Update Kokkos docs for data duplication

needed. Alternatively, one can run with the KOKKOS package by editing

the input script as described below.

NOTE: When using a single OpenMP thread, the Kokkos Serial backend (i.e. 

Makefile.kokkos_mpi_only) will give better performance than the OpenMP 

backend (i.e. Makefile.kokkos_omp) because some of the overhead to make 

the code thread-safe is removed. 

NOTE: The default for the "package kokkos"_package.html command is to

use "full" neighbor lists and set the Newton flag to "off" for both

pairwise and bonded interactions. However, when running on CPUs, it

If the "newton"_newton.html command is used in the input

script, it can also override the Newton flag defaults.

For half neighbor lists and OpenMP, the KOKKOS package uses data 

duplication (i.e. thread-private arrays) by default to avoid 

thread-level write conflicts in the force arrays (and other data 

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 is 

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

atomics.

[Core and Thread Affinity:]

When using multi-threading, it is important for performance to bind

#ifndef KOKKOS_HAVE_SERIAL

  if (num_threads == 1)

    error->warning(FLERR,"Using Kokkos Serial backend (i.e. Makefile.kokkos_mpi_only) performs better with 1 thread");

    error->warning(FLERR,"When using a single thread, the Kokkos Serial backend "

                         "(i.e. Makefile.kokkos_mpi_only) gives better performance "

                         "than the OpenMP backend");

#endif

  Kokkos::InitArguments args;