petsc/include/petscmat.h

/*
     Include file for the matrix component of PETSc
*/
#ifndef __PETSCMAT_H
#define __PETSCMAT_H
#include "petscvec.h"
PETSC_EXTERN_CXX_BEGIN

/*S
     Mat - Abstract PETSc matrix object

   Level: beginner

  Concepts: matrix; linear operator

.seealso:  MatCreate(), MatType, MatSetType()
S*/
typedef struct _p_Mat*           Mat;

/*E
    MatType - String with the name of a PETSc matrix or the creation function
       with an optional dynamic library name, for example
       http://www.mcs.anl.gov/petsc/lib.a:mymatcreate()

   Level: beginner

.seealso: MatSetType(), Mat
E*/
#define MATSAME            "same"
#define MATSEQMAIJ         "seqmaij"
#define MATMPIMAIJ         "mpimaij"
#define MATMAIJ            "maij"
#define MATIS              "is"
#define MATMPIROWBS        "mpirowbs"
#define MATSEQAIJ          "seqaij"
#define MATMPIAIJ          "mpiaij"
#define MATAIJ             "aij"
#define MATSHELL           "shell"
#define MATSEQBDIAG        "seqbdiag"
#define MATMPIBDIAG        "mpibdiag"
#define MATBDIAG           "bdiag"
#define MATSEQDENSE        "seqdense"
#define MATMPIDENSE        "mpidense"
#define MATDENSE           "dense"
#define MATSEQBAIJ         "seqbaij"
#define MATMPIBAIJ         "mpibaij"
#define MATBAIJ            "baij"
#define MATMPIADJ          "mpiadj"
#define MATSEQSBAIJ        "seqsbaij"
#define MATMPISBAIJ        "mpisbaij"
#define MATSBAIJ           "sbaij"
#define MATDAAD            "daad"
#define MATMFFD            "mffd"
#define MATESI             "esi"
#define MATPETSCESI        "petscesi"
#define MATNORMAL          "normal"
#define MATSEQAIJSPOOLES   "seqaijspooles"
#define MATMPIAIJSPOOLES   "mpiaijspooles"
#define MATSEQSBAIJSPOOLES "seqsbaijspooles"
#define MATMPISBAIJSPOOLES "mpisbaijspooles"
#define MATAIJSPOOLES      "aijspooles"
#define MATSBAIJSPOOLES    "sbaijspooles"
#define MATSUPERLU         "superlu"
#define MATSUPERLU_DIST    "superlu_dist"
#define MATUMFPACK         "umfpack"
#define MATESSL            "essl"
#define MATLUSOL           "lusol"
#define MATAIJMUMPS        "aijmumps"
#define MATSBAIJMUMPS      "sbaijmumps"
#define MATDSCPACK         "dscpack"
#define MATMATLAB          "matlab"
#define MatType char*

/* Logging support */
#define    MAT_FILE_COOKIE 1211216    /* used to indicate matrices in binary files */
extern PetscCookie MAT_COOKIE, MATSNESMFCTX_COOKIE, MAT_FDCOLORING_COOKIE, MAT_PARTITIONING_COOKIE, MAT_NULLSPACE_COOKIE;
extern PetscEvent    MAT_Mult, MAT_MultMatrixFree, MAT_Mults, MAT_MultConstrained, MAT_MultAdd, MAT_MultTranspose;
extern PetscEvent    MAT_MultTransposeConstrained, MAT_MultTransposeAdd, MAT_Solve, MAT_Solves, MAT_SolveAdd, MAT_SolveTranspose;
extern PetscEvent    MAT_SolveTransposeAdd, MAT_Relax, MAT_ForwardSolve, MAT_BackwardSolve, MAT_LUFactor, MAT_LUFactorSymbolic;
extern PetscEvent    MAT_LUFactorNumeric, MAT_CholeskyFactor, MAT_CholeskyFactorSymbolic, MAT_CholeskyFactorNumeric, MAT_ILUFactor;
extern PetscEvent    MAT_ILUFactorSymbolic, MAT_ICCFactorSymbolic, MAT_Copy, MAT_Convert, MAT_Scale, MAT_AssemblyBegin;
extern PetscEvent    MAT_AssemblyEnd, MAT_SetValues, MAT_GetValues, MAT_GetRow, MAT_GetSubMatrices, MAT_GetColoring, MAT_GetOrdering;
extern PetscEvent    MAT_IncreaseOverlap, MAT_Partitioning, MAT_ZeroEntries, MAT_Load, MAT_View, MAT_AXPY, MAT_FDColoringCreate;
extern PetscEvent    MAT_FDColoringApply, MAT_Transpose, MAT_FDColoringFunction;
extern PetscEvent    MAT_MatMult, MAT_MatMultSymbolic, MAT_MatMultNumeric;
extern PetscEvent    MAT_PtAP, MAT_PtAPSymbolic, MAT_PtAPNumeric;
extern PetscEvent    MAT_MatMultTranspose, MAT_MatMultTransposeSymbolic, MAT_MatMultTransposeNumeric;

EXTERN PetscErrorCode MatInitializePackage(char *);

EXTERN PetscErrorCode MatCreate(MPI_Comm,int,int,int,int,Mat*);
EXTERN PetscErrorCode MatSetType(Mat,const MatType);
EXTERN PetscErrorCode MatSetFromOptions(Mat);
EXTERN PetscErrorCode MatSetUpPreallocation(Mat);
EXTERN PetscErrorCode MatRegisterAll(const char[]);
EXTERN PetscErrorCode MatRegister(const char[],const char[],const char[],PetscErrorCode(*)(Mat));

/*MC
   MatRegisterDynamic - Adds a new matrix type

   Synopsis:
   int MatRegisterDynamic(char *name,char *path,char *name_create,PetscErrorCode (*routine_create)(Mat))

   Not Collective

   Input Parameters:
+  name - name of a new user-defined matrix type
.  path - path (either absolute or relative) the library containing this solver
.  name_create - name of routine to create method context
-  routine_create - routine to create method context

   Notes:
   MatRegisterDynamic() may be called multiple times to add several user-defined solvers.

   If dynamic libraries are used, then the fourth input argument (routine_create)
   is ignored.

   Sample usage:
.vb
   MatRegisterDynamic("my_mat",/home/username/my_lib/lib/libO/solaris/mylib.a,
               "MyMatCreate",MyMatCreate);
.ve

   Then, your solver can be chosen with the procedural interface via
$     MatSetType(Mat,"my_mat")
   or at runtime via the option
$     -mat_type my_mat

   Level: advanced

   Notes: ${PETSC_ARCH} and ${BOPT} occuring in pathname will be replaced with appropriate values.
         If your function is not being put into a shared library then use VecRegister() instead

.keywords: Mat, register

.seealso: MatRegisterAll(), MatRegisterDestroy()

M*/
#if defined(PETSC_USE_DYNAMIC_LIBRARIES)
#define MatRegisterDynamic(a,b,c,d) MatRegister(a,b,c,0)
#else
#define MatRegisterDynamic(a,b,c,d) MatRegister(a,b,c,d)
#endif

extern PetscTruth MatRegisterAllCalled;
extern PetscFList MatList;

EXTERN PetscErrorCode MatCreateSeqDense(MPI_Comm,int,int,PetscScalar[],Mat*);
EXTERN PetscErrorCode MatCreateMPIDense(MPI_Comm,int,int,int,int,PetscScalar[],Mat*);
EXTERN PetscErrorCode MatCreateSeqAIJ(MPI_Comm,int,int,int,const int[],Mat*);
EXTERN PetscErrorCode MatCreateMPIAIJ(MPI_Comm,int,int,int,int,int,const int[],int,const int[],Mat*);
EXTERN PetscErrorCode MatCreateMPIRowbs(MPI_Comm,int,int,int,const int[],Mat*);
EXTERN PetscErrorCode MatCreateSeqBDiag(MPI_Comm,int,int,int,int,const int[],PetscScalar*[],Mat*);
EXTERN PetscErrorCode MatCreateMPIBDiag(MPI_Comm,int,int,int,int,int,const int[],PetscScalar*[],Mat*);
EXTERN PetscErrorCode MatCreateSeqBAIJ(MPI_Comm,int,int,int,int,const int[],Mat*);
EXTERN PetscErrorCode MatCreateMPIBAIJ(MPI_Comm,int,int,int,int,int,int,const int[],int,const int[],Mat*);
EXTERN PetscErrorCode MatCreateMPIAdj(MPI_Comm,int,int,int[],int[],int[],Mat*);
EXTERN PetscErrorCode MatCreateSeqSBAIJ(MPI_Comm,int,int,int,int,const int[],Mat*);
EXTERN PetscErrorCode MatCreateMPISBAIJ(MPI_Comm,int,int,int,int,int,int,const int[],int,const int[],Mat*);
EXTERN PetscErrorCode MatCreateShell(MPI_Comm,int,int,int,int,void *,Mat*);
EXTERN PetscErrorCode MatCreateAdic(MPI_Comm,int,int,int,int,int,void (*)(void),Mat*);
EXTERN PetscErrorCode MatCreateNormal(Mat,Mat*);
EXTERN PetscErrorCode MatDestroy(Mat);

EXTERN PetscErrorCode MatPrintHelp(Mat);
EXTERN PetscErrorCode MatGetPetscMaps(Mat,PetscMap*,PetscMap*);

/* ------------------------------------------------------------*/
EXTERN PetscErrorCode MatSetValues(Mat,int,const int[],int,const int[],const PetscScalar[],InsertMode);
EXTERN PetscErrorCode MatSetValuesBlocked(Mat,int,const int[],int,const int[],const PetscScalar[],InsertMode);

/*S
     MatStencil - Data structure (C struct) for storing information about a single row or
        column of a matrix as index on an associated grid.

   Level: beginner

  Concepts: matrix; linear operator

.seealso:  MatSetValuesStencil(), MatSetStencil(), MatSetValuesBlockStencil()
S*/
typedef struct {
  int k,j,i,c;
} MatStencil;

EXTERN PetscErrorCode MatSetValuesStencil(Mat,int,const MatStencil[],int,const MatStencil[],const PetscScalar[],InsertMode);
EXTERN PetscErrorCode MatSetValuesBlockedStencil(Mat,int,const MatStencil[],int,const MatStencil[],const PetscScalar[],InsertMode);
EXTERN PetscErrorCode MatSetStencil(Mat,int,const int[],const int[],int);

EXTERN PetscErrorCode MatSetColoring(Mat,ISColoring);
EXTERN PetscErrorCode MatSetValuesAdic(Mat,void*);
EXTERN PetscErrorCode MatSetValuesAdifor(Mat,int,void*);

/*E
    MatAssemblyType - Indicates if the matrix is now to be used, or if you plan
     to continue to add values to it

    Level: beginner

.seealso: MatAssemblyBegin(), MatAssemblyEnd()
E*/
typedef enum {MAT_FLUSH_ASSEMBLY=1,MAT_FINAL_ASSEMBLY=0} MatAssemblyType;
EXTERN PetscErrorCode MatAssemblyBegin(Mat,MatAssemblyType);
EXTERN PetscErrorCode MatAssemblyEnd(Mat,MatAssemblyType);
EXTERN PetscErrorCode MatAssembled(Mat,PetscTruth*);

extern int         MatSetValue_Row, MatSetValue_Column;
extern PetscScalar MatSetValue_Value;

/*MC
   MatSetValue - Set a single entry into a matrix.

   Synopsis:
   int MatSetValue(Mat m,int row,int col,PetscScalar value,InsertMode mode);

   Not collective

   Input Parameters:
+  m - the matrix
.  row - the row location of the entry
.  col - the column location of the entry
.  value - the value to insert
-  mode - either INSERT_VALUES or ADD_VALUES

   Notes:
   For efficiency one should use MatSetValues() and set several or many
   values simultaneously if possible.

   Level: beginner

.seealso: MatSetValues(), MatSetValueLocal()
M*/
#define MatSetValue(v,i,j,va,mode) \
  (MatSetValue_Row = i,MatSetValue_Column = j,MatSetValue_Value = va, \
   MatSetValues(v,1,&MatSetValue_Row,1,&MatSetValue_Column,&MatSetValue_Value,mode))

#define MatGetValue(v,i,j,va) \
  (MatSetValue_Row = i,MatSetValue_Column = j,\
   MatGetValues(v,1,&MatSetValue_Row,1,&MatSetValue_Column,&va))

#define MatSetValueLocal(v,i,j,va,mode) \
  (MatSetValue_Row = i,MatSetValue_Column = j,MatSetValue_Value = va, \
   MatSetValuesLocal(v,1,&MatSetValue_Row,1,&MatSetValue_Column,&MatSetValue_Value,mode))

/*E
    MatOption - Options that may be set for a matrix and its behavior or storage

    Level: beginner

   Any additions/changes here MUST also be made in include/finclude/petscmat.h

.seealso: MatSetOption()
E*/
typedef enum {MAT_ROW_ORIENTED=1,MAT_COLUMN_ORIENTED=2,MAT_ROWS_SORTED=4,
              MAT_COLUMNS_SORTED=8,MAT_NO_NEW_NONZERO_LOCATIONS=16,
              MAT_YES_NEW_NONZERO_LOCATIONS=32,MAT_SYMMETRIC=64,
              MAT_STRUCTURALLY_SYMMETRIC=65,MAT_NO_NEW_DIAGONALS=66,
              MAT_YES_NEW_DIAGONALS=67,MAT_INODE_LIMIT_1=68,MAT_INODE_LIMIT_2=69,
              MAT_INODE_LIMIT_3=70,MAT_INODE_LIMIT_4=71,MAT_INODE_LIMIT_5=72,
              MAT_IGNORE_OFF_PROC_ENTRIES=73,MAT_ROWS_UNSORTED=74,
              MAT_COLUMNS_UNSORTED=75,MAT_NEW_NONZERO_LOCATION_ERR=76,
              MAT_NEW_NONZERO_ALLOCATION_ERR=77,MAT_USE_HASH_TABLE=78,
              MAT_KEEP_ZEROED_ROWS=79,MAT_IGNORE_ZERO_ENTRIES=80,MAT_USE_INODES=81,
              MAT_DO_NOT_USE_INODES=82,MAT_NOT_SYMMETRIC=83,MAT_HERMITIAN=84,
              MAT_NOT_STRUCTURALLY_SYMMETRIC=85,MAT_NOT_HERMITIAN=86,
              MAT_SYMMETRY_ETERNAL=87,MAT_NOT_SYMMETRY_ETERNAL=88} MatOption;
EXTERN PetscErrorCode MatSetOption(Mat,MatOption);
EXTERN PetscErrorCode MatGetType(Mat,MatType*);

EXTERN PetscErrorCode MatGetValues(Mat,int,const int[],int,const int[],PetscScalar[]);
EXTERN PetscErrorCode MatGetRow(Mat,int,int *,const int *[],const PetscScalar*[]);
EXTERN PetscErrorCode MatRestoreRow(Mat,int,int *,const int *[],const PetscScalar*[]);
EXTERN PetscErrorCode MatGetColumn(Mat,int,int *,int *[],PetscScalar*[]);
EXTERN PetscErrorCode MatRestoreColumn(Mat,int,int *,int *[],PetscScalar*[]);
EXTERN PetscErrorCode MatGetColumnVector(Mat,Vec,int);
EXTERN PetscErrorCode MatGetArray(Mat,PetscScalar *[]);
EXTERN PetscErrorCode MatRestoreArray(Mat,PetscScalar *[]);
EXTERN PetscErrorCode MatGetBlockSize(Mat,int *);

EXTERN PetscErrorCode MatMult(Mat,Vec,Vec);
EXTERN PetscErrorCode MatMultAdd(Mat,Vec,Vec,Vec);
EXTERN PetscErrorCode MatMultTranspose(Mat,Vec,Vec);
EXTERN PetscErrorCode MatIsTranspose(Mat,Mat,PetscReal,PetscTruth*);
EXTERN PetscErrorCode MatMultTransposeAdd(Mat,Vec,Vec,Vec);
EXTERN PetscErrorCode MatMultConstrained(Mat,Vec,Vec);
EXTERN PetscErrorCode MatMultTransposeConstrained(Mat,Vec,Vec);

/*E
    MatDuplicateOption - Indicates if a duplicated sparse matrix should have
  its numerical values copied over or just its nonzero structure.

    Level: beginner

   Any additions/changes here MUST also be made in include/finclude/petscmat.h

.seealso: MatDuplicate()
E*/
typedef enum {MAT_DO_NOT_COPY_VALUES,MAT_COPY_VALUES} MatDuplicateOption;

EXTERN PetscErrorCode MatConvertRegister(const char[],const char[],const char[],PetscErrorCode (*)(Mat,MatType,Mat*));
#if defined(PETSC_USE_DYNAMIC_LIBRARIES)
#define MatConvertRegisterDynamic(a,b,c,d) MatConvertRegister(a,b,c,0)
#else
#define MatConvertRegisterDynamic(a,b,c,d) MatConvertRegister(a,b,c,d)
#endif
EXTERN PetscErrorCode        MatConvertRegisterAll(const char[]);
EXTERN PetscErrorCode        MatConvertRegisterDestroy(void);
extern PetscTruth MatConvertRegisterAllCalled;
extern PetscFList MatConvertList;
EXTERN PetscErrorCode        MatConvert(Mat,const MatType,Mat*);
EXTERN PetscErrorCode        MatDuplicate(Mat,MatDuplicateOption,Mat*);

/*E
    MatStructure - Indicates if the matrix has the same nonzero structure

    Level: beginner

   Any additions/changes here MUST also be made in include/finclude/petscmat.h

.seealso: MatCopy(), KSPSetOperators(), PCSetOperators()
E*/
typedef enum {SAME_NONZERO_PATTERN,DIFFERENT_NONZERO_PATTERN,SAME_PRECONDITIONER,SUBSET_NONZERO_PATTERN} MatStructure;

EXTERN PetscErrorCode MatCopy(Mat,Mat,MatStructure);
EXTERN PetscErrorCode MatView(Mat,PetscViewer);
EXTERN PetscErrorCode MatIsSymmetric(Mat,PetscReal,PetscTruth*);
EXTERN PetscErrorCode MatIsSymmetricKnown(Mat,PetscTruth*,PetscTruth*);
EXTERN PetscErrorCode MatLoad(PetscViewer,const MatType,Mat*);

EXTERN PetscErrorCode MatGetRowIJ(Mat,int,PetscTruth,int*,int *[],int *[],PetscTruth *);
EXTERN PetscErrorCode MatRestoreRowIJ(Mat,int,PetscTruth,int *,int *[],int *[],PetscTruth *);
EXTERN PetscErrorCode MatGetColumnIJ(Mat,int,PetscTruth,int*,int *[],int *[],PetscTruth *);
EXTERN PetscErrorCode MatRestoreColumnIJ(Mat,int,PetscTruth,int *,int *[],int *[],PetscTruth *);

/*S
     MatInfo - Context of matrix information, used with MatGetInfo()

   In Fortran this is simply a double precision array of dimension MAT_INFO_SIZE

   Level: intermediate

  Concepts: matrix^nonzero information

.seealso:  MatGetInfo(), MatInfoType
S*/
typedef struct {
  PetscLogDouble rows_global,columns_global;         /* number of global rows and columns */
  PetscLogDouble rows_local,columns_local;           /* number of local rows and columns */
  PetscLogDouble block_size;                         /* block size */
  PetscLogDouble nz_allocated,nz_used,nz_unneeded;   /* number of nonzeros */
  PetscLogDouble memory;                             /* memory allocated */
  PetscLogDouble assemblies;                         /* number of matrix assemblies called */
  PetscLogDouble mallocs;                            /* number of mallocs during MatSetValues() */
  PetscLogDouble fill_ratio_given,fill_ratio_needed; /* fill ratio for LU/ILU */
  PetscLogDouble factor_mallocs;                     /* number of mallocs during factorization */
} MatInfo;

/*E
    MatInfoType - Indicates if you want information about the local part of the matrix,
     the entire parallel matrix or the maximum over all the local parts.

    Level: beginner

   Any additions/changes here MUST also be made in include/finclude/petscmat.h

.seealso: MatGetInfo(), MatInfo
E*/
typedef enum {MAT_LOCAL=1,MAT_GLOBAL_MAX=2,MAT_GLOBAL_SUM=3} MatInfoType;
EXTERN PetscErrorCode MatGetInfo(Mat,MatInfoType,MatInfo*);
EXTERN PetscErrorCode MatValid(Mat,PetscTruth*);
EXTERN PetscErrorCode MatGetDiagonal(Mat,Vec);
EXTERN PetscErrorCode MatGetRowMax(Mat,Vec);
EXTERN PetscErrorCode MatTranspose(Mat,Mat*);
EXTERN PetscErrorCode MatPermute(Mat,IS,IS,Mat *);
EXTERN PetscErrorCode MatPermuteSparsify(Mat,int,PetscReal,PetscReal,IS,IS,Mat *);
EXTERN PetscErrorCode MatDiagonalScale(Mat,Vec,Vec);
EXTERN PetscErrorCode MatDiagonalSet(Mat,Vec,InsertMode);
EXTERN PetscErrorCode MatEqual(Mat,Mat,PetscTruth*);

EXTERN PetscErrorCode MatNorm(Mat,NormType,PetscReal *);
EXTERN PetscErrorCode MatZeroEntries(Mat);
EXTERN PetscErrorCode MatZeroRows(Mat,IS,const PetscScalar*);
EXTERN PetscErrorCode MatZeroColumns(Mat,IS,const PetscScalar*);

EXTERN PetscErrorCode MatUseScaledForm(Mat,PetscTruth);
EXTERN PetscErrorCode MatScaleSystem(Mat,Vec,Vec);
EXTERN PetscErrorCode MatUnScaleSystem(Mat,Vec,Vec);

EXTERN PetscErrorCode MatGetSize(Mat,int*,int*);
EXTERN PetscErrorCode MatGetLocalSize(Mat,int*,int*);
EXTERN PetscErrorCode MatGetOwnershipRange(Mat,int*,int*);

/*E
    MatReuse - Indicates if matrices obtained from a previous call to MatGetSubMatrices()
     or MatGetSubMatrix() are to be reused to store the new matrix values.

    Level: beginner

   Any additions/changes here MUST also be made in include/finclude/petscmat.h

.seealso: MatGetSubMatrices(), MatGetSubMatrix(), MatDestroyMatrices()
E*/
typedef enum {MAT_INITIAL_MATRIX,MAT_REUSE_MATRIX} MatReuse;
EXTERN PetscErrorCode MatGetSubMatrices(Mat,int,const IS[],const IS[],MatReuse,Mat *[]);
EXTERN PetscErrorCode MatDestroyMatrices(int,Mat *[]);
EXTERN PetscErrorCode MatGetSubMatrix(Mat,IS,IS,int,MatReuse,Mat *);
EXTERN PetscErrorCode MatMerge(MPI_Comm,Mat,MatReuse,Mat*);
EXTERN PetscErrorCode MatMerge_SeqsToMPI(MPI_Comm,Mat,MatReuse,Mat*);

EXTERN PetscErrorCode MatIncreaseOverlap(Mat,int,IS[],int);

EXTERN PetscErrorCode MatMatMult(Mat,Mat,MatReuse,PetscReal,Mat*);
EXTERN PetscErrorCode MatMatMultSymbolic(Mat,Mat,PetscReal,Mat*);
EXTERN PetscErrorCode MatMatMultNumeric(Mat,Mat,Mat);

EXTERN PetscErrorCode MatPtAP(Mat,Mat,MatReuse,PetscReal,Mat*);
EXTERN PetscErrorCode MatPtAPSymbolic(Mat,Mat,PetscReal,Mat*);
EXTERN PetscErrorCode MatPtAPNumeric(Mat,Mat,Mat);

EXTERN PetscErrorCode MatMatMultTranspose(Mat,Mat,MatReuse,PetscReal,Mat*);
EXTERN PetscErrorCode MatMatMultTransposeSymbolic(Mat,Mat,PetscReal,Mat*);
EXTERN PetscErrorCode MatMatMultTransposeNumeric(Mat,Mat,Mat);

EXTERN PetscErrorCode MatAXPY(const PetscScalar *,Mat,Mat,MatStructure);
EXTERN PetscErrorCode MatAYPX(const PetscScalar *,Mat,Mat);
EXTERN PetscErrorCode MatCompress(Mat);

EXTERN PetscErrorCode MatScale(const PetscScalar *,Mat);
EXTERN PetscErrorCode MatShift(const PetscScalar *,Mat);

EXTERN PetscErrorCode MatSetLocalToGlobalMapping(Mat,ISLocalToGlobalMapping);
EXTERN PetscErrorCode MatSetLocalToGlobalMappingBlock(Mat,ISLocalToGlobalMapping);
EXTERN PetscErrorCode MatZeroRowsLocal(Mat,IS,const PetscScalar*);
EXTERN PetscErrorCode MatSetValuesLocal(Mat,int,const int[],int,const int[],const PetscScalar[],InsertMode);
EXTERN PetscErrorCode MatSetValuesBlockedLocal(Mat,int,const int[],int,const int[],const PetscScalar[],InsertMode);

EXTERN PetscErrorCode MatStashSetInitialSize(Mat,int,int);
EXTERN PetscErrorCode MatStashGetInfo(Mat,int*,int*,int*,int*);

EXTERN PetscErrorCode MatInterpolateAdd(Mat,Vec,Vec,Vec);
EXTERN PetscErrorCode MatInterpolate(Mat,Vec,Vec);
EXTERN PetscErrorCode MatRestrict(Mat,Vec,Vec);
EXTERN PetscErrorCode MatGetVecs(Mat,Vec*,Vec*);

/*MC
   MatPreallocInitialize - Begins the block of code that will count the number of nonzeros per
       row in a matrix providing the data that one can use to correctly preallocate the matrix.

   Synopsis:
   int MatPreallocateInitialize(MPI_Comm comm, int nrows, int ncols, int *dnz, int *onz)

   Collective on MPI_Comm

   Input Parameters:
+  comm - the communicator that will share the eventually allocated matrix
.  nrows - the number of rows in the matrix
-  ncols - the number of columns in the matrix

   Output Parameters:
+  dnz - the array that will be passed to the matrix preallocation routines
-  ozn - the other array passed to the matrix preallocation routines


   Level: intermediate

   Notes:
   See the chapter in the users manual on performance for more details

   Do not malloc or free dnz and onz, that is handled internally by these routines

   Use MatPreallocateInitializeSymmetric() for symmetric matrices (MPISBAIJ matrices)

  Concepts: preallocation^Matrix

.seealso: MatPreallocateFinalize(), MatPreallocateSet(), MatPreallocateSymmetricSet(), MatPreallocateSetLocal(),
          MatPreallocateInitializeSymmetric(), MatPreallocateSymmetricSetLocal()
M*/
#define MatPreallocateInitialize(comm,nrows,ncols,dnz,onz) 0; \
{ \
  PetscErrorCode _4_ierr; int __tmp = (nrows),__ctmp = (ncols),__rstart,__start,__end; \
  _4_ierr = PetscMalloc(2*__tmp*sizeof(int),&dnz);CHKERRQ(_4_ierr);onz = dnz + __tmp;\
  _4_ierr = PetscMemzero(dnz,2*__tmp*sizeof(int));CHKERRQ(_4_ierr);\
  _4_ierr = MPI_Scan(&__ctmp,&__end,1,MPI_INT,MPI_SUM,comm);CHKERRQ(_4_ierr); __start = __end - __ctmp;\
  _4_ierr = MPI_Scan(&__tmp,&__rstart,1,MPI_INT,MPI_SUM,comm);CHKERRQ(_4_ierr); __rstart = __rstart - __tmp;

/*MC
   MatPreallocSymmetricInitialize - Begins the block of code that will count the number of nonzeros per
       row in a matrix providing the data that one can use to correctly preallocate the matrix.

   Synopsis:
   int MatPreallocateSymmetricInitialize(MPI_Comm comm, int nrows, int ncols, int *dnz, int *onz)

   Collective on MPI_Comm

   Input Parameters:
+  comm - the communicator that will share the eventually allocated matrix
.  nrows - the number of rows in the matrix
-  ncols - the number of columns in the matrix

   Output Parameters:
+  dnz - the array that will be passed to the matrix preallocation routines
-  ozn - the other array passed to the matrix preallocation routines


   Level: intermediate

   Notes:
   See the chapter in the users manual on performance for more details

   Do not malloc or free dnz and onz, that is handled internally by these routines

  Concepts: preallocation^Matrix

.seealso: MatPreallocateFinalize(), MatPreallocateSet(), MatPreallocateSymmetricSet(), MatPreallocateSetLocal(),
          MatPreallocateInitialize(), MatPreallocateSymmetricSetLocal()
M*/
#define MatPreallocateSymmetricInitialize(comm,nrows,ncols,dnz,onz) 0; \
{ \
  PetscErrorCode _4_ierr; int __tmp = (nrows),__ctmp = (ncols),__rstart,__end; \
  _4_ierr = PetscMalloc(2*__tmp*sizeof(int),&dnz);CHKERRQ(_4_ierr);onz = dnz + __tmp;\
  _4_ierr = PetscMemzero(dnz,2*__tmp*sizeof(int));CHKERRQ(_4_ierr);\
  _4_ierr = MPI_Scan(&__ctmp,&__end,1,MPI_INT,MPI_SUM,comm);CHKERRQ(_4_ierr);\
  _4_ierr = MPI_Scan(&__tmp,&__rstart,1,MPI_INT,MPI_SUM,comm);CHKERRQ(_4_ierr); __rstart = __rstart - __tmp;

/*MC
   MatPreallocateSetLocal - Indicates the locations (rows and columns) in the matrix where nonzeros will be
       inserted using a local number of the rows and columns

   Synopsis:
   int MatPreallocateSetLocal(ISLocalToGlobalMappping map,int nrows, int *rows,int ncols, int *cols,int *dnz, int *onz)

   Not Collective

   Input Parameters:
+  map - the mapping between local numbering and global numbering
.  nrows - the number of rows indicated
.  rows - the indices of the rows
.  ncols - the number of columns in the matrix
.  cols - the columns indicated
.  dnz - the array that will be passed to the matrix preallocation routines
-  ozn - the other array passed to the matrix preallocation routines


   Level: intermediate

   Notes:
   See the chapter in the users manual on performance for more details

   Do not malloc or free dnz and onz, that is handled internally by these routines

  Concepts: preallocation^Matrix

.seealso: MatPreallocateFinalize(), MatPreallocateSet(), MatPreallocateSymmetricSet(), MatPreallocateInitialize(),
          MatPreallocateInitialize(), MatPreallocateSymmetricSetLocal()
M*/
#define MatPreallocateSetLocal(map,nrows,rows,ncols,cols,dnz,onz) 0;\
{\
  int __l;\
  _4_ierr = ISLocalToGlobalMappingApply(map,nrows,rows,rows);CHKERRQ(_4_ierr);\
  _4_ierr = ISLocalToGlobalMappingApply(map,ncols,cols,cols);CHKERRQ(_4_ierr);\
  for (__l=0;__l<nrows;__l++) {\
    _4_ierr = MatPreallocateSet((rows)[__l],ncols,cols,dnz,onz);CHKERRQ(_4_ierr);\
  }\
}

/*MC
   MatPreallocateSymmetricSetLocal - Indicates the locations (rows and columns) in the matrix where nonzeros will be
       inserted using a local number of the rows and columns

   Synopsis:
   int MatPreallocateSymmetricSetLocal(ISLocalToGlobalMappping map,int nrows, int *rows,int ncols, int *cols,int *dnz, int *onz)

   Not Collective

   Input Parameters:
+  map - the mapping between local numbering and global numbering
.  nrows - the number of rows indicated
.  rows - the indices of the rows
.  ncols - the number of columns in the matrix
.  cols - the columns indicated
.  dnz - the array that will be passed to the matrix preallocation routines
-  ozn - the other array passed to the matrix preallocation routines


   Level: intermediate

   Notes:
   See the chapter in the users manual on performance for more details

   Do not malloc or free dnz and onz that is handled internally by these routines

  Concepts: preallocation^Matrix

.seealso: MatPreallocateFinalize(), MatPreallocateSet(), MatPreallocateSymmetricSet(), MatPreallocateInitialize(),
          MatPreallocateInitialize(), MatPreallocateSymmetricSetLocal(), MatPreallocateSetLocal()
M*/
#define MatPreallocateSymmetricSetLocal(map,nrows,rows,ncols,cols,dnz,onz) 0;\
{\
  int __l;\
  _4_ierr = ISLocalToGlobalMappingApply(map,nrows,rows,rows);CHKERRQ(_4_ierr);\
  _4_ierr = ISLocalToGlobalMappingApply(map,ncols,cols,cols);CHKERRQ(_4_ierr);\
  for (__l=0;__l<nrows;__l++) {\
    _4_ierr = MatPreallocateSymmetricSet((rows)[__l],ncols,cols,dnz,onz);CHKERRQ(_4_ierr);\
  }\
}

/*MC
   MatPreallocateSet - Indicates the locations (rows and columns) in the matrix where nonzeros will be
       inserted using a local number of the rows and columns

   Synopsis:
   int MatPreallocateSet(int nrows, int *rows,int ncols, int *cols,int *dnz, int *onz)

   Not Collective

   Input Parameters:
+  nrows - the number of rows indicated
.  rows - the indices of the rows
.  ncols - the number of columns in the matrix
-  cols - the columns indicated

   Output Parameters:
+  dnz - the array that will be passed to the matrix preallocation routines
-  ozn - the other array passed to the matrix preallocation routines


   Level: intermediate

   Notes:
   See the chapter in the users manual on performance for more details

   Do not malloc or free dnz and onz that is handled internally by these routines

  Concepts: preallocation^Matrix

.seealso: MatPreallocateFinalize(), MatPreallocateSet(), MatPreallocateSymmetricSet(), MatPreallocateInitialize(),
          MatPreallocateInitialize(), MatPreallocateSymmetricSetLocal(), MatPreallocateSetLocal()
M*/
#define MatPreallocateSet(row,nc,cols,dnz,onz) 0;\
{ int __i; \
  for (__i=0; __i<nc; __i++) {\
    if (cols[__i] < __start || cols[__i] >= __end) onz[row - __rstart]++; \
  }\
  dnz[row - __rstart] = nc - onz[row - __rstart];\
}

/*MC
   MatPreallocateSymmetricSet - Indicates the locations (rows and columns) in the matrix where nonzeros will be
       inserted using a local number of the rows and columns

   Synopsis:
   int MatPreallocateSymmetricSet(int nrows, int *rows,int ncols, int *cols,int *dnz, int *onz)

   Not Collective

   Input Parameters:
+  nrows - the number of rows indicated
.  rows - the indices of the rows
.  ncols - the number of columns in the matrix
.  cols - the columns indicated
.  dnz - the array that will be passed to the matrix preallocation routines
-  ozn - the other array passed to the matrix preallocation routines


   Level: intermediate

   Notes:
   See the chapter in the users manual on performance for more details

   Do not malloc or free dnz and onz that is handled internally by these routines

  Concepts: preallocation^Matrix

.seealso: MatPreallocateFinalize(), MatPreallocateSet(), MatPreallocateSymmetricSet(), MatPreallocateInitialize(),
          MatPreallocateInitialize(), MatPreallocateSymmetricSetLocal(), MatPreallocateSetLocal()
M*/
#define MatPreallocateSymmetricSet(row,nc,cols,dnz,onz) 0;\
{ int __i; \
  for (__i=0; __i<nc; __i++) {\
    if (cols[__i] >= __end) onz[row - __rstart]++; \
    else if (cols[__i] >= row) dnz[row - __rstart]++;\
  }\
}

/*MC
   MatPreallocFinalize - Ends the block of code that will count the number of nonzeros per
       row in a matrix providing the data that one can use to correctly preallocate the matrix.

   Synopsis:
   int MatPreallocateFinalize(int *dnz, int *onz)

   Collective on MPI_Comm

   Input Parameters:
+  dnz - the array that will be passed to the matrix preallocation routines
-  ozn - the other array passed to the matrix preallocation routines


   Level: intermediate

   Notes:
   See the chapter in the users manual on performance for more details

   Do not malloc or free dnz and onz that is handled internally by these routines

  Concepts: preallocation^Matrix

.seealso: MatPreallocateInitialize(), MatPreallocateSet(), MatPreallocateSymmetricSet(), MatPreallocateSetLocal(),
          MatPreallocateSymmetricInitialize(), MatPreallocateSymmetricSetLocal()
M*/
#define MatPreallocateFinalize(dnz,onz) 0;_4_ierr = PetscFree(dnz);CHKERRQ(_4_ierr);}


/* Routines unique to particular data structures */
EXTERN PetscErrorCode MatShellGetContext(Mat,void **);

EXTERN PetscErrorCode MatBDiagGetData(Mat,int*,int*,int*[],int*[],PetscScalar***);
EXTERN PetscErrorCode MatSeqAIJSetColumnIndices(Mat,int[]);
EXTERN PetscErrorCode MatSeqBAIJSetColumnIndices(Mat,int[]);
EXTERN PetscErrorCode MatCreateSeqAIJWithArrays(MPI_Comm,int,int,int[],int[],PetscScalar[],Mat*);

EXTERN PetscErrorCode MatSeqBAIJSetPreallocation(Mat,int,int,const int[]);
EXTERN PetscErrorCode MatSeqSBAIJSetPreallocation(Mat,int,int,const int[]);
EXTERN PetscErrorCode MatSeqAIJSetPreallocation(Mat,int,const int[]);
EXTERN PetscErrorCode MatSeqDensePreallocation(Mat,PetscScalar[]);
EXTERN PetscErrorCode MatSeqBDiagSetPreallocation(Mat,int,int,const int[],PetscScalar*[]);
EXTERN PetscErrorCode MatSeqDenseSetPreallocation(Mat,PetscScalar[]);

EXTERN PetscErrorCode MatMPIBAIJSetPreallocation(Mat,int,int,const int[],int,const int[]);
EXTERN PetscErrorCode MatMPISBAIJSetPreallocation(Mat,int,int,const int[],int,const int[]);
EXTERN PetscErrorCode MatMPIAIJSetPreallocation(Mat,int,const int[],int,const int[]);
EXTERN PetscErrorCode MatMPIDensePreallocation(Mat,PetscScalar[]);
EXTERN PetscErrorCode MatMPIBDiagSetPreallocation(Mat,int,int,const int[],PetscScalar*[]);
EXTERN PetscErrorCode MatMPIAdjSetPreallocation(Mat,int[],int[],int[]);
EXTERN PetscErrorCode MatMPIDenseSetPreallocation(Mat,PetscScalar[]);
EXTERN PetscErrorCode MatMPIRowbsSetPreallocation(Mat,int,const int[]);
EXTERN PetscErrorCode MatMPIAIJGetSeqAIJ(Mat,Mat*,Mat*,int*[]);
EXTERN PetscErrorCode MatMPIBAIJGetSeqBAIJ(Mat,Mat*,Mat*,int*[]);
EXTERN PetscErrorCode MatAdicSetLocalFunction(Mat,void (*)(void));

EXTERN PetscErrorCode MatSeqDenseSetLDA(Mat,int);

EXTERN PetscErrorCode MatStoreValues(Mat);
EXTERN PetscErrorCode MatRetrieveValues(Mat);

EXTERN PetscErrorCode MatDAADSetCtx(Mat,void*);

/*
  These routines are not usually accessed directly, rather solving is
  done through the KSP and PC interfaces.
*/

/*E
    MatOrderingType - String with the name of a PETSc matrix ordering or the creation function
       with an optional dynamic library name, for example
       http://www.mcs.anl.gov/petsc/lib.a:orderingcreate()

   Level: beginner

.seealso: MatGetOrdering()
E*/
#define MatOrderingType char*
#define MATORDERING_NATURAL   "natural"
#define MATORDERING_ND        "nd"
#define MATORDERING_1WD       "1wd"
#define MATORDERING_RCM       "rcm"
#define MATORDERING_QMD       "qmd"
#define MATORDERING_ROWLENGTH "rowlength"
#define MATORDERING_DSC_ND    "dsc_nd"
#define MATORDERING_DSC_MMD   "dsc_mmd"
#define MATORDERING_DSC_MDF   "dsc_mdf"
#define MATORDERING_CONSTRAINED "constrained"
#define MATORDERING_IDENTITY  "identity"
#define MATORDERING_REVERSE   "reverse"

EXTERN PetscErrorCode MatGetOrdering(Mat,const MatOrderingType,IS*,IS*);
EXTERN PetscErrorCode MatOrderingRegister(const char[],const char[],const char[],PetscErrorCode(*)(Mat,const MatOrderingType,IS*,IS*));

/*MC
   MatOrderingRegisterDynamic - Adds a new sparse matrix ordering to the
                               matrix package.

   Synopsis:
   int MatOrderingRegisterDynamic(char *name_ordering,char *path,char *name_create,PetscErrorCode (*routine_create)(MatOrdering))

   Not Collective

   Input Parameters:
+  sname - name of ordering (for example MATORDERING_ND)
.  path - location of library where creation routine is
.  name - name of function that creates the ordering type,a string
-  function - function pointer that creates the ordering

   Level: developer

   If dynamic libraries are used, then the fourth input argument (function)
   is ignored.

   Sample usage:
.vb
   MatOrderingRegisterDynamic("my_order",/home/username/my_lib/lib/libO/solaris/mylib.a,
               "MyOrder",MyOrder);
.ve

   Then, your partitioner can be chosen with the procedural interface via
$     MatOrderingSetType(part,"my_order)
   or at runtime via the option
$     -pc_ilu_mat_ordering_type my_order
$     -pc_lu_mat_ordering_type my_order

   ${PETSC_ARCH} and ${BOPT} occuring in pathname will be replaced with appropriate values.

.keywords: matrix, ordering, register

.seealso: MatOrderingRegisterDestroy(), MatOrderingRegisterAll()
M*/
#if defined(PETSC_USE_DYNAMIC_LIBRARIES)
#define MatOrderingRegisterDynamic(a,b,c,d) MatOrderingRegister(a,b,c,0)
#else
#define MatOrderingRegisterDynamic(a,b,c,d) MatOrderingRegister(a,b,c,d)
#endif

EXTERN PetscErrorCode        MatOrderingRegisterDestroy(void);
EXTERN PetscErrorCode        MatOrderingRegisterAll(const char[]);
extern PetscTruth MatOrderingRegisterAllCalled;
extern PetscFList MatOrderingList;

EXTERN PetscErrorCode MatReorderForNonzeroDiagonal(Mat,PetscReal,IS,IS);

/*S
   MatFactorInfo - Data based into the matrix factorization routines

   In Fortran these are simply double precision arrays of size MAT_FACTORINFO_SIZE

   Notes: These are not usually directly used by users, instead use PC type of LU, ILU, CHOLESKY or ICC.

   Level: developer

.seealso: MatLUFactorSymbolic(), MatILUFactorSymbolic(), MatCholeskyFactorSymbolic(), MatICCFactorSymbolic(), MatICCFactor()

S*/
typedef struct {
  PetscReal     damping;        /* scaling of identity added to matrix to prevent zero pivots */
  PetscReal     shift;          /* if true, shift until positive pivots */
  PetscReal     shift_fraction; /* record shift fraction taken */
  PetscReal     diagonal_fill;  /* force diagonal to fill in if initially not filled */
  PetscReal     dt;             /* drop tolerance */
  PetscReal     dtcol;          /* tolerance for pivoting */
  PetscReal     dtcount;        /* maximum nonzeros to be allowed per row */
  PetscReal     fill;           /* expected fill; nonzeros in factored matrix/nonzeros in original matrix*/
  PetscReal     levels;         /* ICC/ILU(levels) */
  PetscReal     pivotinblocks;  /* for BAIJ and SBAIJ matrices pivot in factorization on blocks, default 1.0
                                   factorization may be faster if do not pivot */
  PetscReal     zeropivot;      /* pivot is called zero if less than this */
} MatFactorInfo;

EXTERN PetscErrorCode MatCholeskyFactor(Mat,IS,MatFactorInfo*);
EXTERN PetscErrorCode MatCholeskyFactorSymbolic(Mat,IS,MatFactorInfo*,Mat*);
EXTERN PetscErrorCode MatCholeskyFactorNumeric(Mat,Mat*);
EXTERN PetscErrorCode MatLUFactor(Mat,IS,IS,MatFactorInfo*);
EXTERN PetscErrorCode MatILUFactor(Mat,IS,IS,MatFactorInfo*);
EXTERN PetscErrorCode MatLUFactorSymbolic(Mat,IS,IS,MatFactorInfo*,Mat*);
EXTERN PetscErrorCode MatILUFactorSymbolic(Mat,IS,IS,MatFactorInfo*,Mat*);
EXTERN PetscErrorCode MatICCFactorSymbolic(Mat,IS,MatFactorInfo*,Mat*);
EXTERN PetscErrorCode MatICCFactor(Mat,IS,MatFactorInfo*);
EXTERN PetscErrorCode MatLUFactorNumeric(Mat,Mat*);
EXTERN PetscErrorCode MatILUDTFactor(Mat,MatFactorInfo*,IS,IS,Mat *);
EXTERN PetscErrorCode MatGetInertia(Mat,int*,int*,int*);
EXTERN PetscErrorCode MatSolve(Mat,Vec,Vec);
EXTERN PetscErrorCode MatForwardSolve(Mat,Vec,Vec);
EXTERN PetscErrorCode MatBackwardSolve(Mat,Vec,Vec);
EXTERN PetscErrorCode MatSolveAdd(Mat,Vec,Vec,Vec);
EXTERN PetscErrorCode MatSolveTranspose(Mat,Vec,Vec);
EXTERN PetscErrorCode MatSolveTransposeAdd(Mat,Vec,Vec,Vec);
EXTERN PetscErrorCode MatSolves(Mat,Vecs,Vecs);

EXTERN PetscErrorCode MatSetUnfactored(Mat);

/*E
    MatSORType - What type of (S)SOR to perform

    Level: beginner

   May be bitwise ORd together

   Any additions/changes here MUST also be made in include/finclude/petscmat.h

   MatSORType may be bitwise ORd together, so do not change the numbers

.seealso: MatRelax(), MatPBRelax()
E*/
typedef enum {SOR_FORWARD_SWEEP=1,SOR_BACKWARD_SWEEP=2,SOR_SYMMETRIC_SWEEP=3,
              SOR_LOCAL_FORWARD_SWEEP=4,SOR_LOCAL_BACKWARD_SWEEP=8,
              SOR_LOCAL_SYMMETRIC_SWEEP=12,SOR_ZERO_INITIAL_GUESS=16,
              SOR_EISENSTAT=32,SOR_APPLY_UPPER=64,SOR_APPLY_LOWER=128} MatSORType;
EXTERN PetscErrorCode MatRelax(Mat,Vec,PetscReal,MatSORType,PetscReal,int,int,Vec);
EXTERN PetscErrorCode MatPBRelax(Mat,Vec,PetscReal,MatSORType,PetscReal,int,int,Vec);

/*
    These routines are for efficiently computing Jacobians via finite differences.
*/

/*E
    MatColoringType - String with the name of a PETSc matrix coloring or the creation function
       with an optional dynamic library name, for example
       http://www.mcs.anl.gov/petsc/lib.a:coloringcreate()

   Level: beginner

.seealso: MatGetColoring()
E*/
#define MatColoringType char*
#define MATCOLORING_NATURAL "natural"
#define MATCOLORING_SL      "sl"
#define MATCOLORING_LF      "lf"
#define MATCOLORING_ID      "id"

EXTERN PetscErrorCode MatGetColoring(Mat,const MatColoringType,ISColoring*);
EXTERN PetscErrorCode MatColoringRegister(const char[],const char[],const char[],PetscErrorCode(*)(Mat,const MatColoringType,ISColoring *));

/*MC
   MatColoringRegisterDynamic - Adds a new sparse matrix coloring to the
                               matrix package.

   Synopsis:
   int MatColoringRegisterDynamic(char *name_coloring,char *path,char *name_create,PetscErrorCode (*routine_create)(MatColoring))

   Not Collective

   Input Parameters:
+  sname - name of Coloring (for example MATCOLORING_SL)
.  path - location of library where creation routine is
.  name - name of function that creates the Coloring type, a string
-  function - function pointer that creates the coloring

   Level: developer

   If dynamic libraries are used, then the fourth input argument (function)
   is ignored.

   Sample usage:
.vb
   MatColoringRegisterDynamic("my_color",/home/username/my_lib/lib/libO/solaris/mylib.a,
               "MyColor",MyColor);
.ve

   Then, your partitioner can be chosen with the procedural interface via
$     MatColoringSetType(part,"my_color")
   or at runtime via the option
$     -mat_coloring_type my_color

   $PETSC_ARCH and $BOPT occuring in pathname will be replaced with appropriate values.

.keywords: matrix, Coloring, register

.seealso: MatColoringRegisterDestroy(), MatColoringRegisterAll()
M*/
#if defined(PETSC_USE_DYNAMIC_LIBRARIES)
#define MatColoringRegisterDynamic(a,b,c,d) MatColoringRegister(a,b,c,0)
#else
#define MatColoringRegisterDynamic(a,b,c,d) MatColoringRegister(a,b,c,d)
#endif

EXTERN PetscErrorCode        MatColoringRegisterAll(const char[]);
extern PetscTruth MatColoringRegisterAllCalled;
EXTERN PetscErrorCode        MatColoringRegisterDestroy(void);
EXTERN PetscErrorCode        MatColoringPatch(Mat,int,int,const ISColoringValue[],ISColoring*);

/*S
     MatFDColoring - Object for computing a sparse Jacobian via finite differences
        and coloring

   Level: beginner

  Concepts: coloring, sparse Jacobian, finite differences

.seealso:  MatFDColoringCreate()
S*/
typedef struct _p_MatFDColoring *MatFDColoring;

EXTERN PetscErrorCode MatFDColoringCreate(Mat,ISColoring,MatFDColoring *);
EXTERN PetscErrorCode MatFDColoringDestroy(MatFDColoring);
EXTERN PetscErrorCode MatFDColoringView(MatFDColoring,PetscViewer);
EXTERN PetscErrorCode MatFDColoringSetFunction(MatFDColoring,PetscErrorCode (*)(void),void*);
EXTERN PetscErrorCode MatFDColoringSetParameters(MatFDColoring,PetscReal,PetscReal);
EXTERN PetscErrorCode MatFDColoringSetFrequency(MatFDColoring,int);
EXTERN PetscErrorCode MatFDColoringGetFrequency(MatFDColoring,int*);
EXTERN PetscErrorCode MatFDColoringSetFromOptions(MatFDColoring);
EXTERN PetscErrorCode MatFDColoringApply(Mat,MatFDColoring,Vec,MatStructure*,void *);
EXTERN PetscErrorCode MatFDColoringApplyTS(Mat,MatFDColoring,PetscReal,Vec,MatStructure*,void *);
EXTERN PetscErrorCode MatFDColoringSetRecompute(MatFDColoring);
EXTERN PetscErrorCode MatFDColoringSetF(MatFDColoring,Vec);
EXTERN PetscErrorCode MatFDColoringGetPerturbedColumns(MatFDColoring,int*,int*[]);
/*
    These routines are for partitioning matrices: currently used only
  for adjacency matrix, MatCreateMPIAdj().
*/

/*S
     MatPartitioning - Object for managing the partitioning of a matrix or graph

   Level: beginner

  Concepts: partitioning

.seealso:  MatPartitioningCreate(), MatPartitioningType
S*/
typedef struct _p_MatPartitioning *MatPartitioning;

/*E
    MatPartitioningType - String with the name of a PETSc matrix partitioning or the creation function
       with an optional dynamic library name, for example
       http://www.mcs.anl.gov/petsc/lib.a:partitioningcreate()

   Level: beginner

.seealso: MatPartitioningCreate(), MatPartitioning
E*/
#define MatPartitioningType char*
#define MAT_PARTITIONING_CURRENT  "current"
#define MAT_PARTITIONING_PARMETIS "parmetis"
#define MAT_PARTITIONING_CHACO    "chaco"
#define MAT_PARTITIONING_JOSTLE   "jostle"
#define MAT_PARTITIONING_PARTY    "party"
#define MAT_PARTITIONING_SCOTCH   "scotch"


EXTERN PetscErrorCode MatPartitioningCreate(MPI_Comm,MatPartitioning*);
EXTERN PetscErrorCode MatPartitioningSetType(MatPartitioning,const MatPartitioningType);
EXTERN PetscErrorCode MatPartitioningSetNParts(MatPartitioning,int);
EXTERN PetscErrorCode MatPartitioningSetAdjacency(MatPartitioning,Mat);
EXTERN PetscErrorCode MatPartitioningSetVertexWeights(MatPartitioning,const int[]);
EXTERN PetscErrorCode MatPartitioningSetPartitionWeights(MatPartitioning,const PetscReal []);
EXTERN PetscErrorCode MatPartitioningApply(MatPartitioning,IS*);
EXTERN PetscErrorCode MatPartitioningDestroy(MatPartitioning);

EXTERN PetscErrorCode MatPartitioningRegister(const char[],const char[],const char[],PetscErrorCode (*)(MatPartitioning));

/*MC
   MatPartitioningRegisterDynamic - Adds a new sparse matrix partitioning to the
   matrix package.

   Synopsis:
   int MatPartitioningRegisterDynamic(char *name_partitioning,char *path,char *name_create,PetscErrorCode (*routine_create)(MatPartitioning))

   Not Collective

   Input Parameters:
+  sname - name of partitioning (for example MAT_PARTITIONING_CURRENT) or parmetis
.  path - location of library where creation routine is
.  name - name of function that creates the partitioning type, a string
-  function - function pointer that creates the partitioning type

   Level: developer

   If dynamic libraries are used, then the fourth input argument (function)
   is ignored.

   Sample usage:
.vb
   MatPartitioningRegisterDynamic("my_part",/home/username/my_lib/lib/libO/solaris/mylib.a,
               "MyPartCreate",MyPartCreate);
.ve

   Then, your partitioner can be chosen with the procedural interface via
$     MatPartitioningSetType(part,"my_part")
   or at runtime via the option
$     -mat_partitioning_type my_part

   $PETSC_ARCH and $BOPT occuring in pathname will be replaced with appropriate values.

.keywords: matrix, partitioning, register

.seealso: MatPartitioningRegisterDestroy(), MatPartitioningRegisterAll()
M*/
#if defined(PETSC_USE_DYNAMIC_LIBRARIES)
#define MatPartitioningRegisterDynamic(a,b,c,d) MatPartitioningRegister(a,b,c,0)
#else
#define MatPartitioningRegisterDynamic(a,b,c,d) MatPartitioningRegister(a,b,c,d)
#endif

EXTERN PetscErrorCode        MatPartitioningRegisterAll(const char[]);
extern PetscTruth MatPartitioningRegisterAllCalled;
EXTERN PetscErrorCode        MatPartitioningRegisterDestroy(void);

EXTERN PetscErrorCode MatPartitioningView(MatPartitioning,PetscViewer);
EXTERN PetscErrorCode MatPartitioningSetFromOptions(MatPartitioning);
EXTERN PetscErrorCode MatPartitioningGetType(MatPartitioning,MatPartitioningType*);

EXTERN PetscErrorCode MatPartitioningParmetisSetCoarseSequential(MatPartitioning);

EXTERN PetscErrorCode MatPartitioningJostleSetCoarseLevel(MatPartitioning,PetscReal);
EXTERN PetscErrorCode MatPartitioningJostleSetCoarseSequential(MatPartitioning);

typedef enum { MP_CHACO_MULTILEVEL_KL, MP_CHACO_SPECTRAL, MP_CHACO_LINEAR,
    MP_CHACO_RANDOM, MP_CHACO_SCATTERED } MPChacoGlobalType;
EXTERN PetscErrorCode MatPartitioningChacoSetGlobal(MatPartitioning, MPChacoGlobalType);
typedef enum { MP_CHACO_KERNIGHAN_LIN, MP_CHACO_NONE } MPChacoLocalType;
EXTERN PetscErrorCode MatPartitioningChacoSetLocal(MatPartitioning, MPChacoLocalType);
EXTERN PetscErrorCode MatPartitioningChacoSetCoarseLevel(MatPartitioning,PetscReal);
typedef enum { MP_CHACO_LANCZOS, MP_CHACO_RQI_SYMMLQ } MPChacoEigenType;
EXTERN PetscErrorCode MatPartitioningChacoSetEigenSolver(MatPartitioning,MPChacoEigenType);
EXTERN PetscErrorCode MatPartitioningChacoSetEigenTol(MatPartitioning, PetscReal);
EXTERN PetscErrorCode MatPartitioningChacoSetEigenNumber(MatPartitioning, int);

#define MP_PARTY_OPT "opt"
#define MP_PARTY_LIN "lin"
#define MP_PARTY_SCA "sca"
#define MP_PARTY_RAN "ran"
#define MP_PARTY_GBF "gbf"
#define MP_PARTY_GCF "gcf"
#define MP_PARTY_BUB "bub"
#define MP_PARTY_DEF "def"
EXTERN PetscErrorCode MatPartitioningPartySetGlobal(MatPartitioning, const char*);
#define MP_PARTY_HELPFUL_SETS "hs"
#define MP_PARTY_KERNIGHAN_LIN "kl"
#define MP_PARTY_NONE "no"
EXTERN PetscErrorCode MatPartitioningPartySetLocal(MatPartitioning, const char*);
EXTERN PetscErrorCode MatPartitioningPartySetCoarseLevel(MatPartitioning,PetscReal);
EXTERN PetscErrorCode MatPartitioningPartySetBipart(MatPartitioning,PetscTruth);
EXTERN PetscErrorCode MatPartitioningPartySetMatchOptimization(MatPartitioning,PetscTruth);

typedef enum { MP_SCOTCH_GREEDY, MP_SCOTCH_GPS, MP_SCOTCH_GR_GPS } MPScotchGlobalType;
EXTERN PetscErrorCode MatPartitioningScotchSetArch(MatPartitioning,const char*);
EXTERN PetscErrorCode MatPartitioningScotchSetMultilevel(MatPartitioning);
EXTERN PetscErrorCode MatPartitioningScotchSetGlobal(MatPartitioning,MPScotchGlobalType);
EXTERN PetscErrorCode MatPartitioningScotchSetCoarseLevel(MatPartitioning,PetscReal);
EXTERN PetscErrorCode MatPartitioningScotchSetHostList(MatPartitioning,const char*);
typedef enum { MP_SCOTCH_KERNIGHAN_LIN, MP_SCOTCH_NONE } MPScotchLocalType;
EXTERN PetscErrorCode MatPartitioningScotchSetLocal(MatPartitioning,MPScotchLocalType);
EXTERN PetscErrorCode MatPartitioningScotchSetMapping(MatPartitioning);
EXTERN PetscErrorCode MatPartitioningScotchSetStrategy(MatPartitioning,char*);

/*
    If you add entries here you must also add them to finclude/petscmat.h
*/
typedef enum { MATOP_SET_VALUES=0,
               MATOP_GET_ROW=1,
               MATOP_RESTORE_ROW=2,
               MATOP_MULT=3,
               MATOP_MULT_ADD=4,
               MATOP_MULT_TRANSPOSE=5,
               MATOP_MULT_TRANSPOSE_ADD=6,
               MATOP_SOLVE=7,
               MATOP_SOLVE_ADD=8,
               MATOP_SOLVE_TRANSPOSE=9,
               MATOP_SOLVE_TRANSPOSE_ADD=10,
               MATOP_LUFACTOR=11,
               MATOP_CHOLESKYFACTOR=12,
               MATOP_RELAX=13,
               MATOP_TRANSPOSE=14,
               MATOP_GETINFO=15,
               MATOP_EQUAL=16,
               MATOP_GET_DIAGONAL=17,
               MATOP_DIAGONAL_SCALE=18,
               MATOP_NORM=19,
               MATOP_ASSEMBLY_BEGIN=20,
               MATOP_ASSEMBLY_END=21,
               MATOP_COMPRESS=22,
               MATOP_SET_OPTION=23,
               MATOP_ZERO_ENTRIES=24,
               MATOP_ZERO_ROWS=25,
               MATOP_LUFACTOR_SYMBOLIC=26,
               MATOP_LUFACTOR_NUMERIC=27,
               MATOP_CHOLESKY_FACTOR_SYMBOLIC=28,
               MATOP_CHOLESKY_FACTOR_NUMERIC=29,
               MATOP_SETUP_PREALLOCATION=30,
               MATOP_ILUFACTOR_SYMBOLIC=31,
               MATOP_ICCFACTOR_SYMBOLIC=32,
               MATOP_GET_ARRAY=33,
               MATOP_RESTORE_ARRAY=34,
               MATOP_DUPLCIATE=35,
               MATOP_FORWARD_SOLVE=36,
               MATOP_BACKWARD_SOLVE=37,
               MATOP_ILUFACTOR=38,
               MATOP_ICCFACTOR=39,
               MATOP_AXPY=40,
               MATOP_GET_SUBMATRICES=41,
               MATOP_INCREASE_OVERLAP=42,
               MATOP_GET_VALUES=43,
               MATOP_COPY=44,
               MATOP_PRINT_HELP=45,
               MATOP_SCALE=46,
               MATOP_SHIFT=47,
               MATOP_DIAGONAL_SHIFT=48,
               MATOP_ILUDT_FACTOR=49,
               MATOP_GET_BLOCK_SIZE=50,
               MATOP_GET_ROW_IJ=51,
               MATOP_RESTORE_ROW_IJ=52,
               MATOP_GET_COLUMN_IJ=53,
               MATOP_RESTORE_COLUMN_IJ=54,
               MATOP_FDCOLORING_CREATE=55,
               MATOP_COLORING_PATCH=56,
               MATOP_SET_UNFACTORED=57,
               MATOP_PERMUTE=58,
               MATOP_SET_VALUES_BLOCKED=59,
               MATOP_GET_SUBMATRIX=60,
               MATOP_DESTROY=61,
               MATOP_VIEW=62,
               MATOP_GET_MAPS=63,
               MATOP_USE_SCALED_FORM=64,
               MATOP_SCALE_SYSTEM=65,
               MATOP_UNSCALE_SYSTEM=66,
               MATOP_SET_LOCAL_TO_GLOBAL_MAP=67,
               MATOP_SET_VALUES_LOCAL=68,
               MATOP_ZERO_ROWS_LOCAL=69,
               MATOP_GET_ROW_MAX=70,
               MATOP_CONVERT=71,
               MATOP_SET_COLORING=72,
               MATOP_SET_VALUES_ADIC=73,
               MATOP_SET_VALUES_ADIFOR=74,
               MATOP_FD_COLORING_APPLY=75,
               MATOP_SET_FROM_OPTIONS=76,
               MATOP_MULT_CON=77,
               MATOP_MULT_TRANSPOSE_CON=78,
               MATOP_ILU_FACTOR_SYMBOLIC_CON=79,
               MATOP_PERMUTE_SPARSIFY=80,
               MATOP_MULT_MULTIPLE=81,
               MATOP_SOLVE_MULTIPLE=82,
               MATOP_GET_INERTIA=83,
               MATOP_LOAD=84,
               MATOP_IS_SYMMETRIC=85,
               MATOP_IS_HERMITIAN=86,
               MATOP_IS_STRUCTURALLY_SYMMETRIC=87,
               MATOP_PB_RELAX=88,
               MATOP_GET_VECS=89,
               MATOP_MAT_MULT=90,
               MATOP_MAT_MULT_SYMBOLIC=91,
               MATOP_MAT_MULT_NUMERIC=92,
               MATOP_PTAP=93,
               MATOP_PTAP_SYMBOLIC=94,
               MATOP_PTAP_NUMERIC=95,
               MATOP_MAT_MULTTRANSPOSE=96,
               MATOP_MAT_MULTTRANSPOSE_SYMBOLIC=97,
               MATOP_MAT_MULTTRANSPOSE_NUMERIC=98,
             } MatOperation;
EXTERN PetscErrorCode MatHasOperation(Mat,MatOperation,PetscTruth*);
EXTERN PetscErrorCode MatShellSetOperation(Mat,MatOperation,void(*)(void));
EXTERN PetscErrorCode MatShellGetOperation(Mat,MatOperation,void(**)(void));
EXTERN PetscErrorCode MatShellSetContext(Mat,void*);

/*
   Codes for matrices stored on disk. By default they are
 stored in a universal format. By changing the format with
 PetscViewerSetFormat(viewer,PETSC_VIEWER_BINARY_NATIVE); the matrices will
 be stored in a way natural for the matrix, for example dense matrices
 would be stored as dense. Matrices stored this way may only be
 read into matrices of the same time.
*/
#define MATRIX_BINARY_FORMAT_DENSE -1

EXTERN PetscErrorCode MatMPIBAIJSetHashTableFactor(Mat,PetscReal);
EXTERN PetscErrorCode MatSeqAIJGetInodeSizes(Mat,int *,int *[],int *);
EXTERN PetscErrorCode MatMPIRowbsGetColor(Mat,ISColoring *);

EXTERN PetscErrorCode MatISGetLocalMat(Mat,Mat*);

/*S
     MatNullSpace - Object that removes a null space from a vector, i.e.
         orthogonalizes the vector to a subsapce

   Level: advanced

  Concepts: matrix; linear operator, null space

  Users manual sections:
.   sec_singular

.seealso:  MatNullSpaceCreate()
S*/
typedef struct _p_MatNullSpace* MatNullSpace;

EXTERN PetscErrorCode MatNullSpaceCreate(MPI_Comm,int,int,const Vec[],MatNullSpace*);
EXTERN PetscErrorCode MatNullSpaceDestroy(MatNullSpace);
EXTERN PetscErrorCode MatNullSpaceRemove(MatNullSpace,Vec,Vec*);
EXTERN PetscErrorCode MatNullSpaceAttach(Mat,MatNullSpace);
EXTERN PetscErrorCode MatNullSpaceTest(MatNullSpace,Mat);

EXTERN PetscErrorCode MatReorderingSeqSBAIJ(Mat,IS);
EXTERN PetscErrorCode MatMPISBAIJSetHashTableFactor(Mat,PetscReal);
EXTERN PetscErrorCode MatSeqSBAIJSetColumnIndices(Mat,int *);


EXTERN PetscErrorCode MatCreateMAIJ(Mat,int,Mat*);
EXTERN PetscErrorCode MatMAIJRedimension(Mat,int,Mat*);
EXTERN PetscErrorCode MatMAIJGetAIJ(Mat,Mat*);

EXTERN PetscErrorCode MatComputeExplicitOperator(Mat,Mat*);

EXTERN PetscErrorCode MatESISetType(Mat,const char*);
EXTERN PetscErrorCode MatESISetFromOptions(Mat);

EXTERN PetscErrorCode MatDiagonalScaleLocal(Mat,Vec);

EXTERN PetscErrorCode PetscViewerMathematicaPutMatrix(PetscViewer, int, int, PetscReal *);
EXTERN PetscErrorCode PetscViewerMathematicaPutCSRMatrix(PetscViewer, int, int, int *, int *, PetscReal *);

PETSC_EXTERN_CXX_END
#endif