The post processing tools are located in the
directory and each one of them has a help text. To see the help text
use the option
--help depending on the tool.
The actual output files generated by the program are in a
TrajectoryFiles. When you start a new simulation in the
same directory, this will be moved to
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_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
Sq.dat to obtain figure 2.
rumd_msd. This generates a
msd.datfile 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.datwith a similar structure. Before it can be run however, you must create a file called
qvalues.datwhich 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
rumd_msdalso calculates gaussian parameter
alpha2.dat. See figure 3 and 4 for mean square displacement and self part of incoherent scattering function.
rumd_rdfhas to be performed before
rumd_msd. If you only are interested in the mean square displacement and know which q-values to use it is not necessary to run
rumd_sqfirst. Then you just have to create a file called
qvalues.datwith the appropriate q-values before running
Heine Larsen 2017-07-21