LAMMPS Large-Scale Atomic/Molecular Massively Parallel Simulator

LAAMPS – A simulator / interpreter for molecular dynamics simulation. Molecular dynamics – a simulation of a many body problem. Dynamics calculated based on Newton’s equations. Forces are calculated based on a given potential – classical or quantum mechanical. In my simulations, I use the Tersoff potential which takes the form: It has the general shape of a pair potential, but the coefficients are not constant. This is the concept of bond order – the strength of the bonds is not constant, but depends on local environment.

Bellow is the simulation I am running in my project: # Initialization units metal atom_style atomic boundary p p s newton on processors * * * # Create Atoms lattice diamond 3.57 region diamondBox block units lattice create_box 1 diamondBox create_atoms 1 region diamondBox mass *

# Potential Defs pair_style tersoff pair_coeff * * SiC.tersoff C # Simulation Settings neighbor 2.0 bin neigh_modify delay 3 timestep thermo_style custom step pe etotal temp thermo 10 dump diamond all atom out.diamond.*.xyz # Relaxation min_style cg minimize 1e-6 1e

# Dynamics fix frlax all nve fix tempControlH all temp/rescale run unfix tempControlH fix tempControlC all temp/rescale run unfix tempControlC # Simulation End unfix frlax undump diamond

Running a LAMMPS simulation on Tamnun Running the simulation is done using the mpirun command, utilizing the many cores Tamnun offers. As with all jobs on tamnun, scheduling is done using the PBS queueing system. #!/bin/sh #PBS -N DmndGrpht6 ##PBS -j eo #PBS -q simphony_q #PBS -l select=1:ncpus=4:mpiprocs=4 ##PBS_O_WORKDIR=$HOME/CompPhys PBS_O_WORKDIR=$HOME/DiamondGraphitized6 cd $PBS_O_WORKDIR mpirun -np 50 lmp_BigMechSim<in.diamondBig