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.
| silica pore flow | flow of water and ions thru a silica pore |
| Brazil nut | Brazil nut effect |
| polyethylene | crystallization of polyethylene melt |
| nanowire2 | Cu nanowire loading and unloading |
| nanowire | Au nanowire formation and extension |
| stick/slip flow | shear flow on a corrugated slip/stick surface |
| 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 "=".
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.
4.0 Mb AVI movie
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.
3.5 Mb QuickTime movies
This paper gives details of the work:
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)
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.
Image and 3.5 Mb QuickTime movie
This paper gives full details of the work:
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)
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.
1.0 Mb AVI movies of loading (left) and unloading (right)
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)
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.
5.0 Mb QuickTime movie
This WWW page gives further details of the work, as does this paper:
Modeling inelasticity and failure in gold nanowires, H. S. Park and J. A. Zimmerman, Phys Rev B, 72, 054106 (2005). (abstract)
This is work due to Nikolai Priezjev (priezjev at princeton.edu) at Princeton. It's a study 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. This movie shows the varying structure above the 2 regions.
2.0 Mb animated GIF movie
The write-up on this page gives further details, as does this paper:
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)
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.
2.2 Mb movie
This WWW site and this research highlight have further details.
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.
6.4 Mb movie
This paper and related ones on this page have further details:
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)
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.
These movies were made with VMD.
5.5 Mb and 5.1 Mb movies
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.
2.0 Mb QuickTime movie
This paper has further details:
Molecular and continuum boundary conditions for a miscible binary fluid, C. Denniston and M. O. Robbins, Phys Rev Lett, 87, 178302 (2001). (abstract)
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.
4.2 Mb movie
This paper and related ones on this page have further details:
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)
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.
1.5 Mb movie
This paper has further details:
Modeling a nematic liquid crystal, S. S. Patnaik, S. J. Plimpton, R. Pachter, W. W. Adams, Liquid Crystals, 19, 213-220 (1995). (abstract)
Input script for this problem.
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.
3.3 Mb QuickTime movie
Input script for this problem.
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.
2.0 Mb movie
Input script for this problem.
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.
4.2 Mb QuickTime movie
Input script for this problem.
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.
3.3 Mb QuickTime movie
Input script1 and script2 for these problems.
2.0 Mb and 3.1 Mb movies
Input script for this problem.
Two half-sphere asperities rub against each other.
1.6 Mb movie
Input script for this problem.
The indenter pushes into the top surface and is then removed. Some healing of the lattice is observed after removal.
1.4 Mb movie
Input script for this problem.
The 3-atom lipids have a hydrophilic head that likes solvent and a hydrophobic tail that doesn't like solvent.
2.7 Mb movie
Input script for this problem.
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.
1.9 Mb QuickTime movie
Input script for this problem.
Two spherical voids in a flowing atomic fluid.
1.7 Mb movie
Input script for this problem.
Side view of 3d container into which particles are poured. Gravity is then set at an angle to induce chute flow.
2.3 Mb movie
Input script1 and script2 for these problems.
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.
1.7 Mb and 1.7 Mb movies
