Update Kokkos docs

When running on Maxwell or Kepler GPUs, this will typically be

best. For Pascal GPUs, using "half" neighbor lists and setting the

Newton flag to "on" may be faster. For many pair styles, setting the

neighbor binsize equal to the ghost atom cutoff will give speedup.

neighbor binsize equal to twice the CPU default value will give speedup,

which is the default when running on GPUs.

Use the "-pk kokkos" "command-line switch"_Run_options.html to change

the default "package kokkos"_package.html options. See its doc page

for details and default settings. Experimenting with its options can

provide a speed-up for specific calculations. For example:

mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj      # Set binsize = neighbor ghost cutoff

mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre

NOTE: For good performance of the KOKKOS package on GPUs, you must

The {binsize} keyword sets the size of bins used to bin atoms in 

neighbor list builds. The same value can be set by the "neigh_modify 

binsize"_neigh_modify.html command.  Making it an option in the

package kokkos command allows it to be set from the command line.  The

default value is 0.0, which means the LAMMPS default will be used,

binsize"_neigh_modify.html command. Making it an option in the package 

kokkos command allows it to be set from the command line. The default 

value for CPUs is 0.0, which means the LAMMPS default will be used, 

which is bins = 1/2 the size of the pairwise cutoff + neighbor skin 

distance.  This is fine when neighbor lists are built on the CPU.  For

GPU builds, a 2x larger binsize equal to the pairwise cutoff +

neighbor skin, is often faster, which can be set by this keyword.

Note that if you use a longer-than-usual pairwise cutoff, e.g. to

allow for a smaller fraction of KSpace work with a "long-range

Coulombic solver"_kspace_style.html because the GPU is faster at

performing pairwise interactions, then this rule of thumb may give too

large a binsize.

distance. This is fine when neighbor lists are built on the CPU. For GPU 

builds, a 2x larger binsize equal to the pairwise cutoff + neighbor skin 

is often faster, which is the default. Note that if you use a 

longer-than-usual pairwise cutoff, e.g. to allow for a smaller fraction 

of KSpace work with a "long-range Coulombic solver"_kspace_style.html 

because the GPU is faster at performing pairwise interactions, then this 

rule of thumb may give too large a binsize and the default should be 

overridden with a smaller value. 

The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse} keywords determine

whether the host or device performs the packing and unpacking of data

switch"_Run_options.html.

For the KOKKOS package, the option defaults neigh = full, neigh/qeq = 

full, newton = off, binsize = 0.0, and comm = device, gpu/direct = on.

When LAMMPS can safely detect, that GPU-direct is not available, the

default value of gpu/direct becomes "off".

These settings are made automatically by the required "-k on"

"command-line switch"_Run_options.html. You can change them by

using the package kokkos command in your input script or via the

full, newton = off, binsize for CPUs = 0.0, binsize for GPUs = 2x LAMMPS 

default value, and comm = device, gpu/direct = on. When LAMMPS can 

safely detect, that GPU-direct is not available, the default value of 

gpu/direct becomes "off". These settings are made automatically by the 

required "-k on" "command-line switch"_Run_options.html. You can change 

them by using the package kokkos command in your input script or via the 

"-pk kokkos command-line switch"_Run_options.html. 

For the OMP package, the default is Nthreads = 0 and the option