NWChem: Scripts

These may be useful for setting up your NWChem environment variables and cleaning up jobs.

Setting up scripts

First of all, you need to know how Linux uses scripts. A script is a bit of code that can be run. These two given here are what are called BASH scripts. They are a list of commands that you could type on the command line, but, instead, we have put them in a file and made the file executable. What do we mean by that? An executable file can be run just by typing its name on the command line - with one caveat: Linux needs to know where to find it. I suggest the following:

• In your home directory create a directory $HOME/bin/''' ('''$HOME is a variable that contains the name of your home directory. Try typing: echo $HOME):

$ cd
$ mkdir bin

• We will put all executable files in bin/.

• Next we will tell the bash shell that it should recognise any executable files in bin/. This is done as follows:

$ export PATH=$PATH:${HOME}/bin

• Now all executable files in bin/ will be available on the command line. But you will need to type the above command each time you log into //comanche//. This is tedious so we do one more step. Edit your .bashrc file to contain the above command. This file will be executed each time you log in, and so will the commands it contains. So, if all goes well, each time you log in, your PATH will be modified as above and all commands in $HOME/bin/ will be available for you to use.

Set up environment

$ cd 
$ vi .bashrc

Go into edit (insert) mode and include the following lines at the end of the file:

export NWCHEM_TOP=/home/alston/NWChem/6.1.1-ifort/
export NWCHEM_TARGET=LINUX64
export PATH=$PATH:${NWCHEM_TOP}/bin/${NWCHEM_TARGET}/

Save the file (unsure how to do this? See the Vim tutorial on the previous page). And execute it using

$ source .bashrc
$ echo $PATH

Does the PATH now include the path to NWChem?

Call this setup-nwchem.bash

bash

export NWCHEM_TOP=/home/alston/NWChem/6.1.1-ifort/
export NWCHEM_TARGET=LINUX64

export PATH=$PATH:${NWCHEM_TOP}/bin/${NWCHEM_TARGET}/

Save it to file. And make the file executable as follows:

$ chmod +x setup-nwchem.bash

Now, to set up your shell variables all you need to do is:

$ ./setup-nwchem.bash

Check to see if it has worked by typing

$ echo $NWCHEM_TOP

It should result in

/home/alston/NWChem/6.1.1-ifort/

Cleaning after an NWChem job

NWChem creates a lot of small temporary file. To erase them this script is handy:

bash(1)

job=$1
rm $job.b
rm $job.b^-1
rm $job.c
rm $job.p
rm $job.zmat
rm $job.movecs
rm $job.db
rm $job.drv.hess
rm $job.lagr

Save it to clean_nwchem.bash. And make it executable as before:

$ chmod +x clean_nwchem.bash

Now say you have run a job using

$ nwchem h2-sto3g.nw > h2-sto3g.out

you can clean up all the unnecessary files using

$ ./clean_nwchem.bash h2-sto3g