Fill in package descriptions

</tr>

<tr>

  <td><code>ENABLE_MOLECULE</code></td>

  <td></td>

  <td>

  A large number of atom, pair, bond, angle, dihedral, improper styles that are

  used to model molecular systems with fixed covalent bonds. The pair styles

  include the Dreiding (hydrogen-bonding) and CHARMM force fields, and a TIP4P

  water model.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_PERI</code></td>

  <td></td>

  <td>

  An atom style, several pair styles which implement different Peridynamics

  materials models, and several computes which calculate diagnostics.

  Peridynamics is a a particle-based meshless continuum model.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_QEQ</code></td>

  <td></td>

  <td>

  Several fixes for performing charge equilibration (QEq) via different

  algorithms. These can be used with pair styles that perform QEq as part of

  their formulation.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_REAX</code></td>

  <td></td>

  <td>

  A pair style which wraps a Fortran library which implements the ReaxFF

  potential, which is a universal reactive force field. See the USER-REAXC

  package for an alternate implementation in C/C++. Also a fix reax/bonds

  command for monitoring molecules as bonds are created and destroyed.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_REPLICA</code></td>

  <td></td>

  <td>

  A collection of multi-replica methods which can be used when running multiple

  LAMMPS simulations (replicas). See Section 6.5 for an overview of how to run

  multi-replica simulations in LAMMPS. Methods in the package include nudged

  elastic band (NEB), parallel replica dynamics (PRD), temperature accelerated

  dynamics (TAD), parallel tempering, and a verlet/split algorithm for

  performing long-range Coulombics on one set of processors, and the remainder

  of the force field calcalation on another set.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_RIGID</code></td>

  <td></td>

  <td>

  Fixes which enforce rigid constraints on collections of atoms or particles.

  This includes SHAKE and RATTLE, as well as varous rigid-body integrators for a

  few large bodies or many small bodies. Also several computes which calculate

  properties of rigid bodies.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_SHOCK</code></td>

  <td></td>

  <td>

  Fixes for running impact simulations where a shock-wave passes through a

  material.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_SNAP</code></td>

  <td></td>

  <td>

  A pair style for the spectral neighbor analysis potential (SNAP). SNAP is

  methodology for deriving a highly accurate classical potential fit to a large

  archive of quantum mechanical (DFT) data. Also several computes which analyze

  attributes of the potential.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_SRD</code></td>

  <td></td>

  <td>

  A pair of fixes which implement the Stochastic Rotation Dynamics (SRD) method

  for coarse-graining of a solvent, typically around large colloidal particles.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_PYTHON</code></td>

  <td>Enable all default packages</td>

  <td>Enable support for Python scripting inside of LAMMPS.</td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_MSCG</code></td>

  <td>Enable all default packages</td>

  <td>

  A fix mscg command which can parameterize a Multi-Scale Coarse-Graining (MSCG)

  model using the open-source MS-CG library.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_MPIIO</code></td>

  <td>Enable all default packages</td>

  <td>

  Support for parallel output/input of dump and restart files via the MPIIO library.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_POEMS</code></td>

  <td>Enable all default packages</td>

  <td>

  A fix that wraps the Parallelizable Open source Efficient Multibody Software

  (POEMS) library, which is able to simulate the dynamics of articulated body

  systems. These are systems with multiple rigid bodies (collections of

  particles) whose motion is coupled by connections at hinge points.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_LATTE</code></td>

  <td>Enable all default packages</td>

  <td>

  A fix command which wraps the LATTE DFTB code, so that molecular dynamics can

  be run with LAMMPS using density-functional tight-binding quantum forces

  calculated by LATTE.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

<tbody>

<tr>

  <td><code>ENABLE_USER-ATC</code></td>

  <td></td>

  <td>

  ATC stands for atoms-to-continuum. This package implements a fix atc command

  to either couple molecular dynamics with continuum finite element equations or

  perform on-the-fly conversion of atomic information to continuum fields.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-AWPMD</code></td>

  <td></td>

  <td>

  AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This package

  implements an atom, pair, and fix style which allows electrons to be treated

  as explicit particles in a classical molecular dynamics model.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-CGDNA</code></td>

  <td></td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

    <dt><code>on</code></dt>

  </dl>

  Several pair styles, a bond style, and integration fixes for coarse-grained

  models of single- and double-stranded DNA based on the oxDNA model of Doye,

  Louis and Ouldridge at the University of Oxford. This includes Langevin-type

  rigid-body integrators with improved stability.

  </td>

</tr>

<tr>

  <td><code>ENABLE_USER-MESO</code></td>

  <td></td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-CGSDK</code></td>

  <td></td>

  <td>

  Several pair styles and an angle style which implement the coarse-grained SDK

  model of Shinoda, DeVane, and Klein which enables simulation of ionic liquids,

  electrolytes, lipids and charged amino acids.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-COLVARS</code></td>

  <td></td>

  <td>

  COLVARS stands for collective variables, which can be used to implement

  various enhanced sampling methods, including Adaptive Biasing Force,

  Metadynamics, Steered MD, Umbrella Sampling and Restraints. A fix colvars

  command is implemented which wraps a COLVARS library, which implements these

  methods. simulations.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-DIFFRACTION</code></td>

  <td></td>

  <td>

  Two computes and a fix for calculating x-ray and electron diffraction

  intensities based on kinematic diffraction theory.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-DPD</code></td>

  <td></td>

  <td>

  DPD stands for dissipative particle dynamics. This package implements

  coarse-grained DPD-based models for energetic, reactive molecular crystalline

  materials. It includes many pair styles specific to these systems, including

  for reactive DPD, where each particle has internal state for multiple species

  and a coupled set of chemical reaction ODEs are integrated each timestep.

  Highly accurate time integrators for isothermal, isoenergetic, isobaric and

  isenthalpic conditions are included. These enable long timesteps via the

  Shardlow splitting algorithm.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-DRUDE</code></td>

  <td></td>

  <td>

  Fixes, pair styles, and a compute to simulate thermalized Drude oscillators as

  a model of polarization.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-EFF</code></td>

  <td></td>

  <td>

  EFF stands for electron force field which allows a classical MD code to model

  electrons as particles of variable radius. This package contains atom, pair,

  fix and compute styles which implement the eFF as described in A.

  Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC, 2010. The eFF

  potential was first introduced by Su and Goddard, in 2007.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-FEP</code></td>

  <td></td>

  <td>

  FEP stands for free energy perturbation. This package provides methods for

  performing FEP simulations by using a fix adapt/fep command with soft-core

  pair potentials, which have a “soft” in their style name.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-H5MD</code></td>

  <td></td>

  <td>

  H5MD stands for HDF5 for MD. HDF5 is a portable, binary, self-describing file

  format, used by many scientific simulations. H5MD is a format for molecular

  simulations, built on top of HDF5. This package implements a dump h5md command

  to output LAMMPS snapshots in this format.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-LB</code></td>

  <td></td>

  <td>

  Fixes which implement a background Lattice-Boltzmann (LB) fluid, which can be

  used to model MD particles influenced by hydrodynamic forces.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-MANIFOLD</code></td>

  <td></td>

  <td>

  Several fixes and a “manifold” class which enable simulations of particles

  constrained to a manifold (a 2D surface within the 3D simulation box). This is

  done by applying the RATTLE constraint algorithm to formulate single-particle

  constraint functions g(xi,yi,zi) = 0 and their derivative (i.e. the normal of

  the manifold) n = grad(g).

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-MEAMC</code></td>

  <td></td>

  <td>

  A pair style for the modified embedded atom (MEAM) potential translated from

  the Fortran version in the MEAM package to plain C++. In contrast to the MEAM

  package, no library needs to be compiled and the pair style can be

  instantiated multiple times.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

    <dt><code>on</code></dt>

  </dl>

  </td>

</tr>

<tr>

  <td><code>ENABLE_USER-MESO</code></td>

  <td>

  Several extensions of the the dissipative particle dynamics (DPD) method.

  Specifically, energy-conserving DPD (eDPD) that can model non-isothermal

  processes, many-body DPD (mDPD) for simulating vapor-liquid coexistence, and

  transport DPD (tDPD) for modeling advection-diffusion-reaction systems. The

  equations of motion of these DPD extensions are integrated through a modified

  velocity-Verlet (MVV) algorithm.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-MGPT</code></td>

  <td></td>

  <td>

  A pair style which provides a fast implementation of the quantum-based MGPT

  multi-ion potentials. The MGPT or model GPT method derives from

  first-principles DFT-based generalized pseudopotential theory (GPT) through a

  series of systematic approximations valid for mid-period transition metals

  with nearly half-filled d bands. The MGPT method was originally developed by

  John Moriarty at LLNL. The pair style in this package calculates forces and

  energies using an optimized matrix-MGPT algorithm due to Tomas Oppelstrup at

  LLNL.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-MISC</code></td>

  <td></td>

  <td>

  A potpourri of (mostly) unrelated features contributed to LAMMPS by users.

  Each feature is a single fix, compute, pair, bond, angle, dihedral, improper,

  or command style.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-MOFFF</code></td>

  <td></td>

  <td>

  Pair, angle and improper styles needed to employ the MOF-FF force field by

  Schmid and coworkers with LAMMPS. MOF-FF is a first principles derived force

  field with the primary aim to simulate MOFs and related porous framework

  materials, using spherical Gaussian charges. It is described in S. Bureekaew

  et al., Phys. Stat. Sol. B 2013, 250, 1128-1141. For the usage of MOF-FF see

  the example in the example directory as well as the MOF+ website.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-MOLFILE</code></td>

  <td></td>

  <td>

  A dump molfile command which uses molfile plugins that are bundled with the

  VMD molecular visualization and analysis program, to enable LAMMPS to dump

  snapshots in formats compatible with various molecular simulation tools.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-NETCDF</code></td>

  <td></td>

  <td>

  Dump styles for writing NetCDF formatted dump files. NetCDF is a portable,

  binary, self-describing file format developed on top of HDF5. The file

  contents follow the AMBER NetCDF trajectory conventions

  (http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-PHONON</code></td>

  <td></td>

  <td>

  A fix phonon command that calculates dynamical matrices, which can then be

  used to compute phonon dispersion relations, directly from molecular dynamics

  simulations.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

</tr>

<tr>

  <td><code>ENABLE_USER-QTB</code></td>

  <td></td>

  <td>

  Two fixes which provide a self-consistent quantum treatment of vibrational modes in a classical molecular dynamics simulation. By coupling the MD simulation to a colored thermostat, it introduces zero point energy into the system, altering the energy power spectrum and the heat capacity to account for their quantum nature. This is useful when modeling systems at temperatures lower than their classical limits or when temperatures ramp across the classical limits in a simulation.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

  </td>

</tr>

<tr>

  <td><code>ENABLE_USER-REAXC</code></td>

  <td></td>

  <td><code>ENABLE_USER-QUIP</code></td>

  <td>

  A pair_style quip command which wraps the QUIP libAtoms library, which

  includes a variety of interatomic potentials, including Gaussian Approximation

  Potential (GAP) models developed by the Cambridge University group.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

  </td>

</tr>

<tr>

  <td><code>ENABLE_USER-SMD</code></td>

  <td></td>

  <td><code>ENABLE_USER-QMMM</code></td>

  <td>

  A fix qmmm command which allows LAMMPS to be used in a QM/MM simulation,

  currently only in combination with the Quantum ESPRESSO package.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

  </td>

</tr>

<tr>

  <td><code>ENABLE_USER-SMTBQ</code></td>

  <td></td>

  <td><code>ENABLE_USER-REAXC</code></td>

  <td>

  A pair style which implements the ReaxFF potential in C/C++ (in contrast to

  the REAX package and its Fortran library). ReaxFF is universal reactive force

  field. See the src/USER-REAXC/README file for more info on differences between

  the two packages. Also two fixes for monitoring molecules as bonds are created

  and destroyed.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

  </td>

</tr>

<tr>

  <td><code>ENABLE_USER-SPH</code></td>

  <td></td>

  <td><code>ENABLE_USER-SMD</code></td>

  <td>

  An atom style, fixes, computes, and several pair styles which implements

  smoothed Mach dynamics (SMD) for solids, which is a model related to smoothed

  particle hydrodynamics (SPH) for liquids (see the USER-SPH package).

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

  </td>

</tr>

<tr>

  <td><code>ENABLE_USER-UEF</code></td>

  <td></td>

  <td><code>ENABLE_USER-SMTBQ</code></td>

  <td>

  A pair style which implements a Second Moment Tight Binding model with QEq

  charge equilibration (SMTBQ) potential for the description of ionocovalent

  bonds in oxides.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

  </td>

</tr>

<tr>

  <td><code>ENABLE_USER-VTK</code></td>

  <td></td>

  <td><code>ENABLE_USER-SPH</code></td>

  <td>

  An atom style, fixes, computes, and several pair styles which implements

  smoothed particle hydrodynamics (SPH) for liquids. See the related USER-SMD

  package package for smooth Mach dynamics (SMD) for solids.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

  </td>

</tr>

<tr>

  <td><code>ENABLE_USER-QUIP</code></td>

  <td></td>

  <td><code>ENABLE_USER-TALLY</code></td>

  <td>

  Several compute styles that can be called when pairwise interactions are

  calculated to tally information (forces, heat flux, energy, stress, etc) about

  individual interactions.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

  </td>

</tr>

<tr>

  <td><code>ENABLE_USER-QMMM</code></td>

  <td></td>

  <td><code>ENABLE_USER-UEF</code></td>

  <td>

  A fix style for the integration of the equations of motion under extensional

  flow with proper boundary conditions, as well as several supporting compute

  styles and an output option.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

    <dt><code>on</code></dt>

  </dl>

  </td>

</tr>

<tr>

  <td><code>ENABLE_USER-VTK</code></td>

  <td>

  A dump vtk command which outputs snapshot info in the VTK format, enabling

  visualization by Paraview or other visualization packages.

  </td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

<tbody>

<tr>

  <td><code>MKL_INCLUDE_DIRS</code></td>

  <td>Optimization for FFT</td>

  <td></td>

  <td>

  </td>

</tr>

<tr>

  <td><code>MKL_LIBRARIES</code></td>

  <td>Optimization for FFT</td>

  <td></td>

  <td>

  </td>

</tr>

<tbody>

<tr>

  <td><code>FFTW2_INCLUDE_DIRS</code></td>

  <td>Optimization for FFT</td>

  <td></td>

  <td>

  </td>

</tr>

<tr>

  <td><code>FFTW2_LIBRARIES</code></td>

  <td>Optimization for FFT</td>

  <td></td>

  <td>

  </td>

</tr>

<tbody>

<tr>

  <td><code>FFTW3_INCLUDE_DIRS</code></td>

  <td>Optimization for FFT</td>

  <td></td>

  <td>

  </td>

</tr>

<tr>

  <td><code>FFTW3_LIBRARIES</code></td>

  <td>Optimization for FFT</td>

  <td></td>

  <td>

  </td>

</tr>