Hello, thank you for your help.
So first of all I have a lot of .gjf files (Gaussian acceptable format) and I want to run Gaussian on all of them to get energy log files. I think that's a standard procedure in computational chemistry. I've got about 3000 of them so obviously I can't do them individually without making mistakes.
So if I were to run Gaussian on an individual file I would do it like this:
g09 5DKXA_TRP-554-A_ASP-443-A.log &
That basically means import ( < ) a file into Gaussian (g09), and redirect the output with errors ( &>) to a log file after Gaussian does its thing, and then finally run Gaussian in the background to free up the terminal ( & ).
So if I wanted to do this operation on every *.gjf file how would I do it?
Thank you very much for your help!
You can simply tell the shell to execute the calculations one after the other. I'm attaching a script that I have been using for that purpose. It will get the names of all ".gjf" files in the current directory, assign the output filename, check if an output file already exists (to avoid overwriting old results if you rerun the script) and call Gaussian on the input. Put the script in the same directory as your input files, give yourself execution rights for it, and have fun.
Note that it's very important that you don't drop g09 to the background (&) in this script! Otherwise the for loop would start all 3000 calculations at once, and you will obviously have a very bad time.
(The Windows version of Gaussian provides batch capabilities for things like this. I don't think that exists in the Unix version, unfortunately.)
Thank you very much for the script!
It created the log files, but there is an issue. The log files are empty because the g09 program wasn't properly called. Maybe the bash script needs to have the location of the g09 program specified or something.
Okay, I'm pretty sure it's working now! I just specified the program g09 home location with directory slashes. I had to check where it lived with ...
$ which g09
Thanks so much!
Oh, right... I just realized I may have cut out too much from my own script file before uploading it. You will need to tell the script where the Gaussian executable files are located. Try adding below the "#!" line:
export GAUSS_EXEDIR=(path to your gaussian installation)
See if that helps.
You're welcome, great to hear that you got it to work! :) My philosophy about shell scripts is generally "If it's stupid, but it works, then it's not stupid."
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