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