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lammps/doc/manifolds.txt
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
[Description:]
Below is a list of currently supported manifolds, 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
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 dendtritic 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 dendtritic spine
thylakoid || wB LB lB || Various, see "(Paquay)"_#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) :tb(s=||)
:link(Paquay)
[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.
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