legacy scripts

RECENT NOTE (MAY 2023) :  These are old workflows that are not currently  uploaded to a github repo.  

RECENT NOTE (SEPTEMBER 2015) : The development of this procedure has been greatly improved and reported in J. App. Cryst. (see below link, you may also download the reprint from this page as well)

<a href="http://dx.doi.org/10.1107/S1600576715013242">

Journal of Applied Crystallography, 2015, Volume 48, pages

1420-1428</a> 

lmp2diffuse.pl  -  useful PERL script for converting LAMMPS trajectory into the input required for use in the  DIFFUSE (only works for versions that have dynamic allocation of array sizes) 

Figure 1. MD Simulation of coordinates for Aspirin (8x15x8 unit cells under periodic boundary conditions) nano-crystal using DREIDING FF at 98K.

Figure 2. Output of diffuse scattering calculated from the MD simulations of an 8x15x8 unit cell aspirin crystal using the LMP2DIFFUSE.pl script. The top row shows outputs where the LAMMPS rigid body constraints applied thus only non-bonding potentials of the DREIDING FF are used.  The bottom row shows outputs when the rigid body constraint is turned off. Comparison of results to ZMC simulation  (see Chan et. al. Acta Cryst. (2010). B66, 696–707)