Potentials (pele.potentials)

This module exports native potential bindings and Python implementations. The reference below groups the available models and wrappers by purpose.

Potential interface

Python potentials can derive from these base classes.

BasePotential()	Base class for all potentials
PairwisePotentialInterface	this class defines the python interface for c++ pair potentials
BasePotentialAtomistic()	Base class for all potentials that can use interaction lists

When creating a potential, implement getEnergy(). Many routines also use gradients, so implement getEnergyGradient() to avoid calculating them numerically. See Creating Your Potential for a worked example.

Pair potentials

LJ	define the python interface to the c++ LJ implementation
BLJCut	Binary Lennard-Jones with a cutoff
LJCut([eps, sig, rcut, boxl])	lennard jones potential with a cutoff that is continuous and smooth
LJpshift(natoms, ntypeA[, boxl, rcut, ...])	binary lennard jones potential with smooth cutoff
Frenkel	Python interface to the native Frenkel pair potential.
Morse([rho, r0, A, boxvec, rcut])	the morse potential
HS_WCA	Define the python interface to the c++ HS_WCA implementation.
WCA	define the python interface to the c++ WCA implementation
WCANeighborList	define the python interface to the c++ WCA implementation
WCAAtomList	define the python interface to the c++ WCA implementation

Inverse-power potentials

InversePower	define the python interface to the c++ InversePower implementation
InversePowerHS	define the python interface to the c++ InversePowerHS implementation
InversePowerStillinger	Python interface to C++ implementation of InversePowerStillinger.
InversePowerStillingerCut	Python interface to C++ implementation of InversePowerStillingerCut, a smooth potential with cutoff distance.
InversePowerStillingerCutQuad	Python interface to C++ implementation of InversePowerStillingerCutQuad, a smooth repulsive potential with a cutoff distance.
PyInversePower(pow, eps, radii[, ndim, ...])	A python based inversepower potential for small system sizes with periodic boundary conditions.

Many-body potentials

ATLJ([eps, sig, Z])	Lennard Jones + three body Axilrod-Teller term
ATLJCPP	alias of ATLJ

Harmonic and Gaussian potentials

Harmonic	define the python interface to the c++ Harmonic potential implementation
RadialGaussian	define the python interface to the c++ RadialGaussian potential implementation
SumGaussianPot	Sum of GaussianPot

Spin potentials

XYModel([dim, phi, periodic, phases])	XY model of 2d spins on a lattice
HeisenbergModel([dim, field_disorder, fields])	The classical Heisenberg Model of 3d spins on a lattice.
HeisenbergModelRA([dim, field_disorder, fields])	The classical Heisenberg Model of 3d spins on a lattice with random anisotropy.
MeanFieldPSpinSpherical	Python interface to _Cdef_MeanFieldPSpinSpherical

Potential wrappers

CombinedPotential	Sum native potentials added with add_potential.
FrozenPotentialWrapper	Wrapper for a potential object for freezing degrees of freedom

Cost and test functions

MLCost(data[, log_probf, probf])	Cost function to be used for maximum likelihood optimization.
PoweredCosineSum	Python Interface to the c++ PoweredCosineSum potential implementation

External potentials

GMINPotential(GMIN)

Interface to fortran GMIN potential

LAMMPSPotential is available when the optional LAMMPS dependency is installed. See the Python adapter source and native adapter source for its energy and gradient interface.