; sample initialization file for stokes3
; SC lattice config of 8 particles in (5,5,5) box
; $Id: manual.tex,v 1.5 2008/10/12 20:16:53 kichiki Exp $
;; output parameters
(define outfile "stokes3.SC8.nc") ; output filename
(define dt 0.1) ; time step for the integrator
(define nout 10) ; frequency of data output
(define nloop 1000) ; main loop
(define flag-Q #f) ; #t => output quaternion, #f => no quaternion.
;; core libstokes parameters
(define version "F") ; version. "F", "FT", or "FTS"
(define flag-noHI #f) ; #t => no HI, #f => with HI
(define flag-mat #t) ; #t => matrix scheme, #f => atimes scheme
(define flag-lub #t) ; #t => with lub, #f => without lub
(define rmin 0.0) ; param for min distance (ai+aj) * rmin
(define lub-min 2.0000000001) ; min cutoff of distance for lub
(define lub-max 4.0) ; max cutoff of distance for lub
;; periodic systems
(define periodic #t) ; #f => non periodic, #t => periodic
(define ewald-tr 4.1) ; time ratio Tr/Tk for Ewald summation
(define ewald-eps 1.0e-12) ; cut-off limit for Ewald summation
(define lattice '(5.0 5.0 5.0)) ; size of the periodic box
;; iterative solver (ignored if flag-mat is true)
(define IT-solver "otmk") ; solver for libiter
; the following solvers are available
; "cg" conjugate gradient method
; "cgs" conjugate gradient squared (Weiss' Algorithm 11)
; "bicgstab" bi-conjugate gradient stabilized (Weiss' Algorithm 12)
; "sta" bi-cgstab method
; "sta2" bi-cgstab2 method
; "gpb" gpbi-cg method
; "otmk" orthomin method
; "gmres" generalized minimum residual method
(define IT-max 2000) ; max number of iterations
(define IT-n 20) ; restart number
(define IT-eps 1.0e-6) ; accuracy of the solution
(define IT-debug 0) ; set 1 to print the debug info for solve_iter()
;; ODE parameters
(define ode-solver "rkf45")
; the following solvers are available
; "rk2" Embedded Runge-Kutta (2, 3) method.
; "rk4" 4th order (classical) Runge-Kutta.
; "rkf45" Embedded Runge-Kutta-Fehlberg (4, 5) method.
; "rkck" Embedded Runge-Kutta Cash-Karp (4, 5) method.
; "rk8pd" Embedded Runge-Kutta Prince-Dormand (8,9) method.
; "rk2imp" Implicit 2nd order Runge-Kutta at Gaussian points.
; "rk4imp" Implicit 4th order Runge-Kutta at Gaussian points.
; "gear1" M=1 implicit Gear method.
; "gear2" M=2 implicit Gear method.
(define ode-eps 1.0e-6) ; ODE control parameter eps
;; system parameters
(define np 8) ; number of particles
(define nm 8) ; number of free particles
; particle radius
; set '() for monodisperse (a = 1.0 for all particles)
(define a '())
; otherwise, poly codes are used in the calculations
;(define a #(
;1.0
;1.0
;1.0
;1.0
;1.0
;1.0
;1.0
;1.0
;))
; slip length
; set '() for no-slip system (slip = 0 for all particles)
(define slip '())
; otherwise, slip codes are used in the calculations
;(define slip #(
;1.0
;1.0
;1.0
;1.0
;1.0
;1.0
;1.0
;1.0
;))
; initial configuration
(define x #(
0.0 0.0 0.0
2.5 0.0 0.0
0.0 2.5 0.0
0.0 0.0 2.5
0.0 2.5 2.5
2.5 0.0 2.5
2.5 2.5 0.0
2.5 2.5 2.5
))
; imposed-flow parameters
(define Ui '(0.0 0.0 0.0)) ; imposed translational velocity
(define Oi '(0.0 0.0 0.0)) ; imposed angular velocity relative to O
(define Ei '(0.0 0.0 0.0 0.0 0.0)) ; imposed strain relative to O
; auxiliary imposed-flow parameters for simple shear
(define shear-mode 0); 0 == imposed flow is given by Ui, Oi, Ei
; 1 == simple shear (x = flow dir, y = grad dir)
; 2 == simple shear (x = flow dir, z = grad dir)
(define shear-rate 0.0); the shear rate for shear-mode = 1 or 2
(define shear-shift 0.0); the initial condition of cell-shift
; for shear-mode = 1 or 2
(define F0 '(0.0 0.0 -0.1)) ; applied force
(define T0 '(0.0 0.0 0.0)) ; applied torque
(define stokes 0.0) ; effective stokes number
;; Brownian dynamics parameters
(define peclet -1) ; peclet number (negative means no Brownian force)
(define length 1.0) ; the characteristic length [nm] (or [micro m]).
; the parameters above are recognized by this.
; the unit should be the same for parameters below
; just ignored for non-Brownian case (peclet<0).
(define BD-seed 0) ; seed for random number generator for BD.
(define n-cheb-minv 50) ; number of chebyshev coefficients for minv
(define n-cheb-lub 70) ; number of chebyshev coefficients for lub
; time-integration scheme
(define BD-scheme "mid-point")
; the following algorithms are available
; "mid-point" the mid-point algorithm
; "BanchioBrady03" Banchio-Brady (2003)
; "BallMelrose97" Ball-Melrose (1997)
; "JendrejackEtal00" Jendrejack et al (2000)
; "semi-implicit-PC" semi-implicit predictor-corrector
; "SI-connector" semi-implicit for connector vectors
(define BB-n 100) ; step parameter for Banchio-Brady-2003 algorithm
; nonlinear solver for implicit schemes
(define BD-nl-solver "GSL")
; the following solvers are available
; "GSL" GSL multiroot solver
; "NITSOL" Newton-GMRES solver by Pernice and Walker (1998)
; "fastSI" fast semi-implicit solver (only for "SI-connector")
; dt-adjustment parameters
; NOTE: if 'rmin' above is defined by non-zero, dt-adjustment is just skipped.
(define BD-rmin 1.0) ; overlap-param for dt-adjustment process in BD.
; the condition is (r2 <= rmin * a2).
(define dt-lim 1.e-12) ; lower bound to shrink dt to prevent overlaps
; set "dt" (or larger value) if you don't want
; to adjust "dt" but just reject it.
;; constraint parameters
(define constraints '())
; an example of constraints
; note that the distance unit should be the same for "length" above.
;(define constraints '(
; ; system parameters
; 1.0e-6 ; 1) tolerance
; "NITSOL" ; 2) scheme for solving nonlinear equations
; ; "linear" for iterative scheme in linear approximation
; ; "NITSOL" for Newton-GMRES scheme by NITSOL library
; ; the following is for each constraint
; ( ; 3) constraint type 1
; 5.0 ; 3-1) distance [nm]
; ( ; 3-2) list of particle-pairs
; (0 1)
; (1 2)
; (2 3)
; ))
; ( ; 4) constraint type 2
; 10.0 ; 4-1) distance [nm]
; ( ; 4-2) list of particle-pairs
; (3 4)
; (4 5)
; ))
;))
; bond parameters
(define bonds '())
(define flag-relax #f) ; #f => stokesian dynamics with bond interactions
; #t => relaxation dynamics only with bond interactions
(define gamma 1.0) ; friction coefficient for relaxation dynamics
; an example of bonds
; note that the length unit should be the same for "length" above.
;(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
; ))
; 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
;; excluded volume parameters
; note that the length unit should be the same for "length" above.
;(define ev-v '()) ; v [nm^3] (or [micro m^3]) for each chain type
;(define ev-lim 5.0) ; max distance for F^{EV} [nm] (or [micro m])
(define ev '())
; an example
;(define ev '(
; 5.0 ; max distance [nm] (or in the same dimension of "length")
; ( ; for the EV 1
; 0.0012 ; v [nm^3] (or in the same dimension of "length")
; 0 ; fene
; 1.0 ; p1 = A^{sp}, scaled spring const
; 2.1 ; p2 = L_{s} / length, scaled max extension
; (0 1 2); list of particles belongs to the EV parameters
; )
; ( ; for the EV 2
; 0.002 ; v [nm^3] (or in the same dimension of "length")
; 1 ; fene
; 19.8 ; p1 = N_{K,s}, the Kuhn steps for a spring
; 106.0 ; p2 = b_{K} [nm], the Kuhn length
; (3 4) ; list of particles belongs to the EV parameters
; )
;))
;; angle parameters
(define angles '())
; an example
;(define angles '(
; (; angle type 1
; 10.0 ; 1) constant (k^{angle})
; 0.0 ; 2) angle in degree (theta_0)
; 0 ; 3) scale flag (0 == scaled)
; ; in this case, the above value for k is just used.
; ((0 1 2); 4) list of triplets
; (1 2 3)
; (2 3 4)
; )
; )
; (; angle type 2
; 20.0 ; 1) constant (k^{angle})
; 90.0 ; 2) angle in degree (theta_0)
; 1 ; 3) scale flag (1 == not scaled yet)
; ; in this case, the potential is given by
; ; (k/2) * kT * (theta - theta_0)^2
; ((3 4 5); 4) list of triplets
; (4 5 6)
; )
; )
;))
;; excluded volume in Debye-Huckel type
(define ev-dh '())
; an example
; note that the length unit should be the same for "length" above.
;(define ev-dh '(
; ; system parameters
; 1.0e-6 ; 1) epsilon for the cut-off distance of EV_DH interaction
; 298.0 ; 2) temperature [K]
; 80.0 ; 3) dielectric constant of the solution
; 3.07 ; 4) Debye length [nm] (or [micro m])
; ( ; 5) list of chain types
; (; chain type 1
; 2.43 ; 1) nu [e/nm] (or [e/micro m])
; 5.00 ; 2) l0 [nm] (or [micro m])
; (0 1 2) ; 3) list of particles
; )
; (; chain type 2
; 2.00 ; 1) nu [e/nm] (or [e/micro m])
; 4.00 ; 2) l0 [nm] (or [micro m])
; (3 4) ; 3) list of particles
; )
; )
;))
;; excluded volume in Debye-Huckel type
(define ev-LJ '())
; an example
; note that the length unit should be the same for "length" above.
;(define ev-LJ '(
; (; LJ type 1
; 10.0 ; 1) LJ parameter epsilon in kT (so this is dimensionless value)
; 1.0 ; 2) LJ parameter r0 in "length" (so this is dimensionless value)
; ( ; 3) list of particles
; 0 1 2
; )
; )
; (; LJ type 2
; 8.0 ; 1) LJ parameter epsilon in kT (so this is dimensionless value)
; 2.0 ; 2) LJ parameter r0 in "length" (so this is dimensionless value)
; ( ; 3) list of particles
; 3 4
; )
; )
;))
;; confinement force parameters
(define confinement '())
; examples:
; for spherical confinement,
; (define confinement '(
; "sphere"
; 10.0 ;; radius of the cavity at (0, 0, 0)
; ))
; for spherical confinement with a hole,
; (define confinement '(
; "sphere+hole"
; 10.0 ;; radius of the cavity at (0, 0, 0)
; 1.0 ;; radius of the hole at (0, 0, 1) direction
; ))
; for cylindrical confinement,
; (define confinement '(
; "cylinder" ;; the cylinder center goes through (0,0,0) and (x,y,z)
; 10.0 ;; radius of the cylinder
; 1.0 0.0 0.0 ;; direction vector (x, y, z) of the cylinder
; ))
; for dumbbell confinement,
; (define confinement '(
; "dumbbell" ;; the origin is at the center of the cylinder
; 10.0 ;; left cavity radius centered at (center1, 0, 0)
; 10.0 ;; right cavity radius centered at (center2, 0, 0)
; 2.0 ;; length of the cylinder
; 1.0 ;; cylinder radius
; ))
; for 2D hexagonal confinement with cylinder pipe,
; (define confinement '(
; "hex2d"
; 10.0 ;; cavity radius
; 1.0 ;; cylinder radius
; 12.0 ;; lattice spacing
; ))
; for porous media (outside of the 3D hexagonal particle array)
; (define confinement '(
; 10.0 ;; LJ parameter epsilon in kT (so this is dimensionless value)
; 1.0 ;; LJ parameter r0 in "length" (so this is dimensionless value)
; "porous"
; 10.0 ;; particle radius
; 20.0 ;; lattice spacing in x (2R for touching case)
; ))
