<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 <aclass="reference internal"href="Section_howto.html#howto-26"><spanclass="std std-ref">Section howto 6.26</span></a> for an overview of how to use the
<spanclass="n">make</span><spanclass="o">-</span><spanclass="n">f</span><spanclass="n">Makefile</span><spanclass="o">.</span><spanclass="n">linux</span><spanclass="o">.</span><spanclass="n">mixed</span><spanclass="c1"># for example</span>
<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. <aclass="reference internal"href="accelerate_kokkos.html"><spanclass="doc">Section accelerate kokkos</span></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-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 <aclass="reference internal"href="accelerate_kokkos.html"><spanclass="doc">Section accelerate kokkos</span></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>
<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 <aclass="reference internal"href="Section_start.html#start-2-2"><spanclass="std std-ref">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
<spanclass="n">make</span><spanclass="o">-</span><spanclass="n">f</span><spanclass="n">Makefile</span><spanclass="o">.</span><spanclass="n">gfortran</span><spanclass="c1"># for example</span>
<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. <aclass="reference internal"href="accelerate_opt.html"><spanclass="doc">Section accelerate opt</span></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
<spanclass="n">make</span><spanclass="o">-</span><spanclass="n">f</span><spanclass="n">Makefile</span><spanclass="o">.</span><spanclass="n">g</span><spanclass="o">++</span><spanclass="c1"># for example</span>
<spanclass="n">make</span><spanclass="o">-</span><spanclass="n">f</span><spanclass="n">Makefile</span><spanclass="o">.</span><spanclass="n">gfortran</span><spanclass="c1"># for example</span>
<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 <aclass="reference internal"href="Section_howto.html#howto-5"><spanclass="std std-ref">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
Sampling and Restraints. This package implements a <aclass="reference internal"href="fix_colvars.html"><spanclass="doc">fix colvars</span></a> command which wraps a COLVARS library which
can perform those kinds of simulations. See src/USER-COLVARS/README
<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 <aclass="reference internal"href="Section_howto.html#howto-27"><spanclass="std std-ref">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>Contents: FEP stands for free energy perturbation. This package
provides methods for performing FEP simulations by using a <aclass="reference internal"href="fix_adapt_fep.html"><spanclass="doc">fix adapt/fep</span></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>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. <aclass="reference internal"href="accelerate_intel.html"><spanclass="doc">Section accelerate intel</span></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>The persons who created the USER-MGPT package are Tomas Oppelstrup
(<aclass="reference external"href="mailto:oppelstrup2%40llnl.gov">oppelstrup2<span>@</span>llnl<span>.</span>gov</a>) and John Moriarty (<aclass="reference external"href="mailto:moriarty2%40llnl.gov">moriarty2<span>@</span>llnl<span>.</span>gov</a>)
Contact them directly if you have any questions.</p>
<p>This package provides a self-consistent quantum treatment of the
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, alter the energy power spectrum and the
heat capacity towards their quantum nature. This package could be of
interest if one wants to model systems at temperatures lower than
their classical limits or when temperatures ramp up across the
classical limits in the simulation.</p>
<p>See these two doc pages to get started:</p>
<p><aclass="reference internal"href="fix_qtb.html"><spanclass="doc">fix qtb</span></a> provides quantum nulcear correction through a
colored thermostat and can be used with other time integration schemes
like <aclass="reference internal"href="fix_nve.html"><spanclass="doc">fix nve</span></a> or <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix nph</span></a>.</p>
<p><aclass="reference internal"href="fix_qbmsst.html"><spanclass="doc">fix qbmsst</span></a> enables quantum nuclear correction of a
multi-scale shock technique simulation by coupling the quantum thermal
bath with the shocked system.</p>
<p>The person who created this package is Yuan Shen (sy0302 at
stanford.edu) at Stanford University. Contact him directly if you
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