diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 655adf939a..adab09b06b 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -825,10 +825,6 @@ factors (xy,xz,yz) is as follows:

-

The inverse relationship can be written as follows: -

-
-

As discussed on the dump 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:

-
+
c_ID entire scalar, vector, or array
c_ID[I] one element of vector, one column of array
c_ID[I][J] 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.

-
+
diff --git a/doc/Section_start.html b/doc/Section_start.html index 55e6bb352d..6d067a1b84 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -784,43 +784,50 @@ more processors or setup a smaller problem.

2.6 Command-line options

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 +
    • -a or -accelerator +
    • -e or -echo +
    • -i or -in +
    • -l or -log +
    • -p or -partition +
    • -s or -screen +
    • -v or -var

    For example, lmp_ibm might be launched as follows:

    -
    mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy 
+
    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 
 
    
 
    Here are the details on the options:
 
    
 
    -accelerator style 
 
    
-
    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.  Also see the acclerator
-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 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.  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 command for info on how to
-temporarily turn off this option.
+
    As an example, all of the packages provide a pair_style
+lj/cut 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 command doc page for info on how
+to turn off/on the suffix associated with this switch within your
+input script.
 
    
 
    -echo style 
 
    
@@ -831,6 +838,28 @@ 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 command in the input script itself.
 
    
+
    -in file 
+
    
+
    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 
+
    
+
    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 command in the input script will override this setting.
+
    
 
    -partition 8x2 4 5 ... 
 
    
 
    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
 temper command.
 
    
-
    -in file 
-
    
-
    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 
-
    
-
    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 command in the input script will override this setting.
-
    
 
    -screen file 
 
    
 
    Specify a file for LAMMPS to write its screen information to.  In
diff --git a/doc/Section_start.txt b/doc/Section_start.txt
index ea0462ae9a..164f70ec05 100644
--- a/doc/Section_start.txt
+++ b/doc/Section_start.txt
@@ -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
diff --git a/doc/accelerator.html b/doc/accelerator.html
index ff6eca3ec0..dc95be8725 100644
--- a/doc/accelerator.html
+++ b/doc/accelerator.html
@@ -64,8 +64,7 @@ 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
@@ -77,8 +76,8 @@ is released with LAMMPS.
 USER-CUDA package.  See the Making LAMMPS
 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:
 
    
diff --git a/doc/accelerator.txt b/doc/accelerator.txt
index 6f93f33a45..9be285f466 100644
--- a/doc/accelerator.txt
+++ b/doc/accelerator.txt
@@ -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:]
Command Input Output
thermo_style custom global scalars screen, log file
dump custom per-atom vectors dump file