The orderparameter section

The orderparameter section defines which order parameter to use for a path sampling simulation.

Example Orderparameter section:
Orderparameter
--------------
class = Distance
index = (0, 1)
periodic = False

Different order parameters require different settings and this is described in detail below for the different types:

Order parameter Position

This order parameter is defined as the position of a single particle in a specified dimension. It is defined by specifying the class Position, selecting the index of the particle to use, dimension to consider and whether to consider periodic boundaries:

Example Orderparameter section for Position:
Orderparameter
--------------
class = Position
index = 0
dim = x
periodic = False

Keywords for order parameter Position

The following keywords can be set for order parameter Position:

Keyword class

class = Position
Selects the order parameter, should be set to Position.

Keyword index

index = integer

The index selects the particle to use. The particles are numbered sequentially, from 0, in the sequence they appear in the input to PyRETIS.

Default:
Not any. This keyword must be specified.

Keyword dim

dim = string

The dimension to consider for the position. This can be one of:

  • x: For the x-coordinate of the particle
  • y: For the y-coordinate of the particle
  • z: For the z-coordinate of the particle
Default:
Not any. This keyword must be specified.

Keyword periodic

periodic = boolean

This keyword determines if we should apply periodic boundaries to the position or not. If it is set to True periodic boundaries will be applied.

Default:
The default is: periodic = False

Order parameter Distance

This order parameter is defined as the distance between two particles. It is defined by selecting the class Distance, selecting the indices of the particles to consider and then determining if periodic boundaries should be used or not:

Example Orderparameter section for Distance:
Orderparameter
--------------
class = Distance
index = (10, 11)
periodic = True

Keywords for order parameter Distance

The following keywords can be set for order parameter Distance:

Keyword class

class = Distance
Selects the order parameter, should be set to Distance.

Keyword index

index = tuple of integers

The index selects the particles to use. The particles are numbered sequentially, from 0, in the sequence they appear in the input to PyRETIS. This index is selected by specifying the indices as a Python tuple: index = (0, 1)

Default:
Not any. This keyword must be specified.

Keyword periodic

periodic = boolean

This keyword determines if we should apply periodic boundaries to the distance or not. If it is set to True periodic boundaries will be applied.

Default:
The default is: periodic = False.

User defined order parameters

You can also define custom order parameters to use with PyRETIS. Such order parameters should subclass the generic OrderParameter class as described in the user guide.

Example Orderparameter section for a user defined order parameter:
Orderparameter
--------------
class = WCAJCP1
module = ../orderp/orderp.py
index = (7,8)
periodic = True

Keywords for user defined order parameters

At least the following keywords can be set for user defined order parameters:

In addition, user defined keywords can be specified, e.g.:

Example Orderparameter section for a user defined order parameter:
Orderparameter
--------------
class = MyOrderParameter
module = order.py
setting1 = input
setting3 = 123.456
setting2 = True

Keyword class

class = string
This keyword selects the order parameter and it should be set to the class name of the custom order parameter class defined in the given module.

Keyword module

module = string

This keyword specified the location of the file containing the user defined class for the order parameter. This file must be accessible by PyRETIS.

Default
Not any. This keyword must be specified.