LargeScale AtomicMolecular Massively Parallel Simulator LAAMPS A simulator interpreter for molecular dynamics simulation Molecular dynamics a simulation of a many body problem Dynamics calculated based on Newtons equations Forces are calculated based on a given potential ID: 431981
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LaMMPS
Large-Scale Atomic/Molecular Massively Parallel SimulatorSlide2
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.
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Bellow is the simulation I am running in my project:
# --------------------- Initialization -----------------
units metalatom_style atomicboundary p p snewton on
processors * * *# --------------------- Create Atoms -------------------lattice diamond 3.57region diamondBox block 0 9 0 9 0 9 units latticecreate_box 1 diamondBoxcreate_atoms 1 region diamondBoxmass * 12.0107Slide4
# --------------------- Potential
Defs
-----------------pair_style tersoffpair_coeff * * SiC.tersoff C# --------------------- Simulation Settings ------------
neighbor 2.0 binneigh_modify delay 3timestep 0.00001thermo_style custom step pe etotal tempthermo 10dump diamond all atom 100000 out.diamond.*.xyz# --------------------- Relaxation ---------------------min_style cgminimize 1e-6 1e-6 5000 10000Slide5
# --------------------- Dynamics -----------------------
fix
frlax all nvefix tempControlH all temp/rescale 50 300.0 3500.0 0.02 1.0run 1000000unfix tempControlH
fix tempControlC all temp/rescale 50 3500.0 300.0 0.02 1.0run 100000000unfix tempControlC# --------------------- Simulation End -----------------unfix frlaxundump diamondSlide6
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=$HOME/CompPhysPBS_O_WORKDIR=$HOME/DiamondGraphitized6cd $PBS_O_WORKDIRmpirun -np 50 lmp_BigMechSim<in.diamondBig