anchor.diff:  ccc   
         dimension xt(ndim),yt(ndim),zt(ndim) !temporal coordinate
         dimension x_n(ndim),y_n(ndim),z_n(ndim) !native structure
  -cjmht dimension x(ndim,nst),y(ndim,nst),z(ndim,nst) !used structures
  -cjmht dimension amat(nst,nst)    !RMSD matrics
  -      real, allocatable :: x(:,:), y(:,:), z(:,:)
  -      real, allocatable :: amat(:,:)
  +      dimension x(ndim,nst),y(ndim,nst),z(ndim,nst) !used structures
  +      dimension amat(nst,nst)    !RMSD matrics
         dimension mark(nst)       !for removing used structures
         dimension n_str_near(nst) !numbef of neighboring structures
         dimension itra(nst),istr(nst),E(nst)
  
positive.code: cjmht To compile with OpenMP support add the -fopenmp flag with gfortran
  cjmht gfortran -g -static -O3 -ffast-math -lm -fopenmp -o spicker2 spicker.f
  cjmht Compiling with OpenMP changes where variables are stored and can cause the
  cjmht stack to get overloaded. To prevent this happening on Linux I had to set
  cjmht 'ulimit -s unlimited' when running. To get it to work on OSX, I had to add
  cjmht the compiler flags: -Wl,-stack_size,0x2000000 (32Mb - empirically determined)
  cjmht The OMP_STACKSIZE variables controls the stack for _additional_ variables,
  cjmht not the main OMP thread - the default is the ulimit option on Linux or the
  cjmht compile-time option on OSX (I think)
  cjmht The x, y, z and amat matrices are now allocated. This was done to decrease
  cjmht the stack size. This has necessitated adding fortran90 constructs and interfaces
  cjmht for some of the subroutines.
  
  *******************************************************************************
  *     SPICKER_2.0, released on December 29, 2010
  *     
  
negative.code:       
  cjmht Calculate the amat with the all-by-all scores
        if (n_para.eq.-2) then
            call tm_score_all(ndim,nst,n_str,Lch,x,y,z,amat,rmsd_delta,
       &                      rmsd_a)
        elseif (n_para.eq.-3) then
            call read_score_matrix(nst,n_str,amat,rmsd_delta, rmsd_a)
        else
            call rmsd_score_all(ndim,nst,w,n_str,Lch,x,y,z,amat,
       &                        rmsd_delta,rmsd_a)
        endif
  
  