  
  [1X3 [33X[0;0YThe Sparse Matrix Data Type[133X[101X
  
  
  [1X3.1 [33X[0;0YThe inner workings of [5XGauss[105X[101X[1X sparse matrices[133X[101X
  
  [33X[0;0YWhen  doing  any  kind  of  computation there is a constant conflict between
  memory load and speed. On the one hand, memory usage is bounded by the total
  available memory, on the other hand, computation time should also not exceed
  certain  proportions.  Memory  usage  and  CPU  time are generally inversely
  proportional,  because the computer needs more time to perform operations on
  a  compactified  data structure. The idea of sparse matrices mirrors exactly
  the  need  for  less  memory  load,  therefore  it  is  natural  that sparse
  algorithms  take  more  time  than  dense  ones.  However,  if the matrix is
  sufficiently large and sparse at the same time, sparse algorithms can easily
  be faster than dense ones while maintaining minimal memory load.[133X
  
  [33X[0;0YIt  should  be  noted  that,  although  matrices  that  appear  naturally in
  homological  algebra  are  almost  always  sparse,  they do not have to stay
  sparse under (R)REF algorithms, especially when the computation is concerned
  with  transformation matrices. Therefore, in a perfect world there should be
  ways  implemented to not only find out which data structure to use, but also
  at  what  point to convert from one to the other. This was, however, not the
  aim  of  the  [5XGauss[105X  package  and  is  just one of many points in which this
  package could be optimized or extended. Take a look at this matrix [22XM[122X:[133X
  
      ┌──   ─   ─   ─   ──┐
      │ 0   0   2   9   0 │ 
      │ 0   5   0   0   0 │ 
      │ 0   0   0   1   0 │ 
      └──   ─   ─   ─   ──┘
  
  [33X[0;0YThe  matrix  [22XM[122X  carries  the same information as the following table, if and
  only if you know how many rows and columns the matrix has. There is also the
  matter of the base ring, but this is not important for now:[133X
  
      ┌──────   ──────┐
      │ (i,j)   Entry │ 
      ├──────   ──────┤
      │ (1,3)     2   │ 
      │ (1,4)     9   │ 
      │ (2,2)     5   │ 
      │ (3,4)     1   │ 
      └──────   ──────┘
  
  [33X[0;0YThis  table  relates each index tuple to its nonzero entry, all other matrix
  entries  are defined to be zero. This only works for known dimensions of the
  matrix,  otherwise trailing zero rows and columns could get lost (notice how
  the table gives no hint about the existence of a 5th column). To convert the
  above  table  into a sparse data structure, one could list the table entries
  in this way:[133X
  
        [22X[ [ 1, 3, 2 ], [ 1, 4, 9 ], [ 2, 2, 5 ], [ 3, 4, 1 ] ][122X   
  
  [33X[0;0YHowever,  this  data structure would not be very efficient. Whenever you are
  interested  in  a  row  [22Xi[122X  of  [22XM[122X  (this happens all the time when performing
  Gaussian  elimination) the whole list would have to be searched for 3-tuples
  of  the  form  [22X[  i,  *, * ][122X. This is why I tried to manage the row index by
  putting the tuples into the corresponding list entry:[133X
  
        [22X[ [ 3, 2 ], [ 4, 9 ] ],[122X   
        [22X[ [ 2, 5 ] ],[122X             
        [22X[ [ 4, 1 ] ] ][122X            
  
  [33X[0;0YAs you can see, this looks fairly complicated. However, the same information
  can  be stored in this form, which would become the final data structure for
  [5XGauss[105X sparse matrices:[133X
  
        indices :=   [ [ 3, 4 ],   entries:=   [ [ 2, 9 ],   
                     [ 2 ],                    [ 5 ],        
                     [ 4 ] ]                   [ 1 ] ]       
  
  [33X[0;0YAlthough now the number of rows is equal to the Length of both `indices' and
  `entries',  it  is  still stored in the sparse matrix. Here is the full data
  structure (--> [2XSparseMatrix[102X ([14X3.2-1[114X)):[133X
  
  [4X[32X  from SparseMatrix.gi  [32X[104X
    [4X    DeclareRepresentation( "IsSparseMatrixRep",[104X
    [4X         IsSparseMatrix, [ "nrows", "ncols", "indices", "entries", "ring" ] );[104X
    [4X    [104X
  [4X[32X[104X
  
  [33X[0;0YAs  you  can see, the matrix stores its ring to be on the safe side. This is
  especially  important for zero matrices, as there is no way to determine the
  base  ring  from  the  sparse  matrix  structure. For further information on
  sparse matrix construction and converting, refer to [2XSparseMatrix[102X ([14X3.2-1[114X).[133X
  
  
  [1X3.1-1 [33X[0;0YA special case: GF(2)[133X[101X
  
  [4X[32X  from SparseMatrix.gi  [32X[104X
    [4X    DeclareRepresentation( "IsSparseMatrixGF2Rep",[104X
    [4X         IsSparseMatrix, [ "nrows", "ncols", "indices", "ring" ] );[104X
    [4X    [104X
  [4X[32X[104X
  
  [33X[0;0YBecause  the nonzero entries of a matrix over GF(2) are all "1", the entries
  of  M are not stored at all. It is of course crucial that all operations and
  algorithms  make  100% sure that all appearing zero entries are deleted from
  the `indices' as well as the `entries' list as they arise.[133X
  
  
  [1X3.2 [33X[0;0YMethods and functions for sparse matrices[133X[101X
  
  [1X3.2-1 SparseMatrix[101X
  
  [29X[2XSparseMatrix[102X( [3Xmat[103X[, [3XR[103X] ) [32X function
  [6XReturns:[106X  [33X[0;10Ya sparse matrix over the ring [3XR[103X[133X
  
  [29X[2XSparseMatrix[102X( [3Xnrows[103X, [3Xncols[103X, [3Xindices[103X ) [32X function
  [6XReturns:[106X  [33X[0;10Ya sparse matrix over GF(2)[133X
  
  [29X[2XSparseMatrix[102X( [3Xnrows[103X, [3Xncols[103X, [3Xindices[103X, [3Xentries[103X[, [3XR[103X] ) [32X function
  [6XReturns:[106X  [33X[0;10Ya sparse matrix over the ring [3XR[103X[133X
  
  [33X[0;0YThe  sparse  matrix  constructor.  In the one-argument form the SparseMatrix
  constructor  converts  a  [5XGAP[105X matrix to a sparse matrix. If not provided the
  base  ring  [3XR[103X  is found automatically. For the multi-argument form [3Xnrows[103X and
  [3Xncols[103X  are  the  dimensions  of the matrix. [3Xindices[103X must be a list of length
  [3Xnrows[103X  containing  lists  of  the  column indices of the matrix in ascending
  order.[133X
  
  [4X[32X  Example  [32X[104X
    [4X[25Xgap>[125X [27XM := [ [ 0 , 1 ], [ 3, 0 ] ] * One( GF(2) );[127X[104X
    [4X[28X[ [ 0*Z(2), Z(2)^0 ], [ Z(2)^0, 0*Z(2) ] ][128X[104X
    [4X[25Xgap>[125X [27XSM := SparseMatrix( M );[127X[104X
    [4X[28X<a 2 x 2 sparse matrix over GF(2)>[128X[104X
    [4X[25Xgap>[125X [27XIsSparseMatrix( SM );[127X[104X
    [4X[28Xtrue[128X[104X
    [4X[25Xgap>[125X [27XDisplay( SM );[127X[104X
    [4X[28X . 1[128X[104X
    [4X[28X 1 .[128X[104X
    [4X[25Xgap>[125X [27XSN := SparseMatrix( 2, 2, [ [ 2 ], [ 1 ] ] );[127X[104X
    [4X[28X<a 2 x 2 sparse matrix over GF(2)>[128X[104X
    [4X[25Xgap>[125X [27XSN = SM;[127X[104X
    [4X[28Xtrue[128X[104X
    [4X[25Xgap>[125X [27XSN := SparseMatrix( 2, 3,[127X[104X
    [4X[25X>[125X [27X                  [ [ 2 ], [ 1, 3 ] ],[127X[104X
    [4X[25X>[125X [27X                  [ [ 1 ], [ 3, 2 ] ] * One( GF(5) ) );[127X[104X
    [4X[28X<a 2 x 3 sparse matrix over GF(5)>[128X[104X
    [4X[25Xgap>[125X [27XDisplay( SN );[127X[104X
    [4X[28X . 1 .[128X[104X
    [4X[28X 3 . 2[128X[104X
  [4X[32X[104X
  
  [1X3.2-2 ConvertSparseMatrixToMatrix[101X
  
  [29X[2XConvertSparseMatrixToMatrix[102X( [3Xsm[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ya [5XGAP[105X matrix, [], or a list of empty lists[133X
  
  [33X[0;0YThis  function  converts  the sparse matrix [3Xsm[103X into a [5XGAP[105X matrix. In case of
  [10Xnrows(sm)=0[110X  or  [10Xncols(sm)=0[110X the return value is the empty list or a list of
  empty lists, respectively.[133X
  
  [4X[32X  Example  [32X[104X
    [4X[25Xgap>[125X [27XM := [ [ 0 , 1 ], [ 3, 0 ] ] * One( GF(3) );[127X[104X
    [4X[28X[ [ 0*Z(3), Z(3)^0 ], [ 0*Z(3), 0*Z(3) ] ][128X[104X
    [4X[25Xgap>[125X [27XSM := SparseMatrix( M );[127X[104X
    [4X[28X<a 2 x 2 sparse matrix over GF(3)>[128X[104X
    [4X[25Xgap>[125X [27XN := ConvertSparseMatrixToMatrix( SM );[127X[104X
    [4X[28X[ [ 0*Z(3), Z(3)^0 ], [ 0*Z(3), 0*Z(3) ] ][128X[104X
    [4X[25Xgap>[125X [27XM = N;[127X[104X
    [4X[28Xtrue[128X[104X
  [4X[32X[104X
  
  [1X3.2-3 CopyMat[101X
  
  [29X[2XCopyMat[102X( [3Xsm[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ya shallow copy of the sparse matrix [3Xsm[103X[133X
  
  [1X3.2-4 GetEntry[101X
  
  [29X[2XGetEntry[102X( [3Xsm[103X, [3Xi[103X, [3Xj[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ya ring element.[133X
  
  [33X[0;0YThis returns the entry [10Xsm[i,j][110X of the sparse matrix [3Xsm[103X[133X
  
  [1X3.2-5 SetEntry[101X
  
  [29X[2XSetEntry[102X( [3Xsm[103X, [3Xi[103X, [3Xj[103X, [3Xelm[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ynothing.[133X
  
  [33X[0;0YThis sets the entry [10Xsm[i,j][110X of the sparse matrix [3Xsm[103X to [3Xelm[103X.[133X
  
  [1X3.2-6 AddToEntry[101X
  
  [29X[2XAddToEntry[102X( [3Xsm[103X, [3Xi[103X, [3Xj[103X, [3Xelm[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Y[9Xtrue[109X or a ring element[133X
  
  [33X[0;0YAddToEntry  adds  the  element  [3Xelm[103X  to the sparse matrix [3Xsm[103X at the [3X(i,j)[103X-th
  position.  This  is  a  Method  with a side effect which returns true if you
  tried  to  add zero or the sum of [10Xsm[i,j][110X and [3Xelm[103X otherwise. Please use this
  method whenever possible.[133X
  
  [1X3.2-7 SparseZeroMatrix[101X
  
  [29X[2XSparseZeroMatrix[102X( [3Xnrows[103X[, [3Xring[103X] ) [32X function
  [6XReturns:[106X  [33X[0;10Ya sparse <[3Xnrows[103X x [3Xnrows[103X> zero matrix over the ring [3Xring[103X[133X
  
  [29X[2XSparseZeroMatrix[102X( [3Xnrows[103X, [3Xncols[103X[, [3Xring[103X] ) [32X function
  [6XReturns:[106X  [33X[0;10Ya sparse <[3Xnrows[103X x [3Xncols[103X> zero matrix over the ring [3Xring[103X[133X
  
  [1X3.2-8 SparseIdentityMatrix[101X
  
  [29X[2XSparseIdentityMatrix[102X( [3Xdim[103X[, [3Xring[103X] ) [32X function
  [6XReturns:[106X  [33X[0;10Ya  sparse  <[3Xdim[103X  x  [3Xdim[103X> identity matrix over the ring [3Xring[103X. If no
            ring  is  specified (one should try to avoid this if possible) the
            Rationals are the default ring.[133X
  
  [1X3.2-9 TransposedSparseMat[101X
  
  [29X[2XTransposedSparseMat[102X( [3Xsm[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ythe transposed matrix of the sparse matrix [3Xsm[103X[133X
  
  [1X3.2-10 CertainRows[101X
  
  [29X[2XCertainRows[102X( [3Xsm[103X, [3Xlist[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ythe submatrix [10Xsm{[list]}[110X as a sparse matrix[133X
  
  [1X3.2-11 CertainColumns[101X
  
  [29X[2XCertainColumns[102X( [3Xsm[103X, [3Xlist[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ythe submatrix [10Xsm{[1..nrows(sm)]}{[list]}[110X as a sparse matrix[133X
  
  [1X3.2-12 UnionOfRows[101X
  
  [29X[2XUnionOfRows[102X( [3XA[103X, [3XB[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ythe row union of the sparse matrices [3XA[103X and [3XB[103X[133X
  
  [1X3.2-13 UnionOfColumns[101X
  
  [29X[2XUnionOfColumns[102X( [3XA[103X, [3XB[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ythe column union of the sparse matrices [3XA[103X and [3XB[103X[133X
  
  [1X3.2-14 SparseDiagMat[101X
  
  [29X[2XSparseDiagMat[102X( [3Xlist[103X ) [32X function
  [6XReturns:[106X  [33X[0;10Ythe block diagonal matrix composed of the sparse matrices in [3Xlist[103X[133X
  
  [1X3.2-15 Nrows[101X
  
  [29X[2XNrows[102X( [3Xsm[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ythe  number  of  rows  of  the  sparse  matrix  [3Xsm[103X. This should be
            preferred to the equivalent [10Xsm!.nrows[110X.[133X
  
  [1X3.2-16 Ncols[101X
  
  [29X[2XNcols[102X( [3Xsm[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ythe  number  of  columns  of  the sparse matrix [3Xsm[103X. This should be
            preferred to the equivalent [10Xsm!.ncols[110X.[133X
  
  [1X3.2-17 IndicesOfSparseMatrix[101X
  
  [29X[2XIndicesOfSparseMatrix[102X( [3Xsm[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ythe  indices of the sparse matrix [3Xsm[103X as a ListList. This should be
            preferred to the equivalent [10Xsm!.indices[110X.[133X
  
  [1X3.2-18 EntriesOfSparseMatrix[101X
  
  [29X[2XEntriesOfSparseMatrix[102X( [3Xsm[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ythe  entries  of  the  sparse  matrix  [3Xsm[103X  as  a  ListList of ring
            elements.  This  should be preferred to the equivalent [10Xsm!.entries[110X
            and  has  the  additional advantage of working for sparse matrices
            over GF(2) which do not have any entries.[133X
  
  [1X3.2-19 RingOfDefinition[101X
  
  [29X[2XRingOfDefinition[102X( [3Xsm[103X ) [32X method
  [6XReturns:[106X  [33X[0;10Ythe base ring of the sparse matrix [3Xsm[103X. This should be preferred to
            the equivalent [10Xsm!.ring[110X.[133X
  
