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
- Keywords for order parameter Position
Order parameter Distance
- Keywords for order parameter Distance
User-defined order parameters
- Keywords for user-defined order parameters
  - Keyword class
  - Keyword module

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:

Table 24 Keywords for the Position order parameter.¶
Keyword	Description
class	Selects the Position order parameter.
index	Selects the particle to use.
dim	Selects the dimension to consider for the position.
periodic	Determines if periodic boundaries should be used.

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:

Table 25 Keywords for the Distance order parameter.¶
Keyword	Description
class	Selects the Distance order parameter.
index	Selects the particles to use for the distance.
periodic	Determines if periodic boundaries should be applied.

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:

Table 26 Keywords for user-defined order parameters.¶
Keyword	Description
class	Selects a Python class to use as the order parameter.
module	Defines the module where the Python class can be located.

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

In the example the file ´orderp.py´ shall contain the class ´MyOrderParameter´. The class can use the PyRETIS system object, which contains the various information to compute the order parameter(s) (position, velocities, etc). Furthermore, when using an external engine, the name of the file where the latest frame is stored is included in system.particles.config[0]. The index of the frame can be found in system.particles.config[1].

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.