VISUALIZATION OF DEFECTS With AViz

What is AViz?


AViz - Atomistic Visualization software


See AViz Home Page
For more instructions of using AViz see Rebecca Hihinashvili web site

Identify Defects


The method used here to identify defects in the perfect Graphene lattice is searching for every atom nearest neighbours and count them.
In a perfect lattice every atom has 3 neighbours. Less/more than 3 neighbours is a suspect for being a defect and therefore painted in a different color (gets a different atom type in the aviz xyz file).

The input file is the xyz dump file discussed in Molecular Dynamics page
This C++ code reads the input file, finds the number of nearest neighbours for each atom and gives different atom types as follows:

  • 'C' for 3 nearest neighbours (perfect lattice).
  • 'A' for less than 3 nearest neighbours (vacancies).
  • 'H' for more than 3 nearest neighbours (doped atoms).
  • Instructions:
  • To use C++ code open Make_xyz.tar and copy files to your working directory. You will also need to copy your xyz dump file (see example dump file dump_Graphene.xyz) to the same directory.
  • In the command line, type 'make all' to compile the program with your dump file.
  • Type 'MakeAViz' to run the program and get xyz AViz files
  • Run AViz by typing 'aviz' in the command line. To use AViz follow instruction with Rebecca Hihinashvili web site.

    Results


    Animation with AViz:

  • This animation shows the results of looking for defects in a Graphene lattice.
  • The yellow colored atoms are perfectly ordered in the Graphene lattice (each atom has 3 neighbours).
  • The blue colored atoms represent a defect in the lattice.
  • The lattice contains 400 atoms.
  • This example has fully periodic boundaries (in x,y directions).
  • The data file used can be found here. The data file was made with Lammps (more info).

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