pyretis.forcefield.potentials package¶

A collection of potential functions.

This package defines some potential functions. These potential functions can be used to create force fields.

Package structure¶

Modules¶

potentials.py (pyretis.forcefield.potentials.potentials): This module defines some simple potential functions.

Sub-packages¶

pairpotentials (pyretis.forcefield.potentials.pairpotentials): This package defines different pair interactions, for instance the Lennard-Jones 6-12 simple cut potential.

Important classes defined in this package¶

DoubleWell (DoubleWell): A double well potential
RectangularWell (RectangularWell): A rectangular well potential – useful as a bias potential.
PairLennardJonesCut (PairLennardJonesCut): The Lennard-Jones potential in pure python.
PairLennardJonesCutnp (PairLennardJonesCutnp): The Lennard-Jones potential, making use of numpy.
DoubleWellWCA (DoubleWellWCA): A n-dimensional Double Well potential.

Subpackages¶

pyretis.forcefield.potentials.pairpotentials package

List of submodules¶

pyretis.forcefield.potentials.potentials

pyretis.forcefield.potentials.potentials module¶

A collection of simple position dependent potentials.

This module defines some potential functions which are useful as simple models.

Important classes defined here¶

DoubleWell (DoubleWell): This class defines a one-dimensional double well potential.
RectangularWell (RectangularWell): This class defines a one-dimensional rectangular well potential.

class pyretis.forcefield.potentials.potentials.DoubleWell(a=1.0, b=1.0, c=0.0, desc='1D double well potential')[source]¶

Bases: pyretis.forcefield.potential.PotentialFunction

A 1D double well potential.

This class defines a one-dimensional double well potential. The potential energy ( $V_\text{pot}$ ) is given by

$V_\text{pot} = a x^4 - b (x - c)^2$

where $x$ is the position and $a$ , $b$ and $c$ are parameters for the potential. These parameters are stored as attributes of the class. Typically, both $a$ and $b$ are positive quantities, however, we do not explicitly check that here.

params¶

Contains the parameters. The keys are:

a: The a parameter for the potential.
b: The b parameter for the potential.
c: The c parameter for the potential.

These keys corresponds to the parameters in the potential, $V_\text{pot} = a x^4 - b (x - c)^2$ .

Type:	dict

__init__(a=1.0, b=1.0, c=0.0, desc='1D double well potential')[source]¶

Initialise the one dimensional double well potential.

Parameters:	a (float, optional) – Parameter for the potential. b (float, optional) – Parameter for the potential. c (float, optional) – Parameter for the potential. desc (string, optional) – Description of the force field.

force(system)[source]¶

Evaluate forces for the 1D double well potential.

Parameters:	system (object like `System`) – The system we evaluate the potential for. Here, we make use of the positions only.
Returns:	out[0] (numpy.array) – The calculated force. out[1] (numpy.array) – The virial, currently not implemented for this potential!

potential(system)[source]¶

Evaluate the potential for the one-dimensional double well.

Parameters:	system (object like `System`) – The system we evaluate the potential for. Here, we make use of the positions only.
Returns:	out (float) – The potential energy.

potential_and_force(system)[source]¶

Evaluate the potential and the force.

Parameters:	system (object like `System`) – The system we evaluate the potential for. Here, we make use of the positions only.
Returns:	out[0] (float) – The potential energy as a float. out[1] (numpy.array) – The force as a numpy.array of the same shape as the positions in particles.pos. out[2] (numpy.array) – The virial, currently not implemented for this potential!

class pyretis.forcefield.potentials.potentials.RectangularWell(left=0.0, right=1.0, largenumber=inf, desc='1D Rectangular well potential')[source]¶

Bases: pyretis.forcefield.potential.PotentialFunction

A 1D rectangular well potential.

This class defines a one-dimensional rectangular well potential. The potential energy is zero within the potential well and infinite outside. The well is defined with a left and right boundary.

params¶

The parameters for the potential. The keys are:

left: Left boundary of the potential.
right: Right boundary of the potential.
largenumber: Value of potential outside the boundaries.

It is possible to define left > right, however, a warning will be issued then.

Type:	dict

__init__(left=0.0, right=1.0, largenumber=inf, desc='1D Rectangular well potential')[source]¶

Initialise the one-dimensional rectangular well.

Parameters:	left (float, optional) – The left boundary of the potential. right (float, optional) – The right boundary of the potential. largenumber (float, optional) – The value of the potential outside (left, right). desc (string, optional) – Description of the force field.

check_parameters()[source]¶

Check the consistency of the parameters.

Returns:	out (None) – Returns None but might give a warning.

potential(system)[source]¶

Evaluate the potential.

Parameters:	system (object like `System`) – The system we evaluate the potential for. Here, we make use of the positions only.
Returns:	out (float) – The potential energy.