<TR><TD >peptide</TD><TD >  dynamics of a small solvated peptide chain (5-mer)</TD></TR>

<TR><TD >peri</TD><TD >     Peridynamics example of cylinder hit by projectile</TD></TR>

<TR><TD >pour</TD><TD >     pouring of granular particles into a 3d box, then chute flow</TD></TR>

<TR><TD >prd</TD><TD >	  parallel replica dynamics of a vacancy diffusion in bulk Si</TD></TR>

<TR><TD >reax</TD><TD >     simple example for ReaxFF force field</TD></TR>

<TR><TD >rigid</TD><TD >    rigid bodies modeled as independent or coupled</TD></TR>

<TR><TD >shear</TD><TD >    sideways shear applied to 2d solid, with and without a void 

peptide:  dynamics of a small solvated peptide chain (5-mer)

peri:     Peridynamics example of cylinder hit by projectile

pour:     pouring of granular particles into a 3d box, then chute flow

prd:	  parallel replica dynamics of a vacancy diffusion in bulk Si

reax:     simple example for ReaxFF force field

rigid:    rigid bodies modeled as independent or coupled

shear:    sideways shear applied to 2d solid, with and without a void :tb(s=:)

</P>

<P>These are new features we'd like to eventually add to LAMMPS.  Some

are being worked on; some haven't been implemented because of lack of

time or interest; others are just a lot of work!

time or interest; others are just a lot of work!  See <A HREF = "http://lammps.sandia.gov/future.html">this

page</A> on the LAMMPS WWW site for more details.

</P>

<UL><LI>coupling to finite elements

<LI>new ReaxFF implementation (in addition to existing one)

<LI>stochastic rotation dynamics

<UL><LI>Coupling to finite elements for streess-strain

<LI>New ReaxFF implementation

<LI>Nudged elastic band

<LI>Temperature accelerated dynamics

<LI>Triangulated particles

<LI>Stochastic rotation dynamics

<LI>Stokesian dynamics via fast lubrication dynamics

<LI>NPT with changing box shape (Parinello-Rahman)

<LI>long-range point-dipole solver

<LI>torsional shear boundary conditions and temperature calculation 

<LI>Long-range point-dipole solver

<LI>Per-atom energy and stress for long-range Coulombics

<LI>Long-range Coulombics via Ewald and PPPM for triclinic boxes

<LI>Metadynamics

<LI>Direct Simulation Monte Carlo - DSMC 

</UL>

<HR>

These are new features we'd like to eventually add to LAMMPS.  Some

are being worked on; some haven't been implemented because of lack of

time or interest; others are just a lot of work!

time or interest; others are just a lot of work!  See "this

page"_lwsfuture on the LAMMPS WWW site for more details.

coupling to finite elements

new ReaxFF implementation (in addition to existing one)

stochastic rotation dynamics

:link(lwsfuture,http://lammps.sandia.gov/future.html)

Coupling to finite elements for streess-strain

New ReaxFF implementation

Nudged elastic band

Temperature accelerated dynamics

Triangulated particles

Stochastic rotation dynamics

Stokesian dynamics via fast lubrication dynamics

NPT with changing box shape (Parinello-Rahman)

long-range point-dipole solver

torsional shear boundary conditions and temperature calculation :ul

Long-range point-dipole solver

Per-atom energy and stress for long-range Coulombics

Long-range Coulombics via Ewald and PPPM for triclinic boxes

Metadynamics

Direct Simulation Monte Carlo - DSMC :ul

:line

<LI>  spatial-decomposition of simulation domain for parallelism

<LI>  open-source distribution

<LI>  highly portable C++

<LI>  optional libraries needed: MPI and single-processor FFT

<LI>  optional libraries used: MPI and single-processor FFT

<LI>  easy to extend with new features and functionality

<LI>  in parallel, run one or multiple simulations simultaneously

<LI>  runs from an input script

<LI>  syntax for defining and using variables and formulas

<LI>  syntax for looping over runs and breaking out of loops

<LI>  run a series of simluations from one script 

<LI>  run one or multiple simulations simultaneously (in parallel) from one script 

</UL>

<H4>Kinds of systems LAMMPS can simulate 

<H4>Particle and model types 

</H4>

<P>(<A HREF = "atom_style.html">atom style</A> command)

</P>

<UL><LI>  atomic (e.g. box of Lennard-Jonesium)

<LI>  bead-spring polymers

<UL><LI>  atoms

<LI>  coarse-grained particles (e.g. bead-spring polymers)

<LI>  united-atom polymers or organic molecules

<LI>  all-atom polymers, organic molecules, proteins, DNA

<LI>  metals

<LI>  granular materials

<LI>  coarse-grained mesoscale models

<LI>  ellipsoidal particles

<LI>  extended spherical and ellipsoidal particles

<LI>  point dipolar particles

<LI>  rigid collections of particles

<LI>  hybrid combinations of these 

</UL>

<H4>Force fields 

<UL><LI>  pairwise potentials: Lennard-Jones, Buckingham, Morse,     Yukawa, soft, class 2 (COMPASS), tabulated

<LI>  charged pairwise potentials: Coulombic, point-dipole

<LI>  manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM),     Stillinger-Weber, Tersoff, AI-REBO, ReaxFF

<LI>  coarse-grain potentials: DPD, GayBerne, REsquared, colloidal

<LI>  coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO

<LI>  mesoscopic potentials: granular, Peridynamics

<LI>  bond potentials: harmonic, FENE, Morse, nonlinear, class 2,     quartic (breakable)

<LI>  angle potentials: harmonic, CHARMM, cosine, cosine/squared,     class 2 (COMPASS)

<LI>  dihedral potentials: harmonic, CHARMM, multi-harmonic, helix,     class 2 (COMPASS), OPLS

<LI>  improper potentials: harmonic, cvff, class 2 (COMPASS)

<LI>  hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation

<LI>  overlaid potentials: superposition of multiple pair potentials

<LI>  polymer potentials: all-atom, united-atom, bead-spring, breakable

<LI>  water potentials: TIP3P, TIP4P, SPC

<LI>  implicit solvent potentials: hydrodynamic lubrication, Debye

<LI>  long-range Coulombics and dispersion: Ewald,     PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones

<LI>  force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options

<LI>  handful of GPU-enabled pair styles 

</UL>

<H4>Creation of atoms 

<P>  hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation

  overlaid potentials: superposition of multiple pair potentials

</P>

<H4>Atom creation 

</H4>

<P>(<A HREF = "read_data.html">read_data</A>, <A HREF = "lattice.html">lattice</A>,

<A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "delete_atoms.html">delete_atoms</A>,

<A HREF = "displace_atoms.html">displace_atoms</A> commands)

<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "replicate.html">replicate</A> commands)

</P>

<UL><LI>  read in atom coords from files

<LI>  create atoms on one or more lattices (e.g. grain boundaries)

<LI>  delete geometric or logical groups of atoms (e.g. voids)

<LI>  replicate existing atoms multiple times

<LI>  displace atoms 

</UL>

<H4>Ensembles, constraints, and boundary conditions 

<LI>  pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions

<LI>  simulation box deformation (tensile and shear)

<LI>  harmonic (umbrella) constraint forces

<LI>  independent or coupled rigid body integration

<LI>  rigid body constraints

<LI>  SHAKE bond and angle constraints

<LI>  bond breaking, formation, swapping

<LI>  walls of various kinds

<LI>  targeted molecular dynamics (TMD) and steered molecule dynamics (SMD) constraints

<LI>  non-equilibrium molecular dynamics (NEMD)

<LI>  variety of additional boundary conditions and constraints 

</UL>

<H4>Integrators 

</H4>

<P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "temper.html">temper</A> commands) 

<P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A> commands) 

</P>

<UL><LI>  velocity-Verlet integrator

<LI>  Brownian dynamics

<LI>  rigid body integration

<LI>  energy minimization via conjugate gradient or steepest descent relaxation

<LI>  rRESPA hierarchical timestepping 

<LI>  parallel tempering (replica exchange) 

</UL>

<H4>Diagnostics 

</H4>

<P>(<A HREF = "fix.html">fix</A> command, <A HREF = "compute.html">compute</A> command) 

</P>

<UL><LI>  see the various flavors of the fix and compute commands 

<UL><LI>  see the various flavors of the <A HREF = "fix.html">fix</A> and <A HREF = "compute.html">compute</A> commands 

</UL>

<H4>Output 

</H4>

<LI>  user-defined system-wide (log file) or per-atom (dump file) calculations

<LI>  spatial and time averaging of per-atom quantities

<LI>  time averaging of system-wide quantities

<LI>  atom snapshots in native, XYZ, XTC, DCD formats 

<LI>  atom snapshots in native, XYZ, XTC, DCD, CFG formats 

</UL>

<H4>Pre- and post-processing 

</H4>

<P>Our group has also written and released a separate toolkit called

<UL><LI>Various pre- and post-processing serial tools are packaged

with LAMMPS; see these <A HREF = "Section_tools.html">doc pages</A>. 

<LI>Our group has also written and released a separate toolkit called

<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,

plotting, and visualization for LAMMPS simulations.  Pizza.py is

written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the

Pizza.py WWW site</A>. 

</P>

</UL>

<H4>Specialized features 

</H4>

<P>These are LAMMPS capabilities which you may not think of as typical

molecular dynamics options:

</P>

<UL><LI><A HREF = "fix_imd.html">real-time visualization and interactive MD</A>

<LI><A HREF = "fix_atc.html">atom-to-continuum coupling</A> with finite elements

<LI>coupled rigid body integration via the <A HREF = "fix_poems.html">POEMS</A> library

<LI><A HREF = "temper.html">parallel tempering</A>

<LI><A HREF = "prd.html">parallel replica dynamics</A>

<LI><A HREF = "pair_dsmc.html">Direct Simulation Monte Carlo</A> for low-density fluids

<LI><A HREF = "pair_peri.html">Peridynamics mesoscale modeling</A>

<LI><A HREF = "fix_tmd.html">targeted</A> and <A HREF = "fix_smd.html">steered</A> molecular dynamics

<LI><A HREF = "fix_ttm.html">two-temperature electron model</A> 

</UL>

<HR>

<A NAME = "1_3"></A><H4>1.3 LAMMPS non-features 

<DIV ALIGN=center><TABLE  BORDER=1 >

<TR><TD >pair yukawa/colloid </TD><TD > Randy Schunk (Sandia)</TD></TR>

<TR><TD >fix wall/colloid </TD><TD > Jeremy Lechman (Sandia)</TD></TR>

<TR><TD >pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling </TD><TD > Paul Crozier (Sandia)</TD></TR>

<TR><TD >fix imd for real-time viz and interactive MD </TD><TD > Axel Kohlmeyer (Temple Univ)</TD></TR>

<TR><TD >concentration-dependent EAM potential </TD><TD > Alexander Stukowski (Technical University of Darmstadt)</TD></TR>

<TR><TD >parallel replica dymamics (PRD) </TD><TD > Mike Brown (Sandia)</TD></TR>

<TR><TD >min_style hftn </TD><TD > Todd Plantenga (Sandia)</TD></TR>

<TR><TD >fix atc </TD><TD > Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)</TD></TR>

<TR><TD >dump cfg </TD><TD > Liang Wan (Chinese Academy of Sciences)</TD></TR>

<TR><TD >fix nvt with Nose/Hoover chains </TD><TD > Andy Ballard (U Maryland)</TD></TR>

<TR><TD >pair_style lj/cut/gpu, pair_style gayberne/gpu </TD><TD > Mike Brown (Sandia)</TD></TR>

<TR><TD >pair_style lj96/cut, bond_style table, angle_style table </TD><TD > Chuanfu Luo</TD></TR>

<TR><TD >fix langevin tally </TD><TD > Carolyn Phillips (U Michigan)</TD></TR>

<TR><TD >compute heat/flux for Green-Kubo </TD><TD > Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)</TD></TR>

<TR><TD >region cone </TD><TD > Pim Schravendijk</TD></TR>

<TR><TD >fix reax/bonds </TD><TD > Aidan Thompson (Sandia)</TD></TR>