pyretis.orderparameter package

Definition of order parameters.

This package defines order parameters for use with PyRETIS.

Package structure

Modules

orderparameter.py (pyretis.orderparameter.orderparameter)
Defines the base class for order parameters and some simple example order parameters.
orderangle.py (pyretis.orderparameter.orderangle)
Defines a class for an angle order parameter.
orderdihedral.py (pyretis.orderparameter.orderdihedral)
Defines a class for a dihedral angle order parameter.

Important methods defined here

order_factory (order_factory())
A method to create order parameters from settings.
pyretis.orderparameter.order_factory(settings)[source]

Create order parameters according to the given settings.

This function is included as a convenient way of setting up and selecting the order parameter.

Parameters:settings (dict) – This defines how we set up and select the order parameter.
Returns:out (object like OrderParameter) – An object representing the order parameter.

pyretis.orderparameter.orderangle module

This file contains classes to represent angle order parameters.

Important classes defined here

Angle (Angle)
An angle defined by three atoms.
class pyretis.orderparameter.orderangle.Angle(index, periodic=False)[source]

Bases: pyretis.orderparameter.orderparameter.OrderParameter

An angle order parameter.

This class defines an order parameter which is an angle ABC for 3 particles A, B and C. The angle is defined as the angle given by the two vectors BA and BC.

index

These are the indices of atoms to be used for the angle, i.e. system.particles.pos[index] will be used.

Type:list of integers
periodic

This determines if periodic boundaries should be applied to the positions/distances.

Type:boolean
__init__(index, periodic=False)[source]

Initialise the order parameter.

Parameters:
  • index (list/tuple of integers) – The indices for the atoms defining the angle.
  • periodic (boolean, optional) – This determines if periodic boundary conditions should be applied to the distance vectors.
calculate(system)[source]

Calculate the angle.

Parameters:system (object like System) – Object containing the positions and box info we use for the calculation.
Returns:out (list of floats) – The order parameters.

pyretis.orderparameter.orderdihedral module

Definition of a dihedral order parameter.

Important classes defined here

Dihedral (Dihedral)
A dihedral angle order parameter.
class pyretis.orderparameter.orderdihedral.Dihedral(index, periodic=False)[source]

Bases: pyretis.orderparameter.orderparameter.OrderParameter

Calculates the dihedral angle defined by 4 atoms.

The angle definition is given by Blondel and Karplus, J. Comput. Chem., vol. 17, 1996, pp. 1132–1141. If we label the 4 atoms A, B, C and D, then the angle is given by the vectors u = A - B, v = B - C, w = D - C

index

These are the indices for the atoms to use in the definition of the dihedral angle.

Type:list/tuple of integers
periodic

This determines if periodic boundaries should be applied to the position or not.

Type:boolean
__init__(index, periodic=False)[source]

Initialise the order parameter.

Parameters:
  • index (list/tuple of integers) – This list gives the indices for the atoms to use in the definition of the dihedral angle.
  • periodic (boolean, optional) – This determines if periodic boundary conditions should be applied to the distance vectors.
calculate(system)[source]

Calculate the dihedral angle.

Parameters:system (object like System) – The object containing the information we need to calculate the order parameter.
Returns:out (list of float) – The order parameter.

pyretis.orderparameter.orderparameter module

This file contains classes to represent order parameters.

The order parameters are assumed to all be completely determined by the system properties and they will all return at least one value - the order parameter itself. The order parameters can also return several order parameters which can be used for further analysis.

Important classes defined here

OrderParameter (OrderParameter)
Base class for the order parameters.
Position (Position)
An order parameter equal to the position of a particle.
Velocity (Velocity)
An order parameter equal to the velocity of a particle.
Distance (Distance)
A class for a particle-particle distance order parameter.
Distancevel (Distancevel)
A class for the rate of change in a particle-particle distance order parameter.
CompositeOrderParameter (CompositeOrderParameter)
A class for an order parameter which is made up of several order parameters, i.e. of several objects like OrderParameter.
PositionVelocity (PositionVelocity)
An order parameter which is equal to the composition of Position and Velocity.
DistanceVelocity (DistanceVelocity)
An order parameter which is equal to the composition of Distance and Distancevel.
class pyretis.orderparameter.orderparameter.OrderParameter(description='Generic order parameter', velocity=False)[source]

Bases: object

Base class for order parameters.

This class represents an order parameter and other collective variables. The order parameter is assumed to be a function that can uniquely be determined by the system object and its attributes.

description

This is a short description of the order parameter.

Type:string
velocity_dependent

This flag indicates whether or not the order parameter depends on the velocity direction. If so, we need to recalculate the order parameter when reversing trajectories.

Type:boolean
__init__(description='Generic order parameter', velocity=False)[source]

Initialise the OrderParameter object.

Parameters:description (string) – Short description of the order parameter.
__str__()[source]

Return a simple string representation of the order parameter.

calculate(system)[source]

Calculate the main order parameter and return it.

All order parameters should implement this method as this ensures that the order parameter can be calculated.

Parameters:system (object like System) – This object contains the information needed to calculate the order parameter.
Returns:out (list of floats) – The order parameter(s). The first order parameter returned is used as the progress coordinate in path sampling simulations!
class pyretis.orderparameter.orderparameter.Position(index, dim='x', periodic=False)[source]

Bases: pyretis.orderparameter.orderparameter.OrderParameter

A positional order parameter.

This class defines a very simple order parameter which is just the position of a given particle.

index

This is the index of the atom which will be used, i.e. system.particles.pos[index] will be used.

Type:integer
dim

This is the dimension of the coordinate to use. 0, 1 or 2 for ‘x’, ‘y’ or ‘z’.

Type:integer
periodic

This determines if periodic boundaries should be applied to the position or not.

Type:boolean
__init__(index, dim='x', periodic=False)[source]

Initialise the order parameter.

Parameters:
  • index (int) – This is the index of the atom we will use the position of.
  • dim (string) – This select what dimension we should consider, it should equal ‘x’, ‘y’ or ‘z’.
  • periodic (boolean, optional) – This determines if periodic boundary conditions should be applied to the position.
calculate(system)[source]

Calculate the position order parameter.

Parameters:system (object like System) – The object containing the positions.
Returns:out (list of floats) – The position order parameter.
class pyretis.orderparameter.orderparameter.Velocity(index, dim='x')[source]

Bases: pyretis.orderparameter.orderparameter.OrderParameter

Initialise the order parameter.

This class defines a very simple order parameter which is just the velocity of a given particle.

index

This is the index of the atom which will be used, i.e. system.particles.vel[index] will be used.

Type:integer
dim

This is the dimension of the coordinate to use. 0, 1 or 2 for ‘x’, ‘y’ or ‘z’.

Type:integer
__init__(index, dim='x')[source]

Initialise the order parameter.

Parameters:
  • index (int) – This is the index of the atom we will use the velocity of.
  • dim (string) – This select what dimension we should consider, it should equal ‘x’, ‘y’ or ‘z’.
calculate(system)[source]

Calculate the velocity order parameter.

Parameters:system (object like System) – The object containing the velocities.
Returns:out (list of floats) – The velocity order parameter.
class pyretis.orderparameter.orderparameter.Distance(index, periodic=True)[source]

Bases: pyretis.orderparameter.orderparameter.OrderParameter

A distance order parameter.

This class defines a very simple order parameter which is just the scalar distance between two particles.

index

These are the indices used for the two particles. system.particles.pos[index[0]] and system.particles.pos[index[1]] will be used.

Type:tuple of integers
periodic

This determines if periodic boundaries should be applied to the distance or not.

Type:boolean
__init__(index, periodic=True)[source]

Initialise order parameter.

Parameters:
  • index (tuple of ints) – This is the indices of the atom we will use the position of.
  • periodic (boolean, optional) – This determines if periodic boundary conditions should be applied to the position.
calculate(system)[source]

Calculate the order parameter.

Here, the order parameter is just the distance between two particles.

Parameters:system (object like System) – The object containing the positions and box used for the calculation.
Returns:out (list of floats) – The distance order parameter.
class pyretis.orderparameter.orderparameter.Distancevel(index, periodic=True)[source]

Bases: pyretis.orderparameter.orderparameter.OrderParameter

A rate of change of the distance order parameter.

This class defines a very simple order parameter which is just the time derivative of the scalar distance between two particles.

index

These are the indices used for the two particles. system.particles.pos[index[0]] and system.particles.pos[index[1]] will be used.

Type:tuple of integers
periodic

This determines if periodic boundaries should be applied to the distance or not.

Type:boolean
__init__(index, periodic=True)[source]

Initialise the order parameter.

Parameters:
  • index (tuple of ints) – This is the indices of the atom we will use the position of.
  • periodic (boolean, optional) – This determines if periodic boundary conditions should be applied to the position.
calculate(system)[source]

Calculate the order parameter.

Here, the order parameter is just the distance between two particles.

Parameters:system (object like System) – The object containing the positions and box used for the calculation.
Returns:out (list of floats) – The rate-of-chang of the distance order parameter.
class pyretis.orderparameter.orderparameter.DistanceVelocity(index, periodic=True)[source]

Bases: pyretis.orderparameter.orderparameter.CompositeOrderParameter

An order parameter equal to a distance and its rate of change.

__init__(index, periodic=True)[source]

Initialise the order parameter.

Parameters:
  • index (tuple of integers) – These are the indices used for the two particles. system.particles.pos[index[0]] and system.particles.pos[index[1]] will be used.
  • periodic (boolean, optional) – This determines if periodic boundary conditions should be applied to the position.
class pyretis.orderparameter.orderparameter.PositionVelocity(index, dim='x', periodic=False)[source]

Bases: pyretis.orderparameter.orderparameter.CompositeOrderParameter

An order parameter equal to the position & velocity of a given atom.

__init__(index, dim='x', periodic=False)[source]

Initialise the order parameter.

Parameters:
  • index (int) – This is the index of the atom we will use the position and velocity of.
  • dim (string) – This select what dimension we should consider, it should equal ‘x’, ‘y’ or ‘z’.
  • periodic (boolean, optional) – This determines if periodic boundary conditions should be applied to the position.
class pyretis.orderparameter.orderparameter.CompositeOrderParameter(order_parameters=None)[source]

Bases: pyretis.orderparameter.orderparameter.OrderParameter

A composite order parameter.

This class represents a composite order parameter. It does not actually calculate order parameters itself, but it has references to several objects like OrderParameter which it can use to obtain the order parameters. Note that the first one of these objects will be interpreted as the main progress coordinate in path sampling simulations.

extra

This is a list of order parameters to calculate.

Type:list of objects like OrderParameter
__init__(order_parameters=None)[source]

Set up the composite order parameter.

Parameters:order_parameters (list of objects like OrderParameter) – A list of order parameters we can add.
__str__()[source]

Return a simple string representation of the order parameter.

add_orderparameter(order_function)[source]

Add an extra order parameter to calculate.

Parameters:order_function (object like OrderParameter) – An object we can use to calculate the order parameter.
Returns:out (boolean) – Return True if we added the function, False otherwise.
calculate(system)[source]

Calculate the main order parameter and return it.

This is defined as a method just to ensure that at least this method will be defined in the different order parameters.

Parameters:system (object like System) – This object contains the information needed to calculate the order parameter.
Returns:out (list of floats) – The order parameter(s). The first order parameter returned is assumed to be the progress coordinate for path sampling simulations.