The post processing tools are located in the <RUMDHOME>/Tools/
directory and each one of them has a help text. To see the help text
use the option h
or help
depending on the tool.
The actual output files generated by the program are in a
directory called TrajectoryFiles
. When you start a new simulation in the
same directory, this will be moved to TrajectoryFiles.rumd_bak
as
a precaution against accidental overwriting of data. The analysis
programs should be run in the original directory where the simulation was run
(they know they should look in TrajectoryFiles
for the data).
rumd_stats
produces mean values, variances and standard
deviations for specific quantities. The rumd_stats
stdout for
the simulation just performed is shown in table 1.
Here ke is the kinetic energy, pe is the potential energy, p is the
pressure, T is the kinetic temperature, Ps is the Nose Hoover
thermostat, Etot is the total kinetic energy and W is the virial. The
program writes the mean and variance in the files
energies_mean.dat
and energies_var.dat
in one row as the
first column of stdout.
The radial distribution function is computed by typing
rumd_rdf n 1000 m 1.0
where the first argument is the number of bins in radial
distribution function and the second argument, the minimum time
between successive configurations to use, is to avoid wasting
time doing calculations that are very similar (we assume here that the
configurations are uncorrelated after one time unit). Use
rumd_rdf h
for a full list of arguments.
The output is rdf.dat
and for binary systems the columns are:
. (Single component only has two columns). Plot
rdf.dat
to obtain figure 1.
The static structure factor can be obtained when the radial
distribution function is computed. It is done by typing
rumd_sq 2 20 1
where the first argument is the start value, the second
argument is the final value and the third argument is the
density. The stdout is the value for the maximum of the first peak
and it is written in a file called qmax.dat
. The static
structure factor is written in Sq.dat
and is structured like
rdf.dat
. Plot Sq.dat
to obtain figure 2.
rumd_msd
. This generates a msd.dat
file with time as the
first column and the mean square displacement as a function of time as
the second column (for binary systems there will be two columns), and a file
Fs.dat
with a similar structure. Before it can
be run however, you must create a file called qvalues.dat
which contains
one wavenumber for each time of particle. Typically these correspond to the
location of the first peak in the structure factor, so one could copy the file
qmax.dat
crated by rumd_sq
. rumd_msd
also calculates
gaussian parameter alpha2.dat
. See figure 3 and
4 for mean square displacement and self part of incoherent
scattering function.


rumd_rdf
has to be
performed before rumd_sq
and rumd_sq
before
rumd_msd
. If you only are interested in the mean square
displacement and know which qvalues to use it is not necessary to run
rumd_rdf
and rumd_sq
first. Then you just have to create
a file called qvalues.dat
with the appropriate qvalues before
running rumd_msd
.
Heine Larsen 20170721