Commit 16b17f81 authored by Stan Moore's avatar Stan Moore
Browse files

Update docs

parent 22b7e12b
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+19 −7
Original line number Diff line number Diff line
@@ -64,13 +64,16 @@ args = arguments specific to the style :l
      {no_affinity} values = none
  {kokkos} args = keyword value ...
    zero or more keyword/value pairs may be appended
    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {gpu/direct}
    keywords = {neigh} or {neigh/qeq} or {neigh/thread} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {gpu/direct}
      {neigh} value = {full} or {half}
        full = full neighbor list
        half = half neighbor list built in thread-safe manner
      {neigh/qeq} value = {full} or {half}
        full = full neighbor list
        half = half neighbor list built in thread-safe manner
      {neigh/thread} value = {off} or {on}
        off = thread only over atoms
        on = thread over both atoms and neighbors
      {newton} = {off} or {on}
        off = set Newton pairwise and bonded flags off
        on = set Newton pairwise and bonded flags on
@@ -444,6 +447,14 @@ the {neigh/qeq} keyword determines how neighbor lists are built for "fix
qeq/reax/kk"_fix_qeq_reax.html. If not explicitly set, the value of 
{neigh/qeq} will match {neigh}.

If the {neigh/thread} keyword is set to {off}, then the KOKKOS package 
threads only over atoms. However, for small systems, this may not expose 
enough parallelism to keep a GPU busy. When this keyword is set to {on}, 
the KOKKOS package threads over both atoms and neighbors of atoms. 
Using {neigh/thread} {on} may be slower for large systems, so this this 
option is turned on by default only when there are 16K atoms or less 
owned by an MPI rank. 

The {newton} keyword sets the Newton flags for pairwise and bonded 
interactions to {off} or {on}, the same as the "newton"_newton.html 
command allows. The default for GPUs is {off} because this will almost 
@@ -630,11 +641,12 @@ neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default
value, comm = device, gpu/direct = on. When LAMMPS can safely detect 
that GPU-direct is not available, the default value of gpu/direct 
becomes "off". For CPUs or Xeon Phis, the option defaults are neigh = 
half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. 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.
half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The 
option neigh/thread = on when there are 16K atoms or less on an MPI 
rank, otherwise it is "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
defaults are neigh = yes.  These settings are made automatically if