External Harmonic Potential Fix

Overview

Applies an external potential to a group of atoms to mimic confinement in a harmonic well.

\[U_{\text{ext}} = \frac{1}{2} \sum_{d=x,y,z} k_d(r_d - r_{d0})^2,\]

where \(\mathbf{k}=(k_x,k_y,k_z), \mathbf{r}_0=(r_{x0},r_{y0},r_{z0})\) are Vector parameters that must be set to define the harmonic well. As the parameters are vectors, one- and two-dimensional harmonic potentials may be created by setting some of the spring coefficients to zero.

The harmonic potentials are defined directly within the python input script as a Fix using its constructor.

Constructor

FixExternalHarmonic(state,handle,groupHandle,k,r0)

Arguments

state

Simulation state to apply the fix.

handle

A name for the object. Named argument.

groupHandle

Group of atoms to which the fix is applied. Named argument. Defaults to all.

k

Vector of spring constant coefficient for \(k_x,k_y,k_z\) for strength of confining potential in each dimension. These are specified as Vector(kx,ky,kz).

r0

Vector of minima \(r_{x0},r_{y0},r_{z0}\) in each dimension for the harmonic potential. These are specified as Vector(rx,ry,rz).

Examples

Adding and activating the fix

#Add Fix for external harmonic potential
UextHarm = FixExternalHarmonic(state,handle='Uharm',groupHandle='all',
  k = Vector(1.0,0.0,0.5), r0 = Vector(0.0,0.0,1.0))
#Activate fix
state.activateFix(UextHarmt)