The Box section

The box section defines the simulation box. This is useful, for instance if periodic boundary conditions are needed.

Example Box section:
Box settings
length = [10, 10, 10]
periodic = [True, True, False]

Description of keywords for the Box section

For the Box section the following keywords can be set:

  • length: Which defines the cell parameters of the simulation box.
  • low: Which defines the lower boundaries of the box.
  • high: Which defines the upper boundaries of the box.
  • periodic: Which determines if the simulation box has periodic boundaries.

Keyword length

length = list of floats

The length keyword defines the length of the simulation box in each dimension. This is given by a list of numbers:

length = [2, 3, 5]
# or
length = [10, 10, float('inf')]

This will define a simulation box with limits starting from 0 and up to the specified length. In case you want to explicitly define the boundaries you can do this by making use of the keywords low and high described below. Note that if more than three values are given, then the created box will be triclinic. The box is then represented by a matrix:

  • If 6 values are given:

    \begin{bmatrix} a_{0} & a_{3} & a_{4} \\
                0 & a_{1} & a_{5} \\
                0 & 0 & a_{2} \\

  • If 9 values are given:

    \begin{bmatrix} a_{0} & a_{5} & a_{7} \\
                a_{3} & a_{1} & a_{8} \\
                a_{4} & a_{6} & a_{2} \\

If the length is not given in the box section, then the length will be set to infinite in all directions. However, if present, the lengths found in the input configuration will be used.

Keyword low

low = list of floats

Determines the lower boundaries for the simulation box.

low = [0, -1, 0]
The default setting is 0 for each dimension.

Keyword high

high = list of floats

Determines the upper boundaries for the simulation box.

high = [10, -10, 100]
The default setting is low + length.

Keyword periodic

periodic = list of boolean

Determines if the boundaries of the simulation box are periodic or not. This is defined by giving a list of boolean values:

periodic = [True, True, True]

or for a 2D case:

periodic = [True, False]
The default setting is periodic (True) for all directions.