There are two kinds of movies on this page. Some are from large-scale simulations performed with LAMMPS (or its predecessor codes). Others are simple animations of (mostly) 2d problems that illustrate the kinds of simulations that LAMMPS can be easily setup to run. This page has additional LAMMPS snapshots, but without animations.

The animations from large simulations were created using various visualization packages to read LAMMPS output.

brazing	brazing of two-metal system
mesoscale impact	Peridynamics mesoscale modeling of impact fracture
brittle failure	shear faults in a model brittle solid
flow on rough surfaces	stick/slip and polymer flow on rough surfaces
polyethylene	crystallization of polyethylene melt
polycrystalline melt	melting of polycrystalline metal
deformation under shock loading	deformation and void nucleation under shock loading
edge dislocation dynamics	dynamics of an isolated edge dislocation
cavitation	cavitation in liquid metal
nanoprecipitates in shock	nanoprecipitates and shock induced plasticity
Brazil nut	Brazil nut effect
nanowire3	ultra-thin Cu nanowire formation
nanowire2	Cu nanowire loading and unloading
nanowire1	Au nanowire formation and extension
silica pore flow	flow of water and ions thru a silica pore
helium bubbles	metal response to He bubble formation
rhodopsin	dynamics of rhodopsin protein in lipid membrane
carbon dioxide	CO2 escaping from binding pocket of RuBisCO protein
c-terminus	C-terminus of RuBisCO closing over binding pocket
nano-wheel	entropy-driven nano-motor
solidification	metal solidification
liquid crystal	liquid crystal conformations

The simple animations are from the examples sub-directory of the LAMMPS distribution and are described in this section of the LAMMPS documentation. Most of these animations were made using snapshots from the xmovie tool provided in the LAMMPS distribution and described in this section of the LAMMPS documentation.

colloid	large colloidal particles in 2d LJ solvent
crack	crack propagation in a 2d solid
dipole	point dipolar particles in 2d
ellipse	ellipsoidal particles in 2d LJ solvent
flow	Couette and Poiseuille flow in a 2d channel
friction	frictional contact of spherical asperities between 2d surfaces
indent	spherical indenter into a 2d solid
micelle	self-assembly of small lipid-like molecules into 2d bilayers
nemd	non-equilibrium MD (NEMD) shear of 2d LJ fluid
obstacle	flow around two voids in a 2d channel
pour	pouring of granular particles into a 3d box, then chute flow
shear	sideways shear applied to 2d solid, with and without a void

For all movies on this page, click on the small image to trigger the animation. You may need to slow-down/speed-up the MPEG playback on your machine. If your browser uses the xanim program to view MPEG movies, the speed-up key is "-" and the slow-down key is "=".

Brazing of two-metal system

This is work by Ed Webb (ebwebb at sandia.gov) at Sandia and Jeff Hoyt at McMaster University to study the interface between Cu and Ni under conditions of brazing to join the metals. A direct correlation between the free energy of the dissolution reaction and the kinetics of pore infiltration was observed.

The snapshots and movie show liquid Cu infiltration into a 10 nm Ni slit pore at 1750K. Cu and Ni atoms are rendered as light and dark spheres. In the figure, results are shown for the non-dissolutive (left) and the dissolutive (right) simulations at varying simulation times: (a) t = 400 ps, (b) t = 900 ps and (c) t = 1400 ps.

Molecular dynamics study of liquid metal infiltration during brazing, E. B. Webb III and J. J. Hoyt, Acta Materialia, 56, 1802-1812 (2008). (abstract)

Peridynamics mesoscale modeling of impact fracture

This is work of Mike Parks at Sandia (mlparks at sandia.gov). We implemented a Peridynamics (PD) model in LAMMPS to enable meso- and continuum-scale simulations of materials response. PD is a particle-based meshless continuum model that is well-suited for hi-deformation problems, such as impact and fracture scenarios. The theory underlying PD was developed by Stewart Silling at Sandia (sasilli at sandia.gov).

In these images a 1 cm ball (not shown) moving at 100 m/sec impacts a circular disk of brittle material composed of about 100K particles. The timestep is 1 nsec and the simulation runs for 200K timesteps.

This paper gives details of the implementation of PD in LAMMPS and more info about this test problem:

Implementing peridynamics within a molecular dynamics code, M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling, Comp Phys Comm, 179, 777-783 (2008). (abstract)

Shear faults in a model brittle solid

This is work due to Craig Maloney at CMU (craigmaloney at cmu.edu) and Mark Robbins at JHU. They studied fracture in an idealized 2d brittle material using Lennard-Jones potentials and bonds. Initial bonds were inferred from nearby atom pairs in a quenched system, then were allowed to break as the system was strained. When the solid is deformed, it can relax by breaking bonds, resulting in the damage patterns shown in these figures for a model undergoing shear with 200K particles. The two images plot the sine of the local rotation angle due to deformation in black/white and the autocorrelation of the local rotation in color, evidencing strong anisotropy. The right figure plays a movie of the induced damage.

Shear faults in a model brittle solid, C. E. Maloney and M. O. Robbins, Chaos, 17, 041105 (2007). (abstract)

Stick/slip and polymer flow on rough surfaces

This is work due to Nikolai Priezjev (priezjev at egr.msu.edu) and his group at Michigan State. The first study is of how fluid flow is affected by molecular-scale interactions at a solid-liquid interface. The solid surface is patterned with alternating stripes with no-shear and finite-slip attributes, a flow is induced in the liquid above the surface, and the dynamical structure of the fluid is observed. The second study is of short polymer chains flowing over a rough surface. The flow properties are a function of the corrugation wavelength and chain length. A fuller description of these results is given here and here

Rheological study of polymer flow past rough surfaces with slip boundary conditions, A. Niavarani and N. V. Priezjev, J Chem Phys, 129, 144902 (2008). (abstract)

Slip behavior in liquid films on surfaces of patterned wettability: Comparison between continuum and molecular dynamics simulations, N. V. Priezjev, A. A. Darhuber, S. M. Troian, Phys Rev E, 71, 041608 (2005). (abstract)

Crystallization of polyethylene melt

This is work of Richard Gee (gee10 at llnl.gov) and Naida Lacevic (lacevic2 at llnl.gov) at LLNL to study the onset of polymer crystallization via spinodal phase separation. The image (left) shows a snapshot of the polyethylene (PE) melt with an ordered polymer domain in a fringed micelle-like morphology. The movie (right) is a brief animation of the ordering transition from a large simulation of 5832 PE chains each with 768 monomers (4.5M united atoms), run for 45 nanoseconds.

Atomistic Simulations of Spinodal Phase Separation Preceding Polymer Crystallization, R. H. Gee, N. Lacevic, and L. E. Fried, Nature Materials, 5, 39-43 (2006). (abstract)

Melting of polycrystalline metal

This is work by Alexey Kuksin, Vladimir Stegailov, Genri Norman and Alexey Yanilkin (Joint Institute for High Temperatures, Russian Academy of Sciences) on the melting of polycrystalline metal under ultrafast isochoric heating.

The animation shows melting of polycrystalline copper with nanosized grains subjected to ultrafast isochoric bulk heating. Atoms are colored by their centro-symmetry parameter. Lighter atoms correspond to a more disordered local environment that allows distinguishing grain boundaries and melting front propagation. The visualization was done with the AtomEye program.

Surface melting of superheated crystals. Atomistic simulation study, A. Y. Kuksin, G. E. Norman, V. V. Stegailov, and A. V. Yanilkin, Comp Phys Comm, 177, 34-37 (2007). (abstract)

Deformation and void nucleation under shock loading

This is work by Vladimir Stegailov and Alexey Yanilkin (Joint Institute for High Temperatures, Russian Academy of Sciences) on plastic deformation and void nucleation in a single crystal of shock loaded bcc iron.

The picture shows successive stages of the shock-wave loading of a single crystal of bcc iron. During compression, pulse propagation plastic deformation takes place near the lateral open surfaces (only one of the two surfaces is shown because of the symmetry). It results in formation of inhomogeneties that act as void nucleation sites during spallation during the rarefaction wave. The visualization was done with the AtomEye program.

Structural transformations in single-crystal iron during shock-wave compression and tension: Molecular dynamics simulation, V. V. Stegailov and A. V. Yanilkin, J of Expt and Theoretical Physics, 104, 928-935 (2007). (abstract)

Dynamics of an isolated edge dislocation

This is work by Alexey Kuksin, Vladimir Stegailov and Alexey Yanilkin (Joint Institute for High Temperatures, Russian Academy of Sciences).

The animation shows the propagation of an isolated edge dislocation in fcc aluminum under shear deformation. Only atoms in the dislocation glide plane are shown. Atoms are colored by their centro-symmetry parameter (blue/yellow colors correspond to prefect fcc/stacking fault structures). The visualization was done with the AtomEye program.

Molecular-dynamics simulation of edge-dislocation dynamics in aluminum, A. Y. Kuksin, V. V. Stegailov, and A. V. Yanilkin, Doklady Physics, 53, 287-291 (2008). (abstract)

Cavitation in liquid metal

This is work by Timur Bazhirov, Genri Norman and Vladimir Stegailov (Joint Institute for High Temperatures, Russian Academy of Sciences) on homogeneous cavitation in a liquid metal under negative pressure.

The graph and the animation illustrate spontaneous formation of a bubble in liquid Pb under temperatures and pressures close to the spinodal. Atoms are colored by their coordination number. The visualization was done with the AtomEye program.

Cavitation in liquid metals under negative pressures. Molecular dynamics modeling and simulation, T. T. Bazhirov, G. E. Norman, and V. V. Stegailov, J Phys - Condensed Matter, 20, 114113:1-11 (2008). (abstract)

Nanoprecipitates and shock induced plasticity

This is work by (Alexey Kuksin, Vladimir Stegailov, Genri Norman and Alexey Yanilkin (Joint Institute for High Temperatures, Russian Academy of Sciences on the influence of nanoprecipitates on shock induced plasticity and subsequent fracture.

Animations show the propagation of weak (left) and strong (right) shock waves in an aluminum (grey atoms) single crystal doped with amorphous copper (yellow atoms) nanoclusters. Only atoms with broken symmetry in their local environment are shown (point defects, stacking faults, etc.) Only atoms in the rear half of the simulation box are visible (the cutting plane is marked). The final atomic structure in the strong shock case corresponds to the spallation stage and is colored according to potential energy of atoms. The visualization was done with the AtomEye program.

Atomistic study of nanoprecipitates influence on plasticity and fracture of crystalline metals, V. V. Stegailov, A. Yu. Kuksin, G. E. Norman, and A. V. Yanilkin, AIP Conf Proc "Shock Compression of Condensed Matter - 2007", 955, 339-342 (2007). (abstract)

Brazil nut effect

This is work of Jin Sun (jinsun at iastate.edu) with Francine Battaglia and Shankar Subramaniam at Iowa State to study polydispersity and boundary condition effects on segregation in granular flows. These give rise to the well-known "Brazil nut" phenomenon where shaking a can of nuts causes the larger nuts to rise to the top even though they are heavier. These movies are animations of long simulations (9M timesteps) of a cylindrical domain containing 7600 granular particles.

The large "Brazil nut" particle has a diameter 3x larger and a mass 224x greater than the small particles. The system on the left includes particle-wall friction and the large particle rises to the top after about 30 "shakes" of the system. The system on the right includes no particle-wall friction and the large particle does not rise.

Dynamics and structures of segregation in a dense, vibrating granular bed, J. Sun, F. Battaglia, and S. Subramaniam, Phys Rev E, 74 061307. (2006). (abstract)

Ultra-thin Cu nanowire formation

This is work of Vijay Sutrakar in Roy Mahapatra's group at the Indian Institute of Science on how ultrathin Cu nanowires form due to creation of pentagonal multi-shell nanobridge structures.

Formation of stable ultra-thin pentagon Cu nanowires under high strain rate loading, V. K. Sutrakar and D. R. Mahapatra, J Physics - Condensed Matter, 20, 335206 (2008). (abstract)

Cu nanowire loading and unloading

This is work of Wuwei Liang (gtg088c at mail.gatech.edu) in Min Zhou's group at Georgia Tech on how defects in Cu single-crystal nanowires form and propagate under various stress loading and unloading scenarios. Atoms in these movies are colored by their local centro-symmetry value. The movie was made with VMD.

This paper gives further details of the work and the group WWW site has more info:

Pseudoelasticity of Single Crystalline Cu Nanowires through Reversible Lattice Reorientations, W. W. Liang and M. Zhou, J Engr Materials and Technology, 127, 423-433 (2005). (abstract)

Au nanowire formation and extension

This is work due to Harold Park (harold.park at vanderbilt.edu) at Vanderbilt and Jon Zimmerman (jzimmer at sandia.gov) at Sandia to study how nanowires form under tensile loading at differing strain rates. The image and movie show Au atoms colored by their potential energy for an EAM potential. The movie was made with the Ensight visualization package.

Modeling inelasticity and failure in gold nanowires, H. S. Park and J. A. Zimmerman, Phys Rev B, 72, 054106 (2005). (abstract)

Flow of water and ions thru a silica pore

This is the work of Paul Crozier (pscrozi at sandia.gov) at Sandia to study how narrow cylindrical pores in silica can regulate the passage water and ions in the presence of a pressure gradient for purposes of desalination. The animation shows amorphous SiO2 in transparent red and yellow, ions in blue and cyan, and water molecules in red and white. Permeation can be calculated from such simulations as a function of pore diameter, pore length, and pressure gradient magnitude.

Metal response to helium bubble formation

This is work due to Jon Zimmerman (jzimmer at sandia.gov) at Sandia. It's a study of how helium bubble formation in a metal induces defect formation. As nanobubbles grow, they force the surrounding metal to respond. This movie is an animation of bubble growth in Pd. Each atom is colored by the value of its centro-symmetry parameter, which is a measure of local crystal order; only atoms at defects are visualized.

Rhodopsin in solvated lipid bilayer

This is work due to Paul Crozier (pscrozi at sandia.gov) and Mark Stevens (msteve at sandia.gov) at Sandia. It's a study of the conformational properties of rhodopsin in both dark- and light-adapted states.

The movie shows the loop and helix dynamics the rhodopsin protein in a lipid bilayer (red) surrounded by water (blue) and counter-ions. The movie was made using VMD.

Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: Coupling between local retinal and larger scale conformational change, P. S. Crozier, M. J. Stevens, L. R. Forrest, T. B. Woolf, J Molecular Biology, 333, 493-514 (2003). (abstract)

RuBisCO protein simulations

This is work due to Paul Crozier (pscrozi at sandia.gov) at Sandia. It's a study of the properties of the RuBisCO enzyme which is a ubiquitous protein involved in converting CO2 to organic forms of carbon and in the photosynthetic process. Sandia's Genomes-to-Life project is focused on a species of cyanobacteria that uses RuBisCO.

The first movie is an all-atom model (water not shown) with the binding pocket in color. Even though the pocket is closed, a CO2 molecule escapes, which was a surprise. The 2nd movie uses implicit solvent, freezes the protein background, and samples via parallel tempering to model the closing of the binding pocket by the C-terminus of the RuBisCO protein.

Entropy-driven nano-motor

This is work due to Colin Denniston (cdennist at uwo.ca) and Mark Robbins at JHU. It's a miscible binary fluid with the wall/fluid interactions set such that the top wall is wet by the yellow particles and the bottom wall by the red. This drives a continuous fluid flow in the system, which spins the tiny nano-wheel.

Molecular and continuum boundary conditions for a miscible binary fluid, C. Denniston and M. O. Robbins, Phys Rev Lett, 87, 178302 (2001). (abstract)

Metal solidification

This is work by Mark Asta's group at Northwestern and Jeff Hoyt (jjhoyt at sandia.gov) at Sandia. The movie shows the motion of a solidification front in Ni where the temperature of the system is carefully thermostatted so that the velocity of the interface can be accurately measured.

Atomistic simulation methods for computing the kinetic coefficient in solid-liquid systems, J. J. Hoyt, M. Asta, A. Karma, Interfacial Science, 10, 181 (2002). (abstract)

Liquid-crystal conformations

This was work with Ruth Pachter (pachterr%ml%wpafb at mlgate.ml.wpafb.af.mil) at Wright Patterson AFB. We studied the conformation of liquid crystal molecules in crystalline and non-crystalline forms. The movie shows the differences for the 2 cases.

Modeling a nematic liquid crystal, S. S. Patnaik, S. J. Plimpton, R. Pachter, W. W. Adams, Liquid Crystals, 19, 213-220 (1995). (abstract)

Colloids in solvent

Colloids of diameter 5 are put in a background solvent of Lennard-Jones particles (diameter 1). The big-big and big-small particle interactions are calculated via the pair_style colloid potential in a 2d system. The system is initialized very dilute and then run at constant pressure, so the simulation box shrinks and oscillates initially.

Crack propagation

Tensile pull on a 2d solid with 8K atoms to induce crack formation. There is an initial slit crack between the red and green blocks of atoms.

Point dipole particles

Particles with point dipoles interact via the pair_style dipole/cut potential in a 2d system. The viz is done by displahing two particles at each site where they are displaced slightly from each other in the direction of the dipole orientation.

Ellipsoids in LJ background

The pairwise GayBerne potential was used to model ellipsoidal particles in a solvent of spherical particles. This is a 2d simulation. The animation was performed with PyMol after converting LAMMPS output to PyMol format with the pymol_asphere tool.

Couette and Poiseuille flow

Friction between 2 surfaces

Indentation

The indenter pushes into the top surface and is then removed. Some healing of the lattice is observed after removal.

Micelle self-assembly

The 3-atom lipids have a hydrophilic head that likes solvent and a hydrophobic tail that doesn't like solvent.

Non-equilibrium MD (NEMD) shear of a LJ fluid

A 2d Lennard-Jones fluid is sheared in a non-orthogonal non-orthogonal (triclinic) box using the fix deform commmand. The yellow band of particles disorders over time. These images were made with Raster3d.

Flow around an obstacle

Granular pouring and chute flow

Side view of 3d container into which particles are poured. Gravity is then set at an angle to induce chute flow.

Shear of a solid

Fixed-end shear of a quasi-2d solid (thin and periodic in the z dimension). The presence of a void enables stress relaxation without defect formation in the bulk.

LAMMPS Movies