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Wednesday, April 1, 2015

simple sample problems for LAMMPS

LAMMPS ("Large-scale Atomic/Molecular Massively Parallel Simulator") is a molecular dynamics program from Sandia National Laboratories.
LAMMPS is free, open-source software, distributed under the terms of the GNU General Public License GPL v2.

Molecular dynamics (MD) is a computer simulation of physical movements of atoms (and molecules  or particules) in the context of N-body simulation. The atoms are allowed to interact for a period of time, giving a view of the motion of the atoms. In the most common version, the trajectories of atoms and molecules are determined by numerically solving the Newton's equations of motion for a system of interacting particles, where forces between the particles and potential energy are defined by interatomic potentials or molecular mechanics force fields.

Rem: LAMMPS uses neighbor lists to keep track of nearby particles. The lists are optimized for systems with particles that are repulsive at short distances, so that the local density of particles never becomes too large.

The LAMMPS distribution includes an examples sub-directory with several sample problems. Each problem is in a sub-directory of its own. Most are 2d models so that they run quickly, requiring at most a couple of minutes to run on a desktop machine. Each problem has an input script (in.*) and produces a log file (log.*) and dump file (dump.*) when it runs. Some use a data file (data.*) of initial coordinates as additional input. A few sample log file outputs on different machines and different numbers of processors are included in the directories to compare your answers to. E.g. a log file like means it ran on P processors of machine "foo".

These are the sample problems and their output in the various

accelerate:  use of all the various accelerator packages
balance:  dynamic load balancing, 2d system
body:     body particles, 2d system
colloid:  big colloid particles in a small particle solvent, 2d system
comb:  models using the COMB potential
crack:  crack propagation in a 2d solid
deposit:  deposition of atoms and molecules onto a 3d substrate
dipole:   point dipolar particles, 2d system
dreiding: methanol via Dreiding FF
eim:      NaCl using the EIM potential
ellipse:  ellipsoidal particles in spherical solvent, 2d system
flow:  Couette and Poiseuille flow in a 2d channel
friction: frictional contact of spherical asperities between 2d surfaces
hugoniostat: Hugoniostat shock dynamics
indent:  spherical indenter into a 2d solid
kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
meam:  MEAM test for SiC and shear (same as shear examples)
melt:  rapid melt of 3d LJ system
micelle:  self-assembly of small lipid-like molecules into 2d bilayers
min:  energy minimization of 2d LJ melt
msst:  MSST shock dynamics
nb3b:     use of nonbonded 3-body harmonic pair style
neb:  nudged elastic band (NEB) calculation for barrier finding
nemd:  non-equilibrium MD of 2d sheared system
obstacle: flow around two voids in a 2d channel
peptide:  dynamics of a small solvated peptide chain (5-mer)
peri:  Peridynamic model of cylinder impacted by indenter
pour:     pouring of granular particles into a 3d box, then chute flow
prd:      parallel replica dynamics of vacancy diffusion in bulk Si
qeq:      use of the QEQ pacakge for charge equilibration
reax:     RDX and TATB models using the ReaxFF
rigid:    rigid bodies modeled as independent or coupled
shear:    sideways shear applied to 2d solid, with and without a void
snap:     use of SNAP potential for Ta
srd:      stochastic rotation dynamics (SRD) particles as solvent
snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
voronoi:  test of Voronoi tesselation in compute voronoi/atom

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