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IOP Chester 2019

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Lectures

Allocating Computing Nodes and Environment Setup

An interactive shell should be allocated after login. The following command allocates an interactive node with 8 CPUs for 90 minutes

qsub -A y15 -q <queue> -IVl select=1:ncpus=8,walltime=01:30:00,place=scatter:excl

Here <queue> is R1179799 for the 14:00-15:30 and R1171601 for the 16:00-17:30 session, respectively. After successful allocation, one has to setup the environment as follows.

To have access to the vasp binaries, the corresponding module has to be loaded into the environment. Furthermore, the job scripts found in the tutorial tar files (job.sh, doall.sh, etc) work only if the environment variables "vasp_std, vasp_gam, vasp_ncl" are defined. Enter following commands in the terminal window after login, to setup up the environment.

module load vasp/5.4.4-intel18-impi18-wannier90_1.2
export vasp_ncl="mpirun -ppn 8 -np 8 /lustre/home/y07/vasp5/5.4.4-intel18-impi18/bin/vasp_ncl"
export vasp_gam="mpirun -ppn 8 -np 8 /lustre/home/y07/vasp5/5.4.4-intel18-impi18/bin/vasp_gam"
export vasp_std="mpirun -ppn 8 -np 8 /lustre/home/y07/vasp5/5.4.4-intel18-impi18/bin/vasp_std"

Submitting jobs

Alternative to an interactive shell, one may submit jobs to the cluster as follows

qsub vasp.job

where the jobfile "vasp.job" reads

#!/bin/bash --login

#PBS -N VASP-Test
#PBS -l select=1:ncpus=36
#PBS -l place=scatter:excl
#PBS -l walltime=00:30:00
#PBS -A y15 

cd $PBS_O_WORKDIR 
module load vasp
mpiexec_mpt -ppn 36 -n 36 vasp_std | tee vasp.out

Install sumo for post processing

Sumo[1] can be used to plot band structures and density of states. A local installation is possible with following commands

module load anaconda/python3
pip install --user --upgrade pip
pip3 install --user --upgrade scipy
pip3 install --user --upgrade numpy
pip3 install --user sumo

Tutorials

All tutorial files can be extracted to your home folder as follows

cd ~ ; mkdir examples 
cd ~/examples
cp /lustre/home/shared/VASP_Workshop_Chester/examples.tgz .
tar -xvf examples.tgz

Electronic structure examples are located on the following folder on cirrus:

/lustre/home/shared/VASP_Workshop_Chester/COonNi111.zip

For the beginners: A short introduction to the common Input and Output files.

Further Examples

Optimisation in the bulk

Nudge Elastic Band Method and (constrained) Molecular Dynamics

Magnetism in NiO

Surfaces and Interfaces