LJ Pair potential

Overview

Define a pair potential energy function corresponding to the Lennard-Jones potential

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

where \(r_{ij}\) is the distance between particles \(i,j\) \(\varepsilon, \sigma\) are Lennard-Jones potential parameters, and that must be set to define the interaction between atoms, and \(r_{\rm cut}\) is cutoff distance.

parameters of potential can be defined directly within the python input script, read from a LAMMPS data file (using the LAMMPS reader utility), read from a NAMD input file (using the NAMD reader utility) or read from a restart file.

Python Member Functions

Adding Fix

FixLJCut(state=..., handle=...)

Arguments

state

state object to add the fix.

handle

A name for the fix.

Setting parameters from within the Python environment is done with setParameter.

setParameter(param=...,handleA=...,handleB=...,val=...,)

Arguments

param

name of parameter to set. Can be eps, sig, rCut.

rCut parameter has a default value equal to state.rCut. All other parameters have to be set manually.

handleA, handleB

a pair of type names to set parameters.

val

value of the parameter.

It is also possible to get value of the parameters within the Python environment with getParameter.

val = getParameter(param=...,handleA=...,handleB=...)

Arguments

param

name of parameter to set. Can be eps, sig, rCut

handleA, handleB

pair of type names to set parameters for.

val

value of the parameter.

Examples

Adding the fix

#adding  Lennard-Jones potential
ljcut = FixLJCut(state, handle='ljcut')

Setting parameters in python

ljcut.setParameter(param='eps', handleA='A', handleB='B', val=1.0)
ljcut.setParameter(param='sig', handleA='B', handleB='B', val=1.0)

Setting same parameters for all types in python

ljsig=1.0
ljeps=1.0
#list of all types
types=['A','B','C','S','P','N']
for A in types:
    for B in types:
        ljcut.setParameter(param='eps', handleA=A, handleB=B, val=ljeps)
        ljcut.setParameter(param='sig', handleA=A, handleB=B, val=ljsig)

Activating the fix

#Activate fix
state.activateFix(ljcut)

LAMMPS data file parameter order

rCut, eps, sig