The orderparameter section¶
The orderparameter
section defines which order parameter to use
for a path sampling simulation.
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:
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 | 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¶
Position
.Keyword index¶
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¶
The dimension to consider for the position. This can be one of:
x
: For the x-coordinate of the particley
: For the y-coordinate of the particlez
: For the z-coordinate of the particle
- Default:
- Not any. This keyword must be specified.
Keyword periodic¶
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:
Orderparameter
--------------
class = Distance
index = (10, 11)
periodic = True
Keywords for order parameter Distance¶
The following keywords can be set for order parameter Distance:
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¶
Distance
.Keyword index¶
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¶
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.
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:
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.:
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¶
Keyword module¶
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.