8.5.8. Manifolds (surfaces)

Overview:

This doc page is not about a LAMMPS input script command, but about manifolds, which are generalized surfaces, as defined and used by the USER-MANIFOLD package, to track particle motion on the manifolds. See the src/USER-MANIFOLD/README file for more details about the package and its commands.

Below is a list of currently supported manifolds by the USER-MANIFOLD package, their parameters and a short description of them. The parameters listed here are in the same order as they should be passed to the relevant fixes.

manifold

parameters

equation

description

cylinder

R

x^2 + y^2 - R^2 = 0

Cylinder along z-axis, axis going through (0,0,0)

cylinder_dent

R l a

x^2 + y^2 - r(z)^2 = 0, r(x) = R if | z | > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise

A cylinder with a dent around z = 0

dumbbell

a A B c

-( x^2 + y^2 ) + (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0

A dumbbell

ellipsoid

a b c

(x/a)^2 + (y/b)^2 + (z/c)^2 = 0

An ellipsoid

gaussian_bump

A l rc1 rc2

if( x < rc1) -z + A * exp( -x^2 / (2 l^2) ); else if( x < rc2 ) -z + a + b*x + c*x^2 + d*x^3; else z

A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0.

plane

a b c x0 y0 z0

a*(x-x0) + b*(y-y0) + c*(z-z0) = 0

A plane with normal (a,b,c) going through point (x0,y0,z0)

plane_wiggle

a w

z - a*sin(w*x) = 0

A plane with a sinusoidal modulation on z along x.

sphere

R

x^2 + y^2 + z^2 - R^2 = 0

A sphere of radius R

supersphere

R q

| x |^q + | y |^q + | z |^q - R^q = 0

A supersphere of hyperradius R

spine

a, A, B, B2, c

-(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise

An approximation to a dendritic spine

spine_two

a, A, B, B2, c

-(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise

Another approximation to a dendritic spine

thylakoid

wB LB lB

Various, see (Paquay)

A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB

torus

R r

(R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2

A torus with large radius R and small radius r, centered on (0,0,0)

(Paquay) Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at arXiv:1411.3019.