IOP Chester 2019
Lectures
- DFT, PW, and PAW: "VASP: The basics. DFT, plane waves, PAW, ...".
- Hybrid functionals: "VASP: Hybrid functionals".
- Beyond DFT: RPA: "VASP: beyond DFT. The Random-Phase-Approximation".
- Geometry optimization: Tutorial on geometry optimisation by Dr. jonathan Skelton.
- Performance: "VASP: running on HPC resources".
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 4 hours
qsub -A y15 -q R1171598 -IVl select=1:ncpus=8,walltime=02:00:00,place=scatter:excl
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
For the beginners: A short introduction to the common Input and Output files.
- Atoms and Molecules
- Simple Bulk Systems
- A bit of Surface Science
- Hybrid Functionals
- Optical Properties and Dielectric Response
- The Random-Phase-Approximation: GW and ACFDT
- The Bethe-Salpeter equation
- Magnetism