# Copyright (C) 2000 by Peter J. Gawthrop

###############################################################
## Version control history
###############################################################
## $Id$
## $Log$
## Revision 1.5  2000/05/17 16:01:42  peterg
## Fixed bug for n_y>1
##
## Revision 1.4  2000/05/16 18:57:15  peterg
## Still debugging
##
## Revision 1.3  2000/05/16 11:59:34  peterg
## Stard new version with data files not argv.
##
## Revision 1.2  2000/05/11 19:32:29  peterg

  dtime = time-tim;
  T = [T; num2str(dtime)];

  ## main simulation loop
  n_sim = max(1,n_sens);
  for i_sim=1:n_sim
    if i_sim==1
      i_1 = 2;
    i_1 = 2;
    else
      i_1 = 2+n_y;
    endif;

    if doing_state
      i_2 = i_1 + n_y - 1;
      i_3 = i_1 + n_y + 1;
      i_4 = i_1 + n_y + $Nx;
    else
      if doing_sensitivities
        i_2 = 1 + 2*n_y;
        ipars = [ipar; [sensitivities(i_sim) 1]];
        save -ascii   $1_numpar.dat ipars 
      else
        i_2 = i_1 + n_y -1;
      endif
    endif;

    if doing_state # Need to cut twice
      command = sprintf("./$1_ode2odes.out< $1_input.dat | cut -f %i-%i,%i-%i | tail -%i;", i_1,i_2,i_3,i_4,n_t);
    else
      command = sprintf("./$1_ode2odes.out< $1_input.dat | cut -f %i-%i | tail -%i;", i_1,i_2,n_t);
    end;
      if doing_state # Need to cut twice
        command = sprintf("./$1_ode2odes.out< $1_input.dat | cut -f %i-%i,%i-%i | tail -%i;", i_1,i_2,i_3,i_4,n_t);
      else # not doing_state
        command = sprintf("./$1_ode2odes.out< $1_input.dat | cut -f %i-%i | tail -%i;", i_1,i_2,n_t);
      endif

  ## Execute external programme
  S = [S;sprintf("Run %i\t",i_sim)];
  tim = time;
  yy_str=system(command);
  dtime = time-tim;
  T = [T; num2str(dtime)];

  ## Convert data
  S = [S;sprintf("Conv %i\t",i_sim)];
  tim = time;
  yy = str2num(yy_str)'; #'
  dtime = time-tim;
  T = [T; num2str(dtime)];


  [N_yy,M_yy] = size(yy);

  if i_sim==1
    if doing_sensitivities
      y = yy(1:n_y:2*n_y,:);              # Output
      ys = yy(2:n_y:2*n_y,:);
    else
    y = yy(1:n_y,:);              # Output
    i_1 = n_y+1;
      y = yy(1:n_y,:);
    endif;
    if doing_state 
      i_1 = n_y+1;
      i_2 = i_1 + $Nx - 1;
      ys = yy(i_1:i_2,:);
    endif;
  else
  else # i_sim>1
    i_1 = 1;
  endif

  if doing_sensitivities
    if doing_sensitivities
    i_2 = i_1 - 1 + n_y;
    ys =  [ys; yy(i_1:i_2,:)];
  endif; 
      ys =  [ys; yy(2:n_y:2*n_y,:)];
    endif; 
  endif

  endfor;
   endfor;
  ##RealTime = [S T]
endfunction

EOF
    
else