The System section

The system section defines some properties of the system.

Example System section:
System
------
units = reduced
dimensions = 2
temperature = 1.0

Keywords for the System section

The following keywords can be set for the System section:

Table 10 Keywords for the System section

Keyword

Description

dimensions

Specify the dimensionality of the system.

temperature

Specify a set temperature for the system.

units

Sepcify the unit system to use.

Keyword dimensions

dimensions = integer

Specify the dimensionality of the system. Should be 1, 2, or 3 for 1D, 2D or 3D, respectively.

Default:

The default value is dimensions = 3.

Keyword temperature

temperature = float

Specify a set temperature for the system. This temperature, \(T\), is used:

  • to obtain \(\beta = 1/(k_\text{B} \times T)\) where \(k_\text{B}\) is the Boltzmann constant for the system.

  • as a target temperature for velocity generation if no temperature is given in the velocity keyword of the particles section.

  • as the target temperature for the Python Maxwell-Boltzmann draw when an external engine sets velocity_generation = maxwell (otherwise the external engine draws its own velocities; this is the default).

Default:

The default value is temperature = 1.0.

Keyword units

units = string

The units keyword defines the system of units to use by PyRETIS. Currently, the following system of units are defined by PyRETIS (see the definitions of unit systems):

  • lj: A Lennard-Jones type of (reduced) units (based on Argon [1]).

  • real: A system of units similar to the LAMMPS [2] unit real.

  • metal: A system of units similar to the LAMMPS [2] unit metal.

  • au: Atomic units. [3]

  • electron: A system of units similar to the LAMMPS [2] unit electron.

  • si: A system of units similar to the LAMMPS [2] unit si.

  • gromacs: A system of units similar to the units used by GROMACS. [4]

The system of units should be one of the systems defined by PyRETIS listed above. Alternatively, you can define your own unit system by making use of a special unit-system section in combination with the units keyword.

Default:

The default value is units = lj.

References