pyPRISM.potential.LennardJones module¶
-
class
pyPRISM.potential.LennardJones.LennardJones(epsilon, sigma=None, rcut=None, shift=False)[source]¶ Bases:
pyPRISM.potential.Potential.Potential12-6 Lennard-Jones potential
Mathematical Definition
\[U_{\alpha,\beta}(r) = 4\epsilon_{\alpha,\beta}\left[\left(\frac{\sigma_{\alpha,\beta}}{r}\right)^{12.0} - \left(\frac{\sigma_{\alpha,\beta}}{r}\right)^{6.0}\right]\]\[U_{\alpha,\beta}^{shift}(r) = U_{\alpha,\beta}(r) - U_{\alpha,\beta}(r_{cut})\]Variable Definitions
- \(\epsilon_{\alpha,\beta}\)
- Strength of attraction between sites \(\alpha\) and \(\beta\).
- \(\sigma_{\alpha,\beta}\)
- Length scale of interaction between sites \(\alpha\) and \(\beta\).
- \(r\)
- Distance between sites.
- \(r_{cut}\)
- Cutoff distance between sites.
Description
The classic 12-6 LJ potential. To facilitate direct comparison with molecular simulation, the simulation may be cut and shifted to zero at a specified cutoff distance by setting the rcut and shift parameters. The full (non-truncated) LJ potential is accessed using \(r_{cut}\) = None and \(shift\) = False.Example
import pyPRISM #Define a PRISM system and set the A-B interaction potential sys = pyPRISM.System(['A','B'],kT=1.0) sys.domain = pyPRISM.Domain(dr=0.1,length=1024) sys.potential['A','B'] = pyPRISM.potential.LennardJones(epsilon=1.0,sigma=1.0,rcut=2.5,shift=True)
Warning
If sigma is specified such that it does not fall on the solution grid of the
Domainobject specified inSystem, then the sigma will effectively be rounded. A warning should be emitted during the construction of aPRISMobject if this occurs.-
__init__(epsilon, sigma=None, rcut=None, shift=False)[source]¶ Constructor
Parameters: - epsilon (float) – Depth of attractive well
- sigma (float, optional) – Contact distance. If not specified, sigma will be calculated from
the diameters specified in the
Systemobject. - rcut (float, optional) – Cutoff distance for potential. Useful for comparing directly to results from simulations where cutoffs are necessary.
- shift (bool,*optional*) – If \(r_{cut}\) is specified, shift the potential by its value at the cutoff. If \(r_{cut}\) is not specified, this parameter is ignored.