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 11 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]

  • ase: eV, Å and fs, the energy and length units of ASE and the unit of the time step of the ASE engine.

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 is the unit system of the engine: lj for the internal integrators, gromacs for GROMACS, openmm for OpenMM, cp2k for CP2K, reduced for TurtleMD, ase for ASE, and the units command of the LAMMPS input for LAMMPS.

References