git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6220 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-05-26 22:35:54 +00:00
parent 5a8719e38f
commit b220fdbcf5
5 changed files with 119 additions and 111 deletions

View File

@ -825,10 +825,6 @@ factors (xy,xz,yz) is as follows:
</P>
<CENTER><IMG SRC = "Eqs/box.jpg">
</CENTER>
<P>The inverse relationship can be written as follows:
</P>
<CENTER><IMG SRC = "Eqs/box_inverse.jpg">
</CENTER>
<P>As discussed on the <A HREF = "dump.html">dump</A> command doc page, when the BOX
BOUNDS for a snapshot is written to a dump file for a triclinic box,
an orthogonal bounding box which encloses the triclinic simulation box
@ -1162,7 +1158,7 @@ discussed below, it can be referenced via the following bracket
notation, where ID in this case is the ID of a compute. The leading
"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >c_ID </TD><TD > entire scalar, vector, or array</TD></TR>
<TR><TD >c_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
<TR><TD >c_ID[I][J] </TD><TD > one element of array
@ -1356,7 +1352,7 @@ data and scalar/vector/array data.
input, that could be an element of a vector or array. Likewise a
vector input could be a column of an array.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >Command</TD><TD > Input</TD><TD > Output</TD><TD ></TD></TR>
<TR><TD ><A HREF = "thermo_style.html">thermo_style custom</A></TD><TD > global scalars</TD><TD > screen, log file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "dump.html">dump custom</A></TD><TD > per-atom vectors</TD><TD > dump file</TD><TD ></TD></TR>

View File

@ -784,43 +784,50 @@ more processors or setup a smaller problem.
<H4><A NAME = "2_6"></A>2.6 Command-line options
</H4>
<P>At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. Either the full word or the
one-letter abbreviation can be used:
which may be used in any order. Either the full word or a one-letter
abbreviation can be used:
</P>
<UL><LI>-accelerator or -a
<LI>-echo or -e
<LI>-partition or -p
<LI>-in or -i
<LI>-log or -l
<LI>-screen or -s
<LI>-var or -v
<UL><LI>-a or -accelerator
<LI>-e or -echo
<LI>-i or -in
<LI>-l or -log
<LI>-p or -partition
<LI>-s or -screen
<LI>-v or -var
</UL>
<P>For example, lmp_ibm might be launched as follows:
</P>
<PRE>mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy
<PRE>mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -s none < in.alloy
mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy
</PRE>
<P>Here are the details on the options:
</P>
<PRE>-accelerator style
</PRE>
<P>Use accelerated variants of various styles if they exist. The style
can be <I>opt</I> or <I>gpu</I> or <I>cuda</I>. The variant styles are part of
optional packages that LAMMPS can be built with, as described above in
<A HREF = "#2_3">Section 2.3</A>. Also see the <A HREF = "accelerator.html">acclerator</A>
command doc page. The "opt" style corrsponds to the OPT package, the
"gpu" style to the GPU package, and the "cuda" style to the USER-CUDA
package. For example, all of the packages provide a <A HREF = "pair_lj.html">pair_style
lj/cut</A> variant, with style names lj/cut/opt or
lj/cut/gpu or lj/cut/cuda.
<P>Use accelerated variants of various styles if they exist. The
specified style can be <I>none</I> or <I>opt</I> or <I>gpu</I> or <I>cuda</I>. <I>None</I>
means do not attempt to use an accelerated style, unless it is
explicitly specified in the input script. <I>Opt</I>, <I>gpu</I>, and <I>cuda</I>
refer to optional packages that LAMMPS can be built with, as described
above in <A HREF = "#2_3">Section 2.3</A>. The "opt" style corrsponds to the OPT
package, the "gpu" style to the GPU package, and the "cuda" style to
the USER-CUDA package.
</P>
<P>These accelerated styles can be specified explicitly in your input
script, e.g. pair_style lj/cut/gpu. If the -accelerator switch is
used, you do not need to modify your input script. The accelerator
suffix (opt,gpu,cuda) is automatically appended when the style is
created for atom, pair, fix, compute, and integrate styles. If an
accelerated version does not exist, the standard version is created.
See the <A HREF = "accelerator.html">accelerator</A> command for info on how to
temporarily turn off this option.
<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/opt or
lj/cut/gpu or lj/cut/cuda. Any accelerated styles can be specified
explicitly in your input script, e.g. pair_style lj/cut/gpu. If the
-accelerator switch is used, you do not need to modify your input
script. The accelerator suffix (opt,gpu,cuda) is automatically
appended when the style is created for atom, pair, fix, compute, and
integrate styles. If an accelerated version does not exist, the
standard version is created.
</P>
<P>The default value of this switch is "none", unless LAMMPS was built
with the USER-CUDA package, in which case the default value is "cuda".
See the <A HREF = "accelerator.html">acclerator</A> command doc page for info on how
to turn off/on the suffix associated with this switch within your
input script.
</P>
<PRE>-echo style
</PRE>
@ -831,6 +838,28 @@ 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>-in file
</PRE>
<P>Specify a file to use as an input script. This is an optional switch
when running LAMMPS in one-partition mode. If it is not specified,
LAMMPS reads its input script from stdin - e.g. lmp_linux < in.run.
This is a required switch when running LAMMPS in multi-partition mode,
since multiple processors cannot all read from stdin.
</P>
<PRE>-log file
</PRE>
<P>Specify a log file for LAMMPS to write status information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
file log.lammps. If this switch is used, LAMMPS writes to the
specified file. In multi-partition mode, if the switch is not used, a
log.lammps file is created with hi-level status information. Each
partition also writes to a log.lammps.N file where N is the partition
ID. If the switch is specified in multi-partition mode, the hi-level
logfile is named "file" and each partition also logs information to a
file.N. For both one-partition and multi-partition mode, if the
specified file is "none", then no log files are created. Using a
<A HREF = "log.html">log</A> command in the input script will override this setting.
</P>
<PRE>-partition 8x2 4 5 ...
</PRE>
<P>Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
@ -857,28 +886,6 @@ these commands in this way. Simulations running on different
partitions can also communicate with each other; see the
<A HREF = "temper.html">temper</A> command.
</P>
<PRE>-in file
</PRE>
<P>Specify a file to use as an input script. This is an optional switch
when running LAMMPS in one-partition mode. If it is not specified,
LAMMPS reads its input script from stdin - e.g. lmp_linux < in.run.
This is a required switch when running LAMMPS in multi-partition mode,
since multiple processors cannot all read from stdin.
</P>
<PRE>-log file
</PRE>
<P>Specify a log file for LAMMPS to write status information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
file log.lammps. If this switch is used, LAMMPS writes to the
specified file. In multi-partition mode, if the switch is not used, a
log.lammps file is created with hi-level status information. Each
partition also writes to a log.lammps.N file where N is the partition
ID. If the switch is specified in multi-partition mode, the hi-level
logfile is named "file" and each partition also logs information to a
file.N. For both one-partition and multi-partition mode, if the
specified file is "none", then no log files are created. Using a
<A HREF = "log.html">log</A> command in the input script will override this setting.
</P>
<PRE>-screen file
</PRE>
<P>Specify a file for LAMMPS to write its screen information to. In

View File

@ -774,43 +774,50 @@ more processors or setup a smaller problem.
2.6 Command-line options :h4,link(2_6)
At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. Either the full word or the
one-letter abbreviation can be used:
which may be used in any order. Either the full word or a one-letter
abbreviation can be used:
-accelerator or -a
-echo or -e
-partition or -p
-in or -i
-log or -l
-screen or -s
-var or -v :ul
-a or -accelerator
-e or -echo
-i or -in
-l or -log
-p or -partition
-s or -screen
-v or -var :ul
For example, lmp_ibm might be launched as follows:
mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -s none < in.alloy
mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy :pre
Here are the details on the options:
-accelerator style :pre
Use accelerated variants of various styles if they exist. The style
can be {opt} or {gpu} or {cuda}. The variant styles are part of
optional packages that LAMMPS can be built with, as described above in
"Section 2.3"_#2_3. Also see the "acclerator"_accelerator.html
command doc page. The "opt" style corrsponds to the OPT package, the
"gpu" style to the GPU package, and the "cuda" style to the USER-CUDA
package. For example, all of the packages provide a "pair_style
lj/cut"_pair_lj.html variant, with style names lj/cut/opt or
lj/cut/gpu or lj/cut/cuda.
Use accelerated variants of various styles if they exist. The
specified style can be {none} or {opt} or {gpu} or {cuda}. {None}
means do not attempt to use an accelerated style, unless it is
explicitly specified in the input script. {Opt}, {gpu}, and {cuda}
refer to optional packages that LAMMPS can be built with, as described
above in "Section 2.3"_#2_3. The "opt" style corrsponds to the OPT
package, the "gpu" style to the GPU package, and the "cuda" style to
the USER-CUDA package.
These accelerated styles can be specified explicitly in your input
script, e.g. pair_style lj/cut/gpu. If the -accelerator switch is
used, you do not need to modify your input script. The accelerator
suffix (opt,gpu,cuda) is automatically appended when the style is
created for atom, pair, fix, compute, and integrate styles. If an
accelerated version does not exist, the standard version is created.
See the "accelerator"_accelerator.html command for info on how to
temporarily turn off this option.
As an example, all of the packages provide a "pair_style
lj/cut"_pair_lj.html variant, with style names lj/cut/opt or
lj/cut/gpu or lj/cut/cuda. Any accelerated styles can be specified
explicitly in your input script, e.g. pair_style lj/cut/gpu. If the
-accelerator switch is used, you do not need to modify your input
script. The accelerator suffix (opt,gpu,cuda) is automatically
appended when the style is created for atom, pair, fix, compute, and
integrate styles. If an accelerated version does not exist, the
standard version is created.
The default value of this switch is "none", unless LAMMPS was built
with the USER-CUDA package, in which case the default value is "cuda".
See the "acclerator"_accelerator.html command doc page for info on how
to turn off/on the suffix associated with this switch within your
input script.
-echo style :pre
@ -821,6 +828,28 @@ 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.
-in file :pre
Specify a file to use as an input script. This is an optional switch
when running LAMMPS in one-partition mode. If it is not specified,
LAMMPS reads its input script from stdin - e.g. lmp_linux < in.run.
This is a required switch when running LAMMPS in multi-partition mode,
since multiple processors cannot all read from stdin.
-log file :pre
Specify a log file for LAMMPS to write status information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
file log.lammps. If this switch is used, LAMMPS writes to the
specified file. In multi-partition mode, if the switch is not used, a
log.lammps file is created with hi-level status information. Each
partition also writes to a log.lammps.N file where N is the partition
ID. If the switch is specified in multi-partition mode, the hi-level
logfile is named "file" and each partition also logs information to a
file.N. For both one-partition and multi-partition mode, if the
specified file is "none", then no log files are created. Using a
"log"_log.html command in the input script will override this setting.
-partition 8x2 4 5 ... :pre
Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
@ -847,28 +876,6 @@ these commands in this way. Simulations running on different
partitions can also communicate with each other; see the
"temper"_temper.html command.
-in file :pre
Specify a file to use as an input script. This is an optional switch
when running LAMMPS in one-partition mode. If it is not specified,
LAMMPS reads its input script from stdin - e.g. lmp_linux < in.run.
This is a required switch when running LAMMPS in multi-partition mode,
since multiple processors cannot all read from stdin.
-log file :pre
Specify a log file for LAMMPS to write status information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
file log.lammps. If this switch is used, LAMMPS writes to the
specified file. In multi-partition mode, if the switch is not used, a
log.lammps file is created with hi-level status information. Each
partition also writes to a log.lammps.N file where N is the partition
ID. If the switch is specified in multi-partition mode, the hi-level
logfile is named "file" and each partition also logs information to a
file.N. For both one-partition and multi-partition mode, if the
specified file is "none", then no log files are created. Using a
"log"_log.html command in the input script will override this setting.
-screen file :pre
Specify a file for LAMMPS to write its screen information to. In

View File

@ -64,8 +64,7 @@ be useful for performance testing or debugging.
</P>
<P>The <I>off</I> style allows you to do this. The effect of the -accelerator
command-line switch is effectively turned off until another
accelerator command is used with the <I>on</I> style. The <I>on</I> style can
only be used if the -accelerator command-line switch was used.
accelerator command is used with the <I>on</I> style.
</P>
<P>The <I>cuda</I> style invokes options associated with the use of the
USER-CUDA package. These will be described when the USER-CUDA package
@ -77,8 +76,8 @@ is released with LAMMPS.
USER-CUDA package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P>Obviously, you must have GPU hardware and associated software to
build LAMMPS with GPU support.
<P>Obviously, you must have GPU hardware and associated software to build
and use LAMMPS with either the GPU or USER_CUDA packages.
</P>
<P><B>Related commands:</B>
</P>

View File

@ -58,8 +58,7 @@ be useful for performance testing or debugging.
The {off} style allows you to do this. The effect of the -accelerator
command-line switch is effectively turned off until another
accelerator command is used with the {on} style. The {on} style can
only be used if the -accelerator command-line switch was used.
accelerator command is used with the {on} style.
The {cuda} style invokes options associated with the use of the
USER-CUDA package. These will be described when the USER-CUDA package
@ -71,8 +70,8 @@ This cuda style can only be invoked if LAMMPS was built with the
USER-CUDA package. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
Obviously, you must have GPU hardware and associated software to
build LAMMPS with GPU support.
Obviously, you must have GPU hardware and associated software to build
and use LAMMPS with either the GPU or USER_CUDA packages.
[Related commands:]