I have created a shell script (.run) that accepts the prefix for the names of the pictures as a parameter, and then calls gnuplot. However, for some reason, the picture is not saved. The code is:
#!/bin/sh
molecule=$1
echo "Plotting DFT-ADF PY results for $molecule"
echo "Tranmission plot (negatory SO)"
gnuplot -p << EOF
#!/usr/bin/gnuplot
set terminal epslatex size 5,3 color colortext
set output '$molecule_trans.tex'
plot cos(x) w l title 'cos(x)', sin(x) w l title 'sin(x)'
EOF
For my bachelor thesis I have to make several plots that are the same. Additionally, the computational cluster uses a qeueing system. For the purpose of being true to this system, I have created several shell scripts that automatically do stuff. In particular, about 45 simulations are called by the shell scripts, followed by a shell script that enters each simulations' directory and uses python files to evaluate the data into [.dat] files. Next, it should use a gnuplot file to make the graph. I use EPSLaTeX to make my figures, because it is so much nicer. However, in the current implementation this required me to manually edit the various latex files to rename the pictures.
In case you'll need more variables and do not want a $1, $2... mess:
You must use brackets around the variable name
set output '${molecule}_trans.tex'
because the underscore is a valid character for variable names, and bash looks for the variable $molecule_trans, see http://www.gnu.org/software/bash/manual/bashref.html#Shell-Parameter-Expansion.