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30
doc/Manual.html
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@ -137,23 +137,23 @@ it gives quick access to documentation for all LAMMPS commands.
<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
<BR>
5.2 <A HREF = "Section_accelerate.html#acc_2">General strategies</A>
5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A>
<BR>
5.3 <A HREF = "Section_accelerate.html#acc_3">Packages with optimized styles</A>
5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A>
<BR>
5.4 <A HREF = "Section_accelerate.html#acc_4">OPT package</A>
<UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
<BR>
5.5 <A HREF = "Section_accelerate.html#acc_5">USER-OMP package</A>
5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
<BR>
5.6 <A HREF = "Section_accelerate.html#acc_6">GPU package</A>
5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
<BR>
5.7 <A HREF = "Section_accelerate.html#acc_7">USER-CUDA package</A>
5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
<BR>
5.8 <A HREF = "Section_accelerate.html#acc_8">KOKKOS package</A>
5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
<BR>
5.9 <A HREF = "Section_accelerate.html#acc_9">USER-INTEL package</A>
<BR>
5.10 <A HREF = "acc_10">Comparison of GPU and USER-CUDA packages</A>
5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
<BR></UL>
5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A>
<BR></UL>
<LI><A HREF = "Section_howto.html">How-to discussions</A>
@ -402,16 +402,6 @@ it gives quick access to documentation for all LAMMPS commands.

23
doc/Manual.txt
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@ -105,15 +105,15 @@ it gives quick access to documentation for all LAMMPS commands.
4.2 "User packages"_pkg_2 :ule,b
"Accelerating LAMMPS performance"_Section_accelerate.html :l
5.1 "Measuring performance"_acc_1 :ulb,b
5.2 "General strategies"_acc_2 :b
5.3 "Packages with optimized styles"_acc_3 :b
5.4 "OPT package"_acc_4 :b
5.5 "USER-OMP package"_acc_5 :b
5.6 "GPU package"_acc_6 :b
5.7 "USER-CUDA package"_acc_7 :b
5.8 "KOKKOS package"_acc_8 :b
5.9 "USER-INTEL package"_acc_9 :b
5.10 "Comparison of GPU and USER-CUDA packages"_acc_10 :ule,b
5.2 "Algorithms and code options to boost performace"_acc_2 :b
5.3 "Accelerator packages with optimized styles"_acc_3 :b
5.3.1 "USER-CUDA package"_accelerate_cuda.html :ulb,b
5.3.2 "GPU package"_accelerate_gpu.html :b
5.3.3 "USER-INTEL package"_accelerate_intel.html :b
5.3.4 "KOKKOS package"_accelerate_kokkos.html :b
5.3.5 "USER-OMP package"_accelerate_omp.html :b
5.3.6 "OPT package"_accelerate_opt.html :ule,b
5.4 "Comparison of various accelerator packages"_acc_4 :ule,b
"How-to discussions"_Section_howto.html :l
6.1 "Restarting a simulation"_howto_1 :ulb,b
6.2 "2d simulations"_howto_2 :b
@ -201,11 +201,6 @@ it gives quick access to documentation for all LAMMPS commands.
:link(acc_2,Section_accelerate.html#acc_2)
:link(acc_3,Section_accelerate.html#acc_3)
:link(acc_4,Section_accelerate.html#acc_4)
:link(acc_5,Section_accelerate.html#acc_5)
:link(acc_6,Section_accelerate.html#acc_6)
:link(acc_7,Section_accelerate.html#acc_7)
:link(acc_8,Section_accelerate.html#acc_8)
:link(acc_9,Section_accelerate.html#acc_9)
:link(howto_1,Section_howto.html#howto_1)
:link(howto_2,Section_howto.html#howto_2)

107
doc/Section_start.html
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@ -1158,11 +1158,12 @@ letter abbreviation can be used:
</P>
<UL><LI>-c or -cuda
<LI>-e or -echo
<LI>-i or -in
<LI>-h or -help
<LI>-i or -in
<LI>-k or -kokkos
<LI>-l or -log
<LI>-nc or -nocite
<LI>-pk or -package
<LI>-p or -partition
<LI>-pl or -plog
<LI>-ps or -pscreen
@ -1198,6 +1199,15 @@ can be useful to figure out which line of your script is causing an
input error. The default value is <I>log</I>. The echo style can also be
set by using the <A HREF = "echo.html">echo</A> command in the input script itself.
</P>
<PRE>-help
</PRE>
<P>Print a brief help summary and a list of options compiled into this
executable for each LAMMPS style (atom_style, fix, compute,
pair_style, bond_style, etc). This can tell you if the command you
want to use was included via the appropriate package at compile time.
LAMMPS will print the info and immediately exit if this switch is
used.
</P>
<PRE>-in file
</PRE>
<P>Specify a file to use as an input script. This is an optional switch
@ -1210,15 +1220,6 @@ Note that this is a required switch when running LAMMPS in
multi-partition mode, since multiple processors cannot all read from
stdin.
</P>
<PRE>-help
</PRE>
<P>Print a brief help summary and a list of options compiled into this
executable for each LAMMPS style (atom_style, fix, compute,
pair_style, bond_style, etc). This can tell you if the command you
want to use was included via the appropriate package at compile time.
LAMMPS will print the info and immediately exit if this switch is
used.
</P>
<PRE>-kokkos on/off keyword/value ...
</PRE>
<P>Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
@ -1326,6 +1327,20 @@ references for specific cite-able features used during a LAMMPS run.
See the <A HREF = "http://lammps.sandia.gov/cite.html">citation page</A> for more
details.
</P>
<PRE>-package style args ....
</PRE>
<P>Invoke the <A HREF = "package.html">package</A> command with style and args. The
syntax is the same as if the command appeared at the top of the input
script. For example "-package gpu 2" or "-pk gpu 2" is the same as
<A HREF = "package.html">package gpu 2</A> in the input script. The possible styles
and args are documented on the <A HREF = "package.html">package</A> doc page. This
switch can be used multiple times, e.g. to set options for the
USER-INTEL and USER-OMP packages which can be used together.
</P>
<P>Along with the "-suffix" command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without
having to edit an input script.
</P>
<PRE>-partition 8x2 4 5 ...
</PRE>
<P>Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
@ -1484,7 +1499,7 @@ multi-partition mode, if the specified file is "none", then no screen
output is performed. Option -pscreen will override the name of the
partition screen files file.N.
</P>
<PRE>-suffix style args
<PRE>-suffix style
</PRE>
<P>Use variants of various styles if they exist. The specified style can
be <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I>. These refer to
@ -1494,51 +1509,61 @@ package, the "gpu" style to the GPU package, the "intel" style to the
USER-INTEL package, the "kk" style to the KOKKOS package, the "opt"
style to the OPT package, and the "omp" style to the USER-OMP package.
</P>
<P>Along with the "-package" command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without
having to edit an input script.
</P>
<P>As an example, all of the packages provide a <A HREF = "pair_lj.html">pair_style
lj/cut</A> variant, with style names lj/cut/cuda,
lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, or lj/cut/opt. A
variant styles can be specified explicitly in your input script,
e.g. pair_style lj/cut/gpu. If the -suffix switch is used, you do not
need to modify your input script. The specified suffix
(cuda,gpu,intel,kk,omp,opt) is automatically appended whenever your
input script command creates a new <A HREF = "atom_style.html">atom</A>,
<A HREF = "pair_style.html">pair</A>, <A HREF = "fix.html">fix</A>, <A HREF = "compute.html">compute</A>, or
<A HREF = "run_style.html">run</A> style. If the variant version does not exist,
the standard version is created.
lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A
variant style can be specified explicitly in your input script,
e.g. pair_style lj/cut/gpu. If the -suffix switch is used the
specified suffix (cuda,gpu,intel,kk,omp,opt) is automatically appended
whenever your input script command creates a new
<A HREF = "atom_style.html">atom</A>, <A HREF = "pair_style.html">pair</A>, <A HREF = "fix.html">fix</A>,
<A HREF = "compute.html">compute</A>, or <A HREF = "run_style.html">run</A> style. If the variant
version does not exist, the standard version is created.
</P>
<P>For the GPU package, using this command-line switch also invokes the
default GPU settings, as if the command "package gpu force/neigh 0 0
1" were used at the top of your input script. These settings can be
changed by using the <A HREF = "package.html">package gpu</A> command in your script
if desired.
default GPU settings, as if the command "package gpu 1" were used at
the top of your input script. These settings can be changed by using
the "-package gpu" command-line switch or the <A HREF = "package.html">package
gpu</A> command in your script.
</P>
<P>For the USER-INTEL package, using this command-line switch also invokes the
default USER-INTEL settings, as if the command "package intel * mixed
balance -1" were used at the top of your input script. These settings
can be changed by using the <A HREF = "package.html">package intel</A> command in
your script if desired. If the USER-OMP package is installed, the
intel suffix will make the omp suffix a second choice, if a requested
style is not available in the USER-INTEL package.
<P>For the USER-INTEL package, using this command-line switch also
invokes the default USER-INTEL settings, as if the command "package
intel 1" were used at the top of your input script. These settings
can be changed by using the "-package intel" command-line switch or
the <A HREF = "package.html">package intel</A> command in your script. If the
USER-OMP package is also installed, the intel suffix will make the omp
suffix a second choice, if a requested style is not available in the
USER-INTEL package. It will also invoke the default USER-OMP
settings, as if the command "package omp 0" were used at the top of
your input script. These settings can be changed by using the
"-package omp" command-line switch or the <A HREF = "package.html">package omp</A>
command in your script.
</P>
<P>For the KOKKOS package, using this command-line switch also invokes
the default KOKKOS settings, as if the command "package kokkos neigh
full comm/exchange host comm/forward host " were used at the top of
your input script. These settings can be changed by using the
<A HREF = "package.html">package kokkos</A> command in your script if desired.
the default KOKKOS settings, as if the command "package kokkos" were
used at the top of your input script. These settings can be changed
by using the "-package kokkos" command-line switch or the <A HREF = "package.html">package
kokkos</A> command in your script.
</P>
<P>For the OMP package, using this command-line switch also invokes the
default OMP settings, as if the command "package omp *" were used at
default OMP settings, as if the command "package omp 0" were used at
the top of your input script. These settings can be changed by using
the <A HREF = "package.html">package omp</A> command in your script if desired.
the "-package omp" command-line switch or the <A HREF = "package.html">package
omp</A> command in your script.
</P>
<P>The <A HREF = "suffix.html">suffix</A> command can also be used to set a suffix and
it can also turn off or back on any suffix setting made via the
command line.
<P>The <A HREF = "suffix.html">suffix</A> command can also be used within an input
script to set a suffix, or to turn off or back on any suffix setting
made via the command line.
</P>
<PRE>-var name value1 value2 ...
</PRE>
<P>Specify a variable that will be defined for substitution purposes when
the input script is read. "Name" is the variable name which can be a
the input script is read. This switch can be used multiple times to
define multiple variables. "Name" is the variable name which can be a
single character (referenced as $x in the input script) or a full
string (referenced as ${abc}). An <A HREF = "variable.html">index-style
variable</A> will be created and populated with the

107
doc/Section_start.txt
View File

@ -1152,11 +1152,12 @@ letter abbreviation can be used:
-c or -cuda
-e or -echo
-i or -in
-h or -help
-i or -in
-k or -kokkos
-l or -log
-nc or -nocite
-pk or -package
-p or -partition
-pl or -plog
-ps or -pscreen
@ -1192,6 +1193,15 @@ can be useful to figure out which line of your script is causing an
input error. The default value is {log}. The echo style can also be
set by using the "echo"_echo.html command in the input script itself.
-help :pre
Print a brief help summary and a list of options compiled into this
executable for each LAMMPS style (atom_style, fix, compute,
pair_style, bond_style, etc). This can tell you if the command you
want to use was included via the appropriate package at compile time.
LAMMPS will print the info and immediately exit if this switch is
used.
-in file :pre
Specify a file to use as an input script. This is an optional switch
@ -1204,15 +1214,6 @@ Note that this is a required switch when running LAMMPS in
multi-partition mode, since multiple processors cannot all read from
stdin.
-help :pre
Print a brief help summary and a list of options compiled into this
executable for each LAMMPS style (atom_style, fix, compute,
pair_style, bond_style, etc). This can tell you if the command you
want to use was included via the appropriate package at compile time.
LAMMPS will print the info and immediately exit if this switch is
used.
-kokkos on/off keyword/value ... :pre
Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
@ -1320,6 +1321,20 @@ references for specific cite-able features used during a LAMMPS run.
See the "citation page"_http://lammps.sandia.gov/cite.html for more
details.
-package style args .... :pre
Invoke the "package"_package.html command with style and args. The
syntax is the same as if the command appeared at the top of the input
script. For example "-package gpu 2" or "-pk gpu 2" is the same as
"package gpu 2"_package.html in the input script. The possible styles
and args are documented on the "package"_package.html doc page. This
switch can be used multiple times, e.g. to set options for the
USER-INTEL and USER-OMP packages which can be used together.
Along with the "-suffix" command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without
having to edit an input script.
-partition 8x2 4 5 ... :pre
Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
@ -1478,7 +1493,7 @@ multi-partition mode, if the specified file is "none", then no screen
output is performed. Option -pscreen will override the name of the
partition screen files file.N.
-suffix style args :pre
-suffix style :pre
Use variants of various styles if they exist. The specified style can
be {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt}. These refer to
@ -1488,51 +1503,61 @@ package, the "gpu" style to the GPU package, the "intel" style to the
USER-INTEL package, the "kk" style to the KOKKOS package, the "opt"
style to the OPT package, and the "omp" style to the USER-OMP package.
Along with the "-package" command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without
having to edit an input script.
As an example, all of the packages provide a "pair_style
lj/cut"_pair_lj.html variant, with style names lj/cut/cuda,
lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, or lj/cut/opt. A
variant styles can be specified explicitly in your input script,
e.g. pair_style lj/cut/gpu. If the -suffix switch is used, you do not
need to modify your input script. The specified suffix
(cuda,gpu,intel,kk,omp,opt) is automatically appended whenever your
input script command creates a new "atom"_atom_style.html,
"pair"_pair_style.html, "fix"_fix.html, "compute"_compute.html, or
"run"_run_style.html style. If the variant version does not exist,
the standard version is created.
lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A
variant style can be specified explicitly in your input script,
e.g. pair_style lj/cut/gpu. If the -suffix switch is used the
specified suffix (cuda,gpu,intel,kk,omp,opt) is automatically appended
whenever your input script command creates a new
"atom"_atom_style.html, "pair"_pair_style.html, "fix"_fix.html,
"compute"_compute.html, or "run"_run_style.html style. If the variant
version does not exist, the standard version is created.
For the GPU package, using this command-line switch also invokes the
default GPU settings, as if the command "package gpu force/neigh 0 0
1" were used at the top of your input script. These settings can be
changed by using the "package gpu"_package.html command in your script
if desired.
default GPU settings, as if the command "package gpu 1" were used at
the top of your input script. These settings can be changed by using
the "-package gpu" command-line switch or the "package
gpu"_package.html command in your script.
For the USER-INTEL package, using this command-line switch also invokes the
default USER-INTEL settings, as if the command "package intel * mixed
balance -1" were used at the top of your input script. These settings
can be changed by using the "package intel"_package.html command in
your script if desired. If the USER-OMP package is installed, the
intel suffix will make the omp suffix a second choice, if a requested
style is not available in the USER-INTEL package.
For the USER-INTEL package, using this command-line switch also
invokes the default USER-INTEL settings, as if the command "package
intel 1" were used at the top of your input script. These settings
can be changed by using the "-package intel" command-line switch or
the "package intel"_package.html command in your script. If the
USER-OMP package is also installed, the intel suffix will make the omp
suffix a second choice, if a requested style is not available in the
USER-INTEL package. It will also invoke the default USER-OMP
settings, as if the command "package omp 0" were used at the top of
your input script. These settings can be changed by using the
"-package omp" command-line switch or the "package omp"_package.html
command in your script.
For the KOKKOS package, using this command-line switch also invokes
the default KOKKOS settings, as if the command "package kokkos neigh
full comm/exchange host comm/forward host " were used at the top of
your input script. These settings can be changed by using the
"package kokkos"_package.html command in your script if desired.
the default KOKKOS settings, as if the command "package kokkos" were
used at the top of your input script. These settings can be changed
by using the "-package kokkos" command-line switch or the "package
kokkos"_package.html command in your script.
For the OMP package, using this command-line switch also invokes the
default OMP settings, as if the command "package omp *" were used at
default OMP settings, as if the command "package omp 0" were used at
the top of your input script. These settings can be changed by using
the "package omp"_package.html command in your script if desired.
the "-package omp" command-line switch or the "package
omp"_package.html command in your script.
The "suffix"_suffix.html command can also be used to set a suffix and
it can also turn off or back on any suffix setting made via the
command line.
The "suffix"_suffix.html command can also be used within an input
script to set a suffix, or to turn off or back on any suffix setting
made via the command line.
-var name value1 value2 ... :pre
Specify a variable that will be defined for substitution purposes when
the input script is read. "Name" is the variable name which can be a
the input script is read. This switch can be used multiple times to
define multiple variables. "Name" is the variable name which can be a
single character (referenced as $x in the input script) or a full
string (referenced as $\{abc\}). An "index-style
variable"_variable.html will be created and populated with the