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
cell = [10, 10, 10]
periodic = [True, True, False]

Keywords for the Box section

For the Box section the following keywords can be set:

Table 10 Keywords for the Box section
Keyword Description
cell 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 cell

cell = list of floats

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

cell = [2, 3, 5]
# or
cell = [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 cell is not given in the box section, then the cell will be set to infinite in all directions. However, if present, the cell 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 + cell.

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.