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    Lammps Tutorial Oct06

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    euser999
    The document provides an overview of the LAMMPS molecular dynamics simulation software. It describes LAMMPS' philosophy of keeping the parallel kernel simple while avoiding non-parallel operations. The document outlines what tasks LAMMPS does not perform such as building molecular systems or assigning force fields. It also summarizes LAMMPS' input/output features and provides examples of 11 sample problems that can be run in LAMMPS. The document concludes by describing how users can add new features to LAMMPS.

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    Lammps Tutorial Oct06

    Uploaded by

    euser999
    3K views23 pages
    The document provides an overview of the LAMMPS molecular dynamics simulation software. It describes LAMMPS' philosophy of keeping the parallel kernel simple while avoiding non-parallel operations. The document outlines what tasks LAMMPS does not perform such as building molecular systems or assigning force fields. It also summarizes LAMMPS' input/output features and provides examples of 11 sample problems that can be run in LAMMPS. The document concludes by describing how users can add new features to LAMMPS.

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    The document provides an overview of the LAMMPS molecular dynamics simulation software. It describes LAMMPS' philosophy of keeping the parallel kernel simple while avoiding non-parallel operations. The document outlines what tasks LAMMPS does not perform such as building molecular systems or assigning force fields. It also summarizes LAMMPS' input/output features and provides examples of 11 sample problems that can be run in LAMMPS. The document concludes by describing how users can add new features to LAMMPS.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    3K views23 pages

    Lammps Tutorial Oct06

    Uploaded by

    euser999
    The document provides an overview of the LAMMPS molecular dynamics simulation software. It describes LAMMPS' philosophy of keeping the parallel kernel simple while avoiding non-parallel operations. The document outlines what tasks LAMMPS does not perform such as building molecular systems or assigning force fields. It also summarizes LAMMPS' input/output features and provides examples of 11 sample problems that can be run in LAMMPS. The document concludes by describing how users can add new features to LAMMPS.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 23

    LAMMPS 2-1

    LAMMPS Tutorial CNF Fall Workshop, Oct 2006 Steve Plimpton, Sandia National Labs [email protected], lammps.sandia.gov 1. 2. 3. 4. Input and Output 11 example problems Parameters to change Adding a "feature" to LAMMPS

    LAMMPS 2-2

    LAMMPS Philosophy

    LAMMPS is a parallel MD kernel keep the kernel simple and fast avoid non-parallel operations

    LAMMPS doesn't do many pre- and post-processing tasks: other codes already do it limited development resources aren't parallel operations

    LAMMPS 2-3

    LAMMPS doesn't ...


    Build molecular systems use a builder code or write out your own cong le can build lattices, grain boundaries, etc Assign force-eld coefcients auto-magically only hard for molecules, use another MD code Compute lots of diagnostics on-the-y often better left to post-processing you can add it if you want it Visualize your output many packages do this VMD, 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 molecular read_data water.data x 1 all nve run 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 screen thermodynamic info "dump" command outputs snapshots of atom properties default format is simple: id, type, x, y, z other supported formats: XYZ, DCD, XTC conversion tools: PDB, Ensight, XYZ, VTK Rasmol, Raster3d, SVG, etc

    LAMMPS 2-7

    Viz of LAMMPS Snapshots xmovie auxiliary tool distributed with LAMMPS very fast, simple viz 2d projection of 3d systems reads default dump format % /usr/local/bin/xmovie -scale dump.melt VMD learning about this afternoon 3d hi-quality viz dump 1 all xyz 100 dump.melt % vmd (load xyz le 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 script data.* input data le (optional) % lmp_linux -echo screen < in.indent (serial) % mpirun -np 2 lmp_linux -in in.indent (parallel) Each example problem produces: log.lammps logle output (see examples) dump.* series of snapshots LAMMPS doc pages at /usr/local/bin/lammps/doc/Manual.html see Section_commands.html % /usr/local/bin/xmovie -scale dump.indent

    LAMMPS 2-9

    11 Example Problems

    crack: ow: friction: indent: melt: micelle: min: obstacle: peptide: pour: shear:

    crack growth in a LJ crystal (2d) Couette/Poisseuille ow between walls (2d) rubbing of 2 irregular surfaces (2d) crystal response to spherical indenter (2d) LJ lattice (3d) self-assembly of tiny lipid molecules (2d) energy minimization of LJ melt (2d) ow around obstacles (2d) small peptide chain in water (3d) granular particle pour and ow (2d/3d) 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 command else shock waves or worse Need large system & slow pull else defects other than crack Biggest computational test problem run in parallel Options to play with: pull rate pair-wise cutoff turn off velocity ramp change NULL 0.0 in x 2

    LAMMPS 2-11

    Flow Problems Couette ow Poisseuille ow

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

    LAMMPS 2-12

    Friction Problem 2 non-uniform surfaces 2d LJ hex lattice Region commands to build geometry Options to play with: add/change asperities size separation shape x-velocity multiple passes

    LAMMPS 2-13

    Indent Problem 2d LJ solid periodic in x free upper y surface Spherical indenter downward push, remove Defect creation and healing Options to play with: speed & depth of indent size of indenter size of system

    LAMMPS 2-14

    Melt Problem 3d LJ solid periodic in x,y,z Melt an fcc lattice Options to play with: temperature x nvt or npt

    LAMMPS 2-15

    Micelle Problem
    Simple lipid model 2d self-assembly vesicles bilayers Hydrophilic head Hydrophobic tail Monomer solvent Options to play with: timestep size # of timesteps pair-wise coeffs turn off special bonds system size: micelle2d.f

    LAMMPS 2-16

    Minimization Problem Melt of 2d LJ solid Followed by energy minimization Returns to hex lattice but with defects Options to play with: size of system melt temperature minimize tolerance

    LAMMPS 2-17

    Obstacle Problem 2d LJ ow around obstacle(s) Poisseuille kick added to atoms pressure-gradient ow Top surface applies pressure Obstacle creation delete_atoms command x indent command Options to play with: size of force kick size of system size & position of obstacles add a new obstacle

    LAMMPS 2-18

    Peptide Problem
    Full-atom model of 5-mer Met-enkaphalin CHARMM force-eld, PPPM Coulombics SHAKE bond/angle constraints 2 fmsec timestep so cant simulate for long! To see bonds: xmovie scale dump.bonds dump.peptide Options to play with: timestep size, turn off SHAKE, add x drag command

    LAMMPS 2-19

    Pour Problem 3d (or 2d) pour of granular particles into empty box under gravity Change gravity direction to induce chute ow Options to play with: vol fraction for pour # of particles to pour spring constant for atoms direction of gravity

    LAMMPS 2-20

    Shear Problems
    Fixed-end shear in fcc Ni EAM potential quasi-3d non-periodic XY slab thin in Z, periodic Defect formation with and without void Options to play with: size of system shear rate turn off velocity ramp comment in/out void add another void

    LAMMPS 2-21

    Extra Credit: Add new Feature to LAMMPS


    Grab your own copy of LAMMPS source les cp -r /usr/local/bin/lammps/src . Add 2 new les with your feature (from lammps/examples/triangle) region_triangle.cpp & region_triangle.h also region.cpp (one extra line needed, my mistake) Edit style_user.h include "region_triangle.h" #ifdef RegionInclude RegionStyle(triangle,RegTriangle) #ifdef RegionClass Re-build LAMMPS make linux Try it out edit examples/obstacle/in.obstacle to use triangular obstacles edit examples/friction/in.friction to use triangular asperities region 1 triangle x1 y1 x2 y2 x3 y3 run and visualize

    LAMMPS 2-22

    region_triangle.cpp

    35 lines of code constructor(int narg, char **arg) reads arguments: x1 y1 x2 y2 x3 y3 determines 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

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