LAMMPS

I would like to share the codes required to perform an end-to-end molecular dynamics simulation, which will be useful to the novice researchers in the filed of atomistic simulations. I focus on simulating uniaxial tensile tests of a graphene sample in the LAMMPS molecular dynamics simulator, and I have attached two MATLAB scripts to create the input files for LAMMPS and to extract data from the LAMMPS output file.

Job Summary: The successful candidate will join an internationally collaboration team of scientists in the New Technologies – Research Centre at University of West Bohemia, Czech Republic. He or she will contribute to ongoing research projects and have the opportunity to propose, design, and carry out new research efforts within the broader scope of the group's research topics, which focuses on molecular dynamics simulations of piezo-electric phenomena at nanoscale and metal plasticity at nanoscale.

Job Summary: The successful candidate will join an internationally collaboration team of scientists in the New Technologies – Research Centre at University of West Bohemia, Czech Republic. He or she will contribute to ongoing research projects and have the opportunity to propose, design, and carry out new research efforts within the broader scope of the group's research topics, which focuses on molecular dynamics simulations of piezo-electric phenomena at nanoscale and metal plasticity at nanoscale.

A PhD position is open for summer or fall 2017 in Advanced Hierarchical Materials by Design Lab at Louisiana Tech University on multiscale modeling of hierarchical materials with an emphasis on nanocomposites. The candidates must have earned a M.Sc. degree in Mechanical Engineering or related fields and have a solid background in theoretical and computational mechanics, specifically continuum mechanics and finite element modeling, and need to have the knowledge of writing computer code (preferably using C/C++).

In the attached paper, recently appeared on Computer Physics Communications, we have proposed an analytical benchmark and a simple consistent Mathematica program for graphene and carbon nanotubes, that may serve to test any molecular dynamics code implemented with REBO potentials. By exploiting the benchmark, we checked results produced by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) when adopting the second generation Brenner potential, we made evident that this code in its current implementation produces results which are offset from those of the benchmark by a significant amount, and provided evidence of the reason.

 * This is a new open position * 

R. Rahman and J.T. Foster

The 6th International Conference on Computational Methods (ICCM2015) is slated to held in Auckland, New Zealand, on the 14th of July, 2015. It is my greatest pleasure to invite interested participants to submit their abstracts for presentation at a mini-symposium which I am organizing, titled:

MS-049 Computational Modelling of Biological and Biochemical Systems

For further information, please visit the official websites:

http://www.sci-en-tech.com/ICCM/index.php/ICCM2015/2015

Dr. Axel Kohlmeyer , one of the LAMMPS code developers, is organizing FREE School on Molecular Dynamics for Biomolecules and Nanomaterials at Temple University, Philadelphia (August 18th - 22nd, 2014)

 Detail Schedule is Available Here 

Atomistic Mechanism of Phase Boundary Evolution during Initial Lithiatio of Crystaline Silicon

I would like to share with you our recent paper published in the Journal of Applied Mechanics: J. Appl. Mech. 81(8), 081010 (Jun 02, 2014)

Abstract

http://dx.doi.org/10.1166/jctn.2014.3568

It is very important to visualize molecular dynamics (MD) trajectories since there are many aspects of MD simulations which are difficult to identify without a proper visualization tool. Improper bounday condition in MD is one of such examples. I use Visual Molecular Dynamics (VMD) to visualize my MD simulations. Some of my movies, created using VMD, are shown below.

In appendix A of my PhD thesis, I share a MATLAB code to get coordinates of carbon atoms in a graphene sheet. The code also generates the data file required for LAMMPS. In addition, I included a sample input and the corresponding output files from LAMMPS. I hope this will be useful for those who would like to learn MD simulations.

 A postdoctoral position with primary focus on molecular dynamics simulations is available immediately at Shenoy Research Group  under the direction of Prof. Vivek B. Shenoy .  We are looking for a strongly motivated candidate to work on modeling of nanomaterials and soft materials. The ideal candidate will have a background in materials science/computational physics with expertise in molecular dynamics simulations with LAMMPS or other packages.  This individual will have the opportunity to be directly involved in complimentary experimental investigations, both at Penn and our collaborators in industry. 

The National Nanotechnology Infrastructure Network’s computational project (NNIN/C) is a multi-university initiative, funded by the National Science Foundation (NSF) as part of NNIN, to establish a user accessible national computing resource for nanotechnology. This network is open to the academic and industrial research community and provides hardware resources and simulation tools dedicated to nanoscience
research.