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:

Table 35 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 36 Input sections for defining an analysis.
Section Useage
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 37 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