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NCPac (Network Characterization Package)

Posted by: Amanda Barnard

August 22, 2016

A host of modules for analysing the structure and connectivity of materials and nanostructure, in detail.

Each module takes as input atomic coordinate files (in a simple .xyz format), either as a single snaphot or a dynamic trajectory output from molecular dynamics code, and characterizes sets of different types of attributes.

modules
Characterization of gold nanorod and a perfect icosahedral gold cluster with the appropriate bulk and surface signature cells.

NCPac Modules

NCStats (for quantifying the average, and representative structures)

  • Bonding Environment statistics: Element-element bond fraction, 1st neighbour bonding environments, element-element average bond lengths
  • Signature cells characterization: Atomic environment characterization, atomic and global ordering parameters
  • Atomic coordination numbers: Elemental and total coordination histograms, elemental and total average coordination, coordination visualization

NCOrder (for characterizing the type of order)

  • Atomic packing fractions, and packing type characterization
  • Order parameters such as q6
  • Pre-crystallization ordering via spherical harmonic q6 bonds
modules
Dynamic packing characterization of the bulk and surface of heated nanorods; red, blue and yellow surface atoms represent (100), (110) and (111) atom environments while the green shows FCC planes which form upon deformation.
Opletal, G., et al. J. Phys. Chem. C, 115 (2011) 4375-4380.

NCChaos (for characterizing the type of disorder)

  • Fractal dimension
  • Global Lindemann Index
  • Local atomic Lindemann Index

NCHash (for fingerprinting)

  • Partial and total radial distribution functions, g(r)
  • Change in radial distribution functions, g(r)
  • Partial and total bond angle distributions
  • Topological matricies

The current serial version is implemented for CPUs, but future plans include a GPU version.   In additional to this, new modules are under development all the time, and the list will be updated as they become available.

For more information, contact the Principal Developer, Dr George Opletal