fix some spelling errors in the manual

you can browse them locally on your system.  Type "make" from the

lammps/doc dir to see other options.

NOTE: You can also download a tarball of the documention for the

NOTE: You can also download a tarball of the documentation for the

current LAMMPS version (HTML and PDF files), from the website

"download page"_http://lammps.sandia.gov/download.html.

long as the shared PLUMED library is ABI-compatible. The third linkage

mode is "runtime" which allows to switch the PLUMED kernel at runtime

between different variants through setting the PLUMED_KERNEL environment

varible, which has to point to the location of the libplumedKernel.so

variable, which has to point to the location of the libplumedKernel.so

dynamical shared object, which is then loaded at runtime. This is

particularly convenient for doing PLUMED development and comparing

multiple PLUMED versions without having to recompile the hosting MD

"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy :ul

The server doc files give details of the message protocols

for data that is exchanged bewteen the client and server.

for data that is exchanged between the client and server.

These example directories illustrate how to use LAMMPS as either a

client or server code:

structures as necessary). Data duplication is typically fastest for

small numbers of threads (i.e. 8 or less) but does increase memory

footprint and is not scalable to large numbers of threads. An

alternative to data duplication is to use thread-level atomics, which 

don't require duplication. The use of atomics can be forced by compiling 

with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all 

Kokkos-enabled pair_styles support data duplication. Alternatively, full 

neighbor lists avoid the need for duplication or atomics but require 

more compute operations per atom. When using the Kokkos Serial backend 

or the OpenMP backend with a single thread, no duplication or atomics are 

used. For CUDA and half neighbor lists, the KOKKOS package always uses 

atomics.

alternative to data duplication is to use thread-level atomic operations

which do not require data duplication. The use of atomic operations can

be enforced by compiling LAMMPS with the "-DLMP_KOKKOS_USE_ATOMICS"

pre-processor flag. Most but not all Kokkos-enabled pair_styles support

data duplication. Alternatively, full neighbor lists avoid the need for

duplication or atomic operations but require more compute operations per

atom.  When using the Kokkos Serial backend or the OpenMP backend with

a single thread, no duplication or atomic operations are used. For CUDA

and half neighbor lists, the KOKKOS package always uses atomic operations.

[Core and Thread Affinity:]

The system has a spatially inhomogeneous particle density which does

not map well to the "domain decomposition scheme"_processors.html or

"load-balancing"_balance.html options that LAMMPS provides.  This is

because multi-threading achives parallelism over the number of

because multi-threading achieves parallelism over the number of

particles, not via their distribution in space. :l

A machine is being used in "capability mode", i.e. near the point

MPI tasks to be invoked and can speed-up the long-range solver, while

increasing overall performance by parallelizing the pairwise and

bonded calculations via OpenMP.  Likewise additional speedup can be

sometimes be achived by increasing the length of the Coulombic cutoff

sometimes be achieved by increasing the length of the Coulombic cutoff

and thus reducing the work done by the long-range solver.  Using the

"run_style verlet/split"_run_style.html command, which is compatible

with the USER-OMP package, is an alternative way to reduce the number