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Bond Parameters

	bonds      : bonds among particles, list in the following form
	(define bonds '(
	  (; bond 1
	   0       ; 1) spring type
	   (       ; 2) spring parameters (list with 3 elements)
	    0      ;    fene = 0 means (p1, p2) = (A^{sp}, L_{s})
	    1.0    ;    p1   = A^{sp}, scaled spring constant
	    2.1)   ;    p2   = L_{s} / length, scaled max extension
	   ((0 1)  ; 3) list of pairs
	    (1 2)
	    (2 3))
	    -1)    ; 4) number of exclusion for lubrication
	           ;    negative means all particles in the chain is excluded.
	  (; bond 2
	   2       ; 1) spring type
	   (       ; 2) spring parameters (list with 3 elements)
	    1      ;    fene = 1 means (p1, p2) = (N_{K,s}, b_{K})
	    19.8   ;    p1 = N_{K,s}, the Kuhn steps for a spring
	    106.0) ;    p2 = b_{K} [nm], the Kuhn length
	           ;    note that, for dWLC (type == 6),
	           ;    (p1, p2) = (k, r0 [nm]), where the potential is
	           ;    (k/2) * (kT / r0^2) * (r-r0)^2
	   ((4 5)  ; 3) list of pairs
	    (5 6)
	    (6 7))
	    1)     ; 4) number of exclusion for lubrication
	  (; bond 3
	   7       ; 1) spring type (FENE-Fraenkel)
	   (       ; 2) spring parameters (list with 4 elements)
	    0      ;    fene = 0 means (p1, p2, p3) = (H, r0 [nm], tol)
	    1.0e6  ;    p1 = H, the spring constant
	    0.5    ;    p2 = r0 [nm], the natural length of the spring
	    0.01)  ;    p3 = tol, the tolerance parameter "s"
	           ;    note that, for FENE-Fraenkel (type == 7),
	           ;    the scalar part of the force is
	           ;    fr = H * (r/hat(r0) - 1.0) / (1 - ((1-r/hat(r0))/tol)^2)
	           ;    where hat(r0) = r0 / L0 (L0 is given by "length" [nm])
	   ((8 9)  ; 3) list of pairs
	    (9 10))
	    0)     ; 4) number of exclusion for lubrication
	 ))
	where spring types are
	  0 : Hookean spring (Asp * (r - Ls)
	  1 : wormlike chain (WLC)
	  2 : inverse Langevin chain (ILC)
	  3 : Cohen's Pade approximation
	  4 : Warner spring
	  5 : Hookean spring (Asp * r / Ls)
	  6 : Hookean spring for dWLC
	  7 : FENE-Fraenkel
	flag_relax : #f stokesian dynamics,
	           : #t relaxation dynamics for bonds.
	gamma      : friction coefficient for the relaxation dynamics



Kengo Ichiki 2008-10-12