Update Kokkos docs

Kokkos library also provides data abstractions to adjust (at compile

time) the memory layout of data structures like 2d and 3d arrays to

optimize performance on different hardware. For more information on

Kokkos, see `GitHub <https://github.com/kokkos/kokkos>`_. Kokkos is

part of `Trilinos <https://www.trilinos.org/>`_. The Kokkos

library was written primarily by Carter Edwards, Christian Trott, and

Dan Sunderland (all Sandia).

Kokkos, see `GitHub <https://github.com/kokkos/kokkos>`_.

The LAMMPS KOKKOS package contains versions of pair, fix, and atom

styles that use data structures and macros provided by the Kokkos

Moore (Sandia) with contributions of various styles by others,

including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez

(Sandia). For more information on developing using Kokkos abstractions

see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf.

see the Kokkos `Wiki <https://github.com/kokkos/kokkos/wiki>`_.

Kokkos currently provides support for 3 modes of execution (per MPI

task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP

   running on GPUs is to use "full" neighbor lists and set the Newton flag

   to "off" for both pairwise and bonded interactions, along with threaded

   communication. When running on Maxwell or Kepler GPUs, this will

   typically be best. For Pascal GPUs, using "half" neighbor lists and

   typically be best. For Pascal GPUs and beyond, using "half" neighbor lists and

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

   setting the neighbor binsize equal to twice the CPU default value will

   give speedup, which is the default when running on GPUs. Use the "-pk

   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

.. note::

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

   have Kepler generation GPUs (or later). The Kokkos library exploits

   texture cache options not supported by Telsa generation GPUs (or

   older).

.. note::

   When using a GPU, you will achieve the best performance if your

they can be set either as variables on the make command line or in

Makefile.machine, or they can be specified as CMake variables.  Each

takes a value shown below.  The default value is listed, which is set

in the lib/kokkos/Makefile.kokkos file.

in the lib/kokkos/Makefile.kokkos file. For a full listing of all options,

see lib/kokkos/Makefile.kokkos.

* KOKKOS_DEBUG, values = *yes*\ , *no*\ , default = *no*

* KOKKOS_USE_TPLS, values = *hwloc*\ , *librt*\ , *experimental_memkind*, default = *none*

* KOKKOS_CXX_STANDARD, values = *c++11*\ , *c++1z*\ , default = *c++11*

* KOKKOS_OPTIONS, values = *aggressive_vectorization*, *disable_profiling*, default = *none*

* KOKKOS_CUDA_OPTIONS, values = *force_uvm*, *use_ldg*, *rdc*\ , *enable_lambda*, default = *enable_lambda*

* KOKKOS_DEBUG, values = *yes*\ , *no*\ , default = *no*

* KOKKOS_CUDA_OPTIONS, values = *force_uvm*, *use_ldg*, *rdc*\ , *enable_lambda*\ , *enable_constexpr*, default = *enable_lambda*

KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not

migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be

debugging information that can be useful. It also enables runtime

bounds checking on Kokkos data structures.

KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when

building LAMMPS.

KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS

package must be compiled with the *enable_lambda* option when using

GPUs.