#ifdef PETSC_RCS_HEADER
static char vcid[] = "$Id: fdaij.c,v 1.21 1999/06/08 22:55:44 balay Exp balay $";
#endif

#include "src/mat/impls/aij/seq/aij.h"
#include "src/vec/vecimpl.h"
#include "petsc.h"

extern int MatGetColumnIJ_SeqAIJ(Mat,int,PetscTruth,int*,int**,int**,PetscTruth*);
extern int MatRestoreColumnIJ_SeqAIJ(Mat,int,PetscTruth,int*,int**,int**,PetscTruth*);

#undef __FUNC__  
#define __FUNC__ "MatFDColoringCreate_SeqAIJ"
int MatFDColoringCreate_SeqAIJ(Mat mat,ISColoring iscoloring,MatFDColoring c)
{
  int        i,*is,n,nrows,N = mat->N,j,k,m,*rows,ierr,*ci,*cj,ncols,col,flg;
  int        nis = iscoloring->n,*rowhit,*columnsforrow;
  IS         *isa = iscoloring->is;
  PetscTruth done;

  PetscFunctionBegin;
  if (!mat->assembled) {
    SETERRQ(PETSC_ERR_ARG_WRONGSTATE,1,"Matrix must be assembled by calls to MatAssemblyBegin/End();");
  }

  c->M             = mat->M;  /* set total rows, columns and local rows */
  c->N             = mat->N;
  c->m             = mat->M;
  c->rstart        = 0;

  c->ncolors       = nis;
  c->ncolumns      = (int *) PetscMalloc( nis*sizeof(int) );CHKPTRQ(c->ncolumns);
  c->columns       = (int **) PetscMalloc( nis*sizeof(int *));CHKPTRQ(c->columns); 
  c->nrows         = (int *) PetscMalloc( nis*sizeof(int) );CHKPTRQ(c->nrows);
  c->rows          = (int **) PetscMalloc( nis*sizeof(int *));CHKPTRQ(c->rows);
  c->columnsforrow = (int **) PetscMalloc( nis*sizeof(int *));CHKPTRQ(c->columnsforrow);

  /*
      Calls the _SeqAIJ() version of these routines to make sure it does not 
     get the reduced (by inodes) version of I and J
  */
  ierr = MatGetColumnIJ_SeqAIJ(mat,0,PETSC_FALSE,&ncols,&ci,&cj,&done);CHKERRQ(ierr);

  /*
     Temporary option to allow for debugging/testing
  */
  ierr = OptionsHasName(0,"-matfdcoloring_slow",&flg);CHKERRQ(ierr);

  rowhit        = (int *) PetscMalloc( (N+1)*sizeof(int) );CHKPTRQ(rowhit);
  columnsforrow = (int *) PetscMalloc( (N+1)*sizeof(int) );CHKPTRQ(columnsforrow);

  for ( i=0; i<nis; i++ ) {
    ierr = ISGetSize(isa[i],&n);CHKERRQ(ierr);
    ierr = ISGetIndices(isa[i],&is);CHKERRQ(ierr);
    c->ncolumns[i] = n;
    if (n) {
      c->columns[i]  = (int *) PetscMalloc( n*sizeof(int) );CHKPTRQ(c->columns[i]);
      ierr = PetscMemcpy(c->columns[i],is,n*sizeof(int));CHKERRQ(ierr);
    } else {
      c->columns[i]  = 0;
    }

    if (flg) { /* ------------------------------------------------------------------------------*/
      /* crude version requires O(N*N) work */
      ierr = PetscMemzero(rowhit,N*sizeof(int));CHKERRQ(ierr);
      /* loop over columns*/
      for ( j=0; j<n; j++ ) {
        col  = is[j];
        rows = cj + ci[col]; 
        m    = ci[col+1] - ci[col];
        /* loop over columns marking them in rowhit */
        for ( k=0; k<m; k++ ) {
          rowhit[*rows++] = col + 1;
        }
      }
      /* count the number of hits */
      nrows = 0;
      for ( j=0; j<N; j++ ) {
        if (rowhit[j]) nrows++;
      }
      c->nrows[i]         = nrows;
      c->rows[i]          = (int *) PetscMalloc(nrows*sizeof(int));CHKPTRQ(c->rows[i]);
      c->columnsforrow[i] = (int *) PetscMalloc(nrows*sizeof(int));CHKPTRQ(c->columnsforrow[i]);
      nrows = 0;
      for ( j=0; j<N; j++ ) {
        if (rowhit[j]) {
          c->rows[i][nrows]           = j;
          c->columnsforrow[i][nrows] = rowhit[j] - 1;
          nrows++;
        }
      }
    } else {  /*-------------------------------------------------------------------------------*/
      /* efficient version, using rowhit as a linked list */
      int currentcol,fm,mfm;
      rowhit[N] = N;
      nrows     = 0;
      /* loop over columns */
      for ( j=0; j<n; j++ ) {
        col   = is[j];
        rows  = cj + ci[col]; 
        m     = ci[col+1] - ci[col];
        /* loop over columns marking them in rowhit */
        fm    = N; /* fm points to first entry in linked list */
        for ( k=0; k<m; k++ ) {
          currentcol = *rows++;
	  /* is it already in the list? */
          do {
            mfm  = fm;
            fm   = rowhit[fm];
          } while (fm < currentcol);
          /* not in list so add it */
          if (fm != currentcol) {
            nrows++;
            columnsforrow[currentcol] = col;
            /* next three lines insert new entry into linked list */
            rowhit[mfm]               = currentcol;
            rowhit[currentcol]        = fm;
            fm                        = currentcol; 
            /* fm points to present position in list since we know the columns are sorted */
          } else {
            SETERRQ(PETSC_ERR_PLIB,0,"Detected invalid coloring");
          }

        }
      }
      c->nrows[i]         = nrows;
      c->rows[i]          = (int *)PetscMalloc((nrows+1)*sizeof(int));CHKPTRQ(c->rows[i]);
      c->columnsforrow[i] = (int *)PetscMalloc((nrows+1)*sizeof(int));CHKPTRQ(c->columnsforrow[i]);
      /* now store the linked list of rows into c->rows[i] */
      nrows = 0;
      fm    = rowhit[N];
      do {
        c->rows[i][nrows]            = fm;
        c->columnsforrow[i][nrows++] = columnsforrow[fm];
        fm                           = rowhit[fm];
      } while (fm < N);
    } /* ---------------------------------------------------------------------------------------*/
    ierr = ISRestoreIndices(isa[i],&is);CHKERRQ(ierr);  
  }
  ierr = MatRestoreColumnIJ_SeqAIJ(mat,0,PETSC_FALSE,&ncols,&ci,&cj,&done);CHKERRQ(ierr);

  ierr = PetscFree(rowhit);CHKERRQ(ierr);
  ierr = PetscFree(columnsforrow);CHKERRQ(ierr);

  c->scale  = (Scalar *) PetscMalloc( 2*N*sizeof(Scalar) );CHKPTRQ(c->scale);
  c->wscale = c->scale + N;

  PetscFunctionReturn(0);
}

#undef __FUNC__  
#define __FUNC__ "MatColoringPatch_SeqAIJ"
int MatColoringPatch_SeqAIJ(Mat mat,int ncolors,int *coloring,ISColoring *iscoloring)
{
  Mat_SeqAIJ *a = (Mat_SeqAIJ *) mat->data;
  int        n = a->n,*sizes,i,**ii,ierr,tag;
  IS         *is;

  PetscFunctionBegin;
  /* construct the index sets from the coloring array */
  sizes = (int *) PetscMalloc( ncolors*sizeof(int) );CHKPTRQ(sizes);
  ierr = PetscMemzero(sizes,ncolors*sizeof(int));CHKERRQ(ierr);
  for ( i=0; i<n; i++ ) {
    sizes[coloring[i]-1]++;
  }
  ii    = (int **) PetscMalloc( ncolors*sizeof(int*) );CHKPTRQ(ii);
  ii[0] = (int *) PetscMalloc( n*sizeof(int) );CHKPTRQ(ii[0]);
  for ( i=1; i<ncolors; i++ ) {
    ii[i] = ii[i-1] + sizes[i-1];
  }
  ierr = PetscMemzero(sizes,ncolors*sizeof(int));CHKERRQ(ierr);
  for ( i=0; i<n; i++ ) {
    ii[coloring[i]-1][sizes[coloring[i]-1]++] = i;
  }
  is  = (IS *) PetscMalloc( ncolors*sizeof(IS) );CHKPTRQ(is);
  for ( i=0; i<ncolors; i++ ) {
    ierr = ISCreateGeneral(PETSC_COMM_SELF,sizes[i],ii[i],is+i);CHKERRQ(ierr);
  }

  *iscoloring         = (ISColoring) PetscMalloc(sizeof(struct _p_ISColoring));CHKPTRQ(*iscoloring);
  (*iscoloring)->n    = ncolors;
  (*iscoloring)->is   = is;
  ierr = PetscCommDuplicate_Private(mat->comm,&(*iscoloring)->comm,&tag);CHKERRQ(ierr);
  ierr = PetscFree(sizes);CHKERRQ(ierr);
  ierr = PetscFree(ii[0]);CHKERRQ(ierr);
  ierr = PetscFree(ii);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
     Makes a longer coloring[] array and calls the usual code with that
*/
#undef __FUNC__  
#define __FUNC__ "MatColoringPatch_SeqAIJ_Inode"
int MatColoringPatch_SeqAIJ_Inode(Mat mat,int ncolors,int *coloring,ISColoring *iscoloring)
{
  Mat_SeqAIJ *a = (Mat_SeqAIJ *) mat->data;
  int        n = a->n,ierr, m = a->inode.node_count,j,*ns = a->inode.size,row;
  int        *colorused,i,*newcolor;

  PetscFunctionBegin;
  newcolor = (int *) PetscMalloc((n+1)*sizeof(int));CHKPTRQ(newcolor);

  /* loop over inodes, marking a color for each column*/
  row = 0;
  for ( i=0; i<m; i++){
    for ( j=0; j<ns[i]; j++) {
      newcolor[row++] = coloring[i] + j*ncolors;
    }
  }

  /* eliminate unneeded colors */
  colorused = (int *) PetscMalloc( 5*ncolors*sizeof(int) );CHKPTRQ(colorused);
  ierr      = PetscMemzero(colorused,5*ncolors*sizeof(int));CHKERRQ(ierr);
  for ( i=0; i<n; i++ ) {
    colorused[newcolor[i]-1] = 1;
  }

  for ( i=1; i<5*ncolors; i++ ) {
    colorused[i] += colorused[i-1];
  }
  ncolors = colorused[5*ncolors-1];
  for ( i=0; i<n; i++ ) {
    newcolor[i] = colorused[newcolor[i]-1];
  }
  ierr = PetscFree(colorused);CHKERRQ(ierr);

  ierr = MatColoringPatch_SeqAIJ(mat,ncolors,newcolor,iscoloring);CHKERRQ(ierr);
  ierr = PetscFree(newcolor);CHKERRQ(ierr);

  PetscFunctionReturn(0);
}