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 41 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 42 Input sections for defining an analysis.

Section	Usage
analysis	For defining an analysis.

Notation for describing keywords

Each keyword entry is shown as:

keyword = DATA-TYPE

where keyword is the input-file key and DATA-TYPE is the kind of value accepted by that key. The paragraph below each keyword explains what it controls. When a keyword has a default value, the default is listed directly below the description.

Example:

task = string

Selects the simulation task to run.

Default:
  md

The data types used in the keyword reference are listed below.

Table 43 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