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 6 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.
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

[1]Rowley et al., J. Comput. Phys., vol. 17, pp. 401-414, 1975, doi: http://dx.doi.org/10.1016/0021-9991
[2](1, 2, 3, 4) The LAMMPS manual, http://lammps.sandia.gov/doc/units.html
[3]https://en.wikipedia.org/wiki/Atomic_units
[4]The GROMACS manual, version 5.1.1, tables 2.1 and 2.2 on page. 8, http://manual.gromacs.org/documentation/5.1.1/manual-5.1.1.pdf