1. LAMMPS Large-Scale Atomic/Molecular Massively Parallel Simulator

2. 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.

3. 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 0 9 0 9 0 9 units lattice create_box 1 diamondBox create_atoms 1 region diamondBox mass * 12.0107

4. # --------------------- Potential Defs ----------------- pair_style tersoff pair_coeff * * SiC.tersoff C # --------------------- Simulation Settings ------------ neighbor 2.0 bin neigh_modify delay 3 timestep 0.00001 thermo_style custom step pe etotal temp thermo 10 dump diamond all atom 100000 out.diamond.*.xyz # --------------------- Relaxation --------------------- min_style cg minimize 1e-6 1e-6 5000 10000

5. # --------------------- Dynamics ----------------------- fix frlax all nve fix tempControlH all temp/rescale 50 300.0 3500.0 0.02 1.0 run 1000000 unfix tempControlH fix tempControlC all temp/rescale 50 3500.0 300.0 0.02 1.0 run 100000000 unfix tempControlC # --------------------- Simulation End ----------------- unfix frlax undump diamond

6. 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