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:
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, , is used:
- to obtain where 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: https://doi.org/10.1016/0021-9991(75)90042-X |
[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 |