Gwangju Institute of Science and Technology (GIST)

Super Computing & Collaboration Environment Technology Center (SCENT)

LAMMPS for Molecular Dynamics Simulation

Taekhee Ryu
Molecular Modeling Laboratory (MML)
School of Materials Science and Engineering (MSE)
Gwangju Institute of Science and Technology (GIST)

Overview: What is LAMMPS

Lesson 1: Preparing input file
Lesson 2: Running LAMMPS
Lesson 3: Viewing output file

What is LAMMPS
Large-scale Atomic/Molecular Massively Parallel Simulation
- By Dr. S. Plimpton (http://lammps.dandia.gov)
Free open-source code (C++)
Model System with only a few particles up to millions or billions
(depends on computational power)

Designed for Parallel applications

Capable for Atomic, polyatomic, biological, metallic, granular system

LAMMPS doesnt
Build Molecular systems
Use a builder code or write out your own config file
Can build lattices, grain boundaries, etc

Assign force-field coefficients auto-magically

Only hard for molecules, use another MD code

Compute lots of diagnostics on-the-fly

Often better left to post-processing

Visualize your output

Many packages do this
VMD, Rasmol, AtomEye, Ensight,..

Our research using LAMMPS

Multiscale molecular modeling of Nano-device containing fullerene derivatives
l Unimolecular rectifier
Single organic molecule between metals can function as rectif
iers, one-way conductors of electrical current

l Absorption model on Au(111)

l Self-assembled monolayer

Our research using LAMMPS

l P3HT/PCBM BHJ

l Amorphous phase of PVDF Molecular dynamic simulation

Overview of LAMMPS simulation

INPUT

- Boundary
conditions
- Potential energy
function

(log.***, dump.***)

OUTPUT

RUNNING

INPUT

(**.cmd, in.**, data.**)

- Initial positions
and velocities

OUTPUT

RUNNING

- Molecular

- Trajectories
- Forces, Energy

Dynamics

- Temperature

Simulation

- Pressure
- Etc.

- Etc.

LAMMPS Input

Reads an input script (ASCtext)

One command per line

Command name + arguments (in.***)

atom_style molecular
read_data water.data
fix
1 all nve
run
10000

Data files(typical components) (data.***)

Summary of molecular connectivity

Cell dimensions
Force field parameters(pair, bond, angle, dihedral, improper)
Atom info (molecule #, atom type #, charge, xyz coordinates)
Bond info (bonds, angles, etc)

Examples sub-dir has many input scripts

Example Problems in LAMMPS

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:
Micelle:
Min:

rapid melt of 3d LJ system

self-assembly of tiny lipid molecules (2d)
energy minimization of LJ melt (2d)

Obstacle: flow around obstacles (2d)

Peptide:

granular particle pour and flow (2d/3d)

Shear:

shear of a metal slab with void (quasi-3d)

Peptide:

dynamics of a small solvated peptide chain (5-mer)

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Input script

Full-atom model of 5-mer peptide

CHARMM force-field
SHAKE bond/angle constraints
2 fs timestep

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Input script
1. initialization

2. Atom definition

3. Settings

4. Run a simulation

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Input script - initialization

1. initialization

Set parameters that need to be defined before atoms

are created or read-in from a file
Unit, dimension, newton, processors, boundary, atom
style, atom modify

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Input script - initialization

Units
1. initialization
sets the style of units used for a simulation
Beginning of an input script
lj, real, metal, si, cgs, electron

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Input script - initialization

1. initialization
atom_style
Define what style of atoms to use in a simulation
Beginning of an input script

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Input script - initialization

1. initialization

2. Atom definition
Boundary - set the style of boundaries for the global simulatio
n box in each dimension
3. Settings
Processors - Specify how processors are mapped as a 3d logic
al grid to the global simulation box
Dimension - Set the dimensionality of the simulation. By defaul
t LAMMPS runs 3d simulations.

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Input script - initialization

1. initialization

2. Atom definition

pair_style
set the formula uses to compute pairwise interactions
3. Settings

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Input script - initialization

r
1. initialization

2. Atom definition
bond_style
uses to compute bond interactions between pairs of atoms
3. Settings

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Input script - initialization

1. initialization

2. Atom definition
angle_style
uses to compute angle interactions between triplets of atoms
3. Settings

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Input script - initialization

1. initialization

2. Atom definition
dihedral_style
uses to compute dihedral interactions between quadruplets of
atoms
3. Settings

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Input script - initialization

1. initialization

2. Atom definition
improper_style
uses to compute dihedral interactions between quadruplets of
atoms

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Input script - initialization

1. initialization

2. Atom definition

kspace_style
Define a K-space solver for LAMMPS to use each timestep to
compute long-range Coulombic interactions or long-range 1/r^
N interactions
Style none or ewald or pppm or pppm/cg or
The pppm style invokes a particle-particle particle-mesh solver
(Hockney) which maps atom charge to a 3d mesh, uses 3d F
FTs to solve Poisson's equation on the mesh, then interpolate
s electric fields on the mesh points back to the atoms

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Input script - atom definition

1. initialization

2. Atom definition
Read them in from a data or restart file
via the read data or read restart command
3. Settings
Contain molecular topology information
Create atoms on a lattice
with no molecular topology
Lattice, region, create box, create atoms

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Input script
Read_data - Read in a data file containing information LA
MMPS needs to run a simulation (data.***)
1. initialization

# of components
in system

Simulation box
boundaries

Mass

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Input script
Read_data - Read in a data file containing information LA
MMPS needs to run a simulation (data.***)
1. initialization

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Input script
Read_data - Read in a data file containing information LA
MMPS needs to run a simulation (data.***)
1. initialization

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Input script
Read_data - Read in a data file containing information LA
MMPS needs to run a simulation (data.***)
1. initialization

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Input script
Read_data - Read in a data file containing information LA
MMPS needs to run a simulation (data.***)
1. initialization

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Input script
Read_data - Read in a data file containing information LA
MMPS needs to run a simulation (data.***)
1. initialization

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Input script - atom definition

read_data - Read in a data file containing information
LAMMPS needs to run a simulation (data.***)
1. initialization
2. Atom definition

read_restart - Read in a previously saved simulation from

a restart file

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Input script - atom definition

Create atoms on a lattice
with no molecular topology
Lattice, region, create box, create atoms
Lattice
simply a set of points in space
determined by a unit cell with basis atoms
used to define a wide variety of crystallographic
ices
syntax
example

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latt

Input script - atom definition

Create atoms on a lattice
with no molecular topology
Lattice, region, create box, create atoms

region
This command defines a geometric region of
sp
ace
create box
This command creates a simulation box based on t
he specified region
create atoms
This command creates atoms on a lattice, or a si
ngle atom, or a random collection of atoms

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Input script - settings

1. initialization

2. Atom definition

3. Settings

3. Run a simulation

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Input script - settings

neighbor
This command sets parameters that affect the
building of pairwise neighbor lists
The style value selects what algorithm is used to
build the list
The bin style creates the list by binning which is an
operation that scales linearly with N/P, the number
of atoms per processor where N = total number of
atoms and P = number of processors

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Input script - settings

Neigh_modify
This command sets parameters that affect the
building and use of pairwise neighbor lists
The delay setting means never build a new list
until at least N steps after the previous build

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Input script - settings

timestep
Set the timestep size for subsequent molecular
dynamics simulations

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Input script - settings

thermo_style
Set the style and content for printing thermodynamic
data to the screen and log file.
Style multi prints a multiple-line listing of thermodyna
mic info
thermo_style custom etotal ke temp pe ebond eangle
edihed eimp evdwl ecoul elong press

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Input script - settings

thermo
Compute and print thermodynamic info on timesteps
that are a multiple of N and at the beginning and end
of a simulation

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Input script - settings

fix
Set a fix that will be applied to a group of atoms

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Input script - settings

fix
Set a fix that will be applied to a group of atoms

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Input script - settings

group
Identify a collection of atoms as belonging to a group
The example above adds all atoms with IDs from 1 t
o 12 to the group named peptide type

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Input script - settings

dump
snapshot of atom quantities to one or more files every
N timesteps in one of several styles

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Input script
1. initialization

2. Atom definition

3. Settings
run
Run or continue dynamics for a specified number of
timesteps
3. Run a simulation

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Tutorial
INPUT

(**.cmd, in.**, data.**)

RUNNING

VMD Data.*** .

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OUTPUT

(log.***, dump.***)

Tutorial

VMD Data.*** .

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Tutorial

VMD Data.*** .

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Tutorial

VMD Data.*** .

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Tutorial

VMD Data.*** .

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Tutorial

VMD Data.*** .

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Hand-on exercise
Download the files
Xming (http://sourceforge.net/projects/xming/)
VMD (http://www.ks.uiuc.edu/Research/vmd/)
Putty (SSH Access Client Program)
Input file (in.peptide)
Topology file (data.peptide)
Executable file (lammps_kigi.cmd)
Analysis file (thermo_extract.c)
Install the programs
Xming, Putty
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Hand-on exercise
PuTTY SSH Remote Access Client Program

putty

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Hand-on exercise
Connect to the GIST supercomputer (kigi)

localhost:0.0

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Hand-on exercise
Connect to the GIST supercomputer (kigi)

Login01.plsi.or.kr, Port-22

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Hand-on exercise
Connect to the GIST supercomputer (kigi)
$ ssh kigi-lg01

connect to the kigi

$ cp lammps.tar /pwork01/edun/pedunXX
$ cd /pwokr01/edun/pedunXX
$ tar xvf lammps.tar
$ cd lammps

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Hand-on exercise
Lammps_kigi.cmd -> executable file
Job name

Job-time

Input file
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Hand-on exercise
Example-1

Full-atom model of 5-mer peptide

CHARMM force-field
SHAKE bond/angle constraints
2 fs timestep

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Hand-on exercise
Running LAMMPS on PLSI supercomputer
$ llsubmit lammps_kigi.cmd
$ llcancel job_id
$ llq
$ llstatus

# submit the job

# cancel the job

# job status
# system status

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Output
There are two basic types of LAMMPS output.
1. Thermodynamic output (log.***)
1. A list of quantities printed every few time steps to the screen
and log file
2. Dump files (dump.***)
1. Snapshots of atoms and various per-atom values and are w
ritten at a specified frequency.
2. Default format is simple : id, type, x, y, z
3. VMD, Rasmol, AtomEye, XMOVIE

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Output
Example-1 (log.lammps)

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Output
Analysis of thermodynamic output (log.lammps)
thermo_extract.c
To run this program please compile it as
->
gcc -O3 thermo_extract.c -lm -o thermo_extract
-p for thermo parameter to extract
-s if the output format is single line, or
-m is the output format is multi line
-> thermo_extract p PotEng -m log.lammps >&PotEng.tot

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Output
Analysis of thermodynamic output (log.***)
-> gnuplot
-> plot PotEng u 1:2 w l

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Visualizer
AtomEye - http://li.mit.edu/Archive/Graphics/A
Rasmol - http://www.umass.edu/microbio/rasmol/
XMOVIE
Auxiliary tool distributed with LAMMPS
Very fast, simple viz
2d projection of 3d systems
/home01/applic/lammps/lammps-18Apr10/intel/ssh/tools/x
movie/xmovie scale dump.***
VMD - http://www.ks.uiuc.edu/Research/vmd/
Windows, Linux, MacOS X
3d hi-quality viz

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Additional tools
Amber2lmp

AMBER <-> LAMMPS

Binary2txt

binary dump file -> ASC test files

Ch2lmp

CHARMM <-> LAMMPS

Chain

create the chains and solvent

Lmp2arc

LAMMPS -> Accelryss insight MD

Lamp2cfg

LAMMPS -> AtomEYE(*.cfg)

Lmp2vmd

LAMMPS -> VMD

Msi2lmp

LAMMPS -> Accelryss insight MD

Python, micelle2d, matlab, ipp, emacs, eff, eam database, data

2xmovie, creatatoms

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Thank you

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