The script run_pbe.lsf is used for the high-throuput calculation in MatHub.

Web page of the database: www.mathub3d.net

The workflow of this script is as below:

The input of this script is POSCAR and INCAR.*, then you can submit this script to your server.

It is written in Shell script, so it is easy to use.

Before using it, you should make sure some dependent scripts is work.

Generate POTCAR file. Need to modify the PAW file path and POTCAR folder path before use.

• Input

  POSCAR: Elements row in POSCAR is needed.

  PAW: This file contains all elements and corresponding POTCAR name.

• Output

  POTCAR

GETINCAR is for LDA+U calculations. Need to modify the LDAU file path before use.

• Input

  POSCAR: Elements row in POSCAR is needed.

  LDAU: This file contains elements and corresponding U value.

• Output

  Add tags for LDA+U calculation to ICNAR file.

Generate KPOINSTS.band file. The KPOINSTS.band file is a line mode K-points file used for band calculation. This script need phonopy-1.12 to get space_group_number (the variable ${spacegroup} in the script need this value) and space_group_type (for variable ${symbol}). (For different versions of phonopy, you need to modify the script to get the correct value.)

• Input:

  POSCAR

• Output

  KPOINTS.band: Copy KPOINTS.band to KPOINTS to run band calculation.

Get lattice parameters from POSCAR.

• Compiler:

  ifort -o lattice_parameters lattice_parameters.f90

• Input:

  POSCAR

• Output:

  Lattice parameters.

Get band gap.

• Compiler:

  ifort -o getgap getgap.f90

• Input:

  OUTCAR, EIGENVAL

• Output:

  Band gap.

  gap.txt file contans the values and k-points for VBM and CBM.

Density of states (DOS) analysis. The needed file PROCAR can be get by add tag 'LORBIT=11' to INCAR.

• Compiler:

  make dospar

• Input files:

  EIGENVAL, OUTCAR, PROCAR

• Input parameters (after running dospar, you need to enter some parameters. Here is a running example):

  The energy for zero point is: (# fermi energy)
  
  -1.90
  
  The energy starts from (with respect to zero point):
  
  -3
  
  The energy step is:
  
  0.01
  
  How many points in this energy step? 
  
  600
  
  Tell the temperature entering the Fermi-Dirac function: (# change the temperature can generate the projected DOS with different smearing.)
  
  300
  
  What scissors for band gap?(T/F)
  
  F
  
  Want to split the d orbitals(i.e. t2g & eg)? (T/F)
  
  T
  
  Want partial dos for special atoms?(T/F)
  
  F
  
  Want partial dos for each type of atoms? (T/F)
  
  T

• Output:

  tdos.txt: total DOS.

  element.txt: PDOS for each element.

For Bader Charge analysis. For more infomation please refer to http://theory.cm.utexas.edu/henkelman/code/bader/

• Input:

  AECCAR0, AECCAR2, CHGCAR

• Output:

  ACF.dat

Calculate electrical transport properties. For more infomation to this softerware, please refer to https://github.com/yangjio4849/TransOpt.git

After ensuring that all the above dependent scripts and programs are available, modify the job management system and the VASP in the script to adapt to your server. Then you can submit the script.

For example:

$ ls
vasp_pbe.lsf POSCAR INCAR.SCF.pbe  INCAR.band.pbe  INCAR.relax.coarse.pbe  INCAR.relax.fine.pbe  INCAR.test.pbe  INCAR.test_ferro.pbe
$ bsub < vasp_pbe.lsf