Diffusion & Deposition Command Note

1. set site value

Syntax:

set label style args keyword values ...

• label = site or iN or dN 

The label determines which per-site quantity is set. iN and dN mean the Nth integer or floating-point quantity,
with 1 <= N <= Nmax. Nmax is defined by the application.
 

• style = value ... 

value arg = nvalue,  nvalue = value to set sites to

For style value, the per-site quantity is set to the specified nvalue, which should be either an integer or
floating-point numeric value, depending on what kind of per-site quantity is being set.

• keyword = fraction or region or loop or if

The optional keywords enable selection of sites whose label quantity will be reset to a new value. The keyword fraction means that only a fraction of the sites will be reset, where 0 < frac <= 1.0. For each site a random number R is generated and the reset only occurs if R < frac.

2. stats command

Syntax:

stats delta keyword values ...

• delta = time increment between statistical output (seconds)

Print statistics to the screen and log file every so many seconds during a simulation. A value of 0.0 for delta
means only print stats at the beginning and end of the run, in which case no optional keywords can be used.
The quantities printed are elapsed CPU time followed by those provided by the application, followed by those
provided by any diagnostics you have defined. Typically the application reports only the number of events or sweeps executed, followed by the simulation time, but other application-specific quantities may also be reported. Quantities such as the total energy of the system can be included in the output by creating diagnostics via the diag_style command.

3. dump text command

Syntax:

dump dump-ID style delta filename field1 field2 ...

• dump-ID = user-assigned name for the dump
• style = text or sites or vtk or image
• delta = time increment between dumps (seconds)
• filename = name of file to dump snapshots to
• fields = list of arguments for a particular style

The text, sites, and vtk styles dump a snapshot of site values to one or more files at time intervals of delta during a
simulation.

The text style dump file is in the format of a LAMMPS dump file which can thus be read-in by the Pizza.py
toolkit, converted to other formats, or used for visualization.

For the text format, each snapshot begins with lines like these:
ITEM: TIMESTEP TIME
100 3.23945
The first field "100" denotes which snapshot it is, numbered as 0,1,2,etc. Snapshot 0 is thus typically for the state
of the system before the first run command. The second field "3.23945" is the simualtion time when the snapshot
is generated.