diff --git a/doc/src/bonds.txt b/doc/src/bonds.txt index fdc3d23c1..a900fdf61 100644 --- a/doc/src/bonds.txt +++ b/doc/src/bonds.txt @@ -1,22 +1,22 @@ -Bonds :h1 +Bond Styles :h1 diff --git a/doc/src/manifolds.txt b/doc/src/manifolds.txt index 6f7b0a9e2..9f0082d5d 100644 --- a/doc/src/manifolds.txt +++ b/doc/src/manifolds.txt @@ -1,40 +1,40 @@ "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 -Manifolds (surfacse) :h3 +Manifolds (surfaces) :h3 [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 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)"_#Paquay1 @ 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(Paquay1) [(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.