Description

Tool to analyze the charge evolution in a reaction pathway as derived from the nudged elastic band (NEB) method in VASP. The tool makes use of a few scripts included in other codes:

• bader2pqr.py,get_lattice.exe and get_lattice.f90 are part of vaspkit 0.73
• chgsum.pl is part of the VTST tools

baderVis
│   README.md
│   setup.sh
│
└───bin
│   │   baderProc.sh
│   │   baderSet.sh
│   │   baderVis.sh
│   
└───examples
│   └───volmer@Mg
│
└───templates
│   │   INCAR
│   │   runscript
│   
└───utilities
    │   bader.tcl
    │   bader2pqr.py
    │   chgsum.pl
    │   get_lattice.exe
    │   get_lattice.f90

Requirements

• Open Babel 2.4.1
• Bader analysis program
• VMD 1.9.3

Installation

1. Modify setup.sh and add the required system paths
2. Execute \.setup.sh
3. Add .../baderVis/bin to your PATH

Workflow

Visualize the Bader charge evolution of a NEB pathway

1. Start from the NEB folder structure

foo@bar:~$ ls
00 01 02 03 04 05 06 07 08 09

2. Set up Bader charge analyses

• Adapt the template files in .../baderVis/templates/ according to your system and cluster architecture
• Use baderSet.sh -m neb at the base of the NEB folder structure to create a subfolder bader and setup Bader charge anaylses for the respective NEB images.
• Run simulations

foo@bar:~$ baderSet.sh -m neb
foo@bar:~$ cd bader
foo@bar:~$ for i in `seq -w 00 09`; do cd $i; sbatch runscript; cd ..; done

3. Process the Bader charge analyses

foo@bar:~$ baderProc.sh -m neb

4. Visualize the Bader charges in the investigated system

foo@bar:~$ baderVis.sh

Visualize the Bader charges of a single Bader calculation

1. Start from the folder containing your optimized system

2. Set up a Bader charge analysis

• Adapt the template files in .../baderVis/templates/ according to your system and cluster architecture
• Use baderSet.sh -m single in your folder to create a subfolder bader and setup a Bader charge anaylsis for the system.
• Run simulation

foo@bar:~$ baderSet.sh -m single
foo@bar:~$ cd bader
foo@bar:~$ sbatch runscript

3. Process the Bader charge analysis

foo@bar:~$ baderProc.sh -m single

4. Visualize the Bader charges in the investigated system

foo@bar:~$ baderVis.sh