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Tutorials: AIRSS

Learning Objectives

Getting Started

  1. Log on to arcus-b and copy the AIRSS examples to your home directory. You also need to copy over a new bash_profile:

cp /home/jr_yates/jryates/WORKSHOP/bash_profile_castep $HOME/.bash_profile
mkdir ~/AIRSS
cp ~jryates/WORKSHOP/airss_ex2.tgz ~/AIRSS
cd AIRSS
tar -xvf airss_ex2.tgz

You also need to edit the file ~/.bashrc so the last line reads

source ~/.bash_profile

  1. AIRSS calculations can be performed using massive parallelisation. However for this practical we will just use a single node containing 16 cores. Log into an arcus-b node by requesting an interactive session from the scheduler:
    salloc --reservation=castep_2017 -c 16 srun --x11 --pty --preserve-env /bin/bash
  2. Detailed instructions for the examples can be found in:
    ~/AIRSS/Examples/README
  3. If you would also like to see a structure's convergence progress during a CASTEP you can use:
    xmgrace *.conv
    however you must first add the grace module.
    module load grace

Spawn

AIRSS comes with its own job management tool spawn which is designed to set off thousands of AIRSS calculations at once. When a command is executed through spawn, the ~/.spawn file is read containing information about the nodes the calculation should be performed on. To get a flavour of the power of this, create a file in your home directory called ~/.spawn and give it the single line.
localhost slots=16 root= You can run AIRSS on each core of the arcus-b node you are logged into by using:
spawn airss.pl <airss arguments>

Furthermore, the stopairss command will kill all of the AIRSS jobs running on the nodes listed in the spawn file.

Visualization

VESTA has been provided to visualize the structures on the workstations. You will find it in the H drive. AIRSS res files can be read directly by VESTA. Use scp to copy them to your local machine for VESTA to read. The user interface is fairly self explanatory. Useful shortcuts: Ctrl-B to open the Bonding dialogue box and Ctrl-Shift-B to open the Boundary dialogue box. Further details can be obtained from: http://jp-minerals.org/vesta/en/. AIRSS res files are in the shelx format so can easily be converted to input formats for your favourite visualization package using http://openbabel.org.

Basic AIRSS Commands

Cheat Sheet

Further information

Debugging

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Page last modified on August 21, 2017, at 03:04 PM