultsymbolic)(Mat,Mat,PetscReal,Mat*);
    136:   PetscErrorCode (*mattransposemultnumeric)(Mat,Mat,Mat);
    137:   PetscErrorCode (*dummy98)(Mat);
    138:   /*99*/
    139:   PetscErrorCode (*dummy99)(Mat);
    140:   PetscErrorCode (*dummy100)(Mat);
    141:   PetscErrorCode (*dummy101)(Mat);
    142:   PetscErrorCode (*conjugate)(Mat);                              /* complex conjugate */
    143:   PetscErrorCode (*dummy5)(void);
    144:   /*104*/
    145:   PetscErrorCode (*setvaluesrow)(Mat,PetscInt,const PetscScalar[]);
    146:   PetscErrorCode (*realpart)(Mat);
    147:   PetscErrorCode (*imaginarypart)(Mat);
    148:   PetscErrorCode (*getrowuppertriangular)(Mat);
    149:   PetscErrorCode (*restorerowuppertriangular)(Mat);
    150:   /*109*/
    151:   PetscErrorCode (*matsolve)(Mat,Mat,Mat);
    152:   PetscErrorCode (*getredundantmatrix)(Mat,PetscInt,MPI_Comm,PetscInt,MatReuse,Mat*);
    153:   PetscErrorCode (*getrowmin)(Mat,Vec,PetscInt[]);
    154:   PetscErrorCode (*getcolumnvector)(Mat,Vec,PetscInt);
    155:   PetscErrorCode (*missingdiagonal)(Mat,PetscBool *,PetscInt*);
    156:   /*114*/
    157:   PetscErrorCode (*getseqnonzerostructure)(Mat,Mat *);
    158:   PetscErrorCode (*create)(Mat);
    159:   PetscErrorCode (*getghosts)(Mat,PetscInt*,const PetscInt *[]);
    160:   PetscErrorCode (*getlocalsubmatrix)(Mat,IS,IS,Mat*);
    161:   PetscErrorCode (*restorelocalsubmatrix)(Mat,IS,IS,Mat*);
    162:   /*119*/
    163:   PetscErrorCode (*multdiagonalblock)(Mat,Vec,Vec);
    164:   PetscErrorCode (*hermitiantranspose)(Mat,MatReuse,Mat*);
    165:   PetscErrorCode (*multhermitiantranspose)(Mat,Vec,Vec);
    166:   PetscErrorCode (*multhermitiantransposeadd)(Mat,Vec,Vec,Vec);
    167:   PetscErrorCode (*getmultiprocblock)(Mat,MPI_Comm,MatReuse,Mat*);
    168:   /*124*/
    169:   PetscErrorCode (*findnonzerorows)(Mat,IS*);
    170:   PetscErrorCode (*getcolumnnorms)(Mat,NormType,PetscReal*);
    171:   PetscErrorCode (*invertblockdiagonal)(Mat,const PetscScalar**);
    172:   PetscErrorCode (*dummy4)(Mat,Vec,Vec,Vec);
    173:   PetscErrorCode (*getsubmatricesparallel)(Mat,PetscInt,const IS[], const IS[], MatReuse, Mat**);
    174:   /*129*/
    175:   PetscErrorCode (*setvaluesbatch)(Mat,PetscInt,PetscInt,PetscInt*,const PetscScalar*);
    176:   PetscErrorCode (*transposematmult)(Mat,Mat,MatReuse,PetscReal,Mat*);
    177:   PetscErrorCode (*transposematmultsymbolic)(Mat,Mat,PetscReal,Mat*);
    178:   PetscErrorCode (*transposematmultnumeric)(Mat,Mat,Mat);
    179:   PetscErrorCode (*transposecoloringcreate)(Mat,ISColoring,MatTransposeColoring);
    180:   /*134*/
    181:   PetscErrorCode (*transcoloringapplysptoden)(MatTransposeColoring,Mat,Mat);
    182:   PetscErrorCode (*transcoloringapplydentosp)(MatTransposeColoring,Mat,Mat);
    183:   PetscErrorCode (*rart)(Mat,Mat,MatReuse,PetscReal,Mat*);
    184:   PetscErrorCode (*rartsymbolic)(Mat,Mat,PetscReal,Mat*); /* double dispatch wrapper routine */
    185:   PetscErrorCode (*rartnumeric)(Mat,Mat,Mat);             /* double dispatch wrapper routine */
    186:   /*139*/
    187:   PetscErrorCode (*setblocksizes)(Mat,PetscInt,PetscInt);
    188:   PetscErrorCode (*aypx)(Mat,PetscScalar,Mat,MatStructure);
    189: };
    190: /*
    191:     If you add MatOps entries above also add them to the MATOP enum
    192:     in include/petscmat.h and include/finclude/petscmat.h
    193: */

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

    199: typedef struct _p_MatBaseName* MatBaseName;
    200: struct _p_MatBaseName {
    201:   char        *bname,*sname,*mname;
    202:   MatBaseName next;
    203: };

    205: PETSC_EXTERN MatBaseName MatBaseNameList;

    207: /*
    208:    Utility private matrix routines
    209: */
    210: PETSC_INTERN PetscErrorCode MatConvert_Basic(Mat, MatType,MatReuse,Mat*);
    211: PETSC_INTERN PetscErrorCode MatCopy_Basic(Mat,Mat,MatStructure);
    212: PETSC_INTERN PetscErrorCode MatHeaderMerge(Mat,Mat);
    213: PETSC_EXTERN PetscErrorCode MatHeaderReplace(Mat,Mat);
    214: PETSC_INTERN PetscErrorCode MatAXPYGetxtoy_Private(PetscInt,PetscInt*,PetscInt*,PetscInt*, PetscInt*,PetscInt*,PetscInt*, PetscInt**);
    215: PETSC_INTERN PetscErrorCode MatDiagonalSet_Default(Mat,Vec,InsertMode);

    217: #if defined(PETSC_USE_DEBUG)
    218: #  define MatCheckPreallocated(A,arg) do {                              \
    219:     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); \
    220:   } while (0)
    221: #else
    222: #  define MatCheckPreallocated(A,arg) do {} while (0)
    223: #endif

    225: /*
    226:   The stash is used to temporarily store inserted matrix values that
    227:   belong to another processor. During the assembly phase the stashed
    228:   values are moved to the correct processor and
    229: */

    231: typedef struct _MatStashSpace *PetscMatStashSpace;

    233: struct _MatStashSpace {
    234:   PetscMatStashSpace next;
    235:   PetscScalar        *space_head,*val;
    236:   PetscInt           *idx,*idy;
    237:   PetscInt           total_space_size;
    238:   PetscInt           local_used;
    239:   PetscInt           local_remaining;
    240: };

    242: PETSC_EXTERN PetscErrorCode PetscMatStashSpaceGet(PetscInt,PetscInt,PetscMatStashSpace *);
    243: PETSC_EXTERN PetscErrorCode PetscMatStashSpaceContiguous(PetscInt,PetscMatStashSpace *,PetscScalar *,PetscInt *,PetscInt *);
    244: PETSC_EXTERN PetscErrorCode PetscMatStashSpaceDestroy(PetscMatStashSpace*);

    246: typedef struct {
    247:   PetscInt      nmax;                   /* maximum stash size */
    248:   PetscInt      umax;                   /* user specified max-size */
    249:   PetscInt      oldnmax;                /* the nmax value used previously */
    250:   PetscInt      n;                      /* stash size */
    251:   PetscInt      bs;                     /* block size of the stash */
    252:   PetscInt      reallocs;               /* preserve the no of mallocs invoked */
    253:   PetscMatStashSpace space_head,space;  /* linked list to hold stashed global row/column numbers and matrix values */
    254:   /* The following variables are used for communication */
    255:   MPI_Comm      comm;
    256:   PetscMPIInt   size,rank;
    257:   PetscMPIInt   tag1,tag2;
    258:   MPI_Request   *send_waits;            /* array of send requests */
    259:   MPI_Request   *recv_waits;            /* array of receive requests */
    260:   MPI_Status    *send_status;           /* array of send status */
    261:   PetscInt      nsends,nrecvs;          /* numbers of sends and receives */
    262:   PetscScalar   *svalues;               /* sending data */
    263:   PetscInt      *sindices;
    264:   PetscScalar   **rvalues;              /* receiving data (values) */
    265:   PetscInt      **rindices;             /* receiving data (indices) */
    266:   PetscInt      nprocessed;             /* number of messages already processed */
    267:   PetscMPIInt   *flg_v;                 /* indicates what messages have arrived so far and from whom */
    268:   PetscBool     reproduce;
    269:   PetscInt      reproduce_count;
    270: } MatStash;

    272: PETSC_INTERN PetscErrorCode MatStashCreate_Private(MPI_Comm,PetscInt,MatStash*);
    273: PETSC_INTERN PetscErrorCode MatStashDestroy_Private(MatStash*);
    274: PETSC_INTERN PetscErrorCode MatStashScatterEnd_Private(MatStash*);
    275: PETSC_INTERN PetscErrorCode MatStashSetInitialSize_Private(MatStash*,PetscInt);
    276: PETSC_INTERN PetscErrorCode MatStashGetInfo_Private(MatStash*,PetscInt*,PetscInt*);
    277: PETSC_INTERN PetscErrorCode MatStashValuesRow_Private(MatStash*,PetscInt,PetscInt,const PetscInt[],const PetscScalar[],PetscBool );
    278: PETSC_INTERN PetscErrorCode MatStashValuesCol_Private(MatStash*,PetscInt,PetscInt,const PetscInt[],const PetscScalar[],PetscInt,PetscBool );
    279: PETSC_INTERN PetscErrorCode MatStashValuesRowBlocked_Private(MatStash*,PetscInt,PetscInt,const PetscInt[],const PetscScalar[],PetscInt,PetscInt,PetscInt);
    280: PETSC_INTERN PetscErrorCode MatStashValuesColBlocked_Private(MatStash*,PetscInt,PetscInt,const PetscInt[],const PetscScalar[],PetscInt,PetscInt,PetscInt);
    281: PETSC_INTERN PetscErrorCode MatStashScatterBegin_Private(Mat,MatStash*,PetscInt*);
    282: PETSC_INTERN PetscErrorCode MatStashScatterGetMesg_Private(MatStash*,PetscMPIInt*,PetscInt**,PetscInt**,PetscScalar**,PetscInt*);

    284: typedef struct {
    285:   PetscInt   dim;
    286:   PetscInt   dims[4];
    287:   PetscInt   starts[4];
    288:   PetscBool  noc;        /* this is a single component problem, hence user will not set MatStencil.c */
    289: } MatStencilInfo;

    291: /* Info about using compressed row format */
    292: typedef struct {
    293:   PetscBool  check;                         /* indicates that at MatAssembly() it should check if compressed rows will be efficient */
    294:   PetscBool  use;                           /* indicates compressed rows have been checked and will be used */
    295:   PetscInt   nrows;                         /* number of non-zero rows */
    296:   PetscInt   *i;                            /* compressed row pointer  */
    297:   PetscInt   *rindex;                       /* compressed row index               */
    298: } Mat_CompressedRow;
    299: PETSC_EXTERN PetscErrorCode MatCheckCompressedRow(Mat,Mat_CompressedRow*,PetscInt*,PetscInt,PetscReal);

    301: struct _p_Mat {
    302:   PETSCHEADER(struct _MatOps);
    303:   PetscLayout            rmap,cmap;
    304:   void                   *data;            /* implementation-specific data */
    305:   MatFactorType          factortype;       /* MAT_FACTOR_LU, ILU, CHOLESKY or ICC */
    306:   PetscBool              assembled;        /* is the matrix assembled? */
    307:   PetscBool              was_assembled;    /* new values inserted into assembled mat */
    308:   PetscInt               num_ass;          /* number of times matrix has been assembled */
    309:   PetscBool              same_nonzero;     /* matrix has same nonzero pattern as previous */
    310:   MatInfo                info;             /* matrix information */
    311:   InsertMode             insertmode;       /* have values been inserted in matrix or added? */
    312:   MatStash               stash,bstash;     /* used for assembling off-proc mat emements */
    313:   MatNullSpace           nullsp;           /* null space (operator is singular) */
    314:   MatNullSpace           nearnullsp;       /* near null space to be used by multigrid methods */
    315:   PetscBool              preallocated;
    316:   MatStencilInfo         stencil;          /* information for structured grid */
    317:   PetscBool              symmetric,hermitian,structurally_symmetric,spd;
    318:   PetscBool              symmetric_set,hermitian_set,structurally_symmetric_set,spd_set; /* if true, then corresponding flag is correct*/
    319:   PetscBool              symmetric_eternal;
    320:   PetscBool              nooffprocentries,nooffproczerorows;
    321: #if defined(PETSC_HAVE_CUSP)
    322:   PetscCUSPFlag          valid_GPU_matrix; /* flag pointing to the matrix on the gpu*/
    323: #endif
    324:   void                   *spptr;          /* pointer for special library like SuperLU */
    325:   MatSolverPackage       solvertype;
    326:   PetscViewer            viewonassembly;         /* the following are set in MatSetFromOptions() and used in MatAssemblyEnd() */
    327:   PetscViewerFormat      viewformatonassembly;
    328:   PetscBool              checksymmetryonassembly,checknullspaceonassembly;
    329:   PetscReal              checksymmetrytol;
    330:   };

    332: PETSC_INTERN PetscErrorCode MatAXPY_Basic(Mat,PetscScalar,Mat,MatStructure);
    333: PETSC_INTERN PetscErrorCode MatAXPY_BasicWithPreallocation(Mat,Mat,PetscScalar,Mat,MatStructure);
    334: /*
    335:     Object for partitioning graphs
    336: */

    338: typedef struct _MatPartitioningOps *MatPartitioningOps;
    339: struct _MatPartitioningOps {
    340:   PetscErrorCode (*apply)(MatPartitioning,IS*);
    341:   PetscErrorCode (*setfromoptions)(MatPartitioning);
    342:   PetscErrorCode (*destroy)(MatPartitioning);
    343:   PetscErrorCode (*view)(MatPartitioning,PetscViewer);
    344: };

    346: struct _p_MatPartitioning {
    347:   PETSCHEADER(struct _MatPartitioningOps);
    348:   Mat         adj;
    349:   PetscInt    *vertex_weights;
    350:   PetscReal   *part_weights;
    351:   PetscInt    n;                                 /* number of partitions */
    352:   void        *data;
    353:   PetscInt    setupcalled;
    354: };

    356: /*
    357:     Object for coarsen graphs
    358: */
    359: typedef struct _MatCoarsenOps *MatCoarsenOps;
    360: struct _MatCoarsenOps {
    361:   PetscErrorCode (*apply)(MatCoarsen);
    362:   PetscErrorCode (*setfromoptions)(MatCoarsen);
    363:   PetscErrorCode (*destroy)(MatCoarsen);
    364:   PetscErrorCode (*view)(MatCoarsen,PetscViewer);
    365: };

    367: struct _p_MatCoarsen {
    368:   PETSCHEADER(struct _MatCoarsenOps);
    369:   Mat         graph;
    370:   PetscInt    verbose;
    371:   PetscInt    setupcalled;
    372:   void        *subctx;
    373:   /* */
    374:   PetscBool strict_aggs;
    375:   IS perm;
    376:   PetscCoarsenData *agg_lists;
    377: };

    379: PETSC_EXTERN PetscErrorCode PetscCDCreate(PetscInt,PetscCoarsenData**);
    380: PETSC_EXTERN PetscErrorCode PetscCDDestroy(PetscCoarsenData*);
    381: PETSC_EXTERN PetscErrorCode PetscLLNSetID(PetscCDIntNd*,PetscInt);
    382: PETSC_EXTERN PetscErrorCode PetscLLNGetID(const PetscCDIntNd*,PetscInt*);
    383: PETSC_EXTERN PetscErrorCode PetscCDAppendID(PetscCoarsenData*,PetscInt,PetscInt);
    384: PETSC_EXTERN PetscErrorCode PetscCDAppendRemove(PetscCoarsenData*,PetscInt,PetscInt);
    385: PETSC_EXTERN PetscErrorCode PetscCDAppendNode(PetscCoarsenData*,PetscInt,PetscCDIntNd*);
    386: PETSC_EXTERN PetscErrorCode PetscCDRemoveNextNode(PetscCoarsenData*,PetscInt,PetscCDIntNd*);
    387: PETSC_EXTERN PetscErrorCode PetscCDRemoveAllAt(PetscCoarsenData*,PetscInt);
    388: PETSC_EXTERN PetscErrorCode PetscCDSizeAt(const PetscCoarsenData*,PetscInt,PetscInt*);
    389: PETSC_EXTERN PetscErrorCode PetscCDEmptyAt(const PetscCoarsenData*,PetscInt,PetscBool*);
    390: PETSC_EXTERN PetscErrorCode PetscCDSetChuckSize(PetscCoarsenData*,PetscInt);
    391: PETSC_EXTERN PetscErrorCode PetscCDPrint(const PetscCoarsenData*,MPI_Comm);
    392: PETSC_EXTERN PetscErrorCode PetscCDGetMIS(PetscCoarsenData*,IS*);
    393: PETSC_EXTERN PetscErrorCode PetscCDGetMat(const PetscCoarsenData*,Mat*);
    394: PETSC_EXTERN PetscErrorCode PetscCDSetMat(PetscCoarsenData*,Mat);

    396: typedef PetscCDIntNd *PetscCDPos;
    397: PETSC_EXTERN PetscErrorCode PetscCDGetHeadPos(const PetscCoarsenData*,PetscInt,PetscCDPos*);
    398: PETSC_EXTERN PetscErrorCode PetscCDGetNextPos(const PetscCoarsenData*,PetscInt,PetscCDPos*);
    399: PETSC_EXTERN PetscErrorCode PetscCDGetASMBlocks(const PetscCoarsenData*,const PetscInt,PetscInt*,IS**);
    400: /* PetscErrorCode PetscCDSetRemovedIS( PetscCoarsenData *ail, MPI_Comm, const PetscInt, PetscInt[] ); */
    401: /* PetscErrorCode PetscCDGetRemovedIS( PetscCoarsenData *ail, IS * ); */

    403: /*
    404:     MatFDColoring is used to compute Jacobian matrices efficiently
    405:   via coloring. The data structure is explained below in an example.

    407:    Color =   0    1     0    2   |   2      3       0
    408:    ---------------------------------------------------
    409:             00   01              |          05
    410:             10   11              |   14     15               Processor  0
    411:                        22    23  |          25
    412:                        32    33  |
    413:    ===================================================
    414:                                  |   44     45     46
    415:             50                   |          55               Processor 1
    416:                                  |   64            66
    417:    ---------------------------------------------------

    419:     ncolors = 4;

    421:     ncolumns      = {2,1,1,0}
    422:     columns       = {{0,2},{1},{3},{}}
    423:     nrows         = {4,2,3,3}
    424:     rows          = {{0,1,2,3},{0,1},{1,2,3},{0,1,2}}
    425:     columnsforrow = {{0,0,2,2},{1,1},{4,3,3},{5,5,5}}
    426:     vscaleforrow  = {{,,,},{,},{,,},{,,}}
    427:     vwscale       = {dx(0),dx(1),dx(2),dx(3)}               MPI Vec
    428:     vscale        = {dx(0),dx(1),dx(2),dx(3),dx(4),dx(5)}   Seq Vec

    430:     ncolumns      = {1,0,1,1}
    431:     columns       = {{6},{},{4},{5}}
    432:     nrows         = {3,0,2,2}
    433:     rows          = {{0,1,2},{},{1,2},{1,2}}
    434:     columnsforrow = {{6,0,6},{},{4,4},{5,5}}
    435:     vscaleforrow =  {{,,},{},{,},{,}}
    436:     vwscale       = {dx(4),dx(5),dx(6)}              MPI Vec
    437:     vscale        = {dx(0),dx(4),dx(5),dx(6)}        Seq Vec

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

    442: */

    444: struct  _p_MatFDColoring{
    445:   PETSCHEADER(int);
    446:   PetscInt       M,N,m;            /* total rows, columns; local rows */
    447:   PetscInt       rstart;           /* first row owned by local processor */
    448:   PetscInt       ncolors;          /* number of colors */
    449:   PetscInt       *ncolumns;        /* number of local columns for a color */
    450:   PetscInt       **columns;        /* lists the local columns of each color (using global column numbering) */
    451:   PetscInt       *nrows;           /* number of local rows for each color */
    452:   PetscInt       **rows;           /* lists the local rows for each color (using the local row numbering) */
    453:   PetscInt       **columnsforrow;  /* lists the corresponding columns for those rows (using the global column) */
    454:   PetscReal      error_rel;        /* square root of relative error in computing function */
    455:   PetscReal      umin;             /* minimum allowable u'dx value */
    456:   Vec            w1,w2,w3;         /* work vectors used in computing Jacobian */
    457:   PetscBool      fset;             /* indicates that the initial function value F(X) is set */
    458:   PetscErrorCode (*f)(void);       /* function that defines Jacobian */
    459:   void           *fctx;            /* optional user-defined context for use by the function f */
    460:   PetscInt       **vscaleforrow;   /* location in vscale for each columnsforrow[] entry */
    461:   Vec            vscale;           /* holds FD scaling, i.e. 1/dx for each perturbed column */
    462:   PetscInt       currentcolor;     /* color for which function evaluation is being done now */
    463:   const char     *htype;            /* "wp" or "ds" */
    464:   ISColoringType ctype;            /* IS_COLORING_GLOBAL or IS_COLORING_GHOSTED */

    466:   void           *ftn_func_pointer,*ftn_func_cntx; /* serve the same purpose as *fortran_func_pointers in PETSc objects */
    467: };

    469: struct  _p_MatTransposeColoring{
    470:   PETSCHEADER(int);
    471:   PetscInt       M,N,m;            /* total rows, columns; local rows */
    472:   PetscInt       rstart;           /* first row owned by local processor */
    473:   PetscInt       ncolors;          /* number of colors */
    474:   PetscInt       *ncolumns;        /* number of local columns for a color */
    475:   PetscInt       *nrows;           /* number of local rows for each color */
    476:   PetscInt       currentcolor;     /* color for which function evaluation is being done now */
    477:   ISColoringType ctype;            /* IS_COLORING_GLOBAL or IS_COLORING_GHOSTED */

    479:   PetscInt       *colorforrow,*colorforcol;  /* pointer to rows and columns */
    480:   PetscInt       *rows;                  /* lists the local rows for each color (using the local row numbering) */
    481:   PetscInt       *columnsforspidx;       /* maps (row,color) in the dense matrix to index of sparse matrix arrays a->j and a->a */
    482:   PetscInt       *columns;               /* lists the local columns of each color (using global column numbering) */
    483: };

    485: /*
    486:    Null space context for preconditioner/operators
    487: */
    488: struct _p_MatNullSpace {
    489:   PETSCHEADER(int);
    490:   PetscBool      has_cnst;
    491:   PetscInt       n;
    492:   Vec*           vecs;
    493:   PetscScalar*   alpha;                 /* for projections */
    494:   Vec            vec;                   /* for out of place removals */
    495:   PetscErrorCode (*remove)(MatNullSpace,Vec,void*);  /* for user provided removal function */
    496:   void*          rmctx;                 /* context for remove() function */
    497: };

    499: /*
    500:    Checking zero pivot for LU, ILU preconditioners.
    501: */
    502: typedef struct {
    503:   PetscInt       nshift,nshift_max;
    504:   PetscReal      shift_amount,shift_lo,shift_hi,shift_top,shift_fraction;
    505:   PetscBool      newshift;
    506:   PetscReal      rs;  /* active row sum of abs(offdiagonals) */
    507:   PetscScalar    pv;  /* pivot of the active row */
    508: } FactorShiftCtx;

    510: PETSC_EXTERN PetscErrorCode MatFactorDumpMatrix(Mat);

    514: PETSC_STATIC_INLINE PetscErrorCode MatPivotCheck_nz(Mat mat,const MatFactorInfo *info,FactorShiftCtx *sctx,PetscInt row)
    515: {
    516:   PetscReal _rs   = sctx->rs;
    517:   PetscReal _zero = info->zeropivot*_rs;

    520:   if (PetscAbsScalar(sctx->pv) <= _zero){
    521:     /* force |diag| > zeropivot*rs */
    522:     if (!sctx->nshift) sctx->shift_amount = info->shiftamount;
    523:     else sctx->shift_amount *= 2.0;
    524:     sctx->newshift = PETSC_TRUE;
    525:     (sctx->nshift)++;
    526:   } else {
    527:     sctx->newshift = PETSC_FALSE;
    528:   }
    529:   return(0);
    530: }

    534: PETSC_STATIC_INLINE PetscErrorCode MatPivotCheck_pd(Mat mat,const MatFactorInfo *info,FactorShiftCtx *sctx,PetscInt row)
    535: {
    536:   PetscReal _rs   = sctx->rs;
    537:   PetscReal _zero = info->zeropivot*_rs;

    540:   if (PetscRealPart(sctx->pv) <= _zero){
    541:     /* force matfactor to be diagonally dominant */
    542:     if (sctx->nshift == sctx->nshift_max) {
    543:       sctx->shift_fraction = sctx->shift_hi;
    544:     } else {
    545:       sctx->shift_lo = sctx->shift_fraction;
    546:       sctx->shift_fraction = (sctx->shift_hi+sctx->shift_lo)/2.;
    547:     }
    548:     sctx->shift_amount = sctx->shift_fraction * sctx->shift_top;
    549:     sctx->nshift++;
    550:     sctx->newshift = PETSC_TRUE;
    551:   } else {
    552:     sctx->newshift = PETSC_FALSE;
    553:   }
    554:   return(0);
    555: }

    559: PETSC_STATIC_INLINE PetscErrorCode MatPivotCheck_inblocks(Mat mat,const MatFactorInfo *info,FactorShiftCtx *sctx,PetscInt row)
    560: {
    561:   PetscReal _zero = info->zeropivot;

    564:   if (PetscAbsScalar(sctx->pv) <= _zero){
    565:     sctx->pv          += info->shiftamount;
    566:     sctx->shift_amount = 0.0;
    567:     sctx->nshift++;
    568:   }
    569:   sctx->newshift = PETSC_FALSE;
    570:   return(0);
    571: }

    575: PETSC_STATIC_INLINE PetscErrorCode MatPivotCheck_none(Mat mat,const MatFactorInfo *info,FactorShiftCtx *sctx,PetscInt row)
    576: {
    577:   PetscReal _zero = info->zeropivot;

    580:   sctx->newshift = PETSC_FALSE;
    581:   if (PetscAbsScalar(sctx->pv) <= _zero) {
    583:     PetscBool      flg = PETSC_FALSE;

    585:     PetscOptionsGetBool(NULL,"-mat_dump",&flg,NULL);
    586:     if (flg) {
    587:       MatView(mat,PETSC_VIEWER_BINARY_(PetscObjectComm((PetscObject)mat)));
    588:     }
    589:     SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_MAT_LU_ZRPVT,"Zero pivot row %D value %G tolerance %G",row,PetscAbsScalar(sctx->pv),_zero);
    590:   }
    591:   return(0);
    592: }

    596: PETSC_STATIC_INLINE PetscErrorCode MatPivotCheck(Mat mat,const MatFactorInfo *info,FactorShiftCtx *sctx,PetscInt row)
    597: {

    601:   if (info->shifttype == (PetscReal) MAT_SHIFT_NONZERO){
    602:     MatPivotCheck_nz(mat,info,sctx,row);
    603:   } else if (info->shifttype == (PetscReal) MAT_SHIFT_POSITIVE_DEFINITE){
    604:     MatPivotCheck_pd(mat,info,sctx,row);
    605:   } else if (info->shifttype == (PetscReal) MAT_SHIFT_INBLOCKS){
    606:     MatPivotCheck_inblocks(mat,info,sctx,row);
    607:   } else {
    608:     MatPivotCheck_none(mat,info,sctx,row);
    609:   }
    610:   return(0);
    611: }

    613: /*
    614:   Create and initialize a linked list
    615:   Input Parameters:
    616:     idx_start - starting index of the list
    617:     lnk_max   - max value of lnk indicating the end of the list
    618:     nlnk      - max length of the list
    619:   Output Parameters:
    620:     lnk       - list initialized
    621:     bt        - PetscBT (bitarray) with all bits set to false
    622:     lnk_empty - flg indicating the list is empty
    623: */
    624: #define PetscLLCreate(idx_start,lnk_max,nlnk,lnk,bt) \
    625:   (PetscMalloc(nlnk*sizeof(PetscInt),&lnk) || PetscBTCreate(nlnk,&(bt)) || (lnk[idx_start] = lnk_max,0))

    627: #define PetscLLCreate_new(idx_start,lnk_max,nlnk,lnk,bt,lnk_empty)\
    628:   (PetscMalloc(nlnk*sizeof(PetscInt),&lnk) || PetscBTCreate(nlnk,&(bt)) || (lnk_empty = PETSC_TRUE,0) ||(lnk[idx_start] = lnk_max,0))

    630: /*
    631:   Add an index set into a sorted linked list
    632:   Input Parameters:
    633:     nidx      - number of input indices
    634:     indices   - interger array
    635:     idx_start - starting index of the list
    636:     lnk       - linked list(an integer array) that is created
    637:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
    638:   output Parameters:
    639:     nlnk      - number of newly added indices
    640:     lnk       - the sorted(increasing order) linked list containing new and non-redundate entries from indices
    641:     bt        - updated PetscBT (bitarray)
    642: */
    643: #define PetscLLAdd(nidx,indices,idx_start,nlnk,lnk,bt) 0;\
    644: {\
    645:   PetscInt _k,_entry,_location,_lnkdata;\
    646:   nlnk     = 0;\
    647:   _lnkdata = idx_start;\
    648:   for (_k=0; _k<nidx; _k++){\
    649:     _entry = indices[_k];\
    650:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
    651:       /* search for insertion location */\
    652:       /* start from the beginning if _entry < previous _entry */\
    653:       if (_k && _entry < _lnkdata) _lnkdata  = idx_start;\
    654:       do {\
    655:         _location = _lnkdata;\
    656:         _lnkdata  = lnk[_location];\
    657:       } while (_entry > _lnkdata);\
    658:       /* insertion location is found, add entry into lnk */\
    659:       lnk[_location] = _entry;\
    660:       lnk[_entry]    = _lnkdata;\
    661:       nlnk++;\
    662:       _lnkdata = _entry; /* next search starts from here if next_entry > _entry */\
    663:     }\
    664:   }\
    665: }

    667: /*
    668:   Add a permuted index set into a sorted linked list
    669:   Input Parameters:
    670:     nidx      - number of input indices
    671:     indices   - interger array
    672:     perm      - permutation of indices
    673:     idx_start - starting index of the list
    674:     lnk       - linked list(an integer array) that is created
    675:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
    676:   output Parameters:
    677:     nlnk      - number of newly added indices
    678:     lnk       - the sorted(increasing order) linked list containing new and non-redundate entries from indices
    679:     bt        - updated PetscBT (bitarray)
    680: */
    681: #define PetscLLAddPerm(nidx,indices,perm,idx_start,nlnk,lnk,bt) 0;\
    682: {\
    683:   PetscInt _k,_entry,_location,_lnkdata;\
    684:   nlnk     = 0;\
    685:   _lnkdata = idx_start;\
    686:   for (_k=0; _k<nidx; _k++){\
    687:     _entry = perm[indices[_k]];\
    688:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
    689:       /* search for insertion location */\
    690:       /* start from the beginning if _entry < previous _entry */\
    691:       if (_k && _entry < _lnkdata) _lnkdata  = idx_start;\
    692:       do {\
    693:         _location = _lnkdata;\
    694:         _lnkdata  = lnk[_location];\
    695:       } while (_entry > _lnkdata);\
    696:       /* insertion location is found, add entry into lnk */\
    697:       lnk[_location] = _entry;\
    698:       lnk[_entry]    = _lnkdata;\
    699:       nlnk++;\
    700:       _lnkdata = _entry; /* next search starts from here if next_entry > _entry */\
    701:     }\
    702:   }\
    703: }

    705: /*
    706:   Add a SORTED ascending index set into a sorted linked list - same as PetscLLAdd() bus skip 'if (_k && _entry < _lnkdata) _lnkdata  = idx_start;'
    707:   Input Parameters:
    708:     nidx      - number of input indices
    709:     indices   - sorted interger array
    710:     idx_start - starting index of the list
    711:     lnk       - linked list(an integer array) that is created
    712:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
    713:   output Parameters:
    714:     nlnk      - number of newly added indices
    715:     lnk       - the sorted(increasing order) linked list containing new and non-redundate entries from indices
    716:     bt        - updated PetscBT (bitarray)
    717: */
    718: #define PetscLLAddSorted(nidx,indices,idx_start,nlnk,lnk,bt) 0;\
    719: {\
    720:   PetscInt _k,_entry,_location,_lnkdata;\
    721:   nlnk      = 0;\
    722:   _lnkdata  = idx_start;\
    723:   for (_k=0; _k<nidx; _k++){\
    724:     _entry = indices[_k];\
    725:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
    726:       /* search for insertion location */\
    727:       do {\
    728:         _location = _lnkdata;\
    729:         _lnkdata  = lnk[_location];\
    730:       } while (_entry > _lnkdata);\
    731:       /* insertion location is found, add entry into lnk */\
    732:       lnk[_location] = _entry;\
    733:       lnk[_entry]    = _lnkdata;\
    734:       nlnk++;\
    735:       _lnkdata = _entry; /* next search starts from here */\
    736:     }\
    737:   }\
    738: }

    740: #define PetscLLAddSorted_new(nidx,indices,idx_start,lnk_empty,nlnk,lnk,bt) 0; \
    741: {\
    742:   PetscInt _k,_entry,_location,_lnkdata;\
    743:   if (lnk_empty){\
    744:     _lnkdata  = idx_start;                      \
    745:     for (_k=0; _k<nidx; _k++){                  \
    746:       _entry = indices[_k];                             \
    747:       PetscBTSet(bt,_entry);  /* mark the new entry */          \
    748:           _location = _lnkdata;                                 \
    749:           _lnkdata  = lnk[_location];                           \
    750:         /* insertion location is found, add entry into lnk */   \
    751:         lnk[_location] = _entry;                                \
    752:         lnk[_entry]    = _lnkdata;                              \
    753:         _lnkdata = _entry; /* next search starts from here */   \
    754:     }                                                           \
    755:     /*\
    756:     lnk[indices[nidx-1]] = lnk[idx_start];\
    757:     lnk[idx_start]       = indices[0];\
    758:     PetscBTSet(bt,indices[0]);  \
    759:     for (_k=1; _k<nidx; _k++){                  \
    760:       PetscBTSet(bt,indices[_k]);                                          \
    761:       lnk[indices[_k-1]] = indices[_k];                                  \
    762:     }                                                           \
    763:      */\
    764:     nlnk      = nidx;\
    765:     lnk_empty = PETSC_FALSE;\
    766:   } else {\
    767:     nlnk      = 0;                              \
    768:     _lnkdata  = idx_start;                      \
    769:     for (_k=0; _k<nidx; _k++){                  \
    770:       _entry = indices[_k];                             \
    771:       if (!PetscBTLookupSet(bt,_entry)){  /* new entry */       \
    772:         /* search for insertion location */                     \
    773:         do {                                                    \
    774:           _location = _lnkdata;                                 \
    775:           _lnkdata  = lnk[_location];                           \
    776:         } while (_entry > _lnkdata);                            \
    777:         /* insertion location is found, add entry into lnk */   \
    778:         lnk[_location] = _entry;                                \
    779:         lnk[_entry]    = _lnkdata;                              \
    780:         nlnk++;                                                 \
    781:         _lnkdata = _entry; /* next search starts from here */   \
    782:       }                                                         \
    783:     }                                                           \
    784:   }                                                             \
    785: }

    787: /*
    788:   Add a SORTED index set into a sorted linked list used for LUFactorSymbolic()
    789:   Same as PetscLLAddSorted() with an additional operation:
    790:        count the number of input indices that are no larger than 'diag'
    791:   Input Parameters:
    792:     indices   - sorted interger array
    793:     idx_start - starting index of the list, index of pivot row
    794:     lnk       - linked list(an integer array) that is created
    795:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
    796:     diag      - index of the active row in LUFactorSymbolic
    797:     nzbd      - number of input indices with indices <= idx_start
    798:     im        - im[idx_start] is initialized as num of nonzero entries in row=idx_start
    799:   output Parameters:
    800:     nlnk      - number of newly added indices
    801:     lnk       - the sorted(increasing order) linked list containing new and non-redundate entries from indices
    802:     bt        - updated PetscBT (bitarray)
    803:     im        - im[idx_start]: unchanged if diag is not an entry
    804:                              : num of entries with indices <= diag if diag is an entry
    805: */
    806: #define PetscLLAddSortedLU(indices,idx_start,nlnk,lnk,bt,diag,nzbd,im) 0;\
    807: {\
    808:   PetscInt _k,_entry,_location,_lnkdata,_nidx;\
    809:   nlnk     = 0;\
    810:   _lnkdata = idx_start;\
    811:   _nidx = im[idx_start] - nzbd; /* num of entries with idx_start < index <= diag */\
    812:   for (_k=0; _k<_nidx; _k++){\
    813:     _entry = indices[_k];\
    814:     nzbd++;\
    815:     if ( _entry== diag) im[idx_start] = nzbd;\
    816:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
    817:       /* search for insertion location */\
    818:       do {\
    819:         _location = _lnkdata;\
    820:         _lnkdata  = lnk[_location];\
    821:       } while (_entry > _lnkdata);\
    822:       /* insertion location is found, add entry into lnk */\
    823:       lnk[_location] = _entry;\
    824:       lnk[_entry]    = _lnkdata;\
    825:       nlnk++;\
    826:       _lnkdata = _entry; /* next search starts from here */\
    827:     }\
    828:   }\
    829: }

    831: /*
    832:   Copy data on the list into an array, then initialize the list
    833:   Input Parameters:
    834:     idx_start - starting index of the list
    835:     lnk_max   - max value of lnk indicating the end of the list
    836:     nlnk      - number of data on the list to be copied
    837:     lnk       - linked list
    838:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
    839:   output Parameters:
    840:     indices   - array that contains the copied data
    841:     lnk       - linked list that is cleaned and initialize
    842:     bt        - PetscBT (bitarray) with all bits set to false
    843: */
    844: #define PetscLLClean(idx_start,lnk_max,nlnk,lnk,indices,bt) 0;\
    845: {\
    846:   PetscInt _j,_idx=idx_start;\
    847:   for (_j=0; _j<nlnk; _j++){\
    848:     _idx = lnk[_idx];\
    849:     indices[_j] = _idx;\
    850:     PetscBTClear(bt,_idx);\
    851:   }\
    852:   lnk[idx_start] = lnk_max;\
    853: }
    854: /*
    855:   Free memories used by the list
    856: */
    857: #define PetscLLDestroy(lnk,bt) (PetscFree(lnk) || PetscBTDestroy(&(bt)))

    859: /* Routines below are used for incomplete matrix factorization */
    860: /*
    861:   Create and initialize a linked list and its levels
    862:   Input Parameters:
    863:     idx_start - starting index of the list
    864:     lnk_max   - max value of lnk indicating the end of the list
    865:     nlnk      - max length of the list
    866:   Output Parameters:
    867:     lnk       - list initialized
    868:     lnk_lvl   - array of size nlnk for storing levels of lnk
    869:     bt        - PetscBT (bitarray) with all bits set to false
    870: */
    871: #define PetscIncompleteLLCreate(idx_start,lnk_max,nlnk,lnk,lnk_lvl,bt)\
    872:   (PetscMalloc(2*nlnk*sizeof(PetscInt),&lnk) || PetscBTCreate(nlnk,&(bt)) || (lnk[idx_start] = lnk_max,lnk_lvl = lnk + nlnk,0))

    874: /*
    875:   Initialize a sorted linked list used for ILU and ICC
    876:   Input Parameters:
    877:     nidx      - number of input idx
    878:     idx       - interger array used for storing column indices
    879:     idx_start - starting index of the list
    880:     perm      - indices of an IS
    881:     lnk       - linked list(an integer array) that is created
    882:     lnklvl    - levels of lnk
    883:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
    884:   output Parameters:
    885:     nlnk     - number of newly added idx
    886:     lnk      - the sorted(increasing order) linked list containing new and non-redundate entries from idx
    887:     lnklvl   - levels of lnk
    888:     bt       - updated PetscBT (bitarray)
    889: */
    890: #define PetscIncompleteLLInit(nidx,idx,idx_start,perm,nlnk,lnk,lnklvl,bt) 0;\
    891: {\
    892:   PetscInt _k,_entry,_location,_lnkdata;\
    893:   nlnk     = 0;\
    894:   _lnkdata = idx_start;\
    895:   for (_k=0; _k<nidx; _k++){\
    896:     _entry = perm[idx[_k]];\
    897:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
    898:       /* search for insertion location */\
    899:       if (_k && _entry < _lnkdata) _lnkdata  = idx_start;\
    900:       do {\
    901:         _location = _lnkdata;\
    902:         _lnkdata  = lnk[_location];\
    903:       } while (_entry > _lnkdata);\
    904:       /* insertion location is found, add entry into lnk */\
    905:       lnk[_location]  = _entry;\
    906:       lnk[_entry]     = _lnkdata;\
    907:       lnklvl[_entry] = 0;\
    908:       nlnk++;\
    909:       _lnkdata = _entry; /* next search starts from here if next_entry > _entry */\
    910:     }\
    911:   }\
    912: }

    914: /*
    915:   Add a SORTED index set into a sorted linked list for ILU
    916:   Input Parameters:
    917:     nidx      - number of input indices
    918:     idx       - sorted interger array used for storing column indices
    919:     level     - level of fill, e.g., ICC(level)
    920:     idxlvl    - level of idx
    921:     idx_start - starting index of the list
    922:     lnk       - linked list(an integer array) that is created
    923:     lnklvl    - levels of lnk
    924:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
    925:     prow      - the row number of idx
    926:   output Parameters:
    927:     nlnk     - number of newly added idx
    928:     lnk      - the sorted(increasing order) linked list containing new and non-redundate entries from idx
    929:     lnklvl   - levels of lnk
    930:     bt       - updated PetscBT (bitarray)

    932:   Note: the level of factor(i,j) is set as lvl(i,j) = min{ lvl(i,j), lvl(i,prow)+lvl(prow,j)+1)
    933:         where idx = non-zero columns of U(prow,prow+1:n-1), prow<i
    934: */
    935: #define PetscILULLAddSorted(nidx,idx,level,idxlvl,idx_start,nlnk,lnk,lnklvl,bt,lnklvl_prow) 0;\
    936: {\
    937:   PetscInt _k,_entry,_location,_lnkdata,_incrlev,_lnklvl_prow=lnklvl[prow];\
    938:   nlnk     = 0;\
    939:   _lnkdata = idx_start;\
    940:   for (_k=0; _k<nidx; _k++){\
    941:     _incrlev = idxlvl[_k] + _lnklvl_prow + 1;\
    942:     if (_incrlev > level) continue;\
    943:     _entry = idx[_k];\
    944:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
    945:       /* search for insertion location */\
    946:       do {\
    947:         _location = _lnkdata;\
    948:         _lnkdata  = lnk[_location];\
    949:       } while (_entry > _lnkdata);\
    950:       /* insertion location is found, add entry into lnk */\
    951:       lnk[_location]  = _entry;\
    952:       lnk[_entry]     = _lnkdata;\
    953:       lnklvl[_entry] = _incrlev;\
    954:       nlnk++;\
    955:       _lnkdata = _entry; /* next search starts from here if next_entry > _entry */\
    956:     } else { /* existing entry: update lnklvl */\
    957:       if (lnklvl[_entry] > _incrlev) lnklvl[_entry] = _incrlev;\
    958:     }\
    959:   }\
    960: }

    962: /*
    963:   Add a index set into a sorted linked list
    964:   Input Parameters:
    965:     nidx      - number of input idx
    966:     idx   - interger array used for storing column indices
    967:     level     - level of fill, e.g., ICC(level)
    968:     idxlvl - level of idx
    969:     idx_start - starting index of the list
    970:     lnk       - linked list(an integer array) that is created
    971:     lnklvl   - levels of lnk
    972:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
    973:   output Parameters:
    974:     nlnk      - number of newly added idx
    975:     lnk       - the sorted(increasing order) linked list containing new and non-redundate entries from idx
    976:     lnklvl   - levels of lnk
    977:     bt        - updated PetscBT (bitarray)
    978: */
    979: #define PetscIncompleteLLAdd(nidx,idx,level,idxlvl,idx_start,nlnk,lnk,lnklvl,bt) 0;\
    980: {\
    981:   PetscInt _k,_entry,_location,_lnkdata,_incrlev;\
    982:   nlnk     = 0;\
    983:   _lnkdata = idx_start;\
    984:   for (_k=0; _k<nidx; _k++){\
    985:     _incrlev = idxlvl[_k] + 1;\
    986:     if (_incrlev > level) continue;\
    987:     _entry = idx[_k];\
    988:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
    989:       /* search for insertion location */\
    990:       if (_k && _entry < _lnkdata) _lnkdata  = idx_start;\
    991:       do {\
    992:         _location = _lnkdata;\
    993:         _lnkdata  = lnk[_location];\
    994:       } while (_entry > _lnkdata);\
    995:       /* insertion location is found, add entry into lnk */\
    996:       lnk[_location]  = _entry;\
    997:       lnk[_entry]     = _lnkdata;\
    998:       lnklvl[_entry] = _incrlev;\
    999:       nlnk++;\
    1000:       _lnkdata = _entry; /* next search starts from here if next_entry > _entry */\
    1001:     } else { /* existing entry: update lnklvl */\
    1002:       if (lnklvl[_entry] > _incrlev) lnklvl[_entry] = _incrlev;\
    1003:     }\
    1004:   }\
    1005: }

    1007: /*
    1008:   Add a SORTED index set into a sorted linked list
    1009:   Input Parameters:
    1010:     nidx      - number of input indices
    1011:     idx   - sorted interger array used for storing column indices
    1012:     level     - level of fill, e.g., ICC(level)
    1013:     idxlvl - level of idx
    1014:     idx_start - starting index of the list
    1015:     lnk       - linked list(an integer array) that is created
    1016:     lnklvl    - levels of lnk
    1017:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
    1018:   output Parameters:
    1019:     nlnk      - number of newly added idx
    1020:     lnk       - the sorted(increasing order) linked list containing new and non-redundate entries from idx
    1021:     lnklvl    - levels of lnk
    1022:     bt        - updated PetscBT (bitarray)
    1023: */
    1024: #define PetscIncompleteLLAddSorted(nidx,idx,level,idxlvl,idx_start,nlnk,lnk,lnklvl,bt) 0;\
    1025: {\
    1026:   PetscInt _k,_entry,_location,_lnkdata,_incrlev;\
    1027:   nlnk = 0;\
    1028:   _lnkdata = idx_start;\
    1029:   for (_k=0; _k<nidx; _k++){\
    1030:     _incrlev = idxlvl[_k] + 1;\
    1031:     if (_incrlev > level) continue;\
    1032:     _entry = idx[_k];\
    1033:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
    1034:       /* search for insertion location */\
    1035:       do {\
    1036:         _location = _lnkdata;\
    1037:         _lnkdata  = lnk[_location];\
    1038:       } while (_entry > _lnkdata);\
    1039:       /* insertion location is found, add entry into lnk */\
    1040:       lnk[_location] = _entry;\
    1041:       lnk[_entry]    = _lnkdata;\
    1042:       lnklvl[_entry] = _incrlev;\
    1043:       nlnk++;\
    1044:       _lnkdata = _entry; /* next search starts from here */\
    1045:     } else { /* existing entry: update lnklvl */\
    1046:       if (lnklvl[_entry] > _incrlev) lnklvl[_entry] = _incrlev;\
    1047:     }\
    1048:   }\
    1049: }

    1051: /*
    1052:   Add a SORTED index set into a sorted linked list for ICC
    1053:   Input Parameters:
    1054:     nidx      - number of input indices
    1055:     idx       - sorted interger array used for storing column indices
    1056:     level     - level of fill, e.g., ICC(level)
    1057:     idxlvl    - level of idx
    1058:     idx_start - starting index of the list
    1059:     lnk       - linked list(an integer array) that is created
    1060:     lnklvl    - levels of lnk
    1061:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
    1062:     idxlvl_prow - idxlvl[prow], where prow is the row number of the idx
    1063:   output Parameters:
    1064:     nlnk   - number of newly added indices
    1065:     lnk    - the sorted(increasing order) linked list containing new and non-redundate entries from idx
    1066:     lnklvl - levels of lnk
    1067:     bt     - updated PetscBT (bitarray)
    1068:   Note: the level of U(i,j) is set as lvl(i,j) = min{ lvl(i,j), lvl(prow,i)+lvl(prow,j)+1)
    1069:         where idx = non-zero columns of U(prow,prow+1:n-1), prow<i
    1070: */
    1071: #define PetscICCLLAddSorted(nidx,idx,level,idxlvl,idx_start,nlnk,lnk,lnklvl,bt,idxlvl_prow) 0;\
    1072: {\
    1073:   PetscInt _k,_entry,_location,_lnkdata,_incrlev;\
    1074:   nlnk = 0;\
    1075:   _lnkdata = idx_start;\
    1076:   for (_k=0; _k<nidx; _k++){\
    1077:     _incrlev = idxlvl[_k] + idxlvl_prow + 1;\
    1078:     if (_incrlev > level) continue;\
    1079:     _entry = idx[_k];\
    1080:     if (!PetscBTLookupSet(bt,_entry)){  /* new entry */\
    1081:       /* search for insertion location */\
    1082:       do {\
    1083:         _location = _lnkdata;\
    1084:         _lnkdata  = lnk[_location];\
    1085:       } while (_entry > _lnkdata);\
    1086:       /* insertion location is found, add entry into lnk */\
    1087:       lnk[_location] = _entry;\
    1088:       lnk[_entry]    = _lnkdata;\
    1089:       lnklvl[_entry] = _incrlev;\
    1090:       nlnk++;\
    1091:       _lnkdata = _entry; /* next search starts from here */\
    1092:     } else { /* existing entry: update lnklvl */\
    1093:       if (lnklvl[_entry] > _incrlev) lnklvl[_entry] = _incrlev;\
    1094:     }\
    1095:   }\
    1096: }

    1098: /*
    1099:   Copy data on the list into an array, then initialize the list
    1100:   Input Parameters:
    1101:     idx_start - starting index of the list
    1102:     lnk_max   - max value of lnk indicating the end of the list
    1103:     nlnk      - number of data on the list to be copied
    1104:     lnk       - linked list
    1105:     lnklvl    - level of lnk
    1106:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
    1107:   output Parameters:
    1108:     indices - array that contains the copied data
    1109:     lnk     - linked list that is cleaned and initialize
    1110:     lnklvl  - level of lnk that is reinitialized
    1111:     bt      - PetscBT (bitarray) with all bits set to false
    1112: */
    1113: #define PetscIncompleteLLClean(idx_start,lnk_max,nlnk,lnk,lnklvl,indices,indiceslvl,bt) 0;\
    1114: {\
    1115:   PetscInt _j,_idx=idx_start;\
    1116:   for (_j=0; _j<nlnk; _j++){\
    1117:     _idx = lnk[_idx];\
    1118:     *(indices+_j) = _idx;\
    1119:     *(indiceslvl+_j) = lnklvl[_idx];\
    1120:     lnklvl[_idx] = -1;\
    1121:     PetscBTClear(bt,_idx);\
    1122:   }\
    1123:   lnk[idx_start] = lnk_max;\
    1124: }
    1125: /*
    1126:   Free memories used by the list
    1127: */
    1128: #define PetscIncompleteLLDestroy(lnk,bt) (PetscFree(lnk) || PetscBTDestroy(&(bt)))

    1130: /* -------------------------------------------------------------------------------------------------------*/
    1131: #include <petscbt.h>
    1134: /*
    1135:   Create and initialize a condensed linked list -
    1136:     same as PetscLLCreate(), but uses a scalable array 'lnk' with size of max number of entries, not O(N).
    1137:     Barry suggested this approach (Dec. 6, 2011):
    1138:       I've thought of an alternative way of representing a linked list that is efficient but doesn't have the O(N) scaling issue
    1139:       (it may be faster than the O(N) even sequentially due to less crazy memory access).

    1141:       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
    1142:       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
    1143:       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
    1144:       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.
    1145:       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
    1146:       to each other so memory access is much better than using the big array.

    1148:   Example:
    1149:      nlnk_max=5, lnk_max=36:
    1150:      Initial list: [0, 0 | 36, 2 | 0, 0 | 0, 0 | 0, 0 | 0, 0 | 0, 0]
    1151:      here, head_node has index 2 with value lnk[2]=lnk_max=36,
    1152:            0-th entry is used to store the number of entries in the list,
    1153:      The initial lnk represents head -> tail(marked by 36) with number of entries = lnk[0]=0.

    1155:      Now adding a sorted set {2,4}, the list becomes
    1156:      [2, 0 | 36, 4 |2, 6 | 4, 2 | 0, 0 | 0, 0 | 0, 0 ]
    1157:      represents head -> 2 -> 4 -> tail with number of entries = lnk[0]=2.

    1159:      Then adding a sorted set {0,3,35}, the list
    1160:      [5, 0 | 36, 8 | 2, 10 | 4, 12 | 0, 4 | 3, 6 | 35, 2 ]
    1161:      represents head -> 0 -> 2 -> 3 -> 4 -> 35 -> tail with number of entries = lnk[0]=5.

    1163:   Input Parameters:
    1164:     nlnk_max  - max length of the list
    1165:     lnk_max   - max value of the entries
    1166:   Output Parameters:
    1167:     lnk       - list created and initialized
    1168:     bt        - PetscBT (bitarray) with all bits set to false. Note: bt has size lnk_max, not nln_max!
    1169: */
    1170: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedCreate(PetscInt nlnk_max,PetscInt lnk_max,PetscInt **lnk,PetscBT *bt)
    1171: {
    1173:   PetscInt       *llnk;

    1176:   PetscMalloc(2*(nlnk_max+2)*sizeof(PetscInt),lnk);
    1177:   PetscBTCreate(lnk_max,bt);
    1178:   llnk = *lnk;
    1179:   llnk[0] = 0;         /* number of entries on the list */
    1180:   llnk[2] = lnk_max;   /* value in the head node */
    1181:   llnk[3] = 2;         /* next for the head node */
    1182:   return(0);
    1183: }

    1187: /*
    1188:   Add a SORTED ascending index set into a sorted linked list. See PetscLLCondensedCreate() for detailed description.
    1189:   Input Parameters:
    1190:     nidx      - number of input indices
    1191:     indices   - sorted interger array
    1192:     lnk       - condensed linked list(an integer array) that is created
    1193:     bt        - PetscBT (bitarray), bt[idx]=true marks idx is in lnk
    1194:   output Parameters:
    1195:     lnk       - the sorted(increasing order) linked list containing previous and newly added non-redundate indices
    1196:     bt        - updated PetscBT (bitarray)
    1197: */
    1198: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedAddSorted(PetscInt nidx,const PetscInt indices[],PetscInt lnk[],PetscBT bt)
    1199: {
    1200:   PetscInt _k,_entry,_location,_next,_lnkdata,_nlnk,_newnode;

    1203:   _nlnk     = lnk[0]; /* num of entries on the input lnk */
    1204:   _location = 2; /* head */
    1205:     for (_k=0; _k<nidx; _k++){
    1206:       _entry = indices[_k];
    1207:       if (!PetscBTLookupSet(bt,_entry)){  /* new entry */
    1208:         /* search for insertion location */
    1209:         do {
    1210:           _next     = _location + 1; /* link from previous node to next node */
    1211:           _location = lnk[_next];    /* idx of next node */
    1212:           _lnkdata  = lnk[_location];/* value of next node */
    1213:         } while (_entry > _lnkdata);
    1214:         /* insertion location is found, add entry into lnk */
    1215:         _newnode        = 2*(_nlnk+2);   /* index for this new node */
    1216:         lnk[_next]      = _newnode;      /* connect previous node to the new node */
    1217:         lnk[_newnode]   = _entry;        /* set value of the new node */
    1218:         lnk[_newnode+1] = _location;     /* connect new node to next node */
    1219:         _location       = _newnode;      /* next search starts from the new node */
    1220:         _nlnk++;
    1221:       }   \
    1222:     }\
    1223:   lnk[0]   = _nlnk;   /* number of entries in the list */
    1224:   return(0);
    1225: }

    1229: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedClean(PetscInt lnk_max,PetscInt nidx,PetscInt *indices,PetscInt lnk[],PetscBT bt)
    1230: {
    1232:   PetscInt       _k,_next,_nlnk;

    1235:   _next = lnk[3];       /* head node */
    1236:   _nlnk = lnk[0];       /* num of entries on the list */
    1237:   for (_k=0; _k<_nlnk; _k++){
    1238:     indices[_k] = lnk[_next];
    1239:     _next       = lnk[_next + 1];
    1240:     PetscBTClear(bt,indices[_k]);
    1241:   }
    1242:   lnk[0] = 0;          /* num of entries on the list */
    1243:   lnk[2] = lnk_max;    /* initialize head node */
    1244:   lnk[3] = 2;          /* head node */
    1245:   return(0);
    1246: }

    1250: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedView(PetscInt *lnk)
    1251: {
    1253:   PetscInt       k;

    1256:   PetscPrintf(PETSC_COMM_SELF,"LLCondensed of size %d, (val,  next)\n",lnk[0]);
    1257:   for (k=2; k< lnk[0]+2; k++){
    1258:     PetscPrintf(PETSC_COMM_SELF," %D: (%D, %D)\n",2*k,lnk[2*k],lnk[2*k+1]);
    1259:   }
    1260:   return(0);
    1261: }

    1265: /*
    1266:   Free memories used by the list
    1267: */
    1268: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedDestroy(PetscInt *lnk,PetscBT bt)
    1269: {

    1273:   PetscFree(lnk);
    1274:   PetscBTDestroy(&bt);
    1275:   return(0);
    1276: }

    1278: /* -------------------------------------------------------------------------------------------------------*/
    1281: /*
    1282:  Same as PetscLLCondensedCreate(), but does not use non-scalable O(lnk_max) bitarray
    1283:   Input Parameters:
    1284:     nlnk_max  - max length of the list
    1285:   Output Parameters:
    1286:     lnk       - list created and initialized
    1287: */
    1288: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedCreate_Scalable(PetscInt nlnk_max,PetscInt **lnk)
    1289: {
    1291:   PetscInt       *llnk;

    1294:   PetscMalloc(2*(nlnk_max+2)*sizeof(PetscInt),lnk);
    1295:   llnk = *lnk;
    1296:   llnk[0] = 0;               /* number of entries on the list */
    1297:   llnk[2] = PETSC_MAX_INT;   /* value in the head node */
    1298:   llnk[3] = 2;               /* next for the head node */
    1299:   return(0);
    1300: }

    1304: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedAddSorted_Scalable(PetscInt nidx,const PetscInt indices[],PetscInt lnk[])
    1305: {
    1306:   PetscInt _k,_entry,_location,_next,_lnkdata,_nlnk,_newnode;
    1307:   _nlnk     = lnk[0]; /* num of entries on the input lnk */
    1308:   _location = 2; /* head */ \
    1309:     for (_k=0; _k<nidx; _k++){
    1310:       _entry = indices[_k];
    1311:       /* search for insertion location */
    1312:       do {
    1313:         _next     = _location + 1; /* link from previous node to next node */
    1314:         _location = lnk[_next];    /* idx of next node */
    1315:         _lnkdata  = lnk[_location];/* value of next node */
    1316:       } while (_entry > _lnkdata);
    1317:       if (_entry < _lnkdata) {
    1318:         /* insertion location is found, add entry into lnk */
    1319:         _newnode        = 2*(_nlnk+2);   /* index for this new node */
    1320:         lnk[_next]      = _newnode;      /* connect previous node to the new node */
    1321:         lnk[_newnode]   = _entry;        /* set value of the new node */
    1322:         lnk[_newnode+1] = _location;     /* connect new node to next node */
    1323:         _location       = _newnode;      /* next search starts from the new node */
    1324:         _nlnk++;
    1325:       }
    1326:     }
    1327:   lnk[0]   = _nlnk;   /* number of entries in the list */
    1328:   return 0;
    1329: }

    1333: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedClean_Scalable(PetscInt nidx,PetscInt *indices,PetscInt *lnk)
    1334: {
    1335:   PetscInt _k,_next,_nlnk;
    1336:   _next = lnk[3];       /* head node */
    1337:   _nlnk = lnk[0];
    1338:   for (_k=0; _k<_nlnk; _k++){
    1339:     indices[_k] = lnk[_next];
    1340:     _next       = lnk[_next + 1];
    1341:   }
    1342:   lnk[0] = 0;          /* num of entries on the list */
    1343:   lnk[3] = 2;          /* head node */
    1344:   return 0;
    1345: }

    1349: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedDestroy_Scalable(PetscInt *lnk)
    1350: {
    1351:   return PetscFree(lnk);
    1352: }

    1354: /* -------------------------------------------------------------------------------------------------------*/
    1355: /*
    1356:       lnk[0]   number of links
    1357:       lnk[1]   number of entries
    1358:       lnk[3n]  value
    1359:       lnk[3n+1] len
    1360:       lnk[3n+2] link to next value

    1362:       The next three are always the first link

    1364:       lnk[3]    PETSC_MIN_INT+1
    1365:       lnk[4]    1
    1366:       lnk[5]    link to first real entry

    1368:       The next three are always the last link

    1370:       lnk[6]    PETSC_MAX_INT - 1
    1371:       lnk[7]    1
    1372:       lnk[8]    next valid link (this is the same as lnk[0] but without the decreases)
    1373: */

    1377: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedCreate_fast(PetscInt nlnk_max,PetscInt **lnk)
    1378: {
    1380:   PetscInt       *llnk;

    1383:   PetscMalloc(3*(nlnk_max+3)*sizeof(PetscInt),lnk);
    1384:   llnk = *lnk;
    1385:   llnk[0] = 0;   /* nlnk: number of entries on the list */
    1386:   llnk[1] = 0;          /* number of integer entries represented in list */
    1387:   llnk[3] = PETSC_MIN_INT+1;   /* value in the first node */
    1388:   llnk[4] = 1;           /* count for the first node */
    1389:   llnk[5] = 6;         /* next for the first node */
    1390:   llnk[6] = PETSC_MAX_INT-1;   /* value in the last node */
    1391:   llnk[7] = 1;           /* count for the last node */
    1392:   llnk[8] = 0;         /* next valid node to be used */
    1393:   return(0);
    1394: }

    1396: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedAddSorted_fast(PetscInt nidx,const PetscInt indices[],PetscInt lnk[])
    1397: {
    1398:   PetscInt k,entry,prev,next;
    1399:   prev      = 3;      /* first value */
    1400:   next      = lnk[prev+2];
    1401:   for (k=0; k<nidx; k++){
    1402:     entry = indices[k];
    1403:     /* search for insertion location */
    1404:     while (entry >= lnk[next]) {
    1405:       prev = next;
    1406:       next = lnk[next+2];
    1407:     }
    1408:     /* entry is in range of previous list */
    1409:     if (entry < lnk[prev]+lnk[prev+1]) continue;
    1410:     lnk[1]++;
    1411:     /* entry is right after previous list */
    1412:     if (entry == lnk[prev]+lnk[prev+1]) {
    1413:       lnk[prev+1]++;
    1414:       if (lnk[next] == entry+1) { /* combine two contiquous strings */
    1415:         lnk[prev+1] += lnk[next+1];
    1416:         lnk[prev+2]  = lnk[next+2];
    1417:         next         = lnk[next+2];
    1418:         lnk[0]--;
    1419:       }
    1420:       continue;
    1421:     }
    1422:     /* entry is right before next list */
    1423:     if (entry == lnk[next]-1) {
    1424:       lnk[next]--;
    1425:       lnk[next+1]++;
    1426:       prev = next;
    1427:       next = lnk[prev+2];
    1428:       continue;
    1429:     }
    1430:     /*  add entry into lnk */
    1431:     lnk[prev+2]    = 3*((lnk[8]++)+3);      /* connect previous node to the new node */
    1432:     prev           = lnk[prev+2];
    1433:     lnk[prev]      = entry;        /* set value of the new node */
    1434:     lnk[prev+1]    = 1;             /* number of values in contiquous string is one to start */
    1435:     lnk[prev+2]    = next;          /* connect new node to next node */
    1436:     lnk[0]++;
    1437:   }
    1438:   return 0;
    1439: }

    1441: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedClean_fast(PetscInt nidx,PetscInt *indices,PetscInt *lnk)
    1442: {
    1443:   PetscInt _k,_next,_nlnk,cnt,j;
    1444:   _next = lnk[5];       /* first node */
    1445:   _nlnk = lnk[0];
    1446:   cnt   = 0;
    1447:   for (_k=0; _k<_nlnk; _k++){
    1448:     for (j=0; j<lnk[_next+1]; j++) {
    1449:       indices[cnt++] = lnk[_next] + j;
    1450:     }
    1451:     _next       = lnk[_next + 2];
    1452:   }
    1453:   lnk[0] = 0;   /* nlnk: number of links */
    1454:   lnk[1] = 0;          /* number of integer entries represented in list */
    1455:   lnk[3] = PETSC_MIN_INT+1;   /* value in the first node */
    1456:   lnk[4] = 1;           /* count for the first node */
    1457:   lnk[5] = 6;         /* next for the first node */
    1458:   lnk[6] = PETSC_MAX_INT-1;   /* value in the last node */
    1459:   lnk[7] = 1;           /* count for the last node */
    1460:   lnk[8] = 0;         /* next valid location to make link */
    1461:   return 0;
    1462: }

    1464: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedView_fast(PetscInt *lnk)
    1465: {
    1466:   PetscInt k,next,nlnk;
    1467:   next = lnk[5];       /* first node */
    1468:   nlnk = lnk[0];
    1469:   for (k=0; k<nlnk; k++){
    1470: #if 0                           /* Debugging code */
    1471:     printf("%d value %d len %d next %d\n",next,lnk[next],lnk[next+1],lnk[next+2]);
    1472: #endif
    1473:     next = lnk[next + 2];
    1474:   }
    1475:   return 0;
    1476: }

    1478: PETSC_STATIC_INLINE PetscErrorCode PetscLLCondensedDestroy_fast(PetscInt *lnk)
    1479: {
    1480:   return PetscFree(lnk);
    1481: }

    1483: PETSC_EXTERN PetscLogEvent MAT_Mult, MAT_MultMatrixFree, MAT_Mults, MAT_MultConstrained, MAT_MultAdd, MAT_MultTranspose;
    1484: PETSC_EXTERN PetscLogEvent MAT_MultTransposeConstrained, MAT_MultTransposeAdd, MAT_Solve, MAT_Solves, MAT_SolveAdd, MAT_SolveTranspose;
    1485: PETSC_EXTERN PetscLogEvent MAT_SolveTransposeAdd, MAT_SOR, MAT_ForwardSolve, MAT_BackwardSolve, MAT_LUFactor, MAT_LUFactorSymbolic;
    1486: PETSC_EXTERN PetscLogEvent MAT_LUFactorNumeric, MAT_CholeskyFactor, MAT_CholeskyFactorSymbolic, MAT_CholeskyFactorNumeric, MAT_ILUFactor;
    1487: PETSC_EXTERN PetscLogEvent MAT_ILUFactorSymbolic, MAT_ICCFactorSymbolic, MAT_Copy, MAT_Convert, MAT_Scale, MAT_AssemblyBegin;
    1488: PETSC_EXTERN PetscLogEvent MAT_AssemblyEnd, MAT_SetValues, MAT_GetValues, MAT_GetRow, MAT_GetRowIJ, MAT_GetSubMatrices, MAT_GetColoring, MAT_GetOrdering, MAT_GetRedundantMatrix;
    1489: PETSC_EXTERN PetscLogEvent MAT_IncreaseOverlap, MAT_Partitioning, MAT_Coarsen, MAT_ZeroEntries, MAT_Load, MAT_View, MAT_AXPY, MAT_FDColoringCreate, MAT_TransposeColoringCreate;
    1490: PETSC_EXTERN PetscLogEvent MAT_FDColoringApply, MAT_Transpose, MAT_FDColoringFunction;
    1491: PETSC_EXTERN PetscLogEvent MAT_MatMult, MAT_MatSolve,MAT_MatMultSymbolic, MAT_MatMultNumeric,MAT_Getlocalmatcondensed,MAT_GetBrowsOfAcols,MAT_GetBrowsOfAocols;
    1492: PETSC_EXTERN PetscLogEvent MAT_PtAP, MAT_PtAPSymbolic, MAT_PtAPNumeric,MAT_Seqstompinum,MAT_Seqstompisym,MAT_Seqstompi,MAT_Getlocalmat;
    1493: PETSC_EXTERN PetscLogEvent MAT_RARt, MAT_RARtSymbolic, MAT_RARtNumeric;
    1494: PETSC_EXTERN PetscLogEvent MAT_MatTransposeMult, MAT_MatTransposeMultSymbolic, MAT_MatTransposeMultNumeric;
    1495: PETSC_EXTERN PetscLogEvent MAT_TransposeMatMult, MAT_TransposeMatMultSymbolic, MAT_TransposeMatMultNumeric;
    1496: PETSC_EXTERN PetscLogEvent MAT_MatMatMult, MAT_MatMatMultSymbolic, MAT_MatMatMultNumeric;
    1497: PETSC_EXTERN PetscLogEvent MAT_Applypapt, MAT_Applypapt_symbolic, MAT_Applypapt_numeric;
    1498: PETSC_EXTERN PetscLogEvent MAT_Getsymtranspose, MAT_Transpose_SeqAIJ, MAT_Getsymtransreduced,MAT_GetSequentialNonzeroStructure;

    1500: PETSC_EXTERN PetscLogEvent MATMFFD_Mult;
    1501: PETSC_EXTERN PetscLogEvent MAT_GetMultiProcBlock;
    1502: PETSC_EXTERN PetscLogEvent MAT_CUSPCopyToGPU, MAT_CUSPARSECopyToGPU, MAT_SetValuesBatch, MAT_SetValuesBatchI, MAT_SetValuesBatchII, MAT_SetValuesBatchIII, MAT_SetValuesBatchIV;
    1503: PETSC_EXTERN PetscLogEvent MAT_Merge;

    1505: #endif