Input file sections

The PyRETIS input file described in detail in the user guide. The sort 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:

  • 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, there are analysis specific settings which can be set by making use of the following section(s):

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 2 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