LAMMPS for Molecular Dynamics Simulation - GIST · PDF fileLAMMPS for Molecular Dynamics Simulation Taekhee Ryu Gwangju Institute of Science and Technology (GIST) Super Computing &

LAMMPS for Molecular Dynamics Simulation

Taekhee Ryu

Gwangju Institute of Science and Technology (GIST) Super Computing & Collaboration Environment Technology Center (SCENT)

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++)

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

Designed for Parallel applications

Model System with only a few particles up to millions or billions (depends on computational power)

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LAMMPS doesn’t

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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,…..

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Our research using LAMMPS Multiscale molecular modeling of Nano-device containing fullerene derivatives

l  Self-assembled monolayer

Ø  Single organic molecule between metals can function as rectifiers, one-way conductors of electrical current

l  Unimolecular rectifier

l  Absorption model on Au(111)

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Our research using LAMMPS l  P3HT/PCBM BHJ

l  Amorphous phase of PVDF Molecular dynamic simulation

Overview of LAMMPS simulation

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INPU

T

- Initial positions and velocities - Boundary conditions - Potential energy function - Etc.

RU

NN

ING

- Molecular Dynamics Simulation

OU

TPU

T

- Trajectories - Forces, Energy - Temperature - Pressure - Etc.

INPUT (**.cmd, in.**, data.**) RUNNING OUTPUT

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

LAMMPS Input

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•  Reads an input script (ASCⅡtext)

•  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

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•  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: rapid melt of 3d LJ system

•  Micelle: self-assembly of tiny lipid molecules (2d)

•  Min: 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)

Input script

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•  Full-atom model of 5-mer peptide

•  CHARMM force-field

•  SHAKE bond/angle constraints

•  2 fs timestep

Input script

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1. initialization

2. Atom definition

3. Settings

4. Run a simulation

Input script - initialization

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


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


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1. initialization

2. Atom definition

3. Settings

•  Boundary - set the style of boundaries for the global simulation box in each dimension

•  Processors - Specify how processors are mapped as a 3d logical grid to the global simulation box

•  Dimension - Set the dimensionality of the simulation. By default LAMMPS runs 3d simulations.


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1. initialization

2. Atom definition

3. Settings

•  pair_style •  set the formula uses to compute pairwise interactions


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1. initialization

2. Atom definition

3. Settings

•  bond_style •  uses to compute bond interactions between pairs of atoms

r


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1. initialization

2. Atom definition

3. Settings

•  angle_style •  uses to compute angle interactions between triplets of atoms

rr


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1. initialization

2. Atom definition

3. Settings

•  dihedral_style •  uses to compute dihedral interactions between quadruplets of atoms


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1. initialization

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


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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 FFTs to solve Poisson's equation on the mesh, then interpolates electric fields on the mesh points back to the atoms

Input script - atom definition

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1. initialization

2. Atom definition

3. Settings

•  Read them in from a data or restart file •  via the read data or read restart command •  Contain molecular topology information

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

Input script

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1. initialization •  Read_data - Read in a data file containing information LA

MMPS needs to run a simulation (data.***)

# of components in system

Simulation box boundaries

Mass

Input script

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Input script

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Input script

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Input script

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Input script

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1. initialization

2. Atom definition

•  read_data - Read in a data file containing information •  LAMMPS needs to run a simulation (data.***)

•  read_restart - Read in a previously saved simulation from a restart file


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•  Lattice •  simply a set of points in space •  determined by a unit cell with basis atoms •  used to define a wide variety of crystallographic latt

ices

syntax example


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•  region •  This command defines a geometric region of sp

ace •  create box

•  This command creates a simulation box based on the specified region

•  create atoms •  This command creates atoms on a lattice, or a si

ngle atom, or a random collection of atoms

Input script - settings

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1. initialization

2. Atom definition

3. Settings

3. Run a simulation


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•  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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•  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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•  timestep •  Set the timestep size for subsequent molecular dynamics simulations


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•  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 thermodynamic info

•  thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press


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


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


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

Input script

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1. initialization

2. Atom definition

3. Settings

3. Run a simulation

•  run •  Run or continue dynamics for a specified number of timesteps

Tutorial

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•  VMD를 사용한 Data.*** 생성.

INPUT (**.cmd, in.**, data.**) RUNNING OUTPUT

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

Tutorial

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Tutorial

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Tutorial

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Tutorial

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Tutorial

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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

Hand-on exercise

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•  Connect to the GIST supercomputer (kigi)

localhost:0.0

Hand-on exercise

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Login01.plsi.or.kr, Port-22

Hand-on exercise

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$ ssh kigi-lg01 à connect to the kigi $ cp lammps.tar /pwork01/edun/pedunXX $ cd /pwokr01/edun/pedunXX $ tar xvf lammps.tar $ cd lammps

Hand-on exercise

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•  Lammps_kigi.cmd -> executable file

Input file

Job-time

Job name

Hand-on exercise

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•  Example-1

•  Full-atom model of 5-mer peptide

•  CHARMM force-field

•  SHAKE bond/angle constraints

•  2 fs timestep

Hand-on exercise

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•  Running LAMMPS on PLSI supercomputer

$ llsubmit lammps_kigi.cmd # submit the job $ llcancel job_id # cancel the job $ llq # job status $ llstatus # system status

Output

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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

Output

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•  Example-1 (log.lammps)

Output

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•  thermo_extract.c

•  To run this program please compile it as -> gcc -O3 thermo_extract.c -lm -o thermo_extract

Analysis of thermodynamic output (log.lammps)

-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

Output

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Analysis of thermodynamic output (log.***)

-> gnuplot -> plot ‘PotEng’ u 1:2 w l

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 -> ASCⅡ test files

•  Ch2lmp CHARMM <-> LAMMPS

•  Chain create the chains and solvent

•  Lmp2arc LAMMPS -> Accelrys’s insight MD

•  Lamp2cfg LAMMPS -> AtomEYE(*.cfg)

•  Lmp2vmd LAMMPS -> VMD

•  Msi2lmp LAMMPS -> Accelrys’s insight MD

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

2xmovie, creatatoms

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Thank you

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Documents

LAMMPS for Molecular Dynamics Simulation - GIST · PDF fileLAMMPS for Molecular Dynamics Simulation Taekhee Ryu Gwangju Institute of Science and Technology (GIST) Super Computing &