<span id="coreshell"></span><h3>4.1.6. CORESHELL package<a class="headerlink" href="#coreshell-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: Compute and pair styles that implement the adiabatic
core/shell model for polarizability. The compute temp/cs command
measures the temperature of a system with core/shell particles. The
pair styles augment Born, Buckingham, and Lennard-Jones styles with
core/shell capabilities. See <a class="reference internal" href="Section_howto.html#howto-26"><span>Section howto 6.26</span></a> for an overview of how to use the
<span id="kokkos"></span><h3>4.1.11. KOKKOS package<a class="headerlink" href="#kokkos-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles
which run with the Kokkos library to provide optimization for
multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in
native mode). All of them have a “kk” in their style name. <a class="reference internal" href="accelerate_kokkos.html"><em>Section accelerate kokkos</em></a> gives details of what
hardware and software is required on your system, and how to build and
use this package. See the GPU, OPT, USER-CUDA, USER-INTEL, USER-OMP
packages, which also provide optimizations for the same range of
hardware.</p>
<p>Building with the KOKKOS package requires choosing which of 3 hardware
options you are optimizing for: CPU acceleration via OpenMP, GPU
acceleration, or Intel Xeon Phi. (You can build multiple times to
create LAMMPS executables for different hardware.) It also requires a
C++11 compatible compiler. For GPUs, the NVIDIA “nvcc” compiler is
used, and an appopriate KOKKOS_ARCH setting should be made in your
Makefile.machine for your GPU hardware and NVIDIA software.</p>
<p>The simplest way to do this is to use Makefile.kokkos_cuda or
Makefile.kokkos_omp or Makefile.kokkos_phi in src/MAKE/OPTIONS, via
“make kokkos_cuda” or “make kokkos_omp” or “make kokkos_phi”. (Check
the KOKKOS_ARCH setting in Makefile.kokkos_cuda), Or, as illustrated
below, you can use the Make.py script with its “-kokkos” option to
choose which hardware to build for. Type “python src/Make.py -h
-kokkos” to see the details. If these methods do not work on your
system, you will need to read the <a class="reference internal" href="accelerate_kokkos.html"><em>Section accelerate kokkos</em></a> doc page for details of what
Makefile.machine settings are needed.</p>
<p>To install via make or Make.py for each of 3 hardware options:</p>
<span id="kspace"></span><h3>4.1.12. KSPACE package<a class="headerlink" href="#kspace-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: A variety of long-range Coulombic solvers, and pair styles
which compute the corresponding short-range portion of the pairwise
Coulombic interactions. These include Ewald, particle-particle
particle-mesh (PPPM), and multilevel summation method (MSM) solvers.</p>
<p>Building with the KSPACE package requires a 1d FFT library be present
on your system for use by the PPPM solvers. This can be the KISS FFT
library provided with LAMMPS, or 3rd party libraries like FFTW or a
vendor-supplied FFT library. See step 6 of <a class="reference internal" href="Section_start.html#start-2-2"><span>Section start 2.2.2</span></a> of the manual for details of how
to select different FFT options in your machine Makefile. The Make.py
tool has an “-fft” option which can insert these settings into your
machine Makefile automatically. Type “python src/Make.py -h -fft” to
<span id="opt"></span><h3>4.1.19. OPT package<a class="headerlink" href="#opt-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: A handful of pair styles with an “opt” in their style name
which are optimized for improved CPU performance on single or multiple
cores. These include EAM, LJ, CHARMM, and Morse potentials. <a class="reference internal" href="accelerate_opt.html"><em>Section accelerate opt</em></a> gives details of how to build and
use this package. See the KOKKOS, USER-INTEL, and USER-OMP packages,
which also have styles optimized for CPU performance.</p>
<p>Some C++ compilers, like the Intel compiler, require the compile flag
“-restrict” to build LAMMPS with the OPT package. It should be added
to the CCFLAGS line of your Makefile.machine. Or use Makefile.opt in
src/MAKE/OPTIONS, via “make opt”. For compilers that use the flag,
the Make.py command adds it automatically to the Makefile.auto file it
<span id="replica"></span><h3>4.1.25. REPLICA package<a class="headerlink" href="#replica-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: A collection of multi-replica methods that are used by
invoking multiple instances (replicas) of LAMMPS
simulations. Communication between individual replicas is performed in
different ways by the different methods. See <a class="reference internal" href="Section_howto.html#howto-5"><span>Section howto 6.5</span></a> for an overview of how to run
multi-replica simulations in LAMMPS. Multi-replica methods included
in the package are 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 remainded of the force
<p>Authors: Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl
at sandia.gov) and Jon Zimmerman (jzimmer at sandia.gov) at Sandia.
Contact them directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-awpmd-package">
<span id="user-awpmd"></span><h3>4.2.2. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: 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 an MD
calculation. See src/USER-AWPMD/README for more details.</p>
<p>Author: Ilya Valuev at the JIHT in Russia (valuev at
physik.hu-berlin.de). Contact him directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-cg-cmm-package">
<span id="user-cg-cmm"></span><h3>4.2.3. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: CG-CMM stands for coarse-grained ??. This package
implements several pair styles and an angle style using the coarse
grained parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27
(2007) (SDK), with extensions to simulate ionic liquids, electrolytes,
lipids and charged amino acids. See src/USER-CG-CMM/README for more
<p>Author: Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact
him directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-colvars-package">
<span id="user-colvars"></span><h3>4.2.4. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: COLVARS stands for collective variables which can be used to
Sampling and Restraints. This package implements a <a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a> command which wraps a COLVARS library which
can perform those kinds of simulations. See src/USER-COLVARS/README
<span id="user-diffraction"></span><h3>4.2.6. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: This packages implements two computes and a fix for
calculating x-ray and electron diffraction intensities based on
kinematic diffraction theory. See src/USER-DIFFRACTION/README for
<p>Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil),
Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com)
and John Brennan (ARL) (john.k.brennan.civ at mail.mil). Contact them
directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-drude-package">
<span id="user-drude"></span><h3>4.2.8. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: This package contains methods for simulating polarizable
systems using thermalized Drude oscillators. It has computes, fixes,
and pair styles for this purpose. See <a class="reference internal" href="Section_howto.html#howto-27"><span>Section howto 6.27</span></a> for an overview of how to use the
package. See src/USER-DRUDE/README for additional details. There are
auxiliary tools for using this package in tools/drude.</p>
<p>Author: Andres Jaramillo-Botero at CalTech (ajaramil at
wag.caltech.edu). Contact him directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-fep-package">
<span id="user-fep"></span><h3>4.2.10. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: FEP stands for free energy perturbation. This package
provides methods for performing FEP simulations by using a <a class="reference internal" href="fix_adapt_fep.html"><em>fix adapt/fep</em></a> command with soft-core pair potentials,
which have a “soft” in their style name. See src/USER-FEP/README for
more details. There are auxiliary tools for using this package in
<p>Author: Pierre de Buyl at KU Leuven (see <a class="reference external" href="http://pdebuyl.be">http://pdebuyl.be</a>) created
this package as well as the H5MD format and library. Contact him
directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-intel-package">
<span id="user-intel"></span><h3>4.2.12. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: Dozens of pair, bond, angle, dihedral, and improper styles
that are optimized for Intel CPUs and the Intel Xeon Phi (in offload
mode). All of them have an “intel” in their style name. <a class="reference internal" href="accelerate_intel.html"><em>Section accelerate intel</em></a> gives details of what hardware
and compilers are required on your system, and how to build and use
this package. Also see src/USER-INTEL/README for more details. See
the KOKKOS, OPT, and USER-OMP packages, which also have CPU and
<p>User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.</p>
<p>The list of features and author of each is given in the
src/USER-MISC/README file.</p>
<p>You should contact the author directly if you have specific questions
about the feature or its coding.</p>
<p>Examples: examples/USER/misc</p>
<hr class="docutils" />
</div>
<div class="section" id="user-molfile-package">
<span id="user-molfile"></span><h3>4.2.16. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: A <a class="reference internal" href="fix_atc.html"><em>fix atc</em></a> command (atoms to continuum) to
either couple of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields. See
<span id="user-phonon"></span><h3>4.2.18. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: A <a class="reference internal" href="fix_atc.html"><em>fix atc</em></a> command (atoms to continuum) to
either couple of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields. See
<span id="user-reaxc"></span><h3>4.2.22. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: A <a class="reference internal" href="fix_atc.html"><em>fix atc</em></a> command (atoms to continuum) to
either couple of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields. See
<p>This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:</p>
<ul class="simple">
<li>Does liquids via traditional Smooth Particle Hydrodynamics (SPH)</li>
<li>Also solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control.</li>
<li>Can specify hydrostatic interactions independently from material
strength models, i.e. pressure and deviatoric stresses are separated.</li>
<li>Many material models available (Johnson-Cook, plasticity with
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
material models.</li>
<li>Rigid boundary conditions (walls) can be loaded as surface geometries
from <a href="#id7"><span class="problematic" id="id8">*</span></a>.STL files.</li>
</ul>
<p>See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.</p>
<p>There are example scripts for using this package in examples/USER/smd.</p>
<p>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.</p>
<p>Examples: examples/USER/smd</p>
<hr class="docutils" />
</div>
<div class="section" id="user-smtbq-package">
<span id="user-smtbq"></span><h3>4.2.24. USER-SMTBQ package<a class="headerlink" href="#user-smtbq-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: A <a class="reference internal" href="fix_atc.html"><em>fix atc</em></a> command (atoms to continuum) to
either couple of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields. See
<p>This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:</p>
<ul class="simple">
<li>Tait, ideal gas, Lennard-Jones equation of states, full support for
complete (i.e. internal-energy dependent) equations of state</li>
<li>Plain or Monaghans XSPH integration of the equations of motion</li>
<li>Density continuity or density summation to propagate the density field</li>
<li>Commands to set internal energy and density of particles from the
input script</li>
<li>Output commands to access internal energy and density for dumping and
thermo output</li>
</ul>
<p>See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.</p>
<p>There are example scripts for using this package in examples/USER/sph.</p>
<p>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.</p>
<p>Examples: examples/USER/sph</p>
<hr class="docutils" />
</div>
<div class="section" id="user-tally-package">
<span id="user-tally"></span><h3>4.2.26. USER-TALLY package<a class="headerlink" href="#user-tally-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: A <a class="reference internal" href="fix_atc.html"><em>fix atc</em></a> command (atoms to continuum) to
either couple of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields. See
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