1. Introduction to LAMMPS
Laalitha Liyanage
ICME Fall 2012

2. Overview Large-scale Atomic/Molecular Massively Parallel Simulator.
Freely available at
Performs molecular dynamics (MD), molecular statics (MS) and monte-carlo (MC) simulations.
Model systems from a few particles to millions/billions, depending on computational power.
Model systems using multiple no. of processors
Parallel execution
Systems
Atomic, polyatomic, metallic, biological, granular

3. Classical Molecular Dynamics
Solves 𝐹=𝑚𝑎
Uses force fields
Mathematical models to describe interactions between atoms
Time step is in the order of femtoseconds

4. How to compile LAMMPS From ICME website
Quick install for the impatient below
Download source tarball. Point your web browser at
Extract the source code. “tar xvzf lammps.tar.gz” this currently creates a directory named lammps-date where date is 30MAR10 as of this writing
Setup the environment for compilation. “swsetup openmpi-intel-64" to add the Intel compilers and mpi related stuff to your path (or “swsetup openmpi-intel-32" for 32-bit clusters).
Compile the MEAM library. In lib/meam under the newly created source code directory, execute “make -f Makefile.ifort” A small amount of compiling will occur. (The makefile is available at the bottom of this page.)
Install header and source code for MEAM pair style. Execute “make yes-meam” inside the src directory under lammps-date. Should display “Installing package meam”
Compile lammps with MEAM support. Copy the included makefile.raptor to src/MAKE/ and finally in the src directory execute “make raptor” This will take a few minutes and output quite a lot of to the screen. When complete a lmp_raptor executable should be in the src directory. Copy this executable to somewhere convenient perhaps ~/bin.
Test the executable.. There are many example runs included in the source tarball. I suggest at a minium to cd into examples/meam
Execute “mpirun -np 4 ~/bin/lmp_raptor < in.meam”. This should produce output very similar to this.

5. Simulation detail Run Simulation Pre-Process Input Running Output
Post-Process
Build system
Determine force-field coefficients
Set boundary conditions
Define force-field
Specify variables
Specify output
Run Simulation
OUTPUT
New coordinates
Forces
Energy
Temperature
Pressure
Etc
POST-PROCESS
Visualize
Graph data
Calc. material properties

6. Pre-Processing task Build system Determine force field coefficients
Methods include
Making your own scripts using crystal structure data
Using LAMMPS commands
Using commercial software
Accrelys Materials studio
Crystal Maker
Determine force field coefficients
Use fitting procedures to fit coefficients to experimental or first principles data.

7. Input script Sequence of commands is important
Script errors are detected by LAMMPS and an ERROR or WARNING message is printed.
More information in LAMMPS manual
Section on commands and input scripts

8. Input script – initialization
Defines the units of the calculation
real
metal si
cgs
electron
Boundary
Periodic (p)
Non-periodic (f,s,m)

9. Input script – structure definition
Define what style of atoms to use in a simulation
Style affects
What quantities are stored by each atom
What quantities are communicated between processors to enable forces to be computed
What quantities are listed in the data file read by the read_data command.
Line no.
Comment – description of structure
No. of atoms
No. of atom types
5-7 Simulation box bounds
Key word atoms
11 onwards atoms
id, type, x, y, z

10. Input script – Force field
pair_style – Set the formula(s) to compute pairwise interactions
Style meam computes pairwise interactions using modified embedded-atom method (MEAM)
pair_coeff - Specify the pairwise force field coefficients for one or more pairs of atom types
neighbor - sets parameters that affect the building of pairwise neighbor lists.
neigh_modify – delay 10 says to build a new neighbor list after 10 steps of building the last one

11. Input script – output file spec.
thermo_style - Set the style and content for printing thermodynamic data to the screen and log file.
thermo_modify – Set options for how thermodynamic information is computed and printed.
dump - Dump a snapshot of atom quantities to one or more files every N timesteps
log - opens a new file with the specified name, and begins logging information to it

12. Input script – Simulation spec.
Run or continue dynamics for a specified number of timesteps
Non-zero value runs MD steps according specified ensemble.
0 is acceptable; only the thermodynamics of the system are computed and printed without taking a timestep.
Other options include
minimize
Perform an energy minimization of the system, by iteratively adjusting atom coordinates.
Format: minimize etol ftol maxiter maxeval
E.g.:minimize 1.0e-4 1.0e

13. Running Lammps Required files Command Input script Data files
Simulation box and atomic coordinates
Parameters for force fields
Command
mpirun –np <no.of proc.> <path of exe> < <name of input script>
E.g.: mpirun –np 8 ~/bin/lmp_exe < Al.infile

14. group command Identify a collection of atoms as belonging to a group.
Format: group ID style args
Available styles
region - specified by coordinates
type - by atom type
variable - by evaluating a atom-style variables
subtract – involves 2/more groups
union – involves 1/more groups
intersect – involves 2/more groups

15. fix command http://lammps.sandia.gov/doc/fix.html
a "fix" is any operation that is applied to the system during timestepping or minimization.
Fixes can be deleted with the unfix command.
Format
fix ID group-ID style args
E.g.
fix 1 all box/relax iso 0.0 vmax 0.001
fix 3 all nvt temp
fix 2 edge setforce NULL

16. Available fix styles neb - nudged elastic band (NEB) spring forces
nvt/asphere - NVT for aspherical particles
rigid/npt - constrain one or more clusters of atoms to move as a rigid body with NPT integration
ttm - two-temperature model for electronic/atomic coupling
rigid/nve - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
nph - constant NPH time integration via Nose/Hoover
nvt/sllod - NVT for NEMD with SLLOD equations
viscosity - Muller-Plathe momentum exchange for viscosity calculation
nph/asphere - NPH for aspherical particles
nvt/sphere - NVT for spherical particles
rigid/nvt - constrain one or more clusters of atoms to move as a rigid body with NVT integration
viscous - viscous damping for granular simulations
nph/sphere - NPH for spherical particles
orient/fcc - add grain boundary migration force
wall/colloid - Lennard-Jones wall interacting with finite-size particles
nphug - constant-stress Hugoniostat integration
planeforce - constrain atoms to move in a plane
setforce - set the force on each atom
npt - constant NPT time integration via Nose/Hoover
poems - constrain clusters of atoms to move as coupled rigid bodies
shake - SHAKE constraints on bonds and/or angles
wall/gran - frictional wall(s) for granular simulations
npt/asphere - NPT for aspherical particles
spring - apply harmonic spring force to group of atoms
wall/harmonic - harmonic spring wall
pour - pour new atoms into a granular simulation domain
npt/sphere - NPT for spherical particles
spring/rg - spring on radius of gyration of group of atoms
wall/lj126 - Lennard-Jones 12-6 wall
press/berendsen - pressure control by Berendsen barostat
nve - constant NVE time integration
spring/self - spring from each atom to its origin
wall/lj93 - Lennard-Jones 9-3 wall
print - print text and variables during a simulation
wall/piston - moving reflective piston wall
nve/asphere - NVE for aspherical particles
srd - stochastic rotation dynamics (SRD)
reax/bonds - write out ReaxFF bond information recenter - constrain the center-of-mass position of a group of atoms
wall/reflect - reflecting wall(s)
nve/asphere/noforce - NVE for aspherical particles without forces
store/force - store force on each atom
wall/region - use region surface as wall
nve/limit - NVE with limited step length
store/state - store attributes for each atom
wall/srd - slip/no-slip wall for SRD particles
restrain - constrain a bond, angle, dihedral
nve/line - NVE for line segments
temp/berendsen - temperature control by Berendsen thermostat
rigid - constrain one or more clusters of atoms to move as a rigid body with NVE integration
nve/noforce - NVE without forces (v only)
temp/rescale - temperature control by velocity rescaling
nve/sphere - NVE for spherical particles
rigid/nph - constrain one or more clusters of atoms to move as a rigid body with NPH integration
thermal/conductivity - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
nve/tri - NVE for triangles
nvt - constant NVT time integration via Nose/Hoover
tmd - guide a group of atoms to a new configuration

17. compute command http://lammps.sandia.gov/doc/compute.html
Define a computation that will be performed on a group of atoms.
Quantities calculated by a compute are instantaneous values
calculated from information about atoms on the current timestep or iteration
Format: compute ID group-ID style args
E.g.
compute 1 all temp
compute 3 all ke/atom

18. Available compute styles
angle/local - theta and energy of each angle
pair/local - distance/energy/force of each pairwise interaction
atom/molecule - sum per-atom properties for each molecule
pe - potential energy
bond/local - distance and energy of each bond
pe/atom - potential energy for each atom
centro/atom - centro-symmetry parameter for each atom
pressure - total pressure and pressure tensor
cluster/atom - cluster ID for each atom
property/atom - convert atom attributes to per-atom vectors/arrays
cna/atom - common neighbor analysis (CNA) for each atom
property/local - convert local attributes to localvectors/arrays
com - center-of-mass of group of atoms
property/molecule - convert molecule attributes to localvectors/arrays
com/molecule - center-of-mass for each molecule
contact/atom - contact count for each spherical particle
rdf - radial distribution function g(r) histogram of group of atoms
coord/atom - coordination number for each atom
reduce - combine per-atom quantities into a single global value
damage/atom - Peridynamic damage for each atom
reduce/region - same as compute reduce, within a region
dihedral/local - angle of each dihedral
slice - extract values from global vector or array
displace/atom - displacement of each atom
stress/atom - stress tensor for each atom
erotate/asphere - rotational energy of aspherical particles
temp - temperature of group of atoms
erotate/sphere - rotational energy of spherical particles
temp/asphere - temperature of aspherical particles
erotate/sphere/atom - rotational energy for each spherical particle
temp/com - temperature after subtracting center-of-mass velocity
event/displace - detect event on atom displacement
temp/deform - temperature excluding box deformation velocity
group/group - energy/force between two groups of atoms
temp/partial - temperature excluding one or more dimensions of velocity
gyration - radius of gyration of group of atoms
temp/profile - temperature excluding a binned velocity profile
gyration/molecule - radius of gyration for each molecule
temp/ramp - temperature excluding ramped velocity component
heat/flux - heat flux through a group of atoms
temp/region - temperature of a region of atoms
improper/local - angle of each improper
temp/sphere - temperature of spherical particles
ke - translational kinetic energy
ti - thermodyanmic integration free energy values
ke/atom - kinetic energy for each atom
msd - mean-squared displacement of group of atoms
msd/molecule - mean-squared displacement for each molecule
pair - values computed by a pair style

19. Example output Onscreen and log file
Output of volume optimization run for Al (fcc)
Initial structure
a = 4.03 Å
Energy = eV
Final structure
a = 4.05 Å
Energy = eV

20. The dump file
Contains geometry of the simulation box and position of atoms for each time step or iteration.
Can be used to see the trajectory of the system

21. Visualizing the output
OVITO
VMD, Rasmol, Ensight etc.

22. LAMMPS references LAMMPS manual ICME LAMMPS workshops
ICME
LAMMPS workshops