LJ Wall Potential

Overview

Implements a Lennard-Jones 12-6 potential well associated with a boundary of the simulation cell for simulation of non-periodic dimensions. The form of the potential is given by

\[\begin{split}V(r_{ij}) = \left[\begin{array}{cc} 4 \varepsilon \left( \left(\frac{\sigma}{r_{ij}}\right)^{12} - \left(\frac{\sigma}{r_{ij}}\right)^{6}\right),& r<r_{\rm cut}\\ 0, & r\geq r_{\rm cut} \end{array}\right.\end{split}\]

where \(r_{ij}\) is the distance between a particle and the wall, \(\varepsilon, \sigma\) are Lennard-Jones potential parameters, and \(r_{\rm cut}\) is cutoff distance.

Constructor

FixWallLJ126(state,handle,groupHandle,origin,forceDir,dist,sigma,epsilon)

Arguments

state

Simulation state to which the fix is applied.

handle

Name of the fix. String type.

groupHandle

Group of atoms to which the fix is applied. String type.

origin

Location of the wall. Vector type.

forceDir

Direction in which the wall potential is applied. Vector type.

dist

Cutoff distance for the potential. Float type.

sigma

Lennard-Jones :math: sigma parameter associated with the wall. Float type.

epsilon

Lennard-Jones :math: epsilon parameter associated with the wall. Float type.

Python Member Functions

Member data of the FixWallLJ126 potential may be modified directly via the Python interface; namely, ‘sigma’, ‘epsilon’, ‘dist’, ‘forceDir’, and ‘origin’ keywords are directly accessible from an instance of FixWallLJ126.

To modify any these parameters, simply assign them a new value of an appropriate type.

Examples

Example 1: creating an instance of FixWallLJ126

# create a simulation state to which we will add the fix
state = State()

# set the bounds of the state
state.bounds = Bounds(state, lo=Vector(0,0,0), hi=Vector(30,30,30))

# put the wall at (0,0,0)
origin = Vector(0,0,0)

# have the wall be acting in the +x direction
forceDir = Vector(1,0,0)

# cutoff distance of 15 units
dist = 15

# sigma and LJ
sigma = 2.4
epsilon = 1.0

# create an instance of the fix
fixWall = FixWallLJ126(state,"ljwall","all",origin,forceDir,dist,sigma,epsilon)

# activate the fix
state.activateFix(fixWall)

Example 2: Modifying the LJ constants of the above wall

# referring to the instances created above..
# change the sigma parameter
fixWall.sigma=3.0