Springs

Overview

Applies a harmonic potential tethering atoms to user-defined coordinates with a potential given by

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

where {k} is a scalar and mathbf{r}_0=(r_{x0},r_{y0},r_{z0})` is a Vector which denotes each atom’s tether position. Anisotropic springs including one and two dimensional springs can be created by setting different coefficients for different dimensions.

By default each atom is tethered to its position when the spring fix is initialized, however arbitrary positions can be set for each atom as shown in the examples.

Springs differ from external potentials in that springs can tether each atom to a different position, while external potentials simulate all atoms within the relevant group in the same external field.

Constructor

FixSpringStatic(state, handle, groupHandle, k, tetherFunc, multiplier)

Arguments

state

Simulation state to apply the fix. Named argument.

handle

A name for the fix. Named argument.

groupHandle

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

k

Spring coefficient for tethers. Floating point number. Named argument

tetherFunc

Python function which, when passed an atom, must return a Vector which is the position to which that atom will be tethered. Optional. Defaults to tethering to current position. Named argument.

multiplier

Scales k in each dimension. Can be set to create anisotropic potentials or 2d / 1d springs. Optional. Defaults to Vector(1, 1, 1). Named argument.

Python Member Functions

updateTethers()

No arguments. Recalculates atom tether positions based on new atom coordinates. If no tetherFunc is supplied, tethers are set to atoms’ current positions. If a tetherFunc is supplied, tetherFunc is called for each atom in groupHandle and new positions are determined.

Python Members

multiplier

#makes anisotropic spring that acts with kx = k, ky = 2k, kz = 0
spring.multiplier = Vector(1, 2, 0)

k

#sets spring constant for tethers
spring.k = 10

tetherFunc

def myFunc(atom):
    return Vector(round(atom.pos[0]), round(atom.pos[1]), round(atom.pos[2]))
#sets new tetherFunc for the spring
spring.tetherFunc = myFunc

#must call updateTethers to generate new tethers
spring.updateTethers()

Examples

#creates fix which tethers all atoms in the group 'substrateAtoms' to their
#current positions with k=10
spring = FixSpringStatic(state, handle='spring1', groupHandle='substrateAtoms', k=10)
state.activateFix(spring)

def myTetherFunc(atom):
    if atom.pos[0] > 10:
        return Vector(15, atom.pos[1], atom.pos[2]):
    else:
        return atom.pos

#create a spring which will tether only in the x dimension.  Atoms with x>10 will be tethered to x=15 and all others will be tethered to their original x position.
spring = FixSpringStatic(state, handle='spring2', groupHandle='all', k=5, tetherFunc=myTetherFunc, multiplier=Vector(1, 0, 0))

#run the simulation
integrator = IntegratorVerlet(state)
integrator.run(1000)

#change spring constant
spring.k = 10
#now spring applies in y dimension as well
spring.multiplier[1] = 1

#update atom tethers based on current atom positions.
spring.updateTethers()