Input file sections

The PyRETIS input file described in detail in the user guide. The short version is:

1. The input file is organised into sections where keywords are given values:

   Section Title
   -------------
   keyword = value
   

2. Comments are marked with a #.

3. Input is in general not case-sensitive unless you are referring to files and Python classes.

Below, we list the different sections that you can make use of in order to define your simulation:

Table 40 Input sections for defining simulations.

Section	Usage
simulation	For defining the simulation we are going to run.
system	For defining system properties.
box	For defining a simulation box.
particles	For defining the initial state of particles.
forcefield	For defining a forcefield.
potential	For defining potential functions to use in the force field.
engine	For defining the simulation engine.
orderparameter	For defining the order parameter.
retis	For defining settings for a RETIS simulation.
tis	For defining settings for a TIS simulation.
initial-path	For defining how the initial path is generated.
output	For defining output settings.
unit-system	For defining custom unit systems.

In addition, an analysis can be defined using:

Table 41 Input sections for defining an analysis.

Section	Usage
analysis	For defining an analysis.

Notation for describing keywords

In each of these sections, the keywords are described using the following notation:

KEYWORD = DATA-TYPE

Description of the keyword.

Default:

Description of default settings.

Here, KEYWORD is the actual keyword that is set, and DATA-TYPE is the allowed parameter type for the particular keyword. The types you may encounter are described in the table below.

Table 42 The different data types encountered in PyRETIS.

DATA-TYPE	Description	Example
string	A string of characters, i.e. text.	task = retis
integer	An integer.	steps = 100
float	A floating-point number	timestep = 0.002
boolean	A boolean value (True or False).	shift = True
dictionary	A Python dictionary.	mass = {'Ar': 1.0}
list	A Python list.	interfaces = [0.1, 0.2, 0.3]
tuple	A Python tuple.	index = (7,8)
None	This represents an optional value