LAMMPS 2-1

LAMMPS TutorialCNF Fall Workshop, Oct 2006

Steve Plimpton, Sandia National Labssjplimp@sandia.gov, lammps.sandia.gov

1. Input and Output2. 11 example problems3. Parameters to change4. Adding a "feature" to LAMMPS

LAMMPS 2-2

LAMMPS Philosophy

• LAMMPS is a parallel MD kernelkeep the kernel simple and fastavoid non-parallel operations

• LAMMPS doesn't do many pre- and post-processing tasks:other codes already do itlimited development resourcesaren't parallel operations

LAMMPS 2-3

LAMMPS doesn't ...

• Build molecular systemsuse a builder code or write out your own config filecan build lattices, grain boundaries, etc

• Assign force-field coefficients auto-magicallyonly hard for molecules, use another MD code

• Compute lots of diagnostics on-the-flyoften better left to post-processingyou can add it if you want it

• Visualize your outputmany packages do thisVMD, Rasmol, Raster3d, AtomEye, Ensight, ...

• LAMMPS package includes auxiliary tools for some of these tasks• Python-based Pizza.py package distributed separately:

www.cs.sandia.gov/~sjplimp/pizza.html

LAMMPS 2-4

LAMMPS has no GUI

LAMMPS 2-5

LAMMPS Input

• Reads an input script (ASCII text)• One command per line• Command name + arguments

atom_style molecularread_data water.datafix 1 all nverun 10000

• lammps.sandia.gov has link to command doc pages• examples sub-dir has many sample input scripts

LAMMPS 2-6

LAMMPS Output

• log.lammps contains what is printed to screenthermodynamic info

• "dump" command outputs snapshots of atom propertiesdefault format is simple: id, type, x, y, zother supported formats: XYZ, DCD, XTCconversion tools: PDB, Ensight, XYZ, VTK

Rasmol, Raster3d, SVG, etc

LAMMPS 2-7

Viz of LAMMPS Snapshots

• xmovieauxiliary tool distributed with LAMMPSvery fast, simple viz2d projection of 3d systemsreads default dump format% /usr/local/bin/xmovie -scale dump.melt

• VMDlearning about this afternoon3d hi-quality vizdump 1 all xyz 100 dump.melt% vmd (load xyz file thru GUI)

LAMMPS 2-8

Running an Example Problem

• All problems in examples sub-directory• Copy entire dir to your space to run & modify

cp -r /usr/local/bin/lammps/examples/indent .cd indent; cp /usr/local/bin/lmp_linux .

• Each example problem reads:in.* input scriptdata.* input data file (optional)

• % lmp_linux -echo screen < in.indent (serial)• % mpirun -np 2 lmp_linux -in in.indent (parallel)• Each example problem produces:

log.lammps logfile output (see examples)dump.* series of snapshots

• LAMMPS doc pages at /usr/local/bin/lammps/doc/Manual.htmlsee Section_commands.html

• % /usr/local/bin/xmovie -scale dump.indent

LAMMPS 2-9

11 Example Problems

• crack: crack growth in a LJ crystal (2d)• flow: Couette/Poisseuille flow between walls (2d)• friction: rubbing of 2 irregular surfaces (2d)• indent: crystal response to spherical indenter (2d)• melt: LJ lattice (3d)• micelle: self-assembly of tiny lipid molecules (2d)• min: energy minimization of LJ melt (2d)• obstacle: flow around obstacles (2d)• peptide: small peptide chain in water (3d)• pour: granular particle pour and flow (2d/3d)• shear: shear of a metal slab with void (quasi-3d)

LAMMPS 2-10

Crack Problem

• Tensile pull on 2d LJ solid• Initial slit crack between red/green

neigh_modify exclude 2 3• Uniform gradient pull

velocity ramp commandelse shock waves or worse

• Need large system & slow pullelse defects other than crack

• Biggest computational test problemrun in parallel

• Options to play with:pull ratepair-wise cutoffturn off velocity rampchange NULL 0.0 in fix 2

LAMMPS 2-11

Flow Problems

Couette flow Poisseuille flow

Options to play with: wall velocity, force kick, temperature

LAMMPS 2-12

Friction Problem

• 2 non-uniform surfaces2d LJ hex lattice

• Region commandsto build geometry

• Options to play with:add/change asperities

sizeseparationshape

x-velocitymultiple passes

LAMMPS 2-13

Indent Problem

• 2d LJ solidperiodic in xfree upper y surface

• Spherical indenterdownward push, remove

• Defect creation and healing• Options to play with:

speed & depth of indentsize of indentersize of system

LAMMPS 2-14

Melt Problem

• 3d LJ solidperiodic in x,y,z

• Melt an fcc lattice• Options to play with:

temperaturefix nvt or npt

LAMMPS 2-15

Micelle Problem

• Simple lipid model• 2d self-assembly

vesiclesbilayers

• Hydrophilic head• Hydrophobic tail• Monomer solvent• Options to play with:

timestep size# of timestepspair-wise coeffsturn off special bondssystem size: micelle2d.f

LAMMPS 2-16

Minimization Problem

• Melt of 2d LJ solid• Followed by

energyminimization

• Returns to hexlattice butwith defects

• Options to play with:size of systemmelt temperatureminimize tolerance

LAMMPS 2-17

Obstacle Problem

• 2d LJ flow around obstacle(s)• Poisseuille “kick” added to atoms

pressure-gradient flow• Top surface applies pressure• Obstacle creation

delete_atoms commandfix indent command

• Options to play with:size of force kicksize of systemsize & position of obstaclesadd a new obstacle

LAMMPS 2-18

Peptide Problem

• Full-atom model of 5-mer Met-enkaphalinCHARMM force-field, PPPM CoulombicsSHAKE bond/angle constraints

• 2 fmsec timestep so can’t simulate for long!• To see bonds: xmovie –scale dump.bonds dump.peptide• Options to play with:

timestep size, turn off SHAKE, add fix drag command

LAMMPS 2-19

Pour Problem

• 3d (or 2d) pour of granular particlesinto empty boxunder gravity

• Change gravity directionto induce chute flow

• Options to play with:vol fraction for pour# of particles to pourspring constant for atomsdirection of gravity

LAMMPS 2-20

Shear Problems

• Fixed-end shear in fcc NiEAM potentialquasi-3d

non-periodic XY slabthin in Z, periodic

• Defect formation with andwithout void

• Options to play with:size of systemshear rateturn off velocity rampcomment in/out voidadd another void

LAMMPS 2-21

Extra Credit: Add new Feature to LAMMPS

• Grab your own copy of LAMMPS source filescp -r /usr/local/bin/lammps/src .

• Add 2 new files with your feature (from lammps/examples/triangle)region_triangle.cpp & region_triangle.halso region.cpp (one extra line needed, my mistake)

• Edit style_user.hinclude "region_triangle.h" #ifdef RegionIncludeRegionStyle(triangle,RegTriangle) #ifdef RegionClass

• Re-build LAMMPSmake linux

• Try it outedit examples/obstacle/in.obstacle to use triangular obstaclesedit examples/friction/in.friction to use triangular asperitiesregion 1 triangle x1 y1 x2 y2 x3 y3run and visualize

LAMMPS 2-22

region_triangle.cpp

• 35 lines of code

• constructor(int narg, char **arg)reads arguments: x1 y1 x2 y2 x3 y3determines extent = bounding box

• match(double x, double y, double z):determine if (x,y) is inside triangle (2d only)3 positive cross products inside

LAMMPS 2-23

Region triangle for Friction Problem

• examples/friction/in.friction• Replace: region lo-asperity sphere 32 7 0 8

region hi-asperity sphere 18 15 0 8• With: region lo-asperity triangle 26 7 32 14 38 7

region hi-asperity triangle 12 15 24 15 18 8