Input file sections¶
The PyRETIS input file described in detail in the user guide. The short version is:
The input file is organised into
sections
wherekeywords
are given values:Section Title ------------- keyword = value
Comments are marked with a
#
.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:
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:
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.
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 |