anchor.diff: -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
   *     
  
positive.code:       return
        end
  
        subroutine tm_score_all(ndim,n_str,Lch,x,y,z,amat,rmsd_delta,
       &                        rmsd_a)
  c
        implicit none
  
  c     Intent In
        integer ndim
        integer n_str ! Number of structures in use
        integer Lch ! Chain length of the structures (all same)
  c      real x(ndim,nst),y(ndim,nst),z(ndim,nst)
        real, allocatable, intent(in) :: x(:,:),y(:,:), z(:,:)
        real, allocatable, intent(inout) :: amat(:,:)
  c     Intent Out
  c      real amat(nst,nst)
        real rmsd_delta
        double precision rmsd_a
  
  
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
  
  