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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)

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Overview: What is LAMMPS

Lesson 1: Preparing input file

Lesson 2: Running LAMMPS

Lesson 3: Viewing output file

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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 doesnt

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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 LAMMPSMultiscale molecular modeling of Nano-device containing fullerene derivatives

!

Self-assembled monolayer

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

!

Unimolecular rectifier

!

Absorption model on Au(111)

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Our research using LAMMPS

!P3HT/PCBM BHJ

! Amorphous phase of PVDF Molecular dynamic simulation

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LAMMPS Input

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Reads an input script (ASC!text)

One command per line

Command name + arguments (in.***)atom_style molecular

read_data water.datafix 1 all nverun 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

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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)

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Input script

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Full-atom model of 5-mer peptide

CHARMM force-field

SHAKE bond/angle constraints

2 fs timestep

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Input script

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1. initialization

2. Atom definition

3. Settings

4. Run a simulation

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Input script - initialization

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1. initialization

Set parameters that need to be defined before atomsare created or read-in from a file

Unit, dimension, newton, processors, boundary, atomstyle, 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 ofatoms

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1. initialization

2. Atom definition

improper_style

uses to compute dihedral interactions between quadruplets ofatoms

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1. initialization

2. Atom definition

kspace_style

Define a K-space solver for LAMMPS to use each timestep tocompute long-range Coulombic interactions or long-range 1/r^N interactions

Style none or ewald or pppm or pppm/cg or!! Thepppmstyle 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

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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

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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 componentsin system

Simulation boxboundaries

Mass

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Input script

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1. initialization



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Input script

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1. initialization



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Input script

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1. initialization



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Input script

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1. initialization



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Input script

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1. initialization



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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 froma restart file

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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 lattices

syntax

example

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with no molecular topology Lattice, region, create box, create atoms

region

This command defines a geometric region of space

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 single atom, or a random collection of atoms

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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 thebuilding of pairwise neighbor lists

The stylevalue selects what algorithm is used tobuild the list

The binstyle creates the list by binning which is anoperation that scales linearly with N/P, the numberof atoms per processor where N = total number ofatoms 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 delaysetting 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 moleculardynamics simulations

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thermo_style Set the style and content for printing thermodynamic

data to the screen and log file.

Style multiprints a multiple-line listing of thermodynamic info

thermo_style custom etotal ke temp pe ebond eangleedihed eimp evdwl ecoul elong press

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thermo

Compute and print thermodynamic info on timestepsthat are a multiple of N and at the beginning and endof 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 namedpeptide type

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dump snapshot of atom quantities to one or more files every

N timesteps in one of several styles

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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 oftimesteps

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Tutorial

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VMDData.*** .

INPUT

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

OUTPUT

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

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Tutorial

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VMDData.*** .

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Tutorial

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VMDData.*** .

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Tutorial

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VMDData.*** .

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Tutorial

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VMDData.*** .

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Tutorial

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VMDData.*** .

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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

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Connect to the GIST supercomputer (kigi)

localhost:0.0

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Hand-on exercise

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Login01.plsi.or.kr, Port-22

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Hand-on exercise

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$ 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

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Lammps_kigi.cmd -> executable file

Input file

Job-time

Job name

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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

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Hand-on exercise

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Running LAMMPS on PLSI supercomputer

$ llsubmitlammps_kigi.cmd # submit the job

$ llcanceljob_id # cancel the job

$ llq # job status

$ llstatus # system status

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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 screenand log file

2.

Dump files (dump.***)1.

Snapshots of atoms and various per-atom values and are written at a specified frequency.

2. Default format is simple : id, type, x, y, z3.

VMD, Rasmol, AtomEye, XMOVIE

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Output

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Example-1 (log.lammps)

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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

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Output

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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, data2xmovie, creatatoms

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Thank you

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