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SNIC & PRACE VASP Workshop
Workshop webpage:
https://www.nsc.liu.se/support/Events/VASP_workshop_2020/
Quick guide for working on Tetralith:
https://www.nsc.liu.se/support/Events/VASP_workshop_2020/quick_guide/
URL of this document:
https://hackmd.io/fM5moKdoT8idRQSWf1jD2Q
Icebreaker: Please write your name, where you work, and optionally what you're working on
General Questions (day 1)
Sagar Sarkar : What shall be the best value for NBANDS. I mean including more empty states in the calculation makes it more accurate (not sure though.. I have not checked). So shall we have to check for it like the convergence of it?
Sagar: Thank you very much.
grep NBANDS OUTCAR
Sagar : For Si dos plotting a very high k-mesh has been used 21x21x21. How to judge that correctly. I mean if I know the converged k-mesh for example say 17x17x17 for this system, then what will be the mesh size for the corresponding dos calculation.
Sagar : Okay. Thank you very much.
Hands-on Questions (day 1)
Anders: When we use ASE to find the volume of one atom, how do we know that the volume is the shape of a cube and not a sphere? E.g. we find a=(4*V0)^1/3.
grep volume OUTCAR
andgrep volume vasprun.xml
Sagar: For partial dos plot in p4vasp, what is the setting First band = 0, Last band = -1 ?
Sagar: In p4vasp, where is my Fermi energy level?? Specially when I plot the band structure?? Is it at 0.0 shifted or the Fermi energy printed at the OUTCAR file?
okay thank you.
Sagar : Then my band structure for Si says it is gapless / metalic. I expect at least a wrong band gap.
okay thank you.
Sagar : Some points regarding the band structure plotting of Si. When I compare with the band structure given in VASP Wiki, qualitatively it matches with it but there are quantitative differences. (a) There are more bands in my plot. (b) The Fermi energy is wrong. I need to substract the fermi energy of the SCF calculation to make it equivallent to the VASP Wiki example, but still the Fermi energy do not match. However I am using a lattice parameter 3.875 compared to 3.90 used in the Wiki.
okay thanks
Sagar : May be a small error. For DOS calculation of diamond Si, the INCAR suggests ICHARG = 2 in place of ICHARG = 11
okay thanks
General Questions (day 2)
Hands-on Questions (day 2)
Answer: You need to copy your CONTCAR to POSCAR and re-run the simulation - just a simple self-consistent run. This step is preferred if you want more accurate total energies.
Answer: depends how complicated your structure is. If you have a monoclinic structures, it may. Allow me to rephrase: whenever the cell shape changes a lot, it is good to do this step.
Answer: ISIF=3 is faster for the user in the sense that VASP will optimize the structure considering all degress of freedom (volume/shape/internal coordinates). I prefer to keep the volume fixed and optimize the positions and the cell shape, if needed, only.
Answer: You should allow the shape and positions to change for different volumes, as otherwise you may not find the equilibrium structure.
Answer: "If the change in the total (free) energy is smaller than EDIFFG between two ionic steps relaxation will be stopped. If EDIFFG is negative it has a different meaning: In this case the relaxation will stop if all forces are smaller than |EDIFFG| . This is usually a more convenient setting." The negative EDIFFG is typically preferred.
Sagar: Okay .. thanks
Answer: https://www.vasp.at/wiki/index.php/KSPACING
Notes:
Feel free to share any useful links.
KPAR
andNCORE
are the parallelization flags that influence the speed and memory requirements of a job the most. It is a good idea to start optimizing these for your simulation and then move to optimizingNSIM
. The memory requirements increase linearly with KPAR, but not as drastically as decreasing NCORE. The number of cores of the simulation has to be divisible by NCORE*KPAR. [NCORE - how many cores work on one orbital]The optimal NCORE, KPAR, and NSIM will depend a lot on the system you are trying to simulate, the number of k-points used, but also on the architecture of the cluster, the memory available on the node and how many cores or nodes you'd like to use.
You may read further here: https://cms.mpi.univie.ac.at/vasp/vasp/Parallelisation_NPAR_NCORE_LPLANE_KPAR_tag.html, but please keep in mind that this guide is very outdated. I always recommend you do a few tests (with a few), especially when starting out with a new system. You are going to save time on the long run.
tags:
workshop
VASP