Assuming you have built LAMMPS with the appropriate package, these styles can be invoked by specifying them explicitly in your input -script. Or you can use the -suffix command-line +script. Or you can use the -suffix command-line switch to invoke the accelerated versions automatically, without changing your input script. The suffix command allows you to set a suffix explicitly and @@ -318,7 +318,7 @@ and in many cases it will be more efficient to run this way.
All of the above examples work whether you are running on 1 or multiple processors, but assumed you are running LAMMPS on a single partition of processors. LAMMPS can be run on multiple partitions via -the "-partition" command-line switch as described in this +the "-partition" command-line switch as described in this section of the manual.
In the last 2 examples, if LAMMPS were run on 3 partitions, the same @@ -361,7 +361,7 @@ for more info on packages.
In all these cases, you must run with one or more processors per replica. The processors assigned to each replica are determined at -run-time by using the -partition command-line +run-time by using the -partition command-line switch to launch LAMMPS on multiple partitions, which in this context are the same as replicas. E.g. these commands: @@ -370,7 +370,7 @@ these commands: mpirun -np 8 lmp_linux -partition 8x1 -in in.neb
would each run 8 replicas, on either 16 or 8 processors. Note the use -of the -in command-line switch to specify +of the -in command-line switch to specify the input script which is required when running in multi-replica mode.
Also note that with MPI installed on a machine (e.g. your desktop), @@ -665,7 +665,7 @@ strain induced across grain boundaries -
This section of the documentation +
This section of the documentation describes how to build LAMMPS as a library. Once this is done, you can interface with LAMMPS either via C++, C, Fortran, or Python (or any other language that supports a vanilla C-like interface). For @@ -1662,7 +1662,7 @@ converge and requires careful post-processing (Shinoda)
As described in Section_start 4, LAMMPS +
As described in Section_start 4, LAMMPS can be built as a library, so that it can be called by another code, used in a coupled manner with other codes, or driven through a Python interface. @@ -1684,7 +1684,7 @@ void lammps_file(void *, char *); char *lammps_command(void *, char *);
The lammps_open() function is used to initialize LAMMPS, passing in a -list of strings as if they were command-line +list of strings as if they were command-line arguments when LAMMPS is run in stand-alone mode from the command line, and a MPI communicator for LAMMPS to run under. It returns a ptr to the LAMMPS object that is diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 923153d816..a01d088b49 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -315,7 +315,7 @@ All of the above examples work whether you are running on 1 or multiple processors, but assumed you are running LAMMPS on a single partition of processors. LAMMPS can be run on multiple partitions via the "-partition" command-line switch as described in "this -section"_Section_start.html#start_6 of the manual. +section"_Section_start.html#start_7 of the manual. In the last 2 examples, if LAMMPS were run on 3 partitions, the same scripts could be used if the "index" and "loop" variables were @@ -357,7 +357,7 @@ for more info on packages. In all these cases, you must run with one or more processors per replica. The processors assigned to each replica are determined at run-time by using the "-partition command-line -switch"_Section_start.html#start_6 to launch LAMMPS on multiple +switch"_Section_start.html#start_7 to launch LAMMPS on multiple partitions, which in this context are the same as replicas. E.g. these commands: @@ -365,7 +365,7 @@ mpirun -np 16 lmp_linux -partition 8x2 -in in.temper mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre would each run 8 replicas, on either 16 or 8 processors. Note the use -of the "-in command-line switch"_Section_start.html#start_6 to specify +of the "-in command-line switch"_Section_start.html#start_7 to specify the input script which is required when running in multi-replica mode. Also note that with MPI installed on a machine (e.g. your desktop), @@ -659,7 +659,7 @@ strain induced across grain boundaries :l,ule :link(quest,http://dft.sandia.gov/Quest) :link(spparks,http://www.sandia.gov/~sjplimp/spparks.html) -"This section"_Section_start.html#start_4 of the documentation +"This section"_Section_start.html#start_5 of the documentation describes how to build LAMMPS as a library. Once this is done, you can interface with LAMMPS either via C++, C, Fortran, or Python (or any other language that supports a vanilla C-like interface). For @@ -1649,7 +1649,7 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda 6.19 Library interface to LAMMPS :link(howto_19),h4 -As described in "Section_start 4"_Section_start.html#start_4, LAMMPS +As described in "Section_start 4"_Section_start.html#start_5, LAMMPS can be built as a library, so that it can be called by another code, used in a "coupled manner"_Section_howto.html#howto_10 with other codes, or driven through a "Python interface"_Section_python.html. @@ -1672,7 +1672,7 @@ char *lammps_command(void *, char *); :pre The lammps_open() function is used to initialize LAMMPS, passing in a list of strings as if they were "command-line -arguments"_Section_start.html#start_6 when LAMMPS is run in +arguments"_Section_start.html#start_7 when LAMMPS is run in stand-alone mode from the command line, and a MPI communicator for LAMMPS to run under. It returns a ptr to the LAMMPS object that is created, and which is used in subsequent library calls. The diff --git a/doc/Section_python.html b/doc/Section_python.html index 5f09521204..1c3e72ecf2 100644 --- a/doc/Section_python.html +++ b/doc/Section_python.html @@ -34,7 +34,7 @@ packages. It can be used to glue multiple pieces of software together, e.g. to run a coupled or multiscale model. See this section of the manual and the couple directory of the distribution for more ideas about coupling LAMMPS to -other codes. See Section_start 4 about +other codes. See Section_start 4 about how to build LAMMPS as a library, and this section for a description of the library interface provided in src/library.cpp and src/library.h and how to @@ -582,7 +582,7 @@ following steps: src/library.h.
lmp_windows.exe-
Skip to the Running LAMMPS sections for info on how to +
Skip to the Running LAMMPS sections for info on how to launch these executables on a Windows box.
The Windows executables for serial or parallel only include certain @@ -93,18 +94,18 @@ pre-built, etc.
Please read this section carefully. If you are not comfortable with makefiles, or building codes on a Unix platform, or running an MPI job on your machine, please find a local expert to help you. Many -compiling, linking, and run problems that users have are not really +compiling, linking, and run problems that users have are often not LAMMPS issues - they are peculiar to the user's system, compilers, libraries, etc. Such questions are better answered by a local expert.
If you have a build problem that you are convinced is a LAMMPS issue (e.g. the compiler complains about a line of LAMMPS source code), then -please send an email to the -developers. +please post a question to the LAMMPS mail +list.
If you succeed in building LAMMPS on a new kind of machine, for which there isn't a similar Makefile for in the src/MAKE directory, send it -to the developers and we'll include it in future LAMMPS releases. +to the developers and we can include it in the LAMMPS distribution.
You can make LAMMPS for multiple platforms from the same src directory. Each target creates its own object sub-directory called -Obj_name where it stores the system-specific *.o files. +Obj_target where it stores the system-specific *.o files.
(2) Cleaning up.
@@ -476,14 +477,15 @@ secs/timestep. Building for a Mac: -OS X is BSD Unix, so it should just work. See the Makefile.mac file. +
OS X is BSD Unix, so it should just work. See the +src/MAKE/Makefile.mac file.
The LAMMPS download page has an option to download both a serial and -parallel pre-built Windows exeutable. See the Running +parallel pre-built Windows exeutable. See the Running LAMMPS section for instructions for running these executables on a Windows box.
@@ -538,7 +540,7 @@ package. You can also typelmp_machine -h-
to run your executable with the optional -h command-line
+ to run your executable with the optional -h command-line
switch for "help", which will list the styles and commands
known to your executable.
The src directory includes a Make.py script, written +in Python, which can be used to automate various steps +of the build process. +
+You can run the script from the src directory by typing either: +
+Make.py +python Make.py ++
which will give you info about the tool. For the former to work, you +may need to edit the 1st line of the script to point to your local +Python. And you may need to insure the script is executable: +
+chmod +x Make.py ++
The following options are supported as switches: +
+Help on any switch can be listed by using -h, e.g. +
+Make.py -h -i -p ++
At a hi-level, these are the kinds of package management +and build tasks that can be performed easily, using +the Make.py tool: +
+The last bullet can be useful when you wish to build a stripped-down +version of LAMMPS to run a specific script(s). Or when you wish to +move the minimal amount of files to another platform for a remote +LAMMPS build. +
+Note that using Make.py is not a substitute for insuring you have a +valid src/MAKE/Makefile.foo for your system, or that external library +Makefiles in any lib/* directories you use are also valid for your +system. But once you have done that, you can use Make.py to quickly +include/exclude the packages and external libraries needed by your +input scripts. +
+LAMMPS itself can be built as a library, which can then be called from another application or a scripting language. See this @@ -738,7 +797,7 @@ your needs.
By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux < in.file. This means you first create an input script (e.g. in.file) @@ -848,7 +907,7 @@ more processors or setup a smaller problem.
At run time, LAMMPS recognizes several optional command-line switches which may be used in any order. Either the full word or a one-or-two @@ -1117,7 +1176,7 @@ negative numeric value. It is OK if the first value1 starts with a
As LAMMPS reads an input script, it prints information to both the screen and a log file about significant actions it takes to setup a @@ -1214,7 +1273,7 @@ communication, roughly 75% in the example above.
The current C++ began with a complete rewrite of LAMMPS 2001, which was written in F90. Features of earlier versions of LAMMPS are listed diff --git a/doc/Section_start.txt b/doc/Section_start.txt index 59b06386ff..882a16f9cc 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -14,11 +14,12 @@ experienced users. 2.1 "What's in the LAMMPS distribution"_#start_1 2.2 "Making LAMMPS"_#start_2 2.3 "Making LAMMPS with optional packages"_#start_3 -2.4 "Building LAMMPS as a library"_#start_4 -2.5 "Running LAMMPS"_#start_5 -2.6 "Command-line options"_#start_6 -2.7 "Screen output"_#start_7 -2.8 "Tips for users of previous versions"_#start_8 :all(b) +2.4 "Building LAMMPS via the Make.py script"_#start_4 +2.5 "Building LAMMPS as a library"_#start_5 +2.6 "Running LAMMPS"_#start_6 +2.7 "Command-line options"_#start_7 +2.8 "Screen output"_#start_8 +2.9 "Tips for users of previous versions"_#start_9 :all(b) :line :line @@ -50,7 +51,7 @@ then you just get a single file: lmp_windows.exe :pre -Skip to the "Running LAMMPS"_#start_5 sections for info on how to +Skip to the "Running LAMMPS"_#start_6 sections for info on how to launch these executables on a Windows box. The Windows executables for serial or parallel only include certain @@ -87,18 +88,18 @@ pre-built, etc. Please read this section carefully. If you are not comfortable with makefiles, or building codes on a Unix platform, or running an MPI job on your machine, please find a local expert to help you. Many -compiling, linking, and run problems that users have are not really +compiling, linking, and run problems that users have are often not LAMMPS issues - they are peculiar to the user's system, compilers, libraries, etc. Such questions are better answered by a local expert. If you have a build problem that you are convinced is a LAMMPS issue (e.g. the compiler complains about a line of LAMMPS source code), then -please send an email to the -"developers"_http://lammps.sandia.gov/authors.html. +please post a question to the "LAMMPS mail +list"_http://lammps.sandia.gov/mail.html. If you succeed in building LAMMPS on a new kind of machine, for which there isn't a similar Makefile for in the src/MAKE directory, send it -to the developers and we'll include it in future LAMMPS releases. +to the developers and we can include it in the LAMMPS distribution. :line @@ -419,7 +420,7 @@ above in Step 4. You can make LAMMPS for multiple platforms from the same src directory. Each target creates its own object sub-directory called -Obj_name where it stores the system-specific *.o files. +Obj_target where it stores the system-specific *.o files. (2) Cleaning up. @@ -470,7 +471,8 @@ secs/timestep. [{Building for a Mac:}] :link(start_2_5) -OS X is BSD Unix, so it should just work. See the Makefile.mac file. +OS X is BSD Unix, so it should just work. See the +src/MAKE/Makefile.mac file. :line @@ -478,7 +480,7 @@ OS X is BSD Unix, so it should just work. See the Makefile.mac file. The LAMMPS download page has an option to download both a serial and parallel pre-built Windows exeutable. See the "Running -LAMMPS"_#start_5 section for instructions for running these +LAMMPS"_#start_6 section for instructions for running these executables on a Windows box. If the pre-built executable doesn't have the options you want, then @@ -533,7 +535,7 @@ package. You can also type lmp_machine -h :pre to run your executable with the optional "-h command-line -switch"_#start_6 for "help", which will list the styles and commands +switch"_#start_7 for "help", which will list the styles and commands known to your executable. There are two kinds of packages in LAMMPS, standard and user packages. @@ -689,7 +691,64 @@ build will likely fail. :line -2.4 Building LAMMPS as a library :h4,link(start_4) +2.4 Building LAMMPS via the Make.py script :h4,link(start_4) + +The src directory includes a Make.py script, written +in Python, which can be used to automate various steps +of the build process. + +You can run the script from the src directory by typing either: + +Make.py +python Make.py :pre + +which will give you info about the tool. For the former to work, you +may need to edit the 1st line of the script to point to your local +Python. And you may need to insure the script is executable: + +chmod +x Make.py :pre + +The following options are supported as switches: + +-i file1 file2 ... +-p package1 package2 ... +-u package1 package2 ... +-e package1 arg1 arg2 package2 ... +-o dir +-b machine +-s suffix1 suffix2 ... +-l dir +-j N +-h switch1 switch2 ... :ul + +Help on any switch can be listed by using -h, e.g. + +Make.py -h -i -p :pre + +At a hi-level, these are the kinds of package management +and build tasks that can be performed easily, using +the Make.py tool: + +install/uninstall packages and build the associated external libs (use -p and -u and -e) +install packages needed for one or more input scripts (use -i and -p) +build LAMMPS, either in the src dir or new dir (use -b) +create a new dir with only the source code needed for one or more input scripts (use -i and -o) :ul + +The last bullet can be useful when you wish to build a stripped-down +version of LAMMPS to run a specific script(s). Or when you wish to +move the minimal amount of files to another platform for a remote +LAMMPS build. + +Note that using Make.py is not a substitute for insuring you have a +valid src/MAKE/Makefile.foo for your system, or that external library +Makefiles in any lib/* directories you use are also valid for your +system. But once you have done that, you can use Make.py to quickly +include/exclude the packages and external libraries needed by your +input scripts. + +:line + +2.5 Building LAMMPS as a library :h4,link(start_5) LAMMPS itself can be built as a library, which can then be called from another application or a scripting language. See "this @@ -732,7 +791,7 @@ your needs. :line -2.5 Running LAMMPS :h4,link(start_5) +2.6 Running LAMMPS :h4,link(start_6) By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux < in.file. This means you first create an input script (e.g. in.file) @@ -839,7 +898,7 @@ more processors or setup a smaller problem. :line -2.6 Command-line options :h4,link(start_6) +2.7 Command-line options :h4,link(start_7) At run time, LAMMPS recognizes several optional command-line switches which may be used in any order. Either the full word or a one-or-two @@ -1108,7 +1167,7 @@ negative numeric value. It is OK if the first value1 starts with a :line -2.7 LAMMPS screen output :h4,link(start_7) +2.8 LAMMPS screen output :h4,link(start_8) As LAMMPS reads an input script, it prints information to both the screen and a log file about significant actions it takes to setup a @@ -1205,7 +1264,7 @@ communication, roughly 75% in the example above. :line -2.8 Tips for users of previous LAMMPS versions :h4,link(start_8) +2.9 Tips for users of previous LAMMPS versions :h4,link(start_9) The current C++ began with a complete rewrite of LAMMPS 2001, which was written in F90. Features of earlier versions of LAMMPS are listed diff --git a/doc/angle_charmm.html b/doc/angle_charmm.html index 9cc950f568..b4fccf5590 100644 --- a/doc/angle_charmm.html +++ b/doc/angle_charmm.html @@ -63,7 +63,7 @@ those packages. See the Making LAMMPS
You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/angle_charmm.txt b/doc/angle_charmm.txt index 78500a5387..28b9c7c73b 100644 --- a/doc/angle_charmm.txt +++ b/doc/angle_charmm.txt @@ -60,7 +60,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/angle_class2.html b/doc/angle_class2.html index ddc19dd1b2..a80dabcc32 100644 --- a/doc/angle_class2.html +++ b/doc/angle_class2.html @@ -95,7 +95,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/angle_class2.txt b/doc/angle_class2.txt index 36a16e8367..12ec476f26 100644 --- a/doc/angle_class2.txt +++ b/doc/angle_class2.txt @@ -92,7 +92,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/angle_cosine.html b/doc/angle_cosine.html index 1c376614a1..f090e0e47a 100644 --- a/doc/angle_cosine.html +++ b/doc/angle_cosine.html @@ -52,7 +52,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/angle_cosine.txt b/doc/angle_cosine.txt index 9c7b722976..22a6c6b964 100644 --- a/doc/angle_cosine.txt +++ b/doc/angle_cosine.txt @@ -49,7 +49,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/angle_cosine_delta.html b/doc/angle_cosine_delta.html index dd8c9965c9..9996549363 100644 --- a/doc/angle_cosine_delta.html +++ b/doc/angle_cosine_delta.html @@ -57,7 +57,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/angle_cosine_delta.txt b/doc/angle_cosine_delta.txt index 92b809b675..680c43f194 100644 --- a/doc/angle_cosine_delta.txt +++ b/doc/angle_cosine_delta.txt @@ -54,7 +54,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/angle_cosine_periodic.html b/doc/angle_cosine_periodic.html index 55469c2c66..d830d3d05a 100644 --- a/doc/angle_cosine_periodic.html +++ b/doc/angle_cosine_periodic.html @@ -65,7 +65,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/angle_cosine_periodic.txt b/doc/angle_cosine_periodic.txt index c5ea3563bb..3f26b9bc99 100644 --- a/doc/angle_cosine_periodic.txt +++ b/doc/angle_cosine_periodic.txt @@ -62,7 +62,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/angle_cosine_shift.html b/doc/angle_cosine_shift.html index 76b1cea55e..37cf72f554 100644 --- a/doc/angle_cosine_shift.html +++ b/doc/angle_cosine_shift.html @@ -55,7 +55,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/angle_cosine_shift.txt b/doc/angle_cosine_shift.txt index cd2b7fe100..6663516425 100644 --- a/doc/angle_cosine_shift.txt +++ b/doc/angle_cosine_shift.txt @@ -52,7 +52,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/angle_cosine_shift_exp.html b/doc/angle_cosine_shift_exp.html index 3a30784ee5..2761a6bc9c 100644 --- a/doc/angle_cosine_shift_exp.html +++ b/doc/angle_cosine_shift_exp.html @@ -67,7 +67,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/angle_cosine_shift_exp.txt b/doc/angle_cosine_shift_exp.txt index f9b2efdf91..4c7098b104 100644 --- a/doc/angle_cosine_shift_exp.txt +++ b/doc/angle_cosine_shift_exp.txt @@ -64,7 +64,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/angle_cosine_squared.html b/doc/angle_cosine_squared.html index 08af469010..c35373fc42 100644 --- a/doc/angle_cosine_squared.html +++ b/doc/angle_cosine_squared.html @@ -57,7 +57,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/angle_cosine_squared.txt b/doc/angle_cosine_squared.txt index ec7dbd2176..54d9ee1131 100644 --- a/doc/angle_cosine_squared.txt +++ b/doc/angle_cosine_squared.txt @@ -54,7 +54,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/angle_harmonic.html b/doc/angle_harmonic.html index 4242327dbb..29886db36d 100644 --- a/doc/angle_harmonic.html +++ b/doc/angle_harmonic.html @@ -57,7 +57,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/angle_harmonic.txt b/doc/angle_harmonic.txt index b0695631e3..c12239528f 100644 --- a/doc/angle_harmonic.txt +++ b/doc/angle_harmonic.txt @@ -54,7 +54,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/angle_table.html b/doc/angle_table.html index 992eeeb262..390684f9a4 100644 --- a/doc/angle_table.html +++ b/doc/angle_table.html @@ -138,7 +138,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/angle_table.txt b/doc/angle_table.txt index 008d0c21f2..953ebd6100 100644 --- a/doc/angle_table.txt +++ b/doc/angle_table.txt @@ -135,7 +135,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/bond_class2.html b/doc/bond_class2.html index d12a5254a3..d3de624de4 100644 --- a/doc/bond_class2.html +++ b/doc/bond_class2.html @@ -57,7 +57,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/bond_class2.txt b/doc/bond_class2.txt index c6a9c317ed..3d7b8f9e4c 100644 --- a/doc/bond_class2.txt +++ b/doc/bond_class2.txt @@ -54,7 +54,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/bond_fene.html b/doc/bond_fene.html index 06efe05a1d..80965a31ff 100644 --- a/doc/bond_fene.html +++ b/doc/bond_fene.html @@ -59,7 +59,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/bond_fene.txt b/doc/bond_fene.txt index 8ce6ae89c6..966af270fb 100644 --- a/doc/bond_fene.txt +++ b/doc/bond_fene.txt @@ -56,7 +56,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/bond_fene_expand.html b/doc/bond_fene_expand.html index a68e76f04c..54fe2718e5 100644 --- a/doc/bond_fene_expand.html +++ b/doc/bond_fene_expand.html @@ -64,7 +64,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/bond_fene_expand.txt b/doc/bond_fene_expand.txt index 997921cd7d..1a6c3a33ef 100644 --- a/doc/bond_fene_expand.txt +++ b/doc/bond_fene_expand.txt @@ -61,7 +61,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/bond_harmonic.html b/doc/bond_harmonic.html index 3fbe7041ce..cfb1759355 100644 --- a/doc/bond_harmonic.html +++ b/doc/bond_harmonic.html @@ -54,7 +54,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/bond_harmonic.txt b/doc/bond_harmonic.txt index df5bdeeffb..1b341a4b83 100644 --- a/doc/bond_harmonic.txt +++ b/doc/bond_harmonic.txt @@ -51,7 +51,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/bond_harmonic_shift.html b/doc/bond_harmonic_shift.html index 0b9b3f6c18..a7ceef93a3 100644 --- a/doc/bond_harmonic_shift.html +++ b/doc/bond_harmonic_shift.html @@ -59,7 +59,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/bond_harmonic_shift.txt b/doc/bond_harmonic_shift.txt index 0ca376089d..418dbe27ef 100644 --- a/doc/bond_harmonic_shift.txt +++ b/doc/bond_harmonic_shift.txt @@ -54,7 +54,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/bond_harmonic_shift_cut.html b/doc/bond_harmonic_shift_cut.html index b7b8e30649..971bd59217 100644 --- a/doc/bond_harmonic_shift_cut.html +++ b/doc/bond_harmonic_shift_cut.html @@ -57,7 +57,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/bond_harmonic_shift_cut.txt b/doc/bond_harmonic_shift_cut.txt index 847a455413..bd5e2466c0 100644 --- a/doc/bond_harmonic_shift_cut.txt +++ b/doc/bond_harmonic_shift_cut.txt @@ -54,7 +54,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/bond_morse.html b/doc/bond_morse.html index 3c60514382..b0fdef52df 100644 --- a/doc/bond_morse.html +++ b/doc/bond_morse.html @@ -55,7 +55,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/bond_morse.txt b/doc/bond_morse.txt index b399b02e93..4c8415956b 100644 --- a/doc/bond_morse.txt +++ b/doc/bond_morse.txt @@ -52,7 +52,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/bond_nonlinear.html b/doc/bond_nonlinear.html index c511c2c956..8847fb709a 100644 --- a/doc/bond_nonlinear.html +++ b/doc/bond_nonlinear.html @@ -55,7 +55,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/bond_nonlinear.txt b/doc/bond_nonlinear.txt index e0cd987b66..d38d8fff55 100644 --- a/doc/bond_nonlinear.txt +++ b/doc/bond_nonlinear.txt @@ -52,7 +52,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/bond_quartic.html b/doc/bond_quartic.html index fc138a2989..0aa83985ab 100644 --- a/doc/bond_quartic.html +++ b/doc/bond_quartic.html @@ -90,7 +90,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/bond_quartic.txt b/doc/bond_quartic.txt index b0a7ff4bc4..a58deafb9a 100644 --- a/doc/bond_quartic.txt +++ b/doc/bond_quartic.txt @@ -87,7 +87,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/bond_table.html b/doc/bond_table.html index d79c4b4091..76e7fce84c 100644 --- a/doc/bond_table.html +++ b/doc/bond_table.html @@ -135,7 +135,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/bond_table.txt b/doc/bond_table.txt index be9060d595..9b9d7bffbc 100644 --- a/doc/bond_table.txt +++ b/doc/bond_table.txt @@ -132,7 +132,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/compute_pe.html b/doc/compute_pe.html index 75f44af57b..fa71a4c740 100644 --- a/doc/compute_pe.html +++ b/doc/compute_pe.html @@ -70,7 +70,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/compute_pe.txt b/doc/compute_pe.txt index e09ad02b32..0920575b17 100644 --- a/doc/compute_pe.txt +++ b/doc/compute_pe.txt @@ -67,7 +67,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/compute_pressure.html b/doc/compute_pressure.html index f5e729b519..e59fa51001 100644 --- a/doc/compute_pressure.html +++ b/doc/compute_pressure.html @@ -100,7 +100,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/compute_pressure.txt b/doc/compute_pressure.txt index 0e42709481..da4dc251c3 100644 --- a/doc/compute_pressure.txt +++ b/doc/compute_pressure.txt @@ -97,7 +97,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/compute_temp.html b/doc/compute_temp.html index bf7a2615c7..d669eee5e2 100644 --- a/doc/compute_temp.html +++ b/doc/compute_temp.html @@ -80,7 +80,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/compute_temp.txt b/doc/compute_temp.txt index d31b05bd2e..d468f30ce1 100644 --- a/doc/compute_temp.txt +++ b/doc/compute_temp.txt @@ -77,7 +77,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/compute_temp_partial.html b/doc/compute_temp_partial.html index c6b841c2b0..5385c5bfae 100644 --- a/doc/compute_temp_partial.html +++ b/doc/compute_temp_partial.html @@ -88,7 +88,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/compute_temp_partial.txt b/doc/compute_temp_partial.txt index 525ab972a9..1be85c5845 100644 --- a/doc/compute_temp_partial.txt +++ b/doc/compute_temp_partial.txt @@ -85,7 +85,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/dihedral_charmm.html b/doc/dihedral_charmm.html index 37f910922f..74e53f84d7 100644 --- a/doc/dihedral_charmm.html +++ b/doc/dihedral_charmm.html @@ -84,7 +84,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/dihedral_charmm.txt b/doc/dihedral_charmm.txt index 7129673581..2176f83bf3 100644 --- a/doc/dihedral_charmm.txt +++ b/doc/dihedral_charmm.txt @@ -81,7 +81,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/dihedral_class2.html b/doc/dihedral_class2.html index dcc8e8343b..960d968eb7 100644 --- a/doc/dihedral_class2.html +++ b/doc/dihedral_class2.html @@ -154,7 +154,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/dihedral_class2.txt b/doc/dihedral_class2.txt index 391facf945..7d089d32a5 100644 --- a/doc/dihedral_class2.txt +++ b/doc/dihedral_class2.txt @@ -151,7 +151,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/dihedral_cosine_shift_exp.html b/doc/dihedral_cosine_shift_exp.html index f0270280aa..f799606388 100644 --- a/doc/dihedral_cosine_shift_exp.html +++ b/doc/dihedral_cosine_shift_exp.html @@ -66,7 +66,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/dihedral_cosine_shift_exp.txt b/doc/dihedral_cosine_shift_exp.txt index 1807d1c7e0..209b7f177d 100644 --- a/doc/dihedral_cosine_shift_exp.txt +++ b/doc/dihedral_cosine_shift_exp.txt @@ -63,7 +63,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/dihedral_harmonic.html b/doc/dihedral_harmonic.html index ad361cfce4..d548a2a7aa 100644 --- a/doc/dihedral_harmonic.html +++ b/doc/dihedral_harmonic.html @@ -52,7 +52,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/dihedral_harmonic.txt b/doc/dihedral_harmonic.txt index 8eefbc02b3..55c935b9ea 100644 --- a/doc/dihedral_harmonic.txt +++ b/doc/dihedral_harmonic.txt @@ -49,7 +49,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/dihedral_helix.html b/doc/dihedral_helix.html index f95b796e10..e03a88d192 100644 --- a/doc/dihedral_helix.html +++ b/doc/dihedral_helix.html @@ -60,7 +60,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/dihedral_helix.txt b/doc/dihedral_helix.txt index 7706c04c25..7034b96796 100644 --- a/doc/dihedral_helix.txt +++ b/doc/dihedral_helix.txt @@ -57,7 +57,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/dihedral_multi_harmonic.html b/doc/dihedral_multi_harmonic.html index 4872c29348..5f7f06f154 100644 --- a/doc/dihedral_multi_harmonic.html +++ b/doc/dihedral_multi_harmonic.html @@ -54,7 +54,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/dihedral_multi_harmonic.txt b/doc/dihedral_multi_harmonic.txt index 97b87546ad..a5706b0c7f 100644 --- a/doc/dihedral_multi_harmonic.txt +++ b/doc/dihedral_multi_harmonic.txt @@ -51,7 +51,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/dihedral_opls.html b/doc/dihedral_opls.html index 6bedadc0cf..6abb123314 100644 --- a/doc/dihedral_opls.html +++ b/doc/dihedral_opls.html @@ -58,7 +58,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/dihedral_opls.txt b/doc/dihedral_opls.txt index d12ced983e..28c2e4bb19 100644 --- a/doc/dihedral_opls.txt +++ b/doc/dihedral_opls.txt @@ -55,7 +55,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/echo.html b/doc/echo.html index 46068aa832..15ca28365e 100644 --- a/doc/echo.html +++ b/doc/echo.html @@ -29,7 +29,7 @@ command to the screen and/or log file as it is read and processed. If an input script has errors, it can be useful to look at echoed output to see the last command processed. -The command-line switch -echo can be used +
The command-line switch -echo can be used in place of this command.
Restrictions: none diff --git a/doc/echo.txt b/doc/echo.txt index eeac802ae0..8ef8ad05f8 100644 --- a/doc/echo.txt +++ b/doc/echo.txt @@ -26,7 +26,7 @@ command to the screen and/or log file as it is read and processed. If an input script has errors, it can be useful to look at echoed output to see the last command processed. -The "command-line switch"_Section_start.html#start_4 -echo can be used +The "command-line switch"_Section_start.html#start_5 -echo can be used in place of this command. [Restrictions:] none diff --git a/doc/fix_addforce.html b/doc/fix_addforce.html index 60ead37035..c97756d813 100644 --- a/doc/fix_addforce.html +++ b/doc/fix_addforce.html @@ -121,7 +121,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/fix_addforce.txt b/doc/fix_addforce.txt index bd2a159133..3ce5a5d3e0 100644 --- a/doc/fix_addforce.txt +++ b/doc/fix_addforce.txt @@ -111,7 +111,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_aveforce.html b/doc/fix_aveforce.html index 99052a01e2..d7c1011cec 100644 --- a/doc/fix_aveforce.html +++ b/doc/fix_aveforce.html @@ -87,7 +87,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/fix_aveforce.txt b/doc/fix_aveforce.txt index 9759fe4550..2b8aff6618 100644 --- a/doc/fix_aveforce.txt +++ b/doc/fix_aveforce.txt @@ -77,7 +77,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_enforce2d.html b/doc/fix_enforce2d.html index 3bf7b56e4f..87b0546b43 100644 --- a/doc/fix_enforce2d.html +++ b/doc/fix_enforce2d.html @@ -44,7 +44,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/fix_enforce2d.txt b/doc/fix_enforce2d.txt index 46000e9624..6a07e7ec5d 100644 --- a/doc/fix_enforce2d.txt +++ b/doc/fix_enforce2d.txt @@ -41,7 +41,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_freeze.html b/doc/fix_freeze.html index ea95a1fdb3..4e016d5d39 100644 --- a/doc/fix_freeze.html +++ b/doc/fix_freeze.html @@ -46,7 +46,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/fix_freeze.txt b/doc/fix_freeze.txt index 05ad194799..f3c5098b0c 100644 --- a/doc/fix_freeze.txt +++ b/doc/fix_freeze.txt @@ -43,7 +43,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_gravity.html b/doc/fix_gravity.html index b26083d2d3..8f846a6f45 100644 --- a/doc/fix_gravity.html +++ b/doc/fix_gravity.html @@ -104,7 +104,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/fix_gravity.txt b/doc/fix_gravity.txt index 45812ffe45..f7cc10635a 100644 --- a/doc/fix_gravity.txt +++ b/doc/fix_gravity.txt @@ -95,7 +95,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_nh.html b/doc/fix_nh.html index 845d2cd0a2..afe49c95c2 100644 --- a/doc/fix_nh.html +++ b/doc/fix_nh.html @@ -385,7 +385,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/fix_nh.txt b/doc/fix_nh.txt index 749097a8cc..71d219f868 100644 --- a/doc/fix_nh.txt +++ b/doc/fix_nh.txt @@ -376,7 +376,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_nve.html b/doc/fix_nve.html index 2a544abd02..3132bfb294 100644 --- a/doc/fix_nve.html +++ b/doc/fix_nve.html @@ -45,7 +45,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/fix_nve.txt b/doc/fix_nve.txt index 3558efda0d..68333011e6 100644 --- a/doc/fix_nve.txt +++ b/doc/fix_nve.txt @@ -42,7 +42,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_nve_sphere.html b/doc/fix_nve_sphere.html index 2702bcbfb3..0134e8ff68 100644 --- a/doc/fix_nve_sphere.html +++ b/doc/fix_nve_sphere.html @@ -66,7 +66,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/fix_nve_sphere.txt b/doc/fix_nve_sphere.txt index ebaeabd40b..2577be82ad 100755 --- a/doc/fix_nve_sphere.txt +++ b/doc/fix_nve_sphere.txt @@ -58,7 +58,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_qeq_comb.html b/doc/fix_qeq_comb.html index 984b6bd685..91e8fb4b0c 100644 --- a/doc/fix_qeq_comb.html +++ b/doc/fix_qeq_comb.html @@ -83,7 +83,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/fix_qeq_comb.txt b/doc/fix_qeq_comb.txt index 5cce65180b..01f94c96ff 100644 --- a/doc/fix_qeq_comb.txt +++ b/doc/fix_qeq_comb.txt @@ -73,7 +73,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_setforce.html b/doc/fix_setforce.html index 2ac1db341d..da6ffb5d3f 100644 --- a/doc/fix_setforce.html +++ b/doc/fix_setforce.html @@ -88,7 +88,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/fix_setforce.txt b/doc/fix_setforce.txt index c215e3ed25..784d1eb7e8 100644 --- a/doc/fix_setforce.txt +++ b/doc/fix_setforce.txt @@ -78,7 +78,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_shake.html b/doc/fix_shake.html index a83ee5a3eb..29b130866f 100644 --- a/doc/fix_shake.html +++ b/doc/fix_shake.html @@ -113,7 +113,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/fix_shake.txt b/doc/fix_shake.txt index e68f04cebf..1efa2dac4b 100644 --- a/doc/fix_shake.txt +++ b/doc/fix_shake.txt @@ -102,7 +102,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_temp_berendsen.html b/doc/fix_temp_berendsen.html index 494311d17a..49d7e7d408 100644 --- a/doc/fix_temp_berendsen.html +++ b/doc/fix_temp_berendsen.html @@ -109,7 +109,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/fix_temp_berendsen.txt b/doc/fix_temp_berendsen.txt index 4ac7e2b6e4..5a4428923f 100644 --- a/doc/fix_temp_berendsen.txt +++ b/doc/fix_temp_berendsen.txt @@ -106,7 +106,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html index 34fd4ea235..9a800303d5 100644 --- a/doc/fix_temp_rescale.html +++ b/doc/fix_temp_rescale.html @@ -118,7 +118,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/fix_temp_rescale.txt b/doc/fix_temp_rescale.txt index 0215f837f4..3d7b7aec13 100644 --- a/doc/fix_temp_rescale.txt +++ b/doc/fix_temp_rescale.txt @@ -114,7 +114,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/fix_viscous.html b/doc/fix_viscous.html index 94a9c6980a..2140a7e8cc 100644 --- a/doc/fix_viscous.html +++ b/doc/fix_viscous.html @@ -96,7 +96,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script. diff --git a/doc/fix_viscous.txt b/doc/fix_viscous.txt index 2e1b87837b..355a099fad 100644 --- a/doc/fix_viscous.txt +++ b/doc/fix_viscous.txt @@ -88,7 +88,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/improper_class2.html b/doc/improper_class2.html index 03cccdf6a3..73cf13993b 100644 --- a/doc/improper_class2.html +++ b/doc/improper_class2.html @@ -100,7 +100,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/improper_class2.txt b/doc/improper_class2.txt index f6d66b9c7f..dbb0a3d8e7 100644 --- a/doc/improper_class2.txt +++ b/doc/improper_class2.txt @@ -97,7 +97,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/improper_cvff.html b/doc/improper_cvff.html index 211b33f1d5..0201678bd3 100644 --- a/doc/improper_cvff.html +++ b/doc/improper_cvff.html @@ -70,7 +70,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/improper_cvff.txt b/doc/improper_cvff.txt index 94736d3cd2..0a0783b533 100644 --- a/doc/improper_cvff.txt +++ b/doc/improper_cvff.txt @@ -67,7 +67,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/improper_harmonic.html b/doc/improper_harmonic.html index 075a1c1416..140f7228c9 100644 --- a/doc/improper_harmonic.html +++ b/doc/improper_harmonic.html @@ -70,7 +70,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/improper_harmonic.txt b/doc/improper_harmonic.txt index 9a03129909..6f67b47017 100644 --- a/doc/improper_harmonic.txt +++ b/doc/improper_harmonic.txt @@ -67,7 +67,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/improper_umbrella.html b/doc/improper_umbrella.html index 8c74bad45c..149d5c9a04 100644 --- a/doc/improper_umbrella.html +++ b/doc/improper_umbrella.html @@ -65,7 +65,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/improper_umbrella.txt b/doc/improper_umbrella.txt index d5e178ff94..478003bb8e 100644 --- a/doc/improper_umbrella.txt +++ b/doc/improper_umbrella.txt @@ -62,7 +62,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/jump.html b/doc/jump.html index 2d175a6a79..8bd2fdaaf7 100644 --- a/doc/jump.html +++ b/doc/jump.html @@ -43,8 +43,8 @@ e.g.since the SELF option invokes the C-library rewind() call, which may not be supported for stdin on some systems. This can be worked around -by using the -in command-line argument or -the -var command-line argument to pass +by using the -in command-line argument or +the -var command-line argument to pass the script name as a variable to the input script In the latter case, the "fname" variable could be used in place of SELF. E.g. diff --git a/doc/jump.txt b/doc/jump.txt index 83f40af7e9..d3069be3a5 100644 --- a/doc/jump.txt +++ b/doc/jump.txt @@ -40,8 +40,8 @@ lmp_g++ < in.script :pre since the SELF option invokes the C-library rewind() call, which may not be supported for stdin on some systems. This can be worked around -by using the "-in command-line argument"_Section_start.html#start_6 or -the "-var command-line argument"_Section_start.html#start_6 to pass +by using the "-in command-line argument"_Section_start.html#start_7 or +the "-var command-line argument"_Section_start.html#start_7 to pass the script name as a variable to the input script In the latter case, the "fname" "variable"_variable.html could be used in place of SELF. E.g. diff --git a/doc/log.html b/doc/log.html index 10db3c0b4c..28cc762cac 100644 --- a/doc/log.html +++ b/doc/log.html @@ -33,7 +33,7 @@ the same log file.
The file "log.lammps" is the default log file for a LAMMPS run. The name of the initial log file can also be set by the command-line -switch -log. See Section_start 6 for +switch -log. See Section_start 6 for details.
Restrictions: none
diff --git a/doc/log.txt b/doc/log.txt
index bfd4462c47..94678f902d 100644
--- a/doc/log.txt
+++ b/doc/log.txt
@@ -30,7 +30,7 @@ the same log file.
The file "log.lammps" is the default log file for a LAMMPS run. The
name of the initial log file can also be set by the command-line
-switch -log. See "Section_start 6"_Section_start.html#start_6 for
+switch -log. See "Section_start 6"_Section_start.html#start_7 for
details.
[Restrictions:] none
diff --git a/doc/neb.html b/doc/neb.html
index 6549538085..06a82d3180 100644
--- a/doc/neb.html
+++ b/doc/neb.html
@@ -42,7 +42,7 @@ follows the discussion in these 3 papers: (Henkelman1)
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
-switch; see Section_start 6 of the
+switch; see Section_start 6 of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
diff --git a/doc/neb.txt b/doc/neb.txt
index 78c3a927ba..aa630f82bb 100644
--- a/doc/neb.txt
+++ b/doc/neb.txt
@@ -39,7 +39,7 @@ follows the discussion in these 3 papers: "(Henkelman1)"_#Henkelman1,
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
-switch; see "Section_start 6"_Section_start.html#start_6 of the
+switch; see "Section_start 6"_Section_start.html#start_7 of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
diff --git a/doc/neighbor.html b/doc/neighbor.html
index 0a69e18d7e..6efb251466 100644
--- a/doc/neighbor.html
+++ b/doc/neighbor.html
@@ -68,7 +68,7 @@ stored in the list.
When a run is finished, counts of the number of neighbors stored in
the pairwise list and the number of times neighbor lists were built
-are printed to the screen and log file. See this
+are printed to the screen and log file. See this
section for details.
Restrictions: none
diff --git a/doc/neighbor.txt b/doc/neighbor.txt
index 199bd91430..e30fb41d0a 100644
--- a/doc/neighbor.txt
+++ b/doc/neighbor.txt
@@ -66,7 +66,7 @@ stored in the list.
When a run is finished, counts of the number of neighbors stored in
the pairwise list and the number of times neighbor lists were built
are printed to the screen and log file. See "this
-section"_Section_start.html#start_7 for details.
+section"_Section_start.html#start_8 for details.
[Restrictions:] none
diff --git a/doc/next.html b/doc/next.html
index 14647c66fc..31be8e0f5f 100644
--- a/doc/next.html
+++ b/doc/next.html
@@ -60,7 +60,7 @@ the next command is used with universe- or uloop-style variables,
the next value is assigned to whichever processor partition executes
the command first. All processors in the partition are assigned the
same value. Running LAMMPS on multiple partitions of processors via
-the "-partition" command-line switch is described in this
+the "-partition" command-line switch is described in this
section of the manual. Universe- and
uloop-style variables are incremented using the files
"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
diff --git a/doc/next.txt b/doc/next.txt
index fd509e1b0b..f0be628871 100644
--- a/doc/next.txt
+++ b/doc/next.txt
@@ -58,7 +58,7 @@ the next value is assigned to whichever processor partition executes
the command first. All processors in the partition are assigned the
same value. Running LAMMPS on multiple partitions of processors via
the "-partition" command-line switch is described in "this
-section"_Section_start.html#start_6 of the manual. {Universe}- and
+section"_Section_start.html#start_7 of the manual. {Universe}- and
{uloop}-style variables are incremented using the files
"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
see in your directory during such a LAMMPS run.
diff --git a/doc/package.html b/doc/package.html
index 124ae47329..f31f8db721 100644
--- a/doc/package.html
+++ b/doc/package.html
@@ -65,7 +65,7 @@ following packages use it: GPU, USER-CUDA, and USER-OMP.
To use the accelerated GPU and USER-OMP styles, the use of the package
command is required. However, as described in the "Defaults" section
-below, if you use the "-sf gpu" or "-sf omp" command-line
+below, if you use the "-sf gpu" or "-sf omp" command-line
options to enable use of these styles,
then default package settings are enabled. In that case you only need
to use the package command if you want to change the defaults.
@@ -250,17 +250,17 @@ LAMMPS
Default:
-If the "-sf gpu" command-line switch is +
If the "-sf gpu" command-line switch is used then it is as if the command "package gpu force/neigh 0 0 1" were invoked, to specify default settings for the GPU package. If the command-line switch is not used, then no defaults are set, and you must specify the appropriate package command in your input script.
The default settings for the USER CUDA package are "package cuda gpu -2". This is the case whether the "-sf cuda" command-line +2". This is the case whether the "-sf cuda" command-line switch is used or not.
-If the "-sf omp" command-line switch is +
If the "-sf omp" command-line switch is used then it is as if the command "package omp *" were invoked, to specify default settings for the USER-OMP package. If the command-line switch is not used, then no defaults are set, and you diff --git a/doc/package.txt b/doc/package.txt index c8b30217a4..c9b6d9681f 100644 --- a/doc/package.txt +++ b/doc/package.txt @@ -60,7 +60,7 @@ following packages use it: GPU, USER-CUDA, and USER-OMP. To use the accelerated GPU and USER-OMP styles, the use of the package command is required. However, as described in the "Defaults" section below, if you use the "-sf gpu" or "-sf omp" "command-line -options"_Section_start.html#start_6 to enable use of these styles, +options"_Section_start.html#start_7 to enable use of these styles, then default package settings are enabled. In that case you only need to use the package command if you want to change the defaults. @@ -244,7 +244,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Default:] -If the "-sf gpu" "command-line switch"_Section_start.html#start_6 is +If the "-sf gpu" "command-line switch"_Section_start.html#start_7 is used then it is as if the command "package gpu force/neigh 0 0 1" were invoked, to specify default settings for the GPU package. If the command-line switch is not used, then no defaults are set, and you @@ -252,9 +252,9 @@ must specify the appropriate package command in your input script. The default settings for the USER CUDA package are "package cuda gpu 2". This is the case whether the "-sf cuda" "command-line -switch"_Section_start.html#start_6 is used or not. +switch"_Section_start.html#start_7 is used or not. -If the "-sf omp" "command-line switch"_Section_start.html#start_6 is +If the "-sf omp" "command-line switch"_Section_start.html#start_7 is used then it is as if the command "package omp *" were invoked, to specify default settings for the USER-OMP package. If the command-line switch is not used, then no defaults are set, and you diff --git a/doc/pair_adp.html b/doc/pair_adp.html index 230d469cd1..a475fee025 100644 --- a/doc/pair_adp.html +++ b/doc/pair_adp.html @@ -133,7 +133,7 @@ those packages. See the Making LAMMPS
You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_adp.txt b/doc/pair_adp.txt index 4909d738b4..4ddbfdac51 100644 --- a/doc/pair_adp.txt +++ b/doc/pair_adp.txt @@ -130,7 +130,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_airebo.html b/doc/pair_airebo.html index 8bc7126e04..42502af09d 100644 --- a/doc/pair_airebo.html +++ b/doc/pair_airebo.html @@ -137,7 +137,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_airebo.txt b/doc/pair_airebo.txt index 8239d42a36..0d76804a05 100644 --- a/doc/pair_airebo.txt +++ b/doc/pair_airebo.txt @@ -132,7 +132,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_born.html b/doc/pair_born.html index 3d7655c752..084b37bf81 100644 --- a/doc/pair_born.html +++ b/doc/pair_born.html @@ -127,7 +127,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_born.txt b/doc/pair_born.txt index 35bc4fe052..105237289e 100644 --- a/doc/pair_born.txt +++ b/doc/pair_born.txt @@ -119,7 +119,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_brownian.html b/doc/pair_brownian.html index 2430a43343..5028c4625a 100644 --- a/doc/pair_brownian.html +++ b/doc/pair_brownian.html @@ -83,7 +83,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_brownian.txt b/doc/pair_brownian.txt index 2919ce7001..9c828a2b37 100644 --- a/doc/pair_brownian.txt +++ b/doc/pair_brownian.txt @@ -78,7 +78,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "this section"_Section_accelerate.html of the manual for more diff --git a/doc/pair_buck.html b/doc/pair_buck.html index 03f068b096..bc237e4033 100644 --- a/doc/pair_buck.html +++ b/doc/pair_buck.html @@ -135,7 +135,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_buck.txt b/doc/pair_buck.txt index a89062799d..c0de764202 100644 --- a/doc/pair_buck.txt +++ b/doc/pair_buck.txt @@ -121,7 +121,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_buck_coul.html b/doc/pair_buck_coul.html index 863850dbc3..5bf1c92923 100644 --- a/doc/pair_buck_coul.html +++ b/doc/pair_buck_coul.html @@ -118,7 +118,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_buck_coul.txt b/doc/pair_buck_coul.txt index e6eaf14ba4..5e100e7da2 100644 --- a/doc/pair_buck_coul.txt +++ b/doc/pair_buck_coul.txt @@ -110,7 +110,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_charmm.html b/doc/pair_charmm.html index 43fb29de69..d586bb4006 100644 --- a/doc/pair_charmm.html +++ b/doc/pair_charmm.html @@ -144,7 +144,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_charmm.txt b/doc/pair_charmm.txt index bafeed18d6..fa46832205 100644 --- a/doc/pair_charmm.txt +++ b/doc/pair_charmm.txt @@ -130,7 +130,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_class2.html b/doc/pair_class2.html index 17192d1f4d..1f73c4daaf 100644 --- a/doc/pair_class2.html +++ b/doc/pair_class2.html @@ -129,7 +129,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_class2.txt b/doc/pair_class2.txt index 0a0f7a48f8..cc80ed5e68 100644 --- a/doc/pair_class2.txt +++ b/doc/pair_class2.txt @@ -115,7 +115,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_colloid.html b/doc/pair_colloid.html index b8ebae042c..765018a378 100644 --- a/doc/pair_colloid.html +++ b/doc/pair_colloid.html @@ -140,7 +140,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_colloid.txt b/doc/pair_colloid.txt index b68f8d9d6f..1feea7cf6c 100644 --- a/doc/pair_colloid.txt +++ b/doc/pair_colloid.txt @@ -137,7 +137,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_comb.html b/doc/pair_comb.html index 62c64c55ee..1ad0bce3b5 100644 --- a/doc/pair_comb.html +++ b/doc/pair_comb.html @@ -182,7 +182,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_comb.txt b/doc/pair_comb.txt index 2ea8f2fc73..2610141a78 100644 --- a/doc/pair_comb.txt +++ b/doc/pair_comb.txt @@ -179,7 +179,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_coul.html b/doc/pair_coul.html index 460ba19d52..c5f2813709 100644 --- a/doc/pair_coul.html +++ b/doc/pair_coul.html @@ -138,7 +138,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_coul.txt b/doc/pair_coul.txt index 0d2333589a..3fc4d75018 100644 --- a/doc/pair_coul.txt +++ b/doc/pair_coul.txt @@ -128,7 +128,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_dipole.html b/doc/pair_dipole.html index 3f1a5ce949..b1965f692e 100644 --- a/doc/pair_dipole.html +++ b/doc/pair_dipole.html @@ -137,7 +137,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_dipole.txt b/doc/pair_dipole.txt index f41ceb434d..b9f8b24983 100755 --- a/doc/pair_dipole.txt +++ b/doc/pair_dipole.txt @@ -130,7 +130,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_dpd.html b/doc/pair_dpd.html index b6c46cce02..18ec03bbbf 100644 --- a/doc/pair_dpd.html +++ b/doc/pair_dpd.html @@ -111,7 +111,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_dpd.txt b/doc/pair_dpd.txt index 0638e753e8..d2f8b38572 100644 --- a/doc/pair_dpd.txt +++ b/doc/pair_dpd.txt @@ -106,7 +106,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_eam.html b/doc/pair_eam.html index 929485b8cd..a525e32cb2 100644 --- a/doc/pair_eam.html +++ b/doc/pair_eam.html @@ -392,7 +392,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_eam.txt b/doc/pair_eam.txt index c865155061..a9f157b082 100644 --- a/doc/pair_eam.txt +++ b/doc/pair_eam.txt @@ -375,7 +375,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accerlate"_Section_accelerate.html of the manual for more diff --git a/doc/pair_edip.html b/doc/pair_edip.html index fb65ffbda5..0df634cd24 100644 --- a/doc/pair_edip.html +++ b/doc/pair_edip.html @@ -115,7 +115,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_edip.txt b/doc/pair_edip.txt index 5fcf6e5d6c..595070b274 100644 --- a/doc/pair_edip.txt +++ b/doc/pair_edip.txt @@ -112,7 +112,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_eim.html b/doc/pair_eim.html index 680353a8c2..08eb4938a6 100644 --- a/doc/pair_eim.html +++ b/doc/pair_eim.html @@ -147,7 +147,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_eim.txt b/doc/pair_eim.txt index 0c2b5439e3..4590ba85d0 100644 --- a/doc/pair_eim.txt +++ b/doc/pair_eim.txt @@ -144,7 +144,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_gauss.html b/doc/pair_gauss.html index d29ba2e5c2..a21e97898d 100644 --- a/doc/pair_gauss.html +++ b/doc/pair_gauss.html @@ -96,8 +96,8 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can +by including their suffix, or you can use the "-suffix command-line +switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can use the suffix command in your input script.
See Section_accelerate of the manual for diff --git a/doc/pair_gauss.txt b/doc/pair_gauss.txt index 62092ce383..a783380819 100644 --- a/doc/pair_gauss.txt +++ b/doc/pair_gauss.txt @@ -92,7 +92,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_gayberne.html b/doc/pair_gayberne.html index de5b34c3b2..84241fcd9d 100644 --- a/doc/pair_gayberne.html +++ b/doc/pair_gayberne.html @@ -147,7 +147,7 @@ those packages. See the Making LAMMPS
You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_gayberne.txt b/doc/pair_gayberne.txt index a83b4f43c0..ed969b1af8 100755 --- a/doc/pair_gayberne.txt +++ b/doc/pair_gayberne.txt @@ -143,7 +143,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_gran.html b/doc/pair_gran.html index d9862cbe69..cef4ccafab 100644 --- a/doc/pair_gran.html +++ b/doc/pair_gran.html @@ -189,7 +189,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_gran.txt b/doc/pair_gran.txt index d84b2ae48c..e15a6aca5f 100644 --- a/doc/pair_gran.txt +++ b/doc/pair_gran.txt @@ -176,7 +176,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_gromacs.html b/doc/pair_gromacs.html index 3f84634b53..c2ffe88497 100644 --- a/doc/pair_gromacs.html +++ b/doc/pair_gromacs.html @@ -109,7 +109,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_gromacs.txt b/doc/pair_gromacs.txt index d276615d19..361e43744b 100644 --- a/doc/pair_gromacs.txt +++ b/doc/pair_gromacs.txt @@ -101,7 +101,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_hbond_dreiding.html b/doc/pair_hbond_dreiding.html index 32c2e16e1b..3dbf6479ee 100644 --- a/doc/pair_hbond_dreiding.html +++ b/doc/pair_hbond_dreiding.html @@ -165,7 +165,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_hbond_dreiding.txt b/doc/pair_hbond_dreiding.txt index 1b0361fc19..1c41da09ce 100644 --- a/doc/pair_hbond_dreiding.txt +++ b/doc/pair_hbond_dreiding.txt @@ -160,7 +160,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_hybrid.html b/doc/pair_hybrid.html index 7c729a7275..98995090f4 100644 --- a/doc/pair_hybrid.html +++ b/doc/pair_hybrid.html @@ -234,7 +234,7 @@ LAMMPS was built with those packages. See the Making LAMMPS section for more info.You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_hybrid.txt b/doc/pair_hybrid.txt index 2828fc21b0..dceb18e884 100644 --- a/doc/pair_hybrid.txt +++ b/doc/pair_hybrid.txt @@ -229,7 +229,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_line_lj.html b/doc/pair_line_lj.html index 41d106fec3..51ed7fa705 100644 --- a/doc/pair_line_lj.html +++ b/doc/pair_line_lj.html @@ -94,7 +94,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_line_lj.txt b/doc/pair_line_lj.txt index cfa4ffe794..3fe83831e5 100644 --- a/doc/pair_line_lj.txt +++ b/doc/pair_line_lj.txt @@ -91,7 +91,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_lj.html b/doc/pair_lj.html index 1c480cf256..f77df8c47d 100644 --- a/doc/pair_lj.html +++ b/doc/pair_lj.html @@ -210,7 +210,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_lj.txt b/doc/pair_lj.txt index 81fc804afd..7b76d385f6 100644 --- a/doc/pair_lj.txt +++ b/doc/pair_lj.txt @@ -187,7 +187,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_lj96.html b/doc/pair_lj96.html index 940459abb4..1689812c75 100644 --- a/doc/pair_lj96.html +++ b/doc/pair_lj96.html @@ -66,7 +66,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_lj96.txt b/doc/pair_lj96.txt index 2a6280a35f..b6a20ce23c 100644 --- a/doc/pair_lj96.txt +++ b/doc/pair_lj96.txt @@ -61,7 +61,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_lj_coul.html b/doc/pair_lj_coul.html index eae07c2a2e..2c1ff3f9bc 100644 --- a/doc/pair_lj_coul.html +++ b/doc/pair_lj_coul.html @@ -120,7 +120,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_lj_coul.txt b/doc/pair_lj_coul.txt index 2a3ebdc97c..7e8344fe0e 100644 --- a/doc/pair_lj_coul.txt +++ b/doc/pair_lj_coul.txt @@ -112,7 +112,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_lj_cubic.html b/doc/pair_lj_cubic.html index 9bd2996a92..06296cd5f2 100644 --- a/doc/pair_lj_cubic.html +++ b/doc/pair_lj_cubic.html @@ -77,7 +77,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_lj_cubic.txt b/doc/pair_lj_cubic.txt index f1f17c9f9d..4183b4576d 100644 --- a/doc/pair_lj_cubic.txt +++ b/doc/pair_lj_cubic.txt @@ -74,7 +74,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_lj_expand.html b/doc/pair_lj_expand.html index 91b3130a69..f85b51cb99 100644 --- a/doc/pair_lj_expand.html +++ b/doc/pair_lj_expand.html @@ -70,7 +70,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_lj_expand.txt b/doc/pair_lj_expand.txt index d2be5a81c1..7abaa01ed9 100644 --- a/doc/pair_lj_expand.txt +++ b/doc/pair_lj_expand.txt @@ -65,7 +65,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_lj_sf.html b/doc/pair_lj_sf.html index 6da69b3e68..5f3354eab7 100644 --- a/doc/pair_lj_sf.html +++ b/doc/pair_lj_sf.html @@ -61,7 +61,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_lj_sf.txt b/doc/pair_lj_sf.txt index be0d94f5af..d9e54e3781 100644 --- a/doc/pair_lj_sf.txt +++ b/doc/pair_lj_sf.txt @@ -58,7 +58,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_lj_smooth.html b/doc/pair_lj_smooth.html index 9cefda53eb..ae42dd4041 100644 --- a/doc/pair_lj_smooth.html +++ b/doc/pair_lj_smooth.html @@ -78,7 +78,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_lj_smooth.txt b/doc/pair_lj_smooth.txt index 65dd323a3c..d040168e1d 100644 --- a/doc/pair_lj_smooth.txt +++ b/doc/pair_lj_smooth.txt @@ -74,7 +74,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_lj_smooth_linear.html b/doc/pair_lj_smooth_linear.html index 48de111cac..949f4f1378 100644 --- a/doc/pair_lj_smooth_linear.html +++ b/doc/pair_lj_smooth_linear.html @@ -63,7 +63,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_lj_smooth_linear.txt b/doc/pair_lj_smooth_linear.txt index 4b3db57607..d2e67cf59a 100644 --- a/doc/pair_lj_smooth_linear.txt +++ b/doc/pair_lj_smooth_linear.txt @@ -60,7 +60,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_lubricate.html b/doc/pair_lubricate.html index 95ef4e6c29..31d85ec902 100644 --- a/doc/pair_lubricate.html +++ b/doc/pair_lubricate.html @@ -138,7 +138,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_lubricate.txt b/doc/pair_lubricate.txt index 70385effd7..2a195a7ae5 100644 --- a/doc/pair_lubricate.txt +++ b/doc/pair_lubricate.txt @@ -133,7 +133,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "this section"_Section_accelerate.html of the manual for more diff --git a/doc/pair_morse.html b/doc/pair_morse.html index 42ab9eb6d5..3c2d62dcab 100644 --- a/doc/pair_morse.html +++ b/doc/pair_morse.html @@ -68,7 +68,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_morse.txt b/doc/pair_morse.txt index 5c8293e6bf..c5d3ede1c5 100644 --- a/doc/pair_morse.txt +++ b/doc/pair_morse.txt @@ -62,7 +62,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_peri.html b/doc/pair_peri.html index c5871b9820..2a25818c3c 100644 --- a/doc/pair_peri.html +++ b/doc/pair_peri.html @@ -96,7 +96,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_peri.txt b/doc/pair_peri.txt index acaea14e3d..e9ddd4caa9 100644 --- a/doc/pair_peri.txt +++ b/doc/pair_peri.txt @@ -91,7 +91,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_resquared.html b/doc/pair_resquared.html index ebca4fe033..2cd51731b4 100644 --- a/doc/pair_resquared.html +++ b/doc/pair_resquared.html @@ -160,7 +160,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_resquared.txt b/doc/pair_resquared.txt index d364346f7b..1a4c76650d 100755 --- a/doc/pair_resquared.txt +++ b/doc/pair_resquared.txt @@ -156,7 +156,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_sdk.html b/doc/pair_sdk.html index c2f9a76c31..361f83307b 100644 --- a/doc/pair_sdk.html +++ b/doc/pair_sdk.html @@ -103,7 +103,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_sdk.txt b/doc/pair_sdk.txt index 536be2a6e8..cd992297cd 100644 --- a/doc/pair_sdk.txt +++ b/doc/pair_sdk.txt @@ -95,7 +95,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_soft.html b/doc/pair_soft.html index 0376c6fe5b..8d3b45cc09 100644 --- a/doc/pair_soft.html +++ b/doc/pair_soft.html @@ -95,7 +95,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_soft.txt b/doc/pair_soft.txt index d95c0d23c1..3acb16d602 100644 --- a/doc/pair_soft.txt +++ b/doc/pair_soft.txt @@ -92,7 +92,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_sw.html b/doc/pair_sw.html index 67165ac0b1..778a01e096 100644 --- a/doc/pair_sw.html +++ b/doc/pair_sw.html @@ -154,7 +154,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_sw.txt b/doc/pair_sw.txt index b6a8113b7f..5712f81de8 100644 --- a/doc/pair_sw.txt +++ b/doc/pair_sw.txt @@ -150,7 +150,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_table.html b/doc/pair_table.html index cc1f4702b1..5ef2668970 100644 --- a/doc/pair_table.html +++ b/doc/pair_table.html @@ -193,7 +193,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_table.txt b/doc/pair_table.txt index f5629a0fb8..f2220d5c5f 100644 --- a/doc/pair_table.txt +++ b/doc/pair_table.txt @@ -189,7 +189,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_tersoff.html b/doc/pair_tersoff.html index ef109da047..50fefb95e4 100644 --- a/doc/pair_tersoff.html +++ b/doc/pair_tersoff.html @@ -191,7 +191,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_tersoff.txt b/doc/pair_tersoff.txt index 58a88abaaf..cb83f752c3 100644 --- a/doc/pair_tersoff.txt +++ b/doc/pair_tersoff.txt @@ -185,7 +185,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_tersoff_zbl.html b/doc/pair_tersoff_zbl.html index 202601f7a4..9aa63e8be0 100644 --- a/doc/pair_tersoff_zbl.html +++ b/doc/pair_tersoff_zbl.html @@ -193,7 +193,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_tersoff_zbl.txt b/doc/pair_tersoff_zbl.txt index 53888cd032..40d17db4c1 100644 --- a/doc/pair_tersoff_zbl.txt +++ b/doc/pair_tersoff_zbl.txt @@ -190,7 +190,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_tri_lj.html b/doc/pair_tri_lj.html index cbf14115e9..fd419ce4bb 100644 --- a/doc/pair_tri_lj.html +++ b/doc/pair_tri_lj.html @@ -97,7 +97,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_tri_lj.txt b/doc/pair_tri_lj.txt index 6fb9553bb6..4f216df1b6 100644 --- a/doc/pair_tri_lj.txt +++ b/doc/pair_tri_lj.txt @@ -94,7 +94,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_yukawa.html b/doc/pair_yukawa.html index 496aee843c..b630172c92 100644 --- a/doc/pair_yukawa.html +++ b/doc/pair_yukawa.html @@ -63,7 +63,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_yukawa.txt b/doc/pair_yukawa.txt index 173710d6a2..302234f18f 100644 --- a/doc/pair_yukawa.txt +++ b/doc/pair_yukawa.txt @@ -59,7 +59,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/pair_yukawa_colloid.html b/doc/pair_yukawa_colloid.html index b41a2f6697..7e439b1ec7 100644 --- a/doc/pair_yukawa_colloid.html +++ b/doc/pair_yukawa_colloid.html @@ -92,7 +92,7 @@ those packages. See the Making LAMMPSYou can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line +by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
diff --git a/doc/pair_yukawa_colloid.txt b/doc/pair_yukawa_colloid.txt index 70eb071d5b..dbd1093311 100644 --- a/doc/pair_yukawa_colloid.txt +++ b/doc/pair_yukawa_colloid.txt @@ -89,7 +89,7 @@ section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for diff --git a/doc/partition.html b/doc/partition.html index 31e212fdb2..4832823338 100644 --- a/doc/partition.html +++ b/doc/partition.html @@ -30,7 +30,7 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1This command invokes the specified command on a subset of the partitions of processors you have defined via the -partition -command-line switch. See Section_start 6 +command-line switch. See Section_start 6 for an explanation of the switch.
Normally, every input script command in your script is invoked by @@ -51,7 +51,7 @@ will be invoked on all the partitions which do not match the Np argument.
Partitions are numbered from 1 to Np, where Np is the number of -partitions specified by the -partition command-line +partitions specified by the -partition command-line switch.
N can be specified in one of two ways. An explicit numeric value diff --git a/doc/partition.txt b/doc/partition.txt index 1253ef0f65..ab62135c83 100644 --- a/doc/partition.txt +++ b/doc/partition.txt @@ -27,7 +27,7 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1 :pre This command invokes the specified command on a subset of the partitions of processors you have defined via the -partition -command-line switch. See "Section_start 6"_Section_start.html#start_6 +command-line switch. See "Section_start 6"_Section_start.html#start_7 for an explanation of the switch. Normally, every input script command in your script is invoked by @@ -49,7 +49,7 @@ argument. Partitions are numbered from 1 to Np, where Np is the number of partitions specified by the "-partition command-line -switch"_Section_start.html#start_6. +switch"_Section_start.html#start_7. {N} can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can diff --git a/doc/prd.html b/doc/prd.html index baad8b3dfb..0d522853fb 100644 --- a/doc/prd.html +++ b/doc/prd.html @@ -71,7 +71,7 @@ event to occur.
Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see Section_start 6 of the +switch; see Section_start 6 of the manual. Note that if you have MPI installed, you can run a multi-replica simulation with more replicas (partitions) than you have physical processors, e.g you can run a 10-replica simulation on one or diff --git a/doc/prd.txt b/doc/prd.txt index 52c5406eee..717e89fb60 100644 --- a/doc/prd.txt +++ b/doc/prd.txt @@ -58,7 +58,7 @@ event to occur. Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see "Section_start 6"_Section_start.html#start_6 of the +switch; see "Section_start 6"_Section_start.html#start_7 of the manual. Note that if you have MPI installed, you can run a multi-replica simulation with more replicas (partitions) than you have physical processors, e.g you can run a 10-replica simulation on one or diff --git a/doc/processors.html b/doc/processors.html index 945a5d5cb7..4180afea75 100644 --- a/doc/processors.html +++ b/doc/processors.html @@ -89,7 +89,7 @@ communication costs due to the high surface area of each processor's sub-domain.
Also note that if multiple partitions are being used then P is the -number of processors in this partition; see this +number of processors in this partition; see this section for an explanation of the -partition command-line switch. Also note that you can prefix the processors command with the partition command to @@ -236,7 +236,7 @@ dependency bewteen a sending partition Psend and a receiving partition Precv which is enforced when each is setting up their own mapping of their processors to the simulation box. Each of Psend and Precv must be integers from 1 to Np, where Np is the number of -partitions you have defined via the -partition command-line +partitions you have defined via the -partition command-line switch.
A "dependency" means that the sending partition will create its 3d @@ -274,7 +274,7 @@ processors and their mapping to the 3d grid to the specified file processors in the manner you desired, which can be tricky to figure out, especially when running on multiple partitions or on, a multicore machine or when the processor ranks were reordered by use of the --reorder command-line switch or due to +-reorder command-line switch or due to use of MPI-specific launch options such as a config file.
If you have multiple partitions you should insure that each one writes @@ -288,9 +288,9 @@ one-line per processor in this format: universe (of multiple simulations), and the original MPI communicator used to instantiate LAMMPS, respectively. The world and universe IDs will only be different if you are running on more than one partition; -see the -partition command-line switch. +see the -partition command-line switch. The universe and original IDs will only be different if you used the --reorder command-line switch to reorder +-reorder command-line switch to reorder the processors differently than their rank in the original communicator LAMMPS was instantiated with.
@@ -320,7 +320,7 @@ option.Related commands:
-partition, -reorder command-line
+ partition, -reorder command-line
switch
Default:
diff --git a/doc/processors.txt b/doc/processors.txt
index a8123eee1a..e1e410f0fc 100644
--- a/doc/processors.txt
+++ b/doc/processors.txt
@@ -83,7 +83,7 @@ sub-domain.
Also note that if multiple partitions are being used then P is the
number of processors in this partition; see "this
-section"_Section_start.html#start_6 for an explanation of the
+section"_Section_start.html#start_7 for an explanation of the
-partition command-line switch. Also note that you can prefix the
processors command with the "partition"_partition.html command to
easily specify different Px,Py,Pz values for different partitions.
@@ -230,7 +230,7 @@ partition {Precv} which is enforced when each is setting up their own
mapping of their processors to the simulation box. Each of {Psend}
and {Precv} must be integers from 1 to Np, where Np is the number of
partitions you have defined via the "-partition command-line
-switch"_Section_start.html#start_6.
+switch"_Section_start.html#start_7.
A "dependency" means that the sending partition will create its 3d
logical grid as Px by Py by Pz and after it has done this, it will
@@ -267,7 +267,7 @@ processors and their mapping to the 3d grid to the specified file
processors in the manner you desired, which can be tricky to figure
out, especially when running on multiple partitions or on, a multicore
machine or when the processor ranks were reordered by use of the
-"-reorder command-line switch"_Section_start.html#start_6 or due to
+"-reorder command-line switch"_Section_start.html#start_7 or due to
use of MPI-specific launch options such as a config file.
If you have multiple partitions you should insure that each one writes
@@ -281,9 +281,9 @@ The IDs are the processor's rank in this simulation (the world), the
universe (of multiple simulations), and the original MPI communicator
used to instantiate LAMMPS, respectively. The world and universe IDs
will only be different if you are running on more than one partition;
-see the "-partition command-line switch"_Section_start.html#start_6.
+see the "-partition command-line switch"_Section_start.html#start_7.
The universe and original IDs will only be different if you used the
-"-reorder command-line switch"_Section_start.html#start_6 to reorder
+"-reorder command-line switch"_Section_start.html#start_7 to reorder
the processors differently than their rank in the original
communicator LAMMPS was instantiated with.
@@ -314,7 +314,7 @@ The {part} keyword (for the receiving partition) only works with the
[Related commands:]
"partition"_partition.html, "-reorder command-line
-switch"_Section_start.html#start_6
+switch"_Section_start.html#start_7
[Default:]
diff --git a/doc/run_style.html b/doc/run_style.html
index abe21ecdd7..49445df879 100644
--- a/doc/run_style.html
+++ b/doc/run_style.html
@@ -69,7 +69,7 @@ simulations performed by LAMMPS.
The verlet/split style is also a velocity-Verlet integrator, but it
splits the force calculation within each timestep over 2 partitions of
-processors. See Section_start 6 for an
+processors. See Section_start 6 for an
explanation of the -partition command-line switch.
Specifically, this style performs all computation except the
@@ -115,7 +115,7 @@ partition yes 2 processors 3 1 5
thermodyanmic data for the entire simulation will be output to the log
and screen file of the 1st partition, which are log.lammps.0 and
screen.0 by default; see the "-plog and -pscreen command-line
-switches"Section_start.html#start_6 to change this. The log and
+switches"Section_start.html#start_7 to change this. The log and
screen file for the 2nd partition will not contain thermodynamic
output beyone the 1st timestep of the run.
Description:
This command allows you to use variants of various styles if they
-exist. In that respect it operates the same as the -suffix
+exist. In that respect it operates the same as the -suffix
command-line switch. It also has options
to turn off/on any suffix setting made via the command line.
Related commands:
-Default: none
diff --git a/doc/suffix.txt b/doc/suffix.txt index d417d2008b..be2c1c26f8 100644 --- a/doc/suffix.txt +++ b/doc/suffix.txt @@ -24,7 +24,7 @@ suffix gpu :pre This command allows you to use variants of various styles if they exist. In that respect it operates the same as the "-suffix -command-line switch"_Section_start.html#start_6. It also has options +command-line switch"_Section_start.html#start_7. It also has options to turn off/on any suffix setting made via the command line. The specified style can be {opt}, {omp}, {gpu}, or {cuda}. These refer to @@ -77,6 +77,6 @@ commands in your input script. [Related commands:] -"Command-line switch -suffix"_Section_start.html#start_6 +"Command-line switch -suffix"_Section_start.html#start_7 [Default:] none diff --git a/doc/temper.html b/doc/temper.html index 01157902aa..fd5727b883 100644 --- a/doc/temper.html +++ b/doc/temper.html @@ -35,7 +35,7 @@ replicas (ensembles) of a system. Two or more replicas must be used.Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see Section_start 6 of the +switch; see Section_start 6 of the manual. Note that if you have MPI installed, you can run a multi-replica simulation with more replicas (partitions) than you have physical processors, e.g you can run a 10-replica simulation on one or @@ -72,7 +72,7 @@ rejected based on a Boltzmann-weighted Metropolis criterion which uses
As a tempering run proceeds, multiple log files and screen output files are created, one per replica. By default these files are named log.lammps.M and screen.M where M is the replica number from 0 to N-1, -with N = # of replicas. See the section on command-line +with N = # of replicas. See the section on command-line switches for info on how to change these names.
diff --git a/doc/temper.txt b/doc/temper.txt index 803c505cd5..6283c2b460 100644 --- a/doc/temper.txt +++ b/doc/temper.txt @@ -32,7 +32,7 @@ replicas (ensembles) of a system. Two or more replicas must be used. Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see "Section_start 6"_Section_start.html#start_6 of the +switch; see "Section_start 6"_Section_start.html#start_7 of the manual. Note that if you have MPI installed, you can run a multi-replica simulation with more replicas (partitions) than you have physical processors, e.g you can run a 10-replica simulation on one or @@ -70,7 +70,7 @@ As a tempering run proceeds, multiple log files and screen output files are created, one per replica. By default these files are named log.lammps.M and screen.M where M is the replica number from 0 to N-1, with N = # of replicas. See the "section on command-line -switches"_Section_start.html#start_6 for info on how to change these +switches"_Section_start.html#start_7 for info on how to change these names. The main screen and log file (log.lammps) will list information about diff --git a/doc/variable.html b/doc/variable.html index 103674e342..83ac3efd52 100644 --- a/doc/variable.html +++ b/doc/variable.html @@ -129,7 +129,7 @@ is ignored. This means variables can NOT be re-defined in an input script (with 2 exceptions, read further). This is to allow an input script to be processed multiple times without resetting the variables; see the jump or include commands. It also -means that using the command-line switch +means that using the command-line switch -var will override a corresponding index variable setting in the input script. @@ -187,7 +187,7 @@ string is assigned. All processors assign the same string to the variable.Index style variables with a single string value can also be set by -using the command-line switch -var; see this +using the command-line switch -var; see this section for details.
The loop style is identical to the index style except that the @@ -202,7 +202,7 @@ two arguments N1 and N2. In this case the loop runs from N1 to N2 inclusive, and the string N1 is initially assigned to the variable.
For the world style, one or more strings are specified. There must -be one string for each processor partition or "world". See this +be one string for each processor partition or "world". See this section of the manual for information on running LAMMPS with multiple partitions via the "-partition" command-line switch. This variable command assigns one string to each @@ -216,7 +216,7 @@ different partitions.
For the universe style, one or more strings are specified. There must be at least as many strings as there are processor partitions or -"worlds". See this page for information +"worlds". See this page for information on running LAMMPS with multiple partitions via the "-partition" command-line switch. This variable command initially assigns one string to each world. When a next command is encountered diff --git a/doc/variable.txt b/doc/variable.txt index 949e2f6751..d42ae0c99b 100644 --- a/doc/variable.txt +++ b/doc/variable.txt @@ -123,7 +123,7 @@ is ignored. This means variables can NOT be re-defined in an input script (with 2 exceptions, read further). This is to allow an input script to be processed multiple times without resetting the variables; see the "jump"_jump.html or "include"_include.html commands. It also -means that using the "command-line switch"_Section_start.html#start_6 +means that using the "command-line switch"_Section_start.html#start_7 -var will override a corresponding index variable setting in the input script. @@ -182,7 +182,7 @@ variable. {Index} style variables with a single string value can also be set by using the command-line switch -var; see "this -section"_Section_start.html#start_6 for details. +section"_Section_start.html#start_7 for details. The {loop} style is identical to the {index} style except that the strings are the integers from 1 to N inclusive, if only one argument N @@ -197,7 +197,7 @@ inclusive, and the string N1 is initially assigned to the variable. For the {world} style, one or more strings are specified. There must be one string for each processor partition or "world". See "this -section"_Section_start.html#start_6 of the manual for information on +section"_Section_start.html#start_7 of the manual for information on running LAMMPS with multiple partitions via the "-partition" command-line switch. This variable command assigns one string to each world. All processors in the world are assigned the same string. The @@ -210,7 +210,7 @@ different partitions. For the {universe} style, one or more strings are specified. There must be at least as many strings as there are processor partitions or -"worlds". See "this page"_Section_start.html#start_6 for information +"worlds". See "this page"_Section_start.html#start_7 for information on running LAMMPS with multiple partitions via the "-partition" command-line switch. This variable command initially assigns one string to each world. When a "next"_next.html command is encountered