There are two sets of plotting code for AutoChem, one using IDL the other using Matlab.
IDL Plotting
To use the IDL version download the code from here. In your home directory unpack the contents of the plotting code by using:
tar -xvf idl-plotting.tar
This will create a directory called IDL. Add the IDL/lib/ directory to your IDL path. Then using the IDL interactive environment load the file IDL/PlotAssim_2/PlotAssim.pro. Compile it (CTRL+F5), then run it (F5) in the interactive environment. This will open a window, on the top bar of this window there will be a Data menu on the left. From this file menu select Data Assimilation Files. If required, use the Browse button in this window to navigate to the AutoChemV8/Output/ directory. Load in the output file, e.g. box.dat. Then from the Plot Type menu choose X - Data. This will let you plot ay variable against any other variable. You can use the Plot Style Menu to adjust the plot style as required.
Matlab Plotting
There is a simple Matlab plotting script available from here. In your home directory unpack the contents of the plotting code by using:
tar -xvf Matlab-plotting.tar
This will create a directory called Matlab-plotting. Change to this directory in Matlab. In this directory you will find a matlab script called plottraj.m. Edit the file on line 7 to give the correct path of your output file. Edit the file on line 12 to give the correct name of your output file.
There is a much more advanced Matlab version which automatically creates an entire cross linked web site. An example of this can be seen here. This version is not currently available for distribution.