Harmonic Bond Style

Overview

Define a bonding potential energy function corresponding to a harmonic bond style

\[U_{ij} = \frac{1}{2}k(r - r_0)^2,\]

where \(k, r_0\) are parameters that must be set to define the interaction between atoms \(i, j\) .

Bonds and types 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

Bond types and bonds can be set from within the Python environment with simple invocations. In the syntax that follows, parameters with = may be given in any order and are also optionally specified. For example, if an existing bond type has already been set, it is unneccessary to specify its parameters again when creating a bond.

createBond(a,b,k=...,r0=...,type=...)
setBondTypeCoefs(k=...,r0=...,type=...)

Arguments

a,b

Indices for atoms for which the bond is defined.

k

Spring constant coefficient for harmonic interaction.

r0

Equilbrium bond for harmonic bond interaction.

Examples

Adding the fix

#Add Fix for harmonic bond style
bondPot = FixBondHarmonic(state,'bondPot')

Setting bond type coefficients in python

#Setting bond types
bondPot.setBondTypeCoefs(k=100.0,r0=1.0,type=0)

Defining a bond type in python

#Creating a bond between atoms 1,2 and 2,3
a=1     # index for atom 1
b=2     # index for atom 2
c=3     # index for atom 3
bondPot.createBond(a,b,type=0)
# create bond and implicitly create type
bondPot.createBond(b,c,k=80.0,r0=1.5,type=1)

Activating the fix

#Activate fix
state.activateFix(bondPot)

LAMMPS data file parameter order

bond_coeff type k r0