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# LAMMPS Molecular Dynamics Simulator 
http://lammps.sandia.gov/


This directory contains Peter Wirnsberger's contributions to the open-source software package LAMMPS. 
All source files and examples provided were copied from the LAMMPS (20Oct16) version and are licensed under the GPL-v2.
For more information on licensing, I refer to the information provided in 'LICENSE' in the root directory of the LAMMPS distribution.
For the latest version of the source files and information on how to compile the code, please visit 
the LAMMPS homepage and download the lastest archive.


ehex:  
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Implementation of the eHEX/a algorithm proposed by Wirnsberger et al. (2015), 
which is available under http://dx.doi.org/10.1063/1.4931597 or https://arxiv.org/abs/1507.07081.

The source files are located in ehex/src and a several examples of LAMMPS input scripts along
with input and output files are provided in the directory ehex/examples. 


Abstract of the paper:

We propose a new algorithm for non-equilibrium molecular dynamics simulations of thermal gradients. 
The algorithm is an extension of the heat exchange algorithm developed by Hafskjold et al. [Mol. Phys. 80, 1389 (1993); 81, 251 (1994)], 
in which a certain amount of heat is added to one region and removed from another by rescaling velocities appropriately. 
Since the amount of added and removed heat is the same and the dynamics between velocity rescaling steps is Hamiltonian, 
the heat exchange algorithm is expected to conserve the energy. However, it has been reported previously that the original version 
of the heat exchange algorithm exhibits a pronounced drift in the total energy, the exact cause of which remained hitherto unclear. 
Here, we show that the energy drift is due to the truncation error arising from the operator splitting and 
suggest an additional coordinate integration step as a remedy. The new algorithm retains all the advantages of the original one 
whilst exhibiting excellent energy conservation as illustrated for a Lennard-Jones liquid and SPC/E water. 


rattle: 
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The source files provided in rattle/src implement the RATTLE algorithm to keep small molecules rigid
in molecular dynamics simulations [J. Comput. Phys. 52, 24 (1983)]. 

The RATTLE algorithm is also employed by the eHEX/a algorithm and more information on how this is accomplished can 
be found in the ehex paper (see above).