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]
cell = [
    10,
    10,
    10,
]
periodic = [
    true,
    true,
    false,
]

Keywords for the Box section

For the Box section the following keywords can be set:

Table 13 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:

[box]
cell = [2, 3, 5]

or, for a box of infinite length along z:

[box]
cell = [10, 10, 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:

  \[\begin{split}\begin{bmatrix} a_{0} & a_{3} & a_{4} \\ 0 & a_{1} & a_{5} \\ 0 & 0 & a_{2} \\ \end{bmatrix}\end{split}\]

• If 9 values are given:

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

Default:

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.

[box]
low = [
    0,
    -1,
    0,
]

Default:

The default setting is 0 for each dimension.

Keyword high

high = list of floats

Determines the upper boundaries for the simulation box.

[box]
high = [
    10,
    -10,
    100,
]

Default:

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:

[box]
periodic = [
    true,
    true,
    true,
]

or for a 2D case:

[box]
periodic = [
    true,
    false,
]

Default:

Periodic (true) in all directions when the input has a [box] section, or when the initial configuration gives a box (a generated lattice, or a file that holds the box). Without either, the box is not periodic in any direction, and the run says so in a warning.