examples using the visualize code
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to investiagte special configurations you could use something like:

./visualize -d saves/dumbbell -nll -2.4 -2.4 -2.4 -fur 3.8 3.8 3.8 \
            -b -2.03 -2.03 -2.03 3.39 3.39 3.39 -r 0.6 -c 1.5 -15.0 1.5

this visualizes the atoms located in the box specified by -fur and -nll and
draws a box according to the -b values by looking at the atoms which have
a radius of 0.6 angstroms from the location determined by the -c coordinates.