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Update docs

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Stan Moore 2019-04-09 08:51:24 -06:00
parent 22b7e12baf
commit 16b17f812c
1 changed files with 19 additions and 7 deletions
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doc/src/package.txt
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@ -64,13 +64,16 @@ args = arguments specific to the style :l
{no_affinity} values = none {no_affinity} values = none
{kokkos} args = keyword value ... {kokkos} args = keyword value ...
zero or more keyword/value pairs may be appended 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} {neigh} value = {full} or {half}
full = full neighbor list full = full neighbor list
half = half neighbor list built in thread-safe manner half = half neighbor list built in thread-safe manner
{neigh/qeq} value = {full} or {half} {neigh/qeq} value = {full} or {half}
full = full neighbor list full = full neighbor list
half = half neighbor list built in thread-safe manner 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} {newton} = {off} or {on}
off = set Newton pairwise and bonded flags off off = set Newton pairwise and bonded flags off
on = set Newton pairwise and bonded flags on on = set Newton pairwise and bonded flags on
@ -442,7 +445,15 @@ running on CPUs, a {half} neighbor list is the default because it are
often faster, just as it is for non-accelerated pair styles. Similarly, often faster, just as it is for non-accelerated pair styles. Similarly,
the {neigh/qeq} keyword determines how neighbor lists are built for "fix 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 qeq/reax/kk"_fix_qeq_reax.html. If not explicitly set, the value of
{neigh/qeq} will match {neigh}. {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 The {newton} keyword sets the Newton flags for pairwise and bonded
interactions to {off} or {on}, the same as the "newton"_newton.html interactions to {off} or {on}, the same as the "newton"_newton.html
@ -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 value, comm = device, gpu/direct = on. When LAMMPS can safely detect
that GPU-direct is not available, the default value of gpu/direct that GPU-direct is not available, the default value of gpu/direct
becomes "off". For CPUs or Xeon Phis, the option defaults are neigh = 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 half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The
settings are made automatically by the required "-k on" "command-line option neigh/thread = on when there are 16K atoms or less on an MPI
switch"_Run_options.html. You can change them by using the package rank, otherwise it is "off". These settings are made automatically by
kokkos command in your input script or via the "-pk kokkos command-line the required "-k on" "command-line switch"_Run_options.html. You can
switch"_Run_options.html. 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 For the OMP package, the default is Nthreads = 0 and the option
defaults are neigh = yes. These settings are made automatically if defaults are neigh = yes. These settings are made automatically if