A Quick Tour of LAMMPS

Steve Plimpton
Sandia National Labs
sjplimp@sandia.gov

5th LAMMPS Workshop Beginner Tutorial

August 2017 - Albuquerque, NM

Follow along with my slides at:

http://lammps.sandia.gov/workshops/Aug17/workshop.html
Resources for learning LAMMPS

All on web site, most in distro tarball:

Workshops (beginner tutorials) & Tutorials
Features: list of features with links
Glossary: MD terms ⇒ LAMMPS
Manual:
Intro, Commands, Packages, Accelerating,
Howto, Modifying, Errors sections
search bubble at top left of every page
Commands
alphabetized command & style tables: one page per command
Papers: find a paper similar to what you want to model
Mail list: search archives (lammps-users, post Qs to it
http://lammps.sandia.gov/mail.html
Examples: 50 sub-dirs under examples in distro
lower-case = simple, upper-case = more complex
many produce movies: http://lammps.sandia.gov/movies.html
Structure of typical input scripts

1 Units and atom style

2 Create simulation box and atoms
region, create box, create atoms, region commands
lattice command vs box units
read data command
data file is a text file
look at examples/micelle/data.micelle
see read data doc page for full syntax
3 Define groups
4 Set attributes of atoms: mass, velocity
5 Pair style for atom interactions
6 Fixes for time integration and constraints
7 Computes for diagnostics
8 Output: thermo, dump, restart
9 Run or minimize
10 Rinse and repeat (script executed one command at a time)
Obstacle example

input script = examples/obstacle/in.obstacle

Obstacle input script

1st section = setup box and create atoms

# 2d LJ obstacle flow

dimension 2
boundary p s p
atom style atomic
neighbor 0.3 bin
neigh modify delay 5

# create geometry

lattice hex 0.7

region box block 0 40 0 10 -0.25 0.25
create box 3 box
create atoms 1 box
Obstacle input script

2nd section = define potential and groups of atoms

# LJ potentials

pair style lj/cut 1.12246

pair coeff * * 1.0 1.0 1.12246

# define groups

region 1 block INF INF INF 1.25 INF INF

group lower region 1
region 2 block INF INF 8.75 INF INF INF
group upper region 2
group boundary union lower upper
group flow subtract all boundary

set group lower type 2

set group upper type 3
Obstacle input script

3rd section = set velocities and fixes

# initial velocities

mass * 1.0
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix modify 2 temp mobile

# Poiseuille flow

velocity boundary set 0.0 0.0 0.0

fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
Obstacle input script

4th section = create 2 obstacles to flow

# 2 obstacles

region void1 sphere 10 4 0 3

delete atoms region void1
region void2 sphere 20 7 0 3
delete atoms region void2

fix 7 flow indent 100 sphere 10 4 0 4

fix 8 flow indent 100 sphere 20 7 0 4
fix 9 all enforce2d
Obstacle input script

5th section: define output and run simulation (JPG, PNG, PPM)

# run

timestep 0.003
thermo 1000
thermo modify temp mobile

#dump 1 all atom 100 dump.obstacle

dump 2 all image 500 image.*.ppm type type &
zoom 1.6 adiam 1.5
dump modify 2 pad 5

run 25000
Make a movie

50 JPG or PNG or PPM files

image.16500.ppm
ImageMagick display
Mac Preview
Make/view a movie
ImageMagick
convert *.ppm image.gif
open in browser
open -a Safari image.gif
Mac QuickTime
open image sequence
Windows Media Player
Ovito, VMD, AtomEye, ...
Obstacle example

Questions on input script?

Exercise:
run examples/obstacle/in.obstacle on your laptop
examine and visualize output
Examine screen output

LAMMPS (5 Oct 2016)

Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
Created orthogonal box = (0 0 -0.321089)
to (51.3743 22.2457 0.321089)
4 by 1 by 1 MPI processor grid
Created 840 atoms
120 atoms in group lower
120 atoms in group upper
240 atoms in group boundary
600 atoms in group flow
Setting atom values ...
120 settings made for type
Setting atom values ...
120 settings made for type
Deleted 36 atoms, new total = 804
Deleted 35 atoms, new total = 769
Neighbor list and memory info

Neighbor list info ...

update every 1 steps, delay 5 steps, check yes
master list distance cutoff = 1.42246
binsize = 0.71123, bins = 73 32 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.003
Per MPI rank memory allocation (avg) = 3.043 Mbytes
Thermo output

Step Temp E pair E mol TotEng Press Volume

0 1.0004177 0 0 0.68689281 0.46210058 1143.0857
1000 1 -0.32494012 0 0.36166587 1.2240503 1282.5239
2000 1 -0.37815616 0 0.30844982 1.0642877 1312.5691
...
...
...
24000 1 -0.40040333 0 0.28620265 0.94983886 1459.4461
25000 1 -0.37645924 0 0.31014674 1.0526044 1458.7191
Loop time of 0.815388 on 4 procs for 25000 steps
with 769 atoms
Performance: 7947137.172 tau/day,
30660.251 timesteps/s
98.7% CPU use with 4 MPI tasks x no OpenMP threads
Timing info

Loop time of 0.815388 on 4 procs for 25000 steps

with 769 atoms

MPI task timing breakdown:

Section | min | avg | max | %varavg | %total
--------------------------------------------------
Pair | 0.063 | 0.123 | 0.202 | 15.7 | 15.10
Neigh | 0.031 | 0.041 | 0.055 | 4.4 | 5.06
Comm | 0.149 | 0.231 | 0.288 | 11.0 | 28.42
Output | 0.001 | 0.001 | 0.001 | 0.0 | 0.01
Modify | 0.275 | 0.305 | 0.341 | 4.3 | 37.43
Other | ----- | 0.113 | ----- | --- | 13.91
Run statistics

Per-processor values at end of run

Nlocal: 192.25 ave 243 max 151 min

Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 41.75 ave 43 max 39 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 408.5 ave 575 max 266 min
Histogram: 1 1 0 0 0 0 0 1 0 1

Total # of neighbors = 1634

Ave neighs/atom = 2.12484
Neighbor list builds = 1631
Dangerous builds = 1
Run statistics

Per-processor values at end of run

Nlocal: 192.25 ave 243 max 151 min

Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 41.75 ave 43 max 39 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 408.5 ave 575 max 266 min
Histogram: 1 1 0 0 0 0 0 1 0 1

Total # of neighbors = 1634

Ave neighs/atom = 2.12484
Neighbor list builds = 1631
Dangerous builds = 1

Questions on output?
Common input script errors and debugging

Command not recognized

ERROR: Unknown pair style gran/hooke (../force.cpp:246)
LAMMPS not built with style being used
many styles are in packages
lmp mpi -h will list all styles included in build
Syntax error in command
ERROR: Incorrect args for pair coefficients (file/line #)
Last command: pair coeff * * 1.0 1.0 1.12246 9.0
Common input script errors and debugging

Command not recognized

ERROR: Unknown pair style gran/hooke (../force.cpp:246)
LAMMPS not built with style being used
many styles are in packages
lmp mpi -h will list all styles included in build
Syntax error in command
ERROR: Incorrect args for pair coefficients (file/line #)
Last command: pair coeff * * 1.0 1.0 1.12246 9.0
Thermo output blows up immediately
usually due to bad atom coords and/or bad force field
often leads to lost or out-of-range atoms
Don’t start with too complex a script
debug an input script just like a computer program
start simple, add complexity one command at a time
can use print command to examine variables
use thermo/dump output and viz to verify correctness
Additional topics

More complex input scripts

Pre-processing to build a complex system
Force fields: pair, bond, and kspace styles
Fixex and computes
Output
Parallelization and performance
Quick tour of more advanced topics
Extending LAMMPS
Defining variables in input scripts

Styles: index, loop, equal, atom, python, file, ...

variable x index run1 run2 run3 run4
variable x loop 100
variable x trap(f JJ[3])*${scale}
variable x atom -(c p[1]+c p[2]+c p[3])/(3*vol)
Defining variables in input scripts

Styles: index, loop, equal, atom, python, file, ...

variable x index run1 run2 run3 run4
variable x loop 100
variable x trap(f JJ[3])*${scale}
variable x atom -(c p[1]+c p[2]+c p[3])/(3*vol)
Formulas can be complex
see doc/variable.html
thermo keywords (temp, press, ...)
math operators & functions (sqrt, log, cos, ...)
group and region functions (count, xcm, fcm, ...)
various special functions (min, ave, trap, stride, stagger, ...)
per-atom vectors (x, vx, fx, ...)
output from computes, fixes, other variables
Formulas can be time- and/or spatially-dependent
Using variables in input scripts

Substitute in any command via $x or ${myVar}

Immediate formula evaluation via $() syntax:
avoids need to define variable separately
variable xmid equal (xlo+xhi)/2
region 1 block $xmid EDGE INF INF EDGE EDGE
region 1 block $((xlo+xhi)/2) EDGE INF INF EDGE EDGE
Next command increments a variable to next value
Many commands allow variables as arguments
fix addforce 0.0 v fy 1.0
dump modify every v foo
region sphere 0.0 0.0 0.0 v radius
only if command doc page says so
Power tools for input scripts

Filename options:
dump.*.% for per-snapshot or per-processor output
read data data.protein.gz
read restart old.restart.*
If/then/else via if command
Insert another script via include command
useful for long list of params
Power tools for input scripts

Filename options:
dump.*.% for per-snapshot or per-processor output
read data data.protein.gz
read restart old.restart.*
If/then/else via if command
Insert another script via include command
useful for long list of params
Looping via next and jump commands
Invoke a shell command or external program
shell cd subdir1
shell my analyze out.file $n ${param}
Invoke Python from your script: doc/Section python.html
pass LAMMPS data to Python, return values in variables
Python function can callback to LAMMPS
Various ways to run multiple simulations from one script
see doc/Section howto 6.4
Example script for multiple runs

Run 8 successive simulations on P processors:

variable r equal random(1,1000000000,58798)

variable a loop 8
variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
log log.$a
read data.polymer
velocity all create $t $r
fix 1 all nvt $t $t 1.0
dump 1 all atom 1000 dump.$a.*
run 100000
next t
next a
jump in.polymer
Example script for multiple runs

Run 8 successive simulations on P processors:

variable r equal random(1,1000000000,58798)

variable a loop 8
variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
log log.$a
read data.polymer
velocity all create $t $r
fix 1 all nvt $t $t 1.0
dump 1 all atom 1000 dump.$a.*
run 100000
next t
next a
jump in.polymer

Instead, run 8 simulations on 3 partitions until finished:

change a & t to universe-style variables
mpirun -np 12 lmp linux -p 3x4 -in in.polymer
Pre-processing tools to build complex systems

LAMMPS does not build molecular systems or auto-magically

assign force field parameters for you
Pre-processing tools to build complex systems

LAMMPS does not build molecular systems or auto-magically

assign force field parameters for you
Data file must include list of bonds, angles, etc
Data file can include force field assignments
Tools directory has converters for both steps
ch2lmp = CHARMM converter
amber2lmp = AMBER converter
msi2lmp = Accelrys converter
Pre-processing tools to build complex systems

LAMMPS does not build molecular systems or auto-magically

assign force field parameters for you
Data file must include list of bonds, angles, etc
Data file can include force field assignments
Tools directory has converters for both steps
ch2lmp = CHARMM converter
amber2lmp = AMBER converter
msi2lmp = Accelrys converter
Provided builders
Moltemplate (Andrew Jewett)
Pizza.py = chain and patch tools (Python)
Builders that can create LAMMPS input
see website Pre/Post processing page for list
VMD TopoTools (Axel Kohlmeyer)
Avogadro, Packmol, ATB (Auto Topo Builder), EMC
EMC builder tool - Wed PM breakout session
Pair styles

LAMMPS lingo for interaction potentials

Pair styles

LAMMPS lingo for interaction potentials

A pair style can be true pair-wise or many-body
LJ, Coulombic, Buckingham, Morse, Yukawa, ...
EAM, Tersoff, REBO, ReaxFF, ...
Bond/angle/dihedral/improper styles = permanent bonds
Pair styles

LAMMPS lingo for interaction potentials

A pair style can be true pair-wise or many-body
LJ, Coulombic, Buckingham, Morse, Yukawa, ...
EAM, Tersoff, REBO, ReaxFF, ...
Bond/angle/dihedral/improper styles = permanent bonds
Variants optimized for CPU (many-core), KNL, GPU
OPT, GPU, USER-OMP, USER-INTEL, KOKKOS packages
lj/cut, lj/cut/gpu, lj/cut/kk, lj/cut/omp
see doc/Section accelerate.html
Coulomb interactions included in pair style
lj/cut, lj/cut/coul/cut, lj/cut/coul/wolf, lj/cut/coul/long
done to optimize inner loop
Categories of pair styles

Solids
eam, eim, meam, adp, etc
Bio and polymers
charmm, class2, gromacs, dreiding, etc
Reactive
tersoff, bop, airebo, comb, reax/c, etc
Coarse-grained
dpd, granular, sph, peri, colloid, lubricate, brownian, FLD
Aspherical
gayberne, resquared, line, tri, etc
Categories of pair styles

Solids
eam, eim, meam, adp, etc
Bio and polymers
charmm, class2, gromacs, dreiding, etc
Reactive
tersoff, bop, airebo, comb, reax/c, etc
Coarse-grained
dpd, granular, sph, peri, colloid, lubricate, brownian, FLD
Aspherical
gayberne, resquared, line, tri, etc

Pair table for tabulation of any pair-wise interaction

Pair hybrid style enables for hybrid models
polymers on metal
CNTs in water
solid-solid interface between 2 materials
Pair styles

See doc/Section commands.html for full list

Annotated with (gikot) for 5 accelerated variants
Pair styles

See doc/pair style.html for one-line descriptions

Relative CPU cost of potentials

See http://lammps.sandia.gov/bench.html#potentials for details

Can estimate how long your simulation will run
Bond styles (also angle, dihedral, improper)

Used for molecules with fixed bonds

Fix bond/break and bond style quartic can break them
To learn what bond styles LAMMPS has ...
where would you look?
Bond styles (also angle, dihedral, improper)

Used for molecules with fixed bonds

Fix bond/break and bond style quartic can break them
To learn what bond styles LAMMPS has ...
where would you look?
doc/Section commands.html or doc/bond style.html
Long-range Coulombics

KSpace style in LAMMPS lingo, see doc/kspace style.html

Options:
traditional Ewald, scales as O(N 3/2 )
PPPM (like PME), scales as O(N log(N))
MSM, scales as O(N), lj/cut/coul/msm
Additional options:
non-periodic, PPPM (z) vs MSM (xyz)
long-range dispersion (LJ)
Long-range Coulombics

KSpace style in LAMMPS lingo, see doc/kspace style.html

Options:
traditional Ewald, scales as O(N 3/2 )
PPPM (like PME), scales as O(N log(N))
MSM, scales as O(N), lj/cut/coul/msm
Additional options:
non-periodic, PPPM (z) vs MSM (xyz)
long-range dispersion (LJ)
PPPM is fastest choice for most systems
FFTs can scale poorly for large processor counts
MSM can be faster for low-accuracy or large proc counts
Pay attention to cutoff & accuracy settings
can affect performance dramatically (see timing output)
adjust Real vs KSpace work
Fixes

Most flexible feature in LAMMPS

Allow control of “what” happens “when” within each timestep
Loop over timesteps:

communicate ghost atoms

build neighbor list (once in a while)

compute forces
communicate ghost forces

output to screen and files

Fixes

Most flexible feature in LAMMPS

Allow control of “what” happens “when” within each timestep
Loop over timesteps:
fix initial NVE, NVT, NPT, rigid-body integration
communicate ghost atoms
fix neighbor insert particles
build neighbor list (once in a while)
compute forces
communicate ghost forces
fix force SHAKE, langevin drag, wall, spring, gravity
fix final NVE, NVT, NPT, rigid-body integration
fix end volume & T rescaling, diagnostics
output to screen and files
Fixes

∼200 fixes in LAMMPS

You choose what group of atoms to apply fix to
Already saw some in obstacle example:
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix 3 lower setforce 0.0 0.0 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
Fixes

∼200 fixes in LAMMPS

You choose what group of atoms to apply fix to
Already saw some in obstacle example:
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix 3 lower setforce 0.0 0.0 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
To learn what fix styles LAMMPS has ...
where would you look?
Fixes

∼200 fixes in LAMMPS

You choose what group of atoms to apply fix to
Already saw some in obstacle example:
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix 3 lower setforce 0.0 0.0 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
To learn what fix styles LAMMPS has ...
where would you look?
doc/Section commands.html or doc/fix.html
Fixes

∼200 fixes in LAMMPS

You choose what group of atoms to apply fix to
Already saw some in obstacle example:
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix 3 lower setforce 0.0 0.0 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
To learn what fix styles LAMMPS has ...
where would you look?
doc/Section commands.html or doc/fix.html
If you familiarize yourself with fixes,
you’ll know many things LAMMPS can do
Many fixes store output accessible by other commands
thermostat energy
force on wall
rigid body COM
Computes

∼120 computes in LAMMPS

Calculate some property of system, in parallel
Always for the current timestep
To learn what compute styles LAMMPS has ...
Computes

∼120 computes in LAMMPS

Calculate some property of system, in parallel
Always for the current timestep
To learn what compute styles LAMMPS has ...
doc/Section commands.html or doc/compute.html
Computes

Key point:
computes store results of their calculation
other commands invoke them and use the results
e.g. thermo output, dumps, fixes
Output of computes:
global vs per-atom vs local
scalar vs vector vs array
extensive vs intensive values
Computes

Key point:
computes store results of their calculation
other commands invoke them and use the results
e.g. thermo output, dumps, fixes
Output of computes:
global vs per-atom vs local
scalar vs vector vs array
extensive vs intensive values
Examples:
temp & pressure = global scalar or vector
pe/atom = potential energy per atom (vector)
displace/atom = displacement per atom (array)
pair/local & bond/local = per-neighbor or per-bond info
Many computes are useful with averaging fixes:
fix ave/time, ave/chunk (spatial), ave/atom
fix ave/histo, ave/correlate
Thermo output

One line of output every N timesteps to screen and log file

See doc/thermo style.html
Thermo output

One line of output every N timesteps to screen and log file

See doc/thermo style.html
Any scalar can be output:
dozens of keywords: temp, pyy, eangle, lz, cpu
any output of a compute or fix: c ID, f ID[N], c ID[N][M]
fix ave/time stores time-averaged quantities
equal-style variable: v MyVar
one value from atom-style variable: v xx[N]
any property for one atom: q, fx, quat, etc
Thermo output

One line of output every N timesteps to screen and log file

See doc/thermo style.html
Any scalar can be output:
dozens of keywords: temp, pyy, eangle, lz, cpu
any output of a compute or fix: c ID, f ID[N], c ID[N][M]
fix ave/time stores time-averaged quantities
equal-style variable: v MyVar
one value from atom-style variable: v xx[N]
any property for one atom: q, fx, quat, etc
Post-process via:
tools/python/logplot.py log.lammps X Y (via GnuPlot)
tools/python/log2txt.py log.lammps data.txt X Y ...
know how to read thermo output across multiple runs
Dump output

Snapshot of per-atom values every N timesteps

See doc/dump.html
Dump output

Snapshot of per-atom values every N timesteps

See doc/dump.html
Styles
atom, custom (both native LAMMPS)
VMD will auto-read if file named *.lammpstraj
xyz for coords only
cfg for AtomEye
DCD, XTC for CHARMM, NAMD, GROMACS
good for back-and-forth runs and analysis
HDF5 and NetCDF and VTK (Paraview)
Two additional styles
local: per-neighbor, per-bond, etc info
image: instant picture, rendered in parallel
Dump output

Any per-atom quantity can be output

dozens of keywords: id, type, x, xs, xu, mux, omegax, ...
any output of a compute or fix: f ID, c ID[M]
atom-style variable: v foo
Dump output

Any per-atom quantity can be output

dozens of keywords: id, type, x, xs, xu, mux, omegax, ...
any output of a compute or fix: f ID, c ID[M]
atom-style variable: v foo
Additional options:
control which atoms by group or region
control which atoms by threshold
dump modify thresh c pe > 3.0
text or binary or gzipped
one big file or per snapshot or per proc
see dump modify fileper or nfile
MPIIO package for parallel dump output
Dump output

Any per-atom quantity can be output

dozens of keywords: id, type, x, xs, xu, mux, omegax, ...
any output of a compute or fix: f ID, c ID[M]
atom-style variable: v foo
Additional options:
control which atoms by group or region
control which atoms by threshold
dump modify thresh c pe > 3.0
text or binary or gzipped
one big file or per snapshot or per proc
see dump modify fileper or nfile
MPIIO package for parallel dump output
Post-run conversion
tools/python/dump2cfg.py, dump2pdb.py, dump2xyz.py
Pizza.py dump, cfg, ensight, pdb, svg, vtk, xyz
Parallelization in LAMMPS

Physical domain divided into 3d bricks

One brick per processor
Atoms carry properties &
topology as they migrate
Comm of ghost atoms within cutoff
6-way local stencil
Short-range forces ⇒
CPU cost scales as O(N/P)
Parallel performance

See http://lammps.sandia.gov/bench.html
Strong or weak scaling, O(N/P) until too few atoms/proc
Parallel performance

See http://lammps.sandia.gov/bench.html
Strong or weak scaling, O(N/P) until too few atoms/proc

Exercise: run bench/in.lj, change N and P, is it O(N/P) ?

lmp linux -v x 2 -v y 2 -v z 2 < in.lj
mpirun -np 2 lmp linux < in.lj
How to speed-up your simulations

See doc/Section accelerate.html of manual

1 Many ideas for long-range Coulombics
PPPM with 2 vs 4 FFTs (smoothed PPPM)
PPPM with staggered grid
run style verlet/split
processor layout
How to speed-up your simulations

See doc/Section accelerate.html of manual

1 Many ideas for long-range Coulombics
PPPM with 2 vs 4 FFTs (smoothed PPPM)
PPPM with staggered grid
run style verlet/split
processor layout
2 OPT, GPU, USER-INTEL, USER-OMP, KOKKOS packages
OPT for CPU
GPU for NVIDIA GPUs with multiple cores/GPU
USER-INTEL for Intel CPU and KNL
USER-OMP for OpenMP on multicore CPUs
KOKKOS for OpenMP, KNL, GPU
Benchmark info at http://lammps.sandia.gov/bench.html
new version in next month, focus on accelerator packages
Stan Moore, Performance breakout, Wed PM
How to speed-up your simulations

3 Increase time scale via timestep size

fix shake for rigid bonds (2 fs)
run style respa for hierarchical timesteps (4 fs)

4 Increase length scale via coarse graining

all-atom vs united-atom vs bead-spring
mesoscale models:
ASPHERE, BODY, COLLOID, FLD packages
GRANULAR, PERI, RIGID, SRD packages
see doc/Section packages.html for details
Dan Bolintineanu, Coarse-graining breakout, Wed PM
Quick tour of more advanced topics

Units
see doc/units.html
LJ, real, metal, cgs, si
all input/output in one unit system
Ensembles
see doc/Section howto.html 6.16
one or more thermostats (by group)
single barostat
rigid body dynamics
Hybrid models
pair style hybrid and hybrid/overlay
atom style hybrid sphere bond ...
Quick tour of more advanced topics

Aspherical particles
see doc/Section howto.html 6.14
ellipsoidal, lines, triangles, rigid bodies
ASPHERE package
Mesoscale and continuum models
Corase-grained packages mentioned 2 slides ago
PERI package for Peridynamics
USER-ATC package for atom-to-continuum (FE)
USER-SPH, USER-SMD packages for smoothed particle hydro
GRANULAR package for granular media
LIGGGHTS simulator for DEM (external code)
www.liggghts.com/www.cfdem.com
built on top of LAMMPS
Quick tour of more advanced topics

Multi-replica modeling
REPLICA package, see doc/Section howto.html 6.14
parallel tempering, PRD, TAD, NEB
Load balancing
balance command for static LB
fix balance command for dynamic LB
adjusting proc dividers, or recursive coordinate bisection
weighted balancing now an option
Quick tour of more advanced topics

Energy minimization

Via usual dynamics

pair style soft
fix nve/limit and fix viscous
Via gradient-based minimization
min style cg, htfn, sd
Via damped-dynamics minimization
min style quickmin and fire
used for nudged-elastic band (NEB)
Quick tour of more advanced topics

Energy minimization

Via usual dynamics

pair style soft
fix nve/limit and fix viscous
Via gradient-based minimization
min style cg, htfn, sd
Via damped-dynamics minimization
min style quickmin and fire
used for nudged-elastic band (NEB)

Packages, packages, packages ...

package = collection of commands with a theme,
or wrapper on an external or provided library
∼60 packages in LAMMPS, wide variety
see doc/Section packages.html for details
Quick tour of more advanced topics

Use LAMMPS as a library

doc/Section howto.html
6.10 and 6.19
C-style interface
(C, C++, Fortran,
Python)
examples/COUPLE dir
python and
python/examples
directories
Customizing and modifying LAMMPS

95% of LAMMPS is customized add-on classes, via styles

Write a new derived class, drop into src, re-compile
Customizing and modifying LAMMPS

95% of LAMMPS is customized add-on classes, via styles

Write a new derived class, drop into src, re-compile
Resources:
doc/Section modify.html
doc/PDF/Developer.pdf
class hierarchy & timestep structure
Workshops and Tutorial links on LAMMPS web site:
slides for hackers/developers breakout of past workshops
Come to Developers breakout session, Wed PM
Please contribute your new code to the LAMMPS distro!
doc/Section modify 15:
Submitting new features for inclusion in LAMMPS
GitHub site: https://github.com/lammps/lammps
What have people already done with LAMMPS?

Pictures: http://lammps.sandia.gov/pictures.html
Movies: http://lammps.sandia.gov/movies.html
What have people already done with LAMMPS?

Pictures: http://lammps.sandia.gov/pictures.html
Movies: http://lammps.sandia.gov/movies.html

Papers: http://lammps.sandia.gov/papers.html
authors, titles, abstracts for 1000s of papers