LAMMPS for Molecular Dynamics Simulation
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1 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)
2 Overview: What is LAMMPS Lesson 1: Preparing input file Lesson 2: Running LAMMPS Lesson 3: Viewing output file
3 What is LAMMPS Large-scale Atomic/Molecular Massively Parallel Simulation - By Dr. S. Plimpton ( 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 3
4 LAMMPS doesn t 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,.. 4
5 Our research using LAMMPS Multiscale molecular modeling of Nano-device containing fullerene derivatives l Unimolecular rectifier Ø 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 5
6 Our research using LAMMPS l P3HT/PCBM BHJ l Amorphous phase of PVDF Molecular dynamic simulation 6
7 Overview of LAMMPS simulation INPUT (**.cmd, in.**, data.**) RUNNING OUTPUT (log.***, dump.***) INPUT - Initial positions and velocities - Boundary conditions - Potential energy function - Etc. RUNNING - Molecular Dynamics Simulation OUTPUT - Trajectories - Forces, Energy - Temperature - Pressure - Etc. 7
8 LAMMPS Input 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 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 8
9 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: 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) 9
10 Input script Full-atom model of 5-mer peptide CHARMM force-field SHAKE bond/angle constraints 2 fs timestep 10
11 Input script 1. initialization 2. Atom definition 3. Settings 4. Run a simulation 11
12 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 12
13 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 13
14 Input script - initialization atom_style 1. initialization Define what style of atoms to use in a simulation Beginning of an input script 14
15 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. 15
16 Input script - initialization 1. initialization 2. Atom definition pair_style set the formula uses to compute pairwise interactions 3. Settings 16
17 Input script - initialization r 1. initialization 2. Atom definition bond_style uses to compute bond interactions between pairs of atoms 3. Settings 17
18 Input script - initialization 1. initialization r r 2. Atom definition angle_style uses to compute angle interactions between triplets of atoms 3. Settings 18
19 Input script - initialization 1. initialization dihedral_style 2. Atom definition uses to compute dihedral interactions between quadruplets of atoms 3. Settings 19
20 Input script - initialization 1. initialization improper_style 2. Atom definition uses to compute dihedral interactions between quadruplets of atoms 20
21 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 21
22 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 Contain molecular topology information 3. Settings Create atoms on a lattice with no molecular topology Lattice, region, create box, create atoms 22
23 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 23
24 Input script Read_data - Read in a data file containing information LA MMPS needs to run a simulation (data.***) 1. initialization 24
25 Input script Read_data - Read in a data file containing information LA MMPS needs to run a simulation (data.***) 1. initialization 25
26 Input script Read_data - Read in a data file containing information LA MMPS needs to run a simulation (data.***) 1. initialization 26
27 Input script Read_data - Read in a data file containing information LA MMPS needs to run a simulation (data.***) 1. initialization 27
28 Input script Read_data - Read in a data file containing information LA MMPS needs to run a simulation (data.***) 1. initialization 28
29 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 29
30 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 latt ices syntax example 30
31 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 31
32 Input script - settings 1. initialization 2. Atom definition 3. Settings 3. Run a simulation 32
33 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 33
34 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 34
35 Input script - settings timestep Set the timestep size for subsequent molecular dynamics simulations 35
36 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 36
37 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 37
38 Input script - settings fix Set a fix that will be applied to a group of atoms 38
39 Input script - settings fix Set a fix that will be applied to a group of atoms 39
40 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 40
41 Input script - settings dump snapshot of atom quantities to one or more files every N timesteps in one of several styles 41
42 Input script 1. initialization 2. Atom definition 3. Settings run Run or continue dynamics for a specified number of timesteps 3. Run a simulation 42
43 INPUT (**.cmd, in.**, data.**) Tutorial RUNNING OUTPUT (log.***, dump.***) VMD Data.***. 43
44 VMD Data.***. Tutorial 44
45 VMD Data.***. Tutorial 45
46 VMD Data.***. Tutorial 46
47 VMD Data.***. Tutorial 47
48 VMD Data.***. Tutorial 48
49 Hand-on exercise Download the files Xming ( 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 49
50 Hand-on exercise PuTTY SSH Remote Access Client Program putty 50
51 Hand-on exercise Connect to the GIST supercomputer (kigi) localhost:0.0 51
52 Hand-on exercise Connect to the GIST supercomputer (kigi) Login01.plsi.or.kr, Port-22 52
53 Hand-on exercise Connect to the GIST supercomputer (kigi) $ ssh kigi-lg01 à connect to the kigi $ cp lammps.tar /pwork01/edun/pedunxx $ cd /pwokr01/edun/pedunxx $ tar xvf lammps.tar $ cd lammps 53
54 Hand-on exercise Lammps_kigi.cmd -> executable file Job name Job-time Input file 54
55 Example-1 Hand-on exercise Full-atom model of 5-mer peptide CHARMM force-field SHAKE bond/angle constraints 2 fs timestep 55
56 Hand-on exercise Running LAMMPS on PLSI supercomputer $ llsubmit lammps_kigi.cmd # submit the job $ llcancel job_id # cancel the job $ llq # job status $ llstatus # system status 56
57 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 57
58 Output Example-1 (log.lammps) 58
59 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 59
60 Output Analysis of thermodynamic output (log.***) -> gnuplot -> plot PotEng u 1:2 w l 60
61 Visualizer AtomEye - 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 - Windows, Linux, MacOS X 3d hi-quality viz 61
62 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 62
63 Thank you 63
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