If the software that you are using is executable from the command line terminal then you can have a Perl script make those function calls in the terminal with the system() function or back ticks ``. You should be able to integrate all your commands into one script by creating functions for each of your simulation calls with those system calls. You could run into errors where if one simulation fails then your program crashes, so you get around that with error checking the status of your variables.

If you want to input the name of a file to analyze for your functions, then use or @ARGV, depending upon if you want to input the file after the script or when you call the perl script from the terminal. You could also list an array of files to analyze and loop through them.

If you need help, I can help you. However, I am not at a position where I can tell you if the physics assumptions are correct.

Thanks, Adron Ung for your help.

Do you think that will work or are you just being polite? Let me know how it goes.